bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficacité alimentaire en cuniculture : voies d'améliorations, impacts technico-économiques et environnementaux
Authors: GIDENNE Thierry , MAERTENS Luc , DROUILHET Laurence 
Published: December 2019

Comme l'alimentation est le premier poste composant le coût de production (± 60 % du coût total) en élevage, la mesure de l'efficacité alimentaire est un indicateur majeur pour juger la performance et la rentabilité d'un élevage. L'amélioration de l'efficacité alimentaire est aussi un enjeu pour réduire l'impact environnemental de l'élevage, par la réduction des rejets animaux et une moindre production de matières premières alimentaires. Cette efficacité se mesure couramment par l'indice de consommation, et en cuniculture conventionnelle, l'indice de consommation économique (ICe = maternité+engraissement) a été réduit de 10 % (3,8 vs 3,4) ces 15 dernières années, de même que les rejets azotés et phosphorés. Cette amélioration provient des progrès conjoints sur la maîtrise sanitaire, l'alimentation (notamment les stratégies de restriction), la maîtrise du logement et le potentiel génétique des animaux. Cette article de synthèse résume l'impact de ces facteurs pour améliorer l'efficacité alimentaire en cuniculture conventionnelle. Après la gestion sanitaire, les performances reproductives du troupeau sont un levier majeur d'amélioration de l'ICe. L'usage d'aliments préservant la santé digestive du lapin en croissance, associé à une stratégie appropriée de restriction post-sevrage sont aussi de bons leviers. Les recherches en génétique peuvent contribuer à réduire l'ICe par 2 voies, l'amélioration de la vitesse de croissance et/ou la réduction de la consommation d'aliment à croissance fixée. L'impact environnemental de la cuniculture varie entre 7,6 et 10,5 kg d'équivalent CO2/kg de carcasse produite (légèrement supérieure au poulet) et ne diffère pas de celui du porc. À l'avenir, il semble possible d'améliorer encore l'efficacité alimentaire, et donc de réduire à la fois les intrants et les rejets, pour atteindre un ICe proche de 3,0 similaire aux systèmes porcins.
Formation of detrital clay grain coats by dewatering of deep-water sands and significance for reservoir quality
Authors: Porten Kristin W. , Warchoł Michał J. , Kane Ian A. 
Published: December 2019

ABSTRACTWell-developed detrital clay grain coats are observed in deep-marine sandstones of the Upper Cretaceous Springar Formation of the Vøring Basin in the Norwegian Sea. The detrital clay coats form thin and compact rims on individual sand grains and meniscus-shaped bridges between grains. These well-developed coats are found in high-density turbidites and proximal hybrid event beds with common to pervasive dewatering structures deposited in proximity to the base of a syndepositionally active basin high. Here, in one exploration well, detrital clay grain coats are common throughout a sandstone package 100 m thick. High-density turbidites and proximal and distal hybrid event beds drilled in mid- to distal-fan settings unaffected by seismically resolved seafloor topography show common dewatering features, but have only scattered detrital clay coats confined to individual dewatering pipes or dish structures. Hence, we propose that intense sediment dewatering has the potential to form detrital clay coats in deep-marine sandstones by a combination of elutriation and reorganization of clays during fluid escape from sediment bodies with pore fluid pressures significantly higher than the hydrostatic pressure. In submarine fan systems, deposition of sediment with coeval trapping of large volumes of interstitial pore fluid is most likely to occur where gravity flows undergo rapid deceleration in response to an abrupt decrease in confinement or gradient. Such environments include the channel–lobe transition and settings in proximity to seabed topography.The investigated sandstones are quartz arenites and subarkoses, with minor to moderate volumes of quartz cement (up to 6%). However, strongly to completely quartz-cemented intergranular pore space is observed where detrital clay coats or matrix does not cover quartz grains in the deepest part of the studied formation. Modeling of quartz cementation predicts that most intergranular macroporosity in the lower part of the Springar Formation would be quartz cemented if the sandstones were free of detrital clays. Based on our observations and modeling results we propose that intense sediment dewatering has the potential to form detrital clay coats, which can be important for retaining porosity in deeply buried sandstones and in basins with high present or past heat flow.
Landslide Susceptibility and Soil Loss Estimates for Drift Creek Watershed, Lincoln County, Oregon
Authors: Korte David M. , Shakoor Abdul 
Published: December 2019

ABSTRACTDrift Creek watershed, Lincoln County, Oregon, is a source of drinking water as well as a reproductive habitat for endangered salmon and trout species. Landslides, exacerbated by logging, are suspected as a cause of water quality deterioration in the watershed. To investigate the impact of landslides on water quality, we mapped landslide distribution and susceptibility, determined engineering properties of landslide-prone soil and rock, and estimated soil loss resulting from landslide-derived sediment within 30 m of Strahler third-order-or-higher streams in the watershed. We mapped 570 landslides using LiDAR imaging, orthophotographs, and field observations. We used logistic regression to determine the most significant variables contributing to landslide occurrence and to create a watershed-scale landslide susceptibility map. Siletz River Volcanics and the sedimentary Tyee Formation make up 85 percent of the watershed, with the sedimentary Yamhill and Nestucca formations making up the majority of the rest. Sedimentary rocks dominate in the Upper Drift Creek watershed, and volcanic dominate in the lower portion. The largest landslide deposits and the highest susceptibility occur in the sedimentary rock formations. The Siletz River Volcanics has a larger abundance of landslides than the sedimentary rock formations, but they are smaller in size with lower susceptibility of occurrence. The soil loss model indicates that the average annual soil loss from landslide deposits in the Upper Drift Creek watershed is 65 tons/acre/yr compared to 29 tons/acre/yr in the Lower Drift Creek watershed. The model also indicates that soil loss from areas along roads in the watershed is high.
Two-Phase Compositional Flow Simulation in Complex Fractured Media by 3D Unstructured Gridding with Horizontal and Deviated Wells
Authors: Zidane Ali , Firoozabadi Abbas 
Published: December 2019

Summary
A higher-order numerical model for compositional two-phase flow in fractured media is presented in this paper. The simulation of horizontal and deviated wells is incorporated in the formation using unstructured grids. All commonly used types of finite elements are accounted for in the algorithm: quadrangular and triangular elements in 2D, and hexahedra, prisms and tetrahedra elements in 3D.
The fracture crossflow equilibrium (FCFE) approach is applied to model the flow exchange between the fractures and the matrix. FCFE is combined with the hybridized form of the mass conservative mixed finite element (MHFE) and the higher-order discontinuous Galerkin (DG) method. A computer-aided design (CAD) interface is developed that connects the mesh generator to the CAD software. The interface allows to design, mesh, and incorporate horizontal and deviated wells into the higher-order simulator. The algorithm allows flow simulation in fractures in all ranges of permeability values as opposed to the embedded discrete fracture matrix (EDFM) approach where low permeable fractures affect the accuracy of the results. The efficiency, accuracy, and strengths of the model are demonstrated in comparison to alternatives including the embedded discrete fracture approach in different examples. Detailed incorporation of complex wells is presented in this work.
MAAWf: A Multifunctional and Visual Tool for Microbiomic Data Analyses
Authors: Zhu Sibo , Sun Tao , Zhu Chengkai , Qing Tao , Jiang Yanfeng , Ding Ruifeng , Su Haoxuan , Sun Yunwen , Xu Xiulin , Xu Kelin , Suo Chen , Yuan Ziyu , Zhang Tiejun , Zhao Genming , Ye Weimin , Jin Li , Chen Xingdong 
Published: December 2019

Abstract
Background: Microbiomic research has grown in popularity in recent decades. The widespread use of next-generation sequencing technologies, including 16S rRNA gene-based and metagenomic shotgun-based methods, has produced a wealth of microbiome data. At present, most software and analysis workflows for analysis and processing of microbiomic data are command line-based, which requires considerable computing time and makes interaction difficult. Results: To provide a command-line free, multifunctional, user interface friendly and online/local deployable microbiome analysis tool, we developed Microbiome Automated Analysis Workflows (MAAWf). MAAWf is composed of a whole metagenomic shotgun workflow (WMS) and a 16S Sequencing Workflow. The WMS analysis workflow assesses taxonomy, protein-coding genes, metabolic pathways, carbohydrate-active enzymes (CAZy) and antibiotic resistance genes (ARGs). The 16S ribosomal RNA (rRNA) analysis workflow counts and clusters operational taxonomic units (OTUs), estimates alpha- and beta-diversity and inter-group differences, and performs functional analysis. We also compared MAAWf with other commonly avaiable analysis tools using two public datasets. The MAAWf pipeline was established using the Ubuntu 16.04.6 LTS kernel with primary sequence files such as FASTQ format and taxonomic format such as OTU or BIOM formats. Following analysis of public 16S and WMS datasets, MAAWf obtained similar results to DIAMOND-MEGAN6, MG-RAST, DADA2 and QIIME2, but the running time was much shorter. Conclusions: MAAWf is a visual, integrated, rapid analysis tool that enables remote and local computing of microbiome data.
Prenatal diagnosis of a 16p11.2p11.1 mosaic small supernumerary marker chromosome (sSMC)
Authors: Tidrenczel Zsolt , Tardy Erika P , Pikó Henrietta , Sarkadi Edina , Böjtös Ildikó , Vermes Gábor , Demeter János , Kósa János P , Beke Artúr 
Published: December 2019

Abstract
Background. Small supernumerary marker chromosome (sSMC) is a challenge in prenatal diagnosis. Its’ presence is associated with advanced maternal age and distinct ultrasound findings, prediction of postnatal clinical consequences and prenatal counselling is difficult. Exact characterization of an sSMC is augmented by the application of novel molecular methods such as fluorescent in situ hybridization (FISH) and array comparative genome hybridization (aCGH). Case presentation. Chorion villous sampling of a fetus of a 42-year old secundipara was carried out due to advanced maternal age and the conventional banding cytogenetic examination revealed a mosaic sSMC. Detailed prenatal ultrasound scan showed no fetal malformations. The karyotype from confirmatory amniocentesis was 47,XY,+mar[45]/46,XY. The level of mosaicism was 70% from chorionic villus and amnion cells as well. By using FISH and SNP based aCGH the exact origin of the marker was described and the final prenatal karyotype was determined as 47,XY,+mar[70].arr[GRCh38]16p11.2p11.1(31699804_35989873)x3dn/46,XY[30]. The increase in DNA dosage was 4,29 Mb affecting 20 genes with two OMIM ones (ZNF267 and TP53TG3), the SNP analysis excluded the possibility of uniparental disomy (UPD) of the chromosome. The application of the molecular cytogenetic methods allowed us the differentiate the mosaic marker chromosome from the known 16p11.2 duplication syndrome in close neighboring that is connected to developmental delay and autism spectrum disorder. The present case was identified as a harmless de novo euchromatic variant (EV) of the short arm of chromosome 16. Postnatal karyotyping from neonatal peripheral blood confirmed the presence of the marker. FISH analysis with probe D16Z2 on cultured lymphocyte and buccal smear samples revealed a 64% and 45% mosaic state of the sSMC, respectively. The precise karyotype was finally defined as 47,XY,+min(16)(:16p11.2->p11.1:)dn[64]/46,XY. Conclusions. Novel microarray methods combined with molecular cytogenetic analysis is particularly effective in the rapid and accurate diagnosis of sSMCs, especially in a prenatal situation when the exact characterization of a genomic imbalance is of utmost importance. Precise diagnosis facilitates proper genetic counseling, allows informed decision making and helps avoiding unnecessary pregnancy termination.
Identification and prognosis analysis of germline WT1 (p.Arg370Pro) and TET2 (p.Asp1844Asn) mutations in an acute myeloid leukemia patient with t(9;11)(p21.3;q23.3);KM2TA-MLL3&nbsp;
Authors: Ma Qiang , Guo Yixian , Lan Xiaoxi , Wang Guoxiang , Liu Congyan , He Jingjuan , Sun Xuejing , Liu Yan , Wan Suigui , Su Li , Sun Wanling 
Published: December 2019

Abstract
Background: Somatic mutations in WT1 and TET2 were separately perceived as contributors to hematopoietic disorders and thought to have a mutually exclusive effect in acute myeloid leukemia (AML). Here, we report a case in which WT1 and TET2 mutations co-existed at different stages in an AML patient with t(9;11)(p21.3;q23.3), and without abnormal WT1 expression, which did not synchronize with the patient's tumor state. Hence, the origins and prognostic value of these two mutations were investigated. Methods: Bone marrow (BM) and buccal mucosal cells were obtained from a 27-year-old male AML patient, and next-generation sequencing (NGS), targeting multiple genes, was performed after DNA extraction. Single nucleotide variant (SNV) and insertion-deletion (Indel) associated with AML were identified in these two samples by using SAM tools. Then, peripheral blood or buccal mucosal cells were obtained from the patient’s relatives, and NGS targeting multiple genes was applied. Besides, the relationship between overall survival (OS) and alteration of these two genes in AML patients was analyzed by using cBioPortal and UALCAN databases, respectively. Results: SNV of WT1 (NM_024426:exon7:c.1109G>C；p.Arg370Pro) and TET2 (NM_001127208:exon11:c.5530G>A；p.Asp1844Asn) were present in the BM of the patient, and these two mutations were also observed in his buccal mucosal cells, which suggested that they were germline mutations. Variation analysis of samples from other relatives indicated that WT1 (NM_024426:exon7:c.1109G>C;p.Arg370Pro) and TET2 (NM_001127208:exon11:c.5530G>A;p.Asp1844Asn) were also present in his father and mother, respectively. The patient’s brother also carried TET2 (NM_001127208:exon11:c.5530G>A；p.Asp1844Asn) mutations. Bioinformatic analysis suggested that mutations in the WT1 and TET2 genes are both associated with a poor prognosis of AML, and abnormal TET2 expression is associated with a poorer prognosis than abnormal WT1 expression. Conclusion: It is firstly report that WT1 p.Arg370Pro and TET2 p.Asp1844Asn mutations co-existed in an AML patient with t(9;11)(p21.3;q23.3) and no WT1 abnormal expression, which highlight the importance of the identification and prognostic evaluation of germline mutations in clinical practice for AML.
Changes in regional cerebral tissue oxygen saturation during anesthesia induction in female patients undergoing breast cancer surgery
Authors: Sheng Fang , Jin Feng , Tan Wen-fei , Ma Hong 
Published: December 2019

Abstract
Background Although the monitoring of regional cerebral oxygen saturation (rScO 2 ) is widely used for cardiac and non-cardiac surgeries, conflicting reports regarding changes in rScO 2 during anesthesia induction remain. We designed this cohort clinical study to assess precise alterations in rScO 2 and the possible mechanism . Methods This cohort study was designed to examine changes in rScO 2 with anesthesia induced by a target control infusion of propofol from the beginning of anesthesia to 30 minutes after induction in patients undergoing breast cancer surgery. rScO 2 values from the right and left sides of patients’ foreheads were averaged to directly determine cerebral oxygenation from FORE-SIGHT data. Mean arterial pressure (MAP), heart rate (HR), partial pressure of oxygen in arterial blood (PaO 2 ), partial pressure of carbon dioxide in arterial blood (PaCO 2 ), hemoglobin concentration (Hb), and cardiac output (CO) were measured every minute until 30 minutes after anesthesia induction. Results A total of 30 female patients treated between January 2016 and April 2016 were included in this study. The average rScO 2 at 7 minutes was 81.7%, which was higher than the average rScO 2 at baseline (67.3%) and at 15 minutes (68.3%). Average rScO 2 correlated significantly with PaO 2 during the first 7 minutes of anesthesia induction. Conclusion During anesthesia induction, changes in rScO 2 , which increased to a peak value at 7 minutes, may be correlated with increases in PaO 2 , and the return of rScO 2 to baseline at 15 minutes may have occurred due to flow-metabolism coupling and balancing between white matter and gray matter.
Assessment of factors affecting voluntary counseling and testing service utilization among preparatory school students in Gondar town, Amhara region, Ethiopia
Authors: Demeke Getaneh Bizuayehu , Alazbih Nega Mihret 
Published: December 2019

Abstract
Background Globally the adolescent and youths are facing different sexual and reproductive health problems like unwanted pregnancy, unsafe abortion, STI including HIV.HIV / AIDS is continue to be a major global health priority. HIV counseling and testing is a key strategic entry point to prevention, treatment, care and support services .HIV/AIDS counseling is “confidential communication between client and a care provider aimed at enabling the client to cope with stress and to take personal decisions relating to HIV/AIDS.VCT give clients an opportunity to explore their HIV risks and to learn their HIV test results in complete confidence.Objective The objective of the study was to asses factors affecting voluntary counseling and testing service utilization among preparatory school students in Gondar town.Methods Institutional based cross-sectional study design was employed. A multistage sampling procedure was conducted in the study area. Data were collected using pretested self-administered questionnaire and the data entered, clean and analyzed by using SPSS version 16 software. Descriptive, bivariate and multivariate analysis were employed. Multivariate analysis with 95% CI was computed to identify factors associated with voluntary counseling and testing service utilization at P-value <0.05.Results A total of 654 study participants were included in the study with the response rate of 97%. The study indicated that 81.7% of study participants knew about voluntary counseling and testing services utilization .But the practice of voluntary counseling and testing was 48.3% with (95% CI: 44.5 -52.1).Based on the finding of multivariate analysis among independent variables, age, place of birth, mother’s educational level and discussed with parents on the issue of VCT were significantly associated with voluntary counseling and testing services utilization.Conclusion Majority of the study participants were not utilize voluntary counseling and testing services, only few respondents ever had VCT test as well as the proportion of students who had discussed on VCT issues with their parent was also very low. Cultural taboos was the main obstacle to students did not discuss with parents on the issue of VCT in the study area. Therefore; it needs great effort all concerned body to improve their services utilization. In broadly family life education should be encourage for the students and parents to promote VCT utilization.
CpG single nucleotide polymorphisms of the insulin signaling pathway associated with the risk of prediabetic status/type 2 diabetes in Chinese population
Authors: Tang Linlin , Wang Changyi , Han Liyuan , Ma Jianping , Cheng Jia , Duan Shiwei 
Published: December 2019

Abstract
Aims: Cytosine-phosphate-guanine single nucleotide polymorphisms (CpG SNPs) have been identified as new markers in human diseases. We aimed to evaluate the contribution of 29 CpG SNPs in the insulin signaling pathways to the risk of prediabetes and type 2 diabetes (T2D) in Han Chinese. Materials and methods: We recruited 708 T2D subjects, 253 prediabetes subjects and 575 healthy controls from 16 community health service centers (CHSC) in Shenzhen Nanshan district. Detailed clinical information and DNA samples were collected. A total of 29 CpG SNPs of the insulin signaling pathways were sequenced using the MassARRAY platform. Binary logistic regression was applied to evaluate the association between these 29 CpG SNPs with prediabetes and T2D after adjusted the relevant confounding factors. The potential interactions among the 29 CpG SNPs were conducted by the generalized multifactor dimensionality reduction (GMDR). Results: Significant associations are found between KRAS rs7311692 [Padjusted = 0.009, OR = 0.562(0.363-0.868) by allele] and CBLC rs2965143 [Padjusted = 0.008, OR = 1.591(1.128-2.242) under the dominant model] with prediabetes. A further breakdown analysis by gender identify a significant association between MAPK9 rs1363513 and T2D risk in males [Padjusted = 0.004, OR = 0.57(0.399-0.836) by allele], while FLOT2 rs4795473 is associated with prediabetes in females (P = 0.007 by genotype). However, no significant effect of potential interaction is observed among the 29 CpG SNPs. Conclusion: These results indicated that KRAS rs7311692, CBLC rs2965143 and FLOT2 rs4795473 are related with prediabetes, while MAPK9 rs1363513 was associated with male T2D.
MicroRNAs as potential biomarkers for the diagnosis of traumatic brain injury: a systematic review and meta-analysis
Authors: Zhou Qian , Yin Jian , Wang Yadong , Zhuang Xinsuo , He Zhiyang , Chen Zuobing , Yang Xiaofeng 
Published: December 2019

Abstract
Background: Traumatic brain injury (TBI) is a sudden trauma on the head, commonly associated with death and long-term disability. MicroRNAs (miRNAs) are potential biomarkers of diverse diseases, including TBI. However, few systematic reviews and meta-analyses have been conducted to determine the clinical value of miRNAs expression in TBI patients.Methods: We did a comprehensive literature search to identify articles that have reported on the diagnostic and prognostic value of miRNAs expression in TBI patients.Results: Six studies investating the diagnostic value of miRNA in TBI were analyzed in this study. The overall sensitivity, specificity and area under the curve (AUC) of miRNAs in diagnosis of TBI were 92% [95% confidence interval (CI): 0.87–0.95]; 92% (95% CI 0.78–0.97) and 96% (95% CI 0.94–0.97), respectively. We found that panels of multiple miRNAs could improve the diagnostic accuracy of TBI. Compared to saliva, detected samples like blood and brain tissue could significantly enhance diagnostic accuracy. Besides, the AUC of miRNAs in severe TBI was 0.97, with 92% sensitivity and 92% specificity.Conclusions: This systematic review and meta-analysis demonstrated that miRNAs could be potential diagnostic markers in TBI patients. MiRNAs detected in blood and brain tissue display high accuracy for TBI diagnosis.