bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic and biological characterizations of a Newcastle disease virus from swine in china
Authors: Yuan Xiaoyuan , Wang Youling , Yang Jinxing , Xu Huaiying , Zhang Yuxia , Qin Zhuoming , Ai Hongbin , Wang Jinbao 
Published: July 2012

Abstract

Background
Newcastle Disease Virus (NDV) has been considered to only infect avian species. However, one paramyxovirus named as Xiny10 was isolated from swine. The differences of Xiny10, another previous swine NDV (JL01) and vaccine strain La Sota were compared on the basis of sequences of the whole-lengthen Fusion (F) gene and biological characteristics.

Findings
Through serologic tests and sequence alignment, Xiny10 was proved as NDV. It has great differences with JL01 in virulence, biological characteristics, genotype and amino acid homology of F gene. The sequence alignment showed Xiny10 and La Sota both belonged to genotype II. It shared 97.3% to 98.7% identities with genotype II NDVs, which was higher than these strains from the other genotypes.

Conclusions
These above data suggested that the swine virus was NDV and it might be generated from La Sota.
Progressive Retinal Atrophy in the Border Collie: A new XLPRA
Authors: Vilboux Thierry , Chaudieu Gilles , Jeannin Patricia , Delattre Delphine , Hedan Benoit , Bourgain Catherine , Queney Guillaume , Galibert Francis , Thomas Anne , André Catherine 
Published: July 2012

AbstractBackgroundSeveral forms of progressive retinal atrophy (PRA) segregate in more than 100 breeds of dog with each PRA segregating in one or a few breeds. This breed specificity may be accounted for by founder effects and genetic drift, which have reduced the genetic heterogeneity of each breed, thereby facilitating the identification of causal mutations. We report here a new form of PRA segregating in the Border Collie breed. The clinical signs, including the loss of night vision and a progressive loss of day vision, resulting in complete blindness, occur at the age of three to four years and may be detected earlier through systematic ocular fundus examination and electroretinography (ERG).ResultsOphthalmic examinations performed on 487 dogs showed that affected dogs present a classical form of PRA. Of those, 274 have been sampled for DNA extraction and 87 could be connected through a large pedigree. Segregation analysis suggested an X-linked mode of transmission; therefore both XLPRA1 and XLPRA2 mutations were excluded through the genetic tests.ConclusionHaving excluded these mutations, we suggest that this PRA segregating in Border Collie is a new XLPRA (XLPRA3) and propose it as a potential model for the homologous human disease, X-Linked Retinitis Pigmentosa.
GTfold: Enabling parallel RNA secondary structure prediction on multi-core desktops
Authors: Swenson M Shel , Anderson Joshua , Ash Andrew , Gaurav Prashant , Sükösd Zsuzsanna , Bader David A , Harvey Stephen C , Heitsch Christine E 
Published: July 2012

Abstract

Background
Accurate and efficient RNA secondary structure prediction remains an important open problem in computational molecular biology. Historically, advances in computing technology have enabled faster and more accurate RNA secondary structure predictions. Previous parallelized prediction programs achieved significant improvements in runtime, but their implementations were not portable from niche high-performance computers or easily accessible to most RNA researchers. With the increasing prevalence of multi-core desktop machines, a new parallel prediction program is needed to take full advantage of today’s computing technology.

Findings
We present here the first implementation of RNA secondary structure prediction by thermodynamic optimization for modern multi-core computers. We show that GTfold predicts secondary structure in less time than UNAfold and RNAfold, without sacrificing accuracy, on machines with four or more cores.

Conclusions
GTfold supports advances in RNA structural biology by reducing the timescales for secondary structure prediction. The difference will be particularly valuable to researchers working with lengthy RNA sequences, such as RNA viral genomes.
Physical therapies for Achilles tendinopathy: systematic review and meta‐analysis
Authors: Sussmilch‐Leitch Samuel P , Collins Natalie J , Bialocerkowski Andrea E , Warden Stuart J , Crossley Kay M 
Published: July 2012

AbstractBackgroundAchilles tendinopathy (AT) is a common condition, causing considerable morbidity in athletes and non‐athletes alike. Conservative or physical therapies are accepted as first‐line management of AT; however, despite a growing volume of research, there remains a lack of high quality studies evaluating their efficacy. Previous systematic reviews provide preliminary evidence for non‐surgical interventions for AT, but lack key quality components as outlined in the Preferred Reporting Items for Systematic Reviews and Meta‐analyses (PRISMA) Statement. The aim of this study was to conduct a systematic review and meta‐analysis (where possible) of the evidence for physical therapies for AT management.MethodsA comprehensive strategy was used to search 11 electronic databases from inception to September 2011. Search terms included Achilles, tendinopathy, pain, physical therapies, electrotherapy and exercise (English language full‐text publications, human studies). Reference lists of eligible papers were hand‐searched. Randomised controlled trials (RCTs) were included if they evaluated at least one non‐pharmacological, non‐surgical intervention for AT using at least one outcome of pain and/or function. Two independent reviewers screened 2852 search results, identifying 23 suitable studies, and assessed methodological quality and risk of bias using a modified PEDro scale. Effect size calculation and meta‐analyses were based on fixed and random effects models respectively.ResultsMethodological quality ranged from 2 to 12 (/14). Four studies were excluded due to high risk of bias, leaving 19 studies, the majority of which evaluated midportion AT. Effect sizes from individual RCTs support the use of eccentric exercise. Meta‐analyses identified significant effects favouring the addition of laser therapy to eccentric exercise at 12 weeks (pain VAS: standardised mean difference −0.59, 95% confidence interval −1.11 to −0.07), as well as no differences in effect between eccentric exercise and shock wave therapy at 16 weeks (VISA‐A:–0.55,–2.21 to 1.11). Pooled data did not support the addition of night splints to eccentric exercise at 12 weeks (VISA‐A:–0.35,–1.44 to 0.74). Limited evidence from an individual RCT suggests microcurrent therapy to be an effective intervention.ConclusionsPractitioners can consider eccentric exercise as an initial intervention for AT, with the addition of laser therapy as appropriate. Shock wave therapy may represent an effective alternative. High‐quality RCTs following CONSORT guidelines are required to further evaluate the efficacy of physical therapies and determine optimal clinical pathways for AT.
Flexible knowledge repertoires: communication by leaders in trauma teams
Authors: Jacobsson Maritha , Hargestam Maria , Hultin Magnus , Brulin Christine 
Published: July 2012

AbstractBackgroundIn emergency situations, it is important for the trauma team to efficiently communicate their observations and assessments. One common communication strategy is “closed-loop communication”, which can be described as a transmission model in which feedback is of great importance. The role of the leader is to create a shared goal in order to achieve consensus in the work for the safety of the patient. The purpose of this study was to analyze how formal leaders communicate knowledge, create consensus, and position themselves in relation to others in the team.MethodsSixteen trauma teams were audio- and video-recorded during high fidelity training in an emergency department. Each team consisted of six members: one surgeon or emergency physician (the designated team leader), one anaesthesiologist, one nurse anaesthetist, one enrolled nurse from the theatre ward, one registered nurse and one enrolled nurse from the emergency department (ED). The communication was transcribed and analyzed, inspired by discourse psychology and Strauss’ concept of “negotiated order”. The data were organized and coded in NVivo 9.ResultsThe findings suggest that leaders use coercive, educational, discussing and negotiating strategies to work things through. The leaders in this study used different repertoires to convey their knowledge to the team, in order to create a common goal of the priorities of the work. Changes in repertoires were dependent on the urgency of the situation and the interaction between team members. When using these repertoires, the leaders positioned themselves in different ways, either on an authoritarian or a more egalitarian level.ConclusionThis study indicates that communication in trauma teams is complex and consists of more than just transferring messages quickly. It also concerns what the leaders express, and even more importantly, how they speak to and involve other team members.
Predictors for diabetic retinopathy in normoalbuminuric people with type 2 diabetes mellitus
Authors: Ra Ho , Yoo Ji Han , Ban Woo Ho , Song Ho Cheol , Lee Seong Su , Kim Sung Rae , Yoo Soon Jib , Kim Yong-Soo , Choi Euy Jin , Kim Yong Kyun 
Published: July 2012

Abstract

Background
Previous studies have reported that microalbuminuria is an independent risk factor for the prevalence of diabetic retinopathy (DR) in patients with type 2 diabetes mellitus (DM). For this reason, the clinical significance of DR in normoalbuminuric type 2 DM patients may be overlooked. The aim of this study was to investigate the prevalence of DR and predictors for DR in normoalbuminuric patients with type 2 DM.

Methods
A total 310 patients with type 2 DM and normoalbuminuria, who were referred to the Department of Ophthalmology for screening of DR were included in this study. DR was clinically graded according to the International Clinical Diabetic Retinopathy guidelines. The urinary albumin excretion rate (UAER) was assessed via 24-hour urine collection and measured by immunoturbidimetric assay. Normoalbuminuria was defined as a UAER < 20 μg/min in 2 out of 3 consecutive tests taken within 2–3 months.

Results
DR of any grade was present in 64/310 (20.7 %) patients. Mild non-proliferative diabetic retinopathy (NPDR) was most prevalent in patients with DR of any grade (36/64, 56 %). The duration of diabetes (OR 1.01, 95 % CI, 1.01 – 1.02, p < 0.001), hemoglobin levels (OR 0.73, 95 % CI, 0.59 – 0.91, p = 0.004) and a higher tertile of UAER (OR 4.04, 95 % CI, 1.71 – 9.57, p = 0.001) had independently significant association with DR. NPDR as well as PDR was more prevalent in patients with higher tertile of UAER compared with those with lower tertile of UAER (NPDR, p = 0.002 and PDR, p = 0.027, respectively).

Conclusions
Our findings suggest that patients with normoalbuminuric type 2 DM also require close monitoring for the early detection of DR, especially if they have a higher UAER, longer duration of diabetes, or lower hemoglobin levels.
LINE-1 methylation in visceral adipose tissue of severely obese individuals is associated with metabolic syndrome status and related phenotypes
Authors: Turcot Valérie , Tchernof André , Deshaies Yves , Pérusse Louis , Bélisle Alexandre , Marceau Simon , Biron Simon , Lescelleur Odette , Biertho Laurent , Vohl Marie-Claude 
Published: July 2012

AbstractBackgroundEpigenetic mechanisms may be involved in the regulation of genes found to be differentially expressed in the visceral adipose tissue (VAT) of severely obese subjects with (MetS+) versus without (MetS-) metabolic syndrome (MetS). Long interspersed nuclear element 1 (LINE-1) elements DNA methylation levels (%meth) in blood, a marker of global DNA methylation, have recently been associated with fasting glucose, blood lipids, heart diseases and stroke.AimTo test whetherLINE-1%meth levels in VAT are associated with MetS phenotypes and whether they can predict MetS risk in severely obese individuals.MethodsDNA was extracted from VAT of 34 men (MetS-:n = 14, MetS+:n = 20) and 152 premenopausal women (MetS-:n = 84; MetS+:n = 68) undergoing biliopancreatic diversion for the treatment of obesity.LINE-1%meth levels were assessed by pyrosequencing of sodium bisulfite-treated DNA.ResultsThe meanLINE-1%meth in VAT was of 75.8% (SD = 3.0%). Multiple linear regression analyses revealed thatLINE-1%meth was negatively associated with fasting glucose levels (β = -0.04;P = 0.03), diastolic blood pressure (β =  -0.65;P = 0.03) and MetS status (β = -0.04;P = 0.004) after adjustments for the effects of age, sex, waist circumference (except for MetS status) and smoking. While dividing subjects into quartiles based on theirLINE-1%meth (Q1 to Q4: lower %meth to higher %meth levels), greater risk were observed in the first (Q1: odds ratio (OR) = 4.37,P = 0.004) and the second (Q2: OR = 4.76,P = 0.002) quartiles compared to Q4 (1.00) when adjusting for age, sex and smoking.ConclusionsThese results suggest that lower global DNA methylation, assessed byLINE-1repetitive elements methylation analysis, would be associated with a greater risk for MetS in the presence of obesity.
The potential of rice to offer solutions for malnutrition and chronic diseases
Authors: Dipti Sharifa Sultana , Bergman Christine , Indrasari Siti Dewi , Herath Theja , Hall Robert , Lee Hueihong , Habibi Fatemeh , Bassinello Priscila Zaczuk , Graterol Eduardo , Ferraz Julie P , Fitzgerald Melissa 
Published: July 2012

AbstractIt is internationally accepted that malnutrition and chronic diseases in developing countries are key limitations to achieving the Millennium Development Goals. In many developing countries, rice is the primary source of nutrition. In those countries, the major forms of malnutrition are Fe-induced anaemia, Zn deficiency and Vitamin A deficiency, whereas the major chronic disease challenges are Type II diabetes, cardiovascular disease and some cancers. There is a growing corpus of evidence regarding both limitations and opportunities as to how rice could be an effective vehicle by which to tackle key nutrition and health related problems in countries with limited resources. Rice breeding programs are able to focus on developing new varieties carrying enhanced amounts of either Fe, Zn or beta-carotene because of large public investment, and the intuitive link between providing a mineral/vitamin to cure a deficiency in that mineral/vitamin. By contrast, there has been little investment in progressing the development of particular varieties for potential impact on chronic diseases. In this review article we focus on the broad battery of evidence linking rice-related nutritional limitations to their impact on a variety of human health issues. We discuss how rice might offer sometimes even simple solutions to rectifying key problems through targeted biofortification strategies and finally, we draw attention to how recent technological (−omics) developments may facilitate untold new opportunities for more rapidly generating improved rice varieties specifically designed to meet the current and future nutritional needs of a rapidly expanding global population.
The sonographic digital portfolio: a longitudinal ultrasound image tracking program
Authors: Hughes Daralee R , Kube Erika , Gable Brad D , Madore Francis E , Bahner David P 
Published: July 2012

Abstract

Background
Ultrasonography (US) at the medical student level is developing. As clinical skills and simulation centers expand, US equipment miniaturizes, and more students are exposed to ultrasound; a digital portfolio comprised of US images and videos may be useful in demonstrating experience and possibly competency.

Methods
Medical students participated in US curricula consisting of didactics and hands-on training. From 1 July 2006 to 30 June 2008, student images and videos were saved. Total images and videos were evaluated and catalogued.

Results
A total of 10,074 images and 1,227 videos were saved during the 2-year period. For the academic year 2006 to 2007, 159 medical students obtained 3,641 of the images (84.9%) and 270 of the videos (86.0%). First year students obtained 778 images and 20 videos; second year students, 1,174 images and 64 videos; third year students, 211 images and 20 videos; and fourth year students, 1,478 images and 166 videos.
For the academic year 2007 to 2008, 222 medical students obtained 4,340 images (75%) and 619 videos (67.8%). First year students obtained 624 images and 109 videos; second year students, 555 images and 81 videos; third year students, 132 images and 14 videos; and fourth year students, 3,029 images and 415 videos.

Conclusions
The ultrasound digital portfolio allows medical students to collate and document their ultrasound experience. Currently, there is no requirement for ultrasound training, documentation of competency, or minimum numbers of US exams for medical education. The ultrasound digital portfolio may be a useful tool in documenting ultrasound proficiency.
Plectus - a stepping stone in embryonic cell lineage evolution of nematodes
Authors: Schulze Jens , Houthoofd Wouter , Uenk Jana , Vangestel Sandra , Schierenberg Einhard 
Published: July 2012

AbstractBackgroundRecent studies have challenged the widespread view that the pattern of embryogenesis found inCaenorhabditis elegans(clade 9) is characteristic of nematodes in general. To understand this still largely unexplored landscape of developmental events, we set out to examine more distantly related nematodes in detail for temporospatial differences in pattern formation and cell specification. Members of the genusPlectus(clade 6) seem to be suitable candidates to show variety, with certain idiosyncratic features during early development and the convenient availability of cultivatable species.MethodsThe study was conducted using 4-D lineage analysis, 3-D modeling of developing embryos and laser-induced ablation of individual blastomeres.ResultsDetailed cell lineage studies of severalPlectusspecies reveal that pattern formation and cell fate assignment differ markedly fromC. elegans. Descendants of the first somatic founder cell S1 (AB) - but not the progeny of other founder cells - demonstrate extremely variable spatial arrangements illustrating that here distinct early cell-cell interactions between invariant partners, as found inC. elegans, cannot take place. Different fromC. elegans, inPlectusalternative positional variations among early S1 blastomeres resulting in a ‘situs inversus’ pattern, nevertheless give rise to adults with normal left-right asymmetries. In addition, laser ablations of early blastomeres uncover inductions between variable cell partners.ConclusionsOur results suggest that embryonic cell specification inPlectusis not correlated with cell lineage but with position. With this peculiarity,Plectusappears to occupy an intermediate position between basal nematodes displaying a variable early development and theC. elegans-like invariant pattern. We suggest that indeterminate pattern formation associated with late, position-dependent fate assignment represents a plesiomorphic character among nematodes predominant in certain basal clades but lost in derived clades. Thus, the behavior of S1 cells inPlectuscan be considered an evolutionary relict in a transition phase between two different developmental strategies.
Contribution of the ethics committee of the French Intensive Care Society to describing a scenario for implementing organ donation after Maastricht type III cardiocirculatory death in France
Authors: Graftieaux Jean-Pierre , Bollaert Pierre-Edouard , Haddad Lise , Kentish-Barnes Nancy , Nitenberg Gérard , Robert René , Villers Daniel , Dreyfuss Didier 
Published: July 2012

Abstract
French law allows organ donation after death due to cardiocirculatory arrest. In the Maastricht classification, type III non-heart-beating donors are those who experience cardiocirculatory arrest after the withdrawal of life-sustaining treatments. French authorities in charge of regulating organ donation (Agence de la Biomédecine, ABM) are considering organ collection from Maastricht type III donors. We describe a scenario for Maastricht type III organ donation that fully complies with the ethical norms governing care to dying patients. That organ donation may occur after death should have no impact on the care given to the patient and family. The dead-donor rule must be followed scrupulously: the organ retrieval procedure must neither cause nor hasten death. The decision to withdraw life-sustaining treatments, withdrawal modalities, and care provided to the patient and family must adhere strictly to the requirements set forth in patient-rights legislation (the 2005 Léonetti law in France) and should not be influenced in any way by the possibility of organ donation. A major ethical issue regarding the family is how best to transition from discussing treatment-withdrawal decisions to discussing possible organ retrieval for donation should the patient die rapidly after treatment withdrawal. Close cooperation between the healthcare team and the organ retrieval team is crucial to minimize the distress of family members during this transition. Modalities for implementing Maastricht type III organ donation are discussed here, including the best location for withdrawing life-sustaining treatments (operating room or intensive care unit).
Pancreatic stone protein as an early biomarker predicting mortality in a prospective cohort of patients with sepsis requiring ICU management
Authors: Que Yok-Ai , Delodder Frederik , Guessous Idris , Graf Rolf , Bain Martha , Calandra Thierry , Liaudet Lucas , Eggimann Philippe 
Published: July 2012

Abstract
Introduction
Biomarkers, such as C-reactive protein [CRP] and procalcitonin [PCT], are insufficiently sensitive or specific to stratify patients with sepsis. We investigate the prognostic value of pancreatic stone protein/regenerating protein (PSP/reg) concentration in patients with severe infections.

Methods
PSP/reg, CRP, PCT, tumor necrosis factor-alpha (TNF-α), interleukin 1 beta (IL1-β), IL-6 and IL-8 were prospectively measured in cohort of patients ≥ 18 years of age with severe sepsis or septic shock within 24 hours of admission in a medico-surgical intensive care unit (ICU) of a community and referral university hospital, and the ability to predict in-hospital mortality was determined.

Results
We evaluated 107 patients, 33 with severe sepsis and 74 with septic shock, with in-hospital mortality rates of 6% (2/33) and 25% (17/74), respectively. Plasma concentrations of PSP/reg (343.5 vs. 73.5 ng/ml, P < 0.001), PCT (39.3 vs. 12.0 ng/ml, P < 0.001), IL-8 (682 vs. 184 ng/ml, P < 0.001) and IL-6 (1955 vs. 544 pg/ml, P < 0.01) were significantly higher in patients with septic shock than with severe sepsis. Of note, median PSP/reg was 13.0 ng/ml (IQR: 4.8) in 20 severely burned patients without infection. The area under the ROC curve for PSP/reg (0.65 [95% CI: 0.51 to 0.80]) was higher than for CRP (0.44 [0.29 to 0.60]), PCT 0.46 [0.29 to 0.61]), IL-8 (0.61 [0.43 to 0.77]) or IL-6 (0.59 [0.44 to 0.75]) in predicting in-hospital mortality. In patients with septic shock, PSP/reg was the only biomarker associated with in-hospital mortality (P = 0.049). Risk of mortality increased continuously for each ascending quartile of PSP/reg.

Conclusions
Measurement of PSP/reg concentration within 24 hours of ICU admission may predict in-hospital mortality in patients with septic shock, identifying patients who may benefit most from tailored ICU management.