BaySize: Bayesian Sample Size Planning for Phase I Dose-Finding Trials

We propose BaySize, a sample size calculator for phase I clinical trials using Bayesian models. BaySize applies the concept of effect size in dose finding, assuming the MTD is defined based on an equivalence interval. Leveraging a decision framework that involves composite hypotheses, BaySize utilizes two prior distributions, the fitting prior (for model fitting) and sampling prior (for data generation), to conduct sample size calculation under desirable statistical power. Look-up tables are generated to facilitate practical applications. To our knowledge, BaySize is the first sample size tool that can be applied to a broad range of phase I trial designs

H.pylori Infection inhibits Inflammatory Bowel Disease(IBD) by affecting the intestinal flora: A systematic Review

Background: Inflammatory bowel diseases (IBD) are chronic, relapsing-remitting diseases of the gastrointestinal tract, including Crohn’s disease (CD), Ulcerative Colitis (UC), and Unclassified IBD (IBDU). Their pathogenesis involves genes and the environment as cofactors in inducing autoimmunity; mainly, the interactions between enteric pathogens and immunity are studied. For example, Helicobacter pylori (HP) is a common pathogen causing gastric inflammation. However, studies found that the number of people with HP was lower than those with IBD. Therefore, it suggests that HP might protect against IBD. Methods: The search terms "helicobacter pylori," "inflammatory bowel disease," "Crohn's disease," and "ulcerative colitis" were entered into the PubMed database. Embase, Medline, Web of Science, Scopus, PubMed publisher, Cochrane, and Google Scholar were also searched. The HP prevalence rates in IBD patients, CD patients, UC patients, and IBDU patients were calculated. So its to prove that there is an inverse relationship between HP and IBD, each group was compared to a control group. Results: Even when the comparison was made separately between each group of newly diagnosed patients and controls to rule out the possibility of pharmacologic bias, the data showed an inverse relationship between the IBD group and the controls. Conclusion: The results of this review demonstrate a striking inverse association between HP infection and the prevalence of inflammatory bowel disease (IBD), regardless of the type of IBD considered across different geographic regions. Anyway, data should be interpreted with care because more research is needed on this topic that is broader, more prospective, and more consistent. This could lead to new ideas about how the environment could cause IBD. Keywords: Inflammatory bowel disease; Helicobacter pylori; Crohn’s disease; Ulcerative colitis; Colorectal cancer DOI: 10.7176/JMPB/72-04 Publication date: May 31st 202

Efficiency of electrochemical chloride removal from concrete at different environmental temperatures

Electrochemical chloride removal (ECR) is an effective and curative method to treat existed reinforced concrete structures about to suffer or already suffering from chloride attack, however, its application is still limited due to its side effect and efficiency, including the velocity and maximum capacity of chloride removal. This paper presents a temperature related numerical transport model to study the effect of temperature on efficiency of electrochemical chloride removal from concrete. Based on Fick’s law and Nernst-Planck equation with Gauss’ Law, temperature effect, chloride binding, multi-species coupling, electrochemical reactions were taken into account in this model. Temperature effect was considered on diffusion coefficient, chloride binding, ions migration capacity as well as electrolyte concentration. The model was validated by the comparison between the calculated results and experimental data. The results indicate that temperature dose have a considerable influence on electrochemical chloride removal and controlling temperature during treatment is a practical method to improve the electrochemical chloride removal when applied current density is not amplified

Consistent Targets Provide Better Supervision in Semi-supervised Object Detection

In this study, we dive deep into the inconsistency of pseudo targets in semi-supervised object detection (SSOD). Our core observation is that the oscillating pseudo targets undermine the training of an accurate semi-supervised detector. It not only inject noise into student training but also lead to severe overfitting on the classification task. Therefore, we propose a systematic solution, termed Consistent-Teacher, to reduce the inconsistency. First, adaptive anchor assignment~(ASA) substitutes the static IoU-based strategy, which enables the student network to be resistant to noisy pseudo bounding boxes; Then we calibrate the subtask predictions by designing a 3D feature alignment module~(FAM-3D). It allows each classification feature to adaptively query the optimal feature vector for the regression task at arbitrary scales and locations. Lastly, a Gaussian Mixture Model (GMM) dynamically revises the score threshold of the pseudo-bboxes, which stabilizes the number of ground-truths at an early stage and remedies the unreliable supervision signal during training. Consistent-Teacher provides strong results on a large range of SSOD evaluations. It achieves 40.0 mAP with ResNet-50 backbone given only 10\% of annotated MS-COCO data, which surpasses previous baselines using pseudo labels by around 3 mAP. When trained on fully annotated MS-COCO with additional unlabeled data, the performance further increases to 47.2 mAP. Our code will be open-sourced soon

High-density genotyping reveals candidate genomic regions for chicken body size in breeds of Asian origin

Body size is one of the main selection indices in chicken breeding. Although often investigated, knowledge of the underlying genetic mechanisms is incomplete. The aim of the current study was to identify genomic regions associated with body size differences between Asian Game and Asian Bantam type chickens. In this study, 94 and 107 chickens from four Asian Game and five Asian Bantam type breeds, respectively, were genotyped using the chicken 580K single nucleotide polymorphism (SNP) array. A genome-wide association study (GWAS) and principal component analyses (PCA) were performed to identify genomic regions associated with body size related-traits such as wing length, shank length, shank thickness, keel length, and body weight. Hierarchical clustering of genotype data showed a clear genetic difference between the investigated Asian Game and Asian Bantam chicken types. GWAS identified 16 genomic regions associated with wing length (2, FDR ≤ 0.018), shank thickness (6, FDR ≤ 0.008), keel length (5, FDR ≤ 0.023), and body weight (3, FDR ≤ 0.041). PCA showed that the first principal component (PC1) separated the two chicken types and significantly correlated with the measured body size related-traits (p ≤ 2.24e-40). SNPs contributing significantly to PC1 were subjected to a more detailed investigation. This analysis identified 11 regions potentially associated with differences in body size related-traits. A region on chromosome 4 (GGA4) (17.3 - 21.3 Mb) was detected in both analyses GWAS and PCA. This region harbors 60 genes. Among them are myotubularin 1 (MTM1) and secreted frizzled-related protein 2 (SFPR2) which can be considered as potential candidate genes for body size related-traits. Our results clearly show that the investigated Asian Game type chicken breeds are genetically different from the Asian Bantam breeds. A region on GGA4 between 17.3 and 21.3 Mb was identified which contributes to the phenotypic difference, though further validation of candidate genes is necessary

miRNA profiling in intrauterine exosomes of pregnant cattle on day 7

Intrauterine exosomes have been identified to be involved in the embryo development and implantation. The aim of this study was to explore the role of miRNAs in intrauterine exosomes in bovine pregnancy. Intrauterine exosomes were collected from uterine flushing fluids of three donor and three recipient Xianan cows 7 days after fertilization. Intrauterine exosomes miRNAs were extracted and the exosomal miRNAs expression levels were analyzed. Sixty miRNAs differed significantly in their amounts between donors and recipients (p-value 1). Twenty-two miRNAs were upregulated and 38 downregulated in the group of donor cows. The bta-miR-184 was the most significant (PBenjamini-Hochberg < 0.001). A total of 9,775 target genes were predicted using the 60 miRNAs. GO and KEGG analysis showed that the target genes were enriched in several biological processes or pathways associated with embryo implantation and endometrial development, such as cell adhesion, cell junction, focal adhesion, and Rap1 signaling pathway. Our findings suggest that, in cattle early pregnancy stage, these differently expressed miRNAs in intrauterine exosomes involved in embryo implantation and endometrial development, which may exert a significant effect and influence the uterine microenvironment for embryo implantation. These results could provide reference for screening and exploring the intrauterine exosomal miRNA affecting embryo implantation

Reducing the interval of a growth QTL on chromosome 4 in laying hens

Supplementary data for publication: Shijie Lyu, Danny Arends, Mostafa K. Nassar, Annett Weigend, Steffen Weigend, Rudolf Preisinger, and Gudrun A. Brockmann. (2018). Reducing the interval of a growth QTL on chromosome 4 in laying hens. Anim Genet. 2018 Oct;49(5):467-471

Study on thin bedrock deformation and strata behavior in coal seam mining under ultra-thick unconsolidated strata

Taking No.12051 fully-mechanized coal face of Zhaogu No.1 Coal Mine as research object, thin bedrock deformation and strata behavior in coal seam mining under ultra-thick unconsolidated strata were studied by use of UDEC numerical simulation software. The results show that the first weighting interval and periodical weighting interval of the coal face is 55 m and 15 m respectively. Caving zone and fractured zone appear in overlying strata after mining. The height of caving zone and fractured zone is 12.4 m and 36.7 m respectively. Ratio of caving zone height to mining height is 3.54 and ratio of fractured zone height to mining height is 10.48. Affected zone range of front abutment pressure, peak of front abutment pressure and plastic zone range increase with increase of coal face advancing distance. The front abutment pressure is stable after the first weighting at basic roof, which manifests in the maximum stress concentration factor and plastic zone range basically remain unchanged. The research results can provide basis for surrounding rock stability control of fully-mechanized coal face under the similar geological condition