├── .gitignore ├── LICENSE ├── README.md ├── content_sources ├── __init__.py ├── arxiv.py ├── bibtex.py ├── doi2bib.py └── rss.py ├── data └── prepositions.dat ├── examples ├── bad.bib ├── good.bib ├── kw.p └── nb.p └── shakespeare.py /.gitignore: -------------------------------------------------------------------------------- 1 | *.pyc 2 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | The MIT License (MIT) 2 | 3 | Copyright (c) 2014 Benjamin Schultz 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy of 6 | this software and associated documentation files (the "Software"), to deal in 7 | the Software without restriction, including without limitation the rights to 8 | use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of 9 | the Software, and to permit persons to whom the Software is furnished to do so, 10 | subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS 17 | FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR 18 | COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER 19 | IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN 20 | CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. 21 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | shakespeare 2 | =========== 3 | 4 | Identify relevant scientific papers with simple machine learning techniques 5 | 6 | Installation 7 | =========== 8 | Copy shakespeare.py, data and content\_sources to your pythonpath. 9 | 10 | To intsall an example knowledge set, copy examples' contents to $HOME/.shakespeare 11 | 12 | Depends on `bibtexparser`, `feedparser` `scikit-learn` packages, which can be installed via pip 13 | 14 | pip install bibtexparser scikit-learn feedparser 15 | 16 | 17 | 18 | Features 19 | ======== 20 | 21 | * fetch functions for the following journals 22 | 23 | * Phys Rev A-X 24 | * PRL 25 | * PNAS 26 | * Nature + Nature:Stuff 27 | * Science 28 | * Small 29 | * ACS Nano, Nano Letters 30 | * Soft Matter 31 | * Langmuir 32 | * Angewandte Chemie 33 | * JCP, JCP B 34 | 35 | * Fetch functions for arXiv 36 | * support for BibTex Files 37 | * Naive bayes training and classification 38 | 39 | Usage 40 | ====== 41 | 42 | The very first thing to do is to let the code know where 'bad stuff' is 43 | 44 | ./shakespeare.py -g good.bib -k examples/ --overwrite-knowledge --train 45 | 46 | Train naive\_bayes algorithm 47 | 48 | ./shakespeare -g thegoodstuff.bib -b thebadstuff.bib -k examples --train 49 | 50 | Find papers from nature nano and PNAS 51 | 52 | ./shakespeare.py -j natnano pnas -o cool_papers.md 53 | 54 | Find papers from the arxiv cond-mat.soft and math, then review the algorithms selection 55 | 56 | ./shakespeare.py -a cond-mat.soft math --feedback 57 | 58 | 59 | Help printout 60 | 61 | usage: shakespeare.py [-h] [-o OUTPUT] [-b [BIBFILES [BIBFILES ...]]] 62 | [-j [JOURNALS [JOURNALS ...]]] [-a [ARXIV [ARXIV ...]]] 63 | [--all_sources] [--all_good_sources] [--train] 64 | [-g GOOD_SOURCE] [-m METHOD] [-k KNOWLEDGE] 65 | [--overwrite-knowledge] [--feedback] [--review_all] 66 | optional arguments: 67 | -h, --help show this help message and exit 68 | -o OUTPUT, --output OUTPUT 69 | output file name. only supports markdown right now. 70 | -b [BIBFILES [BIBFILES ...]], --bibtex [BIBFILES [BIBFILES ...]] 71 | bibtex files to fetch 72 | -j [JOURNALS [JOURNALS ...]], --journals [JOURNALS [JOURNALS ...]] 73 | journals to fetch. Currently supports physreve 74 | physrevd jchemphysb physreva physrevc pnas nature 75 | jchemphys science natmat physrevb acsnano jphyschem 76 | nanoletters natphys prl small angewantechemie langmuir 77 | physrevx natnano. 78 | -a [ARXIV [ARXIV ...]], --arXiv [ARXIV [ARXIV ...]] 79 | arXiv categories to fetch 80 | --all_sources flag to search from all sources. 81 | --all_good_sources flag to search from good sources. Specfied in your 82 | config file. 83 | --train flag to train. All sources beside "--train-input-good" 84 | are treated as bad/irrelevant papers 85 | -g GOOD_SOURCE, --train_input_good GOOD_SOURCE 86 | bibtex file containing relevant articles. 87 | -m METHOD, --method METHOD 88 | Methods to try to find relevent papers. Right now, 89 | only all, title, author, and abstract are valid fields 90 | -k KNOWLEDGE, --knowledge KNOWLEDGE 91 | path to database containing information about good and 92 | bad keywords. If you are training, you must specifiy 93 | this, as it will be where your output is written 94 | --overwrite-knowledge 95 | flag to overwrite knowledge,if training 96 | --feedback flag to give feedback after sorting content 97 | --review_all review all the new selections. Otherwise, you will 98 | only review the good selections 99 | 100 | 101 | TODO 102 | ====== 103 | * Train a bunch and see if this is worth any more time 104 | * Make an nice installer 105 | * Add support for a config file for setting defaults (which journals to search, etc) 106 | -------------------------------------------------------------------------------- /content_sources/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/pfdamasceno/shakespeare/e77dd82c0853313d0e309f7494fd284a72ff3698/content_sources/__init__.py -------------------------------------------------------------------------------- /content_sources/arxiv.py: -------------------------------------------------------------------------------- 1 | from xml.dom.minidom import parseString 2 | import urllib2 3 | import datetime as dt 4 | arxiv_cats = ['astro-ph', 5 | 'cond-mat', 6 | 'gr-gc', 7 | 'hep-ex', 8 | 'hep-lat', 9 | 'hep-ph', 10 | 'hep-th', 11 | 'math-ph', 12 | 'nlin', 13 | 'nucl-ex', 14 | 'nucl-th', 15 | 'physics', 16 | 'quant-ph', 17 | 'math', 18 | 'CoRR', 19 | 'q-bio', 20 | 'q-fin', 21 | 'stat'] 22 | #Class for interacting with the arXiv 23 | class ArXiv(object): 24 | 25 | def __init__(self,topic='cond-mat'): 26 | self.topic=topic 27 | self.url_base = 'http://export.arxiv.org/api/' 28 | 29 | def __repr__(self): 30 | return 'arXiv:{}'.format(self.topic) 31 | 32 | def fetch(self): 33 | today=dt.date.today() 34 | week_ago = today - dt.timedelta(days=7) 35 | end_date = "{:04d}{:02d}{:02d}2359".format(today.year,today.month,today.day) 36 | start_date = "{:04d}{:02d}{:02d}0000".format(week_ago.year,week_ago.month,week_ago.day) 37 | self.xml = '' 38 | query = 'query?search_query=cat:{}*+AND+submittedDate:[{}+TO+{}]&max_results=100'.format(self.topic,start_date,end_date) 39 | self.xml = urllib2.urlopen(self.url_base + query).read() 40 | 41 | # extract the relevant fields from the xml returned from our arXiv query 42 | def parse(self): 43 | 44 | articles = list() 45 | entries = parseString(self.xml).getElementsByTagName('entry') 46 | 47 | for entry in entries: 48 | article = dict() 49 | article['abstract'] = entry.getElementsByTagName('summary')[0].toxml().replace('','').replace('','') 50 | 51 | authors =list() 52 | for author in entry.getElementsByTagName('author'): 53 | name = entry.getElementsByTagName('name')[0] 54 | authors.append(author.toxml().replace('','').replace('','')) 55 | 56 | article['author']= ', '.join(authors) 57 | 58 | article['title'] = entry.getElementsByTagName('title')[0].toxml().replace('','').replace('','') 59 | article['url'] = entry.getElementsByTagName('id')[0].toxml().replace('','').replace('','') 60 | 61 | articles.append(article) 62 | 63 | return articles 64 | -------------------------------------------------------------------------------- /content_sources/bibtex.py: -------------------------------------------------------------------------------- 1 | import re 2 | import os 3 | from bibtexparser.bparser import BibTexParser 4 | 5 | #Parse Bibtex file and return dictionary 6 | class BibTex(object): 7 | 8 | def __init__(self,filename): 9 | self.filename = filename 10 | 11 | def __repr__(self): 12 | return 'BibTex File {} '.format(self.filename) 13 | 14 | def fetch(self): 15 | if not os.path.exists(self.filename): 16 | raise Exception("Bibtex file {} does not exist".format(self.filename)) 17 | if not os.path.isfile(self.filename): 18 | raise Exception("Bibtex file {} is not a file".format(self.filename)) 19 | 20 | def parse(self): 21 | articles= list() 22 | with open(self.filename,'r') as bibfile: 23 | entries = BibTexParser(bibfile).get_entry_list() 24 | for entry in entries: 25 | article=dict() 26 | for kw,btpkw in zip(['title','author','abstract','url'],['title','author','abstract','link']): 27 | article[kw]= entry[btpkw] if btpkw in entry else '' 28 | articles.append(article) 29 | return articles 30 | -------------------------------------------------------------------------------- /content_sources/doi2bib.py: -------------------------------------------------------------------------------- 1 | #modified from https://gist.github.com/zmwangx 2 | #!/usr/bin/env python 3 | 4 | # Take one argument--the doi, and convert it to bibtex using an API 5 | # call to dx.doi.org. 6 | 7 | from sys import argv 8 | import os, re 9 | 10 | #if argv[0].find('doi') != -1: 11 | # # run as executable 12 | # doi = argv[1] 13 | #else: 14 | # # run from python 15 | # doi = argv[2] 16 | 17 | doi_sub_str="dx.doi.org/" 18 | 19 | f = open("/Users/damascus/Documents/Cloud/Dropbox/HipChat_DOIs/DOI.txt", 'r') 20 | for line in f: 21 | try: 22 | doi_str = line 23 | doi = re.split('\s', doi_str[doi_str.find(doi_sub_str)+(len(doi_sub_str)):])[0] 24 | 25 | 26 | cmd = ('curl -sLH "Accept: text/bibliography; style=bibtex" ' + 27 | 'http://dx.doi.org/' + doi) 28 | bib_oneliner = os.popen(cmd).read() 29 | 30 | # convert bib_oneliner to formatted (multiline) bibtex 31 | bib = '' 32 | # extract type 33 | entry_type = bib_oneliner[bib_oneliner.find('@') + 1: 34 | bib_oneliner.find('{')] 35 | bib += '@' + entry_type + '{' + doi + ',\n'; # use doi as cite key 36 | # parse body 37 | body = bib_oneliner[bib_oneliner.find(',')+2:-2] + ',' 38 | while body: 39 | # match curly braces 40 | left_minus_right = 0 41 | i = 0 42 | while True: 43 | if body[i] == '{': 44 | left_minus_right += 1 45 | if body[i] == '}': 46 | left_minus_right -= 1 47 | if left_minus_right == 0: 48 | # outermost level matched up, one entry finished 49 | # advance one char for the trailing comma 50 | i += 1 51 | break 52 | i += 1 53 | 54 | bib += ' ' + body[:i+1] + '\n' 55 | body = body[i+1:].strip() 56 | 57 | bib += '}' 58 | print(bib) 59 | except: 60 | pass 61 | -------------------------------------------------------------------------------- /content_sources/rss.py: -------------------------------------------------------------------------------- 1 | import feedparser 2 | import datetime as dt 3 | 4 | #rss feed dictionary 5 | rss_feeds = { 6 | 'pnas':'http://www.pnas.org/rss/current.xml', 7 | 'small':'http://onlinelibrary.wiley.com/rss/journal/10.1002/(ISSN)1613-6829', 8 | 'advmat':'http://onlinelibrary.wiley.com/rss/journal/10.1002/(ISSN)1521-4095', 9 | 'nature':'http://feeds.nature.com/nature/rss/current?format=xml', 10 | 'science':'https://www.sciencemag.org/rss/current.xml', 11 | 'prl':'http://feeds.aps.org/rss/recent/prl.xml', 12 | 'physreva':'http://feeds.aps.org/rss/recent/pra.xml', 13 | 'physrevb':'http://feeds.aps.org/rss/recent/prb.xml', 14 | 'physrevc':'http://feeds.aps.org/rss/recent/prc.xml', 15 | 'physrevd':'http://feeds.aps.org/rss/recent/prd.xml', 16 | 'physreve':'http://feeds.aps.org/rss/recent/pre.xml', 17 | 'physrevx':'http://feeds.aps.org/rss/recent/prx.xml', 18 | 'acsnano':'http://feeds.feedburner.com/acs/ancac3', 19 | 'nanoletters':'http://feeds.feedburner.com/acs/nalefd', 20 | 'jchemphys':'http://phys.org/rss-feed/journals/journal-of-chemical-physics/', 21 | 'jchemphysb':'http://feeds.feedburner.com/acs/jpcbfk', 22 | 'angewantechemie':'http://onlinelibrary.wiley.com/rss/journal/10.1002/%28ISSN%291521-3773', 23 | 'jphyschem':'http://academic.research.microsoft.com/rss?id=15120&cata=6', 24 | 'natphys':'http://feeds.nature.com/nphys/rss/current', 25 | 'natmat':'http://feeds.nature.com/nmat/rss/current', 26 | 'natnano':'http://feeds.nature.com/nnano/rss/current?format=xml', 27 | 'langmuir':'http://feeds.feedburner.com/acs/langd5' 28 | } 29 | #Class for interacting with the arXiv 30 | class JournalFeed(object): 31 | 32 | def __init__(self,journal): 33 | self.journal=journal 34 | 35 | def __repr__(self): 36 | return 'rss feed : {}'.format(self.journal) 37 | 38 | def fetch(self): 39 | self.address=rss_feeds[self.journal] 40 | 41 | # extract the relevant fields from the xml returned from our arXiv query 42 | def parse(self): 43 | articles = list() 44 | entries = feedparser.parse(self.address)['entries'] 45 | today = dt.date.today() 46 | for entry in entries: 47 | article = dict() 48 | for kw,fkw in zip(['title','author','abstract','url'],['title','author','summary','link']): 49 | article[kw] = entry[fkw] if fkw in entry else '' 50 | #make sure this article is recent 51 | t_str=None 52 | if 'updated' in entry: 53 | t_str = entry['updated_parsed'] 54 | elif 'published' in entry: 55 | t_str = entry['published_parsed'] 56 | if t_str: 57 | day = t_str.tm_mday 58 | month = t_str.tm_mon 59 | year = t_str.tm_year 60 | pdate = dt.date(day=day,month=month,year=year) 61 | if (today-pdate).days<8: 62 | articles.append(article) 63 | else: 64 | articles.append(article) 65 | 66 | return articles 67 | -------------------------------------------------------------------------------- /data/prepositions.dat: -------------------------------------------------------------------------------- 1 | a 2 | abaft 3 | aboard 4 | about 5 | above 6 | absent 7 | across 8 | afore 9 | after 10 | against 11 | along 12 | alongside 13 | amid 14 | amidst 15 | among 16 | amongst 17 | an 18 | anenst 19 | apropos 20 | apud 21 | around 22 | as 23 | aside 24 | astride 25 | at 26 | athwart 27 | atop 28 | barring 29 | before 30 | behind 31 | below 32 | beneath 33 | beside 34 | besides 35 | between 36 | betwixt 37 | beyond 38 | but 39 | by 40 | circa 41 | concerning 42 | despite 43 | down 44 | during 45 | except 46 | excluding 47 | failing 48 | following 49 | for 50 | forenenst 51 | from 52 | given 53 | in 54 | including 55 | inside 56 | into 57 | lest 58 | like 59 | mid 60 | midst 61 | minus 62 | modulo 63 | near 64 | next 65 | notwithstanding 66 | o' 67 | of 68 | off 69 | on 70 | onto 71 | opposite 72 | out 73 | outside 74 | over 75 | pace 76 | past 77 | per 78 | plus 79 | pro 80 | qua 81 | regarding 82 | round 83 | sans 84 | save 85 | since 86 | than 87 | through, thru 88 | throughout, thruout 89 | till 90 | times 91 | to 92 | toward 93 | towards 94 | under 95 | underneath 96 | unlike 97 | until 98 | unto 99 | up 100 | upon 101 | versus 102 | via 103 | vice 104 | vis-à-vis 105 | with 106 | within 107 | without 108 | worth 109 | according to 110 | ahead of 111 | apart from 112 | as for 113 | as of 114 | as per 115 | as regards 116 | aside from 117 | back to 118 | because of 119 | close to 120 | due to 121 | except for 122 | far from 123 | in to 124 | inside of 125 | instead of 126 | left of 127 | near to 128 | next to 129 | on to 130 | onto 131 | out from 132 | out of 133 | outside of 134 | owing to 135 | prior to 136 | pursuant to 137 | rather than 138 | regardless of 139 | right of 140 | subsequent to 141 | such as 142 | thanks to 143 | that of 144 | up to 145 | where as 146 | the 147 | of 148 | in 149 | on 150 | at 151 | with 152 | while 153 | for 154 | into 155 | by 156 | and 157 | -------------------------------------------------------------------------------- /examples/bad.bib: -------------------------------------------------------------------------------- 1 | @article{Adami2014, 2 | abstract = {Research investigating the origins of life usually focuses on exploring possible life-bearing chemistries in the pre-biotic Earth, or else on synthetic approaches. Little work has been done exploring fundamental issues concerning the spontaneous emergence of life using only concepts (such as information and evolution) that are divorced from any particular chemistry. Here, I advocate studying the probability of spontaneous molecular self-replication as a function of the information contained in the replicator, and the environmental conditions that might enable this emergence. I show that (under certain simplifying assumptions) the probability to discover a self-replicator by chance depends exponentially on the rate of formation of the monomers. If the rate at which monomers are formed is somewhat similar to the rate at which they would occur in a self-replicating polymer, the likelihood to discover such a replicator by chance is increased by many orders of magnitude. I document such an increase in searches for a self-replicator within the digital life system avida}, 3 | archivePrefix = {arXiv}, 4 | arxivId = {1409.0590}, 5 | author = {Adami, Christoph}, 6 | eprint = {1409.0590}, 7 | file = {:Users/damascus/Documents/Mendeley\_papers/Adami - 2014 - Unknown.pdf:pdf}, 8 | month = sep, 9 | pages = {9}, 10 | title = {{Information-theoretic considerations concerning the origin of life}}, 11 | url = {http://arxiv.org/abs/1409.0590}, 12 | year = {2014} 13 | } 14 | @article{Benner2010, 15 | abstract = {Organic chemistry on a planetary scale is likely to have transformed carbon dioxide and reduced carbon species delivered to an accreting Earth. According to various models for the origin of life on Earth, biological molecules that jump-started Darwinian evolution arose via this planetary chemistry. The grandest of these models assumes that ribonucleic acid (RNA) arose prebiotically, together with components for compartments that held it and a primitive metabolism that nourished it. Unfortunately, it has been challenging to identify possible prebiotic chemistry that might have created RNA. Organic molecules, given energy, have a well-known propensity to form multiple products, sometimes referred to collectively as "tar" or "tholin." These mixtures appear to be unsuited to support Darwinian processes, and certainly have never been observed to spontaneously yield a homochiral genetic polymer. To date, proposed solutions to this challenge either involve too much direct human intervention to satisfy many in the community, or generate molecules that are unreactive "dead ends" under standard conditions of temperature and pressure. Carbohydrates, organic species having carbon, hydrogen, and oxygen atoms in a ratio of 1:2:1 and an aldehyde or ketone group, conspicuously embody this challenge. They are components of RNA and their reactivity can support both interesting spontaneous chemistry as part of a "carbohydrate world," but they also easily form mixtures, polymers and tars. We describe here the latest thoughts on how on this challenge, focusing on how it might be resolved using minerals containing borate, silicate, and molybdate, inter alia.}, 16 | author = {Benner, Steven a and Kim, Hyo-Joong and Kim, Myung-Jung and Ricardo, Alonso}, 17 | doi = {10.1101/cshperspect.a003467}, 18 | file = {:Users/damascus/Documents/Mendeley\_papers/Benner et al. - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf}, 19 | issn = {1943-0264}, 20 | journal = {Cold Spring Harbor perspectives in biology}, 21 | keywords = {Carbohydrates,Carbohydrates: chemistry,Chemistry, Organic,Polymers}, 22 | month = jul, 23 | number = {7}, 24 | pages = {a003467}, 25 | pmid = {20504964}, 26 | title = {{Planetary organic chemistry and the origins of biomolecules.}}, 27 | url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2890202\&tool=pmcentrez\&rendertype=abstract}, 28 | volume = {2}, 29 | year = {2010} 30 | } 31 | @article{Blackmond2010, 32 | abstract = {The single-handedness of biological molecules has fascinated scientists and laymen alike since Pasteur's first painstaking separation of the enantiomorphic crystals of a tartrate salt more than 150 yr ago. More recently, a number of theoretical and experimental investigations have helped to delineate models for how one enantiomer might have come to dominate over the other from what presumably was a racemic prebiotic world. This article highlights mechanisms for enantioenrichment that include either chemical or physical processes, or a combination of both. The scientific driving force for this work arises from an interest in understanding the origin of life, because the homochirality of biological molecules is a signature of life.}, 33 | author = {Blackmond, Donna G}, 34 | doi = {10.1101/cshperspect.a002147}, 35 | file = {:Users/damascus/Documents/Mendeley\_papers/Blackmond - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf}, 36 | issn = {1943-0264}, 37 | journal = {Cold Spring Harbor perspectives in biology}, 38 | keywords = {Amino Acids,Amino Acids: chemistry,Carbohydrates,Carbohydrates: chemistry,Stereoisomerism}, 39 | month = may, 40 | number = {5}, 41 | pages = {a002147}, 42 | pmid = {20452962}, 43 | title = {{The origin of biological homochirality.}}, 44 | url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2857173\&tool=pmcentrez\&rendertype=abstract}, 45 | volume = {2}, 46 | year = {2010} 47 | } 48 | @article{Bowler2013, 49 | abstract = {The recent synthesis of pyrimidine ribonucleoside-2',3'-cyclic phosphates under prebiotically plausible conditions has strengthened the case for the involvement of ribonucleic acid (RNA) at an early stage in the origin of life. However, a prebiotic conversion of these weakly activated monomers, and their purine counterparts, to the 3',5'-linked RNA polymers of extant biochemistry has been lacking (previous attempts led only to short oligomers with mixed linkages). Here we show that the 2'-hydroxyl group of oligoribonucleotide-3'-phosphates can be chemoselectively acetylated in water under prebiotically credible conditions, which allows rapid and efficient template-directed ligation. The 2'-O-acetyl group at the ligation junction of the product RNA strand can be removed under conditions that leave the internucleotide bonds intact. Remarkably, acetylation of mixed oligomers that possess either 2'- or 3'-terminal phosphates is selective for the 2'-hydroxyl group of the latter. This newly discovered chemistry thus suggests a prebiotic route from ribonucleoside-2',3'-cyclic phosphates to predominantly 3',5'-linked RNA via partially 2'-O-acetylated RNA.}, 50 | author = {Bowler, Frank R and Chan, Christopher K W and Duffy, Colm D and Gerland, B\'{e}atrice and Islam, Saidul and Powner, Matthew W and Sutherland, John D and Xu, Jianfeng}, 51 | doi = {10.1038/nchem.1626}, 52 | file = {:Users/damascus/Documents/Mendeley\_papers/Bowler et al. - 2013 - Nature chemistry.pdf:pdf}, 53 | issn = {1755-4349}, 54 | journal = {Nature chemistry}, 55 | keywords = {Acetylation,Biomolecular,Biopolymers,Biopolymers: chemistry,Nuclear Magnetic Resonance,Prebiotics,RNA,RNA: chemistry}, 56 | month = may, 57 | number = {5}, 58 | pages = {383--9}, 59 | pmid = {23609088}, 60 | title = {{Prebiotically plausible oligoribonucleotide ligation facilitated by chemoselective acetylation.}}, 61 | url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4074891\&tool=pmcentrez\&rendertype=abstract}, 62 | volume = {5}, 63 | year = {2013} 64 | } 65 | @article{Brewer2014, 66 | abstract = {The route by which the complex and specific molecules of life arose from the 'prebiotic soup' remains an unsolved problem. Evolution provides a large part of the answer, but this requires molecules that can carry information (that is, exist in many variants) and can replicate themselves. The process is commonplace in living organisms, but not so easy to achieve with simple chemical systems. It is especially difficult to contemplate in the chemical chaos of the prebiotic world. Although popular in many quarters, the notion that RNA was the first self-replicator carries many difficulties. Here, we present an alternative view, suggesting that there may be undiscovered self-replication mechanisms possible in much simpler systems. In particular, we highlight the possibility of information coding through stereochemical configurations of substituents in organic polymers. We also show that this coding system leads naturally to enantiopurity, solving the apparent problem of biological homochirality.}, 67 | author = {Brewer, Ashley and Davis, Anthony P}, 68 | doi = {10.1038/nchem.1981}, 69 | file = {:Users/damascus/Documents/Mendeley\_papers/Brewer, Davis - 2014 - Nature chemistry.pdf:pdf}, 70 | issn = {1755-4349}, 71 | journal = {Nature chemistry}, 72 | month = jul, 73 | number = {7}, 74 | pages = {569--74}, 75 | pmid = {24950314}, 76 | title = {{Chiral encoding may provide a simple solution to the origin of life.}}, 77 | url = {http://www.ncbi.nlm.nih.gov/pubmed/24950314}, 78 | volume = {6}, 79 | year = {2014} 80 | } 81 | @article{Chen2010a, 82 | abstract = {Self-assembled vesicles are essential components of primitive cells. We review the importance of vesicles during the origins of life, fundamental thermodynamics and kinetics of self-assembly, and experimental models of simple vesicles, focusing on prebiotically plausible fatty acids and their derivatives. We review recent work on interactions of simple vesicles with RNA and other studies of the transition from vesicles to protocells. Finally we discuss current challenges in understanding the biophysics of protocells, as well as conceptual questions in information transmission and self-replication.}, 83 | author = {Chen, Irene a and Walde, Peter}, 84 | doi = {10.1101/cshperspect.a002170}, 85 | file = {:Users/damascus/Documents/Mendeley\_papers/Chen, Walde - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf}, 86 | issn = {1943-0264}, 87 | journal = {Cold Spring Harbor perspectives in biology}, 88 | keywords = {Cell Membrane,Cell Membrane: metabolism,Cells,Kinetics,Nucleic Acids,Nucleic Acids: metabolism,Thermodynamics}, 89 | month = jul, 90 | number = {7}, 91 | pages = {a002170}, 92 | pmid = {20519344}, 93 | title = {{From self-assembled vesicles to protocells.}}, 94 | url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2890201\&tool=pmcentrez\&rendertype=abstract}, 95 | volume = {2}, 96 | year = {2010} 97 | } 98 | @article{Cheng2010, 99 | abstract = {How life emerged on this planet is one of the most important and fundamental questions of science. Although nearly all details concerning our origins have been lost in the depths of time, there is compelling evidence to suggest that the earliest life might have exploited the catalytic and self-recognition properties of RNA to survive. If an RNA based replicating system could be constructed in the laboratory, it would be much easier to understand the challenges associated with the very earliest steps in evolution and provide important insight into the establishment of the complex metabolic systems that now dominate this planet. Recent progress into the selection and characterization of ribozymes that promote nucleotide synthesis and RNA polymerization are discussed and outstanding problems in the field of RNA-mediated RNA replication are summarized.}, 100 | author = {Cheng, Leslie K L and Unrau, Peter J}, 101 | doi = {10.1101/cshperspect.a002204}, 102 | file = {:Users/damascus/Documents/Mendeley\_papers/Cheng, Unrau - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf}, 103 | issn = {1943-0264}, 104 | journal = {Cold Spring Harbor perspectives in biology}, 105 | keywords = {Biogenesis,DNA-Directed RNA Polymerases,DNA-Directed RNA Polymerases: genetics,DNA-Directed RNA Polymerases: metabolism,Evolution, Molecular,Polynucleotide Ligases,Polynucleotide Ligases: genetics,Polynucleotide Ligases: metabolism,RNA,RNA, Catalytic,RNA, Catalytic: genetics,RNA, Catalytic: metabolism,RNA: biosynthesis,RNA: genetics}, 106 | month = oct, 107 | number = {10}, 108 | pages = {a002204}, 109 | pmid = {20554706}, 110 | title = {{Closing the circle: replicating RNA with RNA.}}, 111 | url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2944364\&tool=pmcentrez\&rendertype=abstract}, 112 | volume = {2}, 113 | year = {2010} 114 | } 115 | @article{Damasceno, 116 | author = {Damasceno, Pablo F and Glotzer, Sharon C.}, 117 | journal = {in prep. (2015)}, 118 | title = {{Self-Assembly of Complex Crystals via Isotropic Potentials Derived from Shape}} 119 | } 120 | @article{Damascenoa, 121 | author = {Damasceno, Pablo F. and Engel, Michael and Glotzer, Sharon C.}, 122 | file = {:Users/damascus/Library/Application Support/Mendeley Desktop/Downloaded/Damasceno, Engel, Glotzer - Unknown - Self-Assembly of Homochiral Colloidal Crystals.pdf:pdf}, 123 | journal = {in prep. (2014)}, 124 | title = {{Self-Assembly of Homochiral Colloidal Crystals}} 125 | } 126 | @article{Damascenob, 127 | author = {Damasceno, Pablo F. and Phillips, Carolyn L. and Engel, Michael and Glotzer, Sharon C.}, 128 | file = {:Users/damascus/Library/Application Support/Mendeley Desktop/Downloaded/Damasceno, Engel, Glotzer - Unknown - Self-Assembly of Homochiral Colloidal Crystals.pdf:pdf}, 129 | journal = {in prep. (2014)}, 130 | title = {{Self-Assembly of Complex Crystals from Simple Pair-Potentials}} 131 | } 132 | @article{Deamer2010, 133 | abstract = {Bioenergetics is central to our understanding of living systems, yet has attracted relatively little attention in origins of life research. This article focuses on energy resources available to drive primitive metabolism and the synthesis of polymers that could be incorporated into molecular systems having properties associated with the living state. The compartmented systems are referred to as protocells, each different from all the rest and representing a kind of natural experiment. The origin of life was marked when a rare few protocells happened to have the ability to capture energy from the environment to initiate catalyzed heterotrophic growth directed by heritable genetic information in the polymers. This article examines potential sources of energy available to protocells, and mechanisms by which the energy could be used to drive polymer synthesis.}, 134 | author = {Deamer, David and Weber, Arthur L}, 135 | doi = {10.1101/cshperspect.a004929}, 136 | file = {:Users/damascus/Documents/Mendeley\_papers/Deamer, Weber - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf}, 137 | issn = {1943-0264}, 138 | journal = {Cold Spring Harbor perspectives in biology}, 139 | keywords = {Animals,Biogenesis,Catalysis,Diphosphates,Diphosphates: chemistry,Energy Metabolism,Humans,Kinetics,Life,Models, Biological,Polymers,Polymers: chemistry,Sunlight,Thermodynamics}, 140 | month = feb, 141 | number = {2}, 142 | pages = {a004929}, 143 | pmid = {20182625}, 144 | title = {{Bioenergetics and life's origins.}}, 145 | url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2828274\&tool=pmcentrez\&rendertype=abstract}, 146 | volume = {2}, 147 | year = {2010} 148 | } 149 | @article{Deck2011, 150 | abstract = {The transition from inanimate materials to the earliest forms of life must have involved multiplication of a catalytically active polymer that is able to replicate. The semiconservative replication that is characteristic of genetic information transfer requires strands that contain more than one type of nucleobase. Short strands of RNA can act as catalysts, but attempts to induce efficient self-copying of mixed sequences (containing four different nucleobases) have been unsuccessful with ribonucleotides. Here we show that inhibition by spent monomers, formed by the hydrolysis of the activated nucleotides, is the cause for incomplete extension of growing daughter strands on RNA templates. Immobilization of strands and periodic displacement of the solution containing the activated monomers overcome this inhibition. Any of the four nucleobases (A/C/G/U) is successfully copied in the absence of enzymes. We conclude therefore that in a prebiotic world, oligoribonucleotides may have formed and undergone self-copying on surfaces.}, 151 | author = {Deck, Christopher and Jauker, Mario and Richert, Clemens}, 152 | doi = {10.1038/nchem.1086}, 153 | file = {:Users/damascus/Documents/Mendeley\_papers/Deck, Jauker, Richert - 2011 - Nature chemistry.pdf:pdf}, 154 | issn = {1755-4349}, 155 | journal = {Nature chemistry}, 156 | keywords = {Base Sequence,RNA,RNA: chemistry,Ribonucleotides,Ribonucleotides: chemistry}, 157 | month = aug, 158 | number = {8}, 159 | pages = {603--8}, 160 | pmid = {21778979}, 161 | publisher = {Nature Publishing Group}, 162 | title = {{Efficient enzyme-free copying of all four nucleobases templated by immobilized RNA.}}, 163 | url = {http://www.ncbi.nlm.nih.gov/pubmed/21778979}, 164 | volume = {3}, 165 | year = {2011} 166 | } 167 | @article{Engela, 168 | author = {Engel, Michael and Damasceno, Pablo F. and Phillips, Carolyn L. and Glotzer, Sharon C.}, 169 | file = {:Users/damascus/Documents/Mendeley\_papers//Engel et al. - Unknown - Nature materials.pdf:pdf}, 170 | journal = {Nature materials}, 171 | title = {{Computational discovery of a one-component icosahedral quasicrystal via self-assembly}} 172 | } 173 | @article{Engelhart2010, 174 | abstract = {Since the structure of DNA was elucidated more than 50 years ago, Watson-Crick base pairing has been widely speculated to be the likely mode of both information storage and transfer in the earliest genetic polymers. The discovery of catalytic RNA molecules subsequently provided support for the hypothesis that RNA was perhaps even the first polymer of life. However, the de novo synthesis of RNA using only plausible prebiotic chemistry has proven difficult, to say the least. Experimental investigations, made possible by the application of synthetic and physical organic chemistry, have now provided evidence that the nucleobases (A, G, C, and T/U), the trifunctional moiety ([deoxy]ribose), and the linkage chemistry (phosphate esters) of contemporary nucleic acids may be optimally suited for their present roles-a situation that suggests refinement by evolution. Here, we consider studies of variations in these three distinct components of nucleic acids with regard to the question: Is RNA, as is generally acknowledged of DNA, the product of evolution? If so, what chemical and structural features might have been more likely and advantageous for a proto-RNA?}, 175 | author = {Engelhart, Aaron E and Hud, Nicholas V}, 176 | doi = {10.1101/cshperspect.a002196}, 177 | file = {:Users/damascus/Documents/Mendeley\_papers/Engelhart, Hud - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf}, 178 | issn = {1943-0264}, 179 | journal = {Cold Spring Harbor perspectives in biology}, 180 | keywords = {Biogenesis,Evolution, Chemical,Molecular Structure,Nucleic Acids,Nucleic Acids: chemistry,Polymerization,RNA,RNA: chemistry}, 181 | month = dec, 182 | number = {12}, 183 | pages = {a002196}, 184 | pmid = {20462999}, 185 | title = {{Primitive genetic polymers.}}, 186 | url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2982173\&tool=pmcentrez\&rendertype=abstract}, 187 | volume = {2}, 188 | year = {2010} 189 | } 190 | @article{Engelhart2013, 191 | abstract = {A plausible process for non-enzymatic RNA replication would greatly simplify models of the transition from prebiotic chemistry to simple biology. However, all known conditions for the chemical copying of an RNA template result in the synthesis of a complementary strand that contains a mixture of 2'-5' and 3'-5' linkages, rather than the selective synthesis of only 3'-5' linkages as found in contemporary RNA. Here we show that such backbone heterogeneity is compatible with RNA folding into defined three-dimensional structures that retain molecular recognition and catalytic properties and, therefore, would not prevent the evolution of functional RNAs such as ribozymes. Moreover, the same backbone heterogeneity lowers the melting temperature of RNA duplexes that would otherwise be too stable for thermal strand separation. By allowing copied strands to dissociate, this heterogeneity may have been one of the essential features that allowed RNA to emerge as the first biopolymer.}, 192 | author = {Engelhart, Aaron E and Powner, Matthew W and Szostak, Jack W}, 193 | doi = {10.1038/nchem.1623}, 194 | file = {:Users/damascus/Documents/Mendeley\_papers/Engelhart, Powner, Szostak - 2013 - Nature chemistry.pdf:pdf}, 195 | issn = {1755-4349}, 196 | journal = {Nature chemistry}, 197 | keywords = {Base Sequence,Models,Nucleic Acid Conformation,RNA,RNA: chemistry,Theoretical}, 198 | month = may, 199 | number = {5}, 200 | pages = {390--4}, 201 | pmid = {23609089}, 202 | publisher = {Nature Publishing Group}, 203 | title = {{Functional RNAs exhibit tolerance for non-heritable 2'-5' versus 3'-5' backbone heterogeneity.}}, 204 | url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4088963\&tool=pmcentrez\&rendertype=abstract}, 205 | volume = {5}, 206 | year = {2013} 207 | } 208 | @article{Eschenmoser1999, 209 | author = {Eschenmoser, A.}, 210 | doi = {10.1126/science.284.5423.2118}, 211 | file = {:Users/damascus/Documents/Mendeley\_papers/Eschenmoser - 1999 - Science.pdf:pdf}, 212 | issn = {00368075}, 213 | journal = {Science}, 214 | month = jun, 215 | number = {5423}, 216 | pages = {2118--2124}, 217 | title = {{Chemical Etiology of Nucleic Acid Structure}}, 218 | url = {http://www.sciencemag.org/cgi/doi/10.1126/science.284.5423.2118}, 219 | volume = {284}, 220 | year = {1999} 221 | } 222 | @article{Fox2010, 223 | abstract = {The modern ribosome was largely formed at the time of the last common ancestor, LUCA. Hence its earliest origins likely lie in the RNA world. Central to its development were RNAs that spawned the modern tRNAs and a symmetrical region deep within the large ribosomal RNA, (rRNA), where the peptidyl transferase reaction occurs. To understand pre-LUCA developments, it is argued that events that are coupled in time are especially useful if one can infer a likely order in which they occurred. Using such timing events, the relative age of various proteins and individual regions within the large rRNA are inferred. An examination of the properties of modern ribosomes strongly suggests that the initial peptides made by the primitive ribosomes were likely enriched for l-amino acids, but did not completely exclude d-amino acids. This has implications for the nature of peptides made by the first ribosomes. From the perspective of ribosome origins, the immediate question regarding coding is when did it arise rather than how did the assignments evolve. The modern ribosome is very dynamic with tRNAs moving in and out and the mRNA moving relative to the ribosome. These movements may have become possible as a result of the addition of a template to hold the tRNAs. That template would subsequently become the mRNA, thereby allowing the evolution of the code and making an RNA genome useful. Finally, a highly speculative timeline of major events in ribosome history is presented and possible future directions discussed.}, 224 | author = {Fox, George E}, 225 | doi = {10.1101/cshperspect.a003483}, 226 | file = {:Users/damascus/Documents/Mendeley\_papers/Fox - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf}, 227 | issn = {1943-0264}, 228 | journal = {Cold Spring Harbor perspectives in biology}, 229 | keywords = {Evolution, Molecular,RNA, Ribosomal,RNA, Ribosomal: genetics,RNA, Ribosomal: physiology,RNA, Transfer,RNA, Transfer: genetics,RNA, Transfer: physiology,Ribosomes,Ribosomes: genetics,Ribosomes: physiology}, 230 | month = sep, 231 | number = {9}, 232 | pages = {a003483}, 233 | pmid = {20534711}, 234 | title = {{Origin and evolution of the ribosome.}}, 235 | url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2926754\&tool=pmcentrez\&rendertype=abstract}, 236 | volume = {2}, 237 | year = {2010} 238 | } 239 | @article{Gaucher2010, 240 | abstract = {The Darwinian concept of biological evolution assumes that life on Earth shares a common ancestor. The diversification of this common ancestor through speciation events and vertical transmission of genetic material implies that the classification of life can be illustrated in a tree-like manner, commonly referred to as the Tree of Life. This article describes features of the Tree of Life, such as how the tree has been both pruned and become bushier throughout the past century as our knowledge of biology has expanded. We present current views that the classification of life may be best illustrated as a ring or even a coral with tree-like characteristics. This article also discusses how the organization of the Tree of Life offers clues about ancient life on Earth. In particular, we focus on the environmental conditions and temperature history of Precambrian life and show how chemical, biological, and geological data can converge to better understand this history."You know, a tree is a tree. How many more do you need to look at?"--Ronald Reagan (Governor of California), quoted in the Sacramento Bee, opposing expansion of Redwood National Park, March 3, 1966.}, 241 | author = {Gaucher, Eric a and Kratzer, James T and Randall, Ryan N}, 242 | doi = {10.1101/cshperspect.a002238}, 243 | file = {:Users/damascus/Documents/Mendeley\_papers/Gaucher, Kratzer, Randall - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf}, 244 | issn = {1943-0264}, 245 | journal = {Cold Spring Harbor perspectives in biology}, 246 | keywords = {Adaptation, Physiological,Biological Evolution,Environment,Escherichia coli,Escherichia coli: metabolism,History, Ancient,Paleontology,Paleontology: methods,Phylogeny,Temperature,Thermus,Thermus: metabolism}, 247 | month = jan, 248 | number = {1}, 249 | pages = {a002238}, 250 | pmid = {20182607}, 251 | title = {{Deep phylogeny--how a tree can help characterize early life on Earth.}}, 252 | url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2827910\&tool=pmcentrez\&rendertype=abstract}, 253 | volume = {2}, 254 | year = {2010} 255 | } 256 | @article{Goldman2010, 257 | abstract = {Delivery of prebiotic compounds to early Earth from an impacting comet is thought to be an unlikely mechanism for the origins of life because of unfavourable chemical conditions on the planet and the high heat from impact. In contrast, we find that impact-induced shock compression of cometary ices followed by expansion to ambient conditions can produce complexes that resemble the amino acid glycine. Our ab initio molecular dynamics simulations show that shock waves drive the synthesis of transient C-N bonded oligomers at extreme pressures and temperatures. On post impact quenching to lower pressures, the oligomers break apart to form a metastable glycine-containing complex. We show that impact from cometary ice could possibly yield amino acids by a synthetic route independent of the pre-existing atmospheric conditions and materials on the planet.}, 258 | author = {Goldman, Nir and Reed, Evan J and Fried, Laurence E and {William Kuo}, I-F and Maiti, Amitesh}, 259 | doi = {10.1038/nchem.827}, 260 | file = {:Users/damascus/Documents/Mendeley\_papers/Goldman et al. - 2010 - Nature chemistry.pdf:pdf}, 261 | issn = {1755-4349}, 262 | journal = {Nature chemistry}, 263 | keywords = {Earth (Planet),Glycine,Glycine: analysis,Meteoroids,Molecular Dynamics Simulation}, 264 | month = nov, 265 | number = {11}, 266 | pages = {949--54}, 267 | pmid = {20966951}, 268 | publisher = {Nature Publishing Group}, 269 | title = {{Synthesis of glycine-containing complexes in impacts of comets on early Earth.}}, 270 | url = {http://www.ncbi.nlm.nih.gov/pubmed/20966951}, 271 | volume = {2}, 272 | year = {2010} 273 | } 274 | @article{Gollihar2014, 275 | author = {Gollihar, Jimmy and Levy, Matthew and Ellington, Andrew D}, 276 | doi = {10.1126/science.1246704}, 277 | file = {:Users/damascus/Documents/Mendeley\_papers/Gollihar, Levy, Ellington - 2014 - Science (New York, N.Y.).pdf:pdf}, 278 | issn = {1095-9203}, 279 | journal = {Science (New York, N.Y.)}, 280 | keywords = {Biogenesis,Carbohydrates,Carbohydrates: chemistry,Earth (Planet),Ligases,Ligases: chemistry,Mars,RNA, Catalytic,RNA, Catalytic: chemistry,Ribose,Ribose: chemistry}, 281 | month = jan, 282 | number = {6168}, 283 | pages = {259--60}, 284 | pmid = {24436411}, 285 | title = {{Biochemistry. Many paths to the origin of life.}}, 286 | url = {http://www.ncbi.nlm.nih.gov/pubmed/24436411}, 287 | volume = {343}, 288 | year = {2014} 289 | } 290 | @article{Hazen2010, 291 | abstract = {Crystalline surfaces of common rock-forming minerals are likely to have played several important roles in life's geochemical origins. Transition metal sulfides and oxides promote a variety of organic reactions, including nitrogen reduction, hydroformylation, amination, and Fischer-Tropsch-type synthesis. Fine-grained clay minerals and hydroxides facilitate lipid self-organization and condensation polymerization reactions, notably of RNA monomers. Surfaces of common rock-forming oxides, silicates, and carbonates select and concentrate specific amino acids, sugars, and other molecular species, while potentially enhancing their thermal stabilities. Chiral surfaces of these minerals also have been shown to separate left- and right-handed molecules. Thus, mineral surfaces may have contributed centrally to the linked prebiotic problems of containment and organization by promoting the transition from a dilute prebiotic "soup" to highly ordered local domains of key biomolecules.}, 292 | author = {Hazen, Robert M and Sverjensky, Dimitri a}, 293 | doi = {10.1101/cshperspect.a002162}, 294 | file = {:Users/damascus/Documents/Mendeley\_papers/Hazen, Sverjensky - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf}, 295 | issn = {1943-0264}, 296 | journal = {Cold Spring Harbor perspectives in biology}, 297 | keywords = {Biogenesis,Crystallization,Minerals,Minerals: chemistry,Surface Properties}, 298 | month = may, 299 | number = {5}, 300 | pages = {a002162}, 301 | pmid = {20452963}, 302 | title = {{Mineral surfaces, geochemical complexities, and the origins of life.}}, 303 | url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2857174\&tool=pmcentrez\&rendertype=abstract}, 304 | volume = {2}, 305 | year = {2010} 306 | } 307 | @article{Hein2011, 308 | abstract = {The single-handedness of biological molecules is critical for molecular recognition and replication processes and would seem to be a prerequisite for the origin of life. A drawback of recently reported synthetic routes to RNA is the requirement for enantioenriched reactants, which fails to address the puzzle of how the single chirality of biological molecules arose. Here, we report the synthesis of highly enantioenriched RNA precursor molecules from racemic starting materials, with the molecular asymmetry derived solely from a small initial imbalance of the amino-acid enantiomers present in the reaction mixture. Acting as spectators to the main reaction chemistry, the amino acids orchestrate a sequence of physical and chemical amplification processes. The emergence of molecules of single chirality from complex, multi-component mixtures supports the robustness of this synthesis process under potential prebiotic conditions and provides a plausible explanation for the single-handedness of biological molecules before the emergence of self-replicating informational polymers.}, 309 | author = {Hein, Jason E and Tse, Eric and Blackmond, Donna G}, 310 | doi = {10.1038/nchem.1108}, 311 | file = {:Users/damascus/Documents/Mendeley\_papers/Hein, Tse, Blackmond - 2011 - Nature chemistry.pdf:pdf}, 312 | issn = {1755-4349}, 313 | journal = {Nature chemistry}, 314 | keywords = {Amino Acids,Amino Acids: chemistry,Glyceraldehyde,Glyceraldehyde: chemistry,Oxazoles,Oxazoles: chemistry,RNA Precursors,RNA Precursors: chemical synthesis,RNA Precursors: chemistry,RNA Precursors: genetics,Stereoisomerism}, 315 | month = sep, 316 | number = {9}, 317 | pages = {704--6}, 318 | pmid = {21860459}, 319 | publisher = {Nature Publishing Group}, 320 | title = {{A route to enantiopure RNA precursors from nearly racemic starting materials.}}, 321 | url = {http://www.ncbi.nlm.nih.gov/pubmed/21860459}, 322 | volume = {3}, 323 | year = {2011} 324 | } 325 | @article{Hernandez2013, 326 | author = {Hern\'{a}ndez, Armando R and Piccirilli, Joseph a}, 327 | doi = {10.1038/nchem.1636}, 328 | file = {:Users/damascus/Documents/Mendeley\_papers/Hern\'{a}ndez, Piccirilli - 2013 - Nature chemistry.pdf:pdf}, 329 | issn = {1755-4349}, 330 | journal = {Nature chemistry}, 331 | keywords = {Models, Theoretical,Prebiotics,RNA,RNA: chemistry}, 332 | month = may, 333 | number = {5}, 334 | pages = {360--2}, 335 | pmid = {23609081}, 336 | publisher = {Nature Publishing Group}, 337 | title = {{Chemical origins of life: Prebiotic RNA unstuck.}}, 338 | url = {http://www.ncbi.nlm.nih.gov/pubmed/23609081}, 339 | volume = {5}, 340 | year = {2013} 341 | } 342 | @article{Hormoz2011, 343 | abstract = {Recent experimental advances have opened up the possibility of equilibrium self-assembly of functionalized nanoblocks with a high degree of controllable specific interactions. Here, we propose design principles for selecting the short-range interactions between self-assembling components to maximize yield. We illustrate the approach with an example from colloidal engineering. We construct an optimal set of local interactions for eight colloidal particles (coated, e.g., with DNA strands) to assemble into a particular polytetrahedral cluster. Maximum yield is attained when the interactions between the colloids follow the design rules: All energetically favorable interactions have the same strength, as do all unfavorable ones, and the number of components and energies fall within the proposed range. In general, it might be necessary to use more component than strictly required for enforcing the ground state configuration. The results motivate design strategies for engineering components that can reliably self-assemble.}, 344 | author = {Hormoz, Sahand and Brenner, Michael P}, 345 | doi = {10.1073/pnas.1014094108}, 346 | file = {:Users/damascus/Documents/Mendeley\_papers/Hormoz, Brenner - 2011 - Proceedings of the National Academy of Sciences of the United States of America.pdf:pdf}, 347 | issn = {1091-6490}, 348 | journal = {Proceedings of the National Academy of Sciences of the United States of America}, 349 | keywords = {Colloids,Colloids: chemistry,Models, Molecular,Molecular Structure,Nanostructures,Nanostructures: chemistry}, 350 | month = mar, 351 | number = {13}, 352 | pages = {5193--8}, 353 | pmid = {21383135}, 354 | title = {{Design principles for self-assembly with short-range interactions.}}, 355 | url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3069168\&tool=pmcentrez\&rendertype=abstract}, 356 | volume = {108}, 357 | year = {2011} 358 | } 359 | @article{Ichihashi2010, 360 | abstract = {Understanding the origin of life requires knowledge not only of the origin of biological molecules such as amino acids, nucleotides and their polymers, but also the manner in which those molecules are integrated into the organized systems that characterize cellular life. In this article, we introduce a constructive approach to understand how biological molecules can be arranged to achieve a higher-order biological function: replication of genetic information.}, 361 | author = {Ichihashi, Norikazu and Matsuura, Tomoaki and Kita, Hiroshi and Sunami, Takeshi and Suzuki, Hiroaki and Yomo, Tetsuya}, 362 | doi = {10.1101/cshperspect.a004945}, 363 | file = {:Users/damascus/Documents/Mendeley\_papers/Ichihashi et al. - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf}, 364 | issn = {1943-0264}, 365 | journal = {Cold Spring Harbor perspectives in biology}, 366 | keywords = {Biological Evolution,DNA Replication,DNA Replication: genetics,Gene Regulatory Networks,Liposomes,Models, Genetic,Templates, Genetic}, 367 | month = jun, 368 | number = {6}, 369 | pages = {a004945}, 370 | pmid = {20516136}, 371 | title = {{Constructing partial models of cells.}}, 372 | url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2869526\&tool=pmcentrez\&rendertype=abstract}, 373 | volume = {2}, 374 | year = {2010} 375 | } 376 | @article{Koga2011, 377 | abstract = {Although phospholipid bilayers are ubiquitous in modern cells, their impermeability, lack of dynamic properties, and synthetic complexity are difficult to reconcile with plausible pathways of proto-metabolism, growth and division. Here, we present an alternative membrane-free model, which demonstrates that low-molecular-weight mononucleotides and simple cationic peptides spontaneously accumulate in water into microdroplets that are stable to changes in temperature and salt concentration, undergo pH-induced cycles of growth and decay, and promote $\alpha$-helical peptide secondary structure. Moreover, the microdroplets selectively sequester porphyrins, inorganic nanoparticles and enzymes to generate supramolecular stacked arrays of light-harvesting molecules, nanoparticle-mediated oxidase activity, and enhanced rates of glucose phosphorylation, respectively. Taken together, our results suggest that peptide-nucleotide microdroplets can be considered as a new type of protocell model that could be used to develop novel bioreactors, primitive artificial cells and plausible pathways to prebiotic organization before the emergence of lipid-based compartmentalization on the early Earth.}, 378 | author = {Koga, Shogo and Williams, David S and Perriman, Adam W and Mann, Stephen}, 379 | doi = {10.1038/nchem.1110}, 380 | file = {:Users/damascus/Documents/Mendeley\_papers/Koga et al. - 2011 - Nature chemistry.pdf:pdf}, 381 | issn = {1755-4349}, 382 | journal = {Nature chemistry}, 383 | keywords = {Artificial Cells,Artificial Cells: chemistry,Catalysis,Nanoparticles,Nanoparticles: chemistry,Nucleotides,Nucleotides: chemistry,Peptides,Peptides: chemistry}, 384 | month = sep, 385 | number = {9}, 386 | pages = {720--4}, 387 | pmid = {21860462}, 388 | publisher = {Nature Publishing Group}, 389 | title = {{Peptide-nucleotide microdroplets as a step towards a membrane-free protocell model.}}, 390 | url = {http://www.ncbi.nlm.nih.gov/pubmed/21860462}, 391 | volume = {3}, 392 | year = {2011} 393 | } 394 | @article{Kurihara2011, 395 | abstract = {The construction of a protocell from a materials point of view is important in understanding the origin of life. Both self-reproduction of a compartment and self-replication of an informational substance have been studied extensively, but these processes have typically been carried out independently, rather than linked to one another. Here, we demonstrate the amplification of DNA (encapsulated guest) within a self-reproducible cationic giant vesicle (host). With the addition of a vesicular membrane precursor, we observe the growth and spontaneous division of the giant vesicles, accompanied by distribution of the DNA to the daughter giant vesicles. In particular, amplification of the DNA accelerated the division of the giant vesicles. This means that self-replication of an informational substance has been linked to self-reproduction of a compartment through the interplay between polyanionic DNA and the cationic vesicular membrane. Our self-reproducing giant vesicle system therefore represents a step forward in the construction of an advanced model protocell.}, 396 | author = {Kurihara, Kensuke and Tamura, Mieko and Shohda, Koh-Ichiroh and Toyota, Taro and Suzuki, Kentaro and Sugawara, Tadashi}, 397 | doi = {10.1038/nchem.1127}, 398 | file = {:Users/damascus/Documents/Mendeley\_papers/Kurihara et al. - 2011 - Nature chemistry.pdf:pdf}, 399 | issn = {1755-4349}, 400 | journal = {Nature chemistry}, 401 | keywords = {Artificial Cells,Artificial Cells: chemistry,Artificial Cells: metabolism,Biogenesis,DNA,DNA: metabolism,Lipid Bilayers,Lipid Bilayers: chemistry,Lipid Bilayers: metabolism,Phosphatidylcholines,Phosphatidylcholines: chemistry,Phosphatidylglycerols,Phosphatidylglycerols: chemistry,Polymerase Chain Reaction,Rhodamines,Rhodamines: chemistry}, 402 | month = oct, 403 | number = {10}, 404 | pages = {775--81}, 405 | pmid = {21941249}, 406 | publisher = {Nature Publishing Group}, 407 | title = {{Self-reproduction of supramolecular giant vesicles combined with the amplification of encapsulated DNA.}}, 408 | url = {http://www.ncbi.nlm.nih.gov/pubmed/21941249}, 409 | volume = {3}, 410 | year = {2011} 411 | } 412 | @article{Lazcano2010, 413 | abstract = {Following the publication of the Origin of Species in 1859, many naturalists adopted the idea that living organisms were the historical outcome of gradual transformation of lifeless matter. These views soon merged with the developments of biochemistry and cell biology and led to proposals in which the origin of protoplasm was equated with the origin of life. The heterotrophic origin of life proposed by Oparin and Haldane in the 1920s was part of this tradition, which Oparin enriched by transforming the discussion of the emergence of the first cells into a workable multidisciplinary research program. On the other hand, the scientific trend toward understanding biological phenomena at the molecular level led authors like Troland, Muller, and others to propose that single molecules or viruses represented primordial living systems. The contrast between these opposing views on the origin of life represents not only contrasting views of the nature of life itself, but also major ideological discussions that reached a surprising intensity in the years following Stanley Miller's seminal result which showed the ease with which organic compounds of biochemical significance could be synthesized under putative primitive conditions. In fact, during the years following the Miller experiment, attempts to understand the origin of life were strongly influenced by research on DNA replication and protein biosynthesis, and, in socio-political terms, by the atmosphere created by Cold War tensions. The catalytic versatility of RNA molecules clearly merits a critical reappraisal of Muller's viewpoint. However, the discovery of ribozymes does not imply that autocatalytic nucleic acid molecules ready to be used as primordial genes were floating in the primitive oceans, or that the RNA world emerged completely assembled from simple precursors present in the prebiotic soup. The evidence supporting the presence of a wide range of organic molecules on the primitive Earth, including membrane-forming compounds, suggests that the evolution of membrane-bounded molecular systems preceded cellular life on our planet, and that life is the evolutionary outcome of a process, not of a single, fortuitous event.}, 414 | author = {Lazcano, Antonio}, 415 | doi = {10.1101/cshperspect.a002089}, 416 | file = {:Users/damascus/Documents/Mendeley\_papers/Lazcano - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf}, 417 | issn = {1943-0264}, 418 | journal = {Cold Spring Harbor perspectives in biology}, 419 | keywords = {Biogenesis,Biological Evolution,Biology,Biology: history,History, 19th Century,History, 20th Century}, 420 | month = nov, 421 | number = {11}, 422 | pages = {a002089}, 423 | pmid = {20534710}, 424 | title = {{Historical development of origins research.}}, 425 | url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2964185\&tool=pmcentrez\&rendertype=abstract}, 426 | volume = {2}, 427 | year = {2010} 428 | } 429 | @article{Li2014, 430 | abstract = {The five-membered furanose ring is a central component of the chemical structure of biological nucleic acids. The conformations of the furanose ring can be analytically described using the concept of pseudorotation, and for RNA and DNA they are dominated by the C2'-endo and C3'-endo conformers. While the free energy difference between these two conformers can be inferred from NMR measurements, a free energy landscape of the complete pseudorotation cycle of nucleic acids in solution has remained elusive. Here, we describe a new free energy calculation method for molecular dynamics (MD) simulations using the two pseudorotation parameters directly as the collective variables. To validate our approach, we calculated the free energy surface of ribose pseudorotation in guanosine and 2'-deoxyguanosine. The calculated free energy landscape reveals not only the relative stability of the different pseudorotation conformers, but also the main transition path between the stable conformations. Applying this method to a standard A-form RNA duplex uncovered the expected minimum at the C3'-endo state. However, at a 2'-5' linkage, the minimum shifts to the C2'-endo conformation. The free energy of the C3'-endo conformation is 3 kcal/mol higher due to a weaker hydrogen bond and a reduced base stacking interaction. Unrestrained MD simulations suggest that the conversion from C3'-endo to C2'-endo and vice versa is on the nanosecond and microsecond time scale, respectively. These calculations suggest that 2'-5' linkages may enable folded RNAs to sample a wider spectrum of their pseudorotation conformations.}, 431 | author = {Li, Li and Szostak, Jack W}, 432 | doi = {10.1021/ja412079b}, 433 | file = {:Users/damascus/Documents/Mendeley\_papers/Li, Szostak - 2014 - Journal of the American Chemical Society.pdf:pdf}, 434 | issn = {1520-5126}, 435 | journal = {Journal of the American Chemical Society}, 436 | month = feb, 437 | number = {7}, 438 | pages = {2858--65}, 439 | pmid = {24499340}, 440 | title = {{The free energy landscape of pseudorotation in 3'-5' and 2'-5' linked nucleic acids.}}, 441 | url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3982932\&tool=pmcentrez\&rendertype=abstract}, 442 | volume = {136}, 443 | year = {2014} 444 | } 445 | @article{Luisi2011, 446 | author = {Luisi, Pier Luigi and Stano, Pasquale}, 447 | doi = {10.1038/nchem.1156}, 448 | file = {:Users/damascus/Documents/Mendeley\_papers/Luisi, Stano - 2011 - Nature chemistry.pdf:pdf}, 449 | issn = {1755-4349}, 450 | journal = {Nature chemistry}, 451 | keywords = {Artificial Cells,Artificial Cells: metabolism,DNA,DNA: metabolism,Lipid Bilayers,Lipid Bilayers: chemistry}, 452 | month = oct, 453 | number = {10}, 454 | pages = {755--6}, 455 | pmid = {21941243}, 456 | publisher = {Nature Publishing Group}, 457 | title = {{Synthetic biology: minimal cell mimicry.}}, 458 | url = {http://www.ncbi.nlm.nih.gov/pubmed/21941243}, 459 | volume = {3}, 460 | year = {2011} 461 | } 462 | @article{Mansy2010, 463 | abstract = {Although model protocellular membranes consisting of monoacyl lipids are similar to membranes composed of contemporary diacyl lipids, they differ in at least one important aspect. Model protocellular membranes allow for the passage of polar solutes and thus can potentially support cell-to functions without the aid of transport machinery. The ability to transport polar molecules likely stems from increased lipid dynamics. Selectively permeable vesicle membranes composed of monoacyl lipids allow for many lifelike processes to emerge from a remarkably small set of molecules.}, 464 | author = {Mansy, Sheref S}, 465 | doi = {10.1101/cshperspect.a002188}, 466 | file = {:Users/damascus/Documents/Mendeley\_papers/Mansy - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf}, 467 | issn = {1943-0264}, 468 | journal = {Cold Spring Harbor perspectives in biology}, 469 | keywords = {Biological Evolution,Biological Transport,Cell Membrane,Cell Membrane: metabolism,Diffusion,Fatty Acids,Fatty Acids: chemistry,Lipids,Lipids: chemistry,Membrane Lipids,Membrane Lipids: metabolism,Models, Biological,Models, Chemical,Permeability,Protein Transport,Solubility}, 470 | month = aug, 471 | number = {8}, 472 | pages = {a002188}, 473 | pmid = {20679338}, 474 | title = {{Membrane transport in primitive cells.}}, 475 | url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2908771\&tool=pmcentrez\&rendertype=abstract}, 476 | volume = {2}, 477 | year = {2010} 478 | } 479 | @article{McKay2010, 480 | abstract = {Evidence of past liquid water on the surface of Mars suggests that this world once had habitable conditions and leads to the question of life. If there was life on Mars, it would be interesting to determine if it represented a separate origin from life on Earth. To determine the biochemistry and genetics of life on Mars requires that we have access to an organism or the biological remains of one-possibly preserved in ancient permafrost. A way to determine if organic material found on Mars represents the remains of an alien biological system could be based on the observation that biological systems select certain organic molecules over others that are chemically similar (e.g., chirality in amino acids).}, 481 | author = {McKay, Christopher P}, 482 | doi = {10.1101/cshperspect.a003509}, 483 | file = {:Users/damascus/Documents/Mendeley\_papers/McKay - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf}, 484 | issn = {1943-0264}, 485 | journal = {Cold Spring Harbor perspectives in biology}, 486 | keywords = {Biogenesis,Exobiology,Mars,Water}, 487 | month = apr, 488 | number = {4}, 489 | pages = {a003509}, 490 | pmid = {20452949}, 491 | title = {{An origin of life on Mars.}}, 492 | url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2845199\&tool=pmcentrez\&rendertype=abstract}, 493 | volume = {2}, 494 | year = {2010} 495 | } 496 | @article{Pizzarello2010, 497 | abstract = {Carbon-containing meteorites provide a natural sample of the extraterrestrial organic chemistry that occurred in the solar system ahead of life's origin on the Earth. Analyses of 40 years have shown the organic content of these meteorites to be materials as diverse as kerogen-like macromolecules and simpler soluble compounds such as amino acids and polyols. Many meteoritic molecules have identical counterpart in the biosphere and, in a primitive group of meteorites, represent the majority of their carbon. Most of the compounds in meteorites have isotopic compositions that date their formation to presolar environments and reveal a long and active cosmochemical evolution of the biogenic elements. Whether this evolution resumed on the Earth to foster biogenesis after exogenous delivery of meteoritic and cometary materials is not known, yet, the selective abundance of biomolecule precursors evident in some cosmic environments and the unique L-asymmetry of some meteoritic amino acids are suggestive of their possible contribution to terrestrial molecular evolution.}, 498 | author = {Pizzarello, Sandra and Shock, Everett}, 499 | doi = {10.1101/cshperspect.a002105}, 500 | file = {:Users/damascus/Documents/Mendeley\_papers/Pizzarello, Shock - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf}, 501 | issn = {1943-0264}, 502 | journal = {Cold Spring Harbor perspectives in biology}, 503 | keywords = {Biogenesis,Carbon,Carbon: chemistry,Chemistry, Organic,Chemistry, Organic: methods,Earth (Planet),Evolution, Chemical,Extraterrestrial Environment,Meteoroids,Solar System}, 504 | month = mar, 505 | number = {3}, 506 | pages = {a002105}, 507 | pmid = {20300213}, 508 | title = {{The organic composition of carbonaceous meteorites: the evolutionary story ahead of biochemistry.}}, 509 | url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2829962\&tool=pmcentrez\&rendertype=abstract}, 510 | volume = {2}, 511 | year = {2010} 512 | } 513 | @article{Powner2013, 514 | author = {Powner, Matthew}, 515 | doi = {10.1038/nchem.1629}, 516 | file = {:Users/damascus/Documents/Mendeley\_papers/Powner - 2013 - Nature chemistry.pdf:pdf}, 517 | issn = {1755-4349}, 518 | journal = {Nature chemistry}, 519 | month = may, 520 | number = {5}, 521 | pages = {355--7}, 522 | pmid = {23609075}, 523 | title = {{Asking original questions. Interview by Stephen Davey.}}, 524 | url = {http://www.ncbi.nlm.nih.gov/pubmed/23609075}, 525 | volume = {5}, 526 | year = {2013} 527 | } 528 | @article{Ritson2012, 529 | abstract = {A recent synthesis of activated pyrimidine ribonucleotides under prebiotically plausible conditions relied on mixed oxygenous and nitrogenous systems chemistry. As it stands, this synthesis provides support for the involvement of RNA in the origin of life, but such support would be considerably strengthened if the sugar building blocks for the synthesis--glycolaldehyde and glyceraldehyde--could be shown to derive from one carbon feedstock molecules using similarly mixed oxygenous and nitrogenous systems chemistry. Here, we show that these sugars can be formed from hydrogen cyanide by ultraviolet irradiation in the presence of cyanometallates in a remarkable systems chemistry process. Using copper cyanide complexes, the process operates catalytically to disproportionate hydrogen cyanide, first generating the sugars and then sequestering them as simple derivatives.}, 530 | author = {Ritson, Dougal and Sutherland, John D}, 531 | doi = {10.1038/nchem.1467}, 532 | file = {:Users/damascus/Documents/Mendeley\_papers/Ritson, Sutherland - 2012 - Nature chemistry.pdf:pdf}, 533 | issn = {1755-4349}, 534 | journal = {Nature chemistry}, 535 | keywords = {Carbohydrates,Carbohydrates: chemical synthesis,Carbohydrates: chemistry,Chemistry Techniques,Hydrogen Cyanide,Hydrogen Cyanide: chemistry,Oxidation-Reduction,Photochemical Processes,Prebiotics,Synthetic}, 536 | month = nov, 537 | number = {11}, 538 | pages = {895--9}, 539 | pmid = {23089863}, 540 | publisher = {Nature Publishing Group}, 541 | title = {{Prebiotic synthesis of simple sugars by photoredox systems chemistry.}}, 542 | url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3589744\&tool=pmcentrez\&rendertype=abstract}, 543 | volume = {4}, 544 | year = {2012} 545 | } 546 | @article{Rodrigo2012, 547 | abstract = {A grand challenge in synthetic biology is to use our current knowledge of RNA science to perform the automatic engineering of completely synthetic sequences encoding functional RNAs in living cells. We report here a fully automated design methodology and experimental validation of synthetic RNA interaction circuits working in a cellular environment. The computational algorithm, based on a physicochemical model, produces novel RNA sequences by exploring the space of possible sequences compatible with predefined structures. We tested our methodology in Escherichia coli by designing several positive riboregulators with diverse structures and interaction models, suggesting that only the energy of formation and the activation energy (free energy barrier to overcome for initiating the hybridization reaction) are sufficient criteria to engineer RNA interaction and regulation in bacteria. The designed sequences exhibit nonsignificant similarity to any known noncoding RNA sequence. Our riboregulatory devices work independently and in combination with transcription regulation to create complex logic circuits. Our results demonstrate that a computational methodology based on first-principles can be used to engineer interacting RNAs with allosteric behavior in living cells.}, 548 | author = {Rodrigo, Guillermo and Landrain, Thomas E and Jaramillo, Alfonso}, 549 | doi = {10.1073/pnas.1203831109}, 550 | file = {:Users/damascus/Documents/Mendeley\_papers/Rodrigo, Landrain, Jaramillo - 2012 - Proceedings of the National Academy of Sciences of the United States of America.pdf:pdf}, 551 | issn = {1091-6490}, 552 | journal = {Proceedings of the National Academy of Sciences of the United States of America}, 553 | keywords = {Automation,Chemistry, Physical,Chemistry, Physical: methods,Computational Biology,Computational Biology: methods,Escherichia coli,Escherichia coli: genetics,Escherichia coli: metabolism,Evolution, Molecular,Flow Cytometry,Flow Cytometry: methods,Genes, Reporter,Genetic Engineering,Genetic Engineering: methods,Models, Genetic,Nucleic Acid Conformation,Plasmids,Plasmids: metabolism,Promoter Regions, Genetic,RNA,RNA Processing, Post-Transcriptional,RNA Processing, Post-Transcriptional: genetics,RNA: chemistry,RNA: genetics,Spectrometry, Fluorescence,Spectrometry, Fluorescence: methods,Synthetic Biology,Synthetic Biology: methods,Thermodynamics}, 554 | month = sep, 555 | number = {38}, 556 | pages = {15271--6}, 557 | pmid = {22949707}, 558 | title = {{De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells.}}, 559 | url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3458397\&tool=pmcentrez\&rendertype=abstract}, 560 | volume = {109}, 561 | year = {2012} 562 | } 563 | @article{Schoning2000, 564 | author = {Schoning, K.-U. and Scholz, P. and Guntha, S. and Wu, X. and Krishnamurthy, R. and Eschenmoser, A.}, 565 | doi = {10.1126/science.290.5495.1347}, 566 | file = {:Users/damascus/Documents/Mendeley\_papers/Schoning et al. - 2000 - Science.pdf:pdf}, 567 | issn = {00368075}, 568 | journal = {Science}, 569 | month = nov, 570 | number = {5495}, 571 | pages = {1347--1351}, 572 | title = {{Chemical Etiology of Nucleic Acid Structure: The alpha -Threofuranosyl-(3'rightarrow 2') Oligonucleotide System}}, 573 | url = {http://www.sciencemag.org/cgi/doi/10.1126/science.290.5495.1347}, 574 | volume = {290}, 575 | year = {2000} 576 | } 577 | @article{Schrum2010, 578 | abstract = {Understanding the origin of cellular life on Earth requires the discovery of plausible pathways for the transition from complex prebiotic chemistry to simple biology, defined as the emergence of chemical assemblies capable of Darwinian evolution. We have proposed that a simple primitive cell, or protocell, would consist of two key components: a protocell membrane that defines a spatially localized compartment, and an informational polymer that allows for the replication and inheritance of functional information. Recent studies of vesicles composed of fatty-acid membranes have shed considerable light on pathways for protocell growth and division, as well as means by which protocells could take up nutrients from their environment. Additional work with genetic polymers has provided insight into the potential for chemical genome replication and compatibility with membrane encapsulation. The integration of a dynamic fatty-acid compartment with robust, generalized genetic polymer replication would yield a laboratory model of a protocell with the potential for classical Darwinian biological evolution, and may help to evaluate potential pathways for the emergence of life on the early Earth. Here we discuss efforts to devise such an integrated protocell model.}, 579 | author = {Schrum, Jason P and Zhu, Ting F and Szostak, Jack W}, 580 | doi = {10.1101/cshperspect.a002212}, 581 | file = {:Users/damascus/Documents/Mendeley\_papers/Schrum, Zhu, Szostak - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf}, 582 | issn = {1943-0264}, 583 | journal = {Cold Spring Harbor perspectives in biology}, 584 | keywords = {Artificial Cells,Artificial Cells: chemistry,Biogenesis,Cell Membrane,Cell Membrane: chemistry,Evolution, Chemical,Fatty Acids,Fatty Acids: chemistry}, 585 | month = sep, 586 | number = {9}, 587 | pages = {a002212}, 588 | pmid = {20484387}, 589 | title = {{The origins of cellular life.}}, 590 | url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2926753\&tool=pmcentrez\&rendertype=abstract}, 591 | volume = {2}, 592 | year = {2010} 593 | } 594 | @article{Sheng2014, 595 | abstract = {The mixture of 2'-5' and 3'-5' linkages generated during the nonenzymatic replication of RNA has long been regarded as a central problem for the origin of the RNA world. However, we recently observed that both a ribozyme and an RNA aptamer retain considerable functionality in the presence of prebiotically plausible levels of linkage heterogeneity. To better understand the RNA structure and function in the presence of backbone linkage heterogeneity, we obtained high-resolution X-ray crystal structures of a native 10-mer RNA duplex (1.32 \AA) and two variants: one containing one 2'-5' linkage per strand (1.55 \AA) and one containing three such linkages per strand (1.20 \AA). We found that RNA duplexes adjust their local structures to accommodate the perturbation caused by 2'-5' linkages, with the flanking nucleotides buffering the disruptive effects of the isomeric linkage and resulting in a minimally altered global structure. Although most 2'-linked sugars were in the expected 2'-endo conformation, some were partially or fully in the 3'-endo conformation, suggesting that the energy difference between these conformations was relatively small. Our structural and molecular dynamic studies also provide insight into the diminished thermal and chemical stability of the duplex state associated with the presence of 2'-5' linkages. Our results contribute to the view that a low level of 2'-5' substitution would not have been fatal in an early RNA world and may in contrast have been helpful for both the emergence of nonenzymatic RNA replication and the early evolution of functional RNAs.}, 596 | author = {Sheng, Jia and Li, Li and Engelhart, Aaron E and Gan, Jianhua and Wang, Jiawei and Szostak, Jack W}, 597 | doi = {10.1073/pnas.1317799111}, 598 | file = {:Users/damascus/Documents/Mendeley\_papers/Sheng et al. - 2014 - Proceedings of the National Academy of Sciences of the United States of America.pdf:pdf}, 599 | issn = {1091-6490}, 600 | journal = {Proceedings of the National Academy of Sciences of the United States of America}, 601 | keywords = {Base Sequence,Crystallography, X-Ray,Models, Molecular,Molecular Dynamics Simulation,Nucleic Acid Conformation,Nucleic Acid Heteroduplexes,Nucleic Acid Heteroduplexes: chemistry,Oligonucleotides,Oligonucleotides: genetics,RNA,RNA: chemistry}, 602 | month = feb, 603 | number = {8}, 604 | pages = {3050--5}, 605 | pmid = {24516151}, 606 | title = {{Structural insights into the effects of 2'-5' linkages on the RNA duplex.}}, 607 | url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3939906\&tool=pmcentrez\&rendertype=abstract}, 608 | volume = {111}, 609 | year = {2014} 610 | } 611 | @article{Sleep2010, 612 | abstract = {A sparse geological record combined with physics and molecular phylogeny constrains the environmental conditions on the early Earth. The Earth began hot after the moon-forming impact and cooled to the point where liquid water was present in approximately 10 million years. Subsequently, a few asteroid impacts may have briefly heated surface environments, leaving only thermophile survivors in kilometer-deep rocks. A warm 500 K, 100 bar CO(2) greenhouse persisted until subducted oceanic crust sequestered CO(2) into the mantle. It is not known whether the Earth's surface lingered in a approximately 70 degrees C thermophile environment well into the Archaean or cooled to clement or freezing conditions in the Hadean. Recently discovered approximately 4.3 Ga rocks near Hudson Bay may have formed during the warm greenhouse. Alkalic rocks in India indicate carbonate subduction by 4.26 Ga. The presence of 3.8 Ga black shales in Greenland indicates that S-based photosynthesis had evolved in the oceans and likely Fe-based photosynthesis and efficient chemical weathering on land. Overall, mantle derived rocks, especially kimberlites and similar CO(2)-rich magmas, preserve evidence of subducted upper oceanic crust, ancient surface environments, and biosignatures of photosynthesis.}, 613 | author = {Sleep, Norman H}, 614 | doi = {10.1101/cshperspect.a002527}, 615 | file = {:Users/damascus/Documents/Mendeley\_papers/Sleep - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf}, 616 | issn = {1943-0264}, 617 | journal = {Cold Spring Harbor perspectives in biology}, 618 | keywords = {Earth (Planet),Environment,Evolution, Planetary,Geologic Sediments,Geologic Sediments: chemistry,Minerals,Minerals: chemistry}, 619 | month = jun, 620 | number = {6}, 621 | pages = {a002527}, 622 | pmid = {20516134}, 623 | title = {{The Hadean-Archaean environment.}}, 624 | url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2869525\&tool=pmcentrez\&rendertype=abstract}, 625 | volume = {2}, 626 | year = {2010} 627 | } 628 | @article{Strulson2012, 629 | abstract = {RNA performs important cellular functions in contemporary life forms. Its ability to act both as a catalyst and a storage mechanism for genetic information is also an important part of the RNA world hypothesis. Compartmentalization within modern cells allows the local concentration of RNA to be controlled and it has been suggested that this was also important in early life forms. Here, we mimic intracellular compartmentalization and macromolecular crowding by partitioning RNA in an aqueous two-phase system (ATPS). We show that the concentration of RNA is enriched by up to 3,000-fold in the dextran-rich phase of a polyethylene glycol/dextran ATPS and demonstrate that this can lead to approximately 70-fold increase in the rate of ribozyme cleavage. This rate enhancement can be tuned by the relative volumes of the two phases in the ATPS. Our observations support the importance of compartmentalization in the attainment of function in an RNA World as well as in modern biology.}, 630 | author = {Strulson, Christopher a and Molden, Rosalynn C and Keating, Christine D and Bevilacqua, Philip C}, 631 | doi = {10.1038/nchem.1466}, 632 | file = {:Users/damascus/Documents/Mendeley\_papers/Strulson et al. - 2012 - Nature chemistry.pdf:pdf}, 633 | issn = {1755-4349}, 634 | journal = {Nature chemistry}, 635 | keywords = {Biocatalysis,Biomimetics,Catalytic,Catalytic: metabolism,Cell Compartmentation,Dextrans,Dextrans: chemistry,Intracellular Space,Intracellular Space: metabolism,Polyethylene Glycols,Polyethylene Glycols: chemistry,RNA,Water,Water: chemistry}, 636 | month = nov, 637 | number = {11}, 638 | pages = {941--6}, 639 | pmid = {23089870}, 640 | publisher = {Nature Publishing Group}, 641 | title = {{RNA catalysis through compartmentalization.}}, 642 | url = {http://www.ncbi.nlm.nih.gov/pubmed/23089870}, 643 | volume = {4}, 644 | year = {2012} 645 | } 646 | @article{Sutherland2010, 647 | abstract = {It has normally been assumed that ribonucleotides arose on the early Earth through a process in which ribose, the nucleobases, and phosphate became conjoined. However, under plausible prebiotic conditions, condensation of nucleobases with ribose to give beta-ribonucleosides is fraught with difficulties. The reaction with purine nucleobases is low-yielding and the reaction with the canonical pyrimidine nucleobases does not work at all. The reasons for these difficulties are considered and an alternative high-yielding synthesis of pyrimidine nucleotides is discussed. Fitting the new synthesis to a plausible geochemical scenario is a remaining challenge but the prospects appear good. Discovery of an improved method of purine synthesis, and an efficient means of stringing activated nucleotides together, will provide underpinning support to those theories that posit a central role for RNA in the origins of life.}, 648 | author = {Sutherland, John D}, 649 | doi = {10.1101/cshperspect.a005439}, 650 | file = {:Users/damascus/Documents/Mendeley\_papers/Sutherland - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf}, 651 | issn = {1943-0264}, 652 | journal = {Cold Spring Harbor perspectives in biology}, 653 | keywords = {Biogenesis,Evolution, Chemical,Ribonucleotides,Ribonucleotides: biosynthesis,Ribonucleotides: chemistry,Ribonucleotides: genetics}, 654 | month = apr, 655 | number = {4}, 656 | pages = {a005439}, 657 | pmid = {20452951}, 658 | title = {{Ribonucleotides.}}, 659 | url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2845210\&tool=pmcentrez\&rendertype=abstract}, 660 | volume = {2}, 661 | year = {2010} 662 | } 663 | @article{Walker2014, 664 | author = {Walker, Sara}, 665 | doi = {10.3390/info5030424}, 666 | file = {:Users/damascus/Documents/Mendeley\_papers/Walker - 2014 - Information.pdf:pdf}, 667 | issn = {2078-2489}, 668 | journal = {Information}, 669 | keywords = {"origin of life,emergence,origin of life,top-down causation,top-down causation"}, 670 | month = jul, 671 | number = {3}, 672 | pages = {424--439}, 673 | title = {{Top-Down Causation and the Rise of Information in the Emergence of Life}}, 674 | url = {http://www.mdpi.com/2078-2489/5/3/424/}, 675 | volume = {5}, 676 | year = {2014} 677 | } 678 | @article{Xayaphoummine2007, 679 | abstract = {RNA co-transcriptional folding has long been suspected to play an active role in helping proper native folding of ribozymes and structured regulatory motifs in mRNA untranslated regions (UTRs). Yet, the underlying mechanisms and coding requirements for efficient co-transcriptional folding remain unclear. Traditional approaches have intrinsic limitations to dissect RNA folding paths, as they rely on sequence mutations or circular permutations that typically perturb both RNA folding paths and equilibrium structures. Here, we show that exploiting sequence symmetries instead of mutations can circumvent this problem by essentially decoupling folding paths from equilibrium structures of designed RNA sequences. Using bistable RNA switches with symmetrical helices conserved under sequence reversal, we demonstrate experimentally that native and transiently formed helices can guide efficient co-transcriptional folding into either long-lived structure of these RNA switches. Their folding path is controlled by the order of helix nucleations and subsequent exchanges during transcription, and may also be redirected by transient antisense interactions. Hence, transient intra- and inter-molecular base pair interactions can effectively regulate the folding of nascent RNA molecules into different native structures, provided limited coding requirements, as discussed from an information theory perspective. This constitutive coupling between RNA synthesis and RNA folding regulation may have enabled the early emergence of autonomous RNA-based regulation networks.}, 680 | author = {Xayaphoummine, a and Viasnoff, V and Harlepp, S and Isambert, H}, 681 | doi = {10.1093/nar/gkl1036}, 682 | file = {:Users/damascus/Documents/Mendeley\_papers/Xayaphoummine et al. - 2007 - Nucleic acids research.pdf:pdf}, 683 | issn = {1362-4962}, 684 | journal = {Nucleic acids research}, 685 | keywords = {Base Sequence,Molecular Sequence Data,Nucleic Acid Conformation,RNA,RNA: chemistry,Regulatory Sequences, Ribonucleic Acid,Sequence Alignment,Transcription, Genetic}, 686 | month = jan, 687 | number = {2}, 688 | pages = {614--22}, 689 | pmid = {17178750}, 690 | title = {{Encoding folding paths of RNA switches.}}, 691 | url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1802593\&tool=pmcentrez\&rendertype=abstract}, 692 | volume = {35}, 693 | year = {2007} 694 | } 695 | @article{Yu2012, 696 | abstract = {The pre-RNA world hypothesis postulates that RNA was preceded in the evolution of life by a simpler genetic material, but it is not known if such systems can fold into structures capable of eliciting a desired function. Presumably, whatever chemistry gave rise to RNA would have produced other RNA analogues, some of which may have preceded or competed directly with RNA. Threose nucleic acid (TNA), a potentially natural derivative of RNA, has received considerable interest as a possible RNA progenitor due to its chemical simplicity and ability to exchange genetic information with itself and RNA. Here, we have applied Darwinian evolution methods to evolve, in vitro, a TNA receptor that binds to an arbitrary target with high affinity and specificity. This demonstration shows that TNA has the ability to fold into tertiary structures with sophisticated chemical functions, which provides evidence that TNA could have served as an ancestral genetic system during an early stage of life.}, 697 | author = {Yu, Hanyang and Zhang, Su and Chaput, John C}, 698 | doi = {10.1038/nchem.1241}, 699 | file = {:Users/damascus/Documents/Mendeley\_papers/Yu, Zhang, Chaput - 2012 - Nature chemistry.pdf:pdf}, 700 | issn = {1755-4349}, 701 | journal = {Nature chemistry}, 702 | keywords = {Animals,Aptamers, Nucleotide,Aptamers, Nucleotide: chemistry,Aptamers, Nucleotide: genetics,Base Sequence,Cattle,DNA,DNA: chemistry,DNA: genetics,DNA: metabolism,Evolution, Molecular,Gene Library,Humans,Models, Genetic,Molecular Sequence Data,Protein Binding,RNA,RNA: chemistry,RNA: genetics,RNA: metabolism,Serum Albumin, Bovine,Serum Albumin, Bovine: chemistry,Serum Albumin, Bovine: genetics,Streptavidin,Streptavidin: chemistry,Streptavidin: genetics,Tetroses,Tetroses: chemistry,Tetroses: genetics,Thrombin,Thrombin: chemistry,Thrombin: genetics}, 703 | month = mar, 704 | number = {3}, 705 | pages = {183--7}, 706 | pmid = {22354431}, 707 | publisher = {Nature Publishing Group}, 708 | title = {{Darwinian evolution of an alternative genetic system provides support for TNA as an RNA progenitor.}}, 709 | url = {http://www.ncbi.nlm.nih.gov/pubmed/22354431}, 710 | volume = {4}, 711 | year = {2012} 712 | } 713 | @article{Zahnle2010, 714 | abstract = {Earth is the one known example of an inhabited planet and to current knowledge the likeliest site of the one known origin of life. Here we discuss the origin of Earth's atmosphere and ocean and some of the environmental conditions of the early Earth as they may relate to the origin of life. A key punctuating event in the narrative is the Moon-forming impact, partly because it made Earth for a short time absolutely uninhabitable, and partly because it sets the boundary conditions for Earth's subsequent evolution. If life began on Earth, as opposed to having migrated here, it would have done so after the Moon-forming impact. What took place before the Moon formed determined the bulk properties of the Earth and probably determined the overall compositions and sizes of its atmospheres and oceans. What took place afterward animated these materials. One interesting consequence of the Moon-forming impact is that the mantle is devolatized, so that the volatiles subsequently fell out in a kind of condensation sequence. This ensures that the volatiles were concentrated toward the surface so that, for example, the oceans were likely salty from the start. We also point out that an atmosphere generated by impact degassing would tend to have a composition reflective of the impacting bodies (rather than the mantle), and these are almost without exception strongly reducing and volatile-rich. A consequence is that, although CO- or methane-rich atmospheres are not necessarily stable as steady states, they are quite likely to have existed as long-lived transients, many times. With CO comes abundant chemical energy in a metastable package, and with methane comes hydrogen cyanide and ammonia as important albeit less abundant gases.}, 715 | author = {Zahnle, Kevin and Schaefer, Laura and Fegley, Bruce}, 716 | doi = {10.1101/cshperspect.a004895}, 717 | file = {:Users/damascus/Documents/Mendeley\_papers/Zahnle, Schaefer, Fegley - 2010 - Cold Spring Harbor perspectives in biology.pdf:pdf}, 718 | issn = {1943-0264}, 719 | journal = {Cold Spring Harbor perspectives in biology}, 720 | keywords = {Atmosphere,Atmosphere: chemistry,Biogenesis,Earth (Planet),Moon}, 721 | month = oct, 722 | number = {10}, 723 | pages = {a004895}, 724 | pmid = {20573713}, 725 | title = {{Earth's earliest atmospheres.}}, 726 | url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2944365\&tool=pmcentrez\&rendertype=abstract}, 727 | volume = {2}, 728 | year = {2010} 729 | } 730 | @article{Zeravcic2014, 731 | author = {Zeravcic, Z and Brenner, M P}, 732 | doi = {10.1073/pnas.1313601111}, 733 | file = {:Users/damascus/Desktop/toRead/Brenner.pdf:pdf}, 734 | journal = {Proceedings of the National Academy of Sciences}, 735 | month = jan, 736 | number = {13}, 737 | pages = {1--6}, 738 | title = {{Self-replicating colloidal clusters}}, 739 | url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1313601111}, 740 | volume = {2013}, 741 | year = {2014} 742 | } 743 | @misc{, 744 | file = {:Users/damascus/Documents/Mendeley\_papers/Unknown - Unknown - Unknown(3).pdf:pdf}, 745 | title = {{Isambert\_1.pdf}} 746 | } 747 | @article{, 748 | doi = {10.1038/nchem.1647}, 749 | file = {:Users/damascus/Documents/Mendeley\_papers/Unknown - 2013 - Nature chemistry.pdf:pdf}, 750 | issn = {1755-4349}, 751 | journal = {Nature chemistry}, 752 | month = may, 753 | number = {5}, 754 | pages = {349}, 755 | pmid = {23609072}, 756 | title = {{The ascent of molecules.}}, 757 | url = {http://www.ncbi.nlm.nih.gov/pubmed/23609072}, 758 | volume = {5}, 759 | year = {2013} 760 | } 761 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aS'ROD' 3545 | p1765 3546 | aS'SODIUM' 3547 | p1766 3548 | aS'CONSCIOUS' 3549 | p1767 3550 | aS'DECOMPOSITION' 3551 | p1768 3552 | aS'SWITCHING' 3553 | p1769 3554 | aS'POINTS' 3555 | p1770 3556 | aS'FIRST' 3557 | p1771 3558 | aS'EVENTS' 3559 | p1772 3560 | aS'DEPLETION-INTERACTION' 3561 | p1773 3562 | aS'MELTING' 3563 | p1774 3564 | aS'CAVEATS' 3565 | p1775 3566 | aS'BUILT' 3567 | p1776 3568 | aS'PREDICTING' 3569 | p1777 3570 | aS'VESICULAR' 3571 | p1778 3572 | aS'REDUCTION' 3573 | p1779 3574 | aS'DESIGNED' 3575 | p1780 3576 | aS'GRAND' 3577 | p1781 3578 | aS'TUNNELING' 3579 | p1782 3580 | aS'SPONTANEOUS' 3581 | p1783 3582 | aS'EQUIVALENCES' 3583 | p1784 3584 | aS'LIMITED' 3585 | p1785 3586 | aS'NANOSTRUCTURES' 3587 | p1786 3588 | aS'DOUBLE' 3589 | p1787 3590 | aS'BIPHENOLATE-BASED' 3591 | p1788 3592 | aS'SUPERBALLS' 3593 | p1789 3594 | aS'ANNIHILATION' 3595 | p1790 3596 | aS'NANODECAHEDRA' 3597 | p1791 3598 | aS'LENGTH' 3599 | p1792 3600 | aS'MYSTERIUM' 3601 | p1793 3602 | aS'NANOSTRUCTURED' 3603 | p1794 3604 | aS'LATITUDINALLY' 3605 | p1795 3606 | aS'CONSTRAINED' 3607 | p1796 3608 | aS'HANDS-' 3609 | p1797 3610 | aS'ADVANCE' 3611 | p1798 3612 | aS'POLYMORPHS' 3613 | p1799 3614 | aS'TRANSVERSE' 3615 | p1800 3616 | aS'BALLS' 3617 | p1801 3618 | aS'STABILIZING' 3619 | p1802 3620 | aS'ATOMS' 3621 | p1803 3622 | aS'SIGMA' 3623 | p1804 3624 | aS'TM' 3625 | p1805 3626 | aS'TUNABLE' 3627 | p1806 3628 | aS'MIRRORS' 3629 | p1807 3630 | aS'LIQUID-VAPOR' 3631 | p1808 3632 | aS'MOTION' 3633 | p1809 3634 | aS'POLYMER-TETHERED' 3635 | p1810 3636 | aS'ISING' 3637 | p1811 3638 | aS'PARAMAGNETIC' 3639 | p1812 3640 | aS'INTEGRATED' 3641 | p1813 3642 | aS'INVERSE' 3643 | p1814 3644 | aS'SHEET' 3645 | p1815 3646 | aS'TRAPS' 3647 | p1816 3648 | aS'LOCALIZATION' 3649 | p1817 3650 | aS'LOCKING' 3651 | p1818 3652 | aS'CENTRIFUGATION' 3653 | p1819 3654 | aS'PHENOTYPE' 3655 | p1820 3656 | aS'GRAPHICS' 3657 | p1821 3658 | aS'CONFINED' 3659 | p1822 3660 | aS'1-MICROSECOND' 3661 | p1823 3662 | aS'DIMER' 3663 | p1824 3664 | aS'WIRES' 3665 | p1825 3666 | aS'FLUID-SOLID' 3667 | p1826 3668 | aS'SCAFFOLDED' 3669 | p1827 3670 | aS'POLYOXOMETALATES' 3671 | p1828 3672 | aS'DISSOLUTION' 3673 | p1829 3674 | aS'VICINITY' 3675 | p1830 3676 | aS'QUASICRYSTALS-WHY' 3677 | p1831 3678 | aS'CATALAN' 3679 | p1832 3680 | aS'INVESTIGATION' 3681 | p1833 3682 | aS'NUCLEUS' 3683 | p1834 3684 | aS'STRIPED' 3685 | p1835 3686 | aS'CRYO-EM' 3687 | p1836 3688 | aS'BUCKLING' 3689 | p1837 3690 | aS'MICROMACHINING' 3691 | p1838 3692 | aS'PARAMETER-FREE' 3693 | p1839 3694 | aS'FRICTION' 3695 | p1840 3696 | aS'EMISSIONS' 3697 | p1841 3698 | aS'MORPHOLOGY' 3699 | p1842 3700 | aS'STAR' 3701 | p1843 3702 | aS'-EQUILIBRIUM' 3703 | p1844 3704 | aS'COMPOSITIONALLY' 3705 | p1845 3706 | aS'I4132' 3707 | p1846 3708 | aS'PSEUDO-HARD' 3709 | p1847 3710 | aS'COULOMB' 3711 | p1848 3712 | aS'LIMITED-VALENCE' 3713 | p1849 3714 | aS'NO' 3715 | p1850 3716 | aS'KOTOV' 3717 | p1851 3718 | aS'POPULARITY' 3719 | p1852 3720 | aS'NONCONVEX' 3721 | p1853 3722 | aS'FULFILLMENT' 3723 | p1854 3724 | aS'SPECTROSCOPY' 3725 | p1855 3726 | aS'ORIGAMI' 3727 | p1856 3728 | aS'TETRAHEDRONS' 3729 | p1857 3730 | aS'CAPILLARY' 3731 | p1858 3732 | aS'VISCOUS' 3733 | p1859 3734 | aS'TRIATIC' 3735 | p1860 3736 | aS'CHLORATE' 3737 | p1861 3738 | aS'ONE-DIMENSIONAL' 3739 | p1862 3740 | aS'J' 3741 | aS'NANOSTARS' 3742 | p1863 3743 | aS'MAXIMUM' 3744 | p1864 3745 | aS'NANO-' 3746 | p1865 3747 | aS'STIMULUS-SENSITIVE' 3748 | p1866 3749 | aS'DESIGNING' 3750 | p1867 3751 | aS'OCTAPOD-SHAPED' 3752 | p1868 3753 | aS'CUI' 3754 | p1869 3755 | aS'FF' 3756 | p1870 3757 | aS'MESOPHASE' 3758 | p1871 3759 | aS'LEE' 3760 | p1872 3761 | aS'CAVITIES' 3762 | p1873 3763 | aS'GOVERNS' 3764 | p1874 3765 | aS'TRANSMISSION' 3766 | p1875 3767 | aS'SENSITIVITY' 3768 | p1876 3769 | aS'ANALYSIS' 3770 | p1877 3771 | aS'MOTIFS' 3772 | p1878 3773 | aS'QUENCHED' 3774 | p1879 3775 | aS'USE' 3776 | p1880 3777 | aS'SOFT-CORE' 3778 | p1881 3779 | aS'NANOPARTICLE-BASED' 3780 | p1882 3781 | aS'TEMPLATING' 3782 | p1883 3783 | aS'CHANGE' 3784 | p1884 3785 | aS'SCIENCE' 3786 | p1885 3787 | aS'NANOPYRAMID' 3788 | p1886 3789 | aS'HYDROGENATION' 3790 | p1887 3791 | aS'REMOVAL' 3792 | p1888 3793 | aS'CRYSTALLISATION' 3794 | p1889 3795 | aS'3-D' 3796 | p1890 3797 | aS'COMPARISON' 3798 | p1891 3799 | aS'SHELLS' 3800 | p1892 3801 | aS'VARYING' 3802 | p1893 3803 | aS'GPCR' 3804 | p1894 3805 | aS'FLEXIBLE' 3806 | p1895 3807 | aS'RESOLUTION' 3808 | p1896 3809 | aS'COORDINATION' 3810 | p1897 3811 | aS'PD' 3812 | p1898 3813 | aS'SPACE' 3814 | p1899 3815 | aS'AQUEOUS' 3816 | p1900 3817 | aS'DEPENDENCE' 3818 | p1901 3819 | aS'POSITIONING' 3820 | p1902 3821 | aS'ICE' 3822 | p1903 3823 | aS'PINNING' 3824 | p1904 3825 | aS'MICELLES' 3826 | p1905 3827 | aS'AMBER' 3828 | p1906 3829 | aS'MIXED' 3830 | p1907 3831 | aS'GPUS' 3832 | p1908 3833 | aS'OBSERVED' 3834 | p1909 3835 | aS'JAVA' 3836 | p1910 3837 | aS'MACROMOLECULE' 3838 | p1911 3839 | aS'CONTACTS' 3840 | p1912 3841 | aS'UNCOVERING' 3842 | p1913 3843 | aS'HIGH-INDEX' 3844 | p1914 3845 | aS'MICRORHEOLOGY' 3846 | p1915 3847 | aS'EXACYCLE' 3848 | p1916 3849 | a. -------------------------------------------------------------------------------- /shakespeare.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | import re, glob, sys,os 3 | import argparse 4 | import itertools as it 5 | import numpy as np 6 | import scipy.sparse 7 | import cPickle as pickle 8 | from sklearn.naive_bayes import MultinomialNB 9 | from content_sources import arxiv, bibtex, rss 10 | 11 | #remove punctuation and prepositions from a string 12 | def find_keywords(text): 13 | keywords=re.sub('[{}:?!@#$%^&*\(\)_.\\/,\'\"]','',text).upper() 14 | prepositions = open('data/prepositions.dat').read().upper().split() 15 | 16 | for p in prepositions: 17 | keywords = re.sub(r"\b{!s}\b".format(p),' ',keywords) 18 | 19 | return keywords.encode('ascii','ignore').split() 20 | 21 | #Identify good entries using naive_bayes object 22 | def filter_content(content, 23 | method, 24 | naive_bayes, 25 | keywords): 26 | 27 | new_samples = [find_keywords(entry[method]) for entry in content] 28 | 29 | #compute vector for each new entry 30 | X = scipy.sparse.lil_matrix((len(new_samples),len(keywords))) 31 | 32 | for j,kw in enumerate(keywords): 33 | for i,ns in enumerate(new_samples): 34 | X[i,j]=ns.count(kw) 35 | 36 | categories = naive_bayes.predict(X) 37 | return [e for c,e in zip(categories,content) if c =='good'] 38 | 39 | #Gather content from all sources (BibTex files, arXiv, journal RSS feeds, etc) 40 | def get_content(sources): 41 | all_content = list() 42 | for src in sources: 43 | try: 44 | src.fetch() 45 | except: 46 | print("Fetch of content from {!r} has failed".format(src)) 47 | 48 | content = None 49 | try: 50 | print('parsing {!r}'.format(src)) 51 | content = src.parse() 52 | except: 53 | print("parsing of content from {!r} has failed".format(src)) 54 | 55 | if content: 56 | all_content += content 57 | 58 | return all_content 59 | 60 | #Human review of content classification 61 | #You can review all the content, or just one that the nb classifier thought were good. 62 | #Human input is used to train the NB classifier. 63 | def review_content(good_content,content,method,review_all=False): 64 | to_review=[] 65 | if review_all: 66 | to_review = content 67 | else: 68 | to_review = good_content 69 | 70 | human_class=[] 71 | for entry in to_review: 72 | print("Is \"{}\" a good entry?".format(entry[method].encode('ascii','ignore'))) 73 | decision = raw_input('Y/n?').lower() 74 | human_class.append('good' if decision=='y' else 'bad') 75 | return human_class, to_review 76 | 77 | #Load in a trained naive_bayes object and keyword list 78 | def load_knowledge(knowledge): 79 | #existing naive_bayes object and keyword list 80 | nb=None 81 | kw=list() 82 | if knowledge is not None: 83 | if not os.path.isdir(knowledge): 84 | print("Knowledge bust be a directory") 85 | exit() 86 | 87 | kfiles = glob.glob(knowledge+'/*') 88 | if not any(f.endswith('nb.p') for f in kfiles): 89 | print("Knowledge does not contain nb.p (pickled naive bayes object)") 90 | exit() 91 | if not any(f.endswith('kw.p') for f in kfiles): 92 | print("Knowledge does not contain kw.p (pickled keyword list)") 93 | exit() 94 | 95 | else: 96 | knowledge =os.path.expanduser('~/.shakespeare') 97 | 98 | if os.path.exists(knowledge): 99 | nb=pickle.load(open(knowledge+'/nb.p')) 100 | kw=pickle.load(open(knowledge+'/kw.p')) 101 | 102 | return(nb,kw, knowledge) 103 | 104 | #Train naive_bayes object on a data set 105 | def train(good_sources, bad_sources,method,naive_bayes=None,keywords=list()): 106 | #train the algorithm 107 | good_samples = find_keywords(' '.join([entry[method] for entry in good_sources])) 108 | bad_samples = find_keywords(' '.join([entry[method] for entry in bad_sources])) 109 | 110 | 111 | #if we have an exists knowledge base to append this new information to, do so 112 | if naive_bayes: 113 | new_kws = set(good_samples+bad_samples) 114 | print('Using old keywords as well') 115 | print("# old keywords = {}\n # new keywords = {}".format(len(keywords),len(new_kws))) 116 | new_kws = set(good_samples+bad_samples).difference(keywords) 117 | print("# fresh keywords = {}\n".format(len(new_kws))) 118 | 119 | #make some call to naive_bayes.partial_fssit in here 120 | X = np.concatenate((naive_bayes.feature_count_, np.zeros((naive_bayes.feature_count_.shape[0],len(new_kws)))),1) 121 | all_kw = keywords + list(new_kws) 122 | 123 | else: 124 | print('Only using keywords from this content set') 125 | all_kw = list(set(good_samples+bad_samples)) 126 | X = np.zeros((2,len(all_kw))) 127 | 128 | for j,kw in enumerate(all_kw): 129 | X[0,j] += good_samples.count(kw) 130 | X[1,j] += bad_samples.count(kw) 131 | 132 | y = ['good','bad'] 133 | 134 | naive_bayes = MultinomialNB() 135 | naive_bayes.fit(X,y) 136 | 137 | return naive_bayes, all_kw 138 | 139 | #export content to simple markdown format 140 | def to_markdown(content,output_file): 141 | try: 142 | with open(output_file,'w') as outf: 143 | outf.write('# Relevant articles\n') 144 | for article in content: 145 | outf.write("## {}\n".format(re.sub(r'\n',' ',article['title']).encode('ascii','ignore'))) 146 | outf.write("* authors: {}\n".format(re.sub(r'\n',' ',article['author']).encode('ascii','ignore'))) 147 | outf.write("* abstract: {}\n".format(re.sub(r'\n',' ',article['abstract']).encode('ascii','ignore'))) 148 | outf.write("* [link]({})\n\n".format(re.sub(r'\n',' ',article['url']).encode('ascii','ignore'))) 149 | except: 150 | print("Failed to write markdown file") 151 | 152 | def main(argv): 153 | 154 | #add command line options for sources, output prefs, database of "good" keywords 155 | parser = argparse.ArgumentParser() 156 | parser.add_argument('-o','--output', help='output file name. only supports markdown right now.',dest ='output',default=None) 157 | parser.add_argument('-b','--bibtex', help='bibtex files to fetch',dest='bibfiles', nargs='*',default=list()) 158 | parser.add_argument('-j','--journals', help='journals to fetch. Currently supports {}.'.format(' '.join(rss.rss_feeds.keys())), 159 | nargs='*',dest='journals',default=list()) 160 | parser.add_argument('-a','--arXiv', help='arXiv categories to fetch', 161 | nargs='*',dest='arXiv',default=list()) 162 | parser.add_argument('--all_sources', help='flag to search from all sources.',action ='store_true') 163 | parser.add_argument('--all_good_sources', help='flag to search from good sources. Specfied in your config file.',action ='store_true') 164 | parser.add_argument('--train', help='flag to train. All sources beside "--train-input-good" are treated as bad/irrelevant papers',action ='store_true') 165 | parser.add_argument('-g','--train_input_good', help='bibtex file containing relevant articles.',dest ='good_source',default=None) 166 | parser.add_argument('-m','--method', help='Methods to try to find relevent papers. Right now, only all, title, author, and abstract are valid fields', 167 | dest='method',default='title') 168 | parser.add_argument('-k', '--knowledge', 169 | help='path to database containing information about good and bad keywords. \ 170 | If you are training, you must specifiy this, as it will be where your output is written ', 171 | dest='knowledge',default=None) 172 | parser.add_argument('--overwrite-knowledge', help='flag to overwrite knowledge,if training',action ='store_true',default=False, dest='overwrite_knowledge') 173 | parser.add_argument('--feedback', help='flag to give feedback after sorting content',action ='store_true',default=False, dest='feedback') 174 | parser.add_argument('--review_all', help='review all the new selections. Otherwise, you will only review the good selections',action ='store_true',default=False, dest='review_all') 175 | args = parser.parse_args(argv) 176 | 177 | if not args.method in ['title','abstract','author, all']: 178 | print("Invalid method. Options are title, abstract, author, and all") 179 | exit() 180 | 181 | method = args.method 182 | 183 | #Set up training if that's what we're doing 184 | if args.train: 185 | 186 | #check to make sure we have a good training input 187 | if args.good_source is None: 188 | print("When training, you must specify one good source") 189 | exit() 190 | if not os.path.exists(args.good_source): 191 | print("Specified training input does not exist") 192 | exit() 193 | if not os.path.isfile(args.good_source): 194 | print("Specified training input is not a file") 195 | exit() 196 | if not os.path.splitext(args.good_source)[1] == '.bib' : 197 | print("Training input must be in bibtex format") 198 | exit() 199 | 200 | #load the existing knowledge 201 | nb,kw,knowledge = load_knowledge(args.knowledge) 202 | if args.overwrite_knowledge: 203 | nb=None 204 | kw=list() 205 | 206 | good_content = get_content([bibtex.BibTex(args.good_source)]) 207 | 208 | if args.all_sources: 209 | bad_content = get_content([arxiv.ArXiv(cat) for cat in arxiv.arxiv_cats] + 210 | [rss.JournalFeed(journal) for journal in rss.rss_feeds.keys()]) 211 | else: 212 | bad_content = get_content([arxiv.ArXiv(cat) for cat in args.arXiv] + 213 | [bibtex.BibTex(bibfile) for bibfile in args.bibfiles] + 214 | [rss.JournalFeed(journal) for journal in args.journals]) 215 | 216 | #train, and write out knowledge (naive_bayes class and keywords) 217 | nb, kw = train(good_content,bad_content,method,naive_bayes=nb, keywords=kw) 218 | pickle.dump(nb,open(knowledge+'/nb.p','w')) 219 | pickle.dump(kw,open(knowledge+'/kw.p','w')) 220 | 221 | #we are filtering new content through our existing knowledge 222 | else: 223 | 224 | #load the old knowledge 225 | nb,kw,knowledge = load_knowledge(args.knowledge) 226 | if args.all_sources: 227 | sources = [arxiv.ArXiv(cat) for cat in arxiv.arxiv_cats] + \ 228 | [rss.JournalFeed(journal) for journal in rss.rss_feeds.keys()] 229 | elif args.all_good_sources: 230 | arxiv_cats = ['cond-mat','stat'] 231 | journals = ['science','nature','small','prl','pnas', 232 | 'physreve','physrevx','acsnano', 233 | 'advmat','jchemphysb','natphys', 234 | 'natmat','natnano','langmuir'] 235 | 236 | sources = [arxiv.ArXiv(cat) for cat in arxiv_cats] + \ 237 | [rss.JournalFeed(journal) for journal in journals] 238 | else: 239 | sources = [arxiv.ArXiv(cat) for cat in args.arXiv] + \ 240 | [ bibtex.BibTex (bibfile) for bibfile in args.bibfiles] + \ 241 | [rss.JournalFeed(journal) for journal in args.journals] 242 | 243 | new_content = get_content(sources) 244 | good_content = filter_content(new_content,method,nb,kw) 245 | print("Fraction of good new content: {!r}".format(len(good_content)*1.0/len(new_content))) 246 | print("total content parsed: {!r}".format(len(new_content))) 247 | 248 | if (args.output): 249 | to_markdown(good_content,args.output) 250 | else: 251 | pass 252 | #print(good_content) 253 | 254 | if(args.feedback): 255 | human_class, reviewed_content = review_content(good_content,new_content,method,args.review_all) 256 | good_content = [entry for cat,entry in zip(human_class,reviewed_content) if cat=='good'] 257 | bad_content = [entry for cat,entry in zip(human_class,reviewed_content) if cat=='bad'] 258 | nb, kw = train(good_content,bad_content,method,naive_bayes=nb, keywords=kw) 259 | pickle.dump(nb,open(knowledge+'/nb.p','w')) 260 | pickle.dump(kw,open(knowledge+'/kw.p','w')) 261 | 262 | 263 | 264 | 265 | if __name__=="__main__": 266 | main(sys.argv[1:]) 267 | --------------------------------------------------------------------------------