bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tablets in the Library: Trialling eBooks and iPads at Middle Temple Library
Authors: Satterley Renae 
Published: June 2014

AbstractThis article by Renae Satterley discusses a trial conducted over a four month period at Middle Temple Library where members were allowed to borrow iPads for a week, free of charge. The iPads were lent to the library by LexisNexis and had ebooks and a subscription to LexisLibrary loaded on to them. In this article the author discusses the pros and cons of lending tablets to library users and whether law ebooks are as popular as some claim. It also examines the possibilities of integrating tablet computers into legal research training sessions.
The largest Silurian vertebrate and its palaeoecological implications
Authors: Choo Brian , Zhu Min , Zhao Wenjin , Jia Liaotao , Zhu You'an 
Published: June 2014

AbstractAn apparent absence of Silurian fishes more than half-a-metre in length has been viewed as evidence that gnathostomes were restricted in size and diversity prior to the Devonian. Here we describe the largest pre-Devonian vertebrate (Megamastax amblyodusgen. et sp. nov.), a predatory marine osteichthyan from the Silurian Kuanti Formation (late Ludlow, ~423 million years ago) of Yunnan, China, with an estimated length of about 1 meter. The unusual dentition of the new form suggests a durophagous diet which, combined with its large size, indicates a considerable degree of trophic specialisation among early osteichthyans. The lack of large Silurian vertebrates has recently been used as constraint in palaeoatmospheric modelling, with purported lower oxygen levels imposing a physiological size limit. Regardless of the exact causal relationship between oxygen availability and evolutionary success, this finding refutes the assumption that pre-Emsian vertebrates were restricted to small body sizes.
Stable acetate production in extreme-thermophilic (70°C) mixed culture fermentation by selective enrichment of hydrogenotrophic methanogens
Authors: Zhang Fang , Zhang Yan , Ding Jing , Dai Kun , van Loosdrecht Mark C. M. , Zeng Raymond J. 
Published: June 2014

AbstractThe control of metabolite production is difficult in mixed culture fermentation. This is particularly related to hydrogen inhibition. In this work, hydrogenotrophic methanogens were selectively enriched to reduce the hydrogen partial pressure and to realize efficient acetate production in extreme-thermophilic (70°C) mixed culture fermentation. The continuous stirred tank reactor (CSTR) was stable operated during 100 days, in which acetate accounted for more than 90% of metabolites in liquid solutions. The yields of acetate, methane and biomass in CSTR were 1.5 ± 0.06, 1.0 ± 0.13 and 0.4 ± 0.05 mol/mol glucose, respectively, close to the theoretical expected values. The CSTR effluent was stable and no further conversion occurred when incubated for 14 days in a batch reactor. In fed-batch experiments, acetate could be produced up to 34.4 g/L, significantly higher than observed in common hydrogen producing fermentations. Acetate also accounted for more than 90% of soluble products formed in these fed-batch fermentations. The microbial community analysis revealed hydrogenotrophic methanogens (mainly Methanothermobacter thermautotrophicus and Methanobacterium thermoaggregans) as 98% of Archaea, confirming that high temperature will select hydrogenotrophic methanogens over aceticlastic methanogens effectively. This work demonstrated a potential application to effectively produce acetate as a value chemical and methane as an energy gas together via mixed culture fermentation.
Wheat germin vitrotranslation to produce one of the most toxic sodium channel specific toxins
Authors: Gad Wael , Ben-Abderrazek Rahma , Wahni Khadija , Vertommen Didier , Muyldermans Serge , Bouhaouala-Zahar Balkiss , Messens Joris 
Published: June 2014

Envenoming following scorpion sting is a common emergency in many parts of the world. During scorpion envenoming, highly toxic small polypeptides of the venom diffuse rapidly within the victim causing serious medical problems. The exploration of toxin structure-function relationship would benefit from the generation of soluble recombinant scorpion toxins in Escherichia coli. We developed an in vitro wheat germ translation system for the expression of the highly toxic Aah (Androctonus australis hector)II protein that requires the proper formation of four disulphide bonds. Soluble, recombinant N-terminal GST (glutathione S-transferase)-tagged AahII toxin is obtained in this in vitro translation system. After proteolytic removal of the GST-tag, purified rAahII (recombinant AahII) toxin, which contains two extra amino acids at its N terminal relative to the native AahII, is highly toxic after i.c.v. (intracerebroventricular) injection in Swiss mice. An LD50 (median lethal dose)-value of 10 ng (or 1.33 pmol), close to that of the native toxin (LD50 of 3 ng) indicates that the wheat germ in vitro translation system produces properly folded and biological active rAahII. In addition, NbAahII10 (Androctonus australis hector nanobody 10), a camel single domain antibody fragment, raised against the native AahII toxin, recognizes its cognate conformational epitope on the recombinant toxin and neutralizes the toxicity of purified rAahII upon injection in mice.
Efficiency‐enhanced self‐biased PA driver for multi‐standard applications
Authors: Yin Yun , Chi Baoyong , Wang Zhihua 
Published: June 2014

An efficiency‐enhanced multiband power amplifier (PA) driver is proposed. It introduces a self‐biasing circuit and improved switch‐capacitor banks to enhance the efficiency. The presented PA driver has been implemented in 65 nm CMOS technology. Measurement results demonstrate a broad frequency coverage of 0.7–5.6 GHz and a flat gain within 2 dB variation. The PA driver has an output power above 6 dBm over the broadband, and it consumes a comparatively low power of 38 mA from a 2.5 V supply.
1.3 μm InGaAlAs asymmetric corrugation‐pitch‐modulated DFB lasers with high mask margin at 28 Gbit/s
Authors: Nakahara K. , Wakayama Y. , Kitatani T. , Fukamachi T. , Sakuma Y. , Tanaka S. 
Published: June 2014

Direct modulation of a 1.3 µm InGaAlAs asymmetric corrugation‐pitch‐modulated (ACPM) distributed feedback (DFB) laser operated at 28 Gbit/s was experimentally demonstrated. The laser exhibits linear light–current characteristics and a high‐frequency response with a small roll‐off at low frequency compared with a conventional λ/4‐shifted DFB laser. Moreover, it attains a high mask margin (20%) under 28 Gbit/s operation at 55°C. These superior properties are due to a superior ACPM grating that suppresses longitudinal spatial hole‐burning.
Iron–cobalt–graphite core–shell nanoparticles as efficient electromagnetic wave absorbers at X‐band frequency range
Authors: Seyyed Afghahi Seyyed Salman , Shokuhfar Ali , Saberi Behzad , Javidan Abdollah 
Published: June 2014

In this reported work, FeCo@C core–shell nanoparticles were synthesised using a novel two‐step process. Characterisation of samples confirms the formation of graphite‐coated FeCo nanoparticles. The electromagnetic wave absorption of nanocomposites containing 40%wt of FeCo@C and FeCo nanoparticles in the paraffin matrix was measured at 8–12.4 GHz frequency range. Two samples were prepared with thickness of 9 mm for FeCo and FeCo@C nanoparticles, respectively. Then the reflection loss was measured at ten different thicknesses between 9 and 1.4 mm by slicing the samples and measuring the scattering parameter S11 for each sample thickness using a metal backing. Results show that by graphite coating of FeCo nanoparticles the maximum reflection loss (−5.5 dB) grows up to four times higher (−19.2 dB) and the corresponding thickness reduces to half. The reason lies in active dielectric‐magnetic loss mechanisms in FeCo@C nanoparticles.
Comparison of optimised conditions for inductively coupled plasma‐reactive ion etching of quartz substrates and its optical applications
Authors: Tang Yu‐Hsiang , Lin Yu‐Hsin , Chen Po‐Li , Shiao Ming‐Hua , Hsiao Chien‐Nan 
Published: June 2014

A C4F8/He inductively coupled plasma‐reactive ion etching (ICP‐RIE) was studied to improve the etching conditions of quartz glass. The influences of C4F8 flow rate, He flow rate, chamber pressure, inductively coupled plasma (ICP) power, bias power and cooling temperature were investigated. A report is presented on an optimum etching condition for fabricating quartz‐based optical components considering their application in diffractive optical element (DOE) devices. As per these etching results, the etched microstructure exhibited a depth of 44.2 μm and a vertical sidewall angle of 89° resulting from an ICP power of 3000 W, a bias power of 200 W, a chamber pressure of 2.5 mTorr and an etching time of 120 min in a mixture of C4F8 and He gases with 30 and 100 sccm flow rates, respectively. The successful fabrication of the DOE component by ICP‐RIE is reported. This can be used to provide the uniform light intensity distribution for a DOE device.
Preparation of Ag2SO3 sub‐microparticles with high visible‐light photocatalytic activity
Authors: Dong Chao , Wu Kong‐Lin , Wei Xian‐Wen , Wang Jing , Liu Li , Hu Yu , Xia Shan‐Hui 
Published: June 2014

A visible‐light sensitive Ag2SO3 semiconductor photocatalyst with size of ca. 500 nm was prepared by a simple precipitation method. This photocatalyst exhibits high‐efficiency degradation ability for typical three dyes, which can be ascribed to the efficient photosensitised electron injection and slow electron recombination. The photocatalytic reaction follows a pseudo‐first‐order reaction and the rate constant of Ag2SO3 for the degradation of rhodamine B is estimated to be 1.7 times that of commercial TiO2. The stability of unstable Ag2SO3 was remarkably enhanced by the addition of Na2SO3. The h+ and •O2− played relatively major roles during the photocatalytic reaction.
Evaluating synteny for improved comparative studies
Authors: Ghiurcuta Cristina G. , Moret Bernard M. E. 
Published: June 2014

Abstract
Motivation: Comparative genomics aims to understand the structure and function of genomes by translating knowledge gained about some genomes to the object of study. Early approaches used pairwise comparisons, but today researchers are attempting to leverage the larger potential of multi-way comparisons. Comparative genomics relies on the structuring of genomes into syntenic blocks: blocks of sequence that exhibit conserved features across the genomes. Syntenic blocs are required for complex computations to scale to the billions of nucleotides present in many genomes; they enable comparisons across broad ranges of genomes because they filter out much of the individual variability; they highlight candidate regions for in-depth studies; and they facilitate whole-genome comparisons through visualization tools. However, the concept of syntenic block remains loosely defined. Tools for the identification of syntenic blocks yield quite different results, thereby preventing a systematic assessment of the next steps in an analysis. Current tools do not include measurable quality objectives and thus cannot be benchmarked against themselves. Comparisons among tools have also been neglected—what few results are given use superficial measures unrelated to quality or consistency.
Results: We present a theoretical model as well as an experimental basis for comparing syntenic blocks and thus also for improving or designing tools for the identification of syntenic blocks. We illustrate the application of the model and the measures by applying them to syntenic blocks produced by three different contemporary tools (DRIMM-Synteny, i-ADHoRe and Cyntenator) on a dataset of eight yeast genomes. Our findings highlight the need for a well founded, systematic approach to the decomposition of genomes into syntenic blocks. Our experiments demonstrate widely divergent results among these tools, throwing into question the robustness of the basic approach in comparative genomics. We have taken the first step towards a formal approach to the construction of syntenic blocks by developing a simple quality criterion based on sound evolutionary principles.
Contact: cristinagabriela.ghiurcuta@epfl.ch
BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles
Authors: Videm Pavankumar , Rose Dominic , Costa Fabrizio , Backofen Rolf 
Published: June 2014

Abstract
Summary: Non-coding RNAs (ncRNAs) play a vital role in many cellular processes such as RNA splicing, translation, gene regulation. However the vast majority of ncRNAs still have no functional annotation. One prominent approach for putative function assignment is clustering of transcripts according to sequence and secondary structure. However sequence information is changed by post-transcriptional modifications, and secondary structure is only a proxy for the true 3D conformation of the RNA polymer. A different type of information that does not suffer from these issues and that can be used for the detection of RNA classes, is the pattern of processing and its traces in small RNA-seq reads data. Here we introduce BlockClust, an efficient approach to detect transcripts with similar processing patterns. We propose a novel way to encode expression profiles in compact discrete structures, which can then be processed using fast graph-kernel techniques. We perform both unsupervised clustering and develop family specific discriminative models; finally we show how the proposed approach is scalable, accurate and robust across different organisms, tissues and cell lines.
Availability: The whole BlockClust galaxy workflow including all tool dependencies is available at http://toolshed.g2.bx.psu.edu/view/rnateam/blockclust_workflow.
Contact: backofen@informatik.uni-freiburg.de; costa@informatik.uni-freiburg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Detecting independent and recurrent copy number aberrations using interval graphs
Authors: Wu Hsin-Ta , Hajirasouliha Iman , Raphael Benjamin J. 
Published: June 2014

Abstract
Motivation: Somatic copy number aberrations (SCNAs) are frequent in cancer genomes, but many of these are random, passenger events. A common strategy to distinguish functional aberrations from passengers is to identify those aberrations that are recurrent across multiple samples. However, the extensive variability in the length and position of SCNAs makes the problem of identifying recurrent aberrations notoriously difficult.
Results: We introduce a combinatorial approach to the problem of identifying independent and recurrent SCNAs, focusing on the key challenging of separating the overlaps in aberrations across individuals into independent events. We derive independent and recurrent SCNAs as maximal cliques in an interval graph constructed from overlaps between aberrations. We efficiently enumerate all such cliques, and derive a dynamic programming algorithm to find an optimal selection of non-overlapping cliques, resulting in a very fast algorithm, which we call RAIG (Recurrent Aberrations from Interval Graphs). We show that RAIG outperforms other methods on simulated data and also performs well on data from three cancer types from The Cancer Genome Atlas (TCGA). In contrast to existing approaches that employ various heuristics to select independent aberrations, RAIG optimizes a well-defined objective function. We show that this allows RAIG to identify rare aberrations that are likely functional, but are obscured by overlaps with larger passenger aberrations.
Availability: http://compbio.cs.brown.edu/software.
Contact: braphael@brown.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data
Authors: Hajirasouliha Iman , Mahmoody Ahmad , Raphael Benjamin J. 
Published: June 2014

Abstract
Motivation: High-throughput sequencing of tumor samples has shown that most tumors exhibit extensive intra-tumor heterogeneity, with multiple subpopulations of tumor cells containing different somatic mutations. Recent studies have quantified this intra-tumor heterogeneity by clustering mutations into subpopulations according to the observed counts of DNA sequencing reads containing the variant allele. However, these clustering approaches do not consider that the population frequencies of different tumor subpopulations are correlated by their shared ancestry in the same population of cells.
Results: We introduce the binary tree partition (BTP), a novel combinatorial formulation of the problem of constructing the subpopulations of tumor cells from the variant allele frequencies of somatic mutations. We show that finding a BTP is an NP-complete problem; derive an approximation algorithm for an optimization version of the problem; and present a recursive algorithm to find a BTP with errors in the input. We show that the resulting algorithm outperforms existing clustering approaches on simulated and real sequencing data.
Availability and implementation: Python and MATLAB implementations of our method are available at http://compbio.cs.brown.edu/software/
Contact: braphael@cs.brown.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Gene network inference by probabilistic scoring of relationships from a factorized model of interactions
Authors: Žitnik Marinka , Zupan Blaž 
Published: June 2014

Abstract
Motivation: Epistasis analysis is an essential tool of classical genetics for inferring the order of function of genes in a common pathway. Typically, it considers single and double mutant phenotypes and for a pair of genes observes whether a change in the first gene masks the effects of the mutation in the second gene. Despite the recent emergence of biotechnology techniques that can provide gene interaction data on a large, possibly genomic scale, few methods are available for quantitative epistasis analysis and epistasis-based network reconstruction.
Results: We here propose a conceptually new probabilistic approach to gene network inference from quantitative interaction data. The approach is founded on epistasis analysis. Its features are joint treatment of the mutant phenotype data with a factorized model and probabilistic scoring of pairwise gene relationships that are inferred from the latent gene representation. The resulting gene network is assembled from scored pairwise relationships. In an experimental study, we show that the proposed approach can accurately reconstruct several known pathways and that it surpasses the accuracy of current approaches.
Availability and implementation: Source code is available at http://github.com/biolab/red.
Contact: blaz.zupan@fri.uni-lj.si
Supplementary information: Supplementary data are available at Bioinformatics online.
AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references
Authors: Bao Ergude , Jiang Tao , Girke Thomas 
Published: June 2014

Abstract
Motivation: De novo assemblies of genomes remain one of the most challenging applications in next-generation sequencing. Usually, their results are incomplete and fragmented into hundreds of contigs. Repeats in genomes and sequencing errors are the main reasons for these complications. With the rapidly growing number of sequenced genomes, it is now feasible to improve assemblies by guiding them with genomes from related species.
Results: Here we introduce AlignGraph, an algorithm for extending and joining de novo-assembled contigs or scaffolds guided by closely related reference genomes. It aligns paired-end (PE) reads and preassembled contigs or scaffolds to a close reference. From the obtained alignments, it builds a novel data structure, called the PE multipositional de Bruijn graph. The incorporated positional information from the alignments and PE reads allows us to extend the initial assemblies, while avoiding incorrect extensions and early terminations. In our performance tests, AlignGraph was able to substantially improve the contigs and scaffolds from several assemblers. For instance, 28.7–62.3% of the contigs of Arabidopsis thaliana and human could be extended, resulting in improvements of common assembly metrics, such as an increase of the N50 of the extendable contigs by 89.9–94.5% and 80.3–165.8%, respectively. In another test, AlignGraph was able to improve the assembly of a published genome (Arabidopsis strain Landsberg) by increasing the N50 of its extendable scaffolds by 86.6%. These results demonstrate AlignGraph’s efficiency in improving genome assemblies by taking advantage of closely related references.
Availability and implementation: The AlignGraph software can be downloaded for free from this site: https://github.com/baoe/AlignGraph.
Contact: thomas.girke@ucr.edu
Graph-regularized dual Lasso for robust eQTL mapping
Authors: Cheng Wei , Zhang Xiang , Guo Zhishan , Shi Yu , Wang Wei 
Published: June 2014

AbstractMotivation: As a promising tool for dissecting the genetic basis of complex traits, expression quantitative trait loci (eQTL) mapping has attracted increasing research interest. An important issue in eQTL mapping is how to effectively integrate networks representing interactions among genetic markers and genes. Recently, several Lasso-based methods have been proposed to leverage such network information. Despite their success, existing methods have three common limitations: (i) a preprocessing step is usually needed to cluster the networks; (ii) the incompleteness of the networks and the noise in them are not considered; (iii) other available information, such as location of genetic markers and pathway information are not integrated.Results: To address the limitations of the existing methods, we propose Graph-regularized Dual Lasso (GDL), a robust approach for eQTL mapping. GDL integrates the correlation structures among genetic markers and traits simultaneously. It also takes into account the incompleteness of the networks and is robust to the noise. GDL utilizes graph-based regularizers to model the prior networks and does not require an explicit clustering step. Moreover, it enables further refinement of the partial and noisy networks. We further generalize GDL to incorporate the location of genetic makers and gene-pathway information. We perform extensive experimental evaluations using both simulated and real datasets. Experimental results demonstrate that the proposed methods can effectively integrate various available priori knowledge and significantly outperform the state-of-the-art eQTL mapping methods.Availability: Software for both C++ version and Matlab version is available at http://www.cs.unc.edu/∼weicheng/.Contact: weiwang@cs.ucla.eduSupplementary information: Supplementary data are available at Bioinformatics online.