bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of IFNL3 and IFNL4 polymorphisms with liver‐related mortality in a multiracial cohort of HIV/HCV‐coinfected women
Authors: Sarkar M. , Aouzierat B. , Bacchetti P. , Prokunina‐Olsson L. , French A. , Seaberg E. , O'Brien T. R. , Kuniholm M. H. , Minkoff H. , Plankey M. , Strickler H. D. , Peters M. G. ,   the Women's Interagency HIV
Published: June 2015

SummaryAfrican Americans coinfected with HIV and hepatitis C virus (HCV) have lower liver‐related mortality than Caucasians and Hispanics. While genetic polymorphisms near the IFNL3 and IFNL4 genes explain a significant fraction of racial differences in several HCV‐related outcomes, the impact of these variants on liver‐related mortality has not been investigated. We conducted a cohort study of HIV/HCV‐coinfected women followed in the multicentre, NIH‐funded Women's Interagency HIV Study (WIHS) to investigate whether 10 polymorphisms spanning the IFN‐λ region were associated with liver‐related mortality by dominant, recessive or additive genetic models. We also considered whether these polymorphisms contributed to previously reported differences in liver‐related death by race/ethnicity (ascertained by self‐report and ancestry informative markers). Among 794 coinfected women, there were 471 deaths including 55 liver‐related deaths during up to 18 years of follow‐up. On adjusted analysis, rs12980275 GG genotype compared to AG+AA hazards ratios [(HR) 0.36, 95% CI 0.14–0.90, P = 0.029] and rs8109886 AA genotype compared to CC+AC (HR 0.67, 95% CI 0.45–0.99, P = 0.047) were most strongly associated with liver‐related death although these associations were no longer significant after adjusting for race/ethnicity (HR 0.41, 95% CI 0.16–1.04, P = 0.060 and HR 0.78, 95% CI 0.51–1.19, P = 0.25, respectively). African American women had persistently lower liver‐related death independent of IFN‐λ variants (HRs ≤ 0.44, P values ≤ 0.04). The lower risk of death among African American HIV/HCV‐coinfected women is not explained by genetic variation in the IFN‐λ region suggesting, that other genetic, behavioural and/or environmental factors may contribute to racial/ethnic differences in liver‐related mortality.
Species dynamics of epiphytic macrolichens in relation to time since fire and host tree species in boreal forest
Authors: Bartels Samuel F. , Chen Han Y.H. 
Published: June 2015

AbstractQuestions(1) How is the abundance of individual epiphytic macrolichen species affected by host tree species and stand development, where canopy succession takes place in prolonged absence of stand‐replacing disturbance? (2) Do the associations between individual epiphytic macrolichen species and host tree species change through stand development?LocationThe central boreal forest of Canada (49°23′ N–49°36′ N, 89°31′ W–89°44′ W).MethodsWe estimated the percentage cover of epiphytic macrolichens on individual trees in 51 post‐fire successional stands of varying tree species composition, ranging from 7 to 209 yr since fire. We analysed how epiphytic macrolichen species cover on individual host tree species and community composition change with time since fire and host tree species using GLM and permutational multivariate ANOVA.ResultsCover of individual epiphytic macrolichen species on the host tree species increased continuously, peaked at different time scales or gradually declined through stand development in which canopy succession took place. Some lichen species exhibited exclusive association to particular host tree species. Moreover, stand age‐related trends of the cover of some epiphytic macrolichen species differed with host species. Multivariate analysis indicated that host tree species at each stand development stage supported different epiphytic macrolichen species composition.ConclusionEpiphytic macrolichen species dynamics is strongly influenced by time since fire and host tree species identity. Host‐specific preferences and their interaction with time since fire suggest that epiphytic lichen composition on a particular host tree species is not merely a random sample of the local species pool, but rather related to their time since fire‐dependent preferences for their hosts.
Does drought incite tree decline and death in Austrocedrus chilensis forests?
Authors: Amoroso Mariano M. , Daniels Lori D. , Villalba Ricardo , Cherubini Paolo 
Published: June 2015

AbstractQuestionsIs mal del ciprés, the widespread decline and death of Austrocedrus chilensis trees, caused by a single pathogen or multiple factors? Using a novel dendrochronological approach, we disentangled the influences of climatic variation on the radial growth decline and death of A. chilensis trees in declining forests. We distinguish possible causes of reduced radial growth and mortality from autogenic processes driven by stand development. We present a conceptual model of forest decline including multiple factors that predispose, incite and contributed to decreased radial growth and death of A. chilensis.LocationA. chilensis forests on mesic sites in northern Patagonia, Argentina.MethodsWe used dendrochronology to determine the years of (1) onset of radial growth decline of 301 living and dead trees stratified by canopy position at decline onset, and (2) mortality of 339 trees stratified by radial growth patterns and canopy position at death. Events were years with low or high numbers of trees initiating decline or dying. We tested the hypothesis that onset of decline and mortality were concurrent with drought for individual trees, using contingency tables, and for events, using superposed epoch analysis.ResultsClimatic variability acts as an environmental stress inciting and contributing to stand‐level forest decline. The onset of radial growth decline and mortality of individual trees were significantly associated with summer moisture deficits. High‐magnitude onset‐of‐decline and mortality events were concurrent with adverse climatic conditions.ConclusionsClimatic variation and drought incite and contribute to tree‐ and stand‐level decline and mortality in A. chilensis forests. Deciphering the effects of stand development is critical as autogenic processes independently drive tree mortality and mediate the effects of climatic variability on A. chilensis forest decline. Based on our results, we present a conceptual model within the framework of a forest decline process, and conclude A. chilensis mortality is a forest decline process driven by complex interactions between allogenic abiotic and biotic factors and autogenic stand development processes. Site conditions, genetic variation and sex of trees are predisposing factors that likely interact with the pathogen Phytophthora.
Prizing children's science information books: the text, reading and the reader
Authors: Alexander Joy , Jarman Ruth 
Published: June 2015

AbstractThe Royal Society Young People's Book Prize is awarded annually in the United Kingdom for the best science information book, and the winning book is chosen by panels of young people. This article discusses the findings of a study of the responses to the books and to their judging experience of young people who participated on panels in the 2011 Royal Society Young People's Book Prize. Interviews were conducted with 46 young people, aged from 8 to 14 years, from across the United Kingdom. The nature of contemporary non‐fiction books is discussed, specifically science information books. The impact of their design and format on reading is explored, as is the social nature of reading, which was a consequence of the judging panel context. The young people had opinions on the age range for which each book was most suitable, but they generally did so in such a way as to include themselves. It was found that their judging responsibilities contributed to these young people displaying a positive reading identity and sense of self‐efficacy.
The genetic structure of the exotic ascidian Styela plicata (Tunicata) from Italian ports, with a re‐appraisal of its worldwide genetic pattern
Authors: Maltagliati Ferruccio , Lupi Lisa , Castelli Alberto , Pannacciulli Federica G. 
Published: June 2015

AbstractThe pleated ascidian Styela plicata (Lesueur, 1823) is a solitary species commonly found in ports and marinas around the world. It has been recorded in the Mediterranean region since the mid‐19th century. In the present work, the species’ genetic diversity was analysed, employing a 613‐bp portion of the mitochondrial cytochrome c oxidase subunit I (COI) gene from 149 individuals collected in 14 ports along Italian coasts at spatial scales ranging from 1 to approximately 2200 km. Haplotype and nucleotide diversity values were h = 0–0.933 (total h = 0.789) and π = 0–0.145 (total π = 0.0094), respectively. A general southward trend of increasing within‐population genetic diversity was observed. Analysis of molecular variance revealed significant genetic structuring but no significant differences were detected among basins, and no isolation by distance was found. Our data were integrated with the COI sequences available from previous studies and re‐analysed in order to investigate the possible routes of introduction of this ascidian into the Mediterranean Sea. The presence of the two COI haplogroups detected in previous molecular investigations on S. plicata at intercontinental spatial scale was confirmed in the Mediterranean Sea. The results revealed multiple introductions of S. plicata, although some locations appear to have experienced rapid expansion from few founding individuals with reduced genetic diversity. However, continuous introductions would confound the pattern deriving from single founder events and make it difficult to estimate the time needed for gene diffusion into established populations. This mixing of effects creates difficulties in understanding the past and current dynamics of this introduction, and managing this alien invasive ascidian whose genetic structure is continuously shuffled by vessel‐mediated transport.
SUMOylation of Wor1 by a novel SUMO E3 ligase controls cell fate in Candida albicans
Authors: Yan Minghui , Nie Xinyi , Wang Huafeng , Gao Ning , Liu Haoping , Chen Jiangye 
Published: June 2015

SummaryCandida albicans is the most common human fungal pathogen, yet is a normal commensal resident of the human gut. CO2 levels in the gut are much higher than in air, and it is known that elevated CO2 concentration promotes C. albicans cells to undergo a phenotypic switch from white to opaque phase. Wor1, the master regulator of opaque cell formation, is required for both the white to opaque transition and opaque maintenance. To elucidate the regulatory mechanism of Wor1, we set out to identify Wor1‐interacting proteins using a yeast two‐hybrid screen. A SUMO E3 ligase named Wos1 (Wor1 SUMO‐ligase 1) was identified to interact with Wor1 and regulate Wor1 SUMOylation. WOS1 expression is upregulated in response to high CO2, and the induction by CO2 is dependent on the transcription factor Flo8. Under high CO2 conditions, Wos1 is required for the white to opaque switch and acts downstream of Flo8. At atmospheric CO2 levels, overexpression of Wos1 enhances Wor1 SUMOylation and promotes the white to opaque switch. Wor1 is found to be SUMOylated at lysine 385, and loss of this mark by point mutation leads to a defect in CO2‐mediated opaque cell induction. Together, our genetic and biological data show that Wos1‐mediated Wor1 SUMOylation contributes to the regulation of CO2‐induced white to opaque switching as well as heritable maintenance of the opaque cell type.
Mapping of Re, a gene conferring the red leaf trait in ornamental kale (Brassica oleracea L. var. acephala)
Authors: Ren Jie , Liu Zhiyong , Niu Ruiqing , Feng Hui 
Published: June 2015

AbstractVariegated leaf colour is an important agronomic trait that affects the market value of ornamental kale (Brassica oleracea L. var. acephala). The red leaf phenotype in kale is due to anthocyanin accumulation. To investigate the pattern of inheritance of this trait, we constructed an F2 population by crossing ‘Y005‐15’, a double haploid with red leaves, with a white‐leaved double haploid, ‘Y011‐13‐38’, followed by self‐pollination. An F2 population consisting of 4284 individuals was used to study the inheritance of this trait, which showed that the character was controlled by a dominate gene. All of the 1050 white leaf trait plants in the F2 were used for mapping and developing markers linked to Re gene. Results showed that Re was mapped to a locus on linkage group C09 of Brassica oleracea, and the locus was mapped between six SSR markers (C9Z1, C9Z16‐1, C9Z90, C9Z94, C9Z96 and C9Z99), with a genetic distance of 6.7, 1.0, 0.3, 2.0, 2.1 and 0.4 cM from Re gene, respectively. These results may facilitate marker‐assisted selection of the red leaf trait in kale breeding as well as map‐based cloning of the red leaf trait gene.
Disease state changes and safety of long‐term donepezil hydrochloride administration in patients with Alzheimer's disease: interim results from the long‐term, large‐scale J‐GOLD study in Japan
Authors: Arai Heii , Sumitomo Kenta , Sakata Yukinori , Daidoji Kasumi , Takase Takao , Toyoda Tetsumi 
Published: June 2015

AbstractBackgroundThere have been very few long‐term studies involving a large study population; existing studies usually have no more than a few hundred patients with Alzheimer's disease. For these reasons, there are no detailed investigations regarding changes in activities of daily living evaluated by the Functional Assessment Staging Test (FAST).MethodsA long‐term, large‐scale observational study of donepezil hydrochloride (Aricept®; Eisai Co., Ltd, Tokyo, Japan) is currently in progress. Its objective is to investigate disease state changes associated with the long‐term administration of this drug and its safety in patients with Alzheimer's disease. In this report, data collected over a maximum of 24 months were compiled. Efficacy was assessed using FAST and a cognitive function test (Mini‐Mental State Examination or the Hasegawa's Dementia Scale‐Revised).ResultsThe percentages of patients whose FAST stage improved or remained the same compared to at the start of donepezil hydrochloride administration (baseline) were 91.1% at 6 months, 83.0% at 12 months, 79.5% at 18 months, and 74.8% at 24 months. Multivariate logistic regression analysis was conducted to investigate factors that affect the improvement and maintenance or exacerbation of FAST at 24 months. ‘Independence level in the daily life of elderly with dementia’ and ‘duration of illness’ were identified as variables that affected the improvement and maintenance or exacerbation of FAST.Cognitive function improved significantly at 12 weeks and at 6 months compared to baseline, maintained baseline levels at 12 months and at 18 months, and decreased significantly at 24 months compared to baseline.ConclusionsThis is the largest prospective study involving Alzheimer's disease patients in Japan, and we believe it is an important study that shows the reality of daily clinical practice.
Gait speed in older people: an easy test for detecting cognitive impairment, functional independence, and health state
Authors: Garcia‐Pinillos Felipe , Cozar‐Barba Manuela , Munoz‐Jimenez Marcos , Soto‐Hermoso Victor , Latorre‐Roman Pedro 
Published: June 2015

AbstractBackgroundWith ageing, physical and cognitive functions become impaired. Analyzing and determining the association between both functions can facilitate the prevention and diagnosis of associated problems. Some previous works have proposed batteries of physical performance tests to determine both physical and cognitive functions. However, only a few studies have used the gait speed (GS) test as a tool to evaluate parameters representative of health in the elderly such as functionality, mobility, independence, autonomy, and comorbidity. Therefore, the aim of this study was to determine the association between physical and cognitive functions in older people (over 65 years old) and to detect the most appropriate physical test to assess cognitive impairment, functional independence, comorbidity, and perceived health in this population.MethodsOne hundred six older adults (38 men, 68 women) participated voluntarily in this cross‐sectional study. To assess the physical function handgrip strength, GS, 30‐s chair stand tests, and body composition analysis were performed. To evaluate cognitive function, the Mini‐Mental State Examination, Barthel index, and Charlson index were employed. No significant differences (P ≥ 0.05) between sexes were found.ResultsMultiple regression analysis of the Mini‐Mental State Examination and physical fitness variables, adjusted for age and sex, indicates that GS is a predictor of Mini‐Mental State Examination score (R2 = 0.138).ConclusionThe results showed that GS is an important predictor of functional capacity (physical and cognitive function) in adults over 65 years old.
Suicidal ideation in Chinese patients with chronic obstructive pulmonary disease: a controlled study
Authors: Wong Tak‐Shun , Xiang Yu‐Tao , Tsoh Joshua , Ungvari Gabor S. , Ko Fanny W.S. , Hui David S.C. , Chiu Helen F.K. 
Published: June 2015

AbstractBackgroundNo study has been published on the prevalence of suicidal behaviour in older Chinese patients with chronic obstructive pulmonary disease (COPD). This study examined the 1‐year prevalence of suicidal ideation in older Chinese COPD patients and explored its demographic and clinical correlates.MethodsA consecutive sample of 143 COPD patients and 211 matched control subjects were recruited and interviewed using structured, standardized instruments.ResultsThe 1‐year prevalence of suicidal ideation in COPD patients and controls were 15.4% and 10.9%, respectively. In multivariate analyses, suicidal ideation was significantly associated with the severity of depressive symptoms in COPD patients.ConclusionSuicidal ideation was not higher in COPD patients than in controls.
Grey scale texture analysis of endobronchial ultrasound mini probe images for prediction of benign or malignant aetiology
Authors: Nguyen Phan , Bashirzadeh Farzad , Hundloe Justin , Salvado Olivier , Dowson Nicholas , Ware Robert , Masters Ian Brent , Ravi Kumar Aravind , Fielding David 
Published: June 2015

AbstractBackground and objectiveExpert analysis of endobronchial ultrasound mini probe (EBUS‐MP) images has established subjective criteria for discriminating benign and malignant disease. Minimal data are available for objective analysis of these images. The aim of this study was to determine if greyscale texture analysis could differentiate between benign and malignant lung lesions.MethodsDigital EBUS‐MP images with a gain setting of 10/19 and contrast setting of 4/8 from 2007 until 2012 inclusive were included. These images had an expert‐defined region of interest (ROI) mapped. ROI were analysed for the following greyscale texture features: mean pixel value, difference between maximum and minimum pixel value, standard deviation of the mean pixel value, entropy, correlation, energy and homogeneity. Significant greyscale texture features differentiating benign from malignant disease were used by two physicians to assess a validation set.ResultsA total of 167 images were available. The first 85 lesions were used in the prediction set. Benign lesions had larger differences between maximum and minimum pixel values, larger standard deviations of the mean pixel values and higher entropy than malignant lesions (P < 0.0001 for all values). A total of 82 peripheral lesions were in the validation set. Physician 1 correctly classified 63/82 (76.8%) with a negative predictive value (NPV) for malignancy of 82% and positive predictive value (PPV) of 75%. Physician 2 correctly classified 62/82 (75.6%) with a NPV of 100% and PPV of 71.0%.ConclusionsGreyscale texture analysis of EBUS‐MP images can help establish aetiology with a high NPV for malignancy.
Learning in underserved UK areas: a novel approach
Authors: Crampton Paul , Hetherington Jeanette , McLachlan John , Illing Jan 
Published: June 2015

SummaryBackgroundThere is an insufficient number of medical students intending to pursue general practitioner (GP) careers. The undergraduate curriculum has traditionally prioritised teaching in large hospital settings despite most National Health Service patient contact occurring in primary care. Primary care is faced with providing health care for an ageing population with high levels of co‐morbidities. Patients who live in deprived areas suffer many disadvantages affecting their health and additionally tend to be underserved. Globally, there has been an initiative to provide medical students with extended clinical placements in rural and remote areas. These placements have identified many beneficial outcomes; however, little is known about placements in other underserved, deprived areas. This paper describes an innovative pilot programme to address these issues.ContextThe North East of England has a large proportion of the most deprived communities and worst health care outcomes in England. In Teesside, Phase 1 Medicine at Durham University provides the pre‐clinical curriculum. Durham students then join Newcastle University for Phase 2 Medicine, the clinical years.InnovationThe Difficult and Deprived Areas Programme (DDAP) places fourth‐year students in general practice and community settings in post‐industrial, deprived areas for 14 weeks, thus adopting and applying principles from rural initiatives (continuity and immersion) to other deprived settings. The DDAP allows students to learn about psychosocial determinants of health and to pursue community interests whilst gaining an excellent clinical grounding.There is an insufficient number of medical students intending to pursue general practitioner careersImplicationsThe DDAP provides a model for educators seeking to implement initiatives in similar underserved, deprived settings, which may potentially alleviate GP workforce shortages.
Complete Genome Sequences of Field Isolates of Mycobacterium bovis and Mycobacterium caprae
Authors: de la Fuente José , Díez-Delgado Iratxe , Contreras Marinela , Vicente Joaquín , Cabezas-Cruz Alejandro , Manrique Marina , Tobes Raquel , López Vladimir , Romero Beatriz , Domínguez Lucas , Garrido Joseba M. , Juste Ramón , Gortazar Christian 
Published: June 2015

ABSTRACT

Here we report the complete genome sequences of field isolates of
Mycobacterium bovis
and the related mycobacterial species,
Mycobacterium caprae
. The genomes of three
M. bovis
(MB1, MB3, MB4) and one
M. caprae
(MB2) field isolates with different virulence, prevalence, and host distribution phenotypes were sequenced.
Draft Genome Sequences of
Leviviridae
RNA Phages EC and MB Recovered from San Francisco Wastewater
Authors: Greninger Alexander L. , DeRisi Joseph L. 
Published: June 2015

ABSTRACT

We report here the draft genome sequences of marine RNA phages EC and MB assembled from metagenomic sequencing of organisms in San Francisco wastewater. These phages showed moderate translated amino acid identity to other enterobacteria phages and appear to constitute novel members of the
Leviviridae
family.
Whole-Genome Sequences of 15 Strains of Staphylococcus aureus subsp.
aureus
Isolated from Foodstuff and Human Clinical Samples
Authors: Crovadore Julien , Calmin Gautier , Tonacini Jenna , Chablais Romain , Baumgartner Andreas , Schnyder Bruno , Hodille Elisabeth , Lefort François 
Published: June 2015

ABSTRACT

The whole-genome sequences of 15 strains of
Staphylococcus aureus
(10 strains isolated from foodstuff samples in Switzerland and five from human clinical samples) were obtained by Illumina sequencing. Most strains fit within the known diversity for the species, but one (SA-120) possessed a higher G+C content and a higher number of genes than usual.