Miracle-dz/UniFAR-FTUs huggingface dataset:
INFLUENCE OF FRP WIDTH-TO-SPACING RATIO ON BOND PERFORMANCE OF EXTERNALLY BONDED FRP SYSTEMS ON ONE WAY CONCRETE SLABS

Debonding of externally bonded fiber reinforced polymer (FRP) composite materials used for repair of reinforced concrete elements is commonly observed and is often the critical limit state for such systems. The FRP geometry, as quantified by the ratio of FRP width-to-substrate width, bf/b, (or FRP width-to-FRP spacing, bf/s, for slabs) is expected to affect the ultimate bond performance. Factors accounting for this effect are included in many design guides. An experimental program using concrete slab specimens having identical reinforcement ratios, strengthened with CFRP strips having different bf/s ratios is reported. The focus of the study is the strain in the CFRP and its eventual debonding. Thinner (lower bf/s) CFRP strip are observed to have greater strains at a given load level and to have a higher strain at debonding. The effect of the transverse strain gradient in the CFRP - the CFRP "edge effect" - is also investigated.
Histone hypoacetylation contributes to CXCL12 downregulation in colon cancer: impact on tumor growth and cell migration

CXCL12 has been shown to be involved in colon cancer metastasis, but its expression level and molecular mechanisms regulating its expression remain controversial. We thus evaluated CXCL12 expression in a large cohort of colon adenomas and carcinomas, investigated for an epigenetic mechanism controlling its expression and evaluated the impact of CXCL12 levels on cell migration and tumor growth. CXCL12 expression was measured in human colon adenomas and carcinomas with transcriptome array and RT-qPCR. The promoter methylation was analyzed with whole-genome DNA methylation chips and protein expression by immunohistochemistry. We confirm a reduced expression of CXCL12 in 75% of MSS carcinomas and show that the decrease is an early event as already present in adenomas. The methylome analysis shows that the CXCL12 promoter is methylated in only 30% of microsatellite-stable tumors. In vitro, treatments with HDAC inhibitors, butyrate and valproate restored CXCL12 expression in three colon cell lines, increased acetylation of histone H3 within the CXCL12 promoter and inhibited cell migration. In vivo, valproate diminished (65%) the number of intestinal tumors in APC mutant mice, slowed down xenograft tumor growth concomitant to restored CXCL12 expression. Finally we identified loss of PCAF expression in tumor samples and showed that forced expression of PCAF in colon cancer cell lines restored CXCL12 expression. Thus, reduced PCAF expression may participate to CXCL12 promoter hypoacetylation and its subsequent loss of expression. Our study is of potential clinical interest because agents that promote or maintain histone acetylation through HDAC inhibition and/or HAT stimulation, may help to lower colon adenoma/carcinoma incidence, especially in high-risk families, or could be included in therapeutic protocols to treat advanced colon cancer.
Management of Inflammatory Bowel Disease

Inflammatory bowel disease (IBD) is an inflammatory disease, which involves the digestive tract with still unknown definite etiology. IBD cases are frequently underdiagnosed or even overdiagnosed. Delay in diagnosis often happen due to the unspecific intermittent symptoms. Principally, treatment of IBD is targeted to acute episodes and maintenance of therapy during remission phase. First line therapy drugs include 5-acetil salicylic acid (5-ASA) and corticosteroids are systemic and topical. If failed, then second line therapy, which has immunosuppressive characteristic, is given such as: 6-mercaptopurine, azathioprine, cyclosporine, methotrexate, and anti-TNF (infliximab). Efforts to prevent recurrent inflammation in IBD are to maintain the remission phase as long as possible. Surgery management may be considered if conservative of pharmacological treatment fails or complication happens. Keywords: inflammatory bowel disease, management, treatment
Cold Physical Plasmas in the Field of Hygiene—Relevance, Significance, and Future Applications

Cold physical plasmas ignited a technological spark in industry, biotechnology, and medicine. Especially the field of hygiene benefited of the plasma's exceptional activity against pathogenic microorganisms. Together with plasma-based surface functionalization, these qualities are highly relevant in a variety of processes in health care, such as the decontamination or sterilization of medical devices, food, packaging materials, waste water, or indoor air. In medicine, plasma has proven to show promising antiseptic results on skin and mucosal membranes in infection-related diseases in dermatology and dentistry. This comprehensive review will discuss the current applications of cold plasma in the fields of hygiene, and will provide a promising outlook on many applications yet to come.
Neurodegeneration in an Animal Model of Chronic Amyloid-beta Oligomer Infusion Is Counteracted by Antibody Treatment Infused with Osmotic Pumps

Decline in hippocampal-dependent explicit memory (memory for facts and events) is one of the earliest clinical symptom of Alzheimer's disease (AD). It is well established that synapse loss and ensuing neurodegeneration are the best predictors for memory impairments in AD. Latest studies have emphasized the neurotoxic role of soluble amyloid-beta oligomers (Aβo) that begin to accumulate in the human brain approximately 10 to 15 yr before the clinical symptoms become apparent. Many reports indicate that soluble Aβo correlate with memory deficits in AD models and humans. The Aβo-induced neurodegeneration observed in neuronal and brain slice cultures has been more challenging to reproduce in many animal models. The model of repeated Aβo infusions shown here overcome this issue and allow addressing two key domains for developing new disease modifying therapies: identify biological markers to diagnose early AD, and determine the molecular mechanisms underpinning Aβo-induced memory deficits at the onset of AD. Since soluble Aβo aggregate relatively fast into insoluble Aβ fibrils that correlate poorly with the clinical state of patients, soluble Aβo are prepared freshly and injected once per day during six days to produce marked cell death in the hippocampus. We used cannula specially design for simultaneous infusions of Aβo and continuous infusion of Aβo antibody (6E10) in the hippocampus using osmotic pumps. This innovative in vivo method can now be used in preclinical studies to validate the efficiency of new AD therapies that might prevent the deposition and neurotoxicity of Aβo in pre-dementia patients.
Evolutionary Construction of Multiple Graph Alignments for the Structural Analysis of Biomolecules

The concept of multiple graph alignment (MGA) has recently been introduced as a novel method for the structural analysis of biomolecules. Using approximate graph matching techniques, this method enables the robust identification of approximately conserved patterns in biologically related structures. In particular, MGA enables the characterization of functional protein families independent of sequence or fold homology. This article first recalls the concept of MGA and then addresses the problem of computing optimal alignments from an algorithmic point of view. In this regard, a method from the field of evolutionary algorithms is proposed and empirically compared with a hitherto existing heuristic approach. Empirically, it is shown that the former yields significantly better results than the latter, albeit at the cost of an increased runtime.
Comparative study of joint bioinformatics analysis of underlying potential of ‘neurimmiR’, miR-212-3P/miR-132-3P, being involved in epilepsy and its emerging role in human cancer

Considering the critical roles of miR-132/212 participated in central nervous system, many researches started to explored the contributions of miR-132/212 to epilepsy and achieve something worthwhile. Further illuminates all the genes targeted by miR-132/212 may be a valuable means for us to completely understand the working mechanism playing in epilepsy, by which it can influence diverse biological process. This study attempts to establish macrocontrol regulation system and knowledge that miR-212-3p/132-3p effected the epilepsy, for this literature search, miRbase, Vienna RNAfold webserver, Human miRNA tissue atlas, DIANA-TarBase, miRtarbase, STRING, TargetScanhuman, Cytoscape plugin ClueGO + Cluepedia+STRING, DAVID Bioinformatics Resources, Starbase, GeneCards suite and GEO database are comprehensive employed, miR-132-3p/212-3p and its target gene were found have highly expressed in brain and lots of molecular function and metabolic pathways associated with epilepsy may be intervened by it. Meanwhile, the emerging role of miR-132-3p/212-3p being involved in human cancer also been analyzed by several webtools for TCGA data integrative analysis, most remarkably and well worth exploring in our research conclusion that showed miR-132-3p/212-3p may be the core molecular underlying tumor-induced epileptogenesis.
Condition-Based Maintenance via Simulation and a Targeted Bayesian Network Metamodel

ABSTRACT Condition-based maintenance (CBM) is increasingly applied to operational systems to reduce lifecycle costs. Predicting the performance of various CBM policies is a challenging task addressed in this work. We suggest a CBM framework that is based on system simulations and a targeted Bayesian network model. Simulations explore the robustness of various CBM policies under different scenarios. The Bayesian network, which is learned from the simulation data, is then used as an explanatory compact metamodel for failure prediction. The framework is demonstrated through a study of an operator of a freight rail fleet. This study demonstrates a significant profit improvement compared to other methods.
Trauma induced heterotopic ossification patient serum alters mitogen activated protein kinase signaling in adipose stem cells

Post‐traumatic heterotopic ossification (HO) is the formation of ectopic bone in non‐osseous structures following injury. The precise mechanism for bone development following trauma is unknown; however, early onset of HO may involve the production of pro‐osteogenic serum factors. Here we evaluated serum from a cohort of civilian and military patients post trauma to determine early induction gene signatures in orthopaedic trauma induced HO. To test this, human adipose derived stromal/stem cells (hASCs) were stimulated with human serum from patients who developed HO following trauma and evaluated for a gene panel with qPCR. Pathway gene analysis ontology revealed that hASCs stimulated with serum from patients who developed HO had altered gene expression in the activator protein 1 (AP1) and AP1 transcriptional targets pathways. Notably, there was a significant repression in FOS gene expression in hASCs treated with serum from individuals with HO. Furthermore, the mitogen‐activated protein kinase (MAPK) signaling pathway was activated in hASCs following serum exposure from individuals with HO. Serum from both military and civilian patients with trauma induced HO had elevated downstream genes associated with the MAPK pathways. Stimulation of hASCs with known regulators of osteogenesis (BMP2, IL6, Forskolin, and WNT3A) failed to recapitulate the gene signature observed in hASCs following serum stimulation, suggesting non‐canonical mechanisms for gene regulation in trauma induced HO. These findings provide new insight for the development of HO and support ongoing work linking the systemic response to injury with wound specific outcomes.
Exploring the biochemistry of the prenylome and its role in disease through proteomics: progress and potential

ABSTRACT Introduction: Protein prenylation is a ubiquitous covalent post-translational modification characterized by the addition of farnesyl or geranylgeranyl isoprenoid groups to a cysteine residue located near the carboxyl terminal of a protein. It is essential for the proper localization and cellular activity of numerous proteins, including Ras family GTPases and G-proteins. In addition to its roles in cellular physiology, the prenylation process has important implications in human diseases and in the recent years, it has become attractive target of inhibitors with therapeutic potential. Areas covered: This review attempts to summarize the basic aspects of prenylation integrating them with biological functions in diseases and giving an account of the current status of prenylation inhibitors as potential therapeutics. We also summarize the methodologies for the characterization of this modification. Expert commentary: The growing body of evidence suggesting an important role of prenylation in diseases and the subsequent development of inhibitors of the enzymes responsible for this modification lead to the urgent need to identify the full spectrum of prenylated proteins that are altered in the disease or affected by drugs. Proteomic tools to analyze prenylated proteins are recently emerging, thanks to the advancement in the field of mass spectrometry coupled to enrichment strategies.
Mineral Characteristics Analysis of PM2.5 in Northern China

PM2.5 (sandstorm-related) was sampled at four sites near dust source areas in Northern China in spring 2012. Every site was away from obvious pollution source. After drying 24 hours in a dry dish, X-ray diffraction (XRD), x-ray fluorescence (XRF) and scanning electron microscope (SEM) of all the samples were examined. The main phases were quartz, albite, calcite and mica. SEM observations showed that the particles were mainly irregular shaped, but different sample the particle morphology is slightly different. And the surface was rough because of erosion mark or pores on them. The chemical composition of PM2.5 is characteristic of high SiO2 and CaO, while low K2O, Na2O. Main elements of the samples were Si, Al, Fe, Ca, which were familiar with crust elements and dust fall components [, but some samples also contained low-level heavy metals like As and Pb.
X-ray scattering on ordered colloidal assemblies

Colloidal assemblies and in particular colloidal crystals are built up of colloidal particles ideally arranged in a crystalline structure. They present a promising bottom-up approach towards the fabrication of photonic materials with a complete photonic band gap. These materials have a huge potential for a wide variety of applications. The quality of the colloidal crystals is currently the main challenge of this approach. Therefore, adequate fabrication and characterization methods are imperative. Various techniques for the self-assembly of colloidal crystals have been presented in the last two decades. In the process, convective self-assembly has been established as an approach that yields uniform assemblies over large areas while employing comparatively simple setups. The technique is able to provide close-packed colloids arranged in a fcc lattice with stacking faults. The number of layers of the nal assembly can be tailored by the initial particle concentration. It has been shown that in combination with topologically structured templates, the long-range order of the opals could be increased and their crystallographic symmetry altered. The focus of the presented work was on assessing the potential of grazing incidence small angle X-ray scattering (GISAXS) with respect to the structural characterization of colloidal crystals. For that purpose convective self-assembly has been successfully used to fabricate colloidal crystals from particles with diameters between 277 nm and 740 nm deposited on smooth glass slides. The number of layers of the investigated samples ranged from 1 to 14 layers. The best assemblies exhibited an almost constant number of layers across areas as large as 1 to 2 cm. Colloidal crystals have also been deposited on pDR1M surface relief gratings. This led in general to a less homogeneous coverage. GISAXS data collected on multilayers with 7 and 14 layers, demonstrate that these multilayers have a similar alignment of the domains over the complete sample. The distribution describing the domain misalignment was tted with a Gaussian function and gave for the two investigated samples an almost identical FWHM of 4.4 ± 0.9 deg (7 layers) and 4.3 ± 0.8 deg (14 layers). GISAXS, SEM and AFM investigations consistently show that the preferential orientation of the ordered domains is correlated to
EGF and NRG induce phosphorylation of HER3/ERBB3 by EGFR using distinct oligomeric mechanisms

Significance Signaling by human epidermal growth factor receptor (HER) receptors relies on heteromeric interactions between four members of the family: EGF receptor, HER2, HER3, and HER4. These interactions remain remarkably poorly understood. Using super-resolution microscopy imaging and signaling assays, we demonstrate a rich scope of HER receptor organization patterns that are differentially influenced by ligands and coreceptor expression, resulting in unique phosphorylation signatures of HER receptors. We also show that there are fundamental differences in molecular mechanisms that govern HER receptor cross-activation, which do not always follow the canonical kinase dimerization mechanism. Our data underscore an emerging concept in the field that HER receptor signaling needs to be interpreted in the context of higher-order receptor oligomers, redefining the basic signaling unit relevant for receptor function. Heteromeric interactions between the catalytically impaired human epidermal growth factor receptor (HER3/ERBB3) and its catalytically active homologs EGFR and HER2 are essential for their signaling. Different ligands can activate these receptor pairs but lead to divergent signaling outcomes through mechanisms that remain largely unknown. We used stochastic optical reconstruction microscopy (STORM) with pair-correlation analysis to show that EGF and neuregulin (NRG) can induce different extents of HER3 clustering that are dependent on the nature of the coexpressed HER receptor. We found that the presence of these clusters correlated with distinct patterns and mechanisms of receptor phosphorylation. NRG induction of HER3 phosphorylation depended on the formation of the asymmetric kinase dimer with EGFR in the absence of detectable higher-order oligomers. Upon EGF stimulation, HER3 paralleled previously observed EGFR behavior and formed large clusters within which HER3 was phosphorylated via a noncanonical mechanism. HER3 phosphorylation by HER2 in the presence of NRG proceeded through still another mechanism and involved the formation of clusters within which receptor phosphorylation depended on asymmetric kinase dimerization. Our results demonstrate that the higher-order organization of HER receptors is an essential feature of their ligand-induced behavior and plays an essential role in lateral cross-activation of the receptors. We also show that HER receptor ligands exert unique effects on signaling by modulating this behavior.
Independent active and thermodynamic processes govern the nucleolus assembly in vivo

Significance The role of thermodynamically driven processes in inherently active biological systems has daunted scientists for decades. One such conundrum emerges in the formation of membraneless organelles that, according to in vitro studies, assemble via thermodynamically driven phase separation but harbor numerous active processes within themselves. Disentangling the role of thermodynamic and active processes in their formation is, however, impossible in minimal in vitro systems of individual constituent components. In this work, we introduce a microfluidics-based temperature assay to address this question at its full complexity in vivo and use it to study the assembly of six nucleolar proteins in Drosophila embryos. Although four of these proteins follow the phase separation model, the recruitment of others to the nucleolus is active. Membraneless organelles play a central role in the organization of protoplasm by concentrating macromolecules, which allows efficient cellular processes. Recent studies have shown that, in vitro, certain components in such organelles can assemble through phase separation. Inside the cell, however, such organelles are multicomponent, with numerous intermolecular interactions that can potentially affect the demixing properties of individual components. In addition, the organelles themselves are inherently active, and it is not clear how the active, energy-consuming processes that occur constantly within such organelles affect the phase separation behavior of the constituent macromolecules. Here, we examine the phase separation model for the formation of membraneless organelles in vivo by assessing the two features that collectively distinguish it from active assembly, namely temperature dependence and reversibility. We use a microfluidic device that allows accurate and rapid manipulation of temperature and examine the quantitative dynamics by which six different nucleolar proteins assemble into the nucleoli of Drosophila melanogaster embryos. Our results indicate that, although phase separation is the main mode of recruitment for four of the studied proteins, the assembly of the other two is irreversible and enhanced at higher temperatures, behaviors indicative of active recruitment to the nucleolus. These two subsets of components differ in their requirements for ribosomal DNA; the two actively assembling components fail to assemble in the absence of ribosomal DNA, whereas the thermodynamically driven components assemble but lose temporal and spatial precision.
Epistatic Networks Jointly Influence Phenotypes Related to Metabolic Disease and Gene Expression in Diversity Outbred Mice

In this study, Tyler et al. analyzed the complex genetic architecture of metabolic disease-related traits using the Diversity Outbred mouse population Genetic studies of multidimensional phenotypes can potentially link genetic variation, gene expression, and physiological data to create multi-scale models of complex traits. The challenge of reducing these data to specific hypotheses has become increasingly acute with the advent of genome-scale data resources. Multi-parent populations derived from model organisms provide a resource for developing methods to understand this complexity. In this study, we simultaneously modeled body composition, serum biomarkers, and liver transcript abundances from 474 Diversity Outbred mice. This population contained both sexes and two dietary cohorts. Transcript data were reduced to functional gene modules with weighted gene coexpression network analysis (WGCNA), which were used as summary phenotypes representing enriched biological processes. These module phenotypes were jointly analyzed with body composition and serum biomarkers in a combined analysis of pleiotropy and epistasis (CAPE), which inferred networks of epistatic interactions between quantitative trait loci that affect one or more traits. This network frequently mapped interactions between alleles of different ancestries, providing evidence of both genetic synergy and redundancy between haplotypes. Furthermore, a number of loci interacted with sex and diet to yield sex-specific genetic effects and alleles that potentially protect individuals from the effects of a high-fat diet. Although the epistatic interactions explained small amounts of trait variance, the combination of directional interactions, allelic specificity, and high genomic resolution provided context to generate hypotheses for the roles of specific genes in complex traits. Our approach moves beyond the cataloging of single loci to infer genetic networks that map genetic etiology by simultaneously modeling all phenotypes.