bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predictors of Dissection in Aortic Aneurysms From Giant Cell Arteritis
Authors: Kermani Tanaz A. , Warrington Kenneth J. , Crowson Cynthia S. , Hunder Gene G. , Ytterberg Steven R. , Gabriel Sherine E. , Matteson Eric L. 
Published: May 2016

BackgroundFactors associated with dissection from inflammatory aortic aneurysms may be different from those in the general population.ObjectiveThe aim of this study was to evaluate the risk factors for aortic dissection/rupture in patients with giant cell arteritis (GCA) and aortic aneurysms.MethodsA population-based incident cohort of patients with a diagnosis of GCA from 1950 to 2004 was used. All patients with aortic aneurysms diagnosed 1 year prior to GCA diagnosis or any time thereafter were included. Cox proportional hazard models were used to evaluate risk factors for aortic dissection/rupture.ResultsThe study included 33 patients (91% women) with GCA and aortic aneurysms. Mean age at diagnosis of aortic aneurysm was 83.6 years. There were 27 thoracic aneurysms and 19 abdominal aneurysms. Eight patients developed aortic dissection/rupture (both thoracic and abdominal aorta in 5 cases, thoracic aorta only in 2 cases, and isolated abdominal aorta in 1 case).Older age (hazard ratio [HR], 0.27 per 10 years; 95% confidence interval [CI], 0.09–0.86) and later calendar year at diagnosis of aortic aneurysm (HR, 0.29 per 10 years; 95% CI, 0.13–0.69) were associated with decreased risk of dissection/rupture. Size of the thoracic aneurysm (HR, 1.17; 95% CI, 0.69–1.99) was not associated with dissection/rupture. Histopathology showed active aortitis in 4 of 7 patients with aortic dissection/rupture compared with 0 of 7 patients with aortic aneurysm without dissection/rupture.ConclusionsAneurysm size was not a predictor of aortic dissection/rupture in this cohort of patients with GCA. The higher frequency of active aortitis in patients with dissection suggests that active inflammation may play a role.
Neurological Complications Involving the Central Nervous System After Allogeneic Hematopoietic Stem Cell Transplantation During a Period of Evolution in Transplant Modalities: A Cohort Analysis
Authors: Colombo Anna Amelia , Marchioni Enrico , Diamanti Luca , Di Matteo Angela Maria , Baldanti Fausto , Furione Milena , Cazzola Mario , Ferretti Virginia Valeria , Pascutto Cristiana , Alessandrino Emilio Paolo 
Published: May 2016

Background
Neurological complications (NC) after hematopoietic stem cell transplantation (HSCT) are rare events. The evolution of transplant procedures has resulted in improved survival and has allowed elderly patients or those with comorbidity to receive an HSCT. The risk of NC in these patients has still not been well defined. Therefore, we carried out an observational study to estimate the occurrence and identify the risks associated with NC.

Methods
The study cohort included 452 adult-allogeneic HSCT recipients, transplanted from 1997 to 2012. The median follow up was 1.3 year (0-15.7). A myeloablative regimen was used in 307 patients. Two hundred patients were grafted from matched unrelated donor (MUD), of these, 129 (64.5%) received an in vivo T-cell depletion.

Results
Out of 452 patients, 30 (6.6%) developed NC. Infections were the most frequent causes of NC (30%). Overall survival decreased in patients developing NC (P < 0.001). Univariate survival regression on the cumulative incidence of NC identified period of transplant, linear trend between 4-year periods (1997-2012) (P < 0.001), MUD (P < 0.001), and recipient's age (P = 0.034) as significant risk factors. In multivariate analysis, period of transplant (P < 0.001) and MUD (P = 0.004) remained significant independent risk factors. Matched unrelated donor recipients showed a 3.8-fold elevated risk of developing NC.

Conclusions
Analysis highlights a temporal trend of incidence of NC that progressively increased over time and confirms a strong association between donor type and risk of NC. Our observations suggest that, although relatively uncommon, NC after allo-HSCT, may become more frequent due to the improved overall survival in recent years.
Improved Annotation with de novo Transcriptome Assembly in Four Social Amoeba Species
Authors: Singh Reema , Lawal Hajara M. , Schilde Christina , Glöeckner Gernot , Barton Geoff J. , Schaap Pauline , Cole Christian 
Published: May 2016

ABSTRACTBackground:Annotation of gene models and transcripts is a fundamental step in genome sequencing projects. Often this is performed with automated prediction pipelines, which can miss complex and atypical genes or transcripts. RNA-seq data can aid the annotation with empirical data. Here we present de novo transcriptome assemblies generated from RNA-seq data in four Dictyostelid species: D. discoideum, P. pallidum, D. fasciculatum and D. lacteum. The assemblies were incorporated with existing gene models to determine corrections and improvement on a whole-genome scale. This is the first time this has been performed in these eukaryotic species.Results:An initial de novo transcriptome assembly was generated by Trinity for each species and then refined with Program to Assemble Spliced Alignments (PASA). The completeness and quality were assessed with the Core Eukaryotic Genes Mapping Approach (CEGMA) and Transrate tools at each stage of the assemblies. The final datasets of 11,315-12,849 transcripts contained 5,610-7,712 updates and corrections to >50% of existing gene models including changes to hundreds or thousands of protein products. Putative novel genes are also identified and alternative splice isoforms were observed for the first time in P. pallidum, D. lacteum and D. fasciculatum.Conclusions:In taking a whole transcriptome approach to genome annotation with empirical data we have been able to enrich the annotations of four existing genome sequencing projects. In doing so we have identified updates to the majority of the gene annotations across all four species under study and found putative novel genes and transcripts which could be worthy for follow-up. The new transcriptome data we present here will be a valuable resource for genome curators in the Dictyostelia and we propose this effective methodology for use in other genome annotation projects.
Tissue-Driven Hypothesis of Transcriptome Evolution: An Update
Authors: Hallmark Howard T. , Haltom Jeffrey A , Gu Xun 
Published: May 2016

AbstractIn past decade, many reports have demonstrated that tissues in multi-cellular organisms may play important roles to shape the pattern of genome evolution. The tissue-driven hypothesis was then coined, claiming that tissue-specific factor as the common resource of functional constrain may underlie the positive correlations between tissue expression divergence, sequence divergence, or the expression tolerance of duplication divergence. However, the original version of tissue-driven hypothesis cannot rule out the tissue-specific effect of mutational variance. In this perspective, we solve this problem by modifying the evolutionary model that underlies the tissue expression evolution. Reanalysis of the microarray data reanalysis has revealed the relative importancebetween tissue-specific functional constraints and mutational variances in the tissue evolution. Finally, we outline how to utilize RNA-seq technology to further investigate the tissue expression evolution in the case of multiple tissues and species.
The evolution of CHROMOMETHYLASES and gene body DNA methylation in plants
Authors: Bewick Adam J. , Niederhuth Chad E. , Lexiang Ji , Rohr Nicholas A. , Griffin Patrick T. , Leebens-Mack Jim , Schmitz Robert J. 
Published: May 2016

ABSTRACTBackgroundThe evolution of gene body methylation (gbM), its origins and its functional consequences are poorly understood. By pairing the largest collection of transcriptomes (>1000) and methylomes (77) across Viridiplantae we provide novel insights into the evolution of gbM and its relationship to CHROMOMETHYLASE (CMT) proteins.ResultsCMTs are evolutionary conserved DNA methyltransferases in Viridiplantae. Duplication events gave rise to what are now referred to as CMT1, 2 and 3. Independent losses of CMT1, 2 and 3 in eudicots, CMT2 and ZMET in monocots and monocots/commelinids, variation in copy number and non-neutral evolution suggests overlapping or fluid functional evolution of this gene family. DNA methylation within genes is widespread and is found in all major taxonomic groups of Viridiplantae investigated. Genes enriched with methylated CGs (mCG) were also identified in species sister to angiosperms. The proportion of genes and DNA methylation patterns associated with gbM are restricted to angiosperms with a functional CMT3 or ortholog. However, mCG-enriched genes in the gymnospermPinus taedashared some similarities with gbM genes inAmborella trichopoda. Additionally, gymnosperms and ferns share a CMT homolog closely related to CMT2 and 3. Hence, the dependency of gbM on a CMT most likely extends to all angiosperms and possibly gymnosperms and ferns.ConclusionsThe resulting gene family phylogeny of CMT transcripts from the most diverse sampling of plants to date redefines our understanding of CMT evolution and its evolutionary consequences on DNA methylation. Future, functional tests of homologous and paralogous CMTs will uncover novel roles and consequences to the epigenome.
Centrifuge: rapid and sensitive classification of metagenomic sequences
Authors: Kim Daehwan , Song Li , Breitwieser Florian P. , Salzberg Steven L. 
Published: May 2016

AbstractCentrifuge is a novel microbial classification engine that enables rapid, accurate and sensitive labeling of reads and quantification of species on desktop computers. The system uses an indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.2 GB for 4,078 bacterial and 200 archaeal genomes) and classifies sequences at very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers. Because of its space-optimized indexing schemes, Centrifuge also makes it possible to index the entire NCBI non-redundant nucleotide sequence database (a total of 109 billion bases) with an index size of 69 GB, in contrast to k-mer based indexing schemes, which require far more extensive space. Centrifuge is available as free, open-source software fromwww.ccb.jhu.edu/software/centrifuge
Highly expressed proteins prefer less informative amino acids
Authors: Wang Guang-Zhong 
Published: May 2016

AbstractThe transcriptional and translational systems are essentially information processing systems. However, how to quantify the amount of information decoded during expression remains a mystery. Here, we have proposed a simple method to evaluate the amount of information transcribed and translated during gene expression. We found that although proteins with a high copy number have more information translated, the average number of bits per amino acid is not high. The negative correlation between protein copy number and bits per amino acid indicates the selective pressure to reduce translational errors. Moreover, interacting proteins have similar bits per residue translated. All of these findings highlight the importance of understanding transcription and translation from an information processing perspective.
Potential pitfalls of FISH microscopy as assessment method for anaerobic digesters
Authors: Abendroth Christian , Hahnke Sarah , Klocke Michael , Luschnig Olaf 
Published: May 2016

AbstractIn the present work we investigated how the state of a biogas reactor impacts the enumeration of prokaryotic cells by fluorescencein situhybridisation (FISH). Therefore, the correlation between gas production and FISH hybridisation rates was analysed in different anaerobic digester sludges. High gasification activity coincided with high hybridisation rates. Low hybridisation rates were especially achieved with reactor samples subjected to long starvation periods showing low biogas production.Based on our findings we conclude that samples for FISH analysis should be fixed as soon as possible to prevent a loss of microbial activity resulting in lower FISH signals. Furthermore, the location of sampling is of importance, since samples from different fermenters within the same biogas plant also varied strongly in their FISH hybridisation rate. Our results indicate that FISH could be a useful method for assessing the metabolic state of microorganisms in anaerobic digester plants.
Reference-free comparison of microbial communities via de Bruijn graphs
Authors: Mangul Serghei , Koslicki David 
Published: May 2016

ABSTRACTMicrobial communities inhabiting the human body exhibit significant variability across different individuals and tissues, and are suggested to play an important role in health and disease. High-throughput sequencing offers unprecedented possibilities to profile microbial community composition, but limitations of existing taxonomic classification methods (including incompleteness of existing microbial reference databases) limits the ability to accurately compare microbial communities across different samples. In this paper, we present a method able to overcome these limitations by circumventing the classification step and directly using the sequencing data to compare microbial communities. The proposed method provides a powerful reference-free way to assess differences in microbial abundances across samples. This method, called EMDeBruijn, condenses the sequencing data into a de Bruijn graph. The Earth Mover's Distance (EMD) is then used to measure similarities and differences of the microbial communities associated with the individual graphs. We apply this method to RNA-Seq data sets from a coronary artery calcification (CAC) study and shown that EMDeBruijn is able to differentiate between case and control CAC samples while utilizing all the candidate microbial reads. We compare these results to current reference-based methods, which are shown to have a limited capacity to discriminate between case and control samples. We conclude that this reference-free approach is a viable choice in comparative metatranscriptomic studies.
Prospects of genomic prediction in the USDA Soybean Germplasm Collection: Historical data creates robust models for enhancing selection of accessions
Authors: Jarquin Diego , Specht James , Lorenz Aaron 
Published: May 2016

AbstractThe identification and mobilization of useful genetic variation from germplasm banks for use in breeding programs is critical for future genetic gain and protection against crop pests. Plummeting costs of next-generation sequencing and genotyping is revolutionizing the way in which researchers and breeders interface with plant germplasm collections. An example of this is the high density genotyping of the entire USDA Soybean Germplasm Collection. We assessed the usefulness of 50K SNP data collected on 18,480 domesticated soybean (G. max) accessions and vast historical phenotypic data for developing genomic prediction models for protein, oil, and yield. Resulting genomic prediction models explained an appreciable amount of the variation in accession performance in independent validation trials, with correlations between predicted and observed reaching up to 0.92 for oil and protein and 0.79 for yield. The optimization of training set design was explored using a series of cross-validation schemes. It was found that the target population and environment need to be well represented in the training set. Secondly, genomic prediction training sets appear to be robust to the presence of data from diverse geographical locations and genetic clusters. This finding, however, depends on the influence of shattering and lodging, and may be specific to soybean with its presence of maturity groups. The distribution of 7,608 non-phenotyped accessions was examined through the application of genomic prediction models. The distribution of predictions of phenotyped accessions was representative of the distribution of predictions for non-phenotyped accessions, with no non-phenotyped accessions being predicted to fall far outside the range of predictions of phenotyped accessions.
Not just methods: User expertise explains the variability of outcomes of genome-wide studies
Authors: Lotterhos Katie E. , François Olivier , Blum Michael G.B. 
Published: May 2016

AbstractGenome scan approaches promise to map genomic regions involved in adaptation of individuals to their environment. Outcomes of genome scans have been shown to depend on several factors including the underlying demography, the adaptive scenario, and the software or method used. We took advantage of a pedagogical experiment carried out during a summer school to explore the effect of an unexplored source of variability, which is the degree of user expertise.Participants were asked to analyze three simulated data challenges with methods presented during the summer school. In addition to submitting lists, participants evaluated a priori their level of expertise. We measured the quality of each genome scan analysis by computing a score that depends on false discovery rate and statistical power. In an easy and a difficult challenge, less advanced participants obtained similar scores compared to advanced ones, demonstrating that participants with little background in genome scan methods were able to learn how to use complex software after short introductory tutorials. However, in a challenge ofintermediate difficulty, advanced participants obtained better scores. To explain the difference, we introduce a probabilistic model that shows that a larger variation in scores is expected for SNPs of intermediate difficulty of detection. We conclude that practitioners should develop their statistical and computational expertise to follow the development of complex methods. To encourage training, we release the website of the summer school where users can submit lists of candidate loci, which will be scored and compared to the scores obtained by previous users.
TheC. elegansNF2/Merlin Molecule NFM-1 Non-Autonomously Regulates Neuroblast Migration and Interacts Genetically with the Guidance Cue SLT-1/Slit
Authors: Josephson Matthew P. , Aliani Rana , Lundquist Erik 
Published: May 2016

AbstractDuring nervous system development, neurons and their progenitors often migrate to their final destinations. InCaenorhabditis elegans, the bilateral Q neuroblasts and their descendants migrate long distances in opposite directions, despite being born in the same posterior region. QR on the right migrates anteriorly and generates the AQR neuron positioned near the head, and QL on the left migrates posteriorly, giving rise to the PQR neuron positioned near the tail. In a screen for genes required for AQR and PQR migration, we identified an allele ofnfm-1, which encodes a molecule similar to vertebrate NF2/Merlin, an important tumor suppressor in humans. Mutations inNF2lead to Neurofibromatosis Type II, characterized by benign tumors of glial tissues. These molecules containFour-point-oneEzrinRadixinMoesin (FERM) domains characteristic of cytoskeletal-membrane linkers, and vertebrate NF2 is required for epidermal integrity. Vertebrate NF2 can also regulate several transcriptional pathways including the Hippo pathway. Here we demonstrate that inC. elegans,nfm-1is required for complete migration of AQR and PQR, and that it likely acts outside of the Q cells themselves in a non-autonomous fashion. We also show a genetic interaction betweennfm-1and theC. elegans Slithomologslt-1, which encodes a conserved secreted guidance cue. In vertebrates,NF2can controlSlit2mRNA levels through the hippo pathway in axon pathfinding, suggesting a conserved interaction of NF2 and Slit2 in regulating migration.
A Key Cytoskeletal Regulator of Ubiquitination Amplifies TGFβ Signaling During Mouse Developmental Vascular Patterning
Authors: Shetty Ronak , Joshi Divyesh , Jain Mamta , Vasudevan Madavan , Paul Jasper Chrysolite , Bhat Ganesh , Banerjee Poulomi , Abe Takaya , Kiyonari Hiroshi , Vijayraghavan K. , Inamdar Maneesha S. 
Published: May 2016

AbstractVascular development involvesde novoformation of a capillary plexus, which is then pruned and remodeled by angiogenic events. Cytoskeletal remodeling and directional endothelial migration are essential for developmental and pathological angiogenesis. Smad-dependent TGFβ signaling controls vascular patterning and is negatively regulated by microtubules. Here we show that a positive regulator of TGFβ signaling is essential for developmental vascular patterning and microtubule stability. Rudhira/BCAS3 is known to bind microtubules and to play a nodal role in cytoskeletal remodeling and directional endothelial cell (EC) migration invitro. We demonstrate that the molecular and cellular function of Rudhira is deployed at critical steps in vascular patterning. We generated the first floxed mice forrudhiraand find that global or endothelial knockout ofrudhiraresults in mid-gestation lethality due to aberrant embryonic and extra-embryonic vessel patterning and defective cardiac morphogenesis.Rudhiranull yolk sac ECs show random and retarded migration. Yolk sac transcriptome analysis revealed key mediators of angiogenic processes and TGFβ receptor signaling were perturbed inrudhiranull mutants. Molecular and biochemical analyses showed thatrudhiradepletion reduced microtubule stability but increased expression of pathway inhibitors leading to high levels of SMAD2/3 ubiquitination and reduced activation. These effects were not rescued by exogenous TGFβ. However, TGFβ treatment of wild type ECs increased Rudhira expression. Further, exogenous Rudhira, which promotes directional cell migration, caused increased SMAD2/3 nuclear translocation and reduced inhibitor levels. Therefore, we propose that Rudhira and TGFβ signaling are mutually dependent. Rudhira has a dual function in promoting TGFβ signaling, possibly by sequestering microtubules and simultaneously preventing SMAD2/3 ubiquitination to permit EC migration and vascular patterning. TGFβ signaling and aberrant human Rudhira (Breast Cancer Amplified Sequence 3, BCAS3) expression are both associated with tumour metastasis. Our study identifies a cytoskeletal, cell type-specific modulator of TGFβ signaling important in development and cancer.
Genetic surfing in human populations: from genes to genomes
Authors: Peischl Stephan , Dupanloup Isabelle , Bosshard Lars , Excoffier Laurent 
Published: May 2016

AbstractGenetic surfing describes the spatial spread and increase in frequency of variants that are not lost by genetic drift and serial migrant sampling during a range expansion. Genetic surfing does not modify the total number of derived alleles in a population or in an individual genome, but it leads to a loss of heterozygosity along the expansion axis, implying that derived alleles are more often in homozygous state. Genetic surfing also affects selected variants on the wave front, making them behave almost like neutral variants during the expansion. In agreement with theoretical predictions, human genomic data reveals an increase in recessive mutation load with distance from Africa, an expansion load likely to have developed during the expansion of human populations out of Africa.