bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distance to health services affects local-level vaccine efficacy for pneumococcal conjugate vaccine (PCV) among rural Filipino children
Authors: Root Elisabeth Dowling , Lucero Marilla , Nohynek Hanna , Anthamatten Peter , Thomas Deborah S. K. , Tallo Veronica , Tanskanen Antti , Quiambao Beatriz P. , Puumalainen Taneli , Lupisan Socorro P. , Ruutu Petri , Ladesma Erma , Williams Gail M. , Riley Ian , Simões Eric A. F. 
Published: February 2014

Significance
Although pneumococcal conjugate vaccines (PCVs) are widely available in industrialized nations, the cost of these vaccines and the strategy of universal vaccination of infants, as endorsed by the World Health Organization, are daunting obstacles to the adoption of these vaccines in developing countries. Using spatial epidemiological methods to examine the spatial variation in vaccine efficacy (VE) in an 11-valent PCV trial in Bohol, Philippines, we suggest an alternative strategy to universal vaccination. Our main finding suggests that areas with poor access to healthcare have the highest VE. An alternative vaccination strategy could target vaccination to areas where children are most likely to benefit, rather than focus on nationwide immunization.
Rapid upslope shifts in New Guinean birds illustrate strong distributional responses of tropical montane species to global warming
Authors: Freeman Benjamin G. , Class Freeman Alexandra M. 
Published: February 2014

Significance
Montane species may respond to global warming by shifting their distributions upslope in response to warming temperatures. Such shifts are well documented in the temperate zone, but the situation in the tropics, where species are predicted to be more sensitive to altered temperatures, remains unclear. We found strong upslope shifts in the bird species found on two independent New Guinean mountains originally surveyed in the 1960s. Moreover, we incorporated our results into a metaanalysis that suggests tropical montane species are responding more strongly to climate change than temperate-zone species. Though the magnitude of climate change is higher in the temperate zone, both overall biodiversity and distributional shifts due to warming temperatures are greater in the tropics.
Small-angle X-ray scattering-derived structure of the HIV-1 5′ UTR reveals 3D tRNA mimicry
Authors: Jones Christopher P. , Cantara William A. , Olson Erik D. , Musier-Forsyth Karin 
Published: February 2014

Significance
A highly conserved region of the HIV-1 RNA genome is responsible for regulating numerous steps of the retroviral life cycle, including initiation of reverse transcription. A complete understanding of the mechanisms controlling HIV-1 replication requires structural characterization of this RNA; unfortunately, however, its large size and conformational flexibility makes common methods of solving structures, such as X-ray crystallography and NMR, exceedingly difficult. The present study uses a solution technique, small-angle X-ray scattering coupled with computational molecular modeling, to characterize three ∼100-nucleotide RNAs that play central roles in HIV-1 replication. One of these domains mimics the L-shaped fold of tRNA, providing a structural basis for understanding how this genomic RNA coordinates interactions with a tRNA-binding host factor to facilitate initiation of reverse transcription.
Analysis of the tumor-initiating and metastatic capacity of PDX1-positive cells from the adult pancreas
Authors: Ischenko Irene , Petrenko Oleksi , Hayman Michael J. 
Published: February 2014

Significance
Pancreatic cancer is characterized by aggressive growth and a high propensity for metastatic spread. Despite growing understanding of the genetic causes of pancreatic cancer, the mechanism and timing of cancer metastasis, the main cause of deaths in pancreatic cancer patients, remain relatively unexplored. In this study, we used experimental mouse models of pancreatic carcinogenesis to show that hyperactivation of the Ras/MAPK/ERK pathway and stabilization of the MYC protein are the two main driving forces behind the development of pancreatic cancer cells with high metastatic potential. Our results suggest that pancreatic cells bearing Kras mutation can be induced to differentiate into quasi-normal cells with suppressed tumorigenicity by selective inhibition of the MAPK/ERK/MYC signaling cascade. These findings may have important therapeutic implications.
SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data integrating differential expression and splicing
Authors: Wang Xi , Cairns Murray J. 
Published: February 2014

Abstract
Summary: SeqGSEA is an open-source Bioconductor package for the functional integration of differential expression and splicing analysis in RNA-Seq data. SeqGSEA implements an analysis pipeline, which first computes differential splicing and differential expression scores, followed by integrating them into a per-gene score that quantifies each gene’s association with a phenotype of interest, and finally executes gene set enrichment analysis in a cutoff-free manner to achieve biological insights. SeqGSEA accounts for biological variability and determines the statistical significance of gene pathways and networks using subject permutation, and thus requires at least five samples per group. Real applications show that SeqGSEA detects more biologically meaningful gene sets without biases toward long or highly expressed genes. SeqGSEA can be set up to run in parallel to reduce the analysis time.
Availability and implementation: The SeqGSEA package with a vignette is available at http://bioconductor.org/packages/release/bioc/html/SeqGSEA.html.
Contact: Murray.Carins@newcastle.edu.au
Supplementary information: Supplementary data are available at Bioinformatics online.
First Report of Downy Mildew (Hyaloperonospora lunariae) on White Mustard (Sinapis alba) in Brazil
Authors: Colman A. , Macedo D. M. , Barreto R. W. 
Published: February 2014

Sinapis alba (Brassicaceae), white mustard, is broadly cultivated for its seed used as component of table mustard (4). In June 2013, a group of diseased S. alba were observed in a vegetable garden on the campus of the Universidade Federal de Viçosa (municipality of Viçosa, state of Minas Gerais, Brazil). Foliage of diseased plants showed numerous chlorotic areas that developed into severe leaf blight with abundant downy mildew growth abaxially. A dried representative specimen has been deposited in the herbarium at the Universidade Federal de Viçosa (accession no. VIC 39743). The fungus had the following morphology: Sporangiophores arborescent, dichotomously branched, 540 to 840 × 8 to 10 μm hyaline, smooth, branches 105 to 210 μm long; esterigmata subacutate and curved, in pairs, 15 to 42 μm long; sporangia globose, 18 to 24 × 15 to 18 μm, hyaline, smooth. DNA was extracted using a Wizard Promega purification kit. The cytochrome oxidase subunit II (COX2) region was amplified with COX2f and COX2r primers (3). The sequence has been deposited in GenBank (Accession No. KJ396953). DNA sequences representing morphologically similar taxa were downloaded from GenBank nucleotide database, aligned in MEGA 5, and analyzed using Bayesian inference and Markov chain Monte Carlo simulation implemented in MrBayes 3.0 with five repetitions. A sequence of Albugo candida was used as outgroup in the analysis. The morphological characteristics places the fungus on S. alba in the complex of species of Pernosporaceae that attack the Brassicaceae. These are notoriously difficult to discriminate by morphology but our COX2-based phylogenetic analysis places it in Hyaloperonospora lunariae (1). This species was previously only known to cause downy mildew on other species of Brassicaceae (Lunaria annua and Erucastrum nasturtiifolium) in Europe (2). To our knowledge, this is the first report of this pathogen-host association in the world. References: (1) O. Constantinescu and J. Fatehi. Nova Hediwigia 74:291, 2002 (2) D. F. Farr and A. Y. Rossman. Fungal Databases, Systematic Mycology and Microbiology Laboratory. Online publication. ARS, USDA, 2013. (3) D. S. S. Hudspeth et al. Mycologia 92:674, 2000. (4) B. B. Simpson and M. C. Ogorzaly. Econonic Botany. McGraw Hill, San Diego, CA, 2001.
Inpatient Falls after Total Knee Arthroplasty
Authors: Memtsoudis Stavros G. , Danninger Thomas , Rasul Rehana , Poeran Jashvant , Gerner Philipp , Stundner Ottokar , Mariano Edward R. , Mazumdar Madhu 
Published: February 2014

Abstract

Background:
Much controversy remains on the role of anesthesia technique and peripheral nerve blocks (PNBs) in inpatient falls (IFs) after orthopedic procedures. The aim of the study is to characterize cases of IFs, identify risk factors, and study the role of PNB and anesthesia technique in IF risk in total knee arthroplasty patients.

Methods:
The authors selected total knee arthroplasty patients from the national Premier Perspective database (Premier Inc., Charlotte, NC; 2006–2010; n = 191,570, >400 acute care hospitals). The primary outcome was IF. Patient- and healthcare system–related characteristics, anesthesia technique, and presence of PNB were determined for IF and non-IF patients. Independent risk factors for IFs were determined by using conventional and multilevel logistic regression.

Results:
Overall, IF incidence was 1.6% (n = 3,042). Distribution of anesthesia technique was 10.9% neuraxial, 12.9% combined neuraxial/general, and 76.2% general anesthesia. PNB was used in 12.1%. Patients suffering IFs were older (average age, 68.9 vs. 66.3 yr), had higher comorbidity burden (average Deyo index, 0.77 vs. 0.66), and had more major complications, including 30-day mortality (0.8 vs. 0.1%; all P < 0.001). Use of neuraxial anesthesia (IF incidence, 1.3%; n = 280) had lower adjusted odds of IF compared with adjusted odds of IF with the use of general anesthesia alone (IF incidence, 1.6%; n = 2,393): odds ratio, 0.70 (95% CI, 0.56–0.87). PNB was not significantly associated with IF (odds ratio, 0.85 [CI, 0.71–1.03]).

Conclusions:
This study identifies several risk factors for IF in total knee arthroplasty patients. Contrary to common concerns, no association was found between PNB and IF. Further studies should determine the role of anesthesia practices in the context of fall-prevention programs.
Predicting successful intended vaginal delivery after previous caesarean section: external validation of two predictive models in a Dutch nationwide registration‐based cohort with a high intended vaginal delivery rate
Authors: Schoorel ENC , Melman S , van Kuijk SMJ , Grobman WA , Kwee A , Mol BWJ , Nijhuis JG , Smits LJM , Aardenburg R , de Boer K , Delemarre FMC , van Dooren IM , Franssen MTM , Kleiverda G , Kaplan M , Kuppens SMI , Lim FTH , Sikkema JM , Smid‐Koopman E , Visser H , Vrouenraets FPJM , Woiski M , Hermens RPMG , Scheepers HCJ 
Published: February 2014

ObjectiveTo externally validate two models from the USA (entry‐to‐care [ETC] and close‐to‐delivery [CTD]) that predict successful intended vaginal birth after caesarean (VBAC) for the Dutch population.DesignA nationwide registration‐based cohort study.SettingSeventeen hospitals in the Netherlands.PopulationSeven hundred and sixty‐three pregnant women, each with one previous caesarean section and a viable singleton cephalic pregnancy without a contraindication for an intended VBAC.MethodsThe ETC model comprises the variables maternal age, prepregnancy body mass index (BMI), ethnicity, previous vaginal delivery, previous VBAC and previous nonprogressive labour. The CTD model replaces prepregnancy BMI with third‐trimester BMI and adds estimated gestational age at delivery, hypertensive disease of pregnancy, cervical examination and induction of labour. We included consecutive medical records of eligible women who delivered in 2010. For validation, individual probabilities of women who had an intended VBAC were calculated.Main outcome measuresDiscriminative performance was assessed with the area under the curve (AUC) of the receiver operating characteristic and predictive performance was assessed with calibration plots and the Hosmer–Lemeshow (H‐L) statistic.ResultsFive hundred and fifteen (67%) of the 763 women had an intended VBAC; 72% of these (371) had an actual VBAC. The AUCs of the ETC and CTD models were 68% (95% CI 63–72%) and 72% (95% CI 67–76%), respectively. The H‐L statistic showed a P‐value of 0.167 for the ETC model and P = 0.356 for the CTD model, indicating no lack of fit.ConclusionExternal validation of two predictive models developed in the USA revealed an adequate performance within the Dutch population.
Genetic variants and risk of cervical cancer: epidemiological evidence, meta‐analysis and research review
Authors: Zhang X , Zhang L , Tian C , Yang L , Wang Z 
Published: February 2014

BackgroundMore than 200 articles have been published in the past 20 years on associations between genetic variants and risk of cervical cancer but the results have generally been inconsistent.ObjectiveTo provide a synopsis of the current understanding of the genetic architecture of the risk of cervical cancer by conducting a systematic review and meta‐analysis.Search strategyWe conducted a systematic literature search by a two‐stage strategy using PubMed and other databases on or before 31 March 2012.Selection criteriaCross‐sectional, case–control or cohort studies about the relationship between genetic variants and cervical cancer were included.Data collection and analysisStudy outcomes were presented as odds ratios (ORs) with a 95% confidence interval.We did the meta‐analysis for genetic variants which had at least three data sources and for which the significant associations were assessed using the Venice criteria.Main resultsA total of 5605 publications were screened, of which 286 were eligible. Meta‐analysis was conducted for 58 variants in 25 genes or loci. Fourteen variants in 11 genes or loci could increase the risk of cervical cancer and five variants in three genes or loci could decrease the risk. The epidemiological evidence of the association was graded as strong for four variants in CTLA4 and HLA DQB1, moderate for five variants in IL‐1B, IL‐10, XRCC3 and HLA DQA1, and weak for 10 variants.ConclusionsMany genetic variants were associated with the risk of cervical cancer as supported by the epidemiological evidence in this meta‐analysis.
Rapid Localization of Bone Fragments on Surfaces using Back‐Projection and Hyperspectral Imaging
Authors: Alsberg Bjørn K. , Rosvold Jørgen 
Published: February 2014

AbstractManual localization of bone fragments on the ground or on complex surfaces in relation to accidents or criminal activity may be time‐consuming and challenging. It is here investigated whether combining a near‐infrared hyperspectral camera and chemometric modeling with false color back‐projection can be used for rapid localization of bone fragments. The approach is noninvasive and highlights the spatial distribution of various compounds/properties to facilitate manual inspection of surfaces. Discriminant partial least squares regression is used to classify between bone and nonbone spectra from the hyperspectral camera. A predictive model (>95% prediction ability) is constructed from raw chicken bones mixed with stone, sand, leaves, moss, and wood. The model uses features in the near‐infrared spectrum which may be selective for bones in general and is able to identify a wide variety of bones from different animals and contexts, including aged and weathered bone.
Politically Engaged Geographical Research with the Community Sector: Is It Encouraged by Australia's Higher Education and Research Institutions?
Authors: JACKSON SUE , CRABTREE LOUISE 
Published: February 2014

AbstractWith the application of neoliberal thinking to the higher education sector, measures of research quality and utility have proliferated in efforts to increase academic accountability, innovation, and contributions to public policy. We intend to reignite discussion about community activism and the role of the academic in response to trends in higher education policy and recent debate in Australia about research quality assessment and policy relevance. We challenge the common portrayal of the public sector as the sole locus of policy‐making and argue the case for greater recognition of the role of the community sector and its research partners in policy development and implementation – one that is not given due attention in the discourse on or in measures of research value and impact. Informed by recent literature on governance and interpretative approaches to policy analysis, we draw on our combined experience conducting research with two Australian movements at the forefront of reforms to property rights institutions, legal standards, and norms relating to social and economic equity to outline the institutional tensions and structural impediments facing researchers working with the non‐government sector. The paper documents the progressive roles the academic can play in such work, arguing that institutional change is required within the tertiary sector to support researchers to build closer, more trusting research partnerships in which due attention is given to social impact and relevance.
Effects of rosiglitazone (PPAR γ agonist) on the myocardium in non‐hypertensive diabetic rats 罗格列酮（PPAR γ 激动剂）对非高血压糖尿病大鼠的心肌的影响
Authors: Abou Daya Khodor , Abu Daya Hussein , Nasser Eddine Mohamad , Nahhas Georges , Nuwayri‐Salti Nuha 
Published: February 2014

AbstractBackgroundThere is ongoing controversy regarding the safety of rosiglitazone and its effects on the myocardium, in some cases causing severe cardiac pathology and even in some instances mortality. In this study we aimed at examining the effects of pharmacologic doses of rosiglitazone on cardiomyocytes in diabetic non‐cardiac rats receiving sub‐optimal doses of insulin.MethodsAnimals were distributed into six groups: normal, diabetic, and diabetic receiving insulin, each subdivided into a control group and an experimental group receiving pharmacologic doses of rosiglitazone. Cardiomyocyte hypertrophy was assessed using heart to body weight index and microscopic examination using the number of cardiomyocytes per quadrant of high power field and intercalated disks in a sector of 100 × field. Fibrosis was assessed using Masson Trichrome staining. A number of sections of each group were stained with periodic acid Shiff and others with Sudan III for glycogen and fat accumulation, respectively. One way ANOVA was used for statistical analysis as appropriate.ResultsDiffuse cardiomyopathic changes in diabetic control animals were observed consisting of cardiomyocyte hypertrophy, loss of striations and widespread vacuolation. These changes were reduced and even prevented by treatment with insulin and rosiglitazone. Masson staining showed that all rat groups had no more than +1 fibrosis that is equal to what was present in the normal controls.ConclusionRosiglitazone, in combination with even sub‐optimal doses of insulin therapy, has protective effects on cardiac muscle in diabetic animals especially those expressed as muscle hypertrophy, muscle cell death, and fibrosis.
Relationships among male Coleophora deauratella (Lepidoptera: Coleophoridae) pheromone‐baited trap capture, larval abundance, damage and flight phenology
Authors: Mori Boyd A. , Yoder Calvin , Otani Jennifer , Evenden Maya L. 
Published: February 2014

Abstract

The red clover casebearer Coleophora deauratella Leinig and Zeller is an invasive pest of red clover (Trifolium pratense L.) grown for seed production in Canada. Drastic yield losses (80–99.5%) have been reported in several growing regions over the last 30 years as a result of larval feeding damage.
Field trials conducted in red clover seed production fields in Alberta, Canada, during the summers of 2010–2012 tested the efficacy of pheromone‐baited traps to predict population density and assess male flight phenology of C. deauratella.
Male moth pheromone‐trap capture was positively related to larval abundance and proportion seed damage at both moderate and high population densities.
Phenological models based on degree days (DD11.7) were better at describing median (50%) male flight compared with ordinal date models. Median C. deauratella male flight occurs at 258.39 DD11.7, starting from 1 January each year in the Peace River region of Alberta.
The results obtained in the present study demonstrate that pheromone‐baited traps can be used to detect the spread of this invasive species. Future work could incorporate pheromone‐based monitoring into assessment for the need and timing of control measures to target this invasive pest.
HIV, vascular surgery and cardiovascular outcomes: a South African cohort study
Authors: Redman L. A. , Naidoo P. , Biccard B. M. 
Published: February 2014

SummaryRisk factors for peri‐operative cardiac morbidity are poorly described in HIV‐positive patients. This prospective observational study describes cardiovascular risk factors in a cohort of vascular surgical patients of known HIV status. We recruited 225 patients with 73 (32%) being HIV‐positive. When compared with HIV‐negative patients, the HIV‐positive patients were younger (mean (SD) 56.4 (13.3) vs 40.5 (10.4) years, respectively, p < 0.01). They had fewer Revised Cardiac Risk Index cardiovascular risk factors (median (range [IQR]) 1 (0–5 [0–2]) vs 0 (0–2 [0–0]), respectively, p < 0.001), with the exception of congestive cardiac failure (p = 0.23) and renal dysfunction (p = 0.32), and so were of a significantly lower Revised Cardiac Risk Index risk category (p < 0.01). HIV‐positive and ‐negative patients had similar outcomes in: 30‐day mortality (p = 0.78); three‐day postoperative troponin leak (p = 0.66); and a composite outcome of mortality and troponin release (p = 0.69). We conclude that although HIV‐positive patients have fewer cardiovascular risk factors, they have similar peri‐operative major adverse cardiac events to HIV‐negative patients. Research should focus on why this is the case, and if alternative clinical risk predictors can be developed for HIV patients.
The pharmacokinetics and pharmacodynamics of denosumab in patients with advanced solid tumours and bone metastases: a systematic review
Authors: Sohn Winnie , Simiens Mary Ann , Jaeger Kelly , Hutton Shauna , Jang Graham 
Published: February 2014

AimThe objective of this systematic review was to characterize the pharmacokinetics and pharmacodynamics of denosumab (XGEVA®), a fully human IgG2 monoclonal antibody which binds to receptor activator of nuclear factor kappa‐B ligand (RANKL), for the treatment of skeletal‐related events (SREs) in patients with advanced cancer and bone metastases.MethodsA total of 708 patients (116 healthy patients and 592 patients with solid tumours or multiple myeloma and bone metastases) included in seven clinical studies were evaluated for denosumab pharmacokinetics. Denosumab was administered as a single subcutaneous (s.c.) dose or multiple s.c. doses, ranging from 0.1 to 3.0 mg kg−1 or 30 mg to 180 mg fixed dosing, every 1 or 3 months for up to 45 months.ResultsConsistent with the results in healthy adults, single s.c. doses of denosumab demonstrated dose‐dependent, non‐linear pharmacokinetics in advanced cancer patients with bone metastases across a wide dose range (0.1–3.0 mg kg−1). Reductions in levels of the bone turnover marker, uNTx/Cr, were observed within 1 day. The duration of reductions generally increased with dose and dosing frequency. In patients with solid tumours and bone metastases, pharmacokinetics and pharmacodynamic comparisons across tumour types and concomitant cancer therapies (chemotherapies and/or hormone therapies) suggest that neither tumour type nor type of concomitant therapy markedly affects denosumab pharmacokinetics or pharmacodynamics.ConclusionsDenosumab displayed non‐linear pharmacokinetics at doses below 60 mg but at higher doses, denosumab exposure increased approximately dose‐proportionally in advanced cancer patients with bone metastases. Following a 120 mg, every 4 weeks dosing schedule, similar denosumab pharmacokinetics and pharmacodynamics were observed across tumour types and were independent of concomitant cancer therapies.