bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surveillance for severe acute respiratory infections in Southern Arizona, 2010–2014
Authors: Wansaula Zimy , Olsen Sonja J. , Casal Mariana G. , Golenko Catherine , Erhart Laura M. , Kammerer Peter , Whitfield Natalie , McCotter Orion Z. 
Published: November 2015

BackgroundThe Binational Border Infectious Disease Surveillance program began surveillance for severe acute respiratory infections (SARI) on the US–Mexico border in 2009. Here, we describe patients in Southern Arizona.MethodsPatients admitted to five acute care hospitals that met the SARI case definition (temperature ≥37·8°C or reported fever or chills with history of cough, sore throat, or shortness of breath in a hospitalized person) were enrolled. Staff completed a standard form and collected a nasopharyngeal swab which was tested for selected respiratory viruses by reverse transcription polymerase chain reaction.ResultsFrom October 2010–September 2014, we enrolled 332 SARI patients. Fifty‐two percent were male and 48% were white non‐Hispanic. The median age was 63 years (47% ≥65 years and 5·2% <5 years). During hospitalization, 51 of 230 (22%) patients required intubation, 120 of 297 (40%) were admitted to intensive care unit, and 28 of 278 (10%) died. Influenza vaccination was 56%. Of 309 cases tested, 49 (16%) were positive for influenza viruses, 25 (8·1%) for human metapneumovirus, 20 (6·5%) for parainfluenza viruses, 16 (5·2%) for coronavirus, 11 (3·6%) for respiratory syncytial virus, 10 (3·2%) for rhinovirus, 4 (1·3%) for rhinovirus/enterovirus, 3 (1·0%) for enteroviruses, and 3 (1·0%) for adenovirus. Among the 49 influenza‐positive specimens, 76% were influenza A (19 H3N2, 17 H1N1pdm09, and 1 not subtyped), and 24% were influenza B.ConclusionInfluenza viruses were a frequent cause of SARI in hospitalized patients in Southern Arizona. Monitoring respiratory illness in border populations will help better understand the etiologies. Improving influenza vaccination coverage may help prevent some SARI cases.
Improving the representativeness of influenza viruses shared within the WHO Global Influenza Surveillance and Response System
Authors: Pereyaslov Dmitriy , Zemtsova Galina , Gruessner Christine , Daniels Rodney S. , McCauley John W. , Brown Caroline S. 
Published: November 2015

BackgroundSharing influenza viruses within the WHO Global Influenza Surveillance and Response System is crucial for monitoring evolution of influenza viruses.ObjectivesAnalysis of timeliness and geographic representativeness of viruses shared by National Influenza Centres (NICs) in the WHO European Region with the London WHO Collaborating Centre for Reference and Research on Influenza for the Northern Hemisphere's 2010–2011 and 2011–2012 influenza seasons.Materials and methodsData from NICs on influenza‐positive specimens shared with WHO CC London for the above‐mentioned influenza seasons were analyzed for timeliness of sharing with respect to the February deadline (31 January) for inclusion in the WHO consultations on the composition of influenza virus vaccines for the Northern Hemisphere and geographic representativeness.ResultsThe 2010–2011 and 2011–2012 seasons were different in terms of the seasonal pattern, the timing of the epidemic, and the dominant virus. Consistent patterns of virus sharing across the seasons were observed. Approximately half the viruses collected before the deadline were not shared within the deadline; the average delay between date of specimen collection and shipment receipt was 3 and 1·5 months for the first and second season, respectively.ConclusionA baseline was provided for future work on enhancement of specimen sharing in the WHO European Region and improving the vaccine virus selection process. Greater insight into virus selection criteria applied by countries and the causes of delays in shipment are needed to understand the representativeness of viruses shared and to assess the importance of this for vaccine strain selection.
Ancient river systems and phylogeographical structure in the spring salamander, Gyrinophilus porphyriticus
Authors: Kuchta Shawn R. , Haughey Michael , Wynn Addison H. , Jacobs Jeremy F. , Highton Richard 
Published: November 2015

AbstractAimThe river drainages of the Appalachian Mountains have experienced a dynamic history as glacial cycles, stream capture and other geological processes have led to the fragmentation and fusion of formerly isolated palaeodrainages. Some ancient rivers have gone extinct, including portions of the great Teays River. Here we investigate the contribution of contemporary and historical drainages to patterns of phylogeographical structure in the spring salamander complex, Gyrinophilus porphyriticus.LocationEastern North America, USA.MethodsSampling spanned the range of the G. porphyriticus complex, and included representative samples of the cave species of Gyrinophilus as well. Molecular sequence data included the mitochondrial DNA locus cytochrome b and the nuclear locus recombination‐activating gene 1 (RAG‐1). Time‐calibrated phylogenies were inferred, and Bayes‐LAGRANGE was used to reconstruct ancestral distributions. Contemporary and historical river influences on patterns of genetic diversity were tested using distance‐based redundancy analysis (db‐RDA).ResultsThe G. porphyriticus complex originated prior to the Pleistocene glacial cycles, and historical river systems explained more genetic variation than did contemporary drainages or geographical distance. Patterns of genetic variation suggest that extinct or remodelled palaeodrainages, including the Teays River, played an important role in structuring contemporary patterns of genetic variation.Main conclusionsThe hydrogeological history of eastern North American drainage basins has been instrumental in structuring patterns of regional biodiversity in freshwater species. Here we show that hydrological remodelling has also left its genetic signature in the semi‐aquatic spring salamander complex, G. porphyriticus. Historical drainages accounted for the largest fraction of phylogeographical structure, more so than did contemporary drainages or geographical distance, with spatial and temporal patterns of variation associated with the extinct Teays River.
Moderate alcohol drinking in pregnancy increases risk for children's persistent conduct problems: causal effects in a Mendelian randomisation study
Authors: Murray Joseph , Burgess Stephen , Zuccolo Luisa , Hickman Matthew , Gray Ron , Lewis Sarah J. 
Published: November 2015

BackgroundHeavy alcohol use during pregnancy can cause considerable developmental problems for children, but effects of light‐moderate drinking are uncertain. This study examined possible effects of moderate drinking in pregnancy on children's conduct problems using a Mendelian randomisation design to improve causal inference.MethodsA prospective cohort study (ALSPAC) followed children from their mother's pregnancy to age 13 years. Analyses were based on 3,544 children whose mothers self‐reported either not drinking alcohol during pregnancy or drinking up to six units per week without binge drinking. Children's conduct problem trajectories were classified as low risk, childhood‐limited, adolescence‐onset or early‐onset‐persistent, using six repeated measures of the Strengths and Difficulties Questionnaire between ages 4–13 years. Variants of alcohol‐metabolising genes in children were used to create an instrumental variable for Mendelian randomisation analysis.ResultsChildren's genotype scores were associated with early‐onset‐persistent conduct problems (OR = 1.29, 95% CI = 1.04–1.60, p = .020) if mothers drank moderately in pregnancy, but not if mothers abstained from drinking (OR = 0.94, CI = 0.72–1.25, p = .688). Children's genotype scores did not predict childhood‐limited or adolescence‐onset conduct problems.ConclusionsThis quasi‐experimental study suggests that moderate alcohol drinking in pregnancy contributes to increased risk for children's early‐onset‐persistent conduct problems, but not childhood‐limited or adolescence‐onset conduct problems.
Monitoring and mechanisms of organophosphate resistance in San Jose scale, Diaspidiotus perniciosus (Hemiptera: Diaspididae)
Authors: Buzzetti K. A. , Chorbadjian R. A. , Fuentes‐Contreras E. , Gutiérrez M. , Ríos J. C. , Nauen R. 
Published: November 2015

AbstractSan Jose scale, Diaspidiotus perniciosus (Comstock), is a serious pest in Chilean apple tree orchards, and a number of organophosphate insecticides were used to control them for decades. Recently, control failures with these insecticides were reported and linked to insecticide resistance development. In this study, 40 San Jose scale field populations were collected and their susceptibility to two commonly used organophosphate insecticides, that is chlorpyrifos and methidathion, was assessed. The obtained bioassay data suggest moderate levels of resistance to both insecticides when compared to a reference susceptible strain. The highest resistance ratio (RR) detected for chlorpyrifos and methidathion was 31‐fold and 11‐fold, respectively. The bioassay results suggest the occurrence of a significant cross‐resistance between both compounds. Biochemical measurements revealed a role for esterases in conferring resistance to organophosphates, but not modified acetylcholinesterase. The spatial spread and extend of insecticide resistance were also evaluated. Our result shows that no autocorrelation can be assumed, and then, insecticide resistance is caused by random factors.
A real‐time PCR toolbox for accurate identification of invasive fruit fly species
Authors: Dhami M. K. , Gunawardana D. N. , Voice D. , Kumarasinghe L. 
Published: November 2015

AbstractSignificant plant pests such as fruit flies that travel with fresh produce between countries as eggs or larvae pose a great economic threat to the agriculture and fruit industry worldwide. Time‐limited and expensive quarantine decisions require accurate identification of such pests. Immature stages are often impossible to identify, making them a serious concern for biosecurity agencies. Use of COI barcoding PCR, often the only molecular identification resource, is time‐consuming. We assess the suitability of the COI barcoding region for real‐time PCR assays to identify four pest fruit fly species (Family: Tephritidae), in a diagnostic framework. These species, namely Mediterranean fruit fly (Ceratitis capitata), Queensland fruit fly (Bactrocera tryoni), African invader fly (Bactrocera invadens) and Island fly (Dirioxa pornia) each provide a different set of genetic species delimitation problems. We discuss the benefits and limitations of using a single‐gene TaqMan™ real‐time approach for such species. Our results indicate that COI‐based TaqMan™ real‐time PCR assays, in particular for genetically distinct species, provide an accurate, sensitive and rapid diagnostic tool.
The development of a non‐invasive model to predict the presence of non‐alcoholic steatohepatitis in patients with non‐alcoholic fatty liver disease
Authors: Goh George BB , Issa Danny , Lopez Rocio , Dasarathy Srinivasan , Dasarathy Jaividhya , Sargent Ruth , Hawkins Carol , Pai Rish K , Yerian Lisa , Khiyami Amer , Pagadala Mangesh R , Sourianarayanane Achuthan , Alkhouri Naim , McCullough Arthur J 
Published: November 2015

AbstractBackground:Non‐alcoholic steatohepatitis (NASH) is an advanced and aggressive form of non‐alcoholic fatty liver disease (NAFLD), which remains difficult to diagnose without a liver biopsy. Hyperferritinemia has increasingly been associated with the presence of NASH. Hence, we sought to explore the relationship between ferritin and NASH and to develop a composite model based on ferritin to predict the presence of NASH.Methods:A total of 405 patients with biopsy‐proven NAFLD were enrolled in the study. Comparison was explored to assess differences between patients with and without NASH, upon which a scoring model was established using variables found to be independent predictors of NASH.Results:Among all patients with NAFLD, 291 (72%) had biopsy‐proven NASH, and 114 (28%) had non‐NASH. Mean age was 48 ± 12 years, and 56% were female. Ferritin was significantly higher in NASH compared with non‐NASH patients (184 vs 126, respectively; P < 0.001) but lacked diagnostic accuracy for predicting NASH alone (area under the curve [AUC 0.62]). The addition of other significant variables such as aspartate aminotransferase, body mass index, platelet count, diabetes, and hypertension to ferritin improved the prediction of NASH with an AUC 0.81 (95% confidence interval: 0.76–0.86). Internal validation of the model using imputed data sets demonstrated that AUC did not change materially.Conclusions:While higher ferritin was significantly associated with NASH, ferritin alone lacked diagnostic accuracy to predict NASH. However, incorporating several easily obtainable variables with ferritin allowed the construction of a novel scoring system that can be easily applied in the clinical setting to guide management of NAFLD.
Additive impact of pre‐liver transplant metabolic factors on survival post‐liver transplant
Authors: Adams Leon A , Arauz Oscar , Angus Peter W , Sinclair Marie , MacDonald Graeme A , Chelvaratnam Utti , Wigg Alan J , Yeap Sze , Shackel Nicholas , Lin Linda , Raftopoulos Spiro , McCaughan Geoffrey W , Jeffrey Gary P ,   on behalf of the Australian New Zealand Liver Transplant Study Group
Published: November 2015

AbstractBackground and Aim:Diabetes at time of liver transplantation is associated with reduced post‐transplant survival. We aimed to assess whether additional metabolic conditions such as obesity or hypertension had additive prognostic impact on post‐transplantation survival.Methods:A multi‐center cohort study of 617 adult subjects undergoing liver transplantation between 2003 and 2009 has been used. Dry body mass index was calculated following adjustment for ascites.Results:After a median follow‐up of 5.8 years (range 0–10.5), 112 (18.2%) patients died. Diabetes was associated with reduced post‐transplant survival (hazard ratio 1.89, 95% confidence interval [CI] 1.25–2.86, P = 0.003), whereas obesity, hypertension, dyslipidemia, and the metabolic syndrome itself were not (P > 0.3 for all). Patients with concomitant diabetes and obesity had lower survival (adjusted Hazard Ratio [aHR] 2.40, 95%CI 1.32–4.38, P = 0.004), whereas obese non‐diabetic patients or diabetic non‐obese patients had similar survival compared with non‐diabetic, non‐obese individuals. The presence of hypertension or dyslipidemia did not impact on survival in patients with diabetes (P > 0.1 for both). Obese diabetic patients had longer intensive care and hospital stays than non‐obese diabetic or obese, non‐diabetic patients (P < 0.05). The impact of concomitant obesity and diabetes on survival was greater in subjects aged 50+ years (52.6% 5‐year survival, aHR 3.04, 95% CI 1.54–5.98) or those transplanted with hepatocellular carcinoma (34.1% 5‐year survival, aHR 3.35, 95% CI 1.31–5.57). Diabetes without obesity was not associated with an increased mortality rate in these sub‐groups.Conclusions:Concomitant diabetes and obesity but not each condition in the absence of the other is associated with reduced post‐liver transplant survival. The impact of diabetes and obesity is greater in older patients and those with hepatocellular carcinoma.
Adverse metabolic phenotype of adolescent girls with non‐alcoholic fatty liver disease plus polycystic ovary syndrome compared with other girls and boys
Authors: Ayonrinde Oyekoya T , Adams Leon A , Doherty Dorota A , Mori Trevor A , Beilin Lawrence J , Oddy Wendy H , Hickey Martha , Sloboda Deborah M , Olynyk John K , Hart Roger 
Published: November 2015

AbstractBackground and Aims:Non‐alcoholic fatty liver disease (NAFLD) and polycystic ovary syndrome (PCOS) share risk associations of adiposity and insulin resistance. We examined the impact of a PCOS diagnosis on the metabolic phenotype of adolescent girls with NAFLD and compared this to girls without PCOS or NAFLD and to age‐matched boys.Methods:Community‐based adolescents from the Raine Cohort participated in assessments for NAFLD (572 girls and 592 boys) and PCOS (244 girls). One hundred and ninety‐nine girls attended both assessments.Results:Amongst the 199 girls, PCOS was diagnosed in 16.1% and NAFLD in 18.6%. NAFLD was diagnosed in 10.1% of the boys. NAFLD was more prevalent in girls with PCOS than girls without PCOS (37.5% vs 15.1%, P = 0.003). Girls with NAFLD plus PCOS had greater adiposity (waist circumference, body mass index, suprailiac skinfold thickness [SST], serum androgens, high‐sensitivity C‐reactive protein, ferritin, homeostasis model assessment for insulin resistance (HOMA‐IR), and lower serum sex hormone binding globulin levels than girls with NAFLD without a PCOS diagnosis (all P < 0.05). Girls with NAFLD plus PCOS had similar adiposity, HOMA‐IR, and adiponectin levels to boys with NAFLD, but more adiposity, serum leptin and HOMA‐IR than both girls and boys without NAFLD. PCOS (odds ratios 2.99, 95% confidence intervals 1.01–8.82, P = 0.048) and SST (odds ratios 1.14, 95% confidence intervals 1.08–1.20, P < 0.001) independently predicted NAFLD in adolescent girls, however, serum androgens and HOMA‐IR levels did not.Conclusions:Adolescent girls with NAFLD plus PCOS have a similar metabolic phenotype to boys with NAFLD. Increasing SST and pre‐existing PCOS independently predict NAFLD in adolescent girls.
Valuable New Resistances Ensure Improved Management of Sclerotinia Stem Rot (Sclerotinia sclerotiorum) in Horticultural and Oilseed Brassica Species
Authors: You Ming Pei , Uloth Margaret B. , Li Xi Xiang , Banga Surinder S. , Banga Shashi K. , Barbetti Martin J. 
Published: November 2015

AbstractField resistances against Sclerotinia rot (SR) (Sclerotinia sclerotiorum) were determined in 52 Chinese genotypes of Brassica oleracea var. capitata, 14 Indian Brassica juncea genotypes carrying wild weedy Brassicaceae introgression(s) and four carrying B‐genome introgression, 22 Australian commercial Brassica napus varieties, and 12 B. napus and B. juncea genotypes of known resistance. All plants were individually inoculated by securing an agar disc from a culture of S. sclerotiorum growing on a glucose‐rich medium to the stem above the second internode with Parafilm tape. Mean stem lesion length across tested genotypes ranged from <1 to >68 mm. While there was considerable diversity within the germplasm sets from each country, overall, 65% of the B. oleracea var. capitata genotypes from China showed the highest levels of stem resistance, a level comparable with the highest resistance ever recorded for oilseed B. napus or B. juncea from China or Australia. One Indian B. juncea line carrying weedy introgression displayed a significant level of both stem and leaf resistance. However, the vast majority of commercial Australian oilseed B. napus varieties fell within the most susceptible 40% of genotypes tested for stem disease. There was no correlation between expressions of stem versus leaf resistance, suggesting their independent inheritance. A few Chinese B. oleracea var. capitata genotypes that expressed combined extremely high‐level stem (≤1 mm length) and leaf (≤0.5 mean number of infections/plant) resistance will be particularly significant for developing new SR‐resistant horticultural and oilseed Brassica varieties.
A molecular phylogeny of Chinese orchids
Authors: Li Ming‐He , Zhang Guo‐Qiang , Lan Si‐Ren , Liu Zhong‐Jian ,   China Phylogeny Consortium
Published: November 2015

AbstractWe estimated the molecular phylogenetic relationships of the Chinese members of the family Orchidaceae. Within the Tree of Life for the Genera of Chinese Vascular Plants usingatpB, rbcL, matK, ndhF, andmatR, the currently delimited subfamilies, tribes, and subtribes are highly supported as monophyletic except for the perplexing Epidendroideae. Five genes (rbcL,matK,psaB,ycf1, andXdh), which are more universally used in Orchidaceae, were further analyzed to reconstruct the phylogeny of Epidendroideae. The reconstructed trees were in strong agreement and showed significant support for the tribal and subtribal clades. Based on the highly supported circumscription and arrangement of the suprageneric levels in the Tree of Life and reconstructed trees, we have proposed a new phylogenetic classification of Chinese Orchidaceae that includes five subfamilies, 17 tribes, and 21 subtribes.
Spatial distribution and association patterns in a tropical evergreen broad‐leaved forest of north‐central Vietnam
Authors: Nguyen Hong Hai , Uria‐Diez Jaime , Wiegand Kerstin 
Published: November 2015

AbstractQuestionsWhat are the prevailing types of intraspecific spatial distributions and interspecific association patterns at species and life stage levels of trees in a tropical rain forest? Which ecological processes could structure these patterns? Possible processes include dispersal limitation, self‐thinning, facilitation and competition between species and life stages.LocationA tropical broad‐leaved forest in north‐central Vietnam.MethodsWe used univariate and bivariate pair‐correlation functions to investigate the spatial distribution and association patterns of 18 abundant tree species. To disentangle first‐ and second‐order effects, we used a scale separation approach with the heterogeneous Poisson process as null model.Results(1) Sixteen of 18 species had aggregated patterns at various scales and regardless of their abundance. (2) Significant and aggregated patterns were found in 64% of all specific life stages. (3) At scales up to 15 m, 12.4% species pairs showed significant associations, among that 71% were spatial attractions, 5% were spatial repulsions and 24% were non‐essential interactions. (4) In different life stage associations, attractions (81%) predominated over repulsions (19%) at small scales of up to 15 m.ConclusionsOur findings provide evidence that dispersal limitation may regulate the spatial patterns of tree species. Moreover, positive spatial associations between tree species and life stages suggest the presence of species herd protection and/or facilitation in this forest stand, while the persistence of intraspecific aggregation through life stages suggests a very late onset or even absence of self‐thinning. Habitat heterogeneity plays an important role for species distribution patterns, and the spatial segregation occurs at a scale around 15 m in this forest.
Evaluating the performance of selection scans to detect selective sweeps in domestic dogs
Authors: Schlamp Florencia , van der Made Julian , Stambler Rebecca , Chesebrough Lewis , Boyko Adam R. , Messer Philipp W. 
Published: November 2015

AbstractSelective breeding of dogs has resulted in repeated artificial selection on breed‐specific morphological phenotypes. A number of quantitative trait loci associated with these phenotypes have been identified in genetic mapping studies. We analysed the population genomic signatures observed around the causal mutations for 12 of these loci in 25 dog breeds, for which we genotyped 25 individuals in each breed. By measuring the population frequencies of the causal mutations in each breed, we identified those breeds in which specific mutations most likely experienced positive selection. These instances were then used as positive controls for assessing the performance of popular statistics to detect selection from population genomic data. We found that artificial selection during dog domestication has left characteristic signatures in the haplotype and nucleotide polymorphism patterns around selected loci that can be detected in the genotype data from a single population sample. However, the sensitivity and accuracy at which such signatures were detected varied widely between loci, the particular statistic used and the choice of analysis parameters. We observed examples of both hard and soft selective sweeps and detected strong selective events that removed genetic diversity almost entirely over regions >10 Mbp. Our study demonstrates the power and limitations of selection scans in populations with high levels of linkage disequilibrium due to severe founder effects and recent population bottlenecks.