bluuebunny/crossref_metadata_2025_split huggingface dataset:
Postoperative Steroid Taper Is Associated With Pelvic Sepsis After Ileal Pouch-anal Anastomosis
Authors: Ritter Kaitlin A , Burke John P , Stocchi Luca , Aiello Alexandra , Holubar Stefan , Ashburn Jean H , Lipman Jeremy M , Shawki Sherief , Hull Tracy 
Published: December 2018

AbstractObjectiveWe hypothesized that postoperative oral steroid taper after ileal pouch-anal anastomosis for inflammatory bowel disease would not be associated with pelvic septic complications.BackgroundRecent data has emphasized the possible association between biologic medication use and pelvic sepsis following ileal pouch-anal anastomosis. Limited contemporary data exist examining the effects of steroid use on these complications.MethodsConsecutive patients undergoing ileal pouch-anal anastomosis for inflammatory bowel disease at a single institution from January 2009 to December 2013 were included. Factors associated with anastomotic leak and pelvic sepsis were assessed using univariate and multivariate analysis.ResultsA total of 686 patients were included (mean age 39.5 years, 59% males). Postoperative oral steroid taper was associated with both anastomotic leak and pelvic sepsis on univariate analysis. Stress dose intravenous steroid use was not associated with complications. Multivariate analysis indicated total proctocolectomy (odds ratio [OR] 2.2; confidence interval [CI] 1.01–4.7, P = 0.047), and postoperative oral steroid taper (OR 2.3; CI 1.06–5.1; P = 0.035) as independent factors significantly associated with pelvic sepsis.ConclusionsProlonged postoperative oral steroid taper after ileal pouch-anal anastomosis should be avoided. If preoperative steroid weaning is not possible before a planned total proctocolectomy and ileal pouch-anal anastomosis, patients should undergo an initial total abdominal colectomy.
Results of Phrenic Nerve Transfer to the Musculocutaneous Nerve Using Video-Assisted Thoracoscopy in Patients with Traumatic Brachial Plexus Injury: Series of 28 Cases
Authors: Cardoso Marcio de Mendonça , Gepp Ricardo de Amoreira , Mamare Eduardo , Guedes-Correa José Fernando 
Published: December 2018

Abstract

BACKGROUND
The phrenic nerve can be transferred to the musculocutaneous nerve using video-assisted thoracoscopy, aiming at the recovery of elbow flexion in patients with traumatic brachial plexus injuries. There are few scientific papers in the literature that evaluate the results of this operative technique.

OBJECTIVE
To evaluate biceps strength and pulmonary function after the transfer of the phrenic nerve to the musculocutaneous nerve using video-assisted thoracoscopy.

METHODS
A retrospective study was carried out in a sample composed of 28 patients who were victims of traumatic injury to the brachial plexus from 2008 to 2013. Muscle strength was graded using the British Medical Research Council (BMRC) scale and pulmonary function through spirometry. Statistical tests, with significance level of 5%, were used.

RESULTS
In total, 74.1% of the patients had biceps strength greater than or equal to M3. All patients had a decrease in forced vital capacity and forced expiratory volume in 1 s, with no evidence of recovery over time.

CONCLUSION
Transferring the phrenic nerve to the musculocutaneous nerve using video-assisted thoracoscopy may lead to an increase in biceps strength to BMRC M3 or greater in most patients. Considering the deterioration in the parameters of spirometry observed in our patients and the future effects of aging in the respiratory system, it is not possible at the moment to guarantee the safety of this operative technique in the long term.
An efficient analytical reduction of detailed nonlinear neuron models
Authors: Amsalem Oren , Eyal Guy , Rogozinski Noa , Schürmann Felix , Gevaert Michael , Kumbhar Pramod , Segev Idan 
Published: December 2018

AbstractDetailed conductance-based nonlinear neuron models consisting of thousands of synapses are key for understanding of the computational properties of single neurons and large neuronal networks, and for interpreting experimental results. Simulations of these models are computationally expensive, considerably curtailing their utility.Neuron_Reduceis a new analytical approach to reduce the morphological complexity and computational time of nonlinear neuron models. Synapses and active membrane channels are mapped to the reduced model preserving their transfer impedance to the soma; synapses with identical transfer impedance are merged into one NEURON process still retaining their individual activation times.Neuron_Reduceaccelerates the simulations by 40-250 folds for a variety of cell types and realistic number (10,000-100,000) of synapses while closely replicating voltage dynamics and specific dendritic computations. The reduced neuron-models will enable realistic simulations of neural networks at unprecedented scale, including networks emerging from micro-connectomics efforts and biologically-inspired “deep networks”.Neuron_Reduceis publicly available and is straightforward to implement.
Genomic Prediction of Complex Disease Risk
Authors: Lello Louis , Raben Timothy G. , Yong Soke Yuen , Tellier Laurent CAM , Hsu Stephen D.H. 
Published: December 2018

AbstractWe construct risk predictors using polygenic scores (PGS) computed from common Single Nucleotide Polymorphisms (SNPs) for a number of complex disease conditions, using L1-penalized regression (also known as LASSO) on case-control data from UK Biobank. Among the disease conditions studied are Hypothyroidism, (Resistant) Hypertension, Type 1 and 2 Diabetes, Breast Cancer, Prostate Cancer, Testicular Cancer, Gallstones, Glaucoma, Gout, Atrial Fibrillation, High Cholesterol, Asthma, Basal Cell Carcinoma, Malignant Melanoma, and Heart Attack. We obtain values for the area under the receiver operating characteristic curves (AUC) in the range ~ 0.58 – 0.71 using SNP data alone. Substantially higher predictor AUCs are obtained when incorporating additional variables such as age and sex. Some SNP predictors alone are sufficient to identify outliers (e.g., in the 99th percentile of PGS) with 3 – 8 times higher risk than typical individuals. We validate predictors out-of-sample using the eMERGE dataset, and also with different ancestry subgroups within the UK Biobank population. Our results indicate that substantial improvements in predictive power are attainable using training sets with larger case populations. We anticipate rapid improvement in genomic prediction as more case-control data become available for analysis.
ChIA-PIPE: A fully automated pipeline for ChIA-PET data analysis and visualization
Authors: Capurso Daniel , Wang Jiahui , Tian Simon Zhongyuan , Cai Liuyang , Namburi Sandeep , Lee Byoungkoo , Tjong Harianto , Tang Zhonghui , Wang Ping , Wei Chia-Lin , Ruan Yijun , Li Sheng 
Published: December 2018

AbstractChIA-PET enables the genome-wide discovery of chromatin interactions involving specific protein factors, with base-pair resolution. Interpreting ChIA-PET data depends on having a robust analytic pipeline. Here, we introduce ChIA-PIPE, a fully automated pipeline for ChIA-PET data processing, quality assessment, analysis, and visualization. ChIA-PIPE performs linker filtering, read mapping, peak calling, loop calling, chromatin-contact-domain calling, and can resolve allele-specific peaks and loops. ChIA-PIPE also automates quality-control assessment for each dataset. Furthermore, ChIA-PIPE generates input files for visualizing 2D contact maps with Juicebox and HiGlass, and provides a new dockerized visualization tool for high-resolution, browser-based exploration of peaks and loops. With minimal adjusting, ChIA-PIPE can also be suited for the analysis of other related chromatin-mapping data.
Functional imaging of microbial interactions with tree roots using a microfluidics setup
Authors: Noirot-Gros Marie-Francoise , Shinde Shalaka V. , Akins Chase , Johnson Jessica L. , Zerbs Sarah , Wilton Rosemarie , Kemner Ken , Noirot Philippe , Babnigg Gyorgy 
Published: December 2018

AbstractCoupling microfludics with microscopy has emerged as a powerful approach to study at cellular resolution the dynamics in plant physiology and root-microbe interactions. Most devices have been designed to study the model plant Arabidopsis thaliana at higher throughput than conventional methods. However, there is a need for microfluidic devices which enable in vivo studies of root development and root-microbe interactions in woody plants. Here, we developed the RMI-chip, a simple microfluidic setup in which Populus tremuloides (aspen tree) seedlings can grow for over a month, allowing continuous microscopic observation of interactions between live roots and rhizobacteria. We find that the colonization of growing aspen roots by Pseudomonas fluorescens in the RMI-chip involves dynamic biofilm formation and dispersal, in keeping with previous observations in a different experimental set-up. Also, we find that whole-cell biosensors based on the rhizobacterium Bacillus subtilis can be used to monitor compositional changes in the rhizosphere but that the application of these biosensors is limited by their efficiency at colonizing aspen roots and persisting. These results indicate that functional imaging of dynamic root-bacteria interactions in the RMI-chip requires careful matching between the host plant and the bacterial root colonizer.
Elucidating genomic patterns and recombination events in plant cybrid mitochondria
Authors: Garcia Laura E. , Zubko Mikhajlo K. , Zubko Elena I. , Sanchez-Puerta M. Virginia 
Published: December 2018

AbstractThe maintenance of a dynamic equilibrium between the mitochondrial and nuclear genomes requires continuous communication and a high level of compatibility between them, so that alterations in one genetic compartment need adjustments in the other. The co-evolution of nuclear and mitochondrial genomes has been poorly studied, even though the consequences and effects of this interaction are highly relevant for human health, as well as for crop improvement programs and for genetic engineering. The mitochondria of plants represent an excellent system to understand the mechanisms of genomic rearrangements, chimeric gene formation, incompatibility between nucleus and cytoplasm, and horizontal gene transfer. We carried out detailed analyses of the mitochondrial genome (mtDNA) of a repeated cybrid between the solanaceaeNicotiana tabacumandHyoscyamus niger. The mtDNA of the cybrid was intermediate between the size of parental mtDNAs and the sum of them. Noticeably, most of the homologous sequences inherited from both parents were lost. In contrast, the majority of the sequences exclusive of a single parent were maintained. The mitochondrial gene content included a majority ofN. tabacumderived genes, but also chimeric, two-parent derived, andH. niger-derivedgenes in a tobacco nuclear background. Any of these alterations in the gene content could be the cause of CMS in the cybrid. The parental mtDNAs interacted through 28 homologous recombination events and a single case of illegitimate recombination. Three main homologous recombination mechanisms were recognized in the cybrid mitochondria. Break induced replication (BIR) pathway was the most frequent. We propose that BIR could be one of the mechanisms responsible for the loss of the majority of the repeated regions derived fromH. niger.
A thorough RNA-seq characterization of the porcine sperm transcriptome and its seasonal changes
Authors: Gòdia M. , Estill M. , Castelló A. , Balasch S. , Rodríguez-Gil J.E. , Krawetz S.A. , Sánchez A. , Clop A. 
Published: December 2018

AbstractUnderstanding the molecular basis of cell function and ultimate phenotypes is crucial for the development of biological markers. With this aim, several RNA-seq studies have been devoted to characterize the transcriptome of ejaculated spermatozoa in relation to sperm quality and fertility. Semen quality follows a seasonal pattern and decays in the summer months in several animal species. The aim of this study was to deeply profile the transcriptome of the boar sperm and to evaluate its seasonal changes. We sequenced the total and the short fractions of the sperm RNA from 10 Pietrain boars, 5 collected in summer and 5 five sampled in winter, and identified a complex and rich transcriptome with 4,436 coding genes of moderate to high abundance. Transcript fragmentation was high but less obvious in genes related to spermatogenesis, chromatin compaction and fertility. Short non-coding RNAs mostly included piwi-interacting RNAs, transfer RNAs and micro-RNAs. We also compared the transcriptome of the summer and the winter ejaculates and identified 34 coding genes and 7 micro-RNAs with a significantly distinct distribution. These genes were mostly related to oxidative stress, DNA damage and autophagy. This is the deepest characterization of the boar sperm transcriptome and the first study linking the transcriptome and the seasonal variability of semen quality in animals. The annotation described here can be used as a reference for the identification of markers of sperm quality in pigs.
Mantoniella Beaufortii and Mantoniella Baffinensis sp. nov. (Mamiellales, Mamiellophyceae), Two New Green Algal Species from the High Arctic
Authors: Yau Sheree , dos Santos Adriana Lopes , Eikrem Wenche , Ribero Catherine Gérikas , Gourvil Priscilla , Balzano Sergio , Escande Marie-Line , Moreau Hervé , Vaulot Daniel 
Published: December 2018

AbstractMembers of the class Mamiellophyceae comprise species that can dominate picophytoplankton diversity in polar waters. Yet polar species are often morphologically indistinguishable from temperate species, although clearly separated by molecular features. Here we examine four Mamiellophyceae strains from the Canadian Arctic. The 18S rRNA and Internal Transcribed Spacer 2 (ITS2) gene phylogeny place these strains within the family Mamiellaceae (Mamiellales, Mamiellophyceae) in two separate clades of the genus Mantoniella. ITS2 synapomorphies support their placement as two new species, Mantoniella beaufortii and Mantoniella baffinensis. Both species have round green cells with diameter between 3–5 μm, one long flagellum and a short reduced flagellum (~1 μm) and are covered by spiderweb-like scales, making both species similar to other Mantoniella species. Morphologically, M. beaufortii and M. baffinensis are most similar to the cosmopolitan M. squamata with only minor differences in scale structure distinguishing them. Screening of global marine metabarcoding datasets indicates M. beaufortii has only been recorded in seawater and sea ice samples from the Arctic while no environmental barcode matches M. baffinensis. Like other Mamiellophyceae genera that have distinct polar and temperate species, the polar distribution of these new species suggests they are cold or ice-adapted Mantoniella species.
Wnt signalling is a major determinant of neuroblastoma cell lineages
Authors: Szemes Marianna , Greenhough Alexander , Malik Karim 
Published: December 2018

AbstractThe neural crest, which has been referred to as the fourth germ layer, comprises a multipotent cell population which will specify diverse cells and tissues, including craniofacial cartilage and bones, melanocytes, the adrenal medulla and the peripheral nervous system. These cell fates are known to be determined by gene regulatory networks (GRNs) acting at various stages of neural crest development, such as induction, specification, and migration. Although transcription factor hierarchies and some of their interplay with morphogenetic signalling pathways have been characterised, the full complexity of activities required for regulated development remains uncharted. Deregulation of these pathways may contribute to tumourigenesis, as in the case of neuroblastoma, a frequently lethal embryonic cancer thought to arise from the sympathoadrenal lineage of the neural crest.In this conceptual analysis, we utilise next generation sequencing data from neuroblastoma cells and tumours to evaluate the possible influences of Wnt signalling on neural crest GRNs and on neuroblastoma cell lineages. We provide evidence that Wnt signalling is a major determinant of regulatory networks that underlie mesenchymal/NCC-like cell identities through PRRX1 and YAP/TAZ transcription factors. Furthermore, Wnt may also co-operate with Hedgehog signalling in driving proneural differentiation programmes along the adrenergic lineage. We propose that elucidation of Signalling Regulatory Networks can augment and complement GRNs in characterising cell identities, which will in turn contribute to the design of improved therapeutics tailored to primary and relapsing neuroblastoma.
Enhancer Reprogramming Confers Dependence on Glycolysis and IGF signaling in KMT2D Mutant Melanoma
Authors: Maitituoheti Mayinuer , Keung Emily Z. , Tang Ming , Yan Liang , Alam Hunain , Han Guangchun , Raman Ayush T. , Terranova Christopher , Sarkar Sharmistha , Orouji Elias , Amin Samir B. , Sharma Sneha , Williams Maura , Samant Neha S. , Dhamdhere Mayura , Zheng Norman , Shah Tara , Shah Amiksha , Axelrad Jacob B. , Anvar Nazanin E. , Lin Yu-Hsi , Jiang Shan , Chang Edward Q. , Ingram Davis R. , Wang Wei-Lien , Lazar Alexander , Lee Min Gyu , Muller Florian , Wang Linghua , Ying Haoqiang , Rai Kunal 
Published: December 2018

SUMMARYEpigenetic modifiers have emerged as important regulators of tumor progression. We identified histone methyltransferase KMT2D as a potent tumor-suppressor through an in vivo epigenome-focused pooled RNAi screen in melanoma. KMT2D harbors frequent somatic point mutations in multiple tumor types. How these events contribute to tumorigenesis and whether they impart therapeutic vulnerability are poorly understood. To address these questions, we generated a genetically engineered mouse model of melanoma based on conditional and melanocyte-specific deletion of KMT2D. We demonstrate KMT2D as a bona fide tumor suppressor which cooperates with activated BRAF. KMT2D-deficient tumors showed substantial reprogramming of key metabolic pathways including glycolysis. Glycolysis enzymes, intermediate metabolites and glucose consumption rate were aberrantly upregulated in KMT2D mutant cells. The pharmacological inhibition of glycolysis reduced proliferation and tumorigenesis preferentially in KMT2D mutant cells. Mechanistically, KMT2D loss caused drastic reduction of H3K4me1-marked active enhancer states. Loss of distal enhancer and subsequent reduction in expression of IGFBP5 activated IGF1R-AKT to increase glycolysis in KMT2D-deficient cells. We conclude that KMT2D loss promotes tumorigenesis by facilitating increased usage of glycolysis pathway for enhanced biomass needs via enhancer reprogramming. Our data imply that inhibition of glycolysis or IGFR pathway could be a potential therapeutic strategy in KMT2D mutant tumors.
A quantitative medico-botanical expedition of Fairy Meadows National Park, Diamir, Gilgit Baltistan, Pakistan
Authors: Wali Rahmat , Rahman Khalid , Iqbal Raja Naveed , Qureshi Rahmatullah , Mashwani Ziaur-Rehman 
Published: December 2018

AbstractThis study was conducted to investigate the ethnobotanical knowledge of the population of the Fairy Meadow National Park, Diamir, Gilgit Baltistan. The study area was previously ignored due to physical barriers, remoteness and religious extremism. The use of medicinal plants for various maladies, known to the elders of the community and passed orally to the younger generation was documented. A total of 146 informants were interviewed using semi-structured questionnaires. The data was quantitatively analyzed employing frequency of citation (FC), use value (UV), relative frequency of citation (RFC) along with Pearson correlation coefficient (PCC). A total of 90 plants species belonging to 77 genera and 49 different families have been documented. These medicinal plants were used against 55 diseases, especially stomach problems (23.3%), cough (17.7%), asthma and fever (16.6%). For 31 out of 90 plants species which had been reported either, new uses (28 plants) or new use-report (3 plants) were found. New reported medicinal plants includeAllium gilgitensis, Astragalus gilgitensisandPedicularia flava. The majority of the documented plants were wild collected (86%), herbs (60%), and leaves were the most widely used part (27%). The common method of preparation was powder (27%) mainly administered orally (81.7%). The highest use values were found forBerberis lyceum(5.47),Thymus lineari s(5.07) andRhododendron anthopogon(5.0), while the plants with greater relative frequency of citation wereBerberis lyceum(0.97),Thymus linearis(0.89) andRhododendron anthopogon(0.75). The Pearson correlation coefficient is 0.836 between RFC and UV showing high positive association. This study was an extension to the ethnobotanical work done in Pakistan previously. We documented a wealth of traditional knowledge, and could record the uses of various species for the first time from Pakistan. The new use reports and new plants reported supplement the foundation of pharmacology and new drug development for complex and challenging disease
Influence of nitrite on chemical composition of passivation film of steel bars under the coupling effects of carbonization and chloride
Authors: Liu Junzhe , Geng Jundi , Wang Hui , Ba Mingfang , He Zhiming 
Published: December 2018

Purpose
This paper aims to study the influence of NaNO2 on the chemical composition of passivation film.

Design/methodology/approach
X-ray photoelectron spectroscopy and X-ray diffraction were selected to determine the composition of passivation film of steel bars in mortar. The specimens were exposed to the chloride solution, carbonation environment and the coupling effects of chloride solution and carbonation. The chemical composition and micro structures at 0 and 5 nm from the outer surface of the passivation film of steel bars were analyzed.

Findings
Results showed that the nitrite inhibitor improved the forming rate of the passivation film and increased the mass ratio of Fe3O4 to FeOOH on the surface of steel bars. The component of Fe3O4 at 5 nm of the steel passivation film was more than that at 0 nm. Sodium ferrite in the pore solution was easily hydrolyzed and then FeOOH was formed. Therefore, due to the nitrite inhibitor, a “double layer structure” of the passivation film was formed to prevent steels bars from corrosion.

Originality/value
This is original work and may help the researchers further understand the mechanism of rust resistance by nitrite inhibitor.