bluuebunny/crossref_metadata_2025_split huggingface dataset:
White Matter and Cognitive Decline in Aging: A Focus on Processing Speed and Variability
Authors: Nilsson Jonna , Thomas Alan J. , O'Brien John T. , Gallagher Peter 
Published: February 2014

AbstractWhite matter (WM) change plays an important role in age-related cognitive decline. In this review, we consider methodological advances with particular relevance to the role of WM in age-related changes in processing speed. In this context, intra-individual variability in processing speed performance has emerged as a sensitive proxy of cognitive and neurological decline while neuroimaging techniques used to assess WM change have become increasingly more sensitive. Together with a carefully designed task protocol, we emphasize that the combined implementation of intra-individual variability and neuroimaging techniques hold promise for specifying the WM-processing speed relationship with implications for normative and clinical samples. (JINS, 2014,20, 1–6)
The impact of environmental policies on productivity and market competition
Authors: Sadeghzadeh Javad 
Published: February 2014

AbstractWhile a large body of the literature on environmental policies has focused on the productivity impacts of regulations, less attention has been given to the link between environmental policies and market competition. In this paper, I develop a tractable model that incorporates variable mark-ups to study how a competitive environment is affected by environmental policies in a market with firm heterogeneity and endogenous abatement technology choice. The findings of this study are consistent with the Porter Hypothesis in the sense that environmental regulations motivate abatement technology adoption and enhance productivity and environmental quality. However, the productivity gain is mainly driven by reallocation of resources across firms rather than the induced abatement technological change. Tougher regulations harm the competitive environment by increasing average prices and market concentration. Social welfare also drops because in the absence of strong competition fewer variates are produced in equilibrium.
Super sub-wavelength patterns in photon coincidence detection
Authors: Liu Ruifeng , Zhang Pei , Zhou Yu , Gao Hong , Li Fuli 
Published: February 2014

AbstractHigh-precision measurements implemented with light are desired in all fields of science. However, light acts as a wave and the Rayleigh criterion in classical optics yields a diffraction limit that prevents obtaining a resolution smaller than the wavelength. Sub-wavelength interference has potential application in lithography because it beats the classical Rayleigh resolution limit. Here, we carefully study second-order correlation theory to establish the physics behind sub-wavelength interference in photon coincidence detection. A Young's double slit experiment with pseudo-thermal light is performed to test the second-order correlation pattern. The results show that when two point detectors are scanned in different ways, super sub-wavelength interference patterns can be obtained. We then provide a theoretical explanation for this surprising result and demonstrate that this explanation is also suitable for the results found for entangled light. Furthermore, we discuss the limitations of these types of super sub-wavelength interference patterns in quantum lithography.
Serotonin-2C receptor involved serotonin-induced Ca2+ mobilisations in neuronal progenitors and neurons in rat suprachiasmatic nucleus
Authors: Takeuchi Kouhei , Mohammad Shahid , Ozaki Tomoya , Morioka Eri , Kawaguchi Kaori , Kim Juhyon , Jeong Byeongha , Hong Jin Hee , Lee Kyoung J. , Ikeda Masayuki 
Published: February 2014

AbstractThe hypothalamic suprachiasmatic nucleus (SCN), the central circadian pacemaker in mammals, undergoes serotonergic regulation, but the underlying mechanisms remain obscure. Here, we generated a subclone of an SCN progenitor cell line expressing Ca2+ sensors (SCN2.2YC) and compared its 5-HT receptor signalling with that of rat SCN neurons in brain slices. SCN2.2YC cells expressed 5-HT1A/2A/2B/2C, but not 5A/7, while all six subtypes were expressed in SCN tissues. High K+ or 5-HT increased cytosolic Ca2+ in SCN2.2YC cells. The 5-HT responses were inhibited by ritanserin and SB-221284, but resistant to WAY-100635 and RS-127445, suggesting predominant involvement of 5-HT2C for Ca2+ mobilisations. Consistently, Ca2+ imaging and voltage-clamp electrophysiology using rat SCN slices demonstrated post-synaptic 5-HT2C expression. Because 5-HT2C expression was postnatally increased in the SCN and 5-HT-induced Ca2+ mobilisations were amplified in differentiated SCN2.2YC cells and developed SCN neurons, we suggest that this signalling development occurs in accordance with central clock maturations.
Negative consequences of glacial turbidity for the survival of freshwater planktonic heterotrophic flagellates
Authors: Sommaruga Ruben , Kandolf Georg 
Published: February 2014

AbstractHeterotrophic (phagotrophic) flagellates are key components of planktonic food webs in freshwater and marine ecosystems because they are the main consumers of bacteria. Although they are ubiquitous in aquatic ecosystems, they were numerically undetectable in turbid glacier-fed lakes. Here we show that glacial particles had negative effects on the survival and growth of heterotrophic flagellates. The effect of glacial particles was concentration-dependent and was caused by their interference with bacterial uptake rather than by physical damage. These results are the first to reveal why establishment of heterotrophic flagellates populations is hindered in very turbid glacial lakes. Because glaciers are vanishing around the world, recently formed turbid meltwater lakes represent an excellent opportunity to understand the environmental conditions that probably shaped the establishment of lake communities at the end of the last glaciation.
Direct-potential-fit analyses yield improved empirical potentials for the ground $X\,^1\Sigma _g^+$XΣg+1 state of Be2
Authors: Meshkov Vladimir V. , Stolyarov Andrey V. , Heaven Michael C. , Haugen Carl , LeRoy Robert J. 
Published: February 2014

We have performed new direct-potential-fit (DPF) analyses of the rotationally resolved \documentclass[12pt]{minimal}\begin{document}$A\,^1\Pi _u(v^{\prime }\break=2,3;J^{\prime }=1,2)\rightarrow X\,^1\Sigma _g^+(v^{\prime \prime }\in [0, 11];J^{\prime \prime }\in [0,3])$\end{document}AΠu1(v′=2,3;J′=1,2)→XΣg+1(v″∈[0,11];J″∈[0,3]) stimulated emission pumping spectra of Be2 [J. M. Merritt, V. E. Bondybey, and M. C. Heaven, Science 324, 1548 (2009)] using two quite different analytical potential energy functions that incorporate the correct theoretically known long-range behaviour in different ways. These functions are: the damped Morse/long-range potential [R. J. Le Roy, C. C. Haugen, J. Tao, and H. Li, Mol. Phys. 109, 435 (2011)], and the Chebyshev polynomial expansion potential [L. Busevica, I. Klincare, O. Nikolayeva, M. Tamanis, R. Ferber, V. V. Meshkov, E. A. Pazyuk, and A. V. Stolyarov, J. Chem. Phys. 134, 104307 (2011)]. In contrast with the expanded Morse oscillator potential determined in the original DPF analysis of Merritt et al. [Science 324, 1548 (2009)], both of these functions unambiguously support the existence of the v″ = 11 last vibrational levels which is bound by only ∼0.5 cm−1, and they give equivalent, essentially exact predictions for this level when using the original data set which ended at v″ = 10. These empirical potentials predict an equilibrium distance of re = 2.445(5) Å and a well depth of \documentclass[12pt]{minimal}\begin{document}${\mathfrak {D}}_e=934.9(0.4)$\end{document}De=934.9(0.4) cm−1, values which agree (within the uncertainties) with the best ab initio estimates of 2.444(10) Å and 935(10) cm−1, respectively [J. Koput, Phys. Chem. Chem. Phys. 13, 20311 (2011)].
Multimodal metaphors in contemporary experimental literature
Authors: Gibbons Alison 
Published: February 2014

Multimodal metaphor studies has hitherto neglected one key arena in the creative arts: literature. This article explores four case studies of multimodal metaphor within contemporary experimental literature. In poetry, the metaphor EMOTIONS ARE OBJECTS is discussed within Anne Carson’s (2009) accordion ‘poem in a box’, in which the poet struggles with the death of her brother; in literature, Steve Tomasula and Stephen Farrell’s (1996) fold-out fiction TOC and Mark Z. Danielewski’s (2006) novel Only Revolutions, both thematically interested in time and designed to be rotated in reading, are explored to reveal the metaphor TIME IS CIRCULAR MOTION; and in the graphic novel, analysis of Warren Ellis’ (2011) “SVK”, for which readers use a torch to reveal characters’ thoughts printed in UV ink, exposes the metaphor KNOWLEDGE IS LIGHT.Throughout, it is shown that multimodal metaphors are generated through both the interaction of verbal and visual modes, and through a reader-user’s performative engagement with the text. Moreover, early theorisations of multimodal metaphor in which the two domains (source and target) were required to stem from different modalities, are called into question. Rather, the creative affordances of multimodal literature show such metaphors to be more integrative in nature, both cognitively and semantically.
Discrete mixture modeling to address genetic heterogeneity in time-to-event regression
Authors: Eng Kevin H. , Hanlon Bret M. 
Published: February 2014

AbstractMotivation: Time-to-event regression models are a critical tool for associating survival time outcomes with molecular data. Despite mounting evidence that genetic subgroups of the same clinical disease exist, little attention has been given to exploring how this heterogeneity affects time-to-event model building and how to accommodate it. Methods able to diagnose and model heterogeneity should be valuable additions to the biomarker discovery toolset.Results: We propose a mixture of survival functions that classifies subjects with similar relationships to a time-to-event response. This model incorporates multivariate regression and model selection and can be fit with an expectation maximization algorithm, we call Cox-assisted clustering. We illustrate a likely manifestation of genetic heterogeneity and demonstrate how it may affect survival models with little warning. An application to gene expression in ovarian cancer DNA repair pathways illustrates how the model may be used to learn new genetic subsets for risk stratification. We explore the implications of this model for censored observations and the effect on genomic predictors and diagnostic analysis.Availability and implementation: R implementation of CAC using standard packages is available at https://gist.github.com/programeng/8620b85146b14b6edf8f Data used in the analysis are publicly available.Contact: kevin.eng@roswellpark.orgSupplementary information: Supplementary data are available at Bioinformatics online.
TSSV: a tool for characterization of complex allelic variants in pure and mixed genomes
Authors: Anvar Seyed Yahya , van der Gaag Kristiaan J. , van der Heijden Jaap W. F. , Veltrop Marcel H. A. M. , Vossen Rolf H. A. M. , de Leeuw Rick H. , Breukel Cor , Buermans Henk P. J. , Verbeek J. Sjef , de Knijff Peter , den Dunnen Johan T. , Laros Jeroen F. J. 
Published: February 2014

Abstract
Motivation: Advances in sequencing technologies and computational algorithms have enabled the study of genomic variants to dissect their functional consequence. Despite this unprecedented progress, current tools fail to reliably detect and characterize more complex allelic variants, such as short tandem repeats (STRs). We developed TSSV as an efficient and sensitive tool to specifically profile all allelic variants present in targeted loci. Based on its design, requiring only two short flanking sequences, TSSV can work without the use of a complete reference sequence to reliably profile highly polymorphic, repetitive or uncharacterized regions.
Results: We show that TSSV can accurately determine allelic STR structures in mixtures with 10% representation of minor alleles or complex mixtures in which a single STR allele is shared. Furthermore, we show the universal utility of TSSV in two other independent studies: characterizing de novo mutations introduced by transcription activator-like effector nucleases (TALENs) and profiling the noise and systematic errors in an IonTorrent sequencing experiment. TSSV complements the existing tools by aiding the study of highly polymorphic and complex regions and provides a high-resolution map that can be used in a wide range of applications, from personal genomics to forensic analysis and clinical diagnostics.
Availability and implementation: We have implemented TSSV as a Python package that can be installed through the command-line using pip install TSSV command. Its source code and documentation are available at https://pypi.python.org/pypi/tssv and http://www.lgtc.nl/tssv.
Contact: S.Y.Anvar@lumc.nl
Supplementary information: Supplementary data are available at Bioinformatics online.
SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads
Authors: Xie Yinlong , Wu Gengxiong , Tang Jingbo , Luo Ruibang , Patterson Jordan , Liu Shanlin , Huang Weihua , He Guangzhu , Gu Shengchang , Li Shengkang , Zhou Xin , Lam Tak-Wah , Li Yingrui , Xu Xun , Wong Gane Ka-Shu , Wang Jun 
Published: February 2014

Abstract
Motivation: Transcriptome sequencing has long been the favored method for quickly and inexpensively obtaining a large number of gene sequences from an organism with no reference genome. Owing to the rapid increase in throughputs and decrease in costs of next- generation sequencing, RNA-Seq in particular has become the method of choice. However, the very short reads (e.g. 2 × 90 bp paired ends) from next generation sequencing makes de novo assembly to recover complete or full-length transcript sequences an algorithmic challenge.
Results: Here, we present SOAPdenovo-Trans, a de novo transcriptome assembler designed specifically for RNA-Seq. We evaluated its performance on transcriptome datasets from rice and mouse. Using as our benchmarks the known transcripts from these well-annotated genomes (sequenced a decade ago), we assessed how SOAPdenovo-Trans and two other popular transcriptome assemblers handled such practical issues as alternative splicing and variable expression levels. Our conclusion is that SOAPdenovo-Trans provides higher contiguity, lower redundancy and faster execution.
Availability and implementation: Source code and user manual are available at http://sourceforge.net/projects/soapdenovotrans/.
Contact: xieyl@genomics.cn or bgi-soap@googlegroups.com
Supplementary information: Supplementary data are available at Bioinformatics online.
GUILDify: a web server for phenotypic characterization of genes through biological data integration and network-based prioritization algorithms
Authors: Guney Emre , Garcia-Garcia Javier , Oliva Baldo 
Published: February 2014

Abstract
Summary: Determining genetic factors underlying various phenotypes is hindered by the involvement of multiple genes acting cooperatively. Over the past years, disease–gene prioritization has been central to identify genes implicated in human disorders. Special attention has been paid on using physical interactions between the proteins encoded by the genes to link them with diseases. Such methods exploit the guilt-by-association principle in the protein interaction network to uncover novel disease–gene associations. These methods rely on the proximity of a gene in the network to the genes associated with a phenotype and require a set of initial associations. Here, we present GUILDify, an easy-to-use web server for the phenotypic characterization of genes. GUILDify offers a prioritization approach based on the protein–protein interaction network where the initial phenotype–gene associations are retrieved via free text search on biological databases. GUILDify web server does not restrict the prioritization to any predefined phenotype, supports multiple species and accepts user-specified genes. It also prioritizes drugs based on the ranking of their targets, unleashing opportunities for repurposing drugs for novel therapies.
Availability and implementation: Available online at http://sbi.imim.es/GUILDify.php
Contact: baldo.oliva@upf.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
SBARS: fast creation of dotplots for DNA sequences on different scales using GA-,GC-content
Authors: Pyatkov Maxim I. , Pankratov Anton N. 
Published: February 2014

Abstract
Summary: Structural analysis of long DNA fragments, including chromosomes and whole genomes, is one of the main challenges in modern bioinformatics. Here, we propose an original approach based on spectral methods and its implementation called SBARS (Spectral-Based Approach for Repeats Search. The main idea of our approach is that repeated DNA structures are recognized not within the nucleotide sequence directly but within the function derived from this sequence. This allows us to investigate nucleotide sequences on different scales and decrease time complexity for dotplot creation down to .
Availability and implementation: Pre-compiled versions for Windows and Linux and documentation are available at http://mpyatkov.github.com/sbars/.
Contact: mpyatkov@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
SKINK: a web server for string kernel based kink prediction in α-helices
Authors: Seifert Tim , Lund Andreas , Kneissl Benny , Mueller Sabine C. , Tautermann Christofer S. , Hildebrandt Andreas 
Published: February 2014

Abstract
Motivation: The reasons for distortions from optimal α-helical geometry are widely unknown, but their influences on structural changes of proteins are significant. Hence, their prediction is a crucial problem in structural bioinformatics. Here, we present a new web server, called SKINK, for string kernel based kink prediction. Extending our previous study, we also annotate the most probable kink position in a given α-helix sequence.
Availability and implementation: The SKINK web server is freely accessible at http://biows-inf.zdv.uni-mainz.de/skink. Moreover, SKINK is a module of the BALL software, also freely available at www.ballview.org.
Contact: benny.kneissl@roche.com
fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data
Authors: Hung Ling-Hong , Samudrala Ram 
Published: February 2014

Motivation: fast_protein_cluster is a fast, parallel and memory efficient package used to cluster 60 000 sets of protein models (with up to 550 000 models per set) generated by the Nutritious Rice for the World project.
Results: fast_protein_cluster is an optimized and extensible toolkit that supports Root Mean Square Deviation after optimal superposition (RMSD) and Template Modeling score (TM-score) as metrics. RMSD calculations using a laptop CPU are 60× faster than qcprot and 3× faster than current graphics processing unit (GPU) implementations. New GPU code further increases the speed of RMSD and TM-score calculations. fast_protein_cluster provides novel k-means and hierarchical clustering methods that are up to 250× and 2000× faster, respectively, than Clusco, and identify significantly more accurate models than Spicker and Clusco.
Availability and implementation: fast_protein_cluster is written in C++ using OpenMP for multi-threading support. Custom streaming Single Instruction Multiple Data (SIMD) extensions and advanced vector extension intrinsics code accelerate CPU calculations, and OpenCL kernels support AMD and Nvidia GPUs. fast_protein_cluster is available under the M.I.T. license. (http://software.compbio.washington.edu/fast_protein_cluster)
Contact: lhhung@compbio.washington.edu
Supplementary information: Supplementary Data are available at Bioinformatics online.
ADaCGH2: parallelized analysis of (big) CNA data
Authors: Diaz-Uriarte Ramon 
Published: February 2014

Abstract
Motivation: Studies of genomic DNA copy number alteration can deal with datasets with several million probes and thousands of subjects. Analyzing these data with currently available software (e.g. as available from BioConductor) can be extremely slow and may not be feasible because of memory requirements.
Results: We have developed a BioConductor package, ADaCGH2, that parallelizes the main segmentation algorithms (using forking on multicore computers or parallelization via message passing interface, etc., in clusters of computers) and uses ff objects for reading and data storage. We show examples of data with 6 million probes per array; we can analyze data that would otherwise not fit in memory, and compared with the non-parallelized versions we can achieve speedups of 25–40 times on a 64-cores machine.
Availability and implementation: ADaCGH2 is an R package available from BioConductor. Version 2.3.11 or higher is available from the development branch: http://www.bioconductor.org/packages/devel/bioc/html/ADaCGH2.html.
Contact: ramon.diaz@iib.uam.es
Supplementary information: Supplementary data are available at Bioinformatics online.
Characterizing foodweb structure to identify potential ecosystem effects of fishing in the Ross Sea, Antarctica
Authors: Pinkerton Matthew H. , Bradford-Grieve Janet M. 
Published: February 2014

AbstractThe potential ecosystem effects of fishing for Antarctic toothfish (Dissostichus mawsoni) in the Ross Sea region were investigated. Mixed trophic impact analysis was applied to a model of the Ross Sea foodweb and used to calculate the relative trophic importances of species and trophic groups in the system. The trophic impact of toothfish on medium-sized demersal fish was identified as the strongest top-down interaction in the system based on multiple-step analysis. This suggests a potential for a strong predation-release effect on some piscine prey of toothfish (especially grenadiers and ice-fish on the Ross Sea slope). However, Antarctic toothfish had moderate trophic importance in the Ross Sea foodweb as a whole, and the analysis did not support the hypothesis that changes to toothfish will cascade through the ecosystem by simple trophic effects. Because of limitations of this kind of analysis, cascading effects on the Ross Sea ecosystem due to changes in the abundance of toothfish cannot be ruled out, but for such changes to occur a mechanism other than simple trophic interactions is likely to be involved. Trophic importances were highest in the middle of the foodweb where silverfish and krill are known to have a key role in ecosystem structure and function. The six groups with the highest indices of trophic importance were (in decreasing order): phytoplankton, mesozooplankton, Antarctic silverfish, small demersal fish, Antarctic krill and cephalopods. Crystal krill and small pelagic fish also had high trophic importance in some analyses. Strengths and limitations of this kind of analysis are presented. In particular, it is noted that the analysis only considers trophic interactions at the spatial, temporal and ecological scale of the whole Ross Sea shelf and slope area, averaged over a typical year and in 35 trophic groups. Interference and density-dependent effects were not included in this analysis. Effects at smaller spatial and temporal scales, and effects concerning only parts of populations, were not resolved by the analysis, and this is likely to underestimate the potential risks of fishing to Weddell seals and type-C killer whales.