bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimating abundances of retroviral insertion sites from DNA fragment length data
Authors: Berry Charles C. , Gillet Nicolas A. , Melamed Anat , Gormley Niall , Bangham Charles R. M. , Bushman Frederic D. 
Published: January 2012

Abstract
Motivation: The relative abundance of retroviral insertions in a host genome is important in understanding the persistence and pathogenesis of both natural retroviral infections and retroviral gene therapy vectors. It could be estimated from a sample of cells if only the host genomic sites of retroviral insertions could be directly counted. When host genomic DNA is randomly broken via sonication and then amplified, amplicons of varying lengths are produced. The number of unique lengths of amplicons of an insertion site tends to increase according to its abundance, providing a basis for estimating relative abundance. However, as abundance increases amplicons of the same length arise by chance leading to a non-linear relation between the number of unique lengths and relative abundance. The difficulty in calibrating this relation is compounded by sample-specific variations in the relative frequencies of clones of each length.
Results: A likelihood function is proposed for the discrete lengths observed in each of a collection of insertion sites and is maximized with a hybrid expectation–maximization algorithm. Patient data illustrate the method and simulations show that relative abundance can be estimated with little bias, but that variation in highly abundant sites can be large. In replicated patient samples, variation exceeds what the model implies—requiring adjustment as in Efron (2004) or using jackknife standard errors. Consequently, it is advantageous to collect replicate samples to strengthen inferences about relative abundance.
Availability: An R package implements the algorithm described here. It is available at http://soniclength.r-forge.r-project.org/
Contact: ccberry@ucsd.edu
Supplementary information: Supplementary data are available at at Bioinformatics online.
Predicting folding free energy changes upon single point mutations
Authors: Zhang Zhe , Wang Lin , Gao Yang , Zhang Jie , Zhenirovskyy Maxim , Alexov Emil 
Published: January 2012

Abstract
Motivation: The folding free energy is an important characteristic of proteins stability and is directly related to protein's wild-type function. The changes of protein's stability due to naturally occurring mutations, missense mutations, are typically causing diseases. Single point mutations made in vitro are frequently used to assess the contribution of given amino acid to the stability of the protein. In both cases, it is desirable to predict the change of the folding free energy upon single point mutations in order to either provide insights of the molecular mechanism of the change or to design new experimental studies.
Results: We report an approach that predicts the free energy change upon single point mutation by utilizing the 3D structure of the wild-type protein. It is based on variation of the molecular mechanics Generalized Born (MMGB) method, scaled with optimized parameters (sMMGB) and utilizing specific model of unfolded state. The corresponding mutations are built in silico and the predictions are tested against large dataset of 1109 mutations with experimentally measured changes of the folding free energy. Benchmarking resulted in root mean square deviation = 1.78 kcal/mol and slope of the linear regression fit between the experimental data and the calculations was 1.04. The sMMGB is compared with other leading methods of predicting folding free energy changes upon single mutations and results discussed with respect to various parameters.
Availability: All the pdb files we used in this article can be downloaded from http://compbio.clemson.edu/downloadDir/mentaldisorders/sMMGB_pdb.rar
Contact: ealexov@clemson.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
The evolution of nitrogen fixation in cyanobacteria
Authors: Latysheva Natasha , Junker Vivien L. , Palmer William J. , Codd Geoffrey A. , Barker Daniel 
Published: January 2012

Abstract
Motivation: Fixed nitrogen is an essential requirement for the biosynthesis of cellular nitrogenous compounds. Some cyanobacteria can fix nitrogen, contributing significantly to the nitrogen cycle, agriculture and biogeochemical history of Earth. The rate and position on the species phylogeny of gains and losses of this ability, as well as of the underlying nif genes, are controversial.
Results: We use probabilistic models of trait evolution to investigate the presence and absence of cyanobacterial nitrogen-fixing ability. We estimate rates of change on the species phylogeny, pinpoint probable changes and reconstruct the state and nif gene complement of the ancestor. Our results are consistent with a nitrogen-fixing cyanobacterial ancestor, repeated loss of nitrogen fixation and vertical descent, with little horizontal transfer of the genes involved.
Contact: db60@st-andrews.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
PHACTS, a computational approach to classifying the lifestyle of phages
Authors: McNair Katelyn , Bailey Barbara A. , Edwards Robert A. 
Published: January 2012

Abstract
Motivation: Bacteriophages have two distinct lifestyles: virulent and temperate. The virulent lifestyle has many implications for phage therapy, genomics and microbiology. Determining which lifestyle a newly sequenced phage falls into is currently determined using standard culturing techniques. Such laboratory work is not only costly and time consuming, but also cannot be used on phage genomes constructed from environmental sequencing. Therefore, a computational method that utilizes the sequence data of phage genomes is needed.
Results: Phage Classification Tool Set (PHACTS) utilizes a novel similarity algorithm and a supervised Random Forest classifier to make a prediction whether the lifestyle of a phage, described by its proteome, is virulent or temperate. The similarity algorithm creates a training set from phages with known lifestyles and along with the lifestyle annotation, trains a Random Forest to classify the lifestyle of a phage. PHACTS predictions are shown to have a 99% precision rate.
Availability and implementation: PHACTS was implemented in the PERL programming language and utilizes the FASTA program (Pearson and Lipman, 1988) and the R programming language library ‘Random Forest’ (Liaw and Weiner, 2010). The PHACTS software is open source and is available as downloadable stand-alone version or can be accessed online as a user-friendly web interface. The source code, help files and online version are available at http://www.phantome.org/PHACTS/.
Contact: katelyn@rohan.sdsu.edu; redwards@sciences.sdsu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
SSuMMo: rapid analysis, comparison and visualization of microbial communities
Authors: Leach Alex L. B. , Chong James P. J. , Redeker Kelly R. 
Published: January 2012

Abstract
Motivation: Next-generation sequencing methods are generating increasingly massive datasets, yet still do not fully capture genetic diversity in the richest environments. To understand such complicated and elusive systems, effective tools are needed to assist with delineating the differences found in and between community datasets.
Results: The Small Subunit Markov Modeler (SSuMMo) was developed to probabilistically assign SSU rRNA gene fragments from any sequence dataset to recognized taxonomic clades, producing consistent, comparable cladograms. Accuracy tests predicted &gt;90% of genera correctly for sequences downloaded from public reference databases. Sequences from a next-generation sequence dataset, sampled from lean, overweight and obese individuals, were analysed to demonstrate parallel visualization of comparable datasets. SSuMMo shows potential as a valuable curatorial tool, as numerous incorrect and outdated taxonomic entries and annotations were identified in public databases.
Availability and implementation: SSuMMo is GPLv3 open source Python software, available at http://code.google.com/p/ssummo/. Taxonomy and HMM databases can be downloaded from http://bioltfws1.york.ac.uk/ssummo/.
Contact: albl500@york.ac.uk
Supplementary information: Supplemental materials are available at Bioinformatics Online.
Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS
Authors: Emde Anne-Katrin , Schulz Marcel H. , Weese David , Sun Ruping , Vingron Martin , Kalscheuer Vera M. , Haas Stefan A. , Reinert Knut 
Published: January 2012

Abstract
Motivation: The reliable detection of genomic variation in resequencing data is still a major challenge, especially for variants larger than a few base pairs. Sequencing reads crossing boundaries of structural variation carry the potential for their identification, but are difficult to map.
Results: Here we present a method for ‘split’ read mapping, where prefix and suffix match of a read may be interrupted by a longer gap in the read-to-reference alignment. We use this method to accurately detect medium-sized insertions and long deletions with precise breakpoints in genomic resequencing data. Compared with alternative split mapping methods, SplazerS significantly improves sensitivity for detecting large indel events, especially in variant-rich regions. Our method is robust in the presence of sequencing errors as well as alignment errors due to genomic mutations/divergence, and can be used on reads of variable lengths. Our analysis shows that SplazerS is a versatile tool applicable to unanchored or single-end as well as anchored paired-end reads. In addition, application of SplazerS to targeted resequencing data led to the interesting discovery of a complete, possibly functional gene retrocopy variant.
Availability: SplazerS is available from http://www.seqan.de/projects/ splazers.
Contact: emde@inf.fu-berlin.de
Supplementary information: Supplementary data are available at Bioinformatics online.
GROMACS molecule & liquid database
Authors: van der Spoel David , van Maaren Paul J. , Caleman Carl 
Published: January 2012

AbstractMotivation: The molecular dynamics simulation package GROMACS is a widely used tool used in a broad range of different applications within physics, chemistry and biology. It is freely available, user friendly and extremely efficient. The GROMACS software is force field agnostic, and compatible with many molecular dynamics force fields; coarse-grained, unified atom, all atom as well as polarizable models based on the charge on a spring concept. To validate simulations, it is necessary to compare results from the simulations to experimental data. To ease the process of setting up topologies and structures for simulations, as well as providing pre-calculated physical properties along with experimental values for the same we provide a web-based database, containing 145 organic molecules at present.Results: Liquid properties of 145 organic molecules have been simulated using two different force fields, OPLS all atom and Generalized Amber Force Field. So far, eight properties have been calculated (the density, enthalpy of vaporization, surface tension, heat capacity at constant volume and pressure, isothermal compressibility, volumetric expansion coefficient and the static dielectric constant). The results, together with experimental values are available through the database, along with liquid structures and topologies for the 145 molecules, in the two force fields.Availability: The database is freely available under http://virtualchemistry.org.Contact: spoel@xray.bmc.uu.se; carl.caleman@cfel.de
Surrogate variable analysis using partial least squares (SVA-PLS) in gene expression studies
Authors: Chakraborty Sutirtha , Datta Somnath , Datta Susmita 
Published: January 2012

Abstract
Motivation: In a typical gene expression profiling study, our prime objective is to identify the genes that are differentially expressed between the samples from two different tissue types. Commonly, standard analysis of variance (ANOVA)/regression is implemented to identify the relative effects of these genes over the two types of samples from their respective arrays of expression levels. But, this technique becomes fundamentally flawed when there are unaccounted sources of variability in these arrays (latent variables attributable to different biological, environmental or other factors relevant in the context). These factors distort the true picture of differential gene expression between the two tissue types and introduce spurious signals of expression heterogeneity. As a result, many genes which are actually differentially expressed are not detected, whereas many others are falsely identified as positives. Moreover, these distortions can be different for different genes. Thus, it is also not possible to get rid of these variations by simple array normalizations. This both-way error can lead to a serious loss in sensitivity and specificity, thereby causing a severe inefficiency in the underlying multiple testing problem. In this work, we attempt to identify the hidden effects of the underlying latent factors in a gene expression profiling study by partial least squares (PLS) and apply ANCOVA technique with the PLS-identified signatures of these hidden effects as covariates, in order to identify the genes that are truly differentially expressed between the two concerned tissue types.
Results: We compare the performance of our method SVA-PLS with standard ANOVA and a relatively recent technique of surrogate variable analysis (SVA), on a wide variety of simulation settings (incorporating different effects of the hidden variable, under situations with varying signal intensities and gene groupings). In all settings, our method yields the highest sensitivity while maintaining relatively reasonable values for the specificity, false discovery rate and false non-discovery rate. Application of our method to gene expression profiling for acute megakaryoblastic leukemia shows that our method detects an additional six genes, that are missed by both the standard ANOVA method as well as SVA, but may be relevant to this disease, as can be seen from mining the existing literature.
Availability: The R code for our method, SVA-PLS, is freely available on the Supplementary website http://www.somnathdatta.org/Supp/SVPLS/
Contact: s0chak10@louisville.edu; susmita.datta@louisville.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Interactome–transcriptome integration for predicting distant metastasis in breast cancer
Authors: Garcia Maxime , Millat-Carus Raphaelle , Bertucci François , Finetti Pascal , Birnbaum Daniel , Bidaut Ghislain 
Published: January 2012

Abstract
Motivation: High-throughput gene expression profiling yields genomic signatures that allow the prediction of clinical conditions including patient outcome. However, these signatures have limitations, such as dependency on the training set, and worse, lack of generalization.
Results: We propose a novel algorithm called ITI (interactome–transcriptome integration), to extract a genomic signature predicting distant metastasis in breast cancer by superimposition of large-scale protein–protein interaction data over a compendium of several gene expression datasets. Training on two different compendia showed that the estrogen receptor-specific signatures obtained are more stable (11–35% stability), can be generalized on independent data and performs better than previously published methods (53–74% accuracy).
Availability: The ITI algorithm source code from analysis are available under CeCILL from the ITI companion website: http://bioinformatique.marseille.inserm.fr/iti.
Contact: maxime.garcia@inserm.fr; ghislain.bidaut@inserm.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
‘The World Palpitates’: Globalization and the Religious Faith and Practices of Latin American Women
Authors: Bedford Nancy E. 
Published: January 2012

Abstract
Given the fact that religion and globalization are significantly intertwined, what should we make of the contemporary religious faith and practices of Latin American women? Do religious conversion and active participation in a community of faith amount to “adaptive solutions” to the crisis unleashed by capitalist globalization, analogous to those made by women as economic agents? From the perspective of the sociology of religion, it has become a byword that the faith and religious community-building of women—be it the Pentecostalism of Maya women in Guatemala or the activism of Brazilian women in Roman Catholic base communities—can and do serve as coping or indeed as survival strategies in times of globalization. A theological perspective does not necessarily contradict the sociological insight that discovers ways in which religious faith and practices serve in coping and surviving. Because theology speaks in an engaged voice from within the realm of faith, however, it can allow itself—indeed it must—to delve differently than the social sciences. This chapter explores the observation that religious faith and practices of Latin American women, in these economically globalized times, often serve in rather unexpected ways to make space for life, in all of its messiness and materiality.
First Nation, Empire, and Globalization
Authors: Smith Andrea 
Published: January 2012

AbstractIn his analysis of postmodern theology, which details the imbrication of theology in discourses of power, Gavin Hyman casually evokes the term “Indian territory” to connote the space from which the theologian must resort to the tactics of the “outlaw.” In his larger argument, he evokes an Agamban-like state of exception for theology, where theology must be conducted in the realm of radical undecidability, a theology excluded from but belonging to the law, as it were. So, it is significant that, to make this argument, Hyman relies on the obvious racist connotation of Natives as “outlaws” who live in a place without a home. This chapter argues that this tendency to depict Natives as “outlaws” is not unique to Hyman, but exists even within feminist and liberation theologies. That is, the United States, despite the critiques which many theologians make of it, is still envisaged as a place of law, thereby rending Native peoples, whose genocide is the foundation of the USA, outside the law. Consequently, the theological strategy of engagement with Native peoples does resemble the tactic of “raid and return”: that is, a selective use of “indigenous” principles without engagement in the fundamental contradiction indigenous peoples expose in the project of liberation. Furthermore, this problematic engagement is fundamentally gendered.
Globalization and Women's Bodies in Latin America
Authors: Ventura María Cristina 
Published: January 2012

Abstract
This chapter considers globalization and its relationship to women's bodies in Latin America, both the effects this new face of capitalism is having on women's bodies in this part of the world and the ways in which women construct modalities as creative resistance strategies. It goes beyond a mere analysis of the socioeconomic impact in a variety of situations to examine what women invent, represent, and endow with power in their discourse, practices, and collective quest to redefine the status of all women, and particularly of women excluded from the so-called global economic system.
Globalization, Women's Transnational Migration, and Religious De-traditioning
Authors: Tanner Kathryn 
Published: January 2012

AbstractFar-flung movements of women from disadvantaged areas of the world to more advantaged ones are at the heart of the present configuration of global capitalism. Rather than simply leaving their countries of origin to set up temporary or permanent residence elsewhere, women who move in today's global economy, in order to take jobs as housekeepers or nannies (for example), are typically transnational migrants. Even as they settle into new places, their lives remain bound up with where they came from, in virtue of rather dense social and familial networks bridging national boundaries. Connected simultaneously in this way to at least two places at once, these women are working out in their everyday lives a fundamental reconfiguration of the way cultural traditions are set up and maintained, with significant implications for the understanding of religious traditions in particular. This chapter shows that, in the lives of these women, coming undone is the familiar association of tradition with the intergenerational transmission of an already established way of life by means of face-to-face interactions in a single location.
Editors' Introduction
Authors: Kuusela Oskari , McGinn Marie 
Published: January 2012

Abstract
This Introduction starts by stating that Wittgenstein is a contested figure on the philosophical scene. It talks further about Wittgenstein’s philosophy and his relation to, what is now called, analytical philosophy. It then goes on to talk about the various literature that has been generated by the study of Wittgenstein philosophy, stating that Wittgenstein is best known for his work in the philosophy of language, mind, and mathematics. The Introduction also talks about the differences between Wittgenstein’s views and mainstream analytical philosophy. Finally the topics covered in this book are introduced.
Wittgenstein and Biography
Authors: McGuinness Brian 
Published: January 2012

Abstract
There are obvious ways in which the study of Ludwig Wittgenstein's thought must have recourse to the facts of his life. Much of the most intimate part of Wittgenstein's own diaries was written in a simple code understood in his family, as if it were addressed to them, like one of the ‘confessions’ he often talked about and more than once made. In the notebooks in which he recorded his thoughts for future reflection or use, personal reflections abound. He interrupts his philosophical writing to exclaim, sometimes but not always in code, on his weaknesses, his vanity, his sins, or his aspirations — all of which of course might infect his philosophical writing as much as any other aspect of his life. He constantly felt that he could easily relapse into vanity, in philosophy as elsewhere. In the case of autobiography itself (he said, reflecting on his current activity), this would compound his faults, make him yet schmutziger (sully him yet further).
Assertion, Saying, and Propositional Complexity in Wittgenstein's Tractatus
Authors: Johnston Colin 
Published: January 2012

Abstract
Ludwig Wittgenstein responds in his Notes on Logic to a discussion of Bertrand Russell's 1903 Principles of Mathematics concerning assertion. In Principles of Mathematics, Russell makes a distinction between asserted and unasserted propositions. Whilst this distinction is not given a fully worked-out account, Russell sees it as a point of considerable theoretical importance. It is introduced in the context of a separation by Russell of modus ponens from the proposition that ‘if p and q be propositions then p together with p implies q’. In reply to Russell, Wittgenstein argues that ‘Assertion is merely psychological. In not-p, p is exactly the same as if it stands alone; this point is absolutely fundamental’. Wittgenstein's response is intriguing, not least because of the centrality to his Tractatus Logico-Philosophicus of the idea that a proposition says something.