gebhart/patrepeval huggingface dataset:
Specific Lipid Recruitment by the Retroviral Gag Protein upon HIV-1 Assembly: From Model Membranes to Infected Cells (2020)

The retroviral Gag protein targets the plasma membrane of infected cells for viral particle formation and release. The matrix domain (MA) of Gag is myristoylated for membrane anchoring but also contains a highly basic region that recognizes acidic phospholipids. Gag targets lipid molecules at the inner leaflet of the plasma membrane including phosphatidylinositol (4,5) bisphosphate (PI(4,5)P2) and cholesterol. Here, we addressed the question whether HIV-1 Gag was able to trap PI(4,5)P2 and/or other lipids during HIV-1 assembly in silico, in vitro on reconstituted membranes and in cellulo at the plasma membrane of the host CD4+ T cells. In silico, we could observe the first PI(4,5)P2 preferential recruitment by HIV-1 MA or Gag while protein docked on artificial membranes. In vitro, using biophysical techniques, we observed the specific trapping of PI(4,5)P2, and, to a lesser extent, cholesterol and the exclusion of sphingomyelin, during HIV-1 myr(-)Gag self-assembly on LUVs and SLBs. Finally, in infected living CD4+ T cells, we measured lipid dynamics within and away from HIV-1 assembly sites using super-resolution stimulated emission depletion (STED) microscopy coupled with scanning Fluorescence Correlation Spectroscopy (sSTED-FCS). The analysis of HIV-1 infected CD4+ T lymphocytes revealed that, upon virus assembly, HIV-1 is able to specifically trap PI(4,5)P2, and cholesterol but not phosphatidylethanolamine (PE) or sphingomyelin (SM) at the cellular membrane. Furthermore, analyzing CD4+ T cells expressing only HIV-1 Gag protein showed that Gag is the main driving force restricting the mobility of PI(4,5)P2 and cholesterol at the cell plasma membrane. Our data provide the first direct evidence showing that HIV-1 Gag creates its own specific lipid environment for virus assembly by selectively recruiting lipids to generate PI(4,5)P2/cholesterol-enriched nanodomains favoring virus assembly, and that HIV-1 does not assemble on pre-existing lipid domains.
Differential effect of mode of conception and infertility treatment on fetal growth and prematurity (2016)

Objectives To examine perinatal outcomes in pregnancies conceived by different methods: fertile women with spontaneous pregnancies, infertile women who achieved pregnancy without treatment, pregnancies achieved by ovulation induction (OI) and in vitro fertilization or intra-cytoplasmic sperm injection (IVF/ICSI). Methods Retrospective single-center cohort study including 200 fertile and 748 infertile women stratified according to infertility treatment. The outcome measurements were preterm delivery (PTD), small-for-gestational-age (SGA), gestational diabetes, placenta previa or preeclampsia. Results The overall rate of pregnancy complications was significantly increased in all infertility groups regardless of the infertility treatment (adjusted odds ratio (OR): infertile without treatment 2.3 versus OI 2.2 versus IVF/ICSI 3.4). While PTD was mainly associated to IVF/ICSI (adjusted OR: infertile without treatment 1.3 versus OI 1.6 versus IVF/ICSI 3.3), SGA was significantly associated to both OI and IVF/ICSI (adjusted OR: infertile without treatment 1.9 versus OI 2.7 versus IVF/ICSI 2.6). All these associations remained statistically significant after adjusting by maternal age and twin pregnancy. Conclusions This study confirms the higher prevalence of pregnancy complications in infertile women irrespectively of receiving infertility treatment or not, and further describes a preferential association of prematurity with IVF/ICSI, and SGA with treated infertility (OI and IVF/ICSI).
Vaccine hypersensitivity - update and overview (2010)

Concerns about possible reactions to vaccines or vaccinations are frequently raised. However, the rate of reported vaccine-induced adverse events is low and ranges between 4.8-83.0 per 100,000 doses of the most frequently used vaccines. The number of true allergic reactions to routine vaccines is not known; estimations range from 1 per 500,000 to 1 per 1,000,000 doses for most vaccines. When allergens such as gelatine or egg proteins are components of the formulation, the rate for serious allergic reactions may be higher. Nevertheless, anaphylactic, potentially life-threatening reactions to vaccines are still a rare event (approximately 1 per 1,500,000 doses). The variety of reported vaccine-related adverse events is broad. Most frequently, reactions to vaccines are limited to the injection site and result from a non specific activation of the inflammatory system by, for example, aluminium salts or the active microbial components. If allergy is suspected, an accurate examination followed by algorithms is the key for correct diagnosis, treatment and the decision regarding revaccination in patients with immediate-type reactions to vaccines.
Standards of NGS Data Sharing and Analysis in Ataxias: Recommendations by the NGS Working Group of the Ataxia Global Initiative (2023)

The Ataxia Global Initiative (AGI) is a worldwide multi-stakeholder research platform to systematically enhance trial-readiness in degenerative ataxias. The next-generation sequencing (NGS) working group of the AGI aims to improve methods, platforms, and international standards for ataxia NGS analysis and data sharing, ultimately allowing to increase the number of genetically ataxia patients amenable for natural history and treatment trials. Despite extensive implementation of NGS for ataxia patients in clinical and research settings, the diagnostic gap remains sizeable, as approximately 50% of patients with hereditary ataxia remain genetically undiagnosed. One current shortcoming is the fragmentation of patients and NGS datasets on different analysis platforms and databases around the world. The AGI NGS working group in collaboration with the AGI associated research platforms-CAGC, GENESIS, and RD-Connect GPAP-provides clinicians and scientists access to user-friendly and adaptable interfaces to analyze genome-scale patient data. These platforms also foster collaboration within the ataxia community. These efforts and tools have led to the diagnosis of > 500 ataxia patients and the discovery of > 30 novel ataxia genes. Here, the AGI NGS working group presents their consensus recommendations for NGS data sharing initiatives in the ataxia field, focusing on harmonized NGS variant analysis and standardized clinical and metadata collection, combined with collaborative data and analysis tool sharing across platforms.
An Optimal Model using Goal Programming for Rubber Wood Door Manufacturing Factory in Tripura (2012)

Rubber plantation requires re-planting after 32 to 34 years when collection of latex becomes uneconomical. For commercial utilization and value addition to those rubber logs felled during re-plantation, processing of Rubber Timber is vital, otherwise of no timber value. Restriction on use of Forestry timber, inspires to setting up of Rubber Wood manufacturing unit. Carpentry unit plays a important role to popularize the use of eco-friendly Rubber wood in the country. Making of doors from Solid Rubber wood and Treated timber has good market in the country as plenty of houses are being built in the country. Rubber Wood Door also has immense export potential. In this study, an attempt has been taken to formulate a strategic planning using the Goal Programming approach. The model formulated for this study may help to set up related manufacturing units.
Advantages of Shape Representation using Implicit Surfaces (2004)

近年,ポリゴンメッシュや点群により定義される曲面データを陰関数曲面による表現に変換する方法が盛んに研究されている.本講義では,陰関数曲面で形状を表現することにより,どのような利点があるかをまとめる.
Piezoelectric materials for BAW resonators and filters (2002)

Thin film bulk acoustic wave (BAW) resonators and filters are appropriate for mobile communication systems operating at high frequencies between 0.5 and 10 GHz. c-axis orientated AlN films are used for medium bandwidth applications. Electromechanical coupling factors k/sub t/ of 0.25/spl plusmn/0.03, which are close to the bulk data, have been found in AlN thin films using optimum sputter conditions. The correlation between k/sub t/ and AlN film orientation is discussed. Resonator Q values of approx. 450 are reported at 2.6 GHz and a Q of 250 was realized at 9.2 GHz. A physical model is shown to accurately predict the frequency responses of BAW resonators and band-pass filters. For wide bandwidth applications PbZr/sub x/Ti/sub 1-x/O/sub 3/ (PZT) films are investigated. They exhibit large coupling coefficients.
Threshold conductivity switching in sulfurized antimony selenide nanowires (2011)

We report reversible switching between Ohmic and negative differential resistance states at a threshold voltage in sub-100-nm diameter sulfurized antimony selenide nanowires. We show that threshold switching in our nanowires arises due to high non-equilibrium free carrier concentrations resulting from impact ionization of carriers from defect states traceable to sulfurization and surface dangling bonds. Threshold switching is suppressed because of inhibited carrier generation at air-passivated defect states or at high temperatures due to thermally induced carrier depletion from deep states which preempts impact ionization. Such non-linear phenomena would be important for designing phase-change memories, thermoelectric devices, and sensors using pnictogen chalcogenide nanowires.
Differential lactate and cholesterol synthetic activities in XY and XX Sertoli cells (2017)

SRY, a sex-determining gene, induces testis development in chromosomally female (XX) individuals. However, mouse XX Sertoli cells carrying Sry (XX/Sry Sertoli cells) are incapable of fully supporting germ cell development, even when the karyotype of the germ cells is XY. While it has therefore been assumed that XX/Sry Sertoli cells are not functionally equivalent to XY Sertoli cells, it has remained unclear which specific functions are affected. To elucidate the functional difference, we compared the gene expression of XY and XX/Sry Sertoli cells. Lactate and cholesterol metabolisms, essential for nursing the developing germ cells, were down-regulated in XX/Sry cells, which appears to be caused at least in part by the differential expression of histone modification enzymes SMCX/SMCY (H3K4me3 demethylase) and UTX/UTY (H3K27me3 demethylase) encoded by the sex chromosomes. We suggest that down-regulation of lactate and cholesterol metabolism that may be due to altered epigenetic modification affects the nursing functions of XX/Sry Sertoli cells.
Humoral and Cellular Immune Responses following Vaccination with Purified Recombinant Hemagglutinin from Influenza A (H3N2) Virus (1997)

Adults were immunized with either baculovirus-expressed, purified recombinant hemagglutinin (rHA) from influenza A/Beijing/32/92 (H3N2) virus or saline placebo and evaluated for humoral and in vitro cellular immune responses. Compared with responses in placebo recipients, vaccinees had greater postvaccination H3(Beijing/32) HA (H3)-specific lymphoproliferation and interleukin (IL)-2, IL-10, and interferon-gamma (IFN-gamma) production. Mean increases in the production of IL-10 (> or = 20-fold) and IL-2 (10-fold) were relatively greater than that of IFN-gamma (4-fold) or IL-4 (no change). Serum H3 antibodies were induced in 80% of rHA recipients, and the rise in antibody titer was significantly correlated with changes in IL-2, IL-10, and IFN-gamma concentrations. Vaccination with rHA only minimally enhanced anti-influenza virus cytotoxic T lymphocyte activity. These data demonstrate that rHA immunization of adults elicits a significant recall response by memory B and T lymphocytes and suggest that the cytokine response to vaccination has a T helper cell type 0-like profile.
Prevalence and Molecular Epidemiology of CTX-MExtended-Spectrum β-Lactamase-Producing Escherichia coli and Klebsiella pneumoniae in RussianHospitals (2003)

A total of 904 consecutive nosocomial isolates of Escherichia coli and Klebsiella pneumoniae collected from 28 Russian hospitals were screened for production of extended-spectrum beta-lactamases (ESBLs). The ESBL phenotype was detected in 78 (15.8%) E. coli and 248 (60.8%) K. pneumoniae isolates. One hundred fifteen isolates carried the genes for CTX-M-type beta-lactamases, which, as shown by PCR-restriction fragment length polymorphism analysis, were distributed into the two genetic groups of CTX-M-1 (93%)- and CTX-M-2 (7%)-related enzymes. Isolates producing the enzymes of the first group were found in 20 hospitals from geographically distant regions of the country and were characterized by considerable diversity of genetic types, as was demonstrated by enterobacterial repetitive consensus PCR typing. Within this group the CTX-M-3 and the CTX-M-15 beta-lactamases were identified. In contrast, the enzymes of the CTX-M-2 group (namely, CTX-M-5) were detected only in eight clonally related E. coli isolates from a single hospital. Notably, the levels of resistance to ceftazidime were remarkably variable among the CTX-M producers. This study provides further evidence of the global dissemination of CTX-M type ESBLs and emphasizes the need for their epidemiological monitoring.
Enhancing cognitive performance with repetitive transcranial magnetic stimulation at human individual alpha frequency (2003)

We applied rapid-rate repetitive transcranial magnetic stimulation (rTMS) at individual alpha frequency (IAF) to improve cognitive performance by influencing the dynamics of alpha desynchronization. Previous research indicates that a large upper alpha power in a reference interval preceding a task is related to both large suppression of upper alpha power during the task and good performance. Here, we tested the hypothesis that rTMS at individual upper alpha frequency (IAF + 1 Hz) can enhance alpha power in the reference interval, and can thus improve task performance. Repetitive TMS was delivered to the mesial frontal (Fz) and right parietal (P6) cortex, and as sham condition with 90 degrees-tilted coil (P6 position). The behavioural effect was assessed in a mental rotation task. Further control conditions were rTMS at a lower IAF (IAF - 3 Hz) and at 20 Hz. The results indicate that rTMS at IAF + 1 Hz can enhance task performance and, concomitantly, the extent of task-related alpha desynchronization. This provides further evidence for the functional relevance of oscillatory neuronal activity in the alpha band for the implementation of cognitive performance.
The First Proteomic Study of Nostoc sp. PCC 7120 Exposed to Cyanotoxin BMAA under Nitrogen Starvation (2020)

The oldest prokaryotic photoautotrophic organisms, cyanobacteria, produce many different metabolites. Among them is the water-soluble neurotoxic non-protein amino acid beta-N-methylamino-L-alanine (BMAA), whose biological functions in cyanobacterial metabolism are of fundamental scientific and practical interest. An early BMAA inhibitory effect on nitrogen fixation and heterocyst differentiation was shown in strains of diazotrophic cyanobacteria <i>Nostoc</i> sp. PCC 7120, <i>Nostoc</i><i>punctiforme</i> PCC 73102 (ATCC 29133), and <i>Nostoc</i> sp. strain 8963 under conditions of nitrogen starvation. Herein, we present a comprehensive proteomic study of <i>Nostoc</i> (also called <i>Anabaena</i>) sp. PCC 7120 in the heterocyst formation stage affecting by BMAA treatment under nitrogen starvation conditions. BMAA disturbs proteins involved in nitrogen and carbon metabolic pathways, which are tightly co-regulated in cyanobacteria cells. The presented evidence shows that exogenous BMAA affects a key nitrogen regulatory protein, PII (GlnB), and some of its protein partners, as well as glutamyl-tRNA synthetase gltX and other proteins that are involved in protein synthesis, heterocyst differentiation, and nitrogen metabolism. By taking into account the important regulatory role of PII, it becomes clear that BMAA has a severe negative impact on the carbon and nitrogen metabolism of starving <i>Nostoc</i> sp. PCC 7120 cells. BMAA disturbs carbon fixation and the carbon dioxide concentrating mechanism, photosynthesis, and amino acid metabolism. Stress response proteins and DNA repair enzymes are upregulated in the presence of BMAA, clearly indicating severe intracellular stress. This is the first proteomic study of the effects of BMAA on diazotrophic starving cyanobacteria cells, allowing a deeper insight into the regulation of the intracellular metabolism of cyanobacteria by this non-protein amino acid.
Light Control of the Tet Gene Expression System in Mammalian Cells (2018)

Gene expression and its network structure are dynamically altered in multicellular systems during morphological, functional, and pathological changes. To precisely analyze the functional roles of dynamic gene expression changes, tools that manipulate gene expression at fine spatiotemporal resolution are needed. The tetracycline (Tet)-controlled gene expression system is a reliable drug-inducible method, and it is used widely in many mammalian cultured cells and model organisms. Here, we develop a photoactivatable (PA)-Tet-OFF/ON system for precise temporal control of gene expression at single-cell resolution. By integrating the cryptochrome 2-cryptochrome-interacting basic helix-loop-helix 1 (Cry2-CIB1) light-inducible binding switch, expression of the gene of interest is tightly regulated under the control of light illumination and drug application in our PA-Tet-OFF/ON system. This system has a large dynamic range of downstream gene expression and rapid activation/deactivation kinetics. We also demonstrate the optogenetic regulation of exogenous gene expression in vivo, such as in developing and adult mouse brains.
Abstract 20027: Docosahexaenoic Acid, but Not Eicosapentaenoic Acid, Exerts Anti-Inflammatory Effect and Prevents Pressure Overload Induced Cardiac Left Ventricular Dysfunction (2010)

Omega-3 polyunsaturated fatty acids - docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) - suppress inflammatory pathways that could prevent development and progression of heart failure. Wh...
Ferrocenium Salts—The First Antineoplastic Iron Compounds (1984)

The suprising activity of the action of 1 against Ehrlich ascites tumor in mice must be explainable in terms other than that of the activity of the metallocene dihalogenides of d-electron-deficient transition-metals, since the anions in 1 are not coordinated but bound in a salt-like way. Ferrocene is inactive in the same test.
Targeting human solid tumor xenografts with ex vivo expanded endothelial progenitor cells (2008)

Cellular therapy involves the capability to transplant autologous, non‐transformed cell populations that migrate to sites of tumorogenic development to deliver targeted, anti‐tumor therapy. Exploiting biological processes obligatory to tumorgenicity such as angiogenesis and vasculogenesis, cellular therapies have the potential to circumvent the development of treatment resistance associated with the instability of cancer cell genomes. In this study we investigated the feasibility of homing modified, human, ex vivo expanded endothelial progenitor cells (EPC) to human prostate xenotransplants in immune deficient mice in vivo . Circulating human CD34+/CD133 − EPC were isolated, expanded, infected with adenovirus, fluorescently labeled with dilC18 and injected into the blood stream of athymic nude mice bearing CRL‐2505 prostate xenografts. EPC homed to xenotransplants comprised between 1 and 3% of total tumor cells 5 days following injection as assessed by flow cytometry. Histological analysis revealed that EPC were integrated throughout the developing neovasculature but preferentially accumulated in the peritumoral region of the growing tumor. These data suggest that ex vivo expanded EPC can contribute to vasculogenesis in prostate cancer and may represent a developing tool in cancer therapy.
Stochastic Modeling of a Concrete Mixture Plant with Preventive Maintenance (2014)

In this paper, a stochastic model for concrete mixture plant with Preventive Maintenance (PM) is analyzed in detail by using a supplementary variable technique. In a concrete mixture plant eight subsystems are arranged in a series. The system goes under PM after a maximum operation time and work as new after PM. The time to failure of each subsystem follows a negative exponential distribution while PM and repair time distributions are taken as arbitrary. A sufficient repair facility is provided to the system for conducting PM and repair of the system. Repair, maintenance and switch devices are perfect. All random variables are statistically independent. Various measures of system effectiveness such as reliability, mean time to system failure (MTSF), are derived using a supplementary variable technique. The numerical results for reliability and availability are obtained for particular values of various parameters and costs.
Bio-Inspired Collision Avoidance in Swarm Systems via Deep Reinforcement Learning (2022)

Autonomous vehicles have been highlighted as a major growth area for future transportation systems and the deployment of large numbers of these vehicles is expected when safety and legal challenges are overcome. To meet the necessary safety standards, effective collision avoidance technologies are required to ensure that the number of accidents are kept to a minimum. As large numbers of autonomous vehicles, operating together on roads, can be regarded as a swarm system, we propose a bio-inspired collision avoidance strategy using virtual pheromones; an approach that has evolved effectively in nature over many millions of years. Previous research using virtual pheromones showed the potential of pheromone-based systems to maneuver a swarm of robots. However, designing an individual controller to maximise the performance of the entire swarm is a major challenge. In this paper, we propose a novel deep reinforcement learning (DRL) based approach that is able to train a controller that introduces collision avoidance behaviour. To accelerate training, we propose a novel sampling strategy called <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Highlight Experience Replay</i> and integrate it with a Deep Deterministic Policy Gradient algorithm with noise added to the weights and biases of the artificial neural network to improve exploration. To evaluate the performance of the proposed DRL-based controller, we applied it to navigation and collision avoidance tasks in three different traffic scenarios. The experimental results showed that the proposed DRL-based controller outperformed the manually-tuned controller in terms of stability, effectiveness, robustness and ease of tuning process. Furthermore, the proposed Highlight Experience Replay method outperformed than the popular Prioritized Experience Replay sampling strategy by taking 27% of training time average over three stages.