Miracle-dz/UniFAR-FTUs huggingface dataset:
Hepatitis C Related Chronic Liver Cirrhosis: Feasibility of Texture Analysis of MR Images for Classification of Fibrosis Stage and Necroinflammatory Activity Grade

Purpose To assess the feasibility of texture analysis for classifying fibrosis stage and necroinflammatory activity grade in patients with chronic hepatitis C on T2-weighted (T2W), T1-weighted (T1W) and Gd-EOB-DTPA-enhanced hepatocyte-phase (EOB-HP) imaging. Materials and methods From April 2008 to June 2012, MR images from 123 patients with pathologically proven chronic hepatitis C were retrospectively analyzed. Texture parameters derived from histogram, gradient, run-length matrix, co-occurrence matrix, autoregressive model and wavelet transform methods were estimated with imaging software. Fisher, probability of classification error and average correlation, and mutual information coefficients were used to extract subsets of optimized texture features. Linear discriminant analysis in combination with 1-nearest neighbor classifier (LDA/1-NN) was used for lesion classification. In compliance with the software requirement, classification was performed based on datasets from all patients, the patient group with necroinflammatory activity grade 1, and that with fibrosis stage 4, respectively. Results Based on all patient dataset, LDA/1-NN produced misclassification rates of 28.46%, 35.77% and 20.33% for fibrosis staging and 34.15%, 25.20% and 28.46% for necroinflammatory activity grading in T2W, T1W and EOB-HP images. In the patient group with necroinflammatory activity grade 1, LDA/1-NN yielded misclassification rates of 5.00%, 0% and 12.50% for fibrosis staging in T2W, T1W and EOB-HP images respectively. In the patient group with fibrosis stage 4, LDA/1-NN yielded misclassification rates of 5.88%, 12.94% and 11.76% for necroinflammatory activity grading in T2W, T1W and EOB-HP images respectively. Conclusion Texture quantitative parameters of MR images facilitate classification of the fibrosis stage as well as necroinflammatory activity grade in chronic hepatitis C, especially after categorizing the input dataset according to the activity or fibrosis degree in order to remove the interference between the fibrosis stage and necroinflammatory activity grade on texture features.
Evaluation of tremolite asbestos exposures associated with the use of commercial products

Tremolite is a noncommercial form of amphibole mineral that is present in some chrysotile, talc, and vermiculite deposits. Inhalation of asbestiform tremolite is suspected to have caused or contributed to an increased incidence of mesothelioma in certain mining settings; however, very little is known about the magnitude of tremolite exposure that occurred at these locations, and even less is known regarding tremolite exposures that might have occurred during consumer use of chrysotile, talc, and vermiculite containing products. The purpose of this analysis is to evaluate the exposure-response relationship for tremolite asbestos and mesothelioma in high exposure settings (mining) and to develop estimates of tremolite asbestos exposure for various product use scenarios. Our interpretation of the tremolite asbestos exposure metrics reported for the Thetford chrysotile mines and the Libby vermiculite deposits suggests a lowest-observed-adverse-effect level (LOAEL) for mesothelioma of 35–73 f/cc-year. Using measured and estimated airborne tremolite asbestos concentrations for simulated and actual product use, we conservatively estimated the following cumulative tremolite asbestos exposures: career auto mechanic: 0.028 f/cc-year; non-occupational use of joint compound: 0.0006 f/cc-year; non-occupational use of vermiculite-containing gardening products: 0.034 f/cc-year; home-owner removal of Zonolite insulation: 0.0002 f/cc-year. While the estimated consumer tremolite exposures are far below the tremolite LOAELs derived herein, this analysis examines only a few of the hundreds of chrysotile- and talc-containing products.
Protective Effects of Transforming Growth Factor β2 in Intestinal Epithelial Cells by Regulation of Proteins Associated with Stress and Endotoxin Responses

Transforming growth factor (TGF)-β2 is an important anti-inflammatory protein in milk and colostrum. TGF-β2 supplementation appears to reduce gut inflammatory diseases in early life, such as necrotizing enterocolitis (NEC) in young mice. However, the molecular mechanisms by which TGF-β2 protects immature intestinal epithelial cells (IECs) remain to be more clearly elucidated before interventions in infants can be considered. Porcine IECs PsIc1 were treated with TGF-β2 and/or lipopolysaccharide (LPS), and changes in the cellular proteome were subsequently analyzed using two-dimensional gel electrophoresis-MS and LC-MS-based proteomics. TGF-β2 alone induced the differential expression of 13 proteins and the majority of the identified proteins were associated with stress responses, TGF-β and Toll-like receptor 4 signaling cascades. In particular, a series of heat shock proteins had similar differential trends as previously shown in the intestine of NEC-resistant preterm pigs and young mice. Furthermore, LC-MS-based proteomics and Western blot analyses revealed 20 differentially expressed proteins following treatment with TGF-β2 in LPS-challenged IECs. Thirteen of these proteins were associated with stress response pathways, among which five proteins were altered by LPS and restored by TGF-β2, whereas six were differentially expressed only by TGF-β2 in LPS-challenged IECs. Based on previously reported biological functions, these patterns indicate the anti-stress and anti-inflammatory effects of TGF-β2 in IECs. We conclude that TGF-β2 of dietary or endogenous origin may regulate the IEC responses against LPS stimuli, thereby supporting cellular homeostasis and innate immunity in response to bacterial colonization, and the first enteral feeding in early life.
Functional Mapping of the Human Visual Cortex with Intravoxel Incoherent Motion MRI

Functional imaging with intravoxel incoherent motion (IVIM) magnetic resonance imaging (MRI) is demonstrated. Images were acquired at 3 Tesla using a standard Stejskal-Tanner diffusion-weighted echo-planar imaging sequence with multiple b-values. Cerebro-spinal fluid signal, which is highly incoherent, was suppressed with an inversion recovery preparation pulse. IVIM microvascular perfusion parameters were calculated according to a two-compartment (vascular and non-vascular) diffusion model. The results obtained in 8 healthy human volunteers during visual stimulation are presented. The IVIM blood flow related parameter fD* increased 170% during stimulation in the visual cortex, and 70% in the underlying white matter.
Preschool Externalizing Behavior Predicts Gender-Specific Variation in Adolescent Neural Structure

Dysfunction in the prefrontal cortex, amygdala, and hippocampus is believed to underlie the development of much psychopathology. However, to date only limited longitudinal data relate early behavior with neural structure later in life. Our objective was to examine the relationship of early life externalizing behavior with adolescent brain structure. We report here the first longitudinal study linking externalizing behavior during preschool to brain structure during adolescence. We examined the relationship of preschool externalizing behavior with amygdala, hippocampus, and prefrontal cortex volumes at age 15 years in a community sample of 76 adolescents followed longitudinally since their mothers’ pregnancy. A significant gender by externalizing behavior interaction revealed that males—but not females—with greater early childhood externalizing behavior had smaller amygdala volumes at adolescence (t = 2.33, p = .023). No significant results were found for the hippocampus or the prefrontal cortex. Greater early externalizing behavior also related to smaller volume of a cluster including the angular gyrus and tempoparietal junction across genders. Results were not attributable to the impact of preschool anxiety, preschool maternal stress, school-age internalizing or externalizing behaviors, or adolescent substance use. These findings demonstrate a novel, gender-specific relationship between early-childhood externalizing behavior and adolescent amygdala volume, as well as a cross-gender result for the angular gyrus and tempoparietal junction.
Fate of Antibiotic Resistant Bacteria and Genes during Wastewater Chlorination: Implication for Antibiotic Resistance Control

This study investigated fates of nine antibiotic-resistant bacteria as well as two series of antibiotic resistance genes in wastewater treated by various doses of chlorine (0, 15, 30, 60, 150 and 300 mg Cl2 min/L). The results indicated that chlorination was effective in inactivating antibiotic-resistant bacteria. Most bacteria were inactivated completely at the lowest dose (15 mg Cl2 min/L). By comparison, sulfadiazine- and erythromycin-resistant bacteria exhibited tolerance to low chlorine dose (up to 60 mg Cl2 min/L). However, quantitative real-time PCRs revealed that chlorination decreased limited erythromycin or tetracycline resistance genes, with the removal levels of overall erythromycin and tetracycline resistance genes at 0.42 ± 0.12 log and 0.10 ± 0.02 log, respectively. About 40% of erythromycin-resistance genes and 80% of tetracycline resistance genes could not be removed by chlorination. Chlorination was considered not effective in controlling antimicrobial resistance. More concern needs to be paid to the potential risk of antibiotic resistance genes in the wastewater after chlorination.
Detection of Powdery Mildew in Two Winter Wheat Plant Densities and Prediction of Grain Yield Using Canopy Hyperspectral Reflectance

To determine the influence of plant density and powdery mildew infection of winter wheat and to predict grain yield, hyperspectral canopy reflectance of winter wheat was measured for two plant densities at Feekes growth stage (GS) 10.5. 3, 10.5. 4, and 11.1 in the 2009–2010 and 2010–2011 seasons. Reflectance in near infrared (NIR) regions was significantly correlated with disease index at GS 10.5. 3, 10.5. 4, and 11.1 at two plant densities in both seasons. For the two plant densities, the area of the red edge peak (Σdr 680–760 nm), difference vegetation index (DVI), and triangular vegetation index (TVI) were significantly correlated negatively with disease index at three GSs in two seasons. Compared with other parameters Σdr 680–760 nm was the most sensitive parameter for detecting powdery mildew. Linear regression models relating mildew severity to Σdr 680–760 nm were constructed at three GSs in two seasons for the two plant densities, demonstrating no significant difference in the slope estimates between the two plant densities at three GSs. Σdr 680–760 nm was correlated with grain yield at three GSs in two seasons. The accuracies of partial least square regression (PLSR) models were consistently higher than those of models based on Σdr 680760 nm for disease index and grain yield. PLSR can, therefore, provide more accurate estimation of disease index of wheat powdery mildew and grain yield using canopy reflectance.
Downregulation of cholesteryl ester transfer protein by glucocorticoids: a randomised study on HDL

High density lipoprotein (HDL) cholesterol is not decreased in hypercortisolism despite high triglycerides, which may be ascribed to effects on the cholesteryl ester transfer protein (CETP) pathway. We explored if CETP mRNA expression is modulated by glucocorticoid treatment in vitro. Effects of doubling the hydrocortisone (HCT) replacement dose on plasma CETP activity, and HDL characteristics were tested in patients with secondary adrenal insufficiency.
MUFOLD‐SS: New deep inception‐inside‐inception networks for protein secondary structure prediction

Protein secondary structure prediction can provide important information for protein 3D structure prediction and protein functions. Deep learning offers a new opportunity to significantly improve prediction accuracy. In this article, a new deep neural network architecture, named the Deep inception‐inside‐inception (Deep3I) network, is proposed for protein secondary structure prediction and implemented as a software tool MUFOLD‐SS. The input to MUFOLD‐SS is a carefully designed feature matrix corresponding to the primary amino acid sequence of a protein, which consists of a rich set of information derived from individual amino acid, as well as the context of the protein sequence. Specifically, the feature matrix is a composition of physio‐chemical properties of amino acids, PSI‐BLAST profile, and HHBlits profile. MUFOLD‐SS is composed of a sequence of nested inception modules and maps the input matrix to either eight states or three states of secondary structures. The architecture of MUFOLD‐SS enables effective processing of local and global interactions between amino acids in making accurate prediction. In extensive experiments on multiple datasets, MUFOLD‐SS outperformed the best existing methods and other deep neural networks significantly. MUFold‐SS can be downloaded from http://dslsrv8.cs. missouri.edu/~cf797/MUFoldSS/download.html.
Endogenous Prostaglandins and Afferent Sensory Nerves in Gastroprotective Effect of Hydrogen Sulfide against Stress-Induced Gastric Lesions

Hydrogen sulfide (H2S) plays an important role in human physiology, exerting vasodilatory, neuromodulatory and anti-inflammatory effects. H2S has been implicated in the mechanism of gastrointestinal integrity but whether this gaseous mediator can affect hemorrhagic lesions induced by stress has been little elucidated. We studied the effect of the H2S precursor L-cysteine, H2S-donor NaHS, the H2S synthesizing enzyme (CSE) activity inhibitor- D,L-propargylglycine (PAG) and the gastric H2S production by CSE/CBS/3-MST activity in water immersion and restraint stress (WRS) ulcerogenesis and the accompanying changes in gastric blood flow (GBF). The role of endogenous prostaglandins (PGs) and sensory afferent nerves releasing calcitonin gene-related peptide (CGRP) in the mechanism of gastroprotection induced by H2S was examined in capsaicin-denervated rats and those pretreated with capsazepine to inhibit activity of vanilloid receptors (VR-1). Rats were pretreated with vehicle, NaHS, the donor of H2S and or L-cysteine, the H2S precursor, with or without the concurrent treatment with 1) nonselective (indomethacin) and selective cyclooxygenase (COX)-1 (SC-560) or COX-2 (rofecoxib) inhibitors. The expression of mRNA and protein for COX-1 and COX-2 were analyzed in gastric mucosa pretreated with NaHS with or without PAG. Both NaHS and L-cysteine dose-dependently attenuated severity of WRS-induced gastric lesions and significantly increased GBF. These effects were significantly reduced by pretreatment with PAG and capsaicin denervation. NaHS increased gastric H2S production via CSE/CBS but not 3-MST activity. Inhibition of COX-1 and COX-2 activity significantly diminished NaHS- and L-cysteine-induced protection and hyperemia. NaHS increased expression of COX-1, COX-2 mRNAs and proteins and raised CGRP mRNA expression. These effects of NaHS on COX-1 and COX-2 protein contents were reversed by PAG and capsaicin denervation. We conclude that H2S exerts gastroprotection against WRS-induced gastric lesions by the mechanism involving enhancement in gastric microcirculation mediated by endogenous PGs, sensory afferent nerves releasing CGRP and the activation of VR-1 receptors.
Improving qPCR telomere length assays: Controlling for well position effects increases statistical power

Telomere length (TL) is commonly measured using quantitative PCR (qPCR). Although, easier than the southern blot of terminal restriction fragments (TRF) TL measurement method, one drawback of qPCR is that it introduces greater measurement error and thus reduces the statistical power of analyses. To address a potential source of measurement error, we consider the effect of well position on qPCR TL measurements.
Low Maternal Vitamin D Status during the Second Trimester of Pregnancy: A Cross-Sectional Study in Wuxi, China

Background Vitamin D deficiency is common in pregnant women, but an optimal serum vitamin D level during pregnancy has not been determined and remains an area of active research. Vitamin D data from large populations of pregnant Chinese women are still limited. Objective To evaluate the vitamin D status of women in Eastern China during the second trimester of pregnancy. Methods A hospital-based, cross-sectional, observational study. Serum 25-hydroxyvitamin D [25(OH)D] concentration was measured in samples from 5823 pregnant women in Wuxi City, China (latitude: 31.5o N), from January 2011 to June 2012. Results The median serum 25(OH)D concentration was 34.0 nmol/L [2.5 nmol/L 25(OH)D = 1 ng/mL 25(OH)D]. Vitamin D deficiency [defined as 25(OH)D < 30 nmol/L according to the Institute of Medicine (National Academy of Sciences, Washington, D.C., USA)] or inadequacy [25(OH)D of 30–49.9 nmol/L] was identified in 40.7% and 38.0% of the women, respectively. Only 0.9% had a 25(OH)D level ≥ 80.0 nmol/L, which is the concentration recommended as adequate by the Endocrine Society (Washington, D.C., USA). Compared with older women, younger women were more likely to be deficient in vitamin D. There were significant differences in the 25(OH)D levels according to season. The 25(OH)D levels reached peak values in September and were correlated with (r = 0.337, P < 0.001), and fluctuated with, average monthly air temperatures. Conclusions There is a high prevalence of Vitamin D deficiency among pregnant Chinese women, and 25(OH)D levels varied according to season and air temperature. The results of this study also suggest that currently there is a big gap between the levels of Vitamin D detected in pregnant Chinese women and the levels recommended by the Endocrine Society.
Cost-Effectiveness Analysis of Brief and Expanded Evidence-Based Risk Reduction Interventions for HIV-Infected People Who Inject Drugs in the United States

Aims Two behavioral HIV prevention interventions for people who inject drugs (PWID) infected with HIV include the Holistic Health Recovery Program for HIV+ (HHRP+), a comprehensive evidence-based CDC-supported program, and an abbreviated Holistic Health for HIV (3H+) Program, an adapted HHRP+ version in treatment settings. We compared the projected health benefits and cost-effectiveness of both programs, in addition to opioid substitution therapy (OST), to the status quo in the U.S. Methods A dynamic HIV transmission model calibrated to epidemic data of current US populations was created. Projected outcomes include future HIV incidence, HIV prevalence, and quality-adjusted life years (QALYs) gained under alternative strategies. Total medical costs were estimated to compare the cost-effectiveness of each strategy. Results Over 10 years, expanding HHRP+ access to 80% of PWID could avert up to 29,000 HIV infections, or 6% of the projected total, at a cost of $7,777/QALY gained. Alternatively, 3H+ could avert 19,000 infections, but is slightly more cost-effective ($7,707/QALY), and remains so under widely varying effectiveness and cost assumptions. Nearly two-thirds of infections averted with either program are among non-PWIDs, due to reduced sexual transmission from PWID to their partners. Expanding these programs with broader OST coverage could avert up to 74,000 HIV infections over 10 years and reduce HIV prevalence from 16.5% to 14.1%, but is substantially more expensive than HHRP+ or 3H+ alone. Conclusions Both behavioral interventions were effective and cost-effective at reducing HIV incidence among both PWID and the general adult population; however, 3H+, the economical HHRP+ version, was slightly more cost-effective than HHRP+.
Variation of Burkholderia cenocepacia virulence potential during cystic fibrosis chronic lung infection

ABSTRACT During long-term lung infection in cystic fibrosis (CF) patients, Burkholderia cenocepacia faces multiple selective pressures in this highly stressful and fluctuating environment. As a consequence, the initial infecting strain undergoes genetic changes that result in the diversification of genotypes and phenotypes. Whether this clonal expansion influences the pathogenic potential is unclear. The virulence potential of 39 sequential B. cenocepacia (recA lineage IIIA) isolates, corresponding to 3 different clones retrieved from 3 chronically infected CF patients was compared in this study using the non-mammalian infection hosts Galleria mellonella and Caenorhabditis elegans. The isolates used in this retrospective study were picked randomly from selective agar plates as part of a CF Center routine, from the onset of infection until patients' death after 3.5 and 7.5 y or the more recent isolation date after 12.5 y of chronic infection. The infection models proved useful to assess virulence potential diversification, but for some isolates the relative values diverged in C. elegans and G. mellonella. Results also reinforce the concept of the occurrence of clonal diversification and co-existence of multiple phenotypes within the CF lungs, also with respect to pathogenicity. No clear trend of decrease (or increase) of the virulence potential throughout long-term infection was found but there is an apparent tendency for a clone/patient-dependent decrease of virulence when the G. mellonella model was used. The sole avirulent variant in both infection hosts was found to lack the small third replicon previously associated to virulence. Although possible, the in vivo loss of this nonessential megaplasmid was found to be a rare event (1 among a total of 64 isolates examined).
Assessment of the Contribution of BeiDou GEO, IGSO, and MEO Satellites to PPP in Asia–Pacific Region

In contrast to the US Global Positioning System (GPS), the Russian Global Navigation Satellite System (GLONASS) and the European Galileo, the developing Chinese BeiDou satellite navigation system (BDS) consists of not only Medium Earth Orbit (MEO), but also Geostationary Orbit (GEO) as well as Inclined Geosynchronous Orbit (IGSO) satellites. In this study, the Precise Point Positioning (PPP) and PPP with Integer Ambiguity Resolution (IAR) are obtained. The contributions of these three different types of BDS satellites to PPP in Asia–Pacific region are assessed using data from selected 20 sites over more than four weeks. By using various PPP cases with different satellite combinations, in general, the largest contribution of BDS IGSO among the three kinds of BDS satellites to the reduction of convergence time and the improvement of positioning accuracy, particularly in the east direction, is identified. These PPP cases include static BDS only solutions and static/kinematic ambiguity-float and -fixed PPP with the combination of GPS and BDS. The statistical results demonstrate that the inclusion of BDS GEO and MEO satellites can improve the observation condition and result in better PPP performance as well. When combined with GPS, the contribution of BDS to the reduction of convergence time is, however, not as significant as that of GLONASS. As far as the positioning accuracy is concerned, GLONASS improves the accuracy in vertical component more than BDS does, whereas similar improvement in horizontal component can be achieved by inclusion of BDS IGSO and MEO as GLONASS.