An analytically formulated structural strain method for fatigue evaluation of welded components incorporating nonlinear hardening effects

An analytically formulated structural strain method is presented for performing fatigue evaluation of welded components by incorporating nonlinear material hardening effects by means of a modified Ramberg‐Osgood power law hardening model. The modified Ramberg‐Osgood model enables a consistent partitioning of elastic and plastic strain increments during both loading and unloading. For supporting 2 major forms of welded structures in practice, the new method is applied for computing structural strain defined with respect to a through‐thickness section in plate structures and cross section in piping systems. In both cases, the structural strain is formulated as the linearly deformation gradient on their respective cross sections, consistent with the “plane sections remain plane” assumption in structural mechanics. The structural strain‐based fatigue parameter is proposed and has been shown effective in correlating some well‐known low‐cycle and high‐cycle fatigue test data, ranging from gusset‐to‐plate welded plate connections to pipe girth welds.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146966/1/ffe12900.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146966/2/ffe12900_am.pd

Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes

Synorth is a web resource for exploring and categorizing the syntenic relationships in gene regulatory blocks across multiple genomes

Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes

Genomic regulatory blocks are chromosomal regions spanned by long clusters of highly conserved noncoding elements devoted to long-range regulation of developmental genes, often immobilizing other, unrelated genes into long-lasting syntenic arrangements. Synorth http://synorth.genereg.net/ is a web resource for exploring and categorizing the syntenic relationships in genomic regulatory blocks across multiple genomes, tracing their evolutionary fate after teleost whole genome duplication at the level of genomic regulatory block loci, individual genes, and their phylogenetic context.publishedVersionPeer Reviewe

Transcriptional features of genomic regulatory blocks

CAGE tag mapping of transcription start sites across different human tissues shows that genomic regulatory blocks have unique features that are the likely cause of their ability to respond to regulatory inputs from very long distances

A New Liver Segmentation Based on Digital Liver Portal Vein Ramification Using Computer-Assisted Surgery System: Exploring Artificial Intelligence

A good understanding of liver anatomy is required for performing precise liver resection. However, the currently described methods of liver segmentation based on portal and hepatic veins are inconclusive. We proposed a system of liver segmentation based on previous reports and our data. Three-dimensional computed tomography software based on artificial intelligence was used to analyze the portal vein branching pattern in 759 patients. We analyzed four different types of liver segmentation and measured their respective segmental liver volumes. We classified four types of liver segmentation based on the right portal vein. Median segmental liver volumes were variable for the different types of segmentation. Our system of liver segmentation enables a better classification of individual patients into one of the different types, thus assisting in preoperative surgical planning. Segmental liver volume is useful for the preoperative evaluation of remnant liver volume

Experimental study on treatment of Fe2+ and Mn2+ in AMD with lignite combined with Pseudomonas aeruginosa immobilized SRB particles

Sulfate-Reducing Bacteria (SRB) are easily inhibited by high concentrations of heavy metals, low pH as well as the need to add carbon source materials, the microbial immobilization technology was adopted, with SRB, Pseudomonas aeruginosa and lignite as the main immobilization substrates, to prepare lignite and Pseudomonas aeruginosa immobilized SRB particles (L-P-SRB) and the removal effect of L-P-SRB on Fe2+, Mn2+ and SO4 2− in acid mine wastewater (AMD) was investigated. Based on the reduction kinetics and adsorption kinetics, the mechanism of AMD treatment by L-P-SRB was revealed by means of scanning electron microscope (SEM) and Fourier transform infrared spectroscopy (FT-IR), and the mechanism of L-P-SRB treating AMD was revealed. At the same time, the repair effect of low temperature treatment of L-P-SRB on AMD is explored, which provides a certain basis for the treatment of AMD in mining areas under the condition of low temperature. The results show that the removal rates of Fe2+ and Mn2+ by L-P-SRB are 91% and 79% respectively, and the process of adsorption of Fe2+ and Mn2+ conforms to the pseudo-first-order kinetics; the removal rate of SO4 2− reaches 91.28% and 81.94% respectively, and the process of reducing SO4 2− is in accordance with the first-order kinetics. Compared with Fe2+, Mn2+ has a certain inhibitory effect on the activity of L-P-SRB. L-P-SRB can remove Fe2+, Mn2+ and SO4 2− in wastewater at one time, which well solves the problem that lignite can only adsorb heavy metal ions and SRB needs to add carbon source. Low temperature cold storage treatment will not inhibit the activity of L-P-SRB, which provides a basis for one-time preparation and multiple use. According to the detection of SEM and FT-IR, pseudomonas aeruginosa plays a priority role in the treatment of wastewater by L-P-SRB, destroying the structure of lignite, destroying some functional groups, breaking the C—C bond, C=O bond and side chain of cycloalkanes, alkanes and olefins in lignite, producing a large number of small molecule organic substances, increasing the specific surface area of particles, and improving the adsorption capacity of particles. At the same time, lignite provides a carrier and a large number of carbon sources for the reduction of SO4 2− by SRB, which promotes the growth of SRB and improves the treatment effect of AMD

Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium

The Encyclopedia of DNA Elements (ENCODE) consortium aims to identify all functional elements in the human genome including transcripts, transcriptional regulatory regions, along with their chromatin states and DNA methylation patterns. The ENCODE project generates data utilizing a variety of techniques that can enrich for regulatory regions, such as chromatin immunoprecipitation (ChIP), micrococcal nuclease (MNase) digestion and DNase I digestion, followed by deeply sequencing the resulting DNA. As part of the ENCODE project, we have developed a Web-accessible repository accessible at http://factorbook.org. In Wiki format, factorbook is a transcription factor (TF)-centric repository of all ENCODE ChIP-seq datasets on TF-binding regions, as well as the rich analysis results of these data. In the first release, factorbook contains 457 ChIP-seq datasets on 119 TFs in a number of human cell lines, the average profiles of histone modifications and nucleosome positioning around the TF-binding regions, sequence motifs enriched in the regions and the distance and orientation preferences between motif sites

MicroRNAs Located in the Hox Gene Clusters Are Implicated in Huntington's Disease Pathogenesis

Transcriptional dysregulation has long been recognized as central to the pathogenesis of Huntington's disease (HD). MicroRNAs (miRNAs) represent a major system of post-transcriptional regulation, by either preventing translational initiation or by targeting transcripts for storage or for degradation. Using next-generation miRNA sequencing in prefrontal cortex (Brodmann Area 9) of twelve HD and nine controls, we identified five miRNAs (miR-10b-5p, miR-196a-5p, miR-196b-5p, miR-615-3p and miR-1247-5p) up-regulated in HD at genome-wide significance (FDR q-value<0.05). Three of these, miR-196a-5p, miR-196b-5p and miR-615-3p, were expressed at near zero levels in control brains. Expression was verified for all five miRNAs using reverse transcription quantitative PCR and all but miR-1247-5p were replicated in an independent sample (8HD/8C). Ectopic miR-10b-5p expression in PC12 HTT-Q73 cells increased survival by MTT assay and cell viability staining suggesting increased expression may be a protective response. All of the miRNAs but miR-1247-5p are located in intergenic regions of Hox clusters. Total mRNA sequencing in the same samples identified fifteen of 55 genes within the Hox cluster gene regions as differentially expressed in HD, and the Hox genes immediately adjacent to the four Hox cluster miRNAs as up-regulated. Pathway analysis of mRNA targets of these miRNAs implicated functions for neuronal differentiation, neurite outgrowth, cell death and survival. In regression models among the HD brains, huntingtin CAG repeat size, onset age and age at death were independently found to be inversely related to miR-10b-5p levels. CAG repeat size and onset age were independently inversely related to miR-196a-5p, onset age was inversely related to miR-196b-5p and age at death was inversely related to miR-615-3p expression. These results suggest these Hox-related miRNAs may be involved in neuroprotective response in HD. Recently, miRNAs have shown promise as biomarkers for human diseases and given their relationship to disease expression, these miRNAs are biomarker candidates in HD

An integrated encyclopedia of DNA elements in the human genome

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research

MicroRNAs located in the Hox gene clusters are implicated in huntington\u27s disease pathogenesis

Transcriptional dysregulation has long been recognized as central to the pathogenesis of Huntington\u27s disease (HD). MicroRNAs (miRNAs) represent a major system of post-transcriptional regulation, by either preventing translational initiation or by targeting transcripts for storage or for degradation. Using next-generation miRNA sequencing in prefrontal cortex (Brodmann Area 9) of twelve HD and nine controls, we identified five miRNAs (miR-10b-5p, miR-196a-5p, miR-196b-5p, miR-615-3p and miR-1247-5p) up-regulated in HD at genome-wide significance (FDR q-value \u3c 0.05). Three of these, miR-196a-5p, miR-196b-5p and miR-615-3p, were expressed at near zero levels in control brains. Expression was verified for all five miRNAs using reverse transcription quantitative PCR and all but miR-1247-5p were replicated in an independent sample (8HD/8C). Ectopic miR-10b-5p expression in PC12 HTT-Q73 cells increased survival by MTT assay and cell viability staining suggesting increased expression may be a protective response. All of the miRNAs but miR-1247-5p are located in intergenic regions of Hox clusters. Total mRNA sequencing in the same samples identified fifteen of 55 genes within the Hox cluster gene regions as differentially expressed in HD, and the Hox genes immediately adjacent to the four Hox cluster miRNAs as up-regulated. Pathway analysis of mRNA targets of these miRNAs implicated functions for neuronal differentiation, neurite outgrowth, cell death and survival. In regression models among the HD brains, huntingtin CAG repeat size, onset age and age at death were independently found to be inversely related to miR-10b-5p levels. CAG repeat size and onset age were independently inversely related to miR-196a-5p, onset age was inversely related to miR-196b-5p and age at death was inversely related to miR-615-3p expression. These results suggest these Hox-related miRNAs may be involved in neuroprotective response in HD. Recently, miRNAs have shown promise as biomarkers for human diseases and given their relationship to disease expression, these miRNAs are biomarker candidates in HD