bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ancestral duplications and highly dynamic opsin gene evolution in percomorph fishes
Authors: Cortesi Fabio , Musilová Zuzana , Stieb Sara M. , Hart Nathan S. , Siebeck Ulrike E. , Malmstrøm Martin , Tørresen Ole K. , Jentoft Sissel , Cheney Karen L. , Marshall N. Justin , Carleton Karen L. , Salzburger Walter 
Published: December 2014

Significance
Gene and whole-genome duplications are important evolutionary forces promoting organismal diversification. Teleost fishes, for example, possess many gene duplicates responsible for photoreception (opsins), which emerged through gene duplication and allow fishes to adapt to the various light conditions of the aquatic environment. Here, we reevaluate the evolutionary history of the violet-blue–sensitive opsins [short wavelength-sensitive 2 (SWS2)] in modern teleosts using next generation genome sequencing. We uncover a gene duplication event specific to the most diverse lineage of vertebrates (the percomorphs) and show that SWS2 evolution was highly dynamic and involved gene loss, pseudogenization, and gene conversion. We, thus, clarify previous discrepancies regarding opsin annotations. Our study highlights the importance of integrative approaches to help us understand how species adapt and diversify.
Bacterial growth laws reflect the evolutionary importance of energy efficiency
Authors: Maitra Arijit , Dill Ken A. 
Published: December 2014

Significance
Bacterial cells are remarkable machines. When food is present, bacteria shift gears into a fast-growth mode, whereby they duplicate all their proteins quickly. Cells do this by producing proportionately more ribosomes relative to other proteins. Ribosomes are the 55-protein complexes that a cell makes to synthesize all the cells proteins. Here, we develop a mathematical model of the mechanism of the cell’s gear-shifting and energy utilization under different growth conditions. A major conclusion from this modeling is that we can understand an evolutionary choice made by bacteria. We find that fast growing cells operate close to their optimal energy efficiency, which is a balance between the rates of translation and turnover of proteins and ribosomal assembly.
Detection of Norovirus and Sapovirus from diarrheic dogs and cats in Japan
Authors: Soma Takehisa , Nakagomi Osamu , Nakagomi Toyoko , Mochizuki Masami 
Published: December 2014

ABSTRACTNorovirus (NoV) and sapovirus (SaV) are important causes of human diarrhea. In this study, between 2007 and 2014 fecal samples were collected from 97 dogs and 83 cats with diarrhea and examined to determine the prevalence of NoV and SaV infections in Japan. To detect caliciviruses, approximately 300 bases targeting the polymerase gene were amplified using RT‐PCR and subjected to phylogenetic and homology analyses. Specific PCR products were obtained from four canine and nine feline samples: two canine and one feline isolate were classified as NoV, two canine isolates as SaV and the remaining eight feline isolates as vesivirus (VeV). The three NoV isolates were classified into the same clade as that of known canine and feline NoVs; their homologies (75.9–92.3%) were higher than those with human genogroup IV (GIV) NoVs (59.1–65.9%). The homology of the feline NoV isolate with previously reported feline NoV isolates was particularly high (91.7–92.3%). Regarding SaV, the two canine isolates were classified into the same clade as known canine SaVs and their homologies (72.5–86.5%) were higher than those with other mammal SaVs (20.7–58.0%). The eight feline VeV isolates were assumed to be feline calicivirus. The present study is the first report of the presence of NoV‐ and SaV‐infected dogs and cats in Japan. The findings suggest there are species‐specific circulations of NoV and SaV among dogs and cats, in Japan.
Global women's health: current clinical trials in low‐ and middle‐income countries
Authors: Merriel A , Harb HM , Williams H , Lilford R , Coomarasamy A 
Published: December 2014

BackgroundClinical trials in low‐ and middle‐income countries (LMICs) are necessary to develop evidence‐based approaches to improve women's health. Understanding what research is currently being conducted will allow the identification of research gaps, avoidance of duplication, planning of future studies, collaboration amongst research groups, and geographical targeting for research investments.ObjectivesTo provide an overview of active women's health trials in LMICs.Search strategyThe World Health Organization's International Clinical Trials Registry Platform was searched for trials registered between 1 April 2012 and 31 March 2014.Selection criteriaSelected trials were randomised, conducted in LMICs, active, and with a women's health intervention or a significant outcome for the woman.Data collection and analysisTwo reviewers extracted data. Analysis included geographical spread, speciality areas, pre‐enrolment registration, study size, and funders.Main resultsOf the 8966 records, 509 were eligible for inclusion. Gynaecology trials made up 57% of the research, whereas the remaining 43% of trials were in obstetrics. Research activity focused on fertility (17%), the antenatal period (15%), benign gynaecology (14%), intrapartum care (9%), and pre‐invasive disease and cancers (8%). The majority of trials (84%) took place in middle‐income countries (MICs). In low‐income countries (LICs) 83% of research investigated obstetrics, and in MICs 60% of research investigated gynaecology. Most trials (80%) had a sample size of 500 or fewer participants. The median size of trials in LICs was 815 compared with 128 in MICs. Pre‐enrolment registration occurred in 54% of trials. The majority (62%) of trials were funded locally.Authors' conclusionsMany LMICs are active in women's health research. The majority of registered trials are located in MICs; however, the trials in LICs are often larger. The focus of research in MICs may be driven by local priorities and funding, with fertility being highly researched. In LICs, pregnancy is the focus, perhaps reflecting the international prioritisation of maternal health.
Shock index: an effective predictor of outcome in postpartum haemorrhage?
Authors: Nathan HL , El Ayadi A , Hezelgrave NL , Seed P , Butrick E , Miller S , Briley A , Bewley S , Shennan AH 
Published: December 2014

ObjectivesTo compare the predictive value of the shock index (SI) with conventional vital signs in postpartum haemorrhage (PPH), and to establish ‘alert’ thresholds for use in low‐resource settings.DesignRetrospective cohort study.SettingUK tertiary centre.PopulationWomen with PPH ≥1500 ml (n = 233).MethodsSystolic blood pressure (BP), diastolic BP, mean arterial pressure, pulse pressure, heart rate (HR) and SI (HR/systolic BP) were measured within the first hour following PPH. Values measured at the time of highest SI were selected for analysis. The area under the receiver operating characteristic curve (AUROC) for each parameter, used to predict admission to an intensive care unit and other adverse outcomes, was calculated. Sensitivity, specificity and negative/positive predictive values determined thresholds of the best predictor.Main outcome measuresIntensive care unit (ICU) admission, blood transfusion ≥4 iu, haemoglobin level <7 g/dl, and invasive surgical procedures.ResultsShock index has the highest AUROC to predict ICU admissions (0.75 for SI [95% CI 0.63–0.87] compared with 0.64 [95% CI 0.44–0.83] for systolic BP). SI compared favourably for other outcomes: SI ≥0.9 had 100% sensitivity (95% CI 73.5–100) and 43.4% specificity (95% CI 36.8–50.3), and SI ≥1.7 had 25.0% sensitivity (95% CI 5.5–57.2) and 97.7% specificity (CI 94.8–99.3), for predicting ICU admission.ConclusionsShock index compared favourably with conventional vital signs in predicting ICU admission and other outcomes in PPH, even after adjusting for confounding; SI <0.9 provides reassurance, whereas SI ≥1.7 indicates a need for urgent attention. In low‐resource settings this simple parameter could improve outcomes. It was not possible to adjust for resuscitative measures administered following vital sign measurement that may have influenced the outcome.
The global met need for emergency obstetric care: a systematic review
Authors: Holmer H , Oyerinde K , Meara JG , Gillies R , Liljestrand J , Hagander L 
Published: December 2014

BackgroundOf the 287 000 maternal deaths every year, 99% happen in low‐ and middle‐income countries. The vast majority could be averted with timely access to appropriate emergency obstetric care (EmOC). The proportion of women with complications of pregnancy or childbirth who actually receive treatment is reported as ‘Met need for EmOC’.ObjectiveTo estimate the global met need for EmOC and to examine the correlation between met need, maternal mortality ratio and other indicators.Search strategyA systematic review was performed according to the PRISMA guidelines. Searches were made in PubMed, EMBASE and Google Scholar.Selection criteriaStudies containing data on met need in EmOC were selected.Data collection and analysisAnalysis was performed with data extracted from 62 studies representing 51 countries. World Bank data were used for univariate and multiple linear regression.Main resultsGlobal met need for EmOC was 45% (IQR: 28–57%), with significant disparity between low‐ (21% [12–31%]), middle‐ (32% [15‐56%]), and high‐income countries (99% [99–99%]), (P = 0.041). This corresponds to 11.4 million (8.8–14.8) untreated complications yearly and 951 million (645–1174 million) women without access to EmOC. We found an inverse correlation between met need and maternal mortality ratio (r = −0.42, P < 0.001). Met need was significantly correlated with the proportion of births attended by skilled birth attendants (β = 0.53 [95% CI 0.41–0.65], P < 0.001).Authors’ conclusionsThe results suggest a considerable inadequacy in global met need for EmOC, with vast disparities between countries of different income levels. Met need is a powerful indicator of the response to maternal mortality and strategies to improve EmOC act in synergy with the expansion of skilled birth attendance.
Next‐generation sequencing workflow for assembly of nonmodel mitogenomes exemplified with North Pacific albatrosses (Phoebastria spp.)
Authors: Lounsberry Z. T. , Brown S. K. , Collins P. W. , Henry R. W. , Newsome S. D. , Sacks B. N. 
Published: December 2014

AbstractUse of complete mitochondrial genomes (mitogenomes) can greatly increase the resolution achievable in phylogeographic and historical demographic studies. Using next‐generation sequencing methods, it is now feasible to efficiently sequence mitogenomes of large numbers of individuals once a reference mitogenome is available. However, assembling the initial mitogenomes of nonmodel organisms can present challenges, for example, in birds, where mtDNA is often subject to gene rearrangements and duplications. We developed a workflow based on Illumina paired‐end, whole‐genome shotgun sequencing, which we used to generate complete 19‐kilobase mitogenomes for each of three species of North Pacific albatross, a group of birds known to carry a tandem duplication. Although this duplication had been described previously, our procedure did not depend on this prior knowledge, nor did it require a closely related reference mitogenome (e.g. a mammalian mitogenome was sufficient). We employed an iterative process including de novo assembly, reference‐guided assembly and gap closing, which enabled us to detect duplications, determine gene order and identify sequence for primer positioning to resolve any mitogenome ambiguity (via minimal targeted Sanger sequencing). We present full mtDNA annotations, including 22 tRNAs, 2 rRNAs, 13 protein‐coding genes, a control region and a duplicated feature for all three species. Pairwise comparisons supported previous hypotheses regarding the phylogenetic relationships within this group and occurrence of a shared tandem duplication. The resulting mitogenome sequences will enable rapid, high‐throughput NGS mitogenome sequencing of North Pacific albatrosses via direct reference‐guided assembly. Moreover, our approach to assembling mitogenomes should be applicable to any taxon.
Elevated frequencies of CD4+IL‐21+T, CD4+IL‐21R+T and IL‐21+Th17 cells, and increased levels of IL‐21 in bleomycin‐induced mice may be associated with dermal and pulmonary inflammation and fibrosis
Authors: Lei Ling , He Zhi‐Yi , Zhao Cheng , Sun Xue‐Jiao , Zhong Xiao‐Ning 
Published: December 2014

AbstractAimSystemic sclerosis (SSc) is characterized by immune abnormalities, progressive fibrosis of the skin and internal organs, and microvascular injury and damage. Interleukin‐21 receptor (IL‐21R) is expressed in the epidermis from patients with SSc. However, information describing the role of IL‐21 in SSc is limited.MethodsWe established a mouse model of bleomycin (BLM)‐induced fibrosis. The frequency of CD4+IL‐21+T, CD4+IL‐21R+T and IL‐21+Th17 cells in peripheral blood, skin and lungs of BLM‐induced mice were detected by flow cytometry; IL‐21 levels in the peripheral blood were evaluated by enzyme‐linked immunosorbent assay (ELISA). CD4+T cells were isolated from the spleen of BLM‐induced and control mice and cultured in vitro alone or in the presence of mrIL‐21 or mrIL‐21 plus transforming growth factor (TGF)‐β1. The frequency of Th17 cells was detected by flow cytometry; levels of IL‐17 were evaluated by ELISA, and the expression of IL‐17A and retinoic‐acid‐receptor‐related orphan receptors gamma t (RORγt) messenger RNA were analyzed by real‐time polymerase chain reaction.ResultsCompared to control mice, the frequency of CD4+IL‐21+T, CD4+21R+T and IL‐21+Th17 cells and the levels of IL‐21 were significantly increased in BLM‐induced mice. The frequency of CD4+IL‐21+T, CD4+21R+T and IL‐21+Th17 cells and the levels of IL‐21 were correlated with dermal and pulmonary inflammation and fibrosis. In vitro analyses indicate that IL‐21 promoted the differentiation of Th17 cells from CD4+ cells isolated from the spleen of BLM‐induced mice.ConclusionIL‐21 may play an important role in the pathogenesis of SSc as a Th17 effector cytokine, and IL‐21 may induce the differentiation of Th17 cells in the BLM‐induced SSc mouse model.
Treatment of low back pain: Second extended follow up of an original trial (NCT00600197) comparing a multidisciplinary group‐based rehabilitation program with oral drug treatment alone up to 30 months
Authors: Tavafian Sedigheh S. , Jamshidi Ahmad R. , Mohammad Kazem 
Published: December 2014

AbstractBackgroundThe aim of this study is to investigate the effects of the extended 30‐month follow‐up of an original trial (NCT00600197) which has been published in the Clinical Journal of Pain.MethodsSeventy‐four percent (146/197) of the participants who had taken part in the original study, including 69 patients in the intervention group and 77 patients in the control group, were followed up to 30 months after intervention. The intervention group continued receiving monthly motivational consultation and booster classes plus oral medication but the other group received just medication. Data on measures from the Short Form 36 (SF‐36), Quebec Disability Scale (QDS) and Ronald Morris Disability Questionnaire (RDQ) were collected at 3‐, 6‐, 12‐, 18‐, 24‐ and 30‐month follow‐ups and analyzed through repeated measures analysis of variance.ResultsThe two groups were comparable regarding all baseline characteristics (P > 0.05) except for education level and mental health, which were better in the intervention group (P < 0.05). The two groups improved regarding all studied variables over time up to 30 months (P < 0.001). Moreover, the intervention group in comparison with the control group had consistently better outcomes regarding all variables. There were significant differences within each group by time in terms of mental health (P = 0.01) and disability measured through QDS (P = 0.005) and RDQ (P = 0.014).ConclusionThe proposed multidisciplinary program could improve mental health and disability up to 30 months in chronic low back pain patients.
Reduced efficacy of transcatheter and surgical revascularization in Takayasu arteritis
Authors: Sammel Anthony M. , Wolfenden Hugh D. , Joshua Fredrick , Jepson Nigel 
Published: December 2014

AbstractA 55‐year‐old woman with newly diagnosed Takayasu arteritis was followed for 7 years, during which time she underwent bare metal stenting, drug eluting stenting and coronary bypass grafting for critical coronary and renal artery stenoses. Interventions were initially successful but restenosis occurred within 24 months for all modalities. In contrast, native vessel disease was largely stable after the introduction of immunosuppressive therapy. We advocate a conservative revascularization approach in Takayasu arteritis in the absence of critical end organ ischemia and early optimization of medical therapy.
Histological transformation from non‐small cell to small cell lung carcinoma after treatment with epidermal growth factor receptor‐tyrosine kinase inhibitor
Authors: Kim Woo‐Jin , Kim Sunmin , Choi Hayoung , Chang Jinsun , Shin Hong‐Joon , Park Cheol‐Kyu , Oh In‐Jae , Kim Kyu‐Sik , Kim Young‐Chul , Choi Yoo‐Duk 
Published: December 2014

AbstractSeveral cases of acquired resistance in patients with activating epidermal growth factor receptor (EGFR) mutation have been reported. However, rare clinical cases exist of a transformation to small cell lung cancer (SCLC) following treatment with EGFR‐tyrosine kinase inhibitors (TKIs). We report a case of non‐small cell lung cancer (NSCLC) with L858R mutation at the time of diagnosis. After failure of EGFR‐TKI therapy, we performed additional histopathologic examinations. We confirmed that the patient had a histological transformation from NSCLC to SCLC. We performed chemotherapy with etoposide and cisplatin against the SCLC and radiologic findings were improved.
Incidence of Positive Ventricular Late Potentials Differs in Postural Changes among Supine, Left, and Right Lateral Decubitus, and Prone and Sitting Positions in Brugada Syndrome
Authors: Yoshioka Koichiro , Amino Mari , Nakamura Mari , Kanda Shigetaka , Kobayashi Yoshinori , Ikari Yuji , Shima Makiyoshi , Tanabe Teruhisa 
Published: December 2014

BackgroundHigh‐risk patients with Brugada syndrome (BrS) have inherent late potential (LP) fluctuations that might be explained by autonomic activity, electrolyte abnormality, and body temperature changes. However, the correlation between postural changes and LP determinates remains unknown.MethodsForty patients with BrS (38 men, 43.9 ± 13.5 years) and 15 controls (15 men, 42.4 ± 11.2 years) were enrolled. LP variations were investigated at five body positions using high‐resolution ambulatory monitoring electrocardiography (HR‐ambulatory ECG). The HR‐ambulatory ECG was recorded for 3 hours and LP parameters (fQRSd, LAS40, and RMS40) were obtained for at least 15 minutes in each at the supine, left and right lateral decubitus, and prone and sitting positions.ResultsDeterminate LP in the BrS group was significantly abnormal in all positions. Among the five body positions, positive LP were much more frequent in the supine and left and right lateral decubitus positions than in the prone and sitting positions and normalized in the last two positions in patients with BrS. RMS40 variance by postural change was significantly larger in the coved group than in the saddle back group. Determinate LP improved in the sitting position compared to the supine position in the coved group.ConclusionsPositive LP findings normalized in the sitting position in patients in the coved BrS group with a resuscitation history, suggesting that depolarization instability might be related to the risk of fatal ventricular arrhythmia. Posture‐induced LP variance should be examined using HR‐ambulatory ECG analysis in patients with BrS.
Individual maternal and child exposure to antibiotics in hospital – a national population‐based validation study
Authors: Almqvist C , Örtqvist AK , Gong T , Wallas A , Ahlén KM , Ye W , Lundholm C 
Published: December 2014

AbstractAimExposure to antibiotics in early life may affect future health. Most antibiotics are prescribed in outpatient care, but inpatient exposure is also important. We estimated how specific diagnoses in hospitals corresponded to individual antibiotic exposure.MethodsAll pregnant women and children from birth to 5 years of age with infectious diseases and common inpatient diagnoses between July 2005 and November 2011 were identified from the Swedish National Patient Register. Random samples of individuals from predefined groups were drawn, and medical records received from the clinics were manually reviewed for antibiotics.ResultsMedical records for 4319 hospital visits were requested and 3797 (88%) were received. A quarter (25%) of children diagnosed as premature had received antibiotics, and in children from one to 5 years of age, diagnoses associated with bacterial infections were more commonly treated with antibiotics (62.4–90.6%) than those associated with viruses (6.3–22.2%). Pregnant women who had undergone a Caesarean section were more likely to be treated with antibiotics than those who had had a vaginal delivery (40.1% versus 11.1%).ConclusionThis study defines the proportion of new mothers and young children who received individual antibiotic treatment for specific inpatient diagnoses in Sweden and provides a useful basis for future studies focusing on antibiotic use.
Self‐reflection, growth goals, and academic outcomes: A qualitative study
Authors: Travers Cheryl J. , Morisano Dominique , Locke Edwin A. 
Published: December 2014

BackgroundGoal‐setting theory continues to be among the most popular and influential theories of motivation and performance, although there have been limited academic applications relative to applications in other domains, such as organizational psychology.AimsThis paper summarizes existing quantitative research and then employs a qualitative approach to exploring academic growth via an in‐depth reflective growth goal‐setting methodology.SampleThe study focuses on 92 UK final‐year students enrolled in an elective advanced interpersonal skills and personal development module, with self‐reflection and growth goal setting at its core.MethodQualitative data in the form of regular reflective written diary entries and qualitative questionnaires were collected from students during, on completion of, and 6 months following the personal growth goal‐setting programme.ResultsAbout 20% of students' self‐set growth goals directly related to academic growth and performance; students reported that these had a strong impact on their achievement both during and following the reflective programme. Growth goals that were indirectly related to achievement (e.g., stress management) appeared to positively impact academic growth and other outcomes (e.g., well‐being). A follow‐up survey revealed that growth goal setting continued to impact academic growth factors (e.g., self‐efficacy, academic performance) beyond the reflective programme itself.ConclusionsAcademic growth can result from both academically direct and indirect growth goals, and growth goal setting appears to be aided by the process of simultaneous growth reflection. The implications for promoting academic growth via this unique learning and development approach are discussed.