Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogenetic and temporal dynamics of human immunodeficiency virus type 1 CRF01_AE and CRF07_BC among recently infected antiretroviral therapy-naïve men who have sex with men in Jiangsu province, China, 2012 to 2015

Abstract The prevalence and incidence of human immunodeficiency virus type 1 (HIV-1) among men who have sex with men (MSM) are on the rise throughout China. With a large population of MSM, Jiangsu Province is facing an escalating HIV-1 epidemic. The aim of this study was to explore the phylogenetic and temporal dynamics of HIV-1 CRF01_AE and CRF07_BC among antiretroviral therapy (ART)-naïve MSM recently infected with HIV-1 in Jiangsu Province. We recruited MSM in Jiangsu Province (Suzhou, Wuxi, Nantong, Taizhou and Yancheng) 2012 to 2015. We collected information on demographics and sexual behaviors and a blood sample for HIV genome RNA extraction, RT-PCR amplification, and DNA sequencing. Multiple alignments were made using Gene Cutter, with the selected reference sequences of various subtypes/recombinants from the Los Alamos HIV-1 database. Phylogenetic and Bayesian evolutionary analysis was performed by MEGA version 6.0, Fasttree v2.1. 7. and BEAST v1.6. 2. Categorical variables were analyzed using &khgr;2 test (or Fisher exact test where necessary). &khgr;2 test with trend was used to assess the evolution of HIV-1 subtype distribution over time. All data were analyzed using SPSS20.0 software package (IBM Company, New York, NY). HIV-1 phylogenetic analysis revealed a broad viral diversity including CRF01_AE (60.06%), CRF07_BC (22.29%), subtype B (5.88%), CRF67_01B (5.26%), CRF68_01B (2.79%), CRF55_01B (1.55%), CRF59_01B (0.93%), and CRF08_BC (0.62%). Two unique recombination forms (URFs) (0.62%) were also detected. Four epidemic clusters and 1 major cluster in CRF01_AE and CRF07_BC were identified. The introduction of CRF01_AE strain (2001) was earlier than CRF07_BC strain (2004) into MSM resided in Jiangsu based on the time of the most recent common ancestor. Our study demonstrated HIV-1 subtype diversity among ART-naïve MSM recently infected with HIV-1 in Jiangsu. We first depicted the spatiotemporal dynamics, traced the dates of origin for the HIV-1 CRF01_AE/07_BC strains and made inference for the effective population size among newly infected ART-naïve MSM in Jiangsu from 2012 to 2015. A real-time surveillance of HIV-1 viral diversity and phylodynamics of epidemic cluster would be of great value to the monitoring of the epidemic and control of transmission, improvement of antiretroviral therapy strategies, and design of vaccines.
Bioinformatics analysis of fibroblasts exposed to TGF-β at the early proliferation phase of wound repair

The aim of the current study was to identify gene signatures during the early proliferation stage of wound repair and the effect of TGF-β on fibroblasts and reveal their potential mechanisms. The gene expression profiles of GSE79621 and GSE27165 were obtained from GEO database. Differentially expressed genes (DEGs) were identified using Morpheus and co-expressed DEGs were selected using Venn Diagram. Gene ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs were performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) online tool. Protein-protein interaction (PPI) networks of the DEGs were constructed using Cytoscape software. PPI interaction network was divided into subnetworks using the MCODE algorithm and the function of the top one module was analyzed using DAVID. The results revealed that upregulated DEGs were significantly enriched in biological process, including the Arp2/3 complex-mediated actin nucleation, positive regulation of hyaluronan cable assembly, purine nucleobase biosynthetic process, de novo inosine monophosphate biosynthetic process, positive regulation of epithelial cell proliferation, whereas the downregulated DEGs were enriched in the regulation of blood pressure, negative regulation of cell proliferation, ossification, negative regulation of gene expression and type I interferon signaling pathway. KEGG pathway analysis showed that the upregulated DEGs were enriched in shigellosis, pathogenic Escherichia coli infection, the mitogen-activated protein kinase signaling pathway, Ras signaling pathway and bacterial invasion of epithelial cells. The downregulated DEGs were enriched in systemic lupus erythematosus, lysosome, arachidonic acid metabolism, thyroid cancer and allograft rejection. The top 10 hub genes were identified from the PPI network. The top module analysis revealed that the included genes were involved in ion channel, neuroactive ligand-receptor interaction pathway, purine metabolism and intestinal immune network for IgA production pathway. The functional analysis revealed that TGF-β may promote fibroblast migration and proliferation and defend against microorganisms at the early proliferation stage of wound repair. Furthermore, these results may provide references for chronic wound repair.
Distribution of Virulence-Associated Genes and Genetic Relationships in Non-O1/O139 Vibrio cholerae Aquatic Isolates from China

ABSTRACT Non-O1/O139 Vibrio cholerae is naturally present in aquatic ecosystems and has been linked with cholera-like diarrhea and local outbreaks. The distribution of virulence-associated genes and genetic relationships among aquatic isolates from China are largely unknown. In this study, 295 aquatic isolates of V. cholerae non-O1/O139 serogroups from different regions in China were investigated. Only one isolate was positive for ctxB and harbored a rare genotype; 10 (3.4%) isolates carried several types of rstR sequences, eight of which carried rare types of toxin-coregulated pili (tcpA). Furthermore, 16 (5.4%) isolates carried incomplete (with partial open reading frames [ORFs]) vibrio seventh pandemic island I (VSP-I) or VSP-II clusters, which were further classified as 11 novel types. PCR-based analyses revealed remarkable variations in the distribution of putative virulence genes, including mshA (95.6%), hlyA (95.3%), rtxC (89.8%), rtxA (82.7%), IS1004 (52.9%), chxA (30.2%), SXT (15.3%), type III secretion system (18.0%), and NAG-ST (3.7%) genes. There was no correlation between the prevalence of putative virulence genes and that of CTX prophage or TCP genes, whereas there were correlations among the putative virulence genes. Further multilocus sequence typing (MLST) placed selected isolates (n = 70) into 69 unique sequence types (STs), which were different from those of the toxigenic O1 and O139 counterparts, and each isolate occupied a different position in the MLST tree. The V. cholerae non-O1/O139 aquatic isolates predominant in China have high genotypic diversity; these strains constitute a reservoir of potential virulence genes, which may contribute to evolution of pathogenic isolates.
A QoS guaranteed energy optimized packet transmission technique for the IEEE802.11 WLAN

With the increasing use of smart phones and other portable communications devices the role of WLAN is increasing. The IEEE 802.11 based WLAN is almost becoming the de facto broadband wireless access network. Due to widespread usage of portable devices the demand for energy efficient networking is increasing. It is necessary to design energy efficient algorithms to prolong the battery life of mobile devices. In this paper, we propose a new link adaptation based energy efficient packet transmission technique for the IEEE802.11g standard. The proposed protocol maintains the QoS of different classes of service at the same time it reduces energy requirements of WLAN based devices thus prolonging the battery life of user devices. The performance of the proposed packet transmission technique is analysed using an OPNET based discrete event simulation model. Simulation results show that the proposed protocol can considerably reduce the energy requirements of mobile devices for data transmission.
Modern Self-Lubricating Coatings for Automotive, Aviation and Spacecraft Industry

A series of nanocomposite, self-lubricating coatings designed for dry friction at different temperatures based on amorphous carbon or amorphous MoS2 or amorphous MoO3 matrix was deposited by magnetron sputtering onto high-speed (HS) steel or Ti6Al4V alloy substrates and characterized with use of LM, SEM, TEM and HRTEM microscopy as well as with use of several other techniques. The nanocomposite nc-MeC/a-C(:H) carbon-based coatings (where Me=Cr or Ti or W) were composed of different nanocrystalline phases of a given transition metal of a size of several nanometers embedded in an amorphous hydrogenated or hydrogen-free carbon matrix. The nanocomposite MoS2(Ti,W) coatings were composed of Tiα or Wα or TiS2 nanocrystallites of 3 nm ÷ 10 nm diam. embedded in a semi-crystalline MoS2 matrix with MoS2 clusters of 3 nm÷8 nm diam. The magnetron sputtered MoO3 based coatings after deposition were composed of Ag nanocrystallites of 50 nm÷100 nm diam. embedded in an amorphous fractal-type matrix composed of MoO3 clusters of different size from very small to relatively great ones (not exceeding, however, 400 nm diam.). These amorphous clusters after 3 hours annealing in the ambient atmosphere under normal pressure at 300 °C transform into nanocrystalline MoO3 ones or after same annealing at 450 °C into crystalline silver molybdate Ag2MoO4 ones. The coatings preserve their resistance to wear and their low friction coefficient to approximately 250 °C in case of carbon-based coatings or to 350 °C in case of MoS2-based ones or to 550 °C in case of MoO3-based coatings. Several mechanical and tribological chracteristics of the coatings are given in the paper as well.
A New Approach for Adipose Tissue Regeneration Based on Human Mesenchymal Stem Cells in Contact to Hydrogels—an In Vitro Study

In this study an approach for adipose tissue regeneration based on human mesenchymal stem cells and hydrogels as supporting matrix was evaluated. The gelatin-based hydrogels developed in this study were cytocompatible and stem cell adhesion onto hydrogel surfaces was higher as compared to tissue culture polystyrene. Furthermore, the adipogenic differentiation degree was increased. These results are promising for future applications of hydrogels in adipose tissue regeneration strategies.
Keyword based Automatic Summarization of HTML Documents

Automatic summarization [5] can be defined as the procedure to create a short version of a text by a computer program. Its product still contains the most important points of the existing text. Multi-document summarization [6] can be defined as an automatic procedure which extracts information from multiple texts that is written about the same topic. Resulting summary report allows individual users or professional information consumers, to quickly familiarize themselves with information that is contained in a large cluster of documents. Multi-document summarization creates information reports that are both concise and comprehensive. General terms Text summarization
Trust-Based Communication for the Industrial Internet of Things

Recently, the Industrial Internet of Things (IIoT) is attracting growing attention from both academia and industry. Meanwhile, trust-based communication is widely utilized in various systems. In this article, studying the performance of IIoT, we investigate trust-based communication for IIoT. In particular, devoting attention to sensor- cloud, which is a paradigm of IIoT, we propose three types of trust-based communication mechanisms for sensor-cloud. Furthermore, with numerical results, we show that trust-based communication can greatly enhance the performance of sensor-cloud. Eventually, open research issues with respect to trust-based communication for sensor-cloud are discussed.
Numerical Predictions of Progressive Damage Evolution in Particulate Composites

A method is presented for calculating stresses and strains in a loaded particulate composite structure (specimen) as damage initiates and grows. Load is incrementally applied to a numerically simulated specimen. For every load increment, a finite element method model is used to calculate the composite stresses and strains at each point. A micromechanical model uses the composite strains to calculate the stresses and strains in the composite's component materials, the particles and matrix. A damage model uses the matrix strains to determine values for local matrix damage, and to set reductions in the stiffnesses of damaged matrix material regions, each of which is proportional to the associated damage value. At damaged locations, the micromechanical model uses the reduced matrix stiffnesses to calculate reduced composite stiffnesses. All reduced matrix and composite stiffnesses calculated during a load increment are used in the next load increment. Matrix strain values are set which determine damage initiation, growth, and saturation. Damage saturation indicates matrix material failure, and for saturation the composite stiffness approaches zero. At a specimen point, a matrix crack will form or extend when the point becomes saturated with damage. Numerical simulation predictions are presented, and compared to experimental data. Plots are included showing stress and strain variation, and crack growth.
Stratifying the NHS Diabetic Eye Screening Programme: into the unknown?

In this commentary, we consider the recent recommendation by the UK National Screening Committee (NSC) that people with diabetes at low risk of sight loss should be invited to screening every 2 years rather than annually [1]. We broadly support this recommendation but believe that there are important outstanding questions that require attention before such a policy is implemented. We discuss the decision in the context of the history of the NHS Diabetic Eye Screening Programme (NDESP) and reflect on the current state of evidence, including work cited by the NSC [1–4].
Driver Fatigue Classification With Independent Component by Entropy Rate Bound Minimization Analysis in an EEG-Based System

This paper presents a two-class electroencephal-ography-based classification for classifying of driver fatigue (fatigue state versus alert state) from 43 healthy participants. The system uses independent component by entropy rate bound minimization analysis (ERBM-ICA) for the source separation, autoregressive (AR) modeling for the features extraction, and Bayesian neural network for the classification algorithm. The classification results demonstrate a sensitivity of 89.7%, a specificity of 86.8%, and an accuracy of 88.2%. The combination of ERBM-ICA (source separator), AR (feature extractor), and Bayesian neural network (classifier) provides the best outcome with a p-value < 0.05 with the highest value of area under the receiver operating curve (AUC-ROC = 0.93) against other methods such as power spectral density as feature extractor (AUC-ROC = 0.81). The results of this study suggest the method could be utilized effectively for a countermeasure device for driver fatigue identification and other adverse event applications.
A finite element model of ultrasonic extrusion

Since the 1950's researchers have carried out investigations into the effects of applying ultrasonic excitation to metals undergoing elastic and plastic deformation. Experiments have been conducted where ultrasonic excitation is superimposed in complex metalworking operations such as wire drawing and extrusion, to identify the benefits of ultrasonic vibrations. This study presents a finite element analysis of ultrasonic excitation applied to the extrusion of a cylindrical aluminium bar. The effects of friction on the extrusion load are reported for the two excitation configurations of radially and axially applied ultrasonic vibrations and the results are compared with experimental data reported in the literature.
Dynamic Simulation of Soft Multimaterial 3D-Printed Objects

Abstract This article describes a 2D and 3D simulation engine that quantitatively models the statics, dynamics, and nonlinear deformation of heterogeneous soft bodies in a computationally efficient manner. There is a large body of work simulating compliant mechanisms. These normally assume small deformations with homogeneous material properties actuated with external forces. There is also a large body of research on physically based deformable objects for applications in computer graphics with the purpose of generating realistic appearances at the expense of accuracy. Here we present a simulation framework in which an object may be composed of any number of interspersed materials with varying properties (stiffness, density, Poisson's ratio, thermal expansion coefficient, and friction coefficients) to enable true heterogeneous multimaterial simulation. Collisions are handled to prevent self-penetration due to large deformation, which also allows multiple bodies to interact. A volumetric actuation method is.
Extreme Programming

Summary form only given, as follows. Extreme Programming (XP) is a lightweight design method developed by Kent Beck, Ward Cunningham, and others. After notable successes, XP has been generating huge interest, and no small amount of controversy. Much of the interest stems from XP¿s pragmatic approach to development. Key practices include pair programming, writing tests upfront, frequent refactoring and rebuild, continuous integration and testing. Key principles incremental and iterative development, working with the simplest solution, cutting out extraneous documentation, and collective code ownership.
What happens to an acellular dermal matrix after implantation in the human body? A histological and electron microscopic study

Acellular matrices are used for various purposes and they have been studied extensively for their potential roles in regenerating tissues or organs. The acellular matrix generates physiological cues that mimic the native tissue microenvironment. Acellular dermal matrix (ADM) is a soft connective tissue graft generated by a decellularization process that preserves the intact extracellular skin matrix. Upon implantation, this structure serves as a scaffold for donor-side cells to facilitate subsequent incorporation and revascularization. In breast reconstruction, ADM is used mainly for lower pole coverage and the shaping of a new breast. It helps control the positioning of the implant in the inframammary fold, and prevents the formation of contractile pseudocapsule around the breast implant. In this study, we provide a comprehensive histological description of ADM used for human breast reconstruction over the course of several months following implementation. Using immunohistochemical methods (a panel of 12 antibodies) coupled with optical and transmission electron microscopy, we confirmed that the original acellular dermal matrix became recolonized by fibroblasts and myofibroblasts, and also by various other free cells of the connective tissue (lymphocytes, macrophages and multinucleated giant cells, granulocytes, mast cells) after implantation into the patient’s body. Within the implanted ADM, there was a relatively rapid ingrowth of blood vessels. Lymphatic vessels were only detected in one case 9 months after the implantation of the ADM. These results suggest that lymphangiogenesis is a longer process than angiogenesis.
Biotransformation of Cobicistat: Metabolic Pathways and Enzymes.

BACKGROUND Cobicistat (COBI) is a pharmacoenhancer for antiretroviral therapy. OBJECTIVE The current study was designed to profile the metabolic pathways of COBI and to determine the enzymes that contribute to COBI metabolism. METHOD We screened COBI metabolites in mice and human liver microsomes. We also used cDNAexpressed human cytochromes P450 (CYPs) to explore the role of human enzymes in COBI metabolism. RESULTS Twenty new and three known metabolites of COBI were identified in mouse urine and feces. These new metabolic pathways of COBI include glycine conjugation, N-acetyl cysteine conjugation, morpholine ring-opening, and thiazole ring-opening. Twelve of COBI metabolites were further confirmed in mouse and human liver microsomes, including nine new metabolites. Consistent with the previous report, CYP3A4 and CYP2D6 were determined as the major enzymes that contribute to COBI metabolism. CONCLUSION This study provided a full map of COBI metabolism. These results can be used to manage CYP-mediated drug-drug interactions and adverse drug reactions that are associated with COBI-containing regimens in human.
Scrapie incubation periods and end-point titers in mouse strains differing at the H-2D locus.

In extending findings on the influence of the mouse H-2D locus on the scrapie incubation period, we showed that with the intracerebral (i.c.) route of injection, SJL and NZW mice (s and z alleles, respectively) had shorter incubation periods than C57BL mice (b allele) at several concentrations of two scrapie strains, ME7 and 139A. The three mouse strains have the same Sinc genotype, s7s7. Incubation period data among the three mouse strains after intraperitoneal (i.p.) injection revealed a different rank order of incubation periods from that seen after i.c. injection. End-point titers in the three mouse strains were similar after i.c. injection, but both scrapie strains yielded very low titers in NZW mice after i.p. injection. There were marked differences between 139A and ME7 incubation periods after both i.c. and i.p. injections in the three mouse genotypes, providing an additional parameter that distinguishes these two scrapie strains.
Automatic Spike Removal Algorithm for Raman Spectra

Raman spectroscopy is a powerful technique, widely used in both academia and industry. In part, the technique’s extensive use stems from its ability to uniquely identify and image various material parameters: composition, strain, temperature, lattice/excitation symmetry, and magnetism in bulk, nano, solid, and organic materials. However, in nanomaterials and samples with low thermal conductivity, these measurements require long acquisition times. On the other hand, charge-coupled device (CCD) detectors used in Raman microscopes are vulnerable to cosmic rays. As a result, many spurious spikes occur in the measured spectra, which can distort the result or require the spectra to be ignored. In this paper, we outline a new method that significantly improves upon existing algorithms for removing these spikes. Specifically, we employ wavelet transform and data clustering in a new spike-removal algorithm. This algorithm results in spike-free spectra with negligible spectral distortion. The reduced dependence on the selection of wavelets and intuitive wavelet coefficient adjustment strategy enables non-experts to employ these powerful spectra-filtering techniques.