bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expedient Synthesis of Large‐Ring trans‐Enamide Macrolides by CuI‐Mediated Intramolecular Coupling of Vinyl Iodide with Amide: Total Synthesis of Palmyrolide A
Authors: Yadav Jhillu Singh , Suresh Borra , Srihari Pabbaraja 
Published: April 2016

AbstractAn efficient and improved procedure for copper‐catalyzed coupling of vinyl iodide with amide in an intramolecular fashion is described. The protocol utilizes a combination of copper iodide, CsF and (±)‐1,2‐diaminocyclohexane as ligand. The vinyl iodide couples efficiently with the amide to generate an enamide macrolide without any alteration in the double ‐bond geometry. The developed method was applied in the synthesis of several large‐ring enamide macrolides, and for the total synthesis of natural product palmyrolide A and homologated sanctolide A.
An Introverted Bis‐Au Cavitand and Its Catalytic Dimerization of Terminal Alkynes
Authors: Endo Naoki , Kanaura Mao , Schramm Michael P. , Iwasawa Tetsuo 
Published: April 2016

AbstractA preparative synthesis of an inwardly oriented phosphoramidite‐Au dinuclear resorcinarene cavitand complex is described, including a description of potent catalytic abilities. The cavitand structure was determined by crystallographic analysis, which revealed that the phosphoramidite P–N bonds point outside placing the two Au atoms inside. We explored the catalytic proclivity of the cavitand and found that it effeciently catalyzes selective and direct dimerization of terminal alkynes to afford conjugated enynes. Mixed dimerizations give rise to chemoselective products, and macrocyclization by intramolecular dimerization are both trademark capabilities of the method.
Streamflow response to the rapid retreat of a lake‐calving glacier
Authors: Moyer Alexis N. , Moore R. D. , Koppes Michele N. 
Published: April 2016

AbstractThere has been increasing attention over the last decade to the potential effects of glacier retreat on downstream discharge and aquatic habitat. This study focused on streamflow variability downstream of Bridge Glacier in the southern Coast Mountains of BC between 1979 and 2014, prior to and during a period in which the glacier experienced enhanced calving and rapid retreat across a lake‐filled basin. Here we combined empirical trend detection and a conceptual‐parametric hydrological model to address the following hypotheses: (1) streamflow trends in late summer and early autumn should reflect the opposing influences of climatic warming (which would tend to increase unit‐area meltwater production) and the reduction in glacier area (which would tend to reduce the total volume of meltwater generated), and (2) winter streamflow should increase because of displacement of lake water as ice flows past the grounding line and calves into the lake basin. In relation to the first hypothesis, we found no significant trends in monthly discharge during summer. However, applying regression analysis to account for air temperature and precipitation variations, weak but statistically significant negative trends were detected for August and melt season discharge. The HBV‐EC model was applied using time‐varying glacier cover, as derived from Landsat imagery. Relative to simulations based on constant glacier extent, model results indicated that glacier recession caused a decline in mean monthly streamflow of 9% in August and 11% in September. These declines in late‐summer streamflow are consistent with the results from our empirical analysis. The second hypothesis is supported by the finding of positive trends for December, January, and February discharge. Despite the modelled declines in late‐summer mean monthly streamflow, recorded discharge data exhibited neither positive nor negative trends during the melt season, suggesting that Bridge Glacier may currently be at or close to the point of peak water. Further analysis of the impact of lake‐terminating glaciers on downstream discharge is needed to refine the peak water model. Copyright © 2016 John Wiley & Sons, Ltd.
Detrimental graft survival of size‐mismatched graft for high model for end‐stage liver disease recipients in liver transplantation
Authors: Fukazawa Kyota , Nishida Seigo , Pretto Ernesto A. , Vater Youri , Reyes Jorge D. 
Published: April 2016

AbstractBackgroundIn orthotopic liver transplantation (OLT) size‐mismatch may cause adverse outcomes. We previously reported on a method to predict donor‐recipient size‐mismatch using the body surface area index (BSAi). In this study, we hypothesized that graft survival of size‐mismatch transplantation deteriorates with higher model for end‐stage liver disease (MELD) score at transplantation.MethodsWe evaluated non‐parametrically the association of BSAi and MELD with 1‐year graft survival with a generalized additive model. For derivation, transplantations performed between 2005 and 2010 were used. The associations were then validated by comparing Kaplan–Meier estimates between patient groups stratified according to estimated risk, using transplantations from 2011–2013.ResultsA total of 30,870 OLT were included in the study with 16,466 in the validation group. The derivation model revealed that graft survival significantly decreased with higher or lower BSAi, and with higher MELD (P < 0.0001). Validation confirmed the correlation of observed graft survival with estimated risk categories.ConclusionsWe found that there is an interactive effect between MELD score and size‐mismatch. Also high MELD recipient has a narrower safety margin for size‐mismatched graft. The risk calculated from our nonparametric model with MELD and BSAi well predicts outcome in liver transplantation.
Elevation‐dependent reductions in wind speed over and around the Tibetan Plateau
Authors: Guo Xiaoyu , Wang Lei , Tian Lide , Li Xiuping 
Published: April 2016

ABSTRACTThe Tibetan Plateau (TP) affects its surroundings significantly through thermal and dynamic processes. Reductions in near‐surface wind speed (Ws) have been observed from ground measurements but how the trends of Ws vary with the elevation is less clear. Trends of Ws with respect to elevation were investigated using long‐term daily records taken from 1970 to 2012 of Ws and maximum (Tmax), minimum (Tmin), and mean (Tmean) air temperatures from 139 stations over and around the TP. The major findings are as follows. (1) Pronounced reductions in Ws can be observed in all seasons and annually across the TP. Spring demonstrates the most prominent weakening. The rate of reductions in Ws was amplified with elevation, and higher‐elevation environments experienced greater changes in Ws than lower‐elevation areas. Elevation‐dependent reductions in Ws have intensified from 1970 to 2012. (2) Statistically significant negative correlations between Ws and corresponding near‐surface temperatures were detected. We suggested that the elevation‐dependent warming and thereby the increased surface roughness at higher‐elevation environments may contribute to the elevation‐dependent reductions in Ws over and around the TP. More detailed mechanisms causing this pattern are to be further explored.
Reliability of office‐based narrow‐band imaging–guided flexible laryngoscopic tissue samplings
Authors: Chang Catherine , Lin Wan‐Ni , Hsin Li‐Jen , Lee Li‐Ang , Lin Chien‐Yu , Li Hsueh‐Yu , Liao Chun‐Ta , Fang Tuan‐Jen 
Published: April 2016

Objectives/HypothesisDirect suspension laryngoscopic biopsy performed under general anesthesia is the conventional management for obtaining pathological diagnosis for neoplasms of the larynx, oropharynx, and hypopharynx. Since the development of distal chip laryngoscopy and digital imaging systems, transnasal flexible laryngoscopy tissue sampling has gained popularity as an office‐based procedure. Additional assessment with narrow‐band imaging (NBI) can help to increase the diagnostic yield. The aim of the study was to evaluate the accuracy, sensitivity, and specificity of a novel diagnostic tool: office‐based NBI (OB‐NBI) flexible laryngoscopic tissue sampling.Study DesignRetrospective chart review performed in a tertiary referral medical center in Taiwan.MethodsFrom January 2010 to February 2013, 90 consecutive patients received OB‐NBI biopsies. The accuracies of the OB‐NBI biopsies were compared among locations, tumor sizes, head and neck cancer histories, and other factors.ResultsAll patients had completed the procedure without life‐threatening complications. The overall sensitivity and specificity were 97.2% and 100%, respectively, with a diagnostic accuracy of 98.9%. Accuracy was not affected by tumor size, location, learning curves, or previous head and neck cancer history.ConclusionsWe present an integrated technique that merges the safety and versatility of flexible laryngoscopy with the diagnostic power of NBI to produce a promising method of high accuracy and minimal morbidity.Level of Evidence4 Laryngoscope, 126:2764–2769, 2016
Supramolecular Hydrogel from Nanoparticles and Cyclodextrins for Local and Sustained Nanoparticle Delivery
Authors: Xu Shuxin , Yin Li , Xiang Yuzhang , Deng Hongzhang , Deng Liandong , Fan Hongxia , Tang Hua , Zhang Jianhua , Dong Anjie 
Published: April 2016

Injectable and biodegradable supramolecular hydrogel mPECT NP/α‐CDgel composed of high‐concentration nanoparticle dispersion (≤20% W/V) and α‐cyclodextrins (α‐CD) are prepared by a two‐level physical cross‐linking using amphiphilic block polymer methoxy poly(ethylene glycol)‐b‐poly(ε‐caprolactone‐co‐1,4,8‐trioxa[4.6]spiro‐9‐undecanone) (mPECT) and α‐CD. The gelation behavior depends on the concentration of nanoparticles and α‐CD. The viscoelasticity and shear thinning of mPECT NP/α‐CDgel are confirmed. In vitro hydrogel erosion is demonstrated to be mainly a concentration‐dependent dissociation process with general release of discrete mPECT nanoparticles about 50 nm that can be easily taken up by cells. The in vitro release behavior can be modulated by changing the concentration of nanoparticles or α‐CD. In vitro and in vivo cytotoxicity study demonstrates its biocompatibility and biosafety. Gel formation after subcutaneous injection is also confirmed and mPECT NP/α‐CDgel shows about 2 weeks retention time. This work validates the potential application for this supramolecular hydrogel in local and sustained delivery of nanoparticles.image
Egg consumption and risk of incident type 2 diabetes: a dose–response meta-analysis of prospective cohort studies
Authors: Tamez Martha , Virtanen Jyrki K. , Lajous Martin 
Published: April 2016

AbstractExperimental data suggest that egg intake could have a beneficial impact on several risk factors for type 2 diabetes. In contrast, some recent epidemiological studies have concluded that egg consumption may increase diabetes risk. We performed a dose–response meta-analysis of prospective cohorts on the relation of egg consumption with incident type 2 diabetes. We searched for cohort studies that assessed egg consumption and diabetes risk up to June 2015. We identified 416 articles and extracted data independently and in duplicate from ten eligible studies. We used random-effects generalised least squares models for pooled dose–response estimation based on thirteen estimates. Our study included 251 213 individuals and 12 156 incident type 2 diabetes cases. Egg intake was associated with incident type 2 diabetes (risk ratio (RR)/egg per d 1·13; 95 % CI 1·04, 1·22). We identified study location as a major source of heterogeneity. For studies conducted in the USA, we observed a stronger association (RR 1·47; 95 % CI 1·32, 1·64), whereas results were null for studies conducted elsewhere. Studies considered to be of high quality yielded null findings (RR 0·94; 95 % CI 0·74, 1·19). The association of egg intake with increased risk of incident type 2 diabetes may be restricted to US cohort studies. There are limited data to support a biological mechanism that could underlie this association; thus, the possibility that these results may be due to residual confounding by dietary behaviours restricted to certain populations cannot be excluded.
SAMFIRE: multi-locus variant calling for time-resolved sequence data
Authors: Illingworth C. J. R. 
Published: April 2016

Abstract
Summary: An increasingly common method for studying evolution is the collection of time-resolved short-read sequence data. Such datasets allow for the direct observation of rapid evolutionary processes, as might occur in natural microbial populations and in evolutionary experiments. In many circumstances, evolutionary pressure acting upon single variants can cause genomic changes at multiple nearby loci. SAMFIRE is an open-access software package for processing and analyzing sequence reads from time-resolved data, calling important single- and multi-locus variants over time, identifying alleles potentially affected by selection, calculating linkage disequilibrium statistics, performing haplotype reconstruction and exploiting time-resolved information to estimate the extent of uncertainty in reported genomic data.
Availability and Implementation: C ++ code may be found at https://github.com/cjri/samfire/.
Contact: chris.illingworth@gen.cam.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Pasha: a versatile R package for piling chromatin HTS data
Authors: Fenouil Romain , Descostes Nicolas , Spinelli Lionel , Koch Frederic , Maqbool Muhammad Ahmad , Benoukraf Touati , Cauchy Pierre , Innocenti Charlène , Ferrier Pierre , Andrau Jean-Christophe 
Published: April 2016

Abstract
Summary: We describe an R package designed for processing aligned reads from chromatin-oriented high-throughput sequencing experiments. Pasha (preprocessing of aligned sequences from HTS analyses) allows easy manipulation of aligned reads from short-read sequencing technologies (ChIP-seq, FAIRE-seq, MNase-Seq, …) and offers innovative approaches such as ChIP-seq reads elongation, nucleosome midpoint piling strategy for positioning analyses, or the ability to subset paired-end reads by groups of insert size that can contain biologically relevant information.
Availability and implementation: Pasha is a multi-platform R package, available on CRAN repositories under GPL-3 license (https://cran.r-project.org/web/packages/Pasha/).
Contacts: rfenouil@gmail.com or jean-christophe.andrau@igmm.cnrs.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
Partitioning and correlating subgroup characteristics from Aligned Pattern Clusters
Authors: Lee En-Shiun Annie , Whelan Fiona J. , Bowdish Dawn M. E. , Wong Andrew K. C. 
Published: April 2016

Abstract
Motivation: Evolutionarily conserved amino acids within proteins characterize functional or structural regions. Conversely, less conserved amino acids within these regions are generally areas of evolutionary divergence. A priori knowledge of biological function and species can help interpret the amino acid differences between sequences. However, this information is often erroneous or unavailable, hampering discovery with supervised algorithms. Also, most of the current unsupervised methods depend on full sequence similarity, which become inaccurate when proteins diverge (e.g. inversions, deletions, insertions). Due to these and other shortcomings, we developed a novel unsupervised algorithm which discovers highly conserved regions and uses two types of information measures: (i) data measures computed from input sequences; and (ii) class measures computed using a priori class groupings in order to reveal subgroups (i.e. classes) or functional characteristics.
Results: Using known and putative sequences of two proteins belonging to a relatively uncharacterized protein family we were able to group evolutionarily related sequences and identify conserved regions, which are strong homologous association patterns called Aligned Pattern Clusters, within individual proteins and across the members of this family. An initial synthetic demonstration and in silico results reveal that (i) the data measures are unbiased and (ii) our class measures can accurately rank the quality of the evolutionarily relevant groupings. Furthermore, combining our data and class measures allowed us to interpret the results by inferring regions of biological importance within the binding domain of these proteins. Compared to popular supervised methods, our algorithm has a superior runtime and comparable accuracy.
Availability and implementation: The dataset and results are available at www.pami.uwaterloo.ca/∼ealee/files/classification2015 .
Contact: akcwong@uwaterloo.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
Bayesian nonparametrics in protein remote homology search
Authors: Margelevičius Mindaugas 
Published: April 2016

Abstract
Motivation: Wide application of modeling of three-dimensional protein structures in biomedical research motivates developing protein sequence alignment computer tools featuring high alignment accuracy and sensitivity to remotely homologous proteins. In this paper, we aim at improving the quality of alignments between sequence profiles, encoded multiple sequence alignments. Modeling profile contexts, fixed-length profile fragments, is engaged to achieve this goal.
Results: We develop a hierarchical Dirichlet process mixture model to describe the distribution of profile contexts, which is able to capture dependencies between amino acids in each context position. The model represents an attempt at modeling profile fragments at several hierarchical levels, within the profile and among profiles. Even modeling unit-length contexts leads to greater improvements than processing 13-length contexts previously. We develop a new profile comparison method, called COMER, integrating the model. A benchmark with three other profile-to-profile comparison methods shows an increase in both sensitivity and alignment quality.
Availability and Implementation: COMER is open-source software licensed under the GNU GPLv3, available at https://sourceforge.net/projects/comer.
Contact: mindaugas.margelevicius@bti.vu.lt
Supplementary information: Supplementary data are available at Bioinformatics online.
ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information
Authors: Lachmann Alexander , Giorgi Federico M. , Lopez Gonzalo , Califano Andrea 
Published: April 2016

Abstract
Summary: The accurate reconstruction of gene regulatory networks from large scale molecular profile datasets represents one of the grand challenges of Systems Biology. The Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNe) represents one of the most effective tools to accomplish this goal. However, the initial Fixed Bandwidth (FB) implementation is both inefficient and unable to deal with sample sets providing largely uneven coverage of the probability density space. Here, we present a completely new implementation of the algorithm, based on an Adaptive Partitioning strategy (AP) for estimating the Mutual Information. The new AP implementation (ARACNe-AP) achieves a dramatic improvement in computational performance (200× on average) over the previous methodology, while preserving the Mutual Information estimator and the Network inference accuracy of the original algorithm. Given that the previous version of ARACNe is extremely demanding, the new version of the algorithm will allow even researchers with modest computational resources to build complex regulatory networks from hundreds of gene expression profiles.
Availability and Implementation: A JAVA cross-platform command line executable of ARACNe, together with all source code and a detailed usage guide are freely available on Sourceforge (http://sourceforge.net/projects/aracne-ap). JAVA version 8 or higher is required.
Contact: califano@c2b2.columbia.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
rnaQUAST: a quality assessment tool for de novo transcriptome assemblies
Authors: Bushmanova Elena , Antipov Dmitry , Lapidus Alla , Suvorov Vladimir , Prjibelski Andrey D. 
Published: April 2016

Abstract
Summary: Ability to generate large RNA-Seq datasets created a demand for both de novo and reference-based transcriptome assemblers. However, while many transcriptome assemblers are now available, there is still no unified quality assessment tool for RNA-Seq assemblies. We present rnaQUAST—a tool for evaluating RNA-Seq assembly quality and benchmarking transcriptome assemblers using reference genome and gene database. rnaQUAST calculates various metrics that demonstrate completeness and correctness levels of the assembled transcripts, and outputs them in a user-friendly report.
Availability and Implementation: rnaQUAST is implemented in Python and is freely available at http://bioinf.spbau.ru/en/rnaquast.
Contact: ap@bioinf.spbau.ru
Supplementary information: Supplementary data are available at Bioinformatics online.
Incorporating organelle correlations into semi-supervised learning for protein subcellular localization prediction
Authors: Xu Ying-Ying , Yang Fan , Shen Hong-Bin 
Published: April 2016

Abstract
Motivation: Bioimages of subcellular protein distribution as a new data source have attracted much attention in the field of automated prediction of proteins subcellular localization. Performance of existing systems is significantly limited by the small number of high-quality images with explicit annotations, resulting in the small sample size learning problem. This limitation is more serious for the multi-location proteins that co-exist at two or more organelles, because it is difficult to accurately annotate those proteins by biological experiments or automated systems.
Results: In this study, we designed a new protein subcellular localization prediction pipeline aiming to deal with the small sample size learning and multi-location proteins annotation problems. Five semi-supervised algorithms that can make use of lower-quality data were integrated, and a new multi-label classification approach by incorporating the correlations among different organelles in cells was proposed. The organelle correlations were modeled by the Bayesian network, and the topology of the correlation graph was used to guide the order of binary classifiers training in the multi-label classification to reflect the label dependence relationship. The proposed protocol was applied on both immunohistochemistry and immunofluorescence images, and our experimental results demonstrated its efficiency.
Availability and implementation: The datasets and code are available at: www.csbio.sjtu.edu.cn/bioinf/CorrASemiB.
Contact: hbshen@sjtu.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.