bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trimodality bladder-sparing approach versus radical cystectomy for invasive bladder cancer
Authors: AlGizawy Samy M. , Essa Hoda H. , Abdel-Wanis Mostafa E. , Abdel Raheem Ahmed M. 
Published: March 2014

AbstractPurposeTo compare the outcome among patients with invasive bladder cancer treated with cystectomy alone with outcome among those treated with combined-modality treatment in a randomised phase III trial.Patients and methodsPatients with histologically confirmed invasive non-metastatic bladder cancer T2-3, N0 and M0 were randomly assigned to two arms: Arm 1: of which all patients underwent radical cystectomy (RC) alone; and Arm 2, of which all patients were subjected to maximal transurethral resection of bladder tumour, followed 2 weeks later by combined chemoradiotherapy. The whole pelvis received 46 Gy in 23 fractions over 4·5 weeks. Chemotherapy was administered concomitantly with radiotherapy with: cisplatin 70 mg/m2 q. 3 weeks and Gemcitabine 300 mg/m2 D 1, 8 and 15 q. 3 weeks for two cycles. Patients who had complete response were shifted to phase II treatment: 20 Gy/10 fractions/2 weeks to the bladder. Patients with residual tumour underwent RC.ResultsOf the 80 patients assigned Arm 2, a visibly completed transurethral resection of the bladder tumour was possible in 48 patients (60%). Phase I of combined chemoradiotherapy (CCRT) was accomplished in 74 patients. Post-induction urologic evaluation revealed no evidence of disease in 62 patients (83·8%) and residual disease in 12 patients (16·2%). Phase II of CCRT was completed in 58 of the 62 patients. The median follow-up for all patients is 27 months (range: 4–49). The 3-year overall survival (OS) for the combined-modality group and for the surgery group were 61 and 63%, respectively (p = 0·425), whereas the disease-specific survival (DSS) for each group was 69 and 73%, respectively (p = 0·714). The 3-year OS with bladder preservation for Arm 2 patients was 50%.Multivariate analysis for the whole series showed that tumour stage and performance status (PS) were the only factors independently associated with DSS, although PS was the only factor independently associated with OS. In addition, residual disease after transurethral resection of the bladder tumour in Arm 2 patients was independently associated with both DSS and OS.Acute toxicity was moderate and most of the late toxicities were grade 2 with no grade 4 toxicity and no treatment-related deaths, none required cystectomy for bladder contraction.ConclusionThis study demonstrates that trimodality bladder-preserving approach represents a valid alternative for suitable patients. The OS and DSS rates of patients treated with trimodality bladder-preserving protocol are comparable to the results reported on patients treated with immediate radical cystectomy.
Legal Biography at the British Library: a Particular Perspective on Resources
Authors: Sims Jonathan 
Published: March 2014

AbstractRich personal and institutional archives, antiquarian manuscript collections and published resources make the British Library an obvious choice for biographical research. While these collections include material relating to high ranking legal officials, legislators, renowned legal scholars and their correspondents the article moves beyond this view of legal biographical source materials. Examples of resources from across the Library's diverse collections are presented through a particular perspective on information needs and sources in broadly socio-legal research. In contribution to the theme of methods in legal biographical research this framework is offered, together with signposts to discovery aids as a way of conceptualising the Library's resource. In doing so, various notions of the nature of legal biographical research, its subjects and its source information are considered in this article by Jonathan Sims.
Legal Biography, Oral History and the Cambridge Eminent Scholars Archive (ESA)
Authors: Dingle Lesley 
Published: March 2014

AbstractLesley Dingle describes the ESA, a digital archive based on interviews with prominent personalities associated with the Law Faculty of Cambridge University. It constitutes a unique repository of audio, textual and photographic materials, providing insights into the careers of scholars, jurists and practitioners. Motivations for the establishment of the archive in 2006 were: recording reminiscences of scholars back to WWII and its immediate aftermath; documenting developments in administration and teaching in the Faculty and colleges; archiving voices of scholars taking about their early lives, careers and published works; compiling a cross-indexed reference of personalities mentioned in interviews; and generating an awareness amongst students and younger staff of the rich heritage of the Faculty. The methodology and strategy of conducting interviews and compiling entries is briefly described. Finally, in the broader context of legal biography, it is argued that such oral histories are an essential component because they capture aspects of personality that written accounts cannot and thereby reveal traits that conventional biographies may miss. This claim is illustrated by selected examples from the archive, that currently contains twenty interviewees.
Law Publishers in the Twenty-First Century: Part of the Problem or Part of the Solution? or The Need for a Paradigm Shift in Publishing for the Legal Education Market
Authors: Soetenhorst Wirt 
Published: March 2014

AbstractIn this article Wirt Soetenhorst explores a paradigm shift that is already taking place in the legal education market and that will accelerate over the next five years. This development will have consequences for all the parties that are active in the field of academic legal education: authors, institutions, libraries, students and publishers. The article analyses the current traditional business model (the sale of physical textbooks) and outlines several potential scenarios for the future of legal publishing in which publishers move into teaching and academic institutions.
Design of a broadband passive X-band double-balanced mixer in SiGe HBT technology
Authors: Michaelsen Rasmus S. , Johansen Tom K. , Tamborg Kjeld M. , Zhurbenko Vitaliy 
Published: March 2014

In this paper, a passive double-balanced mixer in SiGe HBT technology is presented. Owing to lack of suitable passive mixing elements in the technology, the mixing elements are formed by diode-connected HBTs. The mixer uses lumped element Marchand baluns on both the local oscillator (LO) and the radio frequency (RF) port. A break out of the Marchand balun is measured. This demonstrates good phase and magnitude match of 0.7° and 0.11 dB, respectively. The Marchand baluns are broadband with a measured 3 dB bandwidth of 6.4 GHz, while still having a magnitude imbalance better than 0.4 dB and a phase imbalance better than 5°. Unfortunately with a rather high loss of 2.5 dB, mainly due to the low Q-factor of the inductors used. The mixer is optimized for use in doppler radars and is highly linear with a 1 dB compression point above 12 dBm IIP2of 66 dBm. The conversion gain at the center frequency of 8.5 GHz is −9.8 dB at an LO drive level of 15 dBm. The whole mixer is very broadband with 3 dB bandwidth from 7 to 12 GHz covering the entire X-band. The LO–IF, RF–IF, and RF–LO isolation is better than 46, 36, and 36 dB, respectively, in the entire band of operation.
VNP: Interactive Visual Network Pharmacology of Diseases, Targets, and Drugs
Authors: Hu Q‐N , Deng Z , Tu W , Yang X , Meng Z‐B , Deng Z‐X , Liu J 
Published: March 2014

In drug discovery, promiscuous targets, multifactorial diseases, and “dirty” drugs construct complex network relationships. Network pharmacology description and analysis not only give a systems‐level understanding of drug action and disease complexity but can also help to improve the efficiency of target selection and drug design. Visual network pharmacology (VNP) is developed to visualize network pharmacology of targets, diseases, and drugs with a graph network by using disease, target or drug names, chemical structures, or protein sequence. To our knowledge, VNP is the first free interactive VNP server that should be very helpful for systems pharmacology research. VNP is freely available at http://cadd.whu.edu.cn/ditad/vnpsearch.CPT Pharmacometrics Syst. Pharmacol. (2014) 3, e105; doi: 10.1038/psp.2014.1; published online 12 March 2014
Brain activation associated with motor imagery of coordination exercises and social abilities
Authors: Mochizuki Akito Azumane , Sudo Michiko Mochizuki , Kirino Eiji , Itoh Kenji 
Published: March 2014

AbstractThe purposes of the present study were: (1) to investigate the brain activation associated with coordination exercises done by one person and those by two persons and (2) to examine the interrelationships between the brain activation and social abilities. We were interested in testing the hypothesis that viewing two‐person coordination exercises evokes more sophisticated brain activation than viewing one‐person coordination exercises. Thirty Japanese college students served as subjects. There were two sessions in this study: the functional magnetic resonance imaging (fMRI) session and the social ability session. In the fMRI session, the subjects were instructed to imagine they were performing coordination exercises. Also, we examined the social abilities from the viewpoint of empathising. Empathising was measured by self‐reports on the Systemising, Empathy and Autism Spectrum Quotients (SQ, EQ and AQ). Regarding brain activation, blood oxygenation level dependent (BOLD) activation was significant in specific areas such as the left cuneus (Brodmann area: BA 17) when the subjects imagined they were performing exercises involving two persons, as compared with the cases when they imagined they were performing exercises involving only one person. The fMRI results showed that exercises done by two persons require more sophisticated communication than those done by one person. Furthermore, the results of this study suggested that those with more autistic traits may undergo difficulties in the exercises done by two persons, especially in the case of playing a role as a follower.
Changes in leg kinematics in response to unpredictability in lateral jump execution
Authors: Mornieux Guillaume , Gehring Dominic , Tokuno Craig , Gollhofer Albert , Taube Wolfgang 
Published: March 2014

AbstractLateral movements like cutting are essential in many team sport disciplines. The aim of the present study was to analyse adaptations in motor control in response to task unpredictability during lateral movement execution. Twelve subjects performed lateral jumps with different landing modalities (stable, sliding or counteracting) that were either known (predictable setting) or unknown (unpredictable setting) prior to movement execution. Results revealed that regardless of the landing modality, hip joint abduction was significantly greater in the unpredictable compared to predictable setting. Furthermore, during the sliding landing modality, hip flexion decreased from 211 ± 7° to 207 ± 7° and knee flexion decreased from 26 ± 4° to 24 ± 4° at the instant of ground contact in the unpredictable compared to predictable condition. During the stable landing modality, the knee joint abduction increased from −0.3 ± 6° to −3 ± 6° after initial ground contact in the unpredictable compared to predictable setting. The present results support our hypothesis that pre‐programmed motor activity depends on the predictability of the landing modality during lateral movements. According to its adaptation in the frontal plane and in some extent in the sagittal plane, the hip joint seems to play the major role in the modulation of the pre‐programmed activity for successful lateral jump execution in an unpredictable setting. However, these kinematic adaptations are concerning since these changes were associated with higher knee abduction during the stable landing modality and therefore with possible higher risk of injury.
The Bio-Community Perl toolkit for microbial ecology
Authors: Angly Florent E. , Fields Christopher J. , Tyson Gene W. 
Published: March 2014

Abstract
Summary: The development of bioinformatic solutions for microbial ecology in Perl is limited by the lack of modules to represent and manipulate microbial community profiles from amplicon and meta-omics studies. Here we introduce Bio-Community, an open-source, collaborative toolkit that extends BioPerl. Bio-Community interfaces with commonly used programs using various file formats, including BIOM, and provides operations such as rarefaction and taxonomic summaries. Bio-Community will help bioinformaticians to quickly piece together custom analysis pipelines and develop novel software.
Availability an implementation: Bio-Community is cross-platform Perl code available from http://search.cpan.org/dist/Bio-Community under the Perl license. A readme file describes software installation and how to contribute.
Contact: f.angly@uq.edu.au
Supplementary information: Supplementary data are available at Bioinformatics online
Probabilistic PCA of censored data: accounting for uncertainties in the visualization of high-throughput single-cell qPCR data
Authors: Buettner Florian , Moignard Victoria , Göttgens Berthold , Theis Fabian J. 
Published: March 2014

Abstract
Motivation: High-throughput single-cell quantitative real-time polymerase chain reaction (qPCR) is a promising technique allowing for new insights in complex cellular processes. However, the PCR reaction can be detected only up to a certain detection limit, whereas failed reactions could be due to low or absent expression, and the true expression level is unknown. Because this censoring can occur for high proportions of the data, it is one of the main challenges when dealing with single-cell qPCR data. Principal component analysis (PCA) is an important tool for visualizing the structure of high-dimensional data as well as for identifying subpopulations of cells. However, to date it is not clear how to perform a PCA of censored data. We present a probabilistic approach that accounts for the censoring and evaluate it for two typical datasets containing single-cell qPCR data.
Results: We use the Gaussian process latent variable model framework to account for censoring by introducing an appropriate noise model and allowing a different kernel for each dimension. We evaluate this new approach for two typical qPCR datasets (of mouse embryonic stem cells and blood stem/progenitor cells, respectively) by performing linear and non-linear probabilistic PCA. Taking the censoring into account results in a 2D representation of the data, which better reflects its known structure: in both datasets, our new approach results in a better separation of known cell types and is able to reveal subpopulations in one dataset that could not be resolved using standard PCA.
Availability and implementation: The implementation was based on the existing Gaussian process latent variable model toolbox ( https://github.com/SheffieldML/GPmat ); extensions for noise models and kernels accounting for censoring are available at http://icb.helmholtz-muenchen.de/censgplvm .
Contact: fbuettner.phys@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Orione, a web-based framework for NGS analysis in microbiology
Authors: Cuccuru Gianmauro , Orsini Massimiliano , Pinna Andrea , Sbardellati Andrea , Soranzo Nicola , Travaglione Antonella , Uva Paolo , Zanetti Gianluigi , Fotia Giorgio 
Published: March 2014

Abstract
Summary: End-to-end next-generation sequencing microbiology data analysis requires a diversity of tools covering bacterial resequencing, de novo assembly, scaffolding, bacterial RNA-Seq, gene annotation and metagenomics. However, the construction of computational pipelines that use different software packages is difficult owing to a lack of interoperability, reproducibility and transparency. To overcome these limitations we present Orione, a Galaxy-based framework consisting of publicly available research software and specifically designed pipelines to build complex, reproducible workflows for next-generation sequencing microbiology data analysis. Enabling microbiology researchers to conduct their own custom analysis and data manipulation without software installation or programming, Orione provides new opportunities for data-intensive computational analyses in microbiology and metagenomics.
Availability and implementation: Orione is available online at http://orione.crs4.it .
Contact: gianmauro.cuccuru@crs4.it
Supplementary information: Supplementary data are available at Bioinformatics online.
pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires
Authors: Vander Heiden Jason A. , Yaari Gur , Uduman Mohamed , Stern Joel N.H. , O’Connor Kevin C. , Hafler David A. , Vigneault Francois , Kleinstein Steven H. 
Published: March 2014

Abstract
Summary: Driven by dramatic technological improvements, large-scale characterization of lymphocyte receptor repertoires via high-throughput sequencing is now feasible. Although promising, the high germline and somatic diversity, especially of B-cell immunoglobulin repertoires, presents challenges for analysis requiring the development of specialized computational pipelines. We developed the REpertoire Sequencing TOolkit (pRESTO) for processing reads from high-throughput lymphocyte receptor studies. pRESTO processes raw sequences to produce error-corrected, sorted and annotated sequence sets, along with a wealth of metrics at each step. The toolkit supports multiplexed primer pools, single- or paired-end reads and emerging technologies that use single-molecule identifiers. pRESTO has been tested on data generated from Roche and Illumina platforms. It has a built-in capacity to parallelize the work between available processors and is able to efficiently process millions of sequences generated by typical high-throughput projects.
Availability and implementation: pRESTO is freely available for academic use. The software package and detailed tutorials may be downloaded from http://clip.med.yale.edu/presto .
Contact: steven.kleinstein@yale.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
An adaptive workflow coupled with Random Forest algorithm to identify intact N-glycopeptides detected from mass spectrometry
Authors: Liang Suh-Yuen , Wu Sz-Wei , Pu Tsung-Hsien , Chang Fang-Yu , Khoo Kay-Hooi 
Published: March 2014

AbstractMotivation: Despite many attempts for algorithm development in recent years, automated identification of intact glycopeptides from LC-MS 2 spectral data is still a challenge in both sensitivity and precision.Results: We implemented a supervised machine learning algorithm, Random Forest, in an automated workflow to identify N-glycopeptides using spectral features derived from ion trap-based LC-MS 2 data. The workflow streamlined high-confident N-glycopeptide spectral data and enabled adaptive model optimization with respect to different sampling strategies, training sample size and feature set. A critical evaluation of the features important for glycopeptide identification further facilitated effective feature selection for model improvement. Using split sample testing method from 577 high-confident N-glycopeptide spectral data, we demonstrated that an optimal true-positive rate, precision and false-positive rate of 73, 88 and 10%, respectively, can be attained for overall N-glycopeptide identificationAvailability and implementation: The workflow developed in this work and the application suite, Sweet-Heart, that the workflow supports for N-glycopeptide identification are available for download at http://sweet-heart.glycoproteomics.proteome.bc.sinica.edu.tw/ .Contact: syliang@gate.sinica.edu.tw or kkhoo@gate.sinica.edu.twSupplementary information: Supplementary data are available at Bioinformatics online.
Genome-wide quantitative analysis of DNA methylation from bisulfite sequencing data
Authors: Akman Kemal , Haaf Thomas , Gravina Silvia , Vijg Jan , Tresch Achim 
Published: March 2014

Abstract
Summary: Here we present the open-source R/ Bioconductor software package BEAT (BS-Seq Epimutation Analysis Toolkit). It implements all bioinformatics steps required for the quantitative high-resolution analysis of DNA methylation patterns from bisulfite sequencing data, including the detection of regional epimutation events, i.e. loss or gain of DNA methylation at CG positions relative to a reference. Using a binomial mixture model, the BEAT package aggregates methylation counts per genomic position, thereby compensating for low coverage, incomplete conversion and sequencing errors.
Availability and implementation: BEAT is freely available as part of Bioconductor at www.bioconductor.org/packages/devel/bioc/html/BEAT.html . The package is distributed under the GNU Lesser General Public License 3.0.
Contact: akman@mpipz.mpg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Bilateral Hypersensitivity to Capsaicin, Thermal, and Mechanical Stimuli in Unilateral Complex Regional Pain Syndrome
Authors: Terkelsen Astrid J. , Gierthmühlen Janne , Finnerup Nanna B. , Højlund Anders P. , Jensen Troels S. 
Published: March 2014

Abstract

Background:
Complex regional pain syndrome is multifactorial. Exaggerated inflammatory responses to limb injury may be involved. The authors hypothesized that capsaicin-induced pain and neurogenic inflammation (skin perfusion and flare area) are increased in patients with complex regional pain syndrome compared with that in controls.

Methods:
Twenty patients with unilateral upper-limb complex regional pain syndrome and 20 age-, sex-, and body mass index–matched controls participated. Topical capsaicin 5% was applied to the back of both hands for 30 min, and pain intensity was assessed on a visual analogue scale. A laser Doppler perfusion imager scanner estimated capsaicin-induced skin perfusion and flare area. Autonomic and small-fiber function was assessed by sensory testing, quantitative sudomotor axon reflex test, and vasoconstrictor responses.

Results:
The authors found bilateral hypersensitivity to capsaicin (P ≤ 0.02), skin fold (P = 0.001), joint pressure (P < 0.0001), cold (P ≤ 0.01), and heat pain (P ≤ 0.04) in patients compared with that in controls and thermal and mechanical hyperalgesia in the complex regional pain syndrome–affected hand compared with that in the unaffected hand (P ≤ 0.001). The patients had normal capsaicin-induced flare areas, thermal detection thresholds, quantitative sudomotor axon reflex test, and vasoconstrictor responses.

Conclusions:
The main finding is bilaterally increased capsaicin-induced pain in patients compared with controls. The flare response to capsaicin was normal, suggesting that the increased pain response was not due to increased neurogenic inflammation. The bilateral hypersensitivity to painful chemical, thermal, and mechanical stimuli not confined to the innervation area of a peripheral nerve or root cannot be explained by a regional change and may partly be due to central sensitization.