bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automatic identification of mixed bacterial species fingerprints in a MALDI-TOF mass-spectrum
Authors: Mahé Pierre , Arsac Maud , Chatellier Sonia , Monnin Valérie , Perrot Nadine , Mailler Sandrine , Girard Victoria , Ramjeet Mahendrasingh , Surre Jérémy , Lacroix Bruno , van Belkum Alex , Veyrieras Jean-Baptiste 
Published: January 2014

Abstract
Motivation: Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry has been broadly adopted by routine clinical microbiology laboratories for bacterial species identification. An isolated colony of the targeted microorganism is the single prerequisite. Currently, MS-based microbial identification directly from clinical specimens can not be routinely performed, as it raises two main challenges: (i) the nature of the sample itself may increase the level of technical variability and bring heterogeneity with respect to the reference database and (ii) the possibility of encountering polymicrobial samples that will yield a ‘mixed’ MS fingerprint. In this article, we introduce a new method to infer the composition of polymicrobial samples on the basis of a single mass spectrum. Our approach relies on a penalized non-negative linear regression framework making use of species-specific prototypes, which can be derived directly from the routine reference database of pure spectra.
Results: A large spectral dataset obtained from in vitro mono- and bi-microbial samples allowed us to evaluate the performance of the method in a comprehensive way. Provided that the reference matrix-assisted laser desorption/ionization time-of-flight mass spectrometry fingerprints were sufficiently distinct for the individual species, the method automatically predicted which bacterial species were present in the sample. Only few samples (5.3%) were misidentified, and bi-microbial samples were correctly identified in up to 61.2% of the cases. This method could be used in routine clinical microbiology practice.
Availability and implementation: The complete dataset including both the reference database and the mock-up mixture spectra is available at http://archive.ics.uci.edu/ml/datasets/MicroMass.
Contact: pierre.mahe@biomerieux.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Exploring genome characteristics and sequence quality without a reference
Authors: Simpson Jared T. 
Published: January 2014

Abstract
Motivation: The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many de novo assembly software packages are available, comparatively little attention has been paid to assisting the user with the assembly.
Results: This article addresses the practical aspects of de novo assembly by introducing new ways to perform quality assessment on a collection of sequence reads. The software implementation calculates per-base error rates, paired-end fragment-size distributions and coverage metrics in the absence of a reference genome. Additionally, the software will estimate characteristics of the sequenced genome, such as repeat content and heterozygosity that are key determinants of assembly difficulty.
Availability: The software described is freely available online (https://github.com/jts/sga) and open source under the GNU Public License.
Contact: jared.simpson@oicr.on.ca
Supplementary Information: Supplementary data are available at Bioinformatics online.
PhyloJIVE: Integrating biodiversity data with the Tree of Life
Authors: Jolley-Rogers Garry , Varghese Temi , Harvey Paul , dos Remedios Nick , Miller Joseph T. 
Published: January 2014

Abstract
Motivation: Rich collections of biodiversity information such as spatial distributions, species descriptions and trait data are now synthesized in publicly available online sources such as GBIF. Also phylogenetic knowledge now provides a sound understanding of the origin of organisms and their place in the tree of life. We demonstrate with PhyloJIVE that any phylogenetic tree can be linked to online biodiversity data in the browser. This evolutionary view of biodiversity data is demonstrated in a case study that suggests that this approach may be useful to scientists and non-experts users.
Contact: joe@acaciamulga.net
Supplementary information: Supplementary data are available at Bioinformatics online.
netClass: an R-package for network based, integrative biomarker signature discovery
Authors: Cun Yupeng , Fröhlich Holger 
Published: January 2014

Abstract
In the past years, there has been a growing interest in methods that incorporate network information into classification algorithms for biomarker signature discovery in personalized medicine. The general hope is that this way the typical low reproducibility of signatures, together with the difficulty to link them to biological knowledge, can be addressed. Complementary to these efforts, there is an increasing interest in integrating different data entities (e.g. gene and miRNA expressions) into comprehensive models. To our knowledge, R-package netClass is the first software that addresses both, network and data integration. Besides several published approaches for network integration, it specifically contains our recently published stSVM method, which allows for additional integration of gene and miRNA expression data into one predictive classifier.
Availability: netClass is available on http://sourceforge.net/p/netclassr and CRAN (http://cran.r-project.org).
Contact: yupeng.cun@gmail.com
IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics
Authors: Rosikiewicz Marta , Robinson-Rechavi Marc 
Published: January 2014

AbstractMotivation: Microarray results accumulated in public repositories are widely reused in meta-analytical studies and secondary databases. The quality of the data obtained with this technology varies from experiment to experiment, and an efficient method for quality assessment is necessary to ensure their reliability.Results: The lack of a good benchmark has hampered evaluation of existing methods for quality control. In this study, we propose a new independent quality metric that is based on evolutionary conservation of expression profiles. We show, using 11 large organ-specific datasets, that IQRray, a new quality metrics developed by us, exhibits the highest correlation with this reference metric, among 14 metrics tested. IQRray outperforms other methods in identification of poor quality arrays in datasets composed of arrays from many independent experiments. In contrast, the performance of methods designed for detecting outliers in a single experiment like Normalized Unscaled Standard Error and Relative Log Expression was low because of the inability of these methods to detect datasets containing only low-quality arrays and because the scores cannot be directly compared between experiments.Availability and implementation: The R implementation of IQRray is available at: ftp://lausanne.isb-sib.ch/pub/databases/Bgee/general/IQRray.R.Contact: Marta.Rosikiewicz@unil.chSupplementary information: Supplementary data are available at Bioinformatics online.
Evidence of fjord spawning by southern Norwegian Atlantic halibut (Hippoglossus hippoglossus)
Authors: Seitz Andrew C. , Michalsen Kathrine , Nielsen Jennifer L. , Evans Mark D. 
Published: January 2014

Abstract
Atlantic halibut (Hippoglossus hippoglossus) in a Norwegian fjord were tagged with pop-up archival transmitting (PAT) tags to investigate whether they join offshore spawning events with halibut from other regions. All fish (n = 4) remained in the fjord throughout the spawning season, suggesting that they may be reproductively segregated from other stocks.
Comparative ribosome profiling reveals extensive translational complexity in differentTrypanosoma bruceilife cycle stages
Authors: Vasquez Juan-José , Hon Chung-Chau , Vanselow Jens T. , Schlosser Andreas , Siegel T. Nicolai 
Published: January 2014

AbstractWhile gene expression is a fundamental and tightly controlled cellular process that is regulated at multiple steps, the exact contribution of each step remains unknown in any organism. The absence of transcription initiation regulation for RNA polymerase II in the protozoan parasite Trypanosoma brucei greatly simplifies the task of elucidating the contribution of translation to global gene expression. Therefore, we have sequenced ribosome-protected mRNA fragments in T. brucei, permitting the genome-wide analysis of RNA translation and translational efficiency. We find that the latter varies greatly between life cycle stages of the parasite and ∼100-fold between genes, thus contributing to gene expression to a similar extent as RNA stability. The ability to map ribosome positions at sub-codon resolution revealed extensive translation from upstream open reading frames located within 5′ UTRs and enabled the identification of hundreds of previously un-annotated putative coding sequences (CDSs). Evaluation of existing proteomics and genome-wide RNAi data confirmed the translation of previously un-annotated CDSs and suggested an important role for &gt;200 of those CDSs in parasite survival, especially in the form that is infective to mammals. Overall our data show that translational control plays a prevalent and important role in different parasite life cycle stages of T. brucei.
Transcriptome analysis of alternative splicing events regulated by SRSF10 reveals position-dependent splicing modulation
Authors: Zhou Xuexia , Wu Wenwu , Li Huang , Cheng Yuanming , Wei Ning , Zong Jie , Feng Xiaoyan , Xie Zhiqin , Chen Dai , Manley James L. , Wang Hui , Feng Ying 
Published: January 2014

Abstract
Splicing factor SRSF10 is known to function as a sequence-specific splicing activator. Here, we used RNA-seq coupled with bioinformatics analysis to identify the extensive splicing network regulated by SRSF10 in chicken cells. We found that SRSF10 promoted both exon inclusion and exclusion. Motif analysis revealed that SRSF10 binding to cassette exons was associated with exon inclusion, whereas the binding of SRSF10 within downstream constitutive exons was associated with exon exclusion. This positional effect was further demonstrated by the mutagenesis of potential SRSF10 binding motifs in two minigene constructs. Functionally, many of SRSF10-verified alternative exons are linked to pathways of stress and apoptosis. Consistent with this observation, cells depleted of SRSF10 expression were far more susceptible to endoplasmic reticulum stress-induced apoptosis than control cells. Importantly, reconstituted SRSF10 in knockout cells recovered wild-type splicing patterns and considerably rescued the stress-related defects. Together, our results provide mechanistic insight into SRSF10-regulated alternative splicing events in vivo and demonstrate that SRSF10 plays a crucial role in cell survival under stress conditions.
A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis
Authors: Pimentel Harold , Parra Marilyn , Gee Sherry , Ghanem Dana , An Xiuli , Li Jie , Mohandas Narla , Pachter Lior , Conboy John G. 
Published: January 2014

Abstract
Alternative pre-messenger RNA splicing remodels the human transcriptome in a spatiotemporal manner during normal development and differentiation. Here we explored the landscape of transcript diversity in the erythroid lineage by RNA-seq analysis of five highly purified populations of morphologically distinct human erythroblasts, representing the last four cell divisions before enucleation. In this unique differentiation system, we found evidence of an extensive and dynamic alternative splicing program encompassing genes with many diverse functions. Alternative splicing was particularly enriched in genes controlling cell cycle, organelle organization, chromatin function and RNA processing. Many alternative exons exhibited differentiation-associated switches in splicing efficiency, mostly in late-stage polychromatophilic and orthochromatophilic erythroblasts, in concert with extensive cellular remodeling that precedes enucleation. A subset of alternative splicing switches introduces premature translation termination codons into selected transcripts in a differentiation stage-specific manner, supporting the hypothesis that alternative splicing-coupled nonsense-mediated decay contributes to regulation of erythroid-expressed genes as a novel part of the overall differentiation program. We conclude that a highly dynamic alternative splicing program in terminally differentiating erythroblasts plays a major role in regulating gene expression to ensure synthesis of appropriate proteome at each stage as the cells remodel in preparation for production of mature red cells.
Expanding the zinc-finger recombinase repertoire: directed evolution and mutational analysis of serine recombinase specificity determinants
Authors: Sirk Shannon J. , Gaj Thomas , Jonsson Andreas , Mercer Andrew C. , Barbas Carlos F. 
Published: January 2014

Abstract
The serine recombinases are a diverse family of modular enzymes that promote high-fidelity DNA rearrangements between specific target sites. Replacement of their native DNA-binding domains with custom-designed Cys2–His2 zinc-finger proteins results in the creation of engineered zinc-finger recombinases (ZFRs) capable of achieving targeted genetic modifications. The flexibility afforded by zinc-finger domains enables the design of hybrid recombinases that recognize a wide variety of potential target sites; however, this technology remains constrained by the strict recognition specificities imposed by the ZFR catalytic domains. In particular, the ability to fully reprogram serine recombinase catalytic specificity has been impeded by conserved base requirements within each recombinase target site and an incomplete understanding of the factors governing DNA recognition. Here we describe an approach to complement the targeting capacity of ZFRs. Using directed evolution, we isolated mutants of the β and Sin recombinases that specifically recognize target sites previously outside the scope of ZFRs. Additionally, we developed a genetic screen to determine the specific base requirements for site-specific recombination and showed that specificity profiling enables the discovery of unique genomic ZFR substrates. Finally, we conducted an extensive and family-wide mutational analysis of the serine recombinase DNA-binding arm region and uncovered a diverse network of residues that confer target specificity. These results demonstrate that the ZFR repertoire is extensible and highlights the potential of ZFRs as a class of flexible tools for targeted genome engineering.
Illumina TruSeq synthetic long-reads empowerde novoassembly and resolve complex, highly repetitive transposable elements
Authors: McCoy Rajiv C. , Taylor Ryan W. , Blauwkamp Timothy A. , Kelley Joanna L. , Kertesz Michael , Pushkarev Dmitry , Petrov Dmitri A. , Fiston-Lavier Anna-Sophie 
Published: January 2014

AbstractHigh-throughput DNA sequencing technologies have revolutionized genomic analysis, including thede novoassembly of whole genomes. Nevertheless, assembly of complex genomes remains challenging, in part due to the presence of dispersed repeats which introduce ambiguity during genome reconstruction. Transposable elements (TEs) can be particularly problematic, especially for TE families exhibiting high sequence identity, high copy number, or present in complex genomic arrangements. While TEs strongly affect genome function and evolution, most currentde novoassembly approaches cannot resolve long, identical, and abundant families of TEs. Here, we applied a novel Illumina technology called TruSeq synthetic long-reads, which are generated through highly parallel library preparation and local assembly of short read data and achieve lengths of 1.5-18.5 Kbp with an extremely low error rate (∼0.03% per base). To test the utility of this technology, we sequenced and assembled the genome of the model organismDrosophila melanogaster(reference genome strainy;cn,bw,sp) achieving an N50 contig size of 69.7 Kbp and covering 96.9% of the euchromatic chromosome arms of the current reference genome. TruSeq synthetic long-read technology enables placement of individual TE copies in their proper genomic locations as well as accurate reconstruction of TE sequences. We entirely recovered and accurately placed 4,229 (77.8%) of the 5,434 of annotated transposable elements with perfect identity to the current reference genome. As TEs are ubiquitous features of genomes of many species, TruSeq synthetic long-reads, and likely other methods that generate long reads, offer a powerful approach to improvede novoassemblies of whole genomes.
Novel Roles for the Polyphenol Oxidase Enzyme in Secondary Metabolism and the Regulation of Cell Death in Walnut
Authors: Araji Soha , Grammer Theresa A. , Gertzen Ross , Anderson Stephen D. , Mikulic-Petkovsek Maja , Veberic Robert , Phu My L. , Solar Anita , Leslie Charles A. , Dandekar Abhaya M. , Escobar Matthew A. 
Published: January 2014

AbstractThe enzyme polyphenol oxidase (PPO) catalyzes the oxidation of phenolic compounds into highly reactive quinones. Polymerization of PPO-derived quinones causes the postharvest browning of cut or bruised fruit, but the native physiological functions of PPOs in undamaged, intact plant cells are not well understood. Walnut (Juglans regia) produces a rich array of phenolic compounds and possesses a single PPO enzyme, rendering it an ideal model to study PPO. We generated a series of PPO-silenced transgenic walnut lines that display less than 5% of wild-type PPO activity. Strikingly, the PPO-silenced plants developed spontaneous necrotic lesions on their leaves in the absence of pathogen challenge (i.e. a lesion mimic phenotype). To gain a clearer perspective on the potential functions of PPO and its possible connection to cell death, we compared the leaf transcriptomes and metabolomes of wild-type and PPO-silenced plants. Silencing of PPO caused major alterations in the metabolism of phenolic compounds and their derivatives (e.g. coumaric acid and catechin) and in the expression of phenylpropanoid pathway genes. Several observed metabolic changes point to a direct role for PPO in the metabolism of tyrosine and in the biosynthesis of the hydroxycoumarin esculetin in vivo. In addition, PPO-silenced plants displayed massive (9-fold) increases in the tyrosine-derived metabolite tyramine, whose exogenous application elicits cell death in walnut and several other plant species. Overall, these results suggest that PPO plays a novel and fundamental role in secondary metabolism and acts as an indirect regulator of cell death in walnut.
Thylakoid FtsH Protease Contributes to Photosystem II and Cytochromeb 6 fRemodeling inChlamydomonas reinhardtiiunder Stress Conditions
Authors: Malnoë Alizée , Wang Fei , Girard-Bascou Jacqueline , Wollman Francis-André , de Vitry Catherine 
Published: January 2014

AbstractFtsH is the major thylakoid membrane protease found in organisms performing oxygenic photosynthesis. Here, we show that FtsH from Chlamydomonas reinhardtii forms heterooligomers comprising two subunits, FtsH1 and FtsH2. We characterized this protease using FtsH mutants that we identified through a genetic suppressor approach that restored phototrophic growth of mutants originally defective for cytochrome b 6 f accumulation. We thus extended the spectrum of FtsH substrates in the thylakoid membranes beyond photosystem II, showing the susceptibility of cytochrome b 6 f complexes (and proteins involved in the c i heme binding pathway to cytochrome b 6) to FtsH. We then show how FtsH is involved in the response of C. reinhardtii to macronutrient stress. Upon phosphorus starvation, photosynthesis inactivation results from an FtsH-sensitive photoinhibition process. In contrast, we identified an FtsH-dependent loss of photosystem II and cytochrome b 6 f complexes in darkness upon sulfur deprivation. The D1 fragmentation pattern observed in the latter condition was similar to that observed in photoinhibitory conditions, which points to a similar degradation pathway in these two widely different environmental conditions. Our experiments thus provide extensive evidence that FtsH plays a major role in the quality control of thylakoid membrane proteins and in the response of C. reinhardtii to light and macronutrient stress.
Fruits and vegetables intake are associated with ethnicity and socio‐demographic factors in Mauritius
Authors: Badurally Adam B.T. , Mahomoodally M.F. , Subratty A.H. , Ramasawmy D. 
Published: January 2014

PurposeFruits and vegetables intake (FVI) in the human diet is strongly related to health status and incidence of diseases. The purpose of this paper is to hypothesize that demographic factors and food insecurity could be associated with the frequency of FVI in a multicultural community such as Mauritius.Design/methodology/approachInformation pertaining to socio‐demographic factors, anthropometric measurements, medical history, lifestyle factors, reason(s) for dietary choice and food insecurity factors were amassed randomly from 374 adults.FindingsThe mean FVI was found to be significantly lower (p<0.05) for the food insecure respondents (n=39). Also, significant (p<0.05) associations between FVI and the level of education (p=0.031 and p=0.012, respectively), ethnic groups (p=0.028 and p=0.013, respectively), income ranges (p<0.001 and p<0.001, respectively), and food insecurity (p<0.001 and p<0.001, respectively) were noted. A high income was also significantly related to a higher FVI. With respect to disease occurrence, a significant (p=0.035) relationship was found with respect to FVI and respiratory diseases.Originality/valueThe paper shows that there is a pressing need to re‐evaluate efficiency of existing nutrition policies and programs. Also that it is important to establish more sensitization campaigns geared towards the above‐mentioned target groups with respect to FVI. Authorities concerned should also endeavour to achieve affordable, accessible and safe fruits and vegetables as a mean to promote a healthy eating culture in Mauritius.
Resource sharing challenges and prospects in Nigerian university libraries
Authors: Anasi Stella , Ali Hussaini 
Published: January 2014

PurposeThe purpose of this paper is to examine the barriers to effective resource sharing among academic libraries in Nigeria.Design/methodology/approachProfessional librarians from six randomly selected federal university libraries representing the six geopolitical zones in Nigeria were surveyed using a descriptive survey research design. Questionnaires were sent to 124 librarians; 85 were returned and found to be usable, for a response rate of 68.5 per cent.FindingsThe study revealed that the prospect for resource sharing among university libraries in Nigeria is high. However, factors that hinder effective resource sharing include inadequate funding, a dearth of skilled librarians, power outages, an absence of web‐accessible OPACs, uneven development of libraries, and slow progress of library automation. It is recommended that each university library have a specific annual budget allocation for ICT development and maintenance and for training of librarians to pilot resource sharing projects.Originality/valueThis paper presents resource‐sharing challenges facing academic libraries in Nigeria. It encourages information professionals to embark on capacity building for effective resource sharing. This paper was prepared for the 12th Interlending and Document Supply Conference, held in September 2011.