bluuebunny/crossref_metadata_2025 huggingface dataset:
Deep sequencing analysis of viral infection and evolution allows rapid and detailed characterization of viral mutant spectrum
Authors: Isakov Ofer , Bordería Antonio V. , Golan David , Hamenahem Amir , Celniker Gershon , Yoffe Liron , Blanc Hervé , Vignuzzi Marco , Shomron Noam
Published: February 2015

Motivation: The study of RNA virus populations is a challenging task. Each population of RNA virus is composed of a collection of different, yet related genomes often referred to as mutant spectra or quasispecies. Virologists using deep sequencing technologies face major obstacles when studying virus population dynamics, both experimentally and in natural settings due to the relatively high error rates of these technologies and the lack of high performance pipelines. In order to overcome these hurdles we developed a computational pipeline, termed ViVan (Viral Variance Analysis). ViVan is a complete pipeline facilitating the identification, characterization and comparison of sequence variance in deep sequenced virus populations.

Results: Applying ViVan on deep sequenced data obtained from samples that were previously characterized by more classical approaches, we uncovered novel and potentially crucial aspects of virus populations. With our experimental work, we illustrate how ViVan can be used for studies ranging from the more practical, detection of resistant mutations and effects of antiviral treatments, to the more theoretical temporal characterization of the population in evolutionary studies.

Availability and implementation: Freely available on the web at http://www.vivanbioinfo.org

Contact: nshomron@post.tau.ac.il

Supplementary information:  Supplementary data are available at Bioinformatics online.
Pattern recognition methods to relate time profiles of gene expression with phenotypic data: a comparative study
Authors: Hendrickx Diana M. , Jennen Danyel G. J. , Briedé Jacob J. , Cavill Rachel , de Kok Theo M. , Kleinjans Jos C. S.
Published: February 2015

Motivation: Comparing time courses of gene expression with time courses of phenotypic data may provide new insights in cellular mechanisms. In this study, we compared the performance of five pattern recognition methods with respect to their ability to relate genes and phenotypic data: one classical method (k-means) and four methods especially developed for time series [Short Time-series Expression Miner (STEM), Linear Mixed Model mixtures, Dynamic Time Warping for -Omics and linear modeling with R/Bioconductor limma package]. The methods were evaluated using data available from toxicological studies that had the aim to relate gene expression with phenotypic endpoints (i.e. to develop biomarkers for adverse outcomes). Additionally, technical aspects (influence of noise, number of time points and number of replicates) were evaluated on simulated data.

Results: None of the methods outperforms the others in terms of biology. Linear modeling with limma is mostly influenced by noise. STEM is mostly influenced by the number of biological replicates in the dataset, whereas k-means and linear modeling with limma are mostly influenced by the number of time points. In most cases, the results of the methods complement each other. We therefore provide recommendations to integrate the five methods.

Availability: The Matlab code for the simulations performed in this research is available in the Supplementary Data (Word file). The microarray data analysed in this paper are available at ArrayExpress (E-TOXM-22 and E-TOXM-23) and Gene Expression Omnibus (GSE39291). The phenotypic data are available in the Supplementary Data (Excel file). Links to the pattern recognition tools compared in this paper are provided in the main text.

Contact:  d.hendrickx@maastrichtuniversity.nl

Supplementary information:  Supplementary data are available at Bioinformatics online.
Population-scale three-dimensional reconstruction and quantitative profiling of microglia arbors
Authors: Megjhani Murad , Rey-Villamizar Nicolas , Merouane Amine , Lu Yanbin , Mukherjee Amit , Trett Kristen , Chong Peter , Harris Carolyn , Shain William , Roysam Badrinath
Published: February 2015

Motivation: The arbor morphologies of brain microglia are important indicators of cell activation. This article fills the need for accurate, robust, adaptive and scalable methods for reconstructing 3-D microglial arbors and quantitatively mapping microglia activation states over extended brain tissue regions.

Results: Thick rat brain sections (100–300 µm) were multiplex immunolabeled for IBA1 and Hoechst, and imaged by step-and-image confocal microscopy with automated 3-D image mosaicing, producing seamless images of extended brain regions (e.g. 5903 × 9874 × 229 voxels). An over-complete dictionary-based model was learned for the image-specific local structure of microglial processes. The microglial arbors were reconstructed seamlessly using an automated and scalable algorithm that exploits microglia-specific constraints. This method detected 80.1 and 92.8% more centered arbor points, and 53.5 and 55.5% fewer spurious points than existing vesselness and LoG-based methods, respectively, and the traces were 13.1 and 15.5% more accurate based on the DIADEM metric. The arbor morphologies were quantified using Scorcioni’s L-measure. Coifman’s harmonic co-clustering revealed four morphologically distinct classes that concord with known microglia activation patterns. This enabled us to map spatial distributions of microglial activation and cell abundances.

Availability and implementation: Experimental protocols, sample datasets, scalable open-source multi-threaded software implementation (C++, MATLAB) in the electronic supplement, and website (www.farsight-toolkit.org). http://www.farsight-toolkit.org/wiki/Population-scale_Three-dimensional_Reconstruction_and_Quanti-tative_Profiling_of_Microglia_Arbors

Contact:  broysam@central.uh.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Oasis: online analysis of small RNA deep sequencing data
Authors: Capece Vincenzo , Garcia Vizcaino Julio C. , Vidal Ramon , Rahman Raza-Ur , Pena Centeno Tonatiuh , Shomroni Orr , Suberviola Irantzu , Fischer Andre , Bonn Stefan
Published: February 2015

Summary: Oasis is a web application that allows for the fast and flexible online analysis of small-RNA-seq (sRNA-seq) data. It was designed for the end user in the lab, providing an easy-to-use web frontend including video tutorials, demo data and best practice step-by-step guidelines on how to analyze sRNA-seq data. Oasis’ exclusive selling points are a differential expression module that allows for the multivariate analysis of samples, a classification module for robust biomarker detection and an advanced programming interface that supports the batch submission of jobs. Both modules include the analysis of novel miRNAs, miRNA targets and functional analyses including GO and pathway enrichment. Oasis generates downloadable interactive web reports for easy visualization, exploration and analysis of data on a local system. Finally, Oasis’ modular workflow enables for the rapid (re-) analysis of data.

Availability and implementation: Oasis is implemented in Python, R, Java, PHP, C++ and JavaScript. It is freely available at http://oasis.dzne.de.

Contact:  stefan.bonn@dzne.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Influenza Circulation in United States Army Training Camps Before and During the 1918 Influenza Pandemic: Clues to Early Detection of Pandemic Viral Emergence
Authors: Chertow Daniel S. , Cai Rongman , Sun Junfeng , Grantham John , Taubenberger Jeffery K. , Morens David M.
Published: February 2015

Background.  Surveillance for respiratory diseases in domestic National Army and National Guard training camps began after the United States’ entry into World War I, 17 months before the “Spanish influenza” pandemic appeared.

Methods.  Morbidity, mortality, and case-fatality data from 605 625 admissions and 18 258 deaths recorded for 7 diagnostic categories of respiratory diseases, including influenza and pneumonia, were examined over prepandemic and pandemic periods.

Results.  High pandemic influenza mortality was primarily due to increased incidence of, but not increased severity of, secondary bacterial pneumonias.

Conclusions.  Two prepandemic incidence peaks of probable influenza, in December 1917–January 1918 and in March–April 1918, differed markedly from the September–October 1918 pandemic onset peak in their clinical-epidemiologic features, and they may have been caused by seasonal or endemic viruses. Nevertheless, rising proportions of very low incidence postinfluenza bronchopneumonia (diagnosed at the time as influenza and bronchopneumonia) in early 1918 could have reflected circulation of the pandemic virus 5 months before it emerged in pandemic form. In this study, we discuss the possibility of detecting pandemic viruses before they emerge, by surveillance of special populations.
Modeling non-local thermodynamic equilibrium plasma using the Flexible Atomic Code data
Authors: Han Bo , Wang Feilu , Salzmann David , Zhao Gang
Published: February 2015

We present a new code, RCF (“Radiative–Collisional code based on FAC”), which is used to simulate steady-state plasmas under non-local thermodynamic equilibrium condition, especially photoinization-dominated plasmas. RCF takes almost all of the radiative and collisional atomic processes into a rate equation to interpret the plasmas systematically. The Flexible Atomic Code (FAC) supplies all the atomic data needed for RCF, which insures calculating completeness and consistency of atomic data. With four input parameters relating to the radiation source and target plasma, RCF calculates the population of levels and charge states, as well as potential emission spectrum. In a preliminary application, RCF successfully reproduced the results of a photoionization experiment with reliable atomic data. The effects of the most important atomic processes on the charge state distribution are also discussed.
An Evaluation of Shared Mental Models and Mutual Trust on General Medical Units: Implications for Collaboration, Teamwork, and Patient Safety
Authors: McComb Sara A. , Lemaster Matthew , Henneman Elizabeth A. , Hinchey Kevin T.
Published: February 2015

Objectives

This study examines nurse-physician teamwork and collaboration, a critical component in the delivery of safe patient care, on general medical units. To that end, we assess shared mental models and mutual trust, 2 coordinating mechanisms that help facilitate teamwork, among nurses and physicians working on general medical units.

Methods

Data were collected from 37 nurses and 42 physicians at an urban teaching medical center in the Northeastern United States. Shared mental model questionnaire items were iteratively developed with experts' input to ensure content validity. Mutual trust items were adapted from an existing scale; items were reliable. Data were analyzed using χ2 and independent 2-tailed t tests.

Results

Physicians and nurses reported significant differences in their perceptions of the professional responsible for a variety of roles (e.g., advocating for the patient [P = 0.0007], identifying a near miss/error [P = 0.003]). Medication reconciliation is only role for which nurses perceive less responsibility than physicians perceive nurses have. Regarding mutual trust, both groups reported significantly more trust within their own professions; both groups reported similar levels of trust in physicians, with physicians reporting significantly less trust in their nursing colleagues than nurses perceive (P < 0.0001).

Conclusions

Although many efforts have been directed at improving nurse-physician collaboration, more work is needed. To that end, we propose increasing knowledge about their respective roles, providing opportunities for nurse and physician collaboration through rounding or committee work and enhancing the preparedness and professionalism of interactions.
Transparency When Things Go Wrong: Physician Attitudes About Reporting Medical Errors to Patients, Peers, and Institutions
Authors: Bell Sigall K. , White Andrew A. , Yi Jean C. , Yi-Frazier Joyce P. , Gallagher Thomas H.
Published: February 2015

Objectives

Transparent communication after medical error includes disclosing the mistake to the patient, discussing the event with colleagues, and reporting to the institution. Little is known about whether attitudes about these transparency practices are related. Understanding these relationships could inform educational and organizational strategies to promote transparency.

Methods

We analyzed responses of 3038 US and Canadian physicians to a medical error communication survey. We used bivariate correlations, principal components analysis, and linear regression to determine whether and how physician attitudes about transparent communication with patients, peers, and the institution after error were related.

Results

Physician attitudes about disclosing errors to patients, peers, and institutions were correlated (all P's < 0.001) and represented 2 principal components analysis factors, namely, communication with patients and communication with peers/institution. Predictors of attitudes supporting transparent communication with patients and peers/institution included female sex, US (vs Canadian) doctors, academic (vs private) practice, the belief that disclosure decreased likelihood of litigation, and the belief that system changes occur after error reporting. In addition, younger physicians, surgeons, and those with previous experience disclosing a serious error were more likely to agree with disclosure to patients. In comparison, doctors who believed that disclosure would decrease patient trust were less likely to agree with error disclosure to patients. Previous disclosure education was associated with attitudes supporting greater transparency with peers/institution.

Conclusions

Physician attitudes about discussing errors with patients, colleagues, and institutions are related. Several predictors of transparency affect all 3 practices and are potentially modifiable by educational and institutional strategies.
“The Jackson Table Is a Pain in the…”: A Qualitative Study of Providers’ Perception Toward a Spinal Surgery Table
Authors: Asiedu Gladys B. , Lowndes Bethany R. , Huddleston Paul M. , Hallbeck Susan
Published: February 2015

Objective

The aim of this study was to define health care providers’ perceptions toward prone patient positioning for spine surgery using the Jackson Table, which has not been hitherto explored.

Methods

We analyzed open-ended questionnaire data and interviews conducted with the spine surgical team regarding the current process of spinal positioning/repositioning using the Jackson Table. Participants were asked to provide an open-ended explanation as to whether they think the current process of spinal positioning/repositioning is safe for the staff or patients. Follow-up qualitative interviews were conducted with 11 of the participants to gain an in-depth understanding of the challenges and safety issues related to prone patient positioning.

Results

Data analysis resulted in 6 main categories: general challenges with patient positioning, role-specific challenges, challenges with the Jackson Table and the “sandwich” mechanism, safety concerns for patients, safety concerns for the medical staff, and recommendations for best practices.

Conclusions

This study is relevant to everyday practice for spinal surgical team members and advances our understanding of how surgical teams qualitatively view the current process of patient positioning for spinal surgery. Providers recommended best practices for using the Jackson Table, which can be achieved through standardized practice for transfer of patients, educational tools, and checklists for equipment before patient transfer and positioning. This research has identified several important practice opportunities for improving provider and patient safety in spine surgery.
Site-Specific Nitrosoproteomic Identification of EndogenouslyS-Nitrosylated Proteins in Arabidopsis
Authors: Hu Jiliang , Huang Xiahe , Chen Lichao , Sun Xuwu , Lu Congming , Zhang Lixin , Wang Yingchun , Zuo Jianru
Published: February 2015

Nitric oxide (NO) regulates multiple developmental events and stress responses in plants. A major biologically active species of NO is S-nitrosoglutathione (GSNO), which is irreversibly degraded by GSNO reductase (GSNOR). The major physiological effect of NO is protein S-nitrosylation, a redox-based posttranslational modification mechanism by covalently linking an NO molecule to a cysteine thiol. However, little is known about the mechanisms of S-nitrosylation-regulated signaling, partly due to limited S-nitrosylated proteins being identified. In this study, we identified 1,195 endogenously S-nitrosylated peptides in 926 proteins from the Arabidopsis (Arabidopsis thaliana) by a site-specific nitrosoproteomic approach, which, to date, is the largest data set of S-nitrosylated proteins among all organisms. Consensus sequence analysis of these peptides identified several motifs that contain acidic, but not basic, amino acid residues flanking the S-nitrosylated cysteine residues. These S-nitrosylated proteins are involved in a wide range of biological processes and are significantly enriched in chlorophyll metabolism, photosynthesis, carbohydrate metabolism, and stress responses. Consistently, the gsnor1-3 mutant shows the decreased chlorophyll content and altered photosynthetic properties, suggesting that S-nitrosylation is an important regulatory mechanism in these processes. These results have provided valuable resources and new clues to the studies on S-nitrosylation-regulated signaling in plants.
Proposing a new approach for evaluating the situational leadership theory based on the Kano model
Authors: Salehzadeh Reza , Shahin Arash , Kazemi Ali , Shaemi Barzoki Ali
Published: February 2015

Purpose

– The purpose of this paper is to propose a new approach for evaluating the situational leadership theory (SLT).

Design/methodology/approach

– Statistical population includes the undergraduate, postgraduate and PhD students of the University of Isfahan. For data analysis, 727 accurate completed questionnaires have been used. Initially, questions were developed for each SLT style, followed by analysis in which the type of styles were determined and classified using the Kano evaluation table.

Findings

– Based on the Kano's classifications, findings imply that, the appropriate leadership styles for undergraduate, postgraduate and PhD students are directing, coaching and supporting styles, respectively.

Originality/value

– The approach and findings of this research contribute to the literature of SLT and the Kano model. Findings can be used as a guideline for lecturers in leading and motivating students.
How salespeople see organizational citizenship behaviors: an exploratory study using the laddering technique
Authors: Guenzi Paolo , Panzeri Federico
Published: February 2015

Purpose

– The purpose of this paper is to more thoroughly investigate the role of organizational citizenship behaviors (OCBs) in sales force settings and the reason why salespeople should practice OCBs. In fact, in spite of the huge body of literature on OCBs and their impact on performance, some important knowledge gaps still remain to be filled. Inconsistent and unexpected findings are particularly apparent in the relatively few studies investigating OCBs in sales forces. The authors argue that some specific characteristics of the selling job and related tasks make the analysis of the practice of these behaviors in the sales context particularly interesting.

Design/methodology/approach

– The authors explore which OCBs salespeople engage in, and analyze the perceived consequences of such behaviors using means-end theory and the laddering technique. They apply means-end theory and the laddering technique to interview a sample of salespersons from three companies operating in different business-to-business settings.

Findings

– The end result of the empirical analysis is the hierarchical value map showing a set of linkages among OCBs and their perceived consequences. In the perceptions of salespeople, OCBs play a strong utilitarian role in that they facilitate personal goal attainment. In salespeople’s minds, there are no relevant trade-offs between OCBs and task-performance as long as the former can be used to improve the latter. For salespeople, the path from OCBs to performance may vary, depending on whether the performance in question is organizational, individual or customer-focused. Finally, some OCBs apparently contribute to creating customer trust in the salesperson.

Research limitations/implications

– The findings add some interesting insights to the discussion regarding some controversies in OCBs literature, especially the interplay of contextual performance and task performance.

Practical implications

– Various types of OCBs can be encouraged through different managerial interventions. As an example, altruism can be fostered by appropriate recruiting criteria (e.g. using “attitude toward teamwork” as a key personnel selection factor), and by training initiatives and leadership style. Altruism can also be stimulated by an adequately designed organizational structure (e.g. team-based) as well as by adopting appropriate integration mechanisms that facilitate interpersonal and interfunctional cooperation. Sales managers can foster some OCBs by promoting knowledge sharing and reciprocal learning among members of the sales team, and by emphasizing the positive consequences of OCBs in all communication with salespeople.

Originality/value

– Findings from this study challenge some widespread assumptions about OCBs in general. In fact, most of the literature holds that OCBs are an example of prosocial behaviors. Actually, the findings suggest that in the specific case of salespeople, OCBs are ultimately self-directed, for the most part.
Less is more: extreme genome complexity reduction with ddRAD using Ion Torrent semiconductor technology
Authors: Pukk Lilian , Ahmad Freed , Hasan Shihab , Kisand Veljo , Gross Riho , Vasemägi Anti
Published: February 2015

Massively parallel sequencing a small proportion of the whole genome at high coverage enables answering a wide range of questions from molecular evolution and evolutionary biology to animal and plant breeding and forensics. In this study, we describe the development of restriction‐site associated DNA (RAD) sequencing approach for Ion Torrent PGM platform. Our protocol results in extreme genome complexity reduction using two rare‐cutting restriction enzymes and strict size selection of the library allowing sequencing of a relatively small number of genomic fragments with high sequencing depth. We applied this approach to a common freshwater fish species, the Eurasian perch (Perca fluviatilis L.), and generated over 2.2 MB of novel sequence data consisting of ~17 000 contigs, identified 1259 single nucleotide polymorphisms (SNPs). We also estimated genetic differentiation between the DNA pools from freshwater (Lake Peipus) and brackish water (the Baltic Sea) populations and identified SNPs with the strongest signal of differentiation that could be used for robust individual assignment in the future. This work represents an important step towards developing genomic resources and genetic tools for the Eurasian perch. We expect that our ddRAD sequencing protocol for semiconductor sequencing technology will be useful alternative for currently available RAD protocols.
Opioid treatment at release from jail using extended‐release naltrexone: a pilot proof‐of‐concept randomized effectiveness trial
Authors: Lee Joshua D. , McDonald Ryan , Grossman Ellie , McNeely Jennifer , Laska Eugene , Rotrosen John , Gourevitch Marc N.
Published: February 2015

Background and Aims

Relapse to addiction following incarceration is common. We estimated the feasibility and effectiveness of extended‐release naltrexone (XR‐NTX) as relapse prevention among opioid‐dependent male adults leaving a large urban jail.

Design

Eight‐week, proof‐of‐concept, open‐label, non‐blinded randomized effectiveness trial.

Setting

New York City jails and Bellevue Hospital Center Adult Primary Care clinics, USA.

Participants

From January 2010 to July 2013, 34 opioid‐dependent adult males with no stated interest in agonist treatments (methadone, buprenorphine) received a counseling and referral intervention and were randomized to XR‐NTX (n = 17) versus no medication (n = 17) within one week prior to jail release.

Intervention

XR‐NTX (Vivitrol®; Alkermes Inc.), a long‐acting injectable mu opioid receptor antagonist.

Measures

The primary intent‐to‐treat outcome was post‐release opioid relapse at week 4, defined as ≥10 days of opioid misuse by self‐report and urine toxicologies. Secondary outcomes were proportion of urine samples negative for opioids and rates of opioid abstinence, intravenous drug use (IVDU), cocaine use, community treatment participation, re‐incarceration and overdose.

Findings

Acceptance of XR‐NTX was high; 15 of 17 initiated treatment. Rates of the primary outcome of week 4 opioid relapse were lower among XR‐NTX participants: 38 versus 88% [P<0.004; odds ratio (OR) = 0.08, 95% confidence interval (CI) = 0.01–0.48]; more XR‐NTX urine samples were negative for opioids, 59 versus 29% (P<0.009; OR = 3.5, 95% CI = 1.4–8.5). There were no significant differences in the remaining secondary outcomes, including rates of IVDU, cocaine use, re‐incarceration and overdose.

Conclusion

Extended‐release naltrexone is associated with significantly lower rates of opioid relapse among men in the United States following release from jail when compared with a no medication treatment‐as‐usual condition.
The Effect of Simvastatin on Infection‐Induced Inflammatory Response of Human Fetal Membranes
Authors: Basraon Sanmaan K. , Costantine Maged M. , Saade George , Menon Ramkumar
Published: February 2015

Problem

Inflammatory cytokines and matrix metalloproteinases (MMPs) contribute to preterm labor pathophysiology. The objective of this study was to test anti‐inflammatory properties of simvastatin in human fetal membranes exposed to lipopolysaccharide (LPS).

Method of study

Normal term human fetal membrane explants (n = 11) were allocated to one of the six study groups: control, LPS only (100 ng/mL), simvastatin only (125 ng/mL), simvastatin given 6 hrs prior to LPS (S‐L), simvastatin given 6 hrs post‐LPS (L‐S), and simvastatin and LPS given simultaneously (L+S). Explants were incubated for 24 hrs. Multiplex ELISA for cytokines: IL‐1β, IL‐6, IL‐10, and TNF‐α; soluble cytokine receptors: sIL‐1R2, sIL‐6R, sTNFR1, and R2; MMPs (1, 2, 7, 9, and 10); and tissue inhibitor of metalloproteinase‐2 (TIMP‐2) was performed on tissue culture supernatants. Pairwise comparison between different groups was conducted by least square mean estimates.

Results

Compared with controls, LPS stimulation increased cytokine production and their tissue bioavailability (measured as the molar ratio of cytokine to its soluble receptor), thus confirming membrane immune reactivity (P < 0.01). Pre‐treatment with simvastatin (S‐L) reduced IL‐6 (P = 0.02), TNF‐α (P = 0.02), and MMP‐9 (P = 0.01); post‐treatment (L‐S) reduced IL‐1β (P = 0.02) and TNF‐α (P = 0.04), while simultaneous treatment (L+S) did not reduce any of the cytokines tested. Simvastatin reduced the molar ratio of TNF‐α/sTNFR1 or R2 and IL‐1β/sIL‐1R2 (P = 0.01 and 0.04 in S‐L group; P = 0.01 and 0.004 in L‐S group, respectively). S‐L additionally reduced MMP‐9/TIMP‐2 molar ratio (P = 0.0007).

Conclusions

Simvastatin downregulates LPS‐induced inflammatory response and restores homeostasis between pro‐ and anti‐inflammatory processes. Simvastatin may reduce fetal inflammatory response associated with infection‐induced preterm birth.
Effect of crossbreeding with Limousine, Rubia Gallega and Belgium Blue on meat quality and fatty acid profile of Holstein calves
Authors: Domingo Gonzalo , Iglesias Antonio , Monserrat Lorenzo , Sanchez Luciano , Cantalapiedra Jesus , Lorenzo Jose Manuel
Published: February 2015

The object of this work was to study the effects of crossbreeding on meat quality and fatty acid profile of Holstein calves. Samples were taken from Longissimus thoracis (LT) muscle of 36 calves of three different groups (Holstein crossed with Rubia Gallega (HF×RG), Holstein crossed with Limousine (HF×LI) and Holstein crossed with Belgian Blue (HF×BB)). Significant differences were observed in carcass weight and killing out percentage (P < 0.001) among, groups reaching the highest values in the HF×BB group (228 kg and 59.4%, respectively), while the cross with Limousine presented the lowest values for carcass weight (191 kg) and the cross with Rubia Gallega showed the lowest killing out percentages (54.9%). Meat from HF×RG animals was redder (a* 13.31) and lightest (L* 39.55) than meat from HF×LI and HF×BB groups. With regard to fatty acid profile, the saturated fatty acids were the most abundant fatty acid, followed by monounsaturated fatty acids (MUFA) and polyunsaturated fatty acids in the three groups. Crossbreeding did not affect the proportion of fatty acid. Finally, live weight, cold carcass weight, killing out, shear force, L* from LT, b*from LT, a* from fat, b* from fat, C14:0, C15:0, C16:0, C18:0, C18:3n‐6, MUFA and price‐to‐sales ratio were the selected variables from discriminant analysis to classify the types of crossbreeding.
Plasma IL‐33 in atopic patients correlates with pro‐inflammatory cytokines and changes cholesterol transport protein expression: a surprising neutral overall impact on atherogenicity
Authors: Voloshyna I. , Mucci T. , Sher J. , Fonacier L. S. , Littlefield M. J. , Carsons S. , Reiss A. B.
Published: February 2015

Objective

Interleukin (IL)‐33 has been associated with atopic and inflammatory conditions. IL‐33 may be atheroprotective inducing a Th1‐to‐Th2 immunologic switch. However, the role of IL‐33 in cardiovascular disease remains unclear. This study examines the effect of physiological and elevated IL‐33 levels in plasma from atopic patients (AP) on cholesterol metabolism in human macrophages as compared to plasma from healthy controls (HC).

Methods

Twenty‐five AP and 25 HC were enrolled in this study. Plasma samples were analysed for levels of IL‐33, IFN‐γ, TNF‐α, IL‐17α, IL‐5 and soluble ST2. THP‐1 differentiated macrophages were exposed to HC and AP plasma. Expression of proteins involved in reverse cholesterol transport (ABCA1, ABCG1 and 27‐hydroxylase) and scavenger receptors, responsible for uptake of modified lipids (CD36, ScR‐A1, CXCL16 and LOX‐1), was measured using QRT‐PCR and immunoblotting techniques.

Results

IL‐33 was significantly higher in AP plasma: 106.7 ± 95 pg/mL versus HC plasma (53.4 ± 23 pg/mL). IL‐33 concentration strongly correlated with levels of IFN‐γ (r = 0.85), TNFα (r = 0.9) and IL‐17α (r = 0.94). No significant difference was found in soluble ST2 levels. An important contrast was observed for 27‐hydroxylase: normal IL‐33 in AP plasma amplified 27‐hydroxylase while increased IL‐33 suppressed it. Expression of CD36 and SR‐A1 was greater in macrophages exposed to plasma with high IL‐33, while CXCL16 was higher in cells grown in the presence of plasma with normal IL‐33.

Conclusions

Here, we demonstrate that high levels of IL‐33 and a high IL‐33/soluble ST2 ratio correlates with elevated levels of IFN‐γ, TNF‐α and IL‐17α as well as IL‐5, demonstrating that IL‐33 has pleiotropic effects. However, elevated IL‐33 did not significantly impact lipid accumulation in macrophages overall. Given the wide variety of cellular responses regulated by IL‐33, further investigation with a larger sample size will allow us to clarify the threshold concentration of IL‐33 that leads to optimal cholesterol balance.
Efficacy and quality of life after transcutaneous posterior tibial neuromodulation for faecal incontinence
Authors: Jiménez‐Toscano M. , Vega D. , Fernandez‐Cebrián J. M. , Valle Martín B. , Jiménez‐Almonacid P. , Rueda Orgaz J. A.
Published: February 2015

Aim

The aim of this study was to evaluate the efficacy of transcutaneous neuromodulation of the posterior tibial nerve for faecal incontinence and to assess quality of life after the procedure.

Method

A prospective non‐randomized cohort study was conducted in a tertiary centre from September 2010 to May 2013. All patients with faecal incontinence who met the inclusion criteria were included and were treated as outpatients during a 3‐month period by unilateral neuromodulation of the posterior tibial nerve. The patients were followed 3‐monthly for 1 year. Severity scales, a bowel diary and quality of life scales were evaluated prospectively before and after treatment.

Results

Twenty‐seven patients of median age 67 (interquartile range 60–69) years and a male to female ratio of 1/6 were included. Faecal incontinence was for solid stools in 48.1% of patients with urgency in 55.6%. About one‐third (34.6%) had a sphincter defect on ultrasound and reduction of anal canal pressure in 85.2%. There was a significant improvement in episodes of incontinence on the Wexner score and visual analogue scale assessment and a decrease in the number of episodes of incontinence per unit time. The Fecal Incontinence Quality of Life score was improved at the end of the follow‐up. No adverse effects were observed. The cost of the treatment was €135 per patient.

Conclusion

Transcutaneous posterior tibial nerve neuromodulation provides good treatment for faecal incontinence in terms of efficacy and quality of life.
Risk factors associated with a reduced response in the treatment of erysipelas
Authors: Linke Miriam , Booken Nina
Published: February 2015

Background

In most cases, erysipelas may be adequately treated using first‐line antibiotic therapy. However, clinicians are sometimes confronted with complicated cases, in which patients do not respond to initial antibiotic therapy. The objective of this study was to identify risk factors associated with a reduced response to antibiotic therapy and, thus, a more complicated disease course.

Patients and Methods

We retrospectively analyzed the clinical course of 98 patients with erysipelas treated with standard antibiotic therapy. Patient groups showing different therapeutic responses were compared with respect to clinical data, medical history, and laboratory parameters.

Results

Patients with bullous or hemorrhagic erysipelas (p = 0.0008), stasis dermatitis (p = 0.01) or chronic venous insufficiency (p = 0.0004) showed a significantly reduced response to initial therapy with cefuroxime or clindamycin, respectively. Furthermore, the response to initial therapy significantly depended on C‐reactive protein (p = 0.007) and neutrophil (p = 0.02) levels.

Conclusion

In erysipelas patients with clinical complications, abnormal laboratory parameters or preexisting local skin damage, an intensified antibiotic regimen should be considered.
Mapping the development of facial expression recognition
Authors: Rodger Helen , Vizioli Luca , Ouyang Xinyi , Caldara Roberto
Published: February 2015

Reading the non‐verbal cues from faces to infer the emotional states of others is central to our daily social interactions from very early in life. Despite the relatively well‐documented ontogeny of facial expression recognition in infancy, our understanding of the development of this critical social skill throughout childhood into adulthood remains limited. To this end, using a psychophysical approach we implemented the QUEST threshold‐seeking algorithm to parametrically manipulate the quantity of signals available in faces normalized for contrast and luminance displaying the six emotional expressions, plus neutral. We thus determined observers' perceptual thresholds for effective discrimination of each emotional expression from 5 years of age up to adulthood. Consistent with previous studies, happiness was most easily recognized with minimum signals (35% on average), whereas fear required the maximum signals (97% on average) across groups. Overall, recognition improved with age for all expressions except happiness and fear, for which all age groups including the youngest remained within the adult range. Uniquely, our findings characterize the recognition trajectories of the six basic emotions into three distinct groupings: expressions that show a steep improvement with age – disgust, neutral, and anger; expressions that show a more gradual improvement with age – sadness, surprise; and those that remain stable from early childhood – happiness and fear, indicating that the coding for these expressions is already mature by 5 years of age. Altogether, our data provide for the first time a fine‐grained mapping of the development of facial expression recognition. This approach significantly increases our understanding of the decoding of emotions across development and offers a novel tool to measure impairments for specific facial expressions in developmental clinical populations.
Neighborhood crime as a predictor of individual differences in emotional processing and regulation
Authors: McCoy Dana Charles , Roy Amanda L. , Raver C. Cybele
Published: February 2015

Emerging research suggests that early exposure to environmental adversity has important implications for the development of brain regions associated with emotion regulation, yet little is known about how such adversity translates into observable differences in children's emotion‐related behavior. The present study examines the relationship between geocoded neighborhood crime and urban pre‐adolescents' emotional attention, appraisal, and response. Results indicate that living in a high‐crime neighborhood is associated with greater selective attention toward negatively valenced emotional stimuli on a dot probe task, less biased appraisal of fear on a facial identification task, and lower rates of teacher‐reported internalizing behaviors in the classroom. These findings suggest that children facing particularly high levels of environmental threat may develop different regulatory processes (e.g. greater use of emotional suppression) than their peers from low‐crime neighborhoods in order to manage the unique stressors and social demands of their communities.
The attentional ‘zoom‐lens’ in 8‐month‐old infants
Authors: Ronconi Luca , Franchin Laura , Valenza Eloisa , Gori Simone , Facoetti Andrea
Published: February 2015

The spatial attention mechanisms of orienting and zooming cooperate to properly select visual information from the environment and plan eye movements accordingly. Despite the fact that orienting ability has been extensively studied in infancy, the zooming mechanism – namely, the ability to distribute the attentional resources to a small or large portion of the visual field – has never been tested before. The aim of the present study was to evaluate the attentional zooming abilities of 8‐month‐old infants. An eye‐tracker device was employed to measure the saccadic latencies (SLs) at the onset of a visual target displayed at two eccentricities. The size of the more eccentric target was adjusted in order to counteract the effect of cortical magnification. Before the target display, attentional resources were automatically focused (zoom‐in) or spread out (zoom‐out) by using a small or large cue, respectively. Two different cue–target intervals were also employed to measure the time course of this attentional mechanism. The results showed that infants'SLs varied as a function of the cue size. Moreover, a clear time course emerged, demonstrating that infants can rapidly adjust the attentional focus size during a pre‐saccadic temporal window. These findings could serve as an early marker for neurodevelopmental disorders associated with attentional zooming dysfunction such as autism and dyslexia.
Discourse bootstrapping: preschoolers use linguistic discourse to learn new words
Authors: Sullivan Jessica , Barner David
Published: February 2015

When children acquire language, they often learn words in the absence of direct instruction (e.g. ‘This is a ball!’) or even social cues to reference (e.g. eye gaze, pointing). However, there are few accounts of how children do this, especially in cases where the referent of a new word is ambiguous. Across two experiments, we test whether preschoolers (2‐ to 4‐year‐olds; n = 239) can learn new words by inferring the referent of a new word from the surrounding linguistic discourse. Across two experiments, we show that children as young as 2 can learn a new word from the linguistic discourse in which it appears. This suggests that children use the linguistic discourse in which a word appears to learn new words.
An endophyte‐rich diet increases ant predation on a specialist herbivorous insect
Authors: HAMMER TOBIN J. , VAN BAEL SUNSHINE A.
Published: February 2015

1. All plants form symbioses with microfungi, known as endophytes, which live within plant tissues. Numerous studies have documented endophyte–herbivore antagonism in grass systems, but plant–endophyte–insect interactions are highly variable for forbs and woody plants.

2. The net effect of endophytes on insect herbivory may be modified by their interactions with higher trophic levels, such as predators. Including these multitrophic dynamics may explain some of the variability among endophyte studies of non‐grass plants, which are currently based exclusively on bitrophic studies.

3. The abundance of natural foliar endophytes in a Neotropical vine was manipulated and beetles were fed high or low endophyte diets. Experimental assays assessed whether dietary endophyte load affected beetle growth, leaf consumption, and susceptibility to ant predation.

4. Beetles feeding on high‐ versus low‐endophyte plants had almost identical growth and leaf consumption rates.

5. In a field bioassay, however, it was discovered that feeding on an endophyte‐rich diet increased a beetle's odds of capture by predatory ants nine‐fold.

6. Endophytes could thus provide an indirect, enemy‐mediated form of plant defence that operates even against specialist herbivores. We argue that a multitrophic approach is necessary to untangle the potentially diverse types of endophyte defence among plants.
Update on paroxysmal nocturnal haemoglobinuria: on the long way to understand the principles of the disease
Authors: Schubert Jörg , Röth Alexander
Published: February 2015

The understanding of the clinical manifestations in paroxysmal nocturnal haemoglobinuria (PNH) has made great progress. The main symptoms of this disease such as abdominal pain, renal failure or pulmonary hypertension and even the basis of the dramatic thrombophilia can be related to intravascular haemolysis and liberation of free haemoglobin resulting in NO depletion. In addition, there has been a recent great progress in elucidating the pathophysiology of clonal expansion within PNH bone marrow. In the majority of patients with haemolytic PNH, there are additional mutations within genes beyond PIG‐A and rather affecting growth and differentiation of clonal bone marrow cells. In contrast to the formerly proposed single mechanism hypotheses such as immune selection or intrinsic gain of clonal dominance, this appears to follow a pattern of a complex clonal hierarchy putatively integrating both earlier anticipated mechanisms. Treatment of PNH is mainly supportive. The only curative approach as allogeneic stem cell transplantation should only be applied to patients with complications such as secondary bone marrow aplasia or transformation into MDS or AML. Symptomatic haemolytic PNH will be treated with eculizumab, an inhibitor of the terminal complement cascade. Treatment with eculizumab can significantly prevent PNH‐related symptoms including the abnormal thrombophilia. Recently, it was demonstrated that in contrast to untreated historic PNH patients, meanwhile a normal life expectancy is observed in eculizumab‐treated patients. The recently approved vaccine against meningococci type B by the European Medical Agency (EMA) could probably further help to prevent meningococcal sepsis due to the induced complement deficiency by eculizumab.
Safe and effective treatment with daclatasvir and asunaprevir in a liver transplant recipient with severe cholestatic hepatitis C
Authors: Ueda Yoshihide , Kaido Toshimi , Hatano Etsuro , Ohtsuru Shigeru , Uemoto Shinji
Published: February 2015

Severe cholestatic hepatitis C (SCH) is a unique variant of recurrent hepatitis C that occurs after liver transplantation. Unfortunately, the prognosis of SCH is poor, and interferon (IFN) therapy has been reported to not improve the prognosis. We herein report a case of progressive SCH with acute cellular rejection (ACR) and bacterial infection, which was successfully treated using IFN‐free therapy with daclatasvir and asunaprevir. A 43‐year‐old man was diagnosed with SCH and mild ACR at day 48 after liver transplantation, and IFN‐free therapy with daclatasvir and asunaprevir was started. Although he experienced catheter‐related bacteremia on the first day, the IFN‐free therapy was safely continued, which immediately caused his liver function to improve. His bilirubin levels decreased from 11.1 to 2.1 mg/dL and serum hepatitis C virus RNA levels became undetectable after 4 weeks of the treatment. This case indicates that IFN‐free therapy for progressive SCH with acute cellular rejection and bacterial infection is safe and effective, and may improve the outcomes of hepatitis C virus positive transplant recipients.
Involving patients in health technology funding decisions: stakeholder perspectives on processes used in Australia
Authors: Lopes Edilene , Street Jackie , Carter Drew , Merlin Tracy
Published: February 2015

Background

Governments use a variety of processes to incorporate public perspectives into policymaking, but few studies have evaluated these processes from participants' point of view.

Objective

The objective of this study was twofold: to understand the perspectives of selected stakeholders with regard to involvement processes used by Australian Advisory Committees to engage the public and patients; and to identify barriers and facilitators to participation.

Design

Twelve semi‐structured interviews were conducted with representatives of different stakeholder groups involved in health technology funding decisions in Australia. Data were collected and analysed using a theoretical framework created by Rowe and Frewer, but adapted to more fully acknowledge issues of power and influence.

Results

Stakeholder groups disagreed as to what constitutes effective and inclusive patient involvement. Barriers reported by interviewees included poor communication, a lack of transparency, unworkable deadlines, and inadequate representativeness. Also described were problems associated with defining the task for patients and their advocates and with the timing of patient input in the decision‐making process. Interviewees suggested that patient participation could be improved by increasing the number of patient organizations engaged in processes and including those organizations at different stages of decision making, especially earlier.

Conclusions

The different evaluations made by stakeholder groups appear to be underpinned by contrasting conceptions of public involvement and its value, in line with Graham Martin's work which distinguishes between ‘technocratic’ and ‘democratic’ public involvement. Understanding stakeholders' perspectives and the contrasting conceptions of public involvement could foster future agreement on which processes should be used to involve the public in decision making.