bluuebunny/crossref_metadata_2025_split huggingface dataset:
TreeEFM: calculating elementary flux modes using linear optimization in a tree-based algorithm
Authors: Pey Jon , Villar Juan A. , Tobalina Luis , Rezola Alberto , García José Manuel , Beasley John E. , Planes Francisco J. 
Published: November 2014

Abstract
Motivation: Elementary flux modes (EFMs) analysis constitutes a fundamental tool in systems biology. However, the efficient calculation of EFMs in genome-scale metabolic networks (GSMNs) is still a challenge. We present a novel algorithm that uses a linear programming-based tree search and efficiently enumerates a subset of EFMs in GSMNs.
Results: Our approach is compared with the EFMEvolver approach, demonstrating a significant improvement in computation time. We also validate the usefulness of our new approach by studying the acetate overflow metabolism in the Escherichia coli bacteria. To do so, we computed 1 million EFMs for each energetic amino acid and then analysed the relevance of each energetic amino acid based on gene/protein expression data and the obtained EFMs. We found good agreement between previous experiments and the conclusions reached using EFMs. Finally, we also analysed the performance of our approach when applied to large GSMNs.
Availability and implementation: The stand-alone software TreeEFM is implemented in C++ and interacts with the open-source linear solver COIN-OR Linear program Solver (CLP).
Contact: fplanes@ceit.es
Supplementary information: Supplementary data are available at Bioinformatics online.
PyFDAP: automated analysis of fluorescence decay after photoconversion (FDAP) experiments
Authors: Bläßle Alexander , Müller Patrick 
Published: November 2014

Abstract
Summary: We developed the graphical user interface PyFDAP for the fitting of linear and non-linear decay functions to data from fluorescence decay after photoconversion (FDAP) experiments. PyFDAP structures and analyses large FDAP datasets and features multiple fitting and plotting options.
Availability and implementation: PyFDAP was written in Python and runs on Ubuntu Linux, Mac OS X and Microsoft Windows operating systems. The software, a user guide and a test FDAP dataset are freely available for download from http://people.tuebingen.mpg.de/mueller-lab.
Contact: pmueller@tue.mpg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Perceptual Training Restores Impaired Cortical Temporal Processing Due to Lead Exposure
Authors: Zhu Xiaoqing , Liu Xia , Wei Fanfan , Wang Fang , Merzenich Michael M. , Schreiner Christoph E. , Sun Xinde , Zhou Xiaoming 
Published: November 2014

Abstract
Low-level lead exposure is a risk factor for cognitive and learning disabilities in children and has been specifically associated with deficits in auditory temporal processing that impair aural language and reading abilities. Here, we show that rats exposed to low levels of lead in early life display a significant behavioral impairment in an auditory temporal rate discrimination task. Lead exposure also results in a degradation of the neuronal repetition-rate following capacity and response synchronization in primary auditory cortex. A modified go/no-go repetition-rate discrimination task applied in adult animals for ∼50 days nearly restores to normal these lead-induced deficits in cortical temporal fidelity. Cortical expressions of parvalbumin, brain-derived neurotrophic factor, and NMDA receptor subunits NR2a and NR2b, which are down-regulated in lead-exposed animals, are also partially reversed with training. These studies in an animal model identify the primary auditory cortex as a novel target for low-level lead exposure and demonstrate that perceptual training can ameliorate lead-induced deficits in cortical discrimination between sound sequences.
An intraplate slow earthquake observed by a dense GPS network in Hokkaido, northernmost Japan
Authors: Ohzono Mako , Takahashi Hiroaki , Ichiyanagi Masayoshi 
Published: November 2014

AbstractAn intraplate slow earthquake was detected in northernmost Hokkaido, Japan, by a dense network of the global navigation satellite system. Transient abnormal acceleration of &lt;12 mm was observed during the period 2012 July to 2013 January (∼5.5 months) at several sites. The spatial displacement distribution suggests that a localized tectonic event caused localized deformation. Estimated fault parameter indicates very shallow-dip reverse faulting in the uppermost crust, with a total seismic moment of 1.75E + 17 N m (Mw 5.4). This fault geometry is probably consistent with detachment structure indicated by geological studies. A simultaneous earthquake swarm with the maximum magnitude M4.1 suggests a possibility that the slow slip triggered the seismic activity for unknown reasons. This slow earthquake is slower than its moment would indicate, with a duration–magnitude scaling relationship unlike either regular earthquakes or subduction slow slip events. This result indicates that even if the area is under different physical property from subduction zones, slow earthquake can occur by some causes. Slow earthquakes exist in remote regions away from subduction zones and might play an important role in strain release and tectonic activity.
Offensive Expression and the Workplace
Authors: Pearson Megan 
Published: November 2014

Abstract
In this article I argue that freedom of expression is an important right even within the employment context. I contend that there should be a presumption in favour of free expression even if the expression is offensive, particularly if it involves a matter of public debate. However, the interests of colleagues and employers should be taken into account and may be decisive. Where expression takes place outside work, employees should only be subject to disciplinary action if there is a clear link between their employment and the expression. I consider the law relating to these issues in the contexts of harassment, unfair dismissal and discrimination on the grounds of religion and belief.
Members, Partners, Employees, Workers? Partnership Law and Employment Status revisited. Clyde & Co LLP v Bates van Winkelhof
Authors: Prassl Jeremias 
Published: November 2014

Abstract
The recent Supreme Court decision in Clyde & Co v Bates van Winkelhof1 at first sight addresses no more than a rather technical point at the intersection of employment and partnership law, brought about as the result of questionable statutory drafting in section 4(4) of the Limited Liability Partnerships Act of 2004. Upon closer inspection, however, the case brings to the forefront a tension underpinning discussions of the personal scope of employment law, between an inclusive approach encompassing all relationships of employment or akin thereto, and the view that ‘private law’ or primarily commercial relationships should fall outside the scope of employment regulation. It will therefore have far-reaching implications for the employment status of partners in all forms of partnership arrangements, as explored in Section 2 of this note. The decision furthermore has the potential significantly to change our understanding of the interrelationship between the notions of employees and workers, by challenging a strand of previous decisions which seemed narrowly to interpret statutory extensions of employment status (Section 3). A brief third section, finally, explores the changing role of ECHR jurisprudence in UK employment law.
Bemovi, software for extracting Behaviour and Morphology from Videos
Authors: Pennekamp Frank , Schtickzelle Nicolas , Petchey Owen L. 
Published: November 2014

SummaryMicrobes are critical components of ecosystems and vital to the services they provide. The essential role of microbes is due to high levels of functional diversity, which are, however, not always mirrored in morphological differentiation hampering their taxonomic identification. In addition, the small size of microbes hinders the measurement of morphological and behavioural traits at the individual level, as well as interactions between individuals.Recent advances in microbial community genetics and genomics, flow cytometry and digital image analysis are promising approaches, however they miss out on a very important aspect of populations and communities: the behaviour of individuals. Video analysis complements these methods by providing in addition to abundance and trait measurements, detailed behavioural information, capturing dynamic processes such as movement, and hence has the potential to describe the interactions between individuals.We introduce bemovi, a package using R - the statistical computing environment - and the free image analysis software ImageJ. Bemovi is an automated digital video processing and analysis work flow to extract abundance and morphological and movement data for numerous individuals on a video, hence characterizing a population or community by multiple traits. Through a set of functions, bemovi identifies individuals present in a video and reconstruct their movement trajectories through space and time, merges measurements from all treated videos into a single database to which information on experimental conditions is added, readily available for further analysis in R.We illustrate the validity, precision and accuracy of the method for experimental multi-species communities of protists in aquatic microcosms. We show the high correspondence between manual and automatic counts of individuals and illustrate how simultaneous time series of abundance, morphology and behaviour are constructed. We demonstrate how the data from videos can be used in combination with supervised machine learning algorithms to automatically classify individuals according to the species they belong to, and that information on movement behaviour can substantially improve the predictive ability and helps to distinguish morphologically similar species. In principle, bemovi should be able to extract from videos information about other types of organism, including “microbes”, so long as the individuals move relatively fast compared to their background.
Tools and Methods from the Anopheles 16 Genome Project
Authors: Steele Aaron , Fontaine Michael C. , Martin Andres , Emrich Scott J. 
Published: November 2014

AbstractThe dramatic reduction in sequencing costs has resulted in many initiatives to sequence certain organisms and populations. These initiatives aim to not only sequence and assemble genomes but also to perform a more broader analysis of the population structure. As part of the Anopheline Genome Consortium, which has a vested interest in studying anpopheline mosquitoes, we developed novel methods and tools to further the communities goals. We provide a brief description of these methods and tools as well as assess the contributions that each offers to the broader study of comparative genomics.
What to compare and how: comparative transcriptomics for Evo-Devo
Authors: Roux Julien , Rosikiewicz Marta , Robinson-Rechavi Marc 
Published: November 2014

AbstractEvolutionary developmental biology has grown historically from the capacity to relate patterns of evolution in anatomy to patterns of evolution of expression of specific genes, whether between very distantly related species, or very closely related species or populations. Scaling up such studies by taking advantage of modern transcriptomics brings promising improvements, allowing us to estimate the overall impact and molecular mechanisms of convergence, constraint or innovation in anatomy and development. But it also presents major challenges, including the computational definitions of anatomical homology and of organ function, the criteria for the comparison of developmental stages, the annotation of transcriptomics data to proper anatomical and developmental terms, and the statistical methods to compare transcriptomic data between species to highlight significant conservation or changes. In this article, we review these challenges, and the ongoing efforts to address them, which are emerging from bioinformatics work on ontologies, evolutionary statistics, and data curation, with a focus on their implementation in the context of the development of our database Bgee (http://bgee.org).
WASP: allele-specific software for robust discovery of molecular quantitative trait loci
Authors: van de Geijn Bryce , McVicker Graham , Gilad Yoav , Pritchard Jonathan K. 
Published: November 2014

AbstractAllele-specific sequencing reads provide a powerful signal for identifying molecular quantitative trait loci (QTLs), however they are challenging to analyze and prone to technical artefacts. Here we describe WASP, a suite of tools for unbiased allele-specific read mapping and discovery of molecular QTLs. Using simulated reads, RNA-seq reads and ChIP-seq reads, we demonstrate that our approach has a low error rate and is far more powerful than existing QTL mapping approaches.
Ectopic Lignification in the Flax lignified bast fiber1 Mutant Stem Is Associated with Tissue-Specific Modifications in Gene Expression and Cell Wall Composition
Authors: Chantreau Maxime , Portelette Antoine , Dauwe Rebecca , Kiyoto Shingo , Crônier David , Morreel Kris , Arribat Sandrine , Neutelings Godfrey , Chabi Malika , Boerjan Wout , Yoshinaga Arata , Mesnard François , Grec Sebastien , Chabbert Brigitte , Hawkins Simon 
Published: November 2014

Abstract
Histochemical screening of a flax ethyl methanesulfonate population led to the identification of 93 independent M2 mutant families showing ectopic lignification in the secondary cell wall of stem bast fibers. We named this core collection the Linum usitatissimum (flax) lbf mutants for lignified bast fibers and believe that this population represents a novel biological resource for investigating how bast fiber plants regulate lignin biosynthesis. As a proof of concept, we characterized the lbf1 mutant and showed that the lignin content increased by 350% in outer stem tissues containing bast fibers but was unchanged in inner stem tissues containing xylem. Chemical and NMR analyses indicated that bast fiber ectopic lignin was highly condensed and rich in G-units. Liquid chromatography-mass spectrometry profiling showed large modifications in the oligolignol pool of lbf1 inner- and outer-stem tissues that could be related to ectopic lignification. Immunological and chemical analyses revealed that lbf1 mutants also showed changes to other cell wall polymers. Whole-genome transcriptomics suggested that ectopic lignification of flax bast fibers could be caused by increased transcript accumulation of (1) the cinnamoyl-CoA reductase, cinnamyl alcohol dehydrogenase, and caffeic acid O-methyltransferase monolignol biosynthesis genes, (2) several lignin-associated peroxidase genes, and (3) genes coding for respiratory burst oxidase homolog NADPH-oxidases necessary to increase H2O2 supply.
ULTRAPETALAtrxG Genes Interact withKANADITranscription Factor Genes to RegulateArabidopsisGynoecium Patterning
Authors: Pires Helena R. , Monfared Mona M. , Shemyakina Elena A. , Fletcher Jennifer C. 
Published: November 2014

AbstractOrgan formation relies upon precise patterns of gene expression that are under tight spatial and temporal regulation. Transcription patterns are specified by several cellular processes during development, including chromatin remodeling, but little is known about how chromatin-remodeling factors contribute to plant organogenesis. We demonstrate that the trithorax group (trxG) gene ULTRAPETALA1 (ULT1) and the GARP transcription factor gene KANADI1 (KAN1) organize the Arabidopsis thaliana gynoecium along two distinct polarity axes. We show that ULT1 activity is required for the kan1 adaxialized polarity defect, indicating that ULT1 and KAN1 act oppositely to regulate the adaxial-abaxial axis. Conversely, ULT1 and KAN1 together establish apical-basal polarity by promoting basal cell fate in the gynoecium, restricting the expression domain of the basic helix-loop-helix transcription factor gene SPATULA. Finally, we show that ult alleles display dose-dependent genetic interactions with kan alleles and that ULT and KAN proteins can associate physically. Our findings identify a dual role for plant trxG factors in organ patterning, with ULT1 and KAN1 acting antagonistically to pattern the adaxial-abaxial polarity axis but jointly to pattern the apical-basal axis. Our data indicate that the ULT proteins function to link chromatin-remodeling factors with DNA binding transcription factors to regulate target gene expression.
Market quality and structural changes in the trading system
Authors: Agudelo Diego A. , Gutiérrez Daza Ángelo , Múnera Montoya Nazly J. 
Published: November 2014

Purpose
The purpose of this paper is to study the effect of X‐Stream, the new trading platform of the Colombian Stock Exchange since February 2009, on the market quality.

Design/methodology/approach
The authors test the effect of X‐Stream on market quality variables, such as liquidity (bid‐ask spread and price impact), daily and intraday volatility and trading activity, using mean tests, panel data and conditional variance models. The authors use a proprietary database of transactions and orders from the exchange.

Findings
The evidence suggests that X‐Stream improved the liquidity and trading activity and reduced the volatility of the overall market, especially of the most liquid stocks.

Practical implications
These results support the investment on more sophisticated trading systems in emerging markets.

Originality/value
Contributing to the literature on market quality, this paper provides novel evidence of the effect of reforms on market design, trading rules and operational capabilities on a small and low‐liquidity emerging stock market.
Gentrification Interrupted in Salford, UK: From New Deal to “Limbo‐Land” in a Contemporary Urban Periphery
Authors: Wallace Andrew 
Published: November 2014

AbstractThis paper examines two potential lacunae in understanding low‐income residents’ experiences of contemporary state‐led gentrification via a study of neighbourhood restructuring in Salford, UK, 2004–2014. The first is the localised politics preparing the ground for neighbourhood “redevelopment” and housing demolition. The second is the blighted social landscape which emerges with the subsequent stalling of this project. A focus on “before” and “after” is adopted in order to disrupt the linear policy and “effects” temporalities that much qualitative gentrification research tends to inhabit. We see how state‐led neighbourhood restructuring does not simply displace, but carries residents from “empowerment” to abandonment and transfers them from active struggle into devitalised limbo. As such, the paper demarcates challenges and opportunities for resident mobilisation inherent in a vacillating urban renewal programme, powerful in its inception but which has since “hit the buffers” (Lees 2014, Antipode 46(4):921–947) in light of global and municipal fiscal crises.
From false belief to friendship: Commentary on Fink, Begeer, Peterson, Slaughter, and de Rosnay
Authors: Lerner Matthew D. , Lillard Angeline S. 
Published: November 2014

Fink, Begeer, Peterson, Slaughter, and de Rosnay (Brit. J. Dev. Psychol, 2015; 33, 1–17) represent a welcome contribution in providing empirical evidence of the link from false belief understanding at Time 1 to mutual friendship 2 years later, controlling for several other possible contributors. This opens a new and important line of inquiry into the practical significance of a Theory of Mind. As is typical of pioneering research, further study is needed to address some issues; here, we point out some of these issues and then briefly discuss the broader implications of Fink et al.'s findings.
Factors predicting survival in peripheral T‐cell lymphoma in the USA: a population‐based analysis of 8802 patients in the modern era
Authors: Petrich Adam M. , Helenowski Irene B. , Bryan Locke J. , Rozell Shaina A. , Galamaga Robert , Nabhan Chadi 
Published: November 2014

SummaryCurrent prognostic models for peripheral T‐cell lymphoma (PTCL) have multiple limitations, and questions exist regarding applicability to current patients. We utilized the Surveillance Epidemiology and End Results (SEER)‐18 database to evaluate factors affecting overall survival (OS) of PTCL in the modern era and identified 8802 patients between 2000–2010. Most subtypes of PTCL increased in incidence during the study period. In univariate analyses, age >55 years, black race, advanced stage, absence of extra‐nodal disease, omission of radiation therapy (RT) and high‐risk histology each predicted inferior OS (P < 0·0001). Multivariate analysis (MVA) demonstrated that hepatosplenic, enteropathy‐associated and extra‐nodal Natural Killer/T cell histologies, each had hazard ratios >1·5 (P ≤ 0·0001) for death. Further, age ≥55 years, black race and advanced stage maintained their significance in the MVA (P < 0·0001 each). Based on the significant factors, a prognostic model was constructed and subsequently validated in an independent cohort. The new model incorporated age, stage, histology and race, with an OS ranging from 9 months (highest risk group) to 120 months (lowest risk group). In summary, this is the largest study of PTCL patients in the modern era that provides risk stratification utilizing a new prognostic model that can be incorporated into future prospective clinical trials.
To what extent is allergen exposure a risk factor for the development of allergic disease?
Authors: Custovic A. 
Published: November 2014

SummaryThe role of allergen exposure in the development of allergic disease has been a matter of considerable debate, and our understanding of the importance of allergens has evolved over the last 25 years. Several observational and primary prevention studies have investigated these relationships, and different studies reported inconsistent, and sometimes opposite findings. It has to be emphasized that a clear understanding of how aeroallergen exposure occurs, and accurate and reproducible measurement of exposure are essential prerequisites for understanding the role of exposure. However, our current understanding of how we get exposed to allergens is not based on solid evidence, but on a number of assumptions, and we urgently need to develop better proxy measures (or indices) of exposure. In addition, the relative importance of the timing of exposure (e.g. early compared to exposure in later life) is unknown. It is also unclear which route of exposure is the most relevant (e.g. inhaled vs. oral vs. transcutaneous). Available data suggest that the dose–response relationship between allergen exposure and allergic disease may differ between different allergens, dose ranges and exposure patterns, and these relationships may further differ between different populations and geographical areas. It is increasingly clear that childhood asthma and atopy are not single phenotypes, and it is likely that allergen exposure has different effect on distinct subgroups under the umbrella terms of ‘sensitization’ and ‘asthma’. Susceptibility to allergen exposure, other environmental exposures and their interactions may also differ between individuals with different genetic predispositions. However, the precise nature of these complex relationships is unclear. We need a holistic approach offered by systems biology, with integration of information on the standardized and reliable measures of exposures (including allergens and other relevant exposures) with genetic and biological data to fully understand the role of allergens in the development of allergic disease.