Miracle-dz/UniFAR-FTUs huggingface dataset:
Microbial Translocation and Inflammation Occur in Hyperacute Immunodeficiency Virus Infection and Compromise Host Control of Virus Replication

Within the first three weeks of human immunodeficiency virus (HIV) infection, virus replication peaks in peripheral blood. Despite the critical, causal role of virus replication in determining transmissibility and kinetics of progression to acquired immune deficiency syndrome (AIDS), there is limited understanding of the conditions required to transform the small localized transmitted founder virus population into a large and heterogeneous systemic infection. Here we show that during the hyperacute “pre-peak” phase of simian immunodeficiency virus (SIV) infection in macaques, high levels of microbial DNA transiently translocate into peripheral blood. This, heretofore unappreciated, hyperacute-phase microbial translocation was accompanied by sustained reduction of lipopolysaccharide (LPS)-specific antibody titer, intestinal permeability, increased abundance of CD4+CCR5+ T cell targets of virus replication, and T cell activation. To test whether increasing gastrointestinal permeability to cause microbial translocation would amplify viremia, we treated two SIV-infected macaque ‘elite controllers’ with a short-course of dextran sulfate sodium (DSS)–stimulating a transient increase in microbial translocation and a prolonged recrudescent viremia. Altogether, our data implicates translocating microbes as amplifiers of immunodeficiency virus replication that effectively undermine the host’s capacity to contain infection.
A systematic review and network meta-analysis protocol of neoadjuvant treatments for patients with gastric cancer

Background: National Comprehensive Cancer Network (NCCN) guidelines recommend surgery, chemotherapy, and radiation therapy for gastric cancer patients. Neoadjuvant treatments as the administration of therapeutic agents before a main treatment gained in more and more attention. However, the role of neoadjuvant treatments is still controversial. The main aim of this systematic review and network meta-analysis is to assess the relative efficacy of different neoadjuvant treatment regimens for gastric cancer using network meta-analysis method. Methods: We will search 5 electronic databases to identify randomized controlled trials (RCTs) and non-RCTs compared the efficacy differences of surgery alone (S), preoperative chemotherapy follow by surgery (CTS), preoperative radiotherapy follow by surgery (RTS), and preoperative chemoradiotherapy follow by surgery (CRTS) for patients with gastric cancer. The risk of bias tool from the Cochrane Handbook version 5.1. 0 will be used to assess the risk of bias of RCTs, and the risk of bias in nonrandomized studies of interventions (ROBINS-I) for non-RCTs. Data will be analyzed using R-3.4. 1 software. Results and conclusion: The results of present network meta-analysis will estimate the relative efficacy among all interventions and rank the interventions even if head-to-head comparisons are lacking and will provide more evidence for clinicians, researchers, and patients in the management of gastric cancer. Protocol registration number: CRD42017074956
Differential Impact of Flavonoids on Redox Modulation, Bioenergetics, and Cell Signaling in Normal and Tumor Cells: A Comprehensive Review

Abstract Significance: Flavonoids can interact with multiple molecular targets to elicit their cellular effects, leading to changes in signal transduction, gene expression, and/or metabolism, which can, subsequently, affect the entire cell and organism. Immortalized cell lines, derived from tumors, are routinely employed as a surrogate for mechanistic studies, with the results extrapolated to tissues in vivo. Recent Advances: We review the activities of selected flavonoids on cultured tumor cells derived from various tissues in comparison to corresponding primary cells or tissues in vivo, mainly using quercetin and flavanols (epicatechin and (−)-epigallocatechin gallate) as exemplars. Several studies have indicated that flavonoids could retard cancer progression in vivo in animal models as well as in tumor cell models. Critical Issues: Extrapolation from in vitro and animal models to humans is not straightforward given both the extensive conjugation and complex microbiota-dependent metabolism of flavonoids after consumption, as well as the heterogeneous metabolism of different tumors. Future Directions: Comparison of data from studies on primary cells or in vivo are essential not only to validate results obtained from cultured cell models, but also to highlight whether any differences may be further exploited in the clinical setting for chemoprevention. Tumor cell models can provide a useful mechanistic tool to study the effects of flavonoids, provided that the limitations of each model are understood and taken into account in interpretation of the data.
Electronic Transmission of Antibacterial Property Into Water at Extremely Low Frequency Range: A Preliminary Study.

OBJECTIVES The aim of this study was to assess the possibility of transmitting the "ampicillin" growth inhibitory property to pure sterile water. DESIGN Three control groups were designed as references of bacterial maximal growth (MG). Different concentrations of ampicillin and pure sterile water used as "positive" and "negative" controls, respectively, and the bacterial cultures supplemented with water that merely exposed to the background carrier waves were set as "sham control. " SETTINGS The electronic characteristic of the ampicillin solution relayed to the water and then it was added to the bacterial culture medium. By this treatment, water received both the carrier wave and ampicillin electronic properties at 1-105 Hz range. RESULTS When the MG of the "treated water" and "positive control" dilutions is getting normalized against either sham or negative control, the treated water competently imitates ampicillin in a way that there is no significant difference with the positive control. These results will be affected to some extent by the time of electronic transmission and the inoculation concentration of bacterial culture. Comparison of electromagnetic signal patterns of "treated water" with the "positive control" shows that they are more similar to each other rather than negative control. CONCLUSION It is believed that the extremely low frequencies can facilitate electronic transmission of ampicillin supramolecular chemistry into water. Imprinting such a property in water could be the result of durable structural configuration in treated water.
Exploring the impact of high intensity interval training on adolescents’ objectively measured physical activity: Findings from a randomized controlled trial

ABSTRACT High Intensity Interval Training (HIIT) may be effective for accumulating VPA. However, the contribution of HIIT to overall physical activity is unknown. Our primary aim was to explore the impact of school-based HIIT on physical activity. The secondary aim was to explore within-individual changes in physical activity after participating in HIIT. Participants [n = 65; 15.8(0.6)years] were randomized to a HIIT or control group. Intervention groups participated in three HIIT sessions/week. GENEActiv accelerometers assessed objective physical activity at baseline and week-one, to detect changes in MPA and VPA. Intervention effects were examined using linear mixed models and evidence of a change in physical activity (i.e., compensation) were examined using multilevel linear regression models. The group-by-time interaction effects for MPA and VPA were small and moderate, respectively. Adjusted difference between groups for VPA was 1.70 min/day, 95%CI –1.96 to 5.36; p = 0.354; d = 0.55). Embedding HIIT within the school-day had a moderate effect on VPA compared to controls. Compensation analyses (i.e., individual level) suggested that adolescents were more active on days when they participated in HIIT. Further studies are needed to test the effects of HIIT on adolescents’ physical activity over extended time periods.
QuadricSLAM: Constrained Dual Quadrics from Object Detections as Landmarks in Semantic SLAM

Research in Simultaneous Localization And Mapping (SLAM) is increasingly moving towards richer world representations involving objects and high level features that enable a semantic model of the world for robots, potentially leading to a more meaningful set of robot-world interactions. Many of these advances are grounded in state-of-the-art computer vision techniques primarily developed in the context of image-based benchmark datasets, leaving several challenges to be addressed in adapting them for use in robotics. In this paper, we derive a SLAM formulation that uses dual quadrics as 3D landmark representations, exploiting their ability to compactly represent the size, position and orientation of an object, and show how 2D bounding boxes (such as those typically obtained from visual object detection systems) can directly constrain the quadric parameters via a novel geometric error formulation. We develop a sensor model for deep-learned object detectors that addresses the challenge of partial object detections often encountered in robotics applications, and demonstrate how to jointly estimate the camera pose and constrained dual quadric parameters in factor graph based SLAM with a general perspective camera.
A Multicenter Pragmatic Interrupted Time Series Analysis of Chlorhexidine Gluconate Bathing in Community Hospital Intensive Care Units

OBJECTIVE To determine whether daily chlorhexidine gluconate (CHG) bathing of intensive care unit (ICU) patients leads to a decrease in hospital-acquired infections (HAIs), particularly infections caused by methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE). DESIGN Interrupted time series analysis. SETTING The study included 33 community hospitals participating in the Duke Infection Control Outreach Network from January 2008 through December 2013. PARTICIPANTS All ICU patients at study hospitals during the study period. METHODS Of the 33 hospitals, 17 hospitals implemented CHG bathing during the study period, and 16 hospitals that did not perform CHG bathing served as controls. Primary pre-specified outcomes included ICU central-line–associated bloodstream infections (CLABSIs), primary bloodstream infections (BSI), ventilator-associated pneumonia (VAP), and catheter-associated urinary tract infections (CAUTIs). MRSA and VRE HAIs were also evaluated. RESULTS Chlorhexidine gluconate (CHG) bathing was associated with a significant downward trend in incidence rates of ICU CLABSI (incidence rate ratio [IRR], 0.96; 95% confidence interval [CI], 0.93–0.99), ICU primary BSI (IRR, 0.96; 95% CI, 0.94–0.99), VRE CLABSIs (IRR, 0.97; 95% CI, 0.97–0.98), and all combined VRE infections (IRR, 0.96; 95% CI, 0.93–1.00). No significant trend in MRSA infection incidence rates was identified prior to or following the implementation of CHG bathing. CONCLUSIONS In this multicenter, real-world analysis of the impact of CHG bathing, hospitals that implemented CHG bathing attained a decrease in ICU CLABSIs, ICU primary BSIs, and VRE CLABSIs. CHG bathing did not affect rates of specific or overall infections due to MRSA. Our findings support daily CHG bathing of ICU patients. Infect Control Hosp Epidemiol 2016;37:791–797
Systematic characterization of autophagy-related genes during the adipocyte differentiation using public-access data

Autophagy contributes to reorganizing intracellular components and forming fat droplets during the adipocyte differentiation. Here, we systematically describe the role of autophagy-related genes and gene sets during the differentiation of adipocytes. We used a public dataset from the European Nucleotide Archive from an RNA-seq experiment in which 3T3-L1 cells were induced by a differentiation induction medium, total RNA was extracted and sequenced at four different time points. Raw reads were aligned to the UCSC mouse reference genome (mm10) using HISAT2, and aligned reads were summarized at the gene or exon level using HTSeq. DESeq2 and DEXSeq were used to model the gene and exon counts and test for differential expression and relative exon usage, respectively. After applying the appropriate transformation, gene counts were used to perform the gene set and pathway enrichment analysis. Data were obtained, processed and annotated using R and Bioconductor. Several autophagy-related genes and autophagy gene sets, as defined in the Gene Ontology, were actively regulated during the course of the adipocyte differentiation. We further characterized these gene sets by clustering their members to a few distinct temporal profiles. Other potential functionally related genes were identified using a machine learning procedure. In summary, we characterized the autophagy gene sets and their members to biologically meaningful groups and elected a number of genes to be functionally related based on their expression patterns, suggesting that autophagy plays a critical role in removal of some intracellular components and supply of energy sources for lipid biogenesis during adipogenesis.
Semantic Hashing for Video Game Levels

We use semantic hashing, an unsupervised machine learning technique based on a type of deep neural network called autoencoders, to categorise video game levels. We show how this technique can be used on dungeon room maps from The Legend of Zelda and segments of 2D-platformer levels from Super Mario Bros. We also discuss how this technique can be useful for game designers, AI-assisted game design, and procedural content generation.
A new textile-based approach to assess the antimicrobial activity of volatiles

Textiles with antimicrobial properties are required in many areas but it is difficult to assess the effect with current assays based on the cultivation of microorganisms. Using confocal laser scanning microscopy (CLSM) we observed that the complex matrix of textiles provides an ideal niche for the adhesion of microorganisms because polyester fibres showed a high number of irregularly appearing notches. In another experiment with green fluorescent protein-labelled Staphylococcus epidermidis cells were found in these notches, tightly bound to the fibres. Staphylococcus cells shielded in the textile were not killed by conventional decontamination techniques like UV irradiation. Cultivation-dependent evaluation of bacterial survival after 10 minutes of irradiation indicated a good reduction of more than 99%, whereas fluorescent viability staining of cells, in combination with CLSM, displayed more than 5% survival. This latter sensitive assay can also be used to assess the activity of volatile antimicrobials. It was shown that volatiles produced by plant-associated bacteria (Pseudomonas chlororaphis and Paenibacillus polymyxa) irreversibly inhibited the growth of human-associated pathogens like Staphylococcus aureus and Candida albicans on textiles. This new approach enables the detection and evaluation of new volatile antimicrobials for their use in disinfection of garments.
Quantification of Intracranial Aneurysm Volume Pulsation with 7T MRI

Tenunruptured aneurysms in 9 patients were studied using a high-resolution 3D gradient-echo sequence with cardiac gating. Semiautomatic segmentation was used to measure aneurysm volume per cardiac phase. Aneurysm pulsation was defined as the relative increase in volume between the phase with the smallest volume and the phase with the largest volume. The accuracy and precision of the measured volume pulsations were addressed by digital phantom simulations and a repeat image analysis. In Stage II, the imaging protocol was optimized and 9 patients with 9 aneurysms were studied with and without administration of a contrast agent. Mean aneurysm pulsation in Stage I was 8%, with a mean volume change of 15 mm3. The artifactual volume pulsations measured with the digital phantom simulations were of the same magnitude as the volume pulsations observed in the patient data. Volume pulsation quantification with the current imaging protocol on 7T MR imaging is not accurate due to multiple imaging artifacts. BACKGROUND AND PURPOSE: Aneurysm volume pulsation is a potential predictor of intracranial aneurysm rupture. We evaluated whether 7T MR imaging can quantify aneurysm volume pulsation. MATERIALS AND METHODS: In Stage I of the study, 10 unruptured aneurysms in 9 patients were studied using a high-resolution (0.6-mm, isotropic) 3D gradient-echo sequence with cardiac gating. Semiautomatic segmentation was used to measure aneurysm volume (in cubic millimeters) per cardiac phase. Aneurysm pulsation was defined as the relative increase in volume between the phase with the smallest volume and the phase with the largest volume. The accuracy and precision of the measured volume pulsations were addressed by digital phantom simulations and a repeat image analysis. In Stage II, the imaging protocol was optimized and 9 patients with 9 aneurysms were studied with and without administration of a contrast agent. RESULTS: The mean aneurysm pulsation in Stage I was 8% ± 7% (range, 2%–27%), with a mean volume change of 15 ± 14 mm3 (range, 3–51 mm3). The mean difference in volume change for the repeat image analysis was 2 ± 6 mm3. The artifactual volume pulsations measured with the digital phantom simulations were of the same magnitude as the volume pulsations observed in the patient data, even after protocol optimization in Stage II. CONCLUSIONS: Volume pulsation quantification with the current imaging protocol on 7T MR imaging is not accurate due to multiple imaging artifacts. Future studies should always include aneurysm-specific accuracy analysis.
The Molecular Targets and Anti-Invasive Effects of 2,6-bis-(4-hydroxyl-3methoxybenzylidine) cyclohexanone or BHMC in MDA-MB-231 Human Breast Cancer Cells

In order to metastasize, tumor cells need to migrate and invade the surrounding tissues. It is important to identify compound(s) capable of disrupting the metastasis of invasive cancer cells, especially for hindering invadopodia formation, so as to provide anti-metastasis targeted therapy. Invadopodia are thought to be specialized actin-rich protrusions formed by highly invasive cancer cells to degrade the extracellular matrix (ECM). A curcuminoid analogue known as 2,6-bis-(4-hydroxy-3-methoxybenzylidine)cyclohexanone or BHMC has shown good potential in inhibiting inflammation and hyperalgesia. It also possesses an anti-tumor effects on 4T1 murine breast cancer cells in vivo. However, there is still a lack of empirical evidence on how BHMC works in preventing human breast cancer invasion. In this study, we investigated the effect of BHMC on MDA-MB-231 breast cancer cells and its underlying mechanism of action to prevent breast cancer invasion, especially during the formation of invadopodia. All MDA-MB-231 cells, which were exposed to the non-cytotoxic concentrations of BHMC, expressed the proliferating cell nuclear antigen (PCNA), which indicate that the anti-proliferative effects of BHMC did not interfere in the subsequent experiments. By using a scratch migration assay, transwell migration and invasion assays, we determined that BHMC reduces the percentage of migration and invasion of MDA-MB-231 cells. The gelatin degradation assay showed that BHMC reduced the number of cells with invadopodia. Analysis of the proteins involved in the invasion showed that there is a significant reduction in the expressions of Rho guanine nucleotide exchange factor 7 (β-PIX), matrix metalloproteinase-9 (MMP-9), and membrane type 1 matrix metalloproteinase (MT1-MMP) in the presence of BHMC treatment at 12.5 µM. Therefore, it can be postulated that BHMC at 12.5 µM is the optimal concentration for preventing breast cancer invasion.
Brain Structural Covariance Network Topology in Remitted Posttraumatic Stress Disorder

Posttraumatic stress disorder (PTSD) is a prevalent, chronic disorder with high psychiatric morbidity; however, a substantial portion of affected individuals experience remission after onset. Alterations in brain network topology derived from cortical thickness correlations are associated with PTSD, but the effects of remitted symptoms on network topology remain essentially unexplored. In this cross-sectional study, US military veterans (N = 317) were partitioned into three diagnostic groups, current PTSD (CURR-PTSD, N = 101), remitted PTSD with lifetime but no current PTSD (REMIT-PTSD, N = 35), and trauma-exposed controls (CONTROL, n = 181). Cortical thickness was assessed for 148 cortical regions (nodes) and suprathreshold interregional partial correlations across subjects constituted connections (edges) in each group. Four centrality measures were compared with characterize between-group differences. The REMIT-PTSD and CONTROL groups showed greater centrality in left frontal pole than the CURR-PTSD group. The REMIT-PTSD group showed greater centrality in right subcallosal gyrus than the other two groups. Both REMIT-PTSD and CURR-PTSD groups showed greater centrality in right superior frontal sulcus than CONTROL group. The centrality in right subcallosal gyrus, left frontal pole, and right superior frontal sulcus may play a role in remission, current symptoms, and PTSD history, respectively. The network centrality changes in critical brain regions and structural networks are associated with remitted PTSD, which typically coincides with enhanced functional behaviors, better emotion regulation, and improved cognitive processing. These brain regions and associated networks may be candidates for developing novel therapies for PTSD. Longitudinal work is needed to characterize vulnerability to chronic PTSD, and resilience to unremitting PTSD.
Group Decision Making With Consistency of Intuitionistic Fuzzy Preference Relations Under Uncertainty

Intuitionistic fuzzy preference relation U+0028 IFPR U+0029 is a suitable technique to express fuzzy preference information by decision makers U+0028 DMs U+0029. This paper aims to provide a group decision making method where DMs use the IFPRs to indicate their preferences with uncertain weights. To begin with, a model to derive weight vectors of alternatives from IFPRs based on multiplicative consistency is presented. Specifically, for any IFPR, by minimizing its absolute deviation from the corresponding consistent IFPR, the weight vectors are generated. Secondly, a method to determine relative weights of DMs depending on preference information is developed. After that we prioritize alternatives based on the obtained weights considering the risk preference of DMs. Finally, this approach is applied to the problem of technical risks assessment of armored equipment to illustrate the applicability and superiority of the proposed method.