bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crystallization behavior and mechanical strength of poly(butylene succinate‐co‐ethylene glycol)‐based nanocomposites using functionalized multiwalled carbon nanotubes
Authors: Tan Licheng , Chen Yiwang , Zhou Weihua , Ye Suwen 
Published: May 2012

AbstractBiodegradable poly(butylene succinate‐co‐ethylene glycol) (PBSG)/multiwalled carbon nanotube (MWCNT) nanocomposites were successfully prepared through physical blending and silication between PBSG and acyl aminopropyltriethoxysilane functionalized multiwalled carbon nanotube (MWCNT‐APTES). Nuclear magnetic resonance (NMR) spectra observations revealed that the PBSG chains were covalently attached to the MWCNT‐APTES by hydrolysis. PBSG/MWCNT‐APTES nanocomposites after hydrolysis showed excellent interfacial compatibility between PBSG and MWCNT‐APTES, which was helpful for the dispersion of MWCNT in the PBSG matrix. The incorporation of MWCNT‐APTES accelerated the crystallization of PBSG in the nanocomposites for both approaches of physical blending and hydrolysis due to the heterogeneous nucleation effect of MWCNT while the crystal structure of PBSG was remained. Furthermore, the crystallization rate of PBSG in PBSG/MWCNT‐APTES nanocomposites after hydrolysis was slower than that in the nanocomposite by physical blend. The tensile strength and modulus of the nanocomposites increased about 6% and 11% with the addition of only 1 wt% MWCNT‐APTES compared with that of neat PBSG, and was larger for the PBSG/MWCNT‐APTES nanocomposites after hydrolysis. POLYM. ENG. SCI., 2012. © 2012 Society of Plastics Engineers
MORE EXOTIC AND FEWER NATIVE PLANT SPECIES: RIVERINE VEGETATION PATTERNS ASSOCIATED WITH ALTERED SEASONAL FLOW PATTERNS
Authors: Greet J. , Cousens R. D. , Webb J. A. 
Published: May 2012

ABSTRACTNatural flow regimes are important for sustaining riverine vegetation. The regulation of river flows to provide water for agriculture often results in changes to flow timing. This study assesses the impact of altered seasonal flow patterns on riverine flora.Within temperate Australia, we surveyed the vegetation of five lowland rivers, three of which have large dams that alter their seasonal flow patterns; the other two are unregulated. From four to six sites were selected on each river, and these were classified into three levels of regulation based on the extent to which the timing of their seasonal flow patterns were altered. Sites were surveyed in winter and the following summer. Permanent quadrats were also established at a number of the surveyed sites and resurveyed every 3 months.Of the 267 plant taxa identified, 145 were exotic (non‐native). More exotic taxa and fewer native taxa were associated with increasing level of seasonal flow inversion (regulation). In particular, greater numbers of short‐lived exotic terrestrial taxa and fewer native woody taxa were associated with increasing level of regulation. Some exotic woody species (e.g. willows) were more common in the unregulated rivers and may have life‐history traits favoured by the natural seasonal flow patterns of study area. Multivariate analyses showed that level of regulation had a significant effect on the overall composition of the riverine vegetation.Our results provide support for the hypotheses that flow regulation adversely affects native species diversity and increases the vulnerability of riparian zones to invasion by exotic species; however, these effects are dependent on plant species' life‐history strategies. Our study highlights the importance of natural seasonal flow patterns for sustaining native riverine plant communities. Flow management aimed at maintaining or restoring ecological values should consider seasonal flow patterns. Winter/spring flow peaks may be particularly important for the recruitment of native riverine plants, especially trees and shrubs, and reducing the extent of exotic annuals and grasses. Copyright © 2012 John Wiley & Sons, Ltd.
Critical window for the vacant set left by random walk on random regular graphs
Authors: Černý Jiří , Teixeira Augusto 
Published: May 2012

AbstractWe consider the simple random walk on a random d ‐regular graph with n vertices, and investigate percolative properties of the set of vertices not visited by the walk until time
\documentclass{article}\usepackage{mathrsfs}\usepackage{amsmath, amssymb}\pagestyle{empty}\begin{document}\begin{align*}\left\lfloor un \right\rfloor\end{align*} \end{document}, where u > 0 is a fixed positive parameter. It was shown in Černý et al., (Ann Inst Henri Poincaré Probab Stat 47 (2011) 929–968) that this so‐called vacant set exhibits a phase transition at u = u⋆: there is a giant component if u < u⋆ and only small components when u > u⋆. In this paper we show the existence of a critical window of size n‐1/3 around u⋆. In this window the size of the largest cluster is of order n2/3. © 2012 Wiley Periodicals, Inc. Random Struct. Alg., 2013
Sharp load thresholds for cuckoo hashing
Authors: Fountoulakis Nikolaos , Panagiotou Konstantinos 
Published: May 2012

AbstractThe paradigm of many choices has influenced significantly the design of efficient data structures and, most notably, hash tables. Cuckoo hashing is a technique that extends this concept. There, we are given a table withnlocations, and we assume that each location can hold one item. Each item to be inserted chooses randomlyk≥ 2 locations and has to be placed in any one of them. How much load can cuckoo hashing handle before collisions prevent the successful assignment of the available items to the chosen locations? Practical evaluations and theoretical analysis of this method have shown that one can allocate a number of elements that is a large proportion of the size of the table, being very close to 1 even for small values ofksuch as 4 or 5.In this paper we show that there is a critical value for this proportion: with high probability, when the amount of available items is below this value, then these can be allocated successfully, but when it exceeds this value, the allocation becomes impossible. We give explicitly for eachk≥ 3 this critical value. This answers an open question posed by Mitzenmacher (ESA '09) and underpins theoretically the experimental results. Our proofs are based on the translation of the question into a hypergraph setting, and the study of the related typical properties of randomk‐uniform hypergraphs.© 2012 Wiley Periodicals, Inc. Random Struct., 2012
Context Memory in Korsakoff’s Syndrome
Authors: Kessels Roy P. C. , Kopelman Michael D. 
Published: May 2012

Abstract
Memory for contextual information and target-context integration are crucial for successful episodic memory formation and are impaired in patients with Korsakoff’s syndrome. In this paper we review the evidence for the notion that a context memory deficit makes an important contribution to the amnesia in these patients. First, we focus on anterograde memory for contextual (spatial and temporal) information. Next, the use of contextual cues in memory retrieval is examined and their role in retrograde amnesia and confabulation. Evidence on the role of contextual cues and associations in working memory is discussed in relation to the underlying neurocognitive mechanisms and their dissociation from long-term encoding. Finally, we focus on implicit learning of contextual information in Korsakoff patients. It can be concluded that Korsakoff patients are impaired in the explicit processing of contextual information and in target-context binding, both in long-term (retrograde and anterograde) memory and in working memory. These results extend the context memory deficit hypothesis. In contrast, implicit contextual learning is relatively preserved in these patients. These findings are discussed in relation to evidence of dysfunction of the extended diencephalic-hippocampal memory circuit in Korsakoff’s syndrome.
Data Quality Challenges in Systemic Lupus Erythematosus Trials: How Can This Be Optimized?
Authors: Pike Marilyn C. , Kelley Lexy 
Published: May 2012

Abstract
Major scientific advances in basic science, pharmacology, and translational medicine have allowed the discovery of new molecular targets whose manipulation by new chemical entities has led to treatments for inflammatory diseases, including rheumatoid arthritis, multiple sclerosis, and inflammatory bowel disease. Development of new agents for systemic lupus erythematosus (SLE) has lagged, however, because the protean manifestations of SLE present challenges for measuring therapeutic effects in a consistent manner. Composite end points combining several Disease Activity Indices (DAIs) are being used in ongoing global studies, but the uniform application of these complex DAIs across large numbers of clinical sites has proven difficult. We describe herein approaches that are being utilized to facilitate collection, review, and analysis of the clinical measures utilizing independent central adjudication committees.
Tuning adaptive computations for the performance improvement of applications in JEE server
Authors: Zhang Ying , Huang Gang , Liu Xuanzhe , Mei Hong 
Published: May 2012

Abstract
With the increasing use of autonomic computing technologies, a Java Enterprise Edition (JEE) application server is implemented with more and more adaptive computations for self-managing the Middleware as well as its hosted applications. However, these adaptive computations consume resources such as CPU and memory, and can interfere with the normal business processing of applications at runtime due to resource competition, especially when the whole system is under heavy load. Tuning these adaptive computations from the perspective of resource management becomes necessary. In this article, we propose a tuning model for adaptive computations. Based on the model, tuning is carried out dynamically by upgrading or degrading the autonomic level of an adaptive computation so as to control its resource consumption. We implement the RSpring tuner and use it to optimize autonomic JEE servers such as PkuAS and JOnAS. RSpring is evaluated on ECperf and RUBiS benchmark applications. The results show that it can effectively improve the application performance by 13.6 % in PkuAS and 19.2 % in JOnAS with the same amount of resources.
Calibration-quality adiabatic potential energy surfaces for ${\rm H}_3^+$H3+ and its isotopologues
Authors: Pavanello Michele , Adamowicz Ludwik , Alijah Alexander , Zobov Nikolai F. , Mizus Irina I. , Polyansky Oleg L. , Tennyson Jonathan , Szidarovszky Tamás , Császár Attila G. 
Published: May 2012

Calibration-quality ab initio adiabatic potential energy surfaces (PES) have been determined for all isotopologues of the molecular ion \documentclass[12pt]{minimal}\begin{document}${\rm H}_3^+$\end{document}H3+. The underlying Born–Oppenheimer electronic structure computations used optimized explicitly correlated shifted Gaussian functions. The surfaces include diagonal Born–Oppenheimer corrections computed from the accurate electronic wave functions. A fit to the 41 655 ab initio points is presented which gives a standard deviation better than 0.1 cm−1 when restricted to the points up to 6000 cm−1 above the first dissociation asymptote. Nuclear motion calculations utilizing this PES, called GLH3P, and an exact kinetic energy operator given in orthogonal internal coordinates are presented. The ro-vibrational transition frequencies for \documentclass[12pt]{minimal}\begin{document}${\rm H}_3^+$\end{document}H3+, H2D+, and \documentclass[12pt]{minimal}\begin{document}${\rm HD}_2^+$\end{document} HD 2+ are compared with high resolution measurements. The most sophisticated and complete procedure employed to compute ro-vibrational energy levels, which makes explicit allowance for the inclusion of non-adiabatic effects, reproduces all the known ro-vibrational levels of the \documentclass[12pt]{minimal}\begin{document}${\rm H}_3^+$\end{document}H3+ isotopologues considered to better than 0.2 cm−1. This represents a significant (order-of-magnitude) improvement compared to previous studies of transitions in the visible. Careful treatment of linear geometries is important for high frequency transitions and leads to new assignments for some of the previously observed lines. Prospects for further investigations of non-adiabatic effects in the \documentclass[12pt]{minimal}\begin{document}${\rm H}_3^+$\end{document}H3+ isotopologues are discussed. In short, the paper presents (a) an extremely accurate global potential energy surface of \documentclass[12pt]{minimal}\begin{document}${\rm H}_3^+$\end{document}H3+ resulting from high accuracy ab initio computations and global fit, (b) very accurate nuclear motion calculations of all available experimental line data up to 16 000 cm−1, and (c) results suggest that we can predict accurately the lines of \documentclass[12pt]{minimal}\begin{document}${\rm H}_3^+$\end{document}H3+ towards dissociation and thus facilitate their experimental observation.
Fast and sensitive mapping of bisulfite-treated sequencing data
Authors: Otto Christian , Stadler Peter F. , Hoffmann Steve 
Published: May 2012

Abstract
Motivation: Cytosine DNA methylation is one of the major epigenetic modifications and influences gene expression, developmental processes, X-chromosome inactivation, and genomic imprinting. Aberrant methylation is furthermore known to be associated with several diseases including cancer. The gold standard to determine DNA methylation on genome-wide scales is ‘bisulfite sequencing’: DNA fragments are treated with sodium bisulfite resulting in the conversion of unmethylated cytosines into uracils, whereas methylated cytosines remain unchanged. The resulting sequencing reads thus exhibit asymmetric bisulfite-related mismatches and suffer from an effective reduction of the alphabet size in the unmethylated regions, rendering the mapping of bisulfite sequencing reads computationally much more demanding. As a consequence, currently available read mapping software often fails to achieve high sensitivity and in many cases requires unrealistic computational resources to cope with large real-life datasets.
Results: In this study, we present a seed-based approach based on enhanced suffix arrays in conjunction with Myers bit-vector algorithm to efficiently extend seeds to optimal semi-global alignments while allowing for bisulfite-related substitutions. It outperforms most current approaches in terms of sensitivity and performs time-competitive in mapping hundreds of millions of sequencing reads to vertebrate genomes.
Availability: The software segemehl is freely available at http://www.bioinf.uni-leipzig.de/Software/segemehl.
Contact: E-mail: steve@bioinf.uni-leipzig.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Software support for SBGN maps: SBGN-ML and LibSBGN
Authors: van Iersel Martijn P. , Villéger Alice C. , Czauderna Tobias , Boyd Sarah E. , Bergmann Frank T. , Luna Augustin , Demir Emek , Sorokin Anatoly , Dogrusoz Ugur , Matsuoka Yukiko , Funahashi Akira , Aladjem Mirit I. , Mi Huaiyu , Moodie Stuart L. , Kitano Hiroaki , Le Novère Nicolas , Schreiber Falk 
Published: May 2012

Abstract
Motivation: LibSBGN is a software library for reading, writing and manipulating Systems Biology Graphical Notation (SBGN) maps stored using the recently developed SBGN-ML file format. The library (available in C++ and Java) makes it easy for developers to add SBGN support to their tools, whereas the file format facilitates the exchange of maps between compatible software applications. The library also supports validation of maps, which simplifies the task of ensuring compliance with the detailed SBGN specifications. With this effort we hope to increase the adoption of SBGN in bioinformatics tools, ultimately enabling more researchers to visualize biological knowledge in a precise and unambiguous manner.
Availability and implementation: Milestone 2 was released in December 2011. Source code, example files and binaries are freely available under the terms of either the LGPL v2.1+ or Apache v2.0 open source licenses from http://libsbgn.sourceforge.net.
Contact: sbgn-libsbgn@lists.sourceforge.net
Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs
Authors: Saunders Christopher T. , Wong Wendy S. W. , Swamy Sajani , Becq Jennifer , Murray Lisa J. , Cheetham R. Keira 
Published: May 2012

Abstract
Motivation: Whole genome and exome sequencing of matched tumor–normal sample pairs is becoming routine in cancer research. The consequent increased demand for somatic variant analysis of paired samples requires methods specialized to model this problem so as to sensitively call variants at any practical level of tumor impurity.
Results: We describe Strelka, a method for somatic SNV and small indel detection from sequencing data of matched tumor–normal samples. The method uses a novel Bayesian approach which represents continuous allele frequencies for both tumor and normal samples, while leveraging the expected genotype structure of the normal. This is achieved by representing the normal sample as a mixture of germline variation with noise, and representing the tumor sample as a mixture of the normal sample with somatic variation. A natural consequence of the model structure is that sensitivity can be maintained at high tumor impurity without requiring purity estimates. We demonstrate that the method has superior accuracy and sensitivity on impure samples compared with approaches based on either diploid genotype likelihoods or general allele-frequency tests.
Availability: The Strelka workflow source code is available at ftp://strelka@ftp.illumina.com/.
Contact: csaunders@illumina.com
Supplementary information: Supplementary data are available at Bioinformatics online
Exhaustive database searching for amino acid mutations in proteomes
Authors: Hyatt Doug , Pan Chongle 
Published: May 2012

Abstract
Motivation: Amino acid mutations in proteins can be found by searching tandem mass spectra acquired in shotgun proteomics experiments against protein sequences predicted from genomes. Traditionally, unconstrained searches for amino acid mutations have been accomplished by using a sequence tagging approach that combines de novo sequencing with database searching. However, this approach is limited by the performance of de novo sequencing.
Results: The Sipros algorithm v2.0 was developed to perform unconstrained database searching using high-resolution tandem mass spectra by exhaustively enumerating all single non-isobaric mutations for every residue in a protein database. The performance of Sipros for amino acid mutation identification exceeded that of an established sequence tagging algorithm, Inspect, based on benchmarking results from a Rhodopseudomonas palustris proteomics dataset. To demonstrate the viability of the algorithm for meta-proteomics, Sipros was used to identify amino acid mutations in a natural microbial community in acid mine drainage.
Availability: The Sipros algorithm is freely available at\newline http://code.google.com/p/sipros.
Contact: panc@ornl.gov
Supplementary information: Supplementary data are available at Bioinformatics online
iFad: an integrative factor analysis model for drug-pathway association inference†
Authors: Ma Haisu , Zhao Hongyu 
Published: May 2012

Abstract
Motivation: Pathway-based drug discovery considers the therapeutic effects of compounds in the global physiological environment. This approach has been gaining popularity in recent years because the target pathways and mechanism of action for many compounds are still unknown, and there are also some unexpected off-target effects. Therefore, the inference of drug-pathway associations is a crucial step to fully realize the potential of system-based pharmacological research. Transcriptome data offer valuable information on drug-pathway targets because the pathway activities may be reflected through gene expression levels. Hence, it is of great interest to jointly analyze the drug sensitivity and gene expression data from the same set of samples to investigate the gene-pathway–drug-pathway associations.
Results: We have developed iFad, a Bayesian sparse factor analysis model to jointly analyze the paired gene expression and drug sensitivity datasets measured across the same panel of samples. The model enables direct incorporation of prior knowledge regarding gene-pathway and/or drug-pathway associations to aid the discovery of new association relationships. We use a collapsed Gibbs sampling algorithm for inference. Satisfactory performance of the proposed model was found for both simulated datasets and real data collected on the NCI-60 cell lines. Our results suggest that iFad is a promising approach for the identification of drug targets. This model also provides a general statistical framework for pathway-based integrative analysis of other types of -omics data.
Availability: The R package ‘iFad’ and real NCI-60 dataset used are available at http://bioinformatics.med.yale.edu/group/.
Contact: hongyu.zhao@yale.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
SRMA: an R package for resequencing array data analysis
Authors: Zhang Nianxiang , Xu Yan , O'Hely Martin , Speed Terence P. , Scharfe Curt , Wang Wenyi 
Published: May 2012

Abstract
Summary: Sequencing by hybridization to oligonucleotides has evolved into an inexpensive, reliable and fast technology for targeted sequencing. Hundreds of human genes can now be sequenced within a day using a single hybridization to a resequencing microarray. However, several issues inherent to these arrays (e.g. cross-hybridization, variable probe/target affinity) cause sequencing errors and have prevented more widespread applications. We developed an R package for resequencing microarray data analysis that integrates a novel statistical algorithm, sequence robust multi-array analysis (SRMA), for rare variant detection with high sensitivity (false negative rate, FNR 5%) and accuracy (false positive rate, FPR 1×10−5). The SRMA package consists of five modules for quality control, data normalization, single array analysis, multi-array analysis and output analysis. The entire workflow is efficient and identifies rare DNA single nucleotide variations and structural changes such as gene deletions with high accuracy and sensitivity.
Availability: http://cran.r-project.org/, http://odin.mdacc.tmc.edu/~wwang7/SRMAIndex.html
Contact: wwang7@mdanderson.org
Supplementary information: Supplementary data are available at Bioinformatics online.