gebhart/patrepeval huggingface dataset:
Evidence for a lack of DNA double-strand break repair in human cells exposed to very low x-ray doses (2003)

DNA double-strand breaks (DSBs) are generally accepted to be the most biologically significant lesion by which ionizing radiation causes cancer and hereditary disease. However, no information on the induction and processing of DSBs after physiologically relevant radiation doses is available. Many of the methods used to measure DSB repair inadvertently introduce this form of damage as part of the methodology, and hence are limited in their sensitivity. Here we present evidence that foci of gamma-H2AX (a phosphorylated histone), detected by immunofluorescence, are quantitatively the same as DSBs and are capable of quantifying the repair of individual DSBs. This finding allows the investigation of DSB repair after radiation doses as low as 1 mGy, an improvement by several orders of magnitude over current methods. Surprisingly, DSBs induced in cultures of nondividing primary human fibroblasts by very low radiation doses (approximately 1 mGy) remain unrepaired for many days, in strong contrast to efficient DSB repair that is observed at higher doses. However, the level of DSBs in irradiated cultures decreases to that of unirradiated cell cultures if the cells are allowed to proliferate after irradiation, and we present evidence that this effect may be caused by an elimination of the cells carrying unrepaired DSBs. The results presented are in contrast to current models of risk assessment that assume that cellular responses are equally efficient at low and high doses, and provide the opportunity to employ gamma-H2AX foci formation as a direct biomarker for human exposure to low quantities of ionizing radiation.
The Roles of Serum Selenium and Selenoproteins on Mercury Toxicity in Environmental and Occupational Exposure (2006)

Many studies have found that mercury (Hg) exposure is associated with selenium (Se) accumulation in vivo. However, human studies are limited. To study the interaction between Se and Hg, we investigated the total Se and Hg concentrations in body fluids and serum Se-containing proteins in individuals exposed to high concentrations of Hg. Our objective was to elucidate the possible roles of serum Se and selenoproteins in transporting and binding Hg in human populations. We collected data from 72 subjects: 35 had very low Hg exposure as evidenced by mean Hg concentrations of 0.91 and 1.25 ng/mL measured in serum and urine, respectively; 37 had high exposure (mean Hg concentrations of 38.5 and 86.8 ng/mL measured in serum and urine, respectively). An association between Se and Hg was found in urine (r = 0.625; p < 0.001) but not in serum. Hg exposure may affect Se concentrations and selenoprotein distribution in human serum. Expression of both selenoprotein P and glutathione peroxidase (GSH-Px) was greatly increased in Hg miners. These increases were accompanied by elevated Se concentrations in serum. In addition, selenoprotein P bound more Hg at higher Hg exposure concentrations. Biochemical observations revealed that both GSH-Px activity and malondialdehyde concentrations increased in serum of the Hg-exposed group. This study aids in the understanding of the interaction between Se and Hg. Selenoproteins play two important roles in protecting against Hg toxicity. First, they may bind more Hg through their highly reactive selenol group, and second, their antioxidative properties help eliminate the reactive oxygen species induced by Hg in vivo.
Electrochemically Induced Deposition of a Polysaccharide Hydrogel onto a Patterned Surface (2003)

Hydrogels are increasingly considered for creating three-dimensional structures in miniaturized devices, yet few techniques exist for creating such hydrogel structures. We report a new approach for creating hydrogels using the amine-containing polysaccharide chitosan. Specifically, electrodes are immersed into a slightly acidic chitosan solution and a voltage is applied to promote the proton-consuming hydrogen evolution reaction at the cathode surface. This reaction leads to a high localized pH in the vicinity of the cathode surface, and if this localized pH exceeds about 6.3, then chitosan becomes insoluble and deposits at the cathode surface. As the current density is increased, the region of high pH is expected to extend further from the cathode surface into the bulk solution. Using moderately high current densities (50 A/m2), we observed that chitosan deposited as a thick hydrogel. Measurements of the water content confirmed that the deposited chitosan was a hydrogel. To suggest the potential utility, we deposited a chitosan hydrogel on a patterned surface to create a channel. Because of chitosan's pH-dependent solubility, this channel could be “disassembled” by mild acid treatment. We envision that electrochemically-induced deposition of chitosan-based hydrogels may offer interesting opportunities for the integration of biological systems into miniaturized devices.
Association between susceptibility to advanced stage endometriosis and the genetic polymorphisms of aryl hydrocarbon receptor repressor and glutathione-S-transferase T1 genes (2007)

These findings suggest that the AhRR codon 185 and GSTT1 polymorphisms are associated with the risk of advanced stage endometriosis.
Emergence of a Wave of Wnt Signaling that Regulates Lung Alveologenesis by Controlling Epithelial Self-Renewal and Differentiation (2016)

Alveologenesis is the culmination of lung development and involves the correct temporal and spatial signals to generate the delicate gas exchange interface required for respiration. Using a Wnt-signaling reporter system, we demonstrate the emergence of a Wnt-responsive alveolar epithelial cell sublineage, which arises during alveologenesis, called the axin2+ alveolar type 2 cell, or AT2<sup>Axin2</sup>. The number of AT2<sup>Axin2</sup> cells increases substantially during late lung development, correlating with a wave of Wnt signaling during alveologenesis. Transcriptome analysis, in vivo clonal analysis, and ex vivo lung organoid assays reveal that AT2s<sup>Axin2</sup> promote enhanced AT2 cell growth during generation of the alveolus. Activating Wnt signaling results in the expansion of AT2s, whereas inhibition of Wnt signaling inhibits AT2 cell development and shunts alveolar epithelial development toward the alveolar type 1 cell lineage. These findings reveal a wave of Wnt-dependent AT2 expansion required for lung alveologenesis and maturation.
Automation Technologies for Genome Characterization (1997)

Laboratory automation: custom hardware and software for genome centre operations - control to databases: automation strategies, a modular approach large-scale library characterization. Control systems: a script directed controller of modular automation (SDCMA) for genome laboratories. Advanced topics: scanning probe microscopy in genomic research.
ZnO: growth, doping & processing (2004)

A review is given here of recent results in developing improved control of growth, doping, and fabrication processes for ZnO devices with possible applications to ultraviolet (UV) light emitters, spin functional devices, gas sensors, transparent electronics, and surface acoustic wave devices. ZnO can be grown on cheap substrates such as glass at relatively low temperatures and may have advantages over the GaN system in some of these applications.
Theoretical and algorithmical optimization of the dead-end elimination theorem. (1997)

The dead-end elimination theorem has proved to be a powerful method to reduce the theoretically accessible conformational space when modeling protein side chains by using a rotameric representation of possible conformations. In this work, theoretical details about variants to the original criterion are discussed. We also provide information on how the equations can be algorithmically implemented in such a way that both computational performance and structural accuracy are optimized. In addition, we discuss the theoretical and practical aspects of three new methods called the "bottom line theorem", dead-end elimination assisted by local modeling and a combinatorial search combined with conventional dead-end elimination. It is shown that the algorithm in its current from enables the determination of the global minimum energy side chain conformation of large proteins on a time scale of hours while for small proteins of up to 30 residues the calculations are done on a time scale of seconds. The latter opens a way to combine a main chain sampling algorithm with the dead-end elimination method to locally model entire fragments of a protein chain.
HIV-1 Neutralizing Monoclonal Antibodies Induced by a Synthetic Peptide (1990)

We have developed a series of murine monoclonal antibodies to a region of the 120 kD envelope glycoprotein (gp120) of human immunodeficiency virus type 1 (HIV-1). This region has previously been implicated as a site for virus neutralization by antisera raised to recombinant proteins and by antibodies made to full-length gp120 purified from virus. The antigen employed was a synthetic peptide containing 15 amino acids, representing amino acid residues 308-322, RIQRGPGRAFVTIGK, of env gp120 (HTLV-IIIB isolate). Five of the monoclonal antibodies raised to this antigen have reactivity with gp120 from divergent strains of HIV-1 in Western blot assays. The two of these five which were tested with live cells infected with the divergent HIV-1 isolates IIIB, MN, and RF were specifically reactive by fluorescence analyses with cells infected with the MN and IIIB isolates. Four of the five monoclonal antibodies blocked the fusion of IIIB-infected cells with uninfected MOLT-4 target cells. The monoclonal antibody most reactive with MN-infected cells by fluorescence, #5025A, blocked the fusion of MN-infected cells with uninfected MOLT-4 cells. Four of the five monoclonal antibodies neutralized the IIIB isolate of HIV-1 in vitro, but none neutralized the MN or RF isolates at the levels of antibody tested (less than or equal to 50 micrograms/ml). Taken together these data indicate that monoclonal antibodies to the immunodominant neutralizing domain of HIV-1 gp120 display different levels of group reactivity depending on the assay system being examined.
ACTIVATOR of Spomin::LUC1/WRINKLED1 of Arabidopsis thaliana Transactivates Sugar-inducible Promoters (2005)

We isolated an enhancer activation-tagged mutant of Arabidopsis thaliana line sGsL carrying the luciferase (LUC) gene under control of a short sugar-inducible promoter derived from a sweet potato sporamin gene (Spomin) that showed high level expression of LUC under non-inducing conditions. The activator of Spomin::LUC1 (ASML1) gene located downstream of the enhancer encoded an APETALA2 (AP2)-type AP2 domain protein, and this gene was shown recently to be responsible for the wrinkled1 mutation which causes defective accumulation of seed storage oil. Overexpression of ASML1 cDNA in sGsL plants resulted in enhanced expression of not only the LUC reporter but also endogenous sugar-inducible genes including Atbeta-Amy encoding beta-amylase. Transient co-expression of 35S::ASML1 with Spomin::LUC or Atbeta-Amy::LUC reporters in protoplasts resulted in an approximately 10-fold transactivation of LUC expression. This transactivation was lost when the C-terminal acidic region of ASML1 was deleted. Expression of ASML1 was high in reproductive organs, and ASML1 mRNA showed transient accumulation in leaves after treatment with 6% sucrose, whereas it did not respond to abscisic acid. These results suggest that ASML1/WRI1 is a transcriptional activator involved in the activation of a subset of sugar-responsive genes and the control of carbon flow from sucrose import to oil accumulation in developing seeds.
Association of Acute Symptoms of COVID-19 and Symptoms of Depression in Adults (2021)

This survey study investigates where acute coronavirus disease 2019 (COVID-19) is associated with the probability of subsequent depressive symptoms among US adults.
CpG Island Hypermethylation in Human Astrocytomas (2010)

Astrocytomas are common and lethal human brain tumors. We have analyzed the methylation status of over 28,000 CpG islands and 18,000 promoters in normal human brain and in astrocytomas of various grades using the methylated CpG island recovery assay. We identified 6,000 to 7,000 methylated CpG islands in normal human brain. Approximately 5% of the promoter-associated CpG islands in the normal brain are methylated. Promoter CpG island methylation is inversely correlated whereas intragenic methylation is directly correlated with gene expression levels in brain tissue. In astrocytomas, several hundred CpG islands undergo specific hypermethylation relative to normal brain with 428 methylation peaks common to more than 25% of the tumors. Genes involved in brain development and neuronal differentiation, such as BMP4, POU4F3, GDNF, OTX2, NEFM, CNTN4, OTP, SIM1, FYN, EN1, CHAT, GSX2, NKX6-1, PAX6, RAX, and DLX2, were strongly enriched among genes frequently methylated in tumors. There was an overrepresentation of homeobox genes and 31% of the most commonly methylated genes represent targets of the Polycomb complex. We identified several chromosomal loci in which many (sometimes more than 20) consecutive CpG islands were hypermethylated in tumors. Seven such loci were near homeobox genes, including the HOXC and HOXD clusters, and the BARHL2, DLX1, and PITX2 genes. Two other clusters of hypermethylated islands were at sequences of recent gene duplication events. Our analysis offers mechanistic insights into brain neoplasia suggesting that methylation of the genes involved in neuronal differentiation, in cooperation with other oncogenic events, may shift the balance from regulated differentiation towards gliomagenesis.
Exploring the industrial placement experience for mechanical engineering undergraduates (2009)

This paper explores the attitudes of undergraduate engineers towards work placements in industry. This research also assesses the placement experience in terms of student learning outcomes and future employment aspirations. Quantitative and qualitative data were collected from three groups: (i) those recently returning from a placement; (ii) those yet to go on placement and (iii) those who elected not to go on placement. Semi-structured interviews gathered experiences and perceptions from all three groups and formed the basis of attitude questionnaires distributed to 276 undergraduates at the University of Bath. Students were asked what value they attached to a year in industry, what improvement in personal transferable skills (such as team-working, time-management, communication and learning) they felt was gained and their perception of the placement experience in terms of aspirations of future employment. Factors influencing the decision of whether or not to undertake a placement were explored. The marks of the students in each of the three populations were scrutinised in order to determine any academic differences between the groups and to assess any value added by a placement in terms of improved performance on returning to university. Finally, this paper identifies reasons why undergraduates do not elect to undertake placements, asking if these important decisions are well-informed or otherwise.
SoSIRe&#x010C;R - IT professional social network (2011)

This paper describes the concept of a social network of the ICT specialists in the regions of the Czech Republic. In particular, we focus on the web portal under development, i.e. a software tool serving for the network implementation. Associated activities concerning collecting and analyzing ICT requirements from companies and educational ICT knowledge of university graduates are presented. The novelty of our approach is in focusing on specificities of the social network (entities and relationships specific for ICT) and in the concept of professional profile (PP). Professional profiles enable to express the ICT focus of a given entity (e.g., person, research team or project) in a structured way. Based of the PP concept, we introduce specific portal functionalities which are not offered by existing portals.
Mapping the Pathways to StaphylococcalPathogenesis by Comparative Secretomics (2006)

SUMMARY The gram-positive bacterium Staphylococcus aureus is a frequent component of the human microbial flora that can turn into a dangerous pathogen. As such, this organism is capable of infecting almost every tissue and organ system in the human body. It does so by actively exporting a variety of virulence factors to the cell surface and extracellular milieu. Upon reaching their respective destinations, these virulence factors have pivotal roles in the colonization and subversion of the human host. It is therefore of major importance to obtain a clear understanding of the protein transport pathways that are active in S. aureus . The present review aims to provide a state-of-the-art roadmap of staphylococcal secretomes, which include both protein transport pathways and the extracytoplasmic proteins of these organisms. Specifically, an overview is presented of the exported virulence factors, pathways for protein transport, signals for cellular protein retention or secretion, and the exoproteomes of different S. aureus isolates. The focus is on S. aureus , but comparisons with Staphylococcus epidermidis and other gram-positive bacteria, such as Bacillus subtilis , are included where appropriate. Importantly, the results of genomic and proteomic studies on S. aureus secretomes are integrated through a comparative “secretomics” approach, resulting in the first definition of the core and variant secretomes of this bacterium. While the core secretome seems to be largely employed for general housekeeping functions which are necessary to thrive in particular niches provided by the human host, the variant secretome seems to contain the “gadgets” that S. aureus needs to conquer these well-protected niches.
Quantum Reservoir Engineering with Laser Cooled Trapped Ions (1996)

We show how to design different couplings between a single ion trapped in a harmonic potential and an environment. The coupling is due to the absorption of a laser photon and subsequent spontaneous emission. The variation of the laser frequencies and intensities allows one to ``engineer'' the coupling and select the master equation describing the motion of the ion.
Novel inhibitors of human CMV. (2008)

Human CMV (HCMV) is an opportunistic pathogen associated with significant morbidity and mortality among immunocompromised patients (in particular immunosuppressed patients with stem cell or solid organ transplantation, AIDS or cancer). Additionally, congenital HCMV infections are a leading cause of birth defects and infections in children, occurring in 1 to 2% of all live births. Drugs currently available for the treatment of HCMV diseases in the immunocompromised individual include ganciclovir, its oral prodrug valganciclovir, cidofovir, foscavir and fomivirsen. Although these drugs have proved successful in the management of HCMV disease in immunocompromised patients, their use is limited because of toxicity, poor oral bioavailability, modest efficacy and the development of drug resistance. Furthermore, no drug has been licensed for use in the treatment of congenital HCMV. Therefore, there is a need to develop new compounds against HCMV diseases. The search for novel inhibitors of HCMV replication has led to the identification of new molecular targets such as the viral protein kinase UL97, and the viral proteins involved in genome replication or in DNA maturation and egress. Moreover, a new strategy based on the identification of specific cellular targets required for viral replication has been developed. This review focuses on non-nucleoside compounds that inhibit specific viral processes and on cell-based approaches that result in the selective inhibition of virus replication.
An application of virtual reality in rehabilitation (2002)

Virtual reality (VR) has been applied in developing systems for vehicle simulation, robot control, decision support and analysis, virtual interfaces to complex systems, entertainment, electronic art, medical science, and education. As an off-spin of virtual reality, a number of sensory hardware components have been developed. One of the greatest potentials of VR exists in medicine and surgery. The author discusses some of the sensory devices developed for VR systems, and then suggests an application in evaluating the performance of impaired hand. The proposed system can be used to monitor patient's progress in therapy and to devise better treatment strategies. The author finally concludes with a discussion on some of the challenges and issues facing the existing technology.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Inflammation enhances myeloid-derived suppressor cell cross-talk by signaling through Toll-like receptor 4 (2009)

Myeloid-derived suppressor cells (MDSC) are potent inhibitors of anti-tumor immunity that facilitate tumor progression by blocking the activation of CD4(+) and CD8(+) T cells and by promoting a type 2 immune response through their production of IL-10 and down-regulation of macrophage production of IL-12. MDSC accumulate in many cancer patients and are a significant impediment to active cancer immunotherapies. Chronic inflammation has been shown recently to enhance the accumulation of MDSC and to increase their suppression of T cells. These findings led us to hypothesize that inflammation contributes to tumor progression through the induction of MDSC, which create a favorable environment for tumor growth. As chronic inflammation also drives type 2 immune responses, which favor tumor growth, we asked if inflammation mediates this effect through MDSC. We find that IL-1beta-induced inflammation increased IL-10 production by MDSC and induces MDSC, which are more effective at down-regulating macrophage production of IL-12 as compared with MDSC isolated from less-inflammatory tumor microenvironments, thereby skewing tumor immunity toward a type 2 response. Inflammation heightens MDSC phenotype by signaling through the TLR4 pathway and involves up-regulation of CD14. Although this pathway is well-recognized in other myeloid cells, it has not been implicated previously in MDSC function. These studies demonstrate that MDSC are an intermediary through which inflammation promotes type 2 immune responses, and they identify the TLR4 pathway in MDSC as a potential target for down-regulating immune suppression and promoting anti-tumor immunity.
Upregulation of Endothelial Nitric Oxide Synthase by HMG CoA Reductase Inhibitors (1998)

Inhibition of endothelial HMG CoA reductase upregulates ecNOS expression predominantly by posttranscriptional mechanisms. These findings suggest that HMG CoA reductase inhibitors may have beneficial effects in atherosclerosis beyond that attributed to the lowering of serum cholesterol by increasing ecNOS activity.
Synthetic inhibitors of human leukocyte elastase Part 1--Sulphated polysaccharides. (1985)

Ten dextran sulphates and six chitosan sulphates of variable Mr and extent of sulphate substitution have been examined for their ability to inhibit human leukocyte elastase (HLE). All were potent partial non-competitive inhibitors of this enzyme, highest activity being obtained with compounds of large molecular weight and maximum sulphate incorporation (Ki = 5.0 X 10(-10)M]. In all cases, the dextran sulphates were more effective inhibitors than chitosan sulphates of similar size and charge, but both classes were inactive against bovine trypsin, chymotrypsin and porcine pancreatic elastase at concentrations less than 10(-4)M. The data suggest that drug binding to HLE occurs by stereospecific electrostatic interactions at site(s) removed from the catalytic reaction centre.