bluuebunny/crossref_metadata_2025_split huggingface dataset:
Top-down analysis of protein samples by de novo sequencing techniques
Authors: Vyatkina Kira , Wu Si , Dekker Lennard J. M. , VanDuijn Martijn M. , Liu Xiaowen , Tolić Nikola , Luider Theo M. , Paša-Tolić Ljiljana , Pevzner Pavel A. 
Published: May 2016

Abstract
Motivation: Recent technological advances have made high-resolution mass spectrometers affordable to many laboratories, thus boosting rapid development of top-down mass spectrometry, and implying a need in efficient methods for analyzing this kind of data.
Results: We describe a method for analysis of protein samples from top-down tandem mass spectrometry data, which capitalizes on de novo sequencing of fragments of the proteins present in the sample. Our algorithm takes as input a set of de novo amino acid strings derived from the given mass spectra using the recently proposed Twister approach, and combines them into aggregated strings endowed with offsets. The former typically constitute accurate sequence fragments of sufficiently well-represented proteins from the sample being analyzed, while the latter indicate their location in the protein sequence, and also bear information on post-translational modifications and fragmentation patterns.
Availability and Implementation: Freely available on the web at http://bioinf.spbau.ru/en/twister.
Contact: vyatkina@spbau.ru or ppevzner@ucsd.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Cost of Herpes Zoster in Patients With Selected Immune-Compromised Conditions in the United States
Authors: Li Qian , Chen Shih-Yin , Burstin Stuart J. , Levin Myron J. , Suaya Jose A. 
Published: May 2016

Abstract
Background.  This retrospective study investigates the healthcare costs of herpes zoster (HZ) in patients with selected immune-compromised (IC) conditions in the United States (US).
Methods.  Patients with incident HZ diagnosis (index date) were selected from nationwide administrative claims databases from 2005 to 2009. Baseline IC groups, analyzed separately, included adults aged 18–64 years with the following: human immunodeficiency virus infection (HIV), solid organ transplant (SOT), bone marrow or stem cell transplant (BMSCT), or cancer; and older adults (aged ≥65 years) with cancer. Herpes zoster patients (n = 2020, n = 1053, n = 286, n = 13 178, and n = 9089, respectively) were 1-to-1 matched to controls without HZ (with randomly selected index date) in the same baseline group. The healthcare resource utilization and costs (2014 US dollars) during the first 2 postindex quarters were compared between matched cohorts with continuous enrollment during the quarter.
Results.  Herpes zoster patients generally had greater use of inpatient, emergency room and outpatient services, and pain medications than matched controls (P &lt; .05). The incremental costs of HZ during the first postindex quarter were $3056, $2649, $13 332, $2549, and $3108 for HIV, SOT, BMSCT, cancer in adults aged 18–64 years, and cancer in older adults, respectively (each P &lt; .05). The incremental costs of HZ during the second quarter were only significant for adults aged 18–64 years with cancer ($1748, P &lt; .05). The national incremental costs of HZ were projected to be $298 million annually across the 5 IC groups.
Conclusions.  The healthcare cost associated with HZ among patients with studied IC conditions was sizable and occurred mainly during the first 90 days after diagnosis.
CMX-2043 Mechanisms of Action In Vitro
Authors: Lader Alan S. , Baguisi Alexander , Casale Ralph , Kates Steven A. , Beeuwkes Reinier 
Published: May 2016

Abstract:
α-Lipoic acid has been shown to provide cytoprotection in some tissues through antioxidant and antiapoptotic mechanisms. We have enhanced these properties by synthetic modification, resulting in a new chemical entity, CMX-2043, with proven efficacy in an animal model of cardiac ischemia-reperfusion injury. The present studies compare cytoprotective cellular pathways of r-α-lipoic acid and CMX-2043. Biochemical and cellular assays were used to compare antioxidant potency, tyrosine kinase activation, and protein kinase B (Akt) phosphorylation. CMX-2043 was more effective than lipoic acid in antioxidant effect, activation of insulin receptor kinase, soluble tyrosine kinase, and Akt phosphorylation. Activation of insulin-like growth factor 1 receptor was similar for both. CMX-2043 stimulation of Akt phosphorylation was abolished by the phosphatidylinositide 3-kinase inhibitor LY294002. Consistent with Akt activation, CMX-2043 reduced carbachol-induced calcium overload. The s-stereoisomer of CMX-2043 was less active in the biochemical assays than the r-isomer. These results are consistent with cytoprotection through activation of Akt and antioxidant action. CMX-2043 may thus provide a pharmacological approach to cytoprotection consistent with established anti-apoptotic mechanisms.
VERSE: a versatile and efficient RNA-Seq read counting tool
Authors: Zhu Qin , Fisher Stephen A , Shallcross Jamie , Kim Junhyong 
Published: May 2016

AbstractMotivationRNA-Seq is a powerful technology that delivers digital gene expression data. To measure expression strength at the gene level, one popular approach is direct read counting after aligning the reads to a reference genome/transcriptome. HTSeq is one of the most popular ways of counting reads, yet its slow running speed of poses a bottleneck to many RNA-Seq pipelines. Gene level counting programs also lack a robust scheme for quantifying reads that map to non-exonic genomic features, such as intronic and intergenic regions, even though these reads are prevalent in most RNA-Seq data.ResultsIn this paper we present VERSE, an RNA-Seq read counting tool which builds upon the speed of featureCounts and implements the counting modes of HTSeq. VERSE is more than 30x faster than HTSeq when computing the same gene counts. VERSE also supports a hierarchical assignment scheme, which allows reads to be assigned uniquely and sequentially to different types of features according to user-defined priorities.AvailabilityVERSE is implemented in C. It is built on top of featureCounts. VERSE is open source and can be downloaded freely from Github (https://github.com/qinzhu/VERSE).Contactjunhyong@sas.upenn.eduSupplementary informationTables and figures illustrating the counting modes implemented in VERSE and the differences between hierarchical and independent assignment.
RefSoil: A reference database of soil microbial genomes
Authors: Choi Jinlyung , Yang Fan , Stepanauskas Ramunas , Cardenas Erick , Garoutte Aaron , Williams Ryan , Flater Jared , Tiedje James M , Hofmockel Kirsten S. , Gelder Brian , Howe Adina 
Published: May 2016

AbstractA database of curated genomes is needed to better assess soil microbial communities and their processes associated with differing land management and environmental impacts. Interpreting soil metagenomic datasets with existing sequence databases is challenging because these datasets are biased towards medical and biotechnology research and can result in misleading annotations. We have curated a database of 922 genomes of soil-associated organisms (888 bacteria and 34 archaea). Using this database, we evaluated phyla and functions that are enriched in soils as well as those that may be underrepresented in RefSoil. Our comparison of RefSoil to soil amplicon datasets allowed us to identify targets that if cultured or sequenced would significantly increase the biodiversity represented within RefSoil. To demonstrate the opportunities to access these underrepresented targets, we employed single cell genomics in a pilot experiment to sequence 14 genomes. This effort demonstrates the value of RefSoil in the guidance of future research efforts and the capability of single cell genomics as a practical means to fill the existing genomic data gaps.
Fractional Dosing of Yellow Fever Vaccine to Extend Supply: A Modeling Study
Authors: Wu Joseph T. , Peak Corey M. , Leung Gabriel M. , Lipsitch Marc 
Published: May 2016

BackgroundThe ongoing yellow fever (YF) epidemic in Angola strains the global vaccine supply, prompting WHO to adopt dose sparing for its vaccination campaign in Kinshasa in July-August 2016. Although a 5-fold fractional-dose vaccine is similar to standard-dose vaccine in safety and immunogenicity, efficacy is untested. There is an urgent need to ensure the robustness of fractional-dose vaccination by elucidating the conditions under which dose fractionation would reduce transmission.MethodsWe estimate the effective reproductive number for YF in Angola using disease natural history and case report data. With simple mathematical models of YF transmission, we calculate the infection attack rate (IAR, the proportion of population infected over the course of an epidemic) under varying levels of transmissibility and five-fold fractional-dose vaccine efficacy for two vaccination scenarios: (i) random vaccination in a hypothetical population that is completely susceptible; (ii) the Kinshasa vaccination campaign in July-August 2016 with different age cutoff for fractional-dose vaccines.FindingsWe estimate the effective reproductive number early in the Angola outbreak was between 5·2 and 7·1. If vaccine action is all-or-nothing (i.e. a proportion VE of vaccinees receives complete and the remainder receive no protection),n-fold fractionation can dramatically reduce IAR as long as efficacy VE exceeds 1/n. This benefit threshold becomes more stringent if vaccine action is leaky (i.e. the susceptibility of each vaccinee is reduced by a factor that is equal to the vaccine efficacy VE). The age cutoff for fractional-dose vaccines chosen by the WHO for the Kinshasa vaccination campaign (namely, 2 years) provides the largest reduction in IAR if the efficacy of five-fold fractional-dose vaccines exceeds 20%.InterpretationDose fractionation is a very effective strategy for reducing infection attack rate that would be robust with a large margin for error in case fractional-dose VE is lower than expected.FundingNIH-MIDAS, HMRF-Hong Kong
Higher classification sensitivity of short metagenomic reads with CLARK-S
Authors: Ounit Rachid , Lonardi Stefano 
Published: May 2016

AbstractThe growing number of metagenomic studies in medicine and environmental sciences is creating increasing demands on the computational infrastructure designed to analyze these very large datasets. Often, the construction of ultra-fast and precise taxonomic classifiers can compromise on their sensitivity (i.e., the number of reads correctly classified). Here we introduce CLARK-S, a new software tool that can classify short reads with high precision, high sensitivity and high speed at the same time.
Further evidence on idiosyncratic risk and REIT pricing: a cross-country analysis
Authors: Mi Lin , Benson Karen , Faff Robert 
Published: May 2016

PurposeThe purpose of this study is to provide new cross-country evidence on the relation between real estate investment trust (REIT) returns and idiosyncratic risk for samples of listed and unlisted REITs in the US and Australia.Design/methodology/approachFive alternative models with exponential GARCH enhancements were employed, in a Fama-MacBeth (1973) setup. The authors assess the statistical significance of the idiosyncratic risk variable and interpret the outcomes.FindingsThe results show that listed REITs in the US and Australia demonstrate a positive idiosyncratic risk-return linkage over the long period of January 1980-November 2013 and April 1994-December 2012, respectively. A further examination by sub-period reveals that this positive relation is only evident in the new REIT era (January 1993-September 2001), absent in the vintage era (before December 1992) and maturity era (November 2001-August 2008). The unlisted REITs in both countries show no relation with idiosyncratic risk. Further, the global financial crisis has no effect on the relation between idiosyncratic risk and REIT returns.Originality/valueA key motivation of this paper stems from the mixed findings documented in the literature. Also very little research has been done on the idiosyncratic risk-REIT returns linkage in the Australian context. This study offers unique insights from comparisons: Australia vs the US; and listed vs unlisted REITs.
CSR communication on corporate websites compared across continents
Authors: Hetze Katharina , Winistörfer Herbert 
Published: May 2016

Purpose– The purpose of this paper is to evaluate how the 106 largest banks in the world use their corporate websites for corporate social responsibility (CSR) communication, identifying CSR communication patterns by continent.Design/methodology/approach– An analysis of the location of CSR information on the banks’ corporate websites, a longitudinal analysis of the publication of CSR reports by the banks from 2000 to 2012, and a content analysis of the most current CSR reports in the recent period of study were undertaken.Findings– Three-quarters of the banks communicate on CSR issues on their corporate website – either located in the section “About Us” or under a separate “CSR” heading which is directly accessible on the front homepage. Company reports published on the website are the most important vehicle for CSR communication. Their publication increased from six for the publication year 2000 to a peak of 63 reports for the year 2011. The reports’ titles are most commonly linked to the concepts of “responsibility” or “sustainability” and refer to ten main stakeholders and topics. In a comparison between continents there is a difference in the use of titles: European banks prefer the title “Sustainability Report”, while Asian and American banks in particular prefer the title “CSR Report”.Research limitations/implications– The paper focuses on corporate communications, and therefore does not address perspectives on CSR communication from other disciplines. Within CSR communication, sources of CSR-related information other than the corporate websites have not been considered.Originality/value– This paper gives the first comprehensive picture of the trend in CSR communication on corporate websites in the global banking sector.
The role of self-esteem, negative affect and normative influence in impulse buying
Authors: Bandyopadhyay Nirmalya 
Published: May 2016

Purpose
– The purpose of this paper is to empirically examine the roles of self-esteem (SE), negative affect (NA), and consumer susceptibility to normative influence in the enactment of impulse buying behavior.

Design/methodology/approach
– A theoretical model is developed through an extensive review of literature. Survey research is conducted to collect the data from respondents. Structural equation modeling is performed to test the model and the hypotheses.

Findings
– The outcome of the study reveals that the act of impulsive buying is preceded by buying impulse (BI). BI is positively influenced by consumer susceptibility to normative influence and impulsive buying tendency (IBT). SE influences the generation of BI partially mediated by IBT.

Research limitations/implications
– The study is limited in its generalizability in terms of its geographic location, culture, and the context of product categories.

Practical implications
– The findings of the study have practical implications in developing marketing communications, merchandising, and personal selling strategies.

Originality/value
– In view of the contradictory empirical evidences in extant literature regarding the role NA the present study re-examines whether NA influences impulse buying. The study, conducted in the field setting also ascertains the external validity of the findings not tested in the prior research. Furthermore, in light of psychology literature, the relationship between SE and IBT was hypothesized and empirically established in the present study.
Does the UK Have Influence in the EU Legislative Process?
Authors: Hix Simon 
Published: May 2016

AbstractThe UK has influenced some major EU policies, such as the creation of the single market and enlargement. But how influential are the UK government and British MEPs in the day‐to‐day EU legislative process? To answer this question, this article analyses recent data from the Council of the European Union and the European Parliament. The evidence is mixed. In the Council, in recent years the UK government has been outvoted more often than any other EU government, yet UK officials remain well connected ‘behind the scenes’. In the European Parliament, British MEPs are now more likely to be on the losing side than are the MEPs of any other member state, yet British MEPs still win key committee chairs and rapporteurships. The evidence suggests that if the UK votes to remain in the EU, Britain's political elites will need to re‐engage with Brussels politics if the UK is to avoid becoming further marginalised from mainstream EU politics.
Industry self‐regulation of alcohol marketing: a systematic review of content and exposure research
Authors: Noel Jonathan K. , Babor Thomas F. , Robaina Katherine 
Published: May 2016

AbstractBackground and AimsWith governments relying increasingly upon the alcohol industry's self‐regulated marketing codes to restrict alcohol marketing activity, there is a need to summarize the findings of research relevant to alcohol marketing controls. This paper provides a systematic review of studies investigating the content of, and exposure to, alcohol marketing in relation to self‐regulated guidelines.MethodsPeer‐reviewed papers were identified through four literature search engines: SCOPUS, Web of Science, PubMed and PsychINFO. Non‐peer‐reviewed reports produced by public health agencies, alcohol research centers, non‐governmental organizations and government research centers were also identified. Ninety‐six publications met the inclusion criteria.ResultsOf the 19 studies evaluating a specific marketing code and 25 content analysis studies reviewed, all detected content that could be considered potentially harmful to children and adolescents, including themes that appeal strongly to young men. Of the 57 studies of alcohol advertising exposure, high levels of youth exposure and high awareness of alcohol advertising were found for television, radio, print, digital and outdoor advertisements. Youth exposure to alcohol advertising has increased over time, even as greater compliance with exposure thresholds has been documented.ConclusionsViolations of the content guidelines within self‐regulated alcohol marketing codes are highly prevalent in certain media. Exposure to alcohol marketing, particularly among youth, is also prevalent. Taken together, the findings suggest that the current self‐regulatory systems that govern alcohol marketing practices are not meeting their intended goal of protecting vulnerable populations.
Unleashing the Kraken: on the maximum length in giant squid (Architeuthis sp.)
Authors: Paxton C. G. M. 
Published: May 2016

AbstractGiant squid are among the largest invertebrates known, but a consensus on their maximum size is lacking. Statistical investigation of various measures of body length and beak size in Architeuthis suggests that squid of at least 2.69 m (99.9% prediction interval: 1.60–3.83 m) mantle length (ML) may be handled by large bull sperm whales but perhaps not females. Given the relationship of squid ML to standard (from tip of mantle to end of arms) and total (from tip of mantle to end of tentacles) length, the observed spread of individual lengths, along with a longest reliably measured ML of 2.79 m, purported squid of 10 m standard length and even 20 m total length are eminently plausible.
Chronological clinical and pathological documentation of porcine ulcerative dermatitis
Authors: Zeeh Friederike , Suter Maja M. , Mueller Eliane , Brünisholz Natalia , Zimmerman Werner , Ricklin Meret , Rüfenacht Silvia , Olivry Thierry , Roosje Petra J. 
Published: May 2016

BackgroundPorcine ulcerative dermatitis syndrome (PUDS) is a rare disease of breeding sows with an unknown pathogenesis.ObjectiveTo describe the evolution of clinical and histopathological lesions over the course of the disease and to elucidate the pathogenesis.AnimalA 24‐month‐old, pluriparous, large white sow presented during gestation with ulcerations around the teats compatible with PUDS.Methods and resultsClinical and histopathological lesions were monitored over the course of the disease (i.e. during and after the subsequent pregnancy). A clear gestation‐dependent flare of the lesions was observed with partial resolution occurring postpartum. The histological pattern presented as a lymphocytic interface dermatitis.Conclusions and clinical importanceThe findings in this case report link gestation with the development of clinical signs and histological changes. Multiparity appears to enhance severity and may finally result in a self‐perpetuating disease. Therefore, it seems advisable to cull breeding sows after they have developed PUDS.
Relationships Between Internal and External Training Load in Team-Sport Athletes: Evidence for an Individualized Approach
Authors: Bartlett Jonathan D. , O’Connor Fergus , Pitchford Nathan , Torres-Ronda Lorena , Robertson Samuel J. 
Published: May 2016

Purpose:The aim of this study was to quantify and predict relationships between rating of perceived exertion (RPE) and GPS training-load (TL) variables in professional Australian football (AF) players using group and individualized modeling approaches.Methods:TL data (GPS and RPE) for 41 professional AF players were obtained over a period of 27 wk. A total of 2711 training observations were analyzed with a total of 66 ± 13 sessions/player (range 39–89). Separate generalized estimating equations (GEEs) and artificial-neural-network analyses (ANNs) were conducted to determine the ability to predict RPE from TL variables (ie, session distance, high-speed running [HSR], HSR %, m/min) on a group and individual basis.Results:Prediction error for the individualized ANN (root-mean-square error [RMSE] 1.24 ± 0.41) was lower than the group ANN (RMSE 1.42 ± 0.44), individualized GEE (RMSE 1.58 ± 0.41), and group GEE (RMSE 1.85 ± 0.49). Both the GEE and ANN models determined session distance as the most important predictor of RPE. Furthermore, importance plots generated from the ANN revealed session distance as most predictive of RPE in 36 of the 41 players, whereas HSR was predictive of RPE in just 3 players and m/min was predictive of RPE in just 2 players.Conclusions:This study demonstrates that machine learning approaches may outperform more traditional methodologies with respect to predicting athlete responses to TL. These approaches enable further individualization of load monitoring, leading to more accurate training prescription and evaluation.
Chronic Bacterial Pathogens: Mechanisms of Persistence
Authors: Byndloss Mariana X. , Tsolis Renee M. 
Published: May 2016

ABSTRACT

Many bacterial pathogens can cause acute infections that are cleared with the onset of adaptive immunity, but a subset of these pathogens can establish persistent, and sometimes lifelong, infections. While bacteria that cause chronic infections are phylogenetically diverse, they share common features in their interactions with the host that enable a protracted period of colonization. This article will compare the persistence strategies of two chronic pathogens from the
Proteobacteria
,
Brucella abortus
and
Salmonella enterica
serovar Typhi, to consider how these two pathogens, which are very different at the genomic level, can utilize common strategies to evade immune clearance to cause chronic intracellular infections of the mononuclear phagocyte system.