Miracle-dz/UniFAR-FTUs huggingface dataset:
Derivation and Characterization of a CD4-Independent, Non-CD4-Tropic Simian Immunodeficiency Virus

ABSTRACT CD4 tropism is conserved among all primate lentiviruses and likely contributes to viral pathogenesis by targeting cells that are critical for adaptive antiviral immune responses. Although CD4-independent variants of human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) have been described that can utilize the coreceptor CCR5 or CXCR4 in the absence of CD4, these viruses typically retain their CD4 binding sites and still can interact with CD4. We describe the derivation of a novel CD4-independent variant of pathogenic SIVmac239, termed iMac239, that was used to derive an infectious R5-tropic SIV lacking a CD4 binding site. Of the seven mutations that differentiate iMac239 from wild-type SIVmac239, a single change (D178G) in the V1/V2 region was sufficient to confer CD4 independence in cell-cell fusion assays, although other mutations were required for replication competence. Like other CD4-independent viruses, iMac239 was highly neutralization sensitive, although mutations were identified that could confer CD4-independent infection without increasing its neutralization sensitivity. Strikingly, iMac239 retained the ability to replicate in cell lines and primary cells even when its CD4 binding site had been ablated by deletion of a highly conserved aspartic acid at position 385, which, for HIV-1, plays a critical role in CD4 binding. iMac239, with and without the D385 deletion, exhibited an expanded host range in primary rhesus peripheral blood mononuclear cells that included CCR5+ CD8+ T cells. As the first non-CD4-tropic SIV, iMac239-ΔD385 will afford the opportunity to directly assess the in vivo role of CD4 targeting on pathogenesis and host immune responses. IMPORTANCE CD4 tropism is an invariant feature of primate lentiviruses and likely plays a key role in pathogenesis by focusing viral infection onto cells that mediate adaptive immune responses and in protecting virions attached to cells from neutralizing antibodies. Although CD4-independent viruses are well described for HIV and SIV, these viruses characteristically retain their CD4 binding site and can engage CD4 if available. We derived a novel CD4-independent, CCR5-tropic variant of the pathogenic molecular clone SIVmac239, termed iMac239. The genetic determinants of iMac239's CD4 independence provide new insights into mechanisms that underlie this phenotype. This virus remained replication competent even after its CD4 binding site had been ablated by mutagenesis. As the first truly non-CD4-tropic SIV, lacking the capacity to interact with CD4, iMac239 will provide the unique opportunity to evaluate SIV pathogenesis and host immune responses in the absence of the immunomodulatory effects of CD4+ T cell targeting and infection.
The French Armed Forces Virology Unit: A Chronological Record of Ongoing Research on Orthopoxvirus

Since the official declaration of smallpox eradication in 1980, the general population vaccination has ceased worldwide. Therefore, people under 40 year old are generally not vaccinated against smallpox and have no cross protection against orthopoxvirus infections. This naïve population may be exposed to natural or intentional orthopoxvirus emergences. The virology unit of the Institut de Recherche Biomédicale des Armées (France) has developed research programs on orthopoxviruses since 2000. Its missions were conceived to improve the diagnosis capabilities, to foster vaccine development, and to develop antivirals targeting specific viral proteins. The role of the virology unit was asserted in 2012 when the responsibility of the National Reference Center for the Orthopoxviruses was given to the unit. This article presents the evolution of the unit activity since 2000, and the past and current research focusing on orthopoxviruses.
Nanocrystal TiO2 Engulfed SiO2-Barium Hexaferrite for Enhanced Electrons Mobility and Solar Harvesting Potential

Barium hexaferrite embedded-silica-titania photocatalyst (TiO2-SiO2-BaFe12O19) was synthesized through sol-gel, liquid catalytic phase transformation and solid reaction routes. The magnetic photocatalyst was aimed to harvest the photoenergy from the sunlight, minimize the electron-holes recombination rate, improve the long lifetime charge-carriers transfer to maximize the photocatalytic activity and enhances the separation and reusability of it. The as-synthesized photocatalyst was characterized and the photocatalytic activity was evaluated for the reduction of 2, 4-dichlorophenol (2, 4-DCP) under direct sunlight. The presence of SiO2 interlayer in TiO2-SiO2-BaFe12O19 prevents the phase transformation of magnetic core. TiO2-SiO2-BaFe12O19 benefits the magnetic separation with appreciable magnitude of coercivity (5035.6 Oe) and saturation magnetization (18.8256E-3 emu/g), respectively. The ferrite ions from the magnetic core which dispersed into TiO2 matrix exhibited an evident shift of the absorption in the visible region. This was again confirmed with the reduced band gap energy of 1.90 eV. Furthermore, TiO2-SiO2-BaFe12O19 destructed 100% of 2, 4-DCP compound within 150 min under very bright sunlight with an average irradiance of 820.8 W/m2 (results not shown). The embedding of BaFe12O19 with a SiO2 layer onto TiO2 nanocrystals contributed for an excellent solar-light utilization and ease magnetic separation of the nanosized photocatalyst.
Discovery of a Glucocorticoid Receptor (GR) Activity Signature Using Selective GR Antagonism in ER-Negative Breast Cancer

Purpose: Although high glucocorticoid receptor (GR) expression in early-stage estrogen receptor (ER)-negative breast cancer is associated with shortened relapse-free survival (RFS), how associated GR transcriptional activity contributes to aggressive breast cancer behavior is not well understood. Using potent GR antagonists and primary tumor gene expression data, we sought to identify a tumor-relevant gene signature based on GR activity that would be more predictive than GR expression alone. Experimental Design: Global gene expression and GR ChIP-sequencing were performed to identify GR-regulated genes inhibited by two chemically distinct GR antagonists, mifepristone and CORT108297. Differentially expressed genes from MDA-MB-231 cells were cross-evaluated with significantly expressed genes in GR-high versus GR-low ER-negative primary breast cancers. The resulting subset of GR-targeted genes was analyzed in two independent ER-negative breast cancer cohorts to derive and then validate the GR activity signature (GRsig). Results: Gene expression pathway analysis of glucocorticoid-regulated genes (inhibited by GR antagonism) revealed cell survival and invasion functions. GR ChIP-seq analysis demonstrated that GR antagonists decreased GR chromatin association for a subset of genes. A GRsig that comprised n = 74 GR activation-associated genes (also reversed by GR antagonists) was derived from an adjuvant chemotherapy-treated Discovery cohort and found to predict probability of relapse in a separate Validation cohort (HR = 1.9; P = 0.012). Conclusions: The GRsig discovered herein identifies high-risk ER-negative/GR-positive breast cancers most likely to relapse despite administration of adjuvant chemotherapy. Because GR antagonism can reverse expression of these genes, we propose that addition of a GR antagonist to chemotherapy may improve outcome for these high-risk patients. Clin Cancer Res; 24(14); 3433–46. ©2018 AACR.
Effect of light on the growth and photosynthesis of an invasive shrub in its native range

We studied the growth and photosynthetic capacity of Berberis darwinii shrub growing under different light conditions in their native area of Argentina to test if plant physiology differs from invaded area (using studies carried out in New Zealand). In its native range B. darwinii grows under different light conditions by adjusting shoot and leaf morphology and physiology. Plants of B. darwinii growing under the same light environments show similar physiology in native and invasive ranges. Therefore, intra-specific variations of the functional traits in native area do not condition successful invasiveness.
Targeting Oxidative Stress Using Nanoparticles as a Theranostic Strategy for Cardiovascular Diseases.

SIGNIFICANCE Nanomedicine is an application of nanotechnology that provides solutions to unmet medical challenges. The unique features of nanoparticles, such as their small size, modifiable components, and diverse functionality, make them attractive and suitable materials for novel diagnostic, therapeutic, or theranostic applications. Cardiovascular diseases (CVDs) are the major cause of noncommunicable illness in both developing and developed countries. Nanomedicine offers novel theranostic options for the treatment of CVDs. Recent Advances: Many innovative nanoparticles to target reactive oxygen species (ROS) have been developed. In this article, we review the characteristics of nanoparticles that are responsive to ROS, their limitations, and their potential clinical uses. Significant advances made in diagnosis of atherosclerosis and treatment of acute coronary syndrome using nanoparticles are discussed. CRITICAL ISSUES Although there is a tremendous potential for the nanoparticle applications in medicine, their safety should be considered while using in humans. We discuss the challenges that may be encountered with some of the innovative nanoparticles used in CVDs. FUTURE DIRECTIONS The unique properties of nanoparticles offer novel diagnostic tool and potential therapeutic strategies. However, nanomedicine is still in its infancy, and further in-depth studies are needed before wide clinical application is achieved.
Laser surface pre-treatment of aluminum for hybrid joints with glass fiber reinforced thermoplastics

Lightweight construction is a major trend in the automotive industry. The connection of fiber reinforced plastics with aluminum is consequently seen as a promising prospect. In this regard, thermal joining is one potential joining technology for bonding of such hybrid joints. Yet a pretreatment of the aluminum surface is necessary to create a load bearing metal-plastic joint. Recent research has shown that a laser surface pretreatment provides high joint strengths. However, there is a variety of laser sources and possible surface topographies with typical structure sizes ranging from macroscopic to nanoscopic profiles. Within this work, two different laser induced structures were generated on aluminum sheets which were subsequently joined to glass fiber reinforced thermoplastics. One of the two laser structures was created with a continuous wave laser using a modified remote ablation cutting process. The other structure was manufactured by a pulsed laser source with a pulse width in the nanosecond-range.
CSF neurofilament light chain and phosphorylated tau 181 predict disease progression in PSP

Objective To determine the ability of CSF biomarkers to predict disease progression in progressive supranuclear palsy (PSP). Methods We compared the ability of baseline CSF β-amyloid1–42, tau, phosphorylated tau 181 (p-tau), and neurofilament light chain (NfL) concentrations, measured by INNO-BIA AlzBio3 or ELISA, to predict 52-week changes in clinical (PSP Rating Scale [PSPRS] and Schwab and England Activities of Daily Living [SEADL]), neuropsychological, and regional brain volumes on MRI using linear mixed effects models controlled for age, sex, and baseline disease severity, and Fisher F density curves to compare effect sizes in 50 patients with PSP. Similar analyses were done using plasma NfL measured by single molecule arrays in 141 patients. Results Higher CSF NfL concentration predicted more rapid decline (biomarker × time interaction) over 52 weeks in PSPRS (p = 0.004, false discovery rate–corrected) and SEADL (p = 0.008), whereas lower baseline CSF p-tau predicted faster decline on PSPRS (p = 0.004). Higher CSF tau concentrations predicted faster decline by SEADL (p = 0.004). The CSF NfL/p-tau ratio was superior for predicting change in PSPRS, compared to p-tau (p = 0.003) or NfL (p = 0.001) alone. Higher NfL concentrations in CSF or blood were associated with greater superior cerebellar peduncle atrophy (fixed effect, p ≤ 0.029 and 0.008, respectively). Conclusions Both CSF p-tau and NfL correlate with disease severity and rate of disease progression in PSP. The inverse correlation of p-tau with disease severity suggests a potentially different mechanism of tau pathology in PSP as compared to Alzheimer disease.
An Initial Cross-Cultural Comparison of Adult Playfulness in Mainland China and German-Speaking Countries

Compared with playfulness in infants and children, playfulness in adults is relatively under-studied. Although there is no empirical research comparing differences in adult playfulness across cultures, one might expect variations between Western and Eastern societies such as China. While playfulness is typically seen as a positive trait in Western culture, there are hints in Chinese culture that being playful has negative connotations (e.g., associations with laziness and seeing play as the opposite of work). The aim of this study was to compare expressions of playfulness in one sample from German-speaking countries (n = 143) and two samples from China (Guangzhou: n = 176; Beijing: n = 100). Participants completed one playfulness scale developed in the West (Short Measure of Adult Playfulness, SMAP) and one from the East (Adult Playfulness Questionnaire, APQ). Additional ratings of the participants were collected to measure: (a) the level of playful behavior expressed by people in different situations (e.g., when being around family members, in public, or on social media), and (b) individuals’ perceptions of society’s expectations concerning the appropriateness of being playful in the given situations. Overall, the results of the comparisons were mixed. Although SMAP scores did not vary significantly across the three samples, people from German-speaking countries tended to score higher on some facets of the APQ and some situational ratings. Stronger effects were found when comparing only the German-speaking sample and the Guangzhou sample. In addition to the cross-cultural differences that we expected, we also detected Chinese regional variations (North vs. South). We conclude that societal rules and cultural factors may impact expressions of playfulness in a society.
Key Mechanisms and Mixture Properties that control Fracture in Asphalt Mixtures

This paper reports a research study aimed at providing insight into key mechanisms and mixture properties that control fracture in asphalt concrete. The experimental analysis was based on the Hot Mix Asphalt (HMA) Fracture Mechanics visco-elastic crack growth law. HMA cracking mechanism was investigated using multiple laboratory test configurations on both unmodified and polymer modified mixtures. A Digital Image Correlation (DIC) was employed to more accurately capture localized or non-uniform stress distributions in asphalt mixtures and as a tool for detecting first fracture. Crack initiation and crack growth were predicted effectively using a Displacement Discontinuity (DD) boundary element method.
Evaluation of the Vitek MS v3.0 Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry System for Identification of Mycobacterium and Nocardia Species

ABSTRACT This multicenter study was designed to assess the accuracy and reproducibility of the Vitek MS v3.0 matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry system for identification of Mycobacterium and Nocardia species compared to DNA sequencing. A total of 963 clinical isolates representing 51 taxa were evaluated. In all, 663 isolates were correctly identified to the species level (69%), with another 231 (24%) correctly identified to the complex or group level. Fifty-five isolates (6%) could not be identified despite repeat testing. All of the tuberculous mycobacteria (45/45; 100%) and most of the nontuberculous mycobacteria (569/606; 94%) were correctly identified at least to the group or complex level. However, not all species or subspecies within the M. tuberculosis, M. abscessus, and M. avium complexes and within the M. fortuitum and M. mucogenicum groups could be differentiated. Among the 312 Nocardia isolates tested, 236 (76%) were correctly identified to the species level, with an additional 44 (14%) correctly identified to the complex level. Species within the N. nova and N. transvalensis complexes could not always be differentiated. Eleven percent of the isolates (103/963) underwent repeat testing in order to get a final result. Identification of a representative set of Mycobacterium and Nocardia species was highly reproducible, with 297 of 300 (99%) replicates correctly identified using multiple kit lots, instruments, analysts, and sites. These findings demonstrate that the system is robust and has utility for the routine identification of mycobacteria and Nocardia in clinical practice.
Thermodynamics and kinetics of oxidation and temperature dependent mechanical characterization of pure indium solder

MicroElectroMechanical System (MEMS) devices often require low-temperature, fluxless soldering techniques due to their high temperature sensitivity and the performance requirements of specific components. While seeking the development of a soldering technology using pure indium, the major focus of this study is to assess the thermodynamics and kinetics of indium oxidation at various solder reflow environments that will ultimately provide a processing window for solder reflow and surface oxide cleaning. The stability of oxidation and reduction reactions for indium is presented in terms of several thermodynamic models. The influence of pO2, pH2O, pH2, pCO, pCO2 on the location of oxidation and reduction zones is calculated using reaction equilibrium. Due to temperature limitations during processing of electronic packaging materials, pH2O was found to be the critical parameter in creating a reducing environment using a hydrogen reaction. Additionally, because of the large enthalpy associated with the formation of In2O3, pO2 was found to have little influence on thermodynamic equilibrium in both H2(g) and CO(g) reducing reactions. Verification of the thermodynamic models is carried out by oxidation experiments performed in various environments. With a glove box employed for precise atmospheric control, pH2O, pO2, and pH2 are varied to examine their effects on the oxidation and reduction behavior of indium. We also explore oxidation mechanisms at different stages of oxide growth, as well as at different regimes of temperature from 145 C-220 C. In particular, electron transport from indium to indium oxide is shown to be the rate
Telomerase reverse transcriptase promotes the proliferation of human laryngeal carcinoma cells through activation of the activator protein 1

TERT is the main functional unit of telomerase, which maintains telomere length and chromosome structure stability. TERT has been shown to act as a key factor in various biological processes, such as cell proliferation, via uncharacterized mechanisms. We transfected HEp-2 laryngeal carcinoma cells with a TERT overexpressing adenovirus (Ad-TERT) and TERT shRNA silencing adenovirus (Ad-sh-TERT), and examined the effect on TERT and the AP-1 transcription factor subunits c-Fos and c-Jun using RT-PCR and western blot analysis. TERT mRNA expression was quantified using RT-PCR in 24 human laryngeal carcinoma samples, and TERT protein co-expression with AP-1 was investigated in a human laryngeal carcinoma tissue microarray using quantum-dot based immunofluorescence. The effect of specific ERK and p38 inhibitors on ERK, p38, c-Jun and c-Fos phosphorylation was investigated in TERT-overexpressing HEp-2 cells. TERT overexpression led to increased TERT, c-Jun and c-Fos mRNA and protein expression and increased cell proliferation, while TERT silencing had the opposite effects. TERT mRNA expression levels were positively correlated with c-Fos and c-Jun mRNA in human laryngeal carcinoma tissue. TERT and AP-1 protein were expressed at high levels and positively correlated in laryngeal carcinoma tissues. Treatment of TERT-overexpressing HEp-2 cells with specific p38 and ERK inhibitors indicated that TERT modulates the expression and phosphorylation of the AP-1 subunits c-Jun and c-Fos through the p38 and ERK signaling pathways. In conclusion, the results of this study indicate that TERT is capable of promoting cell proliferation via activation of the AP-1 subunits, c-Jun and c-Fos, in laryngeal carcinoma cells.
Structural inference embedded adversarial networks for scene parsing

Explicit structural inference is one key point to improve the accuracy of scene parsing. Meanwhile, adversarial training method is able to reinforce spatial contiguity in output segmentations. To take both advantages of the structural learning and adversarial training simultaneously, we propose a novel deep learning network architecture called Structural Inference Embedded Adversarial Networks (SIEANs) for pixel-wise scene labeling. The generator of our SIEANs, a novel designed scene parsing network, makes full use of convolutional neural networks and long short-term memory networks to learn the global contextual information of objects in four different directions from RGB-(D) images, which is able to describe the (three-dimensional) spatial distributions of objects in a more comprehensive and accurate way. To further improve the performance, we explore the adversarial training method to optimize the generator along with a discriminator, which can not only detect and correct higher-order inconsistencies between the predicted segmentations and corresponding ground truths, but also exploit full advantages of the generator by fine-tuning its parameters so as to obtain higher consistencies. The experimental results demonstrate that our proposed SIEANs is able to achieve a better performance on PASCAL VOC 2012, SIFT FLOW, PASCAL Person-Part, Cityscapes, Stanford Background, NYUDv2, and SUN-RGBD datasets compared to the most of state-of-the-art methods.
Reduced Glutathione Mediates Resistance to H2S Toxicity in Oral Streptococci

ABSTRACT Periodontal disease is associated with changes in the composition of the oral microflora, where health-associated oral streptococci decrease while Gram-negative anaerobes predominate in disease. A key feature of periodontal disease-associated anaerobes is their ability to produce hydrogen sulfide (H2S) abundantly as a by-product of anaerobic metabolism. So far, H2S has been reported to be either cytoprotective or cytotoxic by modulating bacterial antioxidant defense systems. Although oral anaerobes produce large amounts of H2S, the potential effects of H2S on oral streptococci are currently unknown. The aim of this study was to determine the effects of H2S on the survival and biofilm formation of oral streptococci. The growth and biofilm formation of Streptococcus mitis and Streptococcus oralis were inhibited by H2S. However, H2S did not significantly affect the growth of Streptococcus gordonii or Streptococcus sanguinis. The differential susceptibility of oral streptococci to H2S was attributed to differences in the intracellular concentrations of reduced glutathione (GSH). In the absence of GSH, H2S elicited its toxicity through an iron-dependent mechanism. Collectively, our results showed that H2S exerts antimicrobial effects on certain oral streptococci, potentially contributing to the decrease in health-associated plaque microflora.