bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anxiety Symptoms and Disease Severity in Children and Adolescents With Crohn Disease
Authors: Reigada Laura C. , Hoogendoorn Claire J. , Walsh Lindsay C. , Lai Joanne , Szigethy Eva , Cohen Barry H. , Bao Ruijun , Isola Kimberly , Benkov Keith J. 
Published: September 2014

ABSTRACTObjectives:Children and adolescents diagnosed as having Crohn disease (CD), a type of inflammatory bowel disease (IBD), have increased vulnerability for anxiety symptoms that may be related to disease‐related processes. The aims of this article are 3‐fold: to report the proportion of pediatric patients with CD whose self‐reported anxiety symptoms are indicative of distress, to describe the constellation of anxiety symptoms, and to examine the relation between anxiety and disease symptoms.Methods:Retrospective medical chart review was performed for 93 youths with CD (ages 9–18 years) who had completed the Screen for Child Anxiety Related Disorders during their gastroenterology visit. Medical records were reviewed for demographic and disease characteristics. the Harvey‐Bradshaw Index (HBI) was used as a measure of CD activity.Results:Thirty percent of the youths reported experiencing elevated anxiety symptoms (Screen for Child Anxiety Related Disorder score >20), and 50% had scored above the cutoff in 1 or more anxiety domains, with school anxiety, general anxiety, and separation anxiety symptoms reported most frequently. Youth rated with moderate/severe disease activity on the HBI (n = 4) self‐reported more anxiety symptoms compared with youth with inactive disease (n = 78,P= 0.03). Greater school anxiety was significantly associated with decreased well‐being (P= 0.003), more abdominal pain (P< 0.001), and the number of loose stools (P= 0.01). Having extraintestinal symptoms was significantly associated with higher somatic/panic anxiety (P=0.01).Conclusions:Implementing a brief anxiety screen in tertiary pediatric settings may be one approach to identify young patients with CD in distress. Health care providers should consider periodic assessment of school anxiety among youth with CD.
A Fast 3 ×NMatrix Multiply Routine for Calculation of Protein RMSD
Authors: Haque Imran S. , Beauchamp Kyle A. , Pande Vijay S. 
Published: September 2014

AbstractThe bottleneck for the rapid calculation of the root-mean-square deviation in atomic coordinates (RMSD) between pairs of protein structures for large numbers of conformations is the evaluation of a 3 ×N×N× 3 matrix product over conformation pairs. Here we describe two matrix multiply routines specialized for the 3 ×Ncase that are able to significantly outperform (by up to 3X) off-the-shelf high-performance linear algebra libraries for this computation, reaching machine limits on performance. The routines are implemented in C and Python libraries, and are available athttps://github.com/simtk/IRMSD.
Direct gamete sequencing reveals no evidence for segregation distortion in house mouse hybrids
Authors: Corbett-Detig Russell , Jacobs-Palmer Emily , Hartl Daniel , Hoekstra Hopi 
Published: September 2014

AbstractUnderstanding the molecular basis of species formation is an important goal in evolutionary genetics, and Dobzhansky-Muller incompatibilities are thought to be a common source of postzygotic reproductive isolation between closely related lineages. However, the evolutionary forces that lead to the accumulation of such incompatibilities between diverging taxa are poorly understood. Segregation distorters are believed to be an important source of Dobzhansky-Muller incompatibilities betweenDrosophilaspecies and crop plants, but it remains unclear if these selfish genetic elements contribute to reproductive isolation in other species. Here, we collected viable sperm from first-generation hybrid male progeny ofMus musculus castaneusandM. m. domesticus, two subspecies of rodent in the earliest stages of speciation. We then genotyped millions of single nucleotide polymorphisms in these gamete pools and tested for a skew in the frequency of parental alleles across the genome. We show that segregation distorters are not measurable contributors to observed infertility in these hybrid males, despite sufficient statistical power to detect even weak segregation distortion with our novel method. Thus, reduced hybrid male fertility in crosses between these nascent species is attributable to other evolutionary forces.
Rate and cost of adaptation in theDrosophilagenome
Authors: Schiffels Stephan , Lässig Michael , Mustonen Ville 
Published: September 2014

AbstractRecent studies have consistently inferred high rates of adaptive molecular evolution betweenDrosophilaspecies. At the same time, theDrosophilagenome evolves under different rates of recombination, which results in partial genetic linkage between alleles at neighboring genomic loci. Here we analyze how linkage correlations affect adaptive evolution. We develop a new inference method for adaptation that takes into account the effect on an allele at a focal site caused by neighboring deleterious alleles (background selection) and by neighboring adaptive substitutions (hitchhiking). Using complete genome sequence data and fine-scale recombination maps, we infer a highly heterogeneous scenario of adaptation inDrosophila. In high-recombining regions, about 50% of all amino acid substitutions are adaptive, together with about 20% of all substitutions in proximal intergenic regions. In low-recombining regions, only a small fraction of the amino acid substitutions are adaptive, while hitchhiking accounts for the majority of these changes. Hitchhiking of deleterious alleles generates a substantial collateral cost of adaptation, leading to a fitness decline of about 30/2N per gene and per million years in the lowest-recombining regions. Our results show how recombination shapes rate and efficacy of the adaptive dynamics in eukaryotic genomes.Author SummaryBecause recombination takes place at a limited rate, alleles at neighboring sites in a genome can remain genetically linked over evolutionary periods. In this paper, we show that evolutionary forces generated by genetic linkage have drastic consequences for the adaptive dynamics in low-recombining parts of theDrosophilagenome. Our study is based on a new method to analyze allele frequencies that is applicable to genome data at both high and low rates of recombination. We show that genes in low-recombining regions of theDrosophilagenome incur a substantial cost of adaptation, because deleterious alleles get fixed more frequently than under high recombination. This cost reduces rate and power of the adaptive process. Our results suggest that theDrosophilagenome has evolved to minimize this cost by placing genes under high adaptive pressure in high-recombining regions.
A Consistent Estimator of the Evolutionary Rate
Authors: Bartoszek Krzysztof , Sagitov Serik 
Published: September 2014

AbstractWe consider a branching particle system where particles reproduce according to the pure birth Yule process with the birth rate λ, conditioned on the observed number of particles to be equaln.Particles are assumed to move independently on the real line according to the Brownian motion with the local variance σ2. In this paper we treatnparticles as a sample of related species. The spatial Brownian motion of a particle describes the development of a trait value of interest (e.g. log-body-size). We propose an unbiased estimatorof the evolutionary rateρ2=σ2/λ. The estimatoris proportional to the sample variancecomputed fromntrait values. We find an approximate formula for the standard error ofbased on a neat asymptotic relation for the variance of.
Phosphaturic mesenchymal tumor, mixed connective tissue type, non‐phosphaturic variant: Report of a case and review of 32 cases from the Japanese published work
Authors: Honda Rie , Kawabata Yuka , Ito Shusaku , Kikuchi Fumihito 
Published: September 2014

AbstractPhosphaturic mesenchymal tumor, mixed connective tissue type (PMTMCT) is a rare neoplasm that can cause tumor‐induced osteomalacia due to overproduction of a phosphaturic hormone, fibroblast growth factor 23 (FGF23). We report here a case of subcutaneous PMTMCT, non‐phosphaturic variant, in the sole. We also review 32 Japanese cases of PMTMCT reported in detail. They occurred in 16 men and 15 women (one was unknown), with ages ranging 20–73 years (median, 48). Tumors were found in soft tissue, bone and sinuses in 17, 11 and four, respectively. A history of long‐standing osteomalacia was noted in all cases except two non‐phosphaturic variant cases. Serum FGF23 level was elevated in 11 of 12 cases examined. In terms of follow‐up information, metastases were found in four patients, and two patients died of disease. In conclusion, PMTMCT is histologically a benign lesion; however, there may be rare metastatic and malignant cases. Wider recognition of the histological features of this unique neoplasm would aid its distinction from the large number of mesenchymal tumors for which it may be mistaken and should enable correct diagnosis of tumors with osteomalacia.
Case of erythema nodosum associated with granulomatous mastitis probably due to Corynebacterium infection
Authors: Hida Tetsuya , Minami Mitsuyoshi , Kawaguchi Hidetoshi , Oshiro Yumi , Kubo Yoshiaki 
Published: September 2014

AbstractGranulomatous mastitis (GM) is a rare chronic inflammatory breast disease that can be mistaken for a variety of inflammatory and neoplastic disorders of the breast. Erythema nodosum (EN) is a common panniculitis, and is often associated with a variety of diseases, yet coexistence of EN and GM is very rare. In this paper, we present a young Japanese woman with EN associated with GM probably due to Corynebacterium infection. Both lesions of EN and GM were successfully treated with oral minocycline and surgical drainage. To the best of our knowledge, this is the first case of EN associated with GM due to Corynebacterium infection in the English‐language published work.
Evaluation of five antibiotics on larval gut bacterial diversity of Plutella xylostella (Lepidoptera: Plutellidae)
Authors: Lin Xiao‐Li , Kang Zhi‐Wei , Pan Qin‐Jian , Liu Tong‐Xian 
Published: September 2014

AbstractLarvae of the diamondback moth, Plutella xylostella L. (Lepidoptera: Plutellidae), have rich microbial communities inhabiting the gut, and these bacteria contribute to the fitness of the pest. In this study we evaluated the effects of five antibiotics (rifampicin, ampicillin, tetracycline, streptomycin sulfate and chloramphenicol) on the gut bacterial diversity of P. xylostella larvae. We screened five different concentrations for each antibiotic in a leaf disc assay, and found that rifampicin and streptomycin sulfate at 3 mg/mL significantly reduced the diversity of the bacterial community, and some bacterial species could be rapidly eliminated. The number of gut bacteria in the rifampicin group and streptomycin sulfate group decreased more rapidly than the others. With the increase of antibiotic concentration, the removal efficiency was improved, whereas toxic effects became more apparent. All antibiotics reduced larval growth and development, and eventually caused high mortality, malformation of the prepupae, and hindered pupation and adult emergence. Among the five antibiotics, tetracycline was the most toxic and streptomycin sulfate was a relatively mild one. Some dominant bacteria were not affected by feeding antibiotics alone. Denaturing gradient gel electrophoresis graph showed that the most abundant and diverse bacteria in P. xylostella larval gut appeared in the cabbage feeding group, and diet change and antibiotics intake influenced gut flora abundance. Species diversity was significantly reduced in the artificial diet and antibiotics treatment groups. After feeding on the artificial diet with rifampicin, streptomycin sulfate and their mixture for 10 days, larval gut bacteria could not be completely removed as detected with the agarose gel electrophoresis method.
Cytometric patterns reveal growth states of Shewanella putrefaciens
Authors: Melzer Susanne , Winter Gudrun , Jäger Kathrin , Hübschmann Thomas , Hause Gerd , Syrowatka Frank , Harms Hauke , Tárnok Attila , Müller Susann 
Published: September 2014

SummaryBacterial growth is often difficult to estimate beyond classical cultivation approaches. Low cell numbers, particles or coloured and dense media may disturb reliable growth assessment. Further difficulties appear when cells are attached to surfaces and detachment is incomplete.Therefore, flow cytometry was tested and used for analysis of bacterial growth on the single‐cell level. Shewanella putrefaciens was cultivated as a model organism in planktonic or biofilm culture. Materials of smooth and rough surfaces were used for biofilm cultivation. Both aerobic and anaerobic as well as feast and famine conditions were applied. Visualization of growth was also done using Environmental Scanning and Phase Contrast Microscopy. Bioinformatic tools were applied for data interpretation.Cytometric proliferation patterns based on distributions of DNA contents per cell corresponded distinctly to the various lifestyles, electron acceptors and substrates tested. Therefore, cell cycling profiles of S. putrefaciens were found to mirror growth conditions.The cytometric patterns were consistently detectable with exception of some biofilm types whose resolution remained challenging. Corresponding heat maps proved to be useful for clear visualization of growth behaviour under all tested conditions. Therefore, flow cytometry in combination with bioinformatic tools proved to be powerful means to determine various growth states of S. putrefaciens, even in constrained environments. The approach is universal and will also be applicable for other bacterial species.
Whole genome and transcriptome analyses of environmental antibiotic sensitive and multi‐resistant Pseudomonas aeruginosa isolates exposed to waste water and tap water
Authors: Schwartz Thomas , Armant Olivier , Bretschneider Nancy , Hahn Alexander , Kirchen Silke , Seifert Martin , Dötsch Andreas 
Published: September 2014

SummaryThe fitness of sensitive and resistant Pseudomonas aeruginosa in different aquatic environments depends on genetic capacities and transcriptional regulation. Therefore, an antibiotic‐sensitive isolate PA30 and a multi‐resistant isolate PA49 originating from waste waters were compared via whole genome and transcriptome Illumina sequencing after exposure to municipal waste water and tap water. A number of different genomic islands (e.g. PAGIs, PAPIs) were identified in the two environmental isolates beside the highly conserved core genome. Exposure to tap water and waste water exhibited similar transcriptional impacts on several gene clusters (antibiotic and metal resistance, genetic mobile elements, efflux pumps) in both environmental P. aeruginosa isolates. The MexCD‐OprJ efflux pump was overexpressed in PA49 in response to waste water. The expression of resistance genes, genetic mobile elements in PA49 was independent from the water matrix. Consistently, the antibiotic sensitive strain PA30 did not show any difference in expression of the intrinsic resistance determinants and genetic mobile elements. Thus, the exposure of both isolates to polluted waste water and oligotrophic tap water resulted in similar expression profiles of mentioned genes. However, changes in environmental milieus resulted in rather unspecific transcriptional responses than selected and stimuli‐specific gene regulation.
Vegetable microbiomes: is there a connection among opportunistic infections, human health and our ‘gut feeling'?
Authors: Berg Gabriele , Erlacher Armin , Smalla Kornelia , Krause Robert 
Published: September 2014

SummaryThe highly diverse microbiomes of vegetables are reservoirs for opportunistic and emerging pathogens. In recent years, an increased consumption, larger scale production and more efficient distribution of vegetables together with an increased number of immunocompromised individuals resulted in an enhanced number of documented outbreaks of human infections associated with the consumption of vegetables. Here we discuss the occurrence of potential pathogens in vegetable microbiomes, the impact of farming and processing practices, and plant and human health issues. Based on these results, we discuss the question if vegetables can serve as a source of infection for immunocompromised individuals as well as possible solutions to avoid outbreaks. Moreover, the potentially positive aspects of the vegetables microbiome for the gut microbiota and human health are presented.
Improved bioethanol production in an engineered Kluyveromyces lactis strain shifted from respiratory to fermentative metabolism by deletion of NDI1
Authors: González‐Siso María Isabel , Touriño Alba , Vizoso Ángel , Pereira‐Rodríguez Ángel , Rodríguez‐Belmonte Esther , Becerra Manuel , Cerdán María Esperanza 
Published: September 2014

SummaryIn this paper, we report the metabolic engineering of the respiratory yeast Kluyveromyces lactis by construction and characterization of a null mutant (Δklndi1) in the single gene encoding a mitochondrial alternative internal dehydrogenase. Isolated mitochondria of the Δklndi1 mutant show unaffected rate of oxidation of exogenous NADH, but no oxidation of matrix NADH; this confirms that KlNdi1p is the only internal NADH dehydrogenase in K. lactis mitochondria. Permeabilized cells of the Δklndi1 mutant do not show oxidation of matrix NADH, which suggests that shuttle systems to transfer the NADH from mitochondrial matrix to cytosol, for being oxidized by external dehydrogenases, are not functional. The Δklndi1 mutation decreases the chronological life span in absence of nutrients. The expression of KlNDI1 is increased by glutathione reductase depletion. The Δklndi1 mutation shifts the K. lactis metabolism from respiratory to fermentative: the Δklndi1 strain shows reduced respiration rate and increased ethanol production from glucose, while it does not grow in non‐fermentable carbon sources such as lactate. The biotechnological benefit of the Δklndi1 mutant for bioethanol production from waste cheese whey lactose was proved.
ITS1: a DNA barcode better than ITS2 in eukaryotes?
Authors: Wang Xin‐Cun , Liu Chang , Huang Liang , Bengtsson‐Palme Johan , Chen Haimei , Zhang Jian‐Hui , Cai Dayong , Li Jian‐Qin 
Published: September 2014

AbstractA DNA barcode is a short piece of DNA sequence used for species determination and discovery. The internal transcribed spacer (ITS/ITS2) region has been proposed as the standard DNA barcode for fungi and seed plants and has been widely used in DNA barcoding analyses for other biological groups, for example algae, protists and animals. The ITS region consists of both ITS1 and ITS2 regions. Here, a large‐scale meta‐analysis was carried out to compare ITS1 and ITS2 from three aspects: PCR amplification, DNA sequencing and species discrimination, in terms of the presence of DNA barcoding gaps, species discrimination efficiency, sequence length distribution, GC content distribution and primer universality. In total, 85 345 sequence pairs in 10 major groups of eukaryotes, including ascomycetes, basidiomycetes, liverworts, mosses, ferns, gymnosperms, monocotyledons, eudicotyledons, insects and fishes, covering 611 families, 3694 genera, and 19 060 species, were analysed. Using similarity‐based methods, we calculated species discrimination efficiencies for ITS1 and ITS2 in all major groups, families and genera. Using Fisher's exact test, we found that ITS1 has significantly higher efficiencies than ITS2 in 17 of the 47 families and 20 of the 49 genera, which are sample‐rich. By in silico PCR amplification evaluation, primer universality of the extensively applied ITS1 primers was found superior to that of ITS2 primers. Additionally, shorter length of amplification product and lower GC content was discovered to be two other advantages of ITS1 for sequencing. In summary, ITS1 represents a better DNA barcode than ITS2 for eukaryotic species.
Design of a 9K illumina BeadChip for polar bears (Ursus maritimus) from RAD and transcriptome sequencing
Authors: Malenfant René M. , Coltman David W. , Davis Corey S. 
Published: September 2014

AbstractSingle‐nucleotide polymorphisms (SNPs) offer numerous advantages over anonymous markers such as microsatellites, including improved estimation of population parameters, finer‐scale resolution of population structure and more precise genomic dissection of quantitative traits. However, many SNPs are needed to equal the resolution of a single microsatellite, and reliable large‐scale genotyping of SNPs remains a challenge in nonmodel species. Here, we document the creation of a 9K Illumina Infinium BeadChip for polar bears (Ursus maritimus), which will be used to investigate: (i) the fine‐scale population structure among Canadian polar bears and (ii) the genomic architecture of phenotypic traits in the Western Hudson Bay subpopulation. To this end, we used restriction‐site associated DNA (RAD) sequencing from 38 bears across their circumpolar range, as well as blood/fat transcriptome sequencing of 10 individuals from Western Hudson Bay. Six‐thousand RAD SNPs and 3000 transcriptomic SNPs were selected for the chip, based primarily on genomic spacing and gene function respectively. Of the 9000 SNPs ordered from Illumina, 8042 were successfully printed, and – after genotyping 1450 polar bears – 5441 of these SNPs were found to be well clustered and polymorphic. Using this array, we show rapid linkage disequilibrium decay among polar bears, we demonstrate that in a subsample of 78 individuals, our SNPs detect known genetic structure more clearly than 24 microsatellites genotyped for the same individuals and that these results are not driven by the SNP ascertainment scheme. Here, we present one of the first large‐scale genotyping resources designed for a threatened species.
Identifying the signal of environmental filtering and competition in invasion patterns – a contest of approaches from community ecology
Authors: Gallien Laure , Carboni Marta , Münkemüller Tamara 
Published: September 2014

Summary

In 1859, Darwin had already identified environmental constraints and competition with the native community as major drivers of invasion success. Since then, a toolbox of indices and statistical approaches has been developed and commonly applied to test for the relative importance of these drivers. This toolbox is largely based on community ecology theory with the underlying hypothesis that patterns of trait (or phylogenetic) similarities between invaders and native species permit to disentangle the signatures of competition and environmental filtering. However, so far the performance of the indices and statistical approaches has not been thoroughly evaluated, and there exists no study exploring the sensitivity of the different methods given common biases in field data. This severely hampers intercomparisons of invasion studies and ultimately prevents the elaboration of general conclusions.

In this study, we developed a mechanistic community assembly model to simulate invasion patterns across a range of communities and tested the performance of four different indices aiming at disentangling environmental filtering vs. competition from these patterns. Furthermore, we evaluated the sensitivity of the statistical methods to biases in the data (resulting from non‐equilibrium dynamics or observation errors).

Our results indicated that the best performing index was mean distance to the native species (the average functional distance between the invader and all the species of the community), especially in heterogeneous landscapes. Further, we demonstrated that the detection of competition was more sensitive to the presence of biases in the data than the detection of environmental filtering.

In conclusion, studying invasion mechanisms based on community patterns is possible when employing the appropriate statistical method, but it is highly sensitive to the quality of the data set used.