bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparing alternative pipelines for cross-platform microarray gene expression data integration with RNA-seq data in breast cancer
Authors: Frolova Alina , Bondarenko Vladyslav , Obolenska Maria 
Published: June 2016

AbstractBackgroundAccording to major public repositories statistics an overwhelming majority of the existing and newly uploaded data originates from microarray experiments. Unfortunately, the potential of this data to bring new insights is limited by the effects of individual study-specific biases due to small number of biological samples. Increasing sample size by direct microarray data integration increases the statistical power to obtain a more precise estimate of gene expression in a population of individuals resulting in lower false discovery rates. However, despite numerous recommendations for gene expression data integration, there is a lack of a systematic comparison of different processing approaches aimed to asses microarray platforms diversity and ambiguous probesets to genes correspondence, leading to low number of studies applying integration.ResultsHere, we investigated five different approaches of the microarrays data processing in comparison with RNA-seq data on breast cancer samples. We aimed to evaluate different probesets annotations as well as different procedures of choosing between probesets mapped to the same gene. We show that pipelines rankings are mostly preserved across Affymetrix and Illumina platforms. BrainArray approach based on updated annotation and redesigned probesets definition and choosing probeset with the maximum average signal across the samples have best correlation with RNA-seq, while averaging probesets signals as well as scoring the quality of probes sequences mapping to the transcripts of the targeted gene have worse correlation. Finally, randomly selecting probeset among probesets mapped to the same gene significantly decreases the correlation with RNA-seq.ConclusionWe show that methods, which rely on actual probesets signal intensities, are advantageous to methods considering biological characteristics of the probes sequences only and that cross-platform integration of datasets improves correlation with the RNA-seq data. We consider the results obtained in this paper contributive to the integrative analysis as a worthwhile alternative to the classical meta-analysis of the multiple gene expression datasets.
Decoding brain activity using a large-scale probabilistic functional-anatomical atlas of human cognition
Authors: Rubin Timothy N. , Koyejo Oluwasanmi , Gorgolewski Krzysztof J. , Jones Michael N. , Poldrack Russell A. , Yarkoni Tal 
Published: June 2016

AbstractA central goal of cognitive neuroscience is to decode human brain activity--i.e., to infer mental processes from observed patterns of whole-brain activation. Previous decoding efforts have focused on classifying brain activity into a small set of discrete cognitive states. To attain maximal utility, a decoding framework must be open-ended, systematic, and context-sensitive--i.e., capable of interpreting numerous brain states, presented in arbitrary combinations, in light of prior information. Here we take steps towards this objective by introducing a Bayesian decoding framework based on a novel topic model---Generalized Correspondence Latent Dirichlet Allocation---that learns latent topics from a database of over 11,000 published fMRI studies. The model produces highly interpretable, spatially-circumscribed topics that enable flexible decoding of whole-brain images. Importantly, the Bayesian nature of the model allows one to “seed” decoder priors with arbitrary images and text--enabling researchers, for the first time, to generative quantitative, context-sensitive interpretations of whole-brain patterns of brain activity.
Efficient inference of recent and ancestral recombination within bacterial populations
Authors: Mostowy Rafal , Croucher Nicholas J. , Andam Cheryl P. , Corander Jukka , Hanage William P. , Marttinen Pekka 
Published: June 2016

AbstractProkaryotic evolution is affected by horizontal transfer of genetic material through recombination. Inference of an evolutionary tree of bacteria thus relies on accurate identification of the population genetic structure and recombination-derived mosaicism. Rapidly growing databases represent a challenge for computational methods to detect recombinations in bacterial genomes. We introduce a novel algorithm calledfastGEARwhich identifies lineages in diverse microbial alignments, and recombinations between them and from external origins. The algorithm detects both recent recombinations (affecting a few isolates) and ancestral recombinations between detected lineages (affecting entire lineages), thus providing insight into recombinations affecting deep branches of the phylogenetic tree. In sim-ulations,fastGEARhad comparable power to detect recent recombinations and outstanding power to detect the ancestral ones, compared to state-of-the-art methods, often with a fraction of computational cost. We demonstrate the utility of the method by analysing a collection of 616 whole-genomes of a recombinogenic pathogenStreptococcus pneumoniae, for which the method provided a high-resolution view of recombination across the genome. We examined in detail the penicillin-binding genes across theStreptococcusgenus, demonstrating previously undetected genetic exchanges between different species at these three loci. Hence,fastGEARcan be readily applied to investigate mosaicism in bacterial genes across multiple species. Finally,fastGEARcorrectly identified many known recombination hotspots and pointed to potential new ones. Matlab code and Linux/Windows executables are available athttps://users.ics.aalto.fi/~pemartti/fastGEAR/
“Gap hunting” to characterize clustered probe signals in Illumina methylation array data
Authors: Andrews Shan V. , Ladd-Acosta Christine , Feinberg Andrew P. , Hansen Kasper D. , Fallin M. Daniele 
Published: June 2016

AbstractBackgroundThe Illumina 450K array has been widely used in epigenetic association studies. Current quality-control (QC) pipelines typically remove certain sets of probes, such as those containing a SNP or with multiple mapping locations. An additional set of potentially problematic probes are those with DNA methylation (DNAm) distributions characterized by two or more distinct clusters separated by gaps. Data-driven identification of such probes may offer additional insights for downstream analyses.ResultsWe developed a procedure, termed “gap hunting”, to identify probes showing clustered distributions. Among 590 peripheral blood samples from the Study to Explore Early Development, we identified 11,007 “gap probes”. The vast majority (9,199) are likely attributed to an underlying SNP(s) or other variant in the probe, although SNP-affected probes exist that do not produce a gap signals. Specific factors predict which SNPs lead to gap signals, including type of nucleotide change, probe type, DNA strand, and overall methylation state. These expected effects are demonstrated in paired genotype and 450k data on the same samples. Gap probes can also serve as a surrogate for the local genetic sequence on a haplotype scale and can be used to adjust for population stratification.ConclusionsThe characteristics of gap probes reflect potentially informative biology. QC pipelines may benefit from an efficient data-driven approach that “flags” gap probes, rather than filtering such probes, followed by careful interpretation of downstream association analyses. Our results should translate directly to the recently released Illumina 850K EPIC array given the similar chemistry and content design.
The role of single occupancy effects on integrase dynamics in a cell-free system
Authors: Artavanis Georgios , Hsiao Victoria , Hayes Clarmyra A. , Murray Richard M. 
Published: June 2016

AbstractPhage integrase-based circuits are an alternative approach to relying on transcriptional and translational repression for biomolecular circuits. Previous research has shown that circuits based on integrases can perform a variety of functions, including counters, Boolean logic operators, memory modules and temporal event detectors. It is therefore essential to develop a principled theoretical and experimental framework for the design, implementation and study of such circuits. One of the fundamental questions that such a framework should address concerns the functionality limitations and temporal dynamics of the integrases as regulatory elements. Here, we test the functionality of several large serine integrases from a recently published library in a cell-free transcription-translation (TX-TL) platform. Additionally, we use a combination of experimental data and models to investigate integrase dynamics as a function of enzyme concentration and number of binding sites.We report that sequestration of integrase molecules, either in the form of monomers or dimers, by the integrase's own binding sites dominates integrase dynamics, and that the delay in the activation of the reporter is negatively correlated with integrase plasmid concentration. We have validated our sequestration hypothesis by building a model with MATLAB’s SimBiology toolbox, and running simulations with various integrase and binding sites concentrations. The simulation results qualitatively match the experimental results, and offer further insights into the system.
Temporal Modulations Reveal Distinct Rhythmic Properties of Speech and Music
Authors: Ding Nai , Patel Aniruddh D. , Chen Lin , Butler Henry , Luo Cheng , Poeppel David 
Published: June 2016

AbstractSpeech and music have structured rhythms, but these rhythms are rarely compared empirically. This study, based on large corpora, quantitatively characterizes and compares a major acoustic correlate of spoken and musical rhythms, the slow (0.25-32 Hz) temporal modulations in sound intensity. We show that the speech modulation spectrum is highly consistent cross 9 languages (including languages with typologically different rhythmic characteristics, such as English, French, and Mandarin Chinese). A different, but similarly consistent modulation spectrum is observed for Western classical music played by 6 different instruments. Western music, including classical music played by single instruments, symphonic, jazz, and rock music, contains more energy than speech in the low modulation frequency range below 4 Hz. The temporal modulations of speech and music show broad but well-separated peaks around 5 and 2 Hz, respectively. These differences in temporal modulations alone, without any spectral details, can discriminate speech and music with high accuracy. Speech and music therefore show distinct and reliable statistical regularities in their temporal modulations that likely facilitate their perceptual analysis and its neural foundations.
Meta population modelling of narwhals in East Canada and West Greenland - 2017
Authors: Witting Lars 
Published: June 2016

ABSTRACTThis paper combines a catch allocation model for narwhals in East Canada and West Greenland with Bayesian population modelling of the eight summer aggregations of narwhals in the region. The catch allocation model allocates the catches in different hunting areas and seasons to the different summer aggregations, and the population models analyse the impact of these catches on the population dynamics of the eight narwhal aggregations.The population models run from 1970, and the catch allocation model needs population trajectories from 1970 to the present in order to estimate the catches taken from the different summer aggregations during this period. In an initial run it uses linear transitions between the available abundance estimates; but more elaborate population trajectories are estimated by the fit of the population models to the abundance data. The two models are therefore run in an iterative manner until the catch histories that are estimated by the allocation model, and the abundance trajectories that are estimated by the population models, converge between runs.Given a converged model and potential future catch options for the different hunts, the model estimates the probabilities of fulfilling management options for the eight summer aggregations of narwhals.
ADAR-Independent A-to-I RNA Editing is Generally Adaptive for Sexual Reproduction in Fungi
Authors: Wang Qinhu , Jiang Cong , Liu Huiquan , Xu Jin-Rong 
Published: June 2016

ABSTRACTADAR-mediated A-to-I RNA editing is a well-known RNA modification mechanism in metazoans that can cause nonsynonymous changes leading to amino acid substitutions. Despite a few cases that are clearly functionally important, the biological significance of most nonsynonymous editing sites in animals remains largely unknown. Recently, genome-wide A-to-I editing was found to occur mainly in the coding regions and specifically during sexual reproduction in the wheat scab fungusFusarium graminearumthat lacks ADAR orthologs. In this study, we found that both the frequency and editing level of nonsynonymous editing is significantly higher than those of synonymous editing, suggesting that nonsynonymous editing is generally beneficial and under positive selection inF. graminearum. We also showed that nonsynonymous editing favorably targets functionally more important and more conserved genes, but at less-conserved sites, indicating that the RNA editing system is adapted to fine turn protein functions by avoiding potentially deleterious editing events. Furthermore, nonsynonymous editing inF. graminearumwas found to be under codon-specific selection and most types of codon changes tend to cause amino acid substitutions with distinct physical-chemical properties and smaller molecular weights, which likely have more profound impact on protein structures and functions. In addition, we found that the most abundant synonymous editing of leucine codons is adapted to fine turn the protein expression by increasing codon usage bias. These results clearly show that A-to-I RNA editing in fungi is generally adaptive and recoding RNA editing may play an important role in sexual development in filamentous ascomycetes.
The role of evolutionary selection in the dynamics of protein structure evolution
Authors: Gilson Amy I. , Marshall-Christensen Ahmee , Choi Jeong-Mo , Shakhnovich Eugene I. 
Published: June 2016

AbstractHomology modeling is a powerful tool for predicting a protein’s structure. This approach is successful because proteins whose sequences are only 30% identical still adopt the same structure, while structure similarity rapidly deteriorates beyond the 30% threshold. By studying the divergence of protein structure as sequence evolves in real proteins and in evolutionary simulations, we show that this non-linear sequence-structure relationship emerges as a result of selection for protein folding stability in divergent evolution. Fitness constraints prevent the emergence of unstable protein evolutionary intermediates thereby enforcing evolutionary paths that preserve protein structure despite broad sequence divergence. However on longer time scales, evolution is punctuated by rare events where the fitness barriers obstructing structure evolution are overcome and discovery of new structures occurs. We outline biophysical and evolutionary rationale for broad variation in protein family sizes, prevalence of compact structures among ancient proteins and more rapid structure evolution of proteins with lower packing density.
Potential energy landscapes reveal the information-theoretic nature of the epigenome
Authors: Jenkinson Garrett , Pujadas Elisabet , Goutsias John , Feinberg Andrew P. 
Published: June 2016

ABSTRACTEpigenetics is defined as genomic modifications carrying information independent of DNA sequence heritable through cell division. In 1940, Waddington coined the term “epigenetic landscape” as a metaphor for pluripotency and differentiation, but epigenetic potential energy landscapes have not yet been rigorously defined. Using well-grounded biological assumptions and principles of statistical physics and information theory, we derive potential energy landscapes from whole genome bisulfite sequencing data that allow us to quantify methylation stochasticity genome-wide and discern epigenetic differences using Shannon’s entropy and the Jensen-Shannon distance. We discover a “developmental wheel” of germ cell lineages and an association between entropy and chromatin structure. Viewing methylation maintenance as a communications system, we introduce methylation channels and show that higher-order chromatin organization can be predicted from their informational properties. Our results provide a fundamental understanding of the information-theoretic nature of the epigenome and a powerful methodology for studying its role in disease and aging.
Shedding light on the grey zone of speciation along a continuum of genomic divergence
Authors: Roux Camille , Fraïsse Christelle , Romiguier Jonathan , Anciaux Yoann , Galtier Nicolas , Bierne Nicolas 
Published: June 2016

AbstractSpeciation results from the progressive accumulation of mutations that decrease the probability of mating between parental populations, or reduce the fitness of hybrids - the so-called species barriers. The speciation genomic literature, however, is mainly a collection of case studies, each with its own approach and specificities, such that a global view of the gradual process of evolution from one to two species is currently lacking. Of primary importance is the prevalence of gene flow between diverging entities, which is central in most species concepts, and has been widely discussed in recent years. Here we explore the continuum of speciation thanks to a comparative analysis of genomic data from 61 pairs of populations/species of animals with variable levels of divergence. Gene flow between diverging gene pools is assessed under an Approximate Bayesian Computation (ABC) framework. We show that the intermediate "grey zone" of speciation, in which taxonomy is often controversial, spans from 0.5% to 2% of net synonymous divergence, irrespective of species life-history traits or ecology. Thanks to appropriate modeling of among-loci variation in genetic drift and introgression rate, we clarify the status of the majority of ambiguous cases and uncover a number of cryptic species. Our analysis also reveals the high incidence in animals of semi-isolated species, when some but not all loci are affected by barriers to gene flow, and highlights the intrinsic difficulty, both statistical and conceptual, of delineating species in the grey zone of speciation.
On portfolio optimization
Authors: Berger Theo , Fieberg Christian 
Published: June 2016

Purpose
The purpose of this paper is to show how investors can incorporate the multi-scale nature of asset and factor returns into their portfolio decisions and to evaluate the out-of-sample performance of such strategies.

Design/methodology/approach
The authors decompose daily return series of common risk factors and of all stocks listed in the Dow Jones Industrial Index (DJI) from 2000 to 2015 into different time scales to separate short-term noise from long-run trends. Then, the authors apply various (multi-scale) factor models to determine variance-covariance matrices which are used for minimum variance portfolio selection. Finally, the portfolios are evaluated by their out-of-sample performance.

Findings
The authors find that portfolios which are constructed on variance-covariance matrices stemming from multi-scale factor models outperform portfolio allocations which do not take the multi-scale nature of asset and factor returns into account.

Practical implications
The results of this paper provide evidence that accounting for the multi-scale nature of return distributions in portfolio decisions might be a promising approach from a portfolio performance perspective.

Originality/value
The authors demonstrate how investors can incorporate the multi-scale nature of returns into their portfolio decisions by applying wavelet filter techniques.
Commentary: enhancing community inclusion for people with complex needs through partnership working
Authors: Carnaby Steve 
Published: June 2016

Purpose
– The purpose of this paper is to serve as a commentary on the work reported by Hilary Johnson and her colleagues, which used partnership working as a lever for developing community inclusion for people with complex communication needs.

Design/methodology/approach
– The commentary uses the wider literature on social inclusion as well as narrative from current policy in England on the development of “Transforming Care Partnerships” to explore some of the issues raised by the research.

Findings
– The conclusion is that physical integration is only the starting point for a vision where people with the most complex needs live the “included life” which evolves by developing partnership working and reciprocal relationships between people with and without disabilities.

Originality/value
– This paper attempts to highlight relevant key research in the area of social integration as a way of reviewing the likely impact of recent policy on the lives of people with intellectual disabilities and the most complex needs.
The effects of physical prehabilitation in elderly patients undergoing colorectal surgery: a systematic review
Authors: Bruns E. R. J. , van den Heuvel B. , Buskens C. J. , van Duijvendijk P. , Festen S. , Wassenaar E. B. , van der Zaag E. S. , Bemelman W. A. , van Munster B. C. 
Published: June 2016

AbstractAimPrehabilitation, defined as enhancement of the preoperative condition of a patient, is a possible strategy for improving postoperative outcome. Lack of muscle strength and poor physical condition, increasingly prevalent in older patients, are risk factors for postoperative complications. Eighty‐five per cent of patients with colorectal cancer are aged over 60 years. Since surgery is the cornerstone of their treatment, this review systemically examined the literature on the effect of physical prehabilitation in older patients undergoing colorectal surgery.MethodTrials and case–control studies investigating the effect of physical prehabilitation in patients over 60 years undergoing colorectal surgery were retrieved from MEDLINE, EMBASE, CINAHL and the Cochrane library. Patient characteristics, the type of intervention and outcome measurements were recorded. The risk of bias and heterogeneity was assessed.ResultsFive studies including 353 patients were identified. They were small, containing an average of 77 patients and were of moderate methodological quality. Compliance rates of the prehabilitation programme varied from 16 to 97%. None of the studies could identify a significant reduction of postoperative complications or length of hospital stay. Four studies showed physical improvement (walking distance, respiratory endurance) in the prehabilitation group. Clinical heterogeneity precluded a meta‐analysis.ConclusionPrehabilitation is a possible means of enhancing the physical condition of patients preoperatively. The quality of studies in older patients undergoing colorectal surgery is poor, despite the increase in elderly people with colorectal cancer. Defining specific patient groups at risk and standardizing the outcome are essential for improving the results of treatment.