bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cryptococcal meningitis is a cause for cross‐reactivity in cerebrospinal fluid assays for anti‐Histoplasma, anti‐Coccidioides and anti‐Blastomyces antibodies
Authors: Bahr Nathan C. , Panackal Anil A. , Durkin Michelle M. , Smedema Melinda L. , Keown Wesley , Davis Thomas E. , Raymond‐Guillen Luke , Park Yoon‐Dong , Marr Kieren A. , Fries Bettina C. , Williamson Peter R. , Boulware David R. , Wheat L. Joseph 
Published: December 2018

SummaryBackground/ObjectivesAntibody detection is commonly used for diagnosis of histoplasmosis, and cross‐reactions have been recognised due to endemic mycoses but not cryptococcosis. We observed cross‐reactions in an anti‐Histoplasma antibody enzyme immunoassay (EIA) in the cerebrospinal fluid (CSF) from a patient with cryptococcal meningitis and sought to assess the risk of cross‐reactive anti‐Histoplasma antibodies in persons with cryptococcal meningitis.MethodsAn anti‐cryptococcal antibody EIA was developed to measure CSF antibody response in HIV‐infected subjects from Kampala, Uganda and previously healthy, HIV‐negative subjects at the National Institutes of Health (NIH) with cryptococcal meningitis. Specimens were tested for cross‐reactivity in assays for IgG anti‐Histoplasma, anti‐Blastomyces and anti‐Coccidioides antibodies.ResultsAmong 61 subjects with cryptococcal meningitis (44 Kampala cohort, 17 NIH cohort), elevated CSF anti‐cryptococcal antibody levels existed in 38% (23/61). Of the 23 CSF specimens containing elevated anti‐cryptococcal antibodies, falsely positive results were detected in antibody EIAs for histoplasmosis (8/23, 35%), coccidioidomycosis (6/23, 26%) and blastomycosis (1/23, 4%). Overall, 2% (2/81) of control CSF specimens had elevated anti‐cryptococcal antibody detected, both from Indiana.ConclusionsCryptococcal meningitis may cause false‐positive results in the CSF for antibodies against Histoplasma, Blastomyces and Coccidioides. Fungal antigen testing should be performed to aid in differentiating true‐ and false‐positive antibody results in the CSF.
An analysis of the development of adolescent and young adult cancer care in the United Kingdom: A Foucauldian perspective
Authors: Cable Maria , Kelly Daniel 
Published: December 2018

AbstractThis paper analyses the development of the specialism of adolescent and young adult (AYA) cancer care via a Foucauldian lens to consider how knowledge and awareness have grown since questions were first raised about unmet needs of AYAs with cancer. The AYA specialism has gathered momentum over the last 30 years in the United Kingdom (UK) and is fast gathering pace internationally. Fundamental to this process has been the combined contribution from nursing and other health professionals, researchers, policy‐makers and philanthropists. From an initial process of problematisation, through a gradual growth in empirical knowledge and resultant shifts in health policy, a new nexus of expertise has emerged that enabled AYA cancer care to become recognised as distinct from either child or adult oncology. Different stakeholders contributed to the discourses that have underpinned this development—a process likely to continue as it expands further. This paper draws on examples from the growth of the AYA specialism, the emergence of new professional roles and a growth in research. It illustrates how the coalescing of multiple perspectives allowed new discourses and, ultimately, new practices to be established that now have global impact.
Nutrient exchange in arbuscular mycorrhizal symbiosis from a thermodynamic point of view
Authors: Dreyer Ingo , Spitz Olivia , Kanonenberg Kerstin , Montag Karolin , Handrich Maria R. , Ahmad Sabahuddin , Schott‐Verdugo Stephan , Navarro‐Retamal Carlos , Rubio‐Meléndez María E. , Gomez‐Porras Judith L. , Riedelsberger Janin , Molina‐Montenegro Marco A. , Succurro Antonella , Zuccaro Alga , Gould Sven B. , Bauer Petra , Schmitt Lutz , Gohlke Holger 
Published: December 2018

Summary

To obtain insights into the dynamics of nutrient exchange in arbuscular mycorrhizal (AM) symbiosis, we modelled mathematically the two‐membrane system at the plant–fungus interface and simulated its dynamics.

In computational cell biology experiments, the full range of nutrient transport pathways was tested for their ability to exchange phosphorus (P)/carbon (C)/nitrogen (N) sources.

As a result, we obtained a thermodynamically justified, independent and comprehensive model of the dynamics of the nutrient exchange at the plant–fungus contact zone. The predicted optimal transporter network coincides with the transporter set independently confirmed in wet‐laboratory experiments previously, indicating that all essential transporter types have been discovered.

The thermodynamic analyses suggest that phosphate is released from the fungus via proton‐coupled phosphate transporters rather than anion channels. Optimal transport pathways, such as cation channels or proton‐coupled symporters, shuttle nutrients together with a positive charge across the membranes. Only in exceptional cases does electroneutral transport via diffusion facilitators appear to be plausible. The thermodynamic models presented here can be generalized and adapted to other forms of mycorrhiza and open the door for future studies combining wet‐laboratory experiments with computational simulations to obtain a deeper understanding of the investigated phenomena.
Symmetrical palatal fibromatosis: Five new cases and a review of the literature
Authors: Vargo Richard J. , Hossino Kenan H. , Clark Ashley , Bouquot Jerry E. 
Published: December 2018

AbstractObjectiveTo present five cases of symmetrical palatal fibromatosis (SPF), a lesion reported very rarely in the English language literature, under more than a dozen different names, and to recommend the most appropriate name.MethodsFive SPF cases are characterized with a literature review.ResultsThree females and two males, aged 20–39 years, presented with bilateral, symmetrical, asymptomatic, sessile, moderately firm, or soft (n = 2) masses of the lateral posterior hard palate; two were isolated to the tuberosities. All masses were normal in color, with smooth, non‐ulcerated surfaces and occasional surface nodularity. Underlying bone was radiographically normal, and adjacent teeth were asymptomatic. All masses originated from supra‐periosteal tissues over palatal bone, only secondarily extending to gingivae and/or crestal tuberosity. Cases were present between 4 months and 15 years, with no familial or environmental etiologies identified. Histopathologically, masses were comprised of dense, avascular fibrous tissue with scattered thick bands of collagen. Surface epithelium showed occasional long, thin, sometimes pointed rete processes, and subepithelial stroma contained scattered large, angular fibroblasts. Conservative surgical excision appeared curative in all cases.ConclusionsThe present investigators propose SPF as the most accurate name for this rare entity.
Development of Beet necrotic yellow vein virus‐based vectors for multiple‐gene expression and guide RNA delivery in plant genome editing
Authors: Jiang Ning , Zhang Chao , Liu Jun‐Ying , Guo Zhi‐Hong , Zhang Zong‐Ying , Han Cheng‐Gui , Wang Ying 
Published: December 2018

SummaryMany plant viruses with monopartite or bipartite genomes have been developed as efficient expression vectors of foreign recombinant proteins. Nonetheless, due to lack of multiple insertion sites in these plant viruses, it is still a big challenge to simultaneously express multiple foreign proteins in single cells. The genome of Beet necrotic yellow vein virus (BNYVV) offers an attractive system for expression of multiple foreign proteins owning to a multipartite genome composed of five positive‐stranded RNAs. Here, we have established a BNYVV full‐length infectious cDNA clone under the control of the Cauliflower mosaic virus 35S promoter. We further developed a set of BNYVV‐based vectors that permit efficient expression of four recombinant proteins, including some large proteins with lengths up to 880 amino acids in the model plant Nicotiana benthamiana and native host sugar beet plants. These vectors can be used to investigate the subcellular co‐localization of multiple proteins in leaf, root and stem tissues of systemically infected plants. Moreover, the BNYVV‐based vectors were used to deliver NbPDS guide RNAs for genome editing in transgenic plants expressing Cas9, which induced a photobleached phenotype in systemically infected leaves. Collectively, the BNYVV‐based vectors will facilitate genomic research and expression of multiple proteins, in sugar beet and related crop plants.
Constitutive expression of a stabilized transcription factor group VII ethylene response factor enhances waterlogging tolerance in wheat without penalizing grain yield
Authors: Wei Xuening , Xu Huijun , Rong Wei , Ye Xingguo , Zhang Zengyan 
Published: December 2018

AbstractWaterlogging causes oxygen deprivation within plant roots and affects crop growth and yield. In crop wheat (Triticum aestivum), molecular responses to waterlogging are poorly understood. Here, we performed a genome‐wide analysis of group VII ethylene response factor (ERFVII) genes in hexaploid wheat and identified 25 genes, which were induced by waterlogging with diverse manner. Among them, TaERFVII.1 exhibited differential expression patterns between waterlogging‐tolerant wheat Nonglin46 and susceptible wheat Yangmai16 under waterlogging. Constitutive expression of TaERFVII.1 with an MYC‐peptide tag at its N terminus in wheat enhanced tolerance to waterlogging as evidenced by increased grain weight per plant, survival rate, and chlorophyll content of leaves and by increased expression of waterlogging‐responsive genes, while silencing of TaERFVII.1 compromised the expression of waterlogging‐responsive genes. Notably, constitutive expression of the stabilized TaERFVII.1 did not negatively impact both plant development and grain yield under standard conditions. We further demonstrated that constitutive expression of stabilized TaERFVII.1 elevated the transcriptional level of TaSAB18.1, the ortholog of Arabidopsis HRA1 and rice SAB18, consequently reduced the expression of waterlogging‐responsive genes under standard conditions. These results suggest that TaERFVII.1 plays an important role in wheat tolerance to waterlogging, and it could be a candidate for improving crop waterlogging tolerance.
Omentin‐1 level in adolescents with polycystic ovarian syndrome
Authors: Özgen İlker Tolga , Oruçlu Şüera , Selek Sahabettin , Kutlu Esra , Guzel Gülsüm , Cesur Yaşar 
Published: December 2018

AbstractBackgroundAdipokines have been suggested to play an important role in the pathogenesis of polycystic ovarian syndrome (PCOS). Omentin is an adipokine secreted essentially by visceral adipose tissue with an insulin‐sensitizing effect. Insulin resistance (IR) is a common feature of PCOS, therefore the aim of this study was to investigate omentin‐1 level in adolescent girls with PCOS and its relationship with IR and androgens.MethodA total of 41 obese girls with PCOS, and 30 age‐ and body mass index (BMI)‐matched obese girls without PCOS were enrolled in the study. The demographic, clinic and laboratory characteristics of the groups were compared. Additionally, bivariate correlation analysis of omentin‐1 with BMI standard deviation score (BMI‐SDS), insulin, glucose, homeostatic model assessment of IR (HOMA‐IR), total and free testosterone was performed.ResultsIn the PCOS group HOMA‐IR, free and total testosterone were higher than in the control group. Omentin‐1 was lower in the PCOS group compared with the controls (55.01 ± 7.99 ng/mL vs 59.10 ± 7.02 ng/mL, respectively; P = 0.027). Omentin‐1 was inversely correlated with free testosterone (r = −0.527, P = 0.030) and BMI‐SDS (r = −0.241, P = 0.046) but it was not correlated with total testosterone, HOMA‐IR, glucose, insulin or serum lipids.ConclusionOmentin‐1 was lower in obese girls with PCOS and hyperandrogenism was associated with this condition.
Identification of Brassica accessions resistant to ‘old’ and ‘new’ pathotypes of Plasmodiophora brassicae from Canada
Authors: Fredua‐Agyeman R. , Hwang S. F. , Strelkov S. E. , Zhou Q. , Manolii V. P. , Feindel D. 
Published: December 2018

Genetic resistance is the main tool used to manage clubroot of canola (Brassica napus) in Canada. However, the emergence of new virulent strains of the clubroot pathogen, Plasmodiophora brassicae, has complicated canola breeding efforts. In this study, 386 Brassica accessions were screened against five single‐spore isolates (represented by pathotypes 2F, 3H, 5I, 6M and 8N on the Canadian Clubroot Differential Set) and 17 field isolates (represented by 12 unique pathotypes: 2B, 3A, 3D, 3O, 5C, 5G, 5K, 5L, 5X, 8E, 8J and 8P) of P. brassicae to identify resistance sources effective against these strains. The results showed that one B. rapa accession (CDCNFG‐046, mean index of disease (ID) = 3.3%) and two B. nigra accessions (CDCNFG‐263, mean ID = 3.1%; and CDCNFG‐262, mean ID = 4.7%) possessed excellent resistance to all 22 of the isolates evaluated. Fifty other accessions showed differential clubroot reactions (resistant, moderately resistant or susceptible), including 27 (one B. napus, two B. rapa, four B. oleracea and 20 B. nigra) accessions that were each resistant to 8–21 P. brassicae isolates, but developed mean IDs in the range of 5.3–29.6%. The remaining 23 accessions (two B. napus, one B. rapa, five B. oleracea and 15 B. nigra) were each resistant to 3–13 isolates, but developed mean IDs in the range of 30.3–47.0%. The three accessions that showed absolute resistance and the 50 accessions that showed differential clubroot reactions could be used to breed for resistance to the new P. brassicae strains.
The Use of Telematics Devices to Improve Automobile Insurance Rates
Authors: Guillen Montserrat , Nielsen Jens Perch , Ayuso Mercedes , Pérez‐Marín Ana M. 
Published: December 2018

AbstractMost automobile insurance databases contain a large number of policyholders with zero claims. This high frequency of zeros may reflect the fact that some insureds make little use of their vehicle, or that they do not wish to make a claim for small accidents in order to avoid an increase in their premium, but it might also be because of good driving. We analyze information on exposure to risk and driving habits using telematics data from a pay‐as‐you‐drive sample of insureds. We include distance traveled per year as part of an offset in a zero‐inflated Poisson model to predict the excess of zeros. We show the existence of a learning effect for large values of distance traveled, so that longer driving should result in higher premiums, but there should be a discount for drivers who accumulate longer distances over time due to the increased proportion of zero claims. We confirm that speed limit violations and driving in urban areas increase the expected number of accident claims. We discuss how telematics information can be used to design better insurance and to improve traffic safety.
Timing and duration of paternal migration and the educational attainment of left‐behind children: Evidence from rural China
Authors: Wang Sophie Xuefei 
Published: December 2018

AbstractThis paper examines the relationship between the migration of men from rural China and the educational attainment of their left‐behind children. The importance of migratory timing and duration are addressed. Using survey data, the study found that compared with rural children of nonmigrant parents, rural children of migrant fathers have a lower probability of being enrolled in school. In addition, the relationship between migratory timing, duration, and school enrollment shows an interesting pattern; children whose fathers migrated when they were infants are more likely to be enrolled in school, but children whose fathers migrated before their birth or after they reached school age are less likely to be enrolled in school. Possible explanations for this pattern are provided.
A Bayesian Model-Free Approach to Combination Therapy Phase I Trials Using Censored Time-to-Toxicity Data
Authors: Wheeler Graham M. , Sweeting Michael J. , Mander Adrian P. 
Published: December 2018

SummaryThe product of independent beta probabilities escalation design for dual agent phase I dose escalation trials is a Bayesian model-free approach for identifying multiple maximum tolerated dose combinations of novel combination therapies. Despite only being published in 2015, the design has been implemented in at least two oncology trials. However, these trials require patients to have completed follow-up before clinicians can make dose escalation decisions. For trials of radiotherapy or advanced therapeutics, this may lead to impractically long trial durations due to late-onset treatment-related toxicities. We extend the product of independent probabilities escalation design to use censored time-to-event toxicity outcomes for making dose escalation decisions. We show via comprehensive simulation studies and sensitivity analyses that trial duration can be reduced by up to 35%, particularly when recruitment is faster than expected, without compromising on other operating characteristics.
Detecting Weak Dependence in Computer Network Traffic Patterns by Using Higher Criticism
Authors: Price-Williams Matthew , Heard Nick , Rubin-Delanchy Patrick 
Published: December 2018

SummaryTo perform robust statistical anomaly detection in cybersecurity, we must build realistic models of the traffic patterns within a computer network. It is therefore important to understand the dependences between the large number of routinely interacting communication pathways within such a network. Pairs of interacting nodes in any directed communication network can be modelled as point processes where events in a process indicate information being sent between two nodes. For two processes A and B denoting the interactions between two distinct pairs of computers, called edges, we wish to assess whether events in A trigger events then to occur in B. A test is introduced to detect such dependence when only a subset of the events in A exhibit a triggering effect on process B; this test will enable us to detect even weakly correlated edges within a computer network graph. Since computer network events occur as a high frequency data stream, we consider the asymptotics of this problem as the number of events goes to ∞, while the proportion exhibiting dependence goes to 0, and examine the performance of tests that are provably consistent in this framework. An example of how this method can be used to detect genuine causal dependences is provided by using real world event data from the enterprise computer network of Los Alamos National Laboratory.
Dose Individualization and Variable Selection by Using the Bayesian Lasso in Early Phase Dose Finding Trials
Authors: Kakurai Yasuyuki , Kaneko Shuhei , Hamada Chikuma , Hirakawa Akihiro 
Published: December 2018

SummaryRecommended phase 2 doses for some drugs may differ according to a patient's clinical or genetic characteristics. We develop a new method that determines the individualized optimal dose according to patterns of patient covariates and selects the covariates that are associated with efficacy and toxicity in early phase trials for evaluating multiple patient covariates of interest. To address the difficulty of high dimensional estimation of model parameters with a limited sample size, we propose the use of the Bayesian least absolute shrinkage and selection operator, which is a penalized regression approach. We demonstrate the potential utility of this proposed method through various simulation studies.
Straw mulching with fertilizer nitrogen: An approach for improving crop yield, soil nutrients and enzyme activities
Authors: Akhtar Kashif , Wang Weiyu , Khan Ahmad , Ren Guangxin , Zaheer Sajjad , Sial Tanveer A. , Feng Yongzhong , Yang Gaihe 
Published: December 2018

AbstractField experiments were conducted to study soil properties, soil enzymes activities, water use efficiency (WUE) and crop productivity after six years of soya bean straw mulching in the semi‐arid conditions of China. The experiment included four treatments: CK (Control), N (240 kg N ha‐1), H (soya bean straw mulching at half rate 700 kg ha‐1 with 240 kg N ha‐1) and F (soya bean straw mulching at full rate 1,400 kg ha‐1 with 240 kg N ha‐1). Soil organic carbon (SOC), soil labile organic carbon (LOC), soil available N (AN), available P (AP) and enzyme activities were analysed after wheat harvesting in 2016 and 2017. Results show that straw amounts had positive effects on the soil fertility indices being higher for treatment F. The SOC, LOC, AN, AP and enzyme activities (i.e. saccharase, urease and alkaline phosphatase) were in the order of F > H > N > CK. High wheat grain yield and WUE were observed for F treatment. A total of six years mulching along with 240 kg ha‐1 nitrogen fertilizer application is sufficient for wheat yield stability and improving soil properties except urease activities in the semi‐arid condition of China. However, the straw mulching amount should be further studied with minimum nitrogen fertilizer for an environment‐friendly and effective approach for improving the soil biological properties with adequate crop production on a sustainable basis in the semi‐arid region of China.
Exploring gene tree incongruence at the origin of ants and bees (Hymenoptera)
Authors: Camacho Gabriela P. , Pie Marcio R. , Feitosa Rodrigo M. , Barbeitos Marcos S. 
Published: December 2018

AbstractThe fact that different phylogenomic data sets can lead to highly supported but inconsistent results suggest that conflict among gene trees in real data sets could be severe. We provide here a detailed exploration of gene tree space to investigate the relationships in Hymenoptera based on data obtained by Johnson et al. (Current Biology, 2013, 23, 2058), in which ants and Apoidea (bees and spheciform wasps) were recovered as sister groups, contradicting previous studies. We found high levels of topological variation among gene trees, several of them disagreeing with previously published hypotheses. To profile the dynamics of emerging support versus conflicting signal in combined analysis of data, we employed a novel method based on the incremental addition of randomized data to coalescence‐based phylogenetic inference. Although the monophyly of Aculeata and of Formicidae were consistently recovered using as little as 6.5% of the 308 available markers, signal for the Formicidae + Apoidea clade prevailed only after more than 50% of the loci were sampled. Still, non‐negligible support for alternative hypotheses remained until all genes were added to the analysis. Our results suggest that phylogenetic conflict is rather pervasive and not scattered as noise across individual gene trees because alternative topologies were recovered not from a specific subset, but from several random combinations of loci. Thus, even though phylogenetic signal recovered from full gene data sets was already dominant in much smaller ensembles, large amounts of data may be indeed necessary to overcome phylogenetic conflict.