gebhart/patrepeval huggingface dataset:
Antigenic differences between two viruses, isolated in Japan and Korea, that cause hemorrhagic fever with renal syndrome (1984)

Hantaan virus (HV) 76-118, isolated from Apodemus agrarius coreae in Korea, and hemorrhagic fever with renal syndrome (HFRS) virus B-1, isolated from a rat in Japan, were examined for polypeptide compositions and for differences in immune responses in rats. In immunoprecipitation experiments, a major polypeptide of ca. 50 kilodaltons (K) was detected with antisera against HV 76-118 in cell extracts from Vero E6 cells infected with HFRS virus B-1, whereas three major polypeptides of 74 K (glycosylated), 57 K (glycosylated), and 50 K were detected with antisera against HFRS virus B-1. On the other hand, two polypeptides with molecular weights of 55,000 (glycosylated) and 50,000 were detected with either antiserum in cell extracts infected with HV 76-118. In neutralizing antibody tests with antisera prepared in rats, a remarkable difference in antibody titer (5 to 30 times higher to the homologous virus than to the heterologous virus) was observed between the two viruses. However, this difference was not so marked (1 to 4 times higher to the homologous virus) in the immunofluorescent antibody test. Twenty hybrid cell lines producing mouse monoclonal antibodies against HV 76-118 were isolated by fusion of spleen cells from BALB/c mice immunized against HV (strain 76-118) with mouse myeloma cells. The specificity of these monoclonal antibodies was established by immunofluorescent antibody, neutralizing antibody, and fluorescent antibody to membrane antigen tests and by analysis with sodium dodecyl sulfate-polyacrylamide gel electrophoresis. These hybrid cell lines were classified into three groups based principally on the IF staining pattern of the HV-infected cells: (i) antibodies which showed a discrete patch pattern in the cytoplasm by the immunofluorescent antibody test, reacting with the membrane antigen of infected cells and immunoprecipitating a 55-K glycoprotein from HV 76-118-infected cell lysates and a 57-K glycoprotein from the heterologous (strain B-1) HFRS virus-infected cell lysates. Among these, depending on the neutralizing antibody activity and the reaction with the heterologous antigen, three subgroups designated I-A, I-B, and I-C were established; (ii) antibodies which showed large granular dots in the cytoplasm, neither having neutralizing antibody activity nor immunoprecipitating any antigen; (iii) antibodies which showed defined granular dots throughout the cytoplasm, reacting with a 50-K polypeptide of both virus strains. These antibodies also classified into two subgroups based on the reactivity with the B-1 strain.(ABSTRACT TRUNCATED AT 400 WORDS)
Inhibition of collagen hydroxylation by 2,7,8-trihydroxyanthraquinone in embryonic-chick tendon cells (1989)

Prolyl 4-hydroxylase (EC 1.14.11.2) is an essential enzyme in the post-translational modification of collagen. Inhibitors of this enzyme are of potential interest for the treatment of diseases involving excessive deposition of collagen. 2,7,8-Trihydroxyanthraquinone (THA) is an effective inhibitor of prolyl 4-hydroxylase by virtue of its ability to compete with the co-substrate 2-oxoglutarate (Ki = 40.3 microM). Using a simple and reproducible assay for collagen hydroxylation, we show that THA inhibits the hydroxylation of collagen in embryonic-chick tendon cells in short-term culture, with an IC50 value (concn. giving 50% inhibition) of 32 microM. In comparison, the ethyl ester of 3,4-dihydroxybenzoic acid has an IC50 value of 0.1 mM against collagen hydroxylation by chick tendon cells, whereas its Ki versus isolated prolyl 4-hydroxylase is 49 microM.
Probing Biomolecular Interactions at Conductive and Semiconductive Surfaces by Impedance Spectroscopy: Routes to Impedimetric Immunosensors, DNA‐Sensors, and Enzyme Biosensors (2003)

Abstract Impedance spectroscopy is a rapidly developing electrochemical technique for the characterization of biomaterial‐functionalized electrodes and biocatalytic transformations at electrode surfaces, and specifically for the transduction of biosensing events at electrodes or field‐effect transistor devices. The immobilization of biomaterials, e.g., enzymes, antigens/antibodies or DNA on electrodes or semiconductor surfaces alters the capacitance and interfacial electron transfer resistance of the conductive or semiconductive electrodes. Impedance spectroscopy allows analysis of interfacial changes originating from biorecognition events at electrode surfaces. Kinetics and mechanisms of electron transfer processes corresponding to biocatalytic reactions occurring at modified electrodes can be also derived from Faradaic impedance spectroscopy. Different immunosensors that use impedance measurements for the transduction of antigen‐antibody complex formation on electronic transducers were developed. Similarly, DNA biosensors using impedance measurements as readout signals were developed. Amplified detection of the analyte DNA using Faradaic impedance spectroscopy was accomplished by the coupling of functionalized liposomes or by the association of biocatalytic conjugates to the sensing interface providing biocatalyzed precipitation of an insoluble product on the electrodes. The amplified detections of viral DNA and single‐base mismatches in DNA were accomplished by similar methods. The changes of interfacial features of gate surfaces of field‐effect transistors (FET) upon the formation of antigen‐antibody complexes or assembly of protein arrays were probed by impedance measurements and specifically by transconductance measurements. Impedance spectroscopy was also applied to characterize enzyme‐based biosensors. The reconstitution of apo‐enzymes on cofactor‐functionalized electrodes and the formation of cofactor‐enzyme affinity complexes on electrodes were probed by Faradaic impedance spectroscopy. Also biocatalyzed reactions occurring on electrode surfaces were analyzed by impedance spectroscopy. The theoretical background of the different methods and their practical applications in analytical procedures were outlined in this article.
Growth factor responsiveness of human articular chondrocytes: Distinct profiles in primary chondrocytes, subcultured chondrocytes, and fibroblasts (1994)

The objectives of this study were to establish a growth factor response profile for adult human articular chondrocytes, to determine whether this is unique for chondrocytes or influenced by the differentiation status of the cells, and to characterize growth factor interactions. It is shown that transforming growth factor-beta (TGF-beta) is the most potent mitogen among a variety of factors tested. All three isoforms of TGF-beta caused similar dose-dependent increases in chondrocyte proliferation. Other members of the TGF-beta family, including bone morphogenetic protein 2B (BMP2B), activin, and inhibin, did not detectably increase chondrocyte proliferation. Platelet-derived growth factor-AA (PDGF-AA), basic fibroblast growth factor (bFGF), and insulin-like growth factor 1 (IGF-1) also stimulated proliferation but were less effective than TGF-beta. In contrast to findings with other cell types, the effects of TGF-beta on chondrocyte proliferation were not dependent on the endogenous production of PDGF. The cytokines Interleukin 1 (IL-1) and tumor necrosis factor-alpha (TNF-alpha) gave no stimulation, but IL-1 inhibited chondrocyte proliferation induced by TGF-beta or serum. This response profile was characteristic for primary chondrocytes from human adults and distinct from subcultured (dedifferentiated) chondrocytes or skin fibroblasts. The latter preferentially responded to PDGF, and IL-1 caused greater increases in proliferation than TGF-beta. In summary, these results describe growth factor responses that are characteristic for chondrocytes and provide a basis for the analysis of changes in chondrocyte growth proliferation that occur in aging and tissue injury.
Surveillance for neuraminidase-inhibitor-resistant influenza viruses in Japan, 1996–2007 (2008)

Our findings suggested possible low-level transmission of resistant variants from oseltamivir-treated patients in several seasons in Japan but no sustained reductions in NAI susceptibility or consistently increased frequency of detecting resistant variants for any strain or subtype, despite high levels of drug use. In particular, although oseltamivir-resistant A(H1N1) viruses with the H274Y mutation spread globally in 2007-2008, we found little evidence for increasing levels of resistant A(H1N1) variants in Japan in preceding years.
Expanding the Clinical Development of Bevacizumab (2004)

Bevacizumab (Avastin; Genentech, Inc.; South San Francisco, CA) is a recombinant, humanized monoclonal antibody to vascular endothelial growth factor, a key regulator of tumor angiogenesis. Bevacizumab demonstrated potent antitumor activity in preclinical models and has also shown biologic activity and clinical benefit in clinical studies. Notably, a randomized, placebo-controlled phase II trial in renal cell carcinoma demonstrated a significantly longer time to tumor progression with bevacizumab monotherapy. Furthermore, in a phase III trial for untreated advanced colorectal cancer, the addition of bevacizumab to chemotherapy led to significantly longer overall survival and progression-free survival times than chemotherapy alone. The clinical development of bevacizumab has been expanded to include confirmatory phase III trials and exploratory phase II trials in a variety of solid tumors and hematologic malignancies. Treatment regimens being examined include bevacizumab alone and in combination with conventional chemotherapy, radiation, immune therapy, and biologically targeted agents.
Parasite-specific interaction of N-[4-(4'nitroanilino)-phenyl]-S-(beta-carboxyethyl)-dithiocar bamic acid-ester with arginyl-tRNA-synthetase from Dirofilaria immitis. (1985)

A potent inhibition of arginyl-tRNA-synthetase from Dirofilaria immitis by N-[4-(4'nitroanilino)-phenyl]-S-(beta-carboxylethyl)-dith iocarbamic acid-ester (CGP 8065) is demonstrated, which indicates the charging of amino acids to tRNA as a possible target for the chemotherapeutic attack by this filaricidal compound. CGP 8065 competes with ATP; the inhibition constant was determined to be 13 micrograms ml-1 (34 microM). The Michaelis constants for arginine and ATP were found to be 5 microM and 0.4 mM, respectively. The inhibition of arginyl-tRNA-synthetase by CGP 8065 was shown to be specific for D. immitis; the isofunctional enzymes from Ascaris suum and rat liver were not affected.
Elimination of Transcriptional Interference between Tandem Genes in Plant Cells (2001)

Plant cells are commonly transformed with two or more tandemly arranged genes, but how orientation affects their expression is not well understood. We investigated the amount of transcriptional interference occurring between two adjacent genes by cloning luciferase and green fluorescent protein (GFP) genes (promoter--coding sequence--terminator) in all possible orientations and expressing the genes in tobacco protoplasts. When two genes are oriented head-to-tail (-->-->), the expression of the downstream gene was reduced 80% by the upstream gene. When two genes are oriented tail-to-tail (--><--), the expression of the upstream gene was reduced 53% by the expression of the downstream gene. There was no interference when the orientation was head-to-head (<---->). Using a chemically inducible gene expression system, we showed that the downstream gene expression was reduced 71% by the induction of an upstream gene. Inserting a mammalian transcription blocker sequence eliminated the interference between the genes in tail-to-tail orientation. The interference in the head-to-tail orientation was eliminated by inserting a 2322-bp lambda phage DNA fragment. The terminators in gene constructs did not prevent the transcriptional interference, and the interference was eliminated by designing the orientation of genes and by placing a transcription blocker or a lambda phage sequence between genes.
Androgens and Estrogens Modulate the Immune and Inflammatory Responses in Rheumatoid Arthritis (2002)

Generally, androgens exert suppressive effects on both humoral and cellular immune responses and seem to represent natural anti-inflammatory hormones; in contrast, estrogens exert immunoenhancing activities, at least on humoral immune response. Low levels of gonadal androgens (testosterone/dihydrotestosterone) and adrenal androgens (dehydroepiandrosterone and its sulfate), as well as lower androgen/estrogen ratios, have been detected in body fluids (that is, blood, synovial fluid, smears, salivary) of both male and female rheumatoid arthritis patients, supporting the possibility of a pathogenic role for the decreased levels of the immune-suppressive androgens. Several physiological, pathological, and therapeutic conditions may change the sex hormone milieu and/or peripheral conversion, including the menstrual cycle, pregnancy, the postpartum period, menopause, chronic stress, and inflammatory cytokines, as well as use of corticosteroids, oral contraceptives, and steroid hormonal replacements, inducing altered androgen/estrogen ratios and related effects. Therefore, sex hormone balance is still a crucial factor in the regulation of immune and inflammatory responses, and the therapeutical modulation of this balance should represent part of advanced biological treatments for rheumatoid arthritis and other autoimmune rheumatic diseases.
Modeling LED street lighting (2014)

LED luminaires may deliver precise illumination patterns to control light pollution, comfort, visibility, and light utilization efficiency. Here, we provide simple equations to determine how the light distributes in the streets. In particular, we model the illuminance spatial distribution as a function of Cartesian coordinates on a floor, road, or street. The equations show explicit dependence on the luminary position (pole height and arm length), luminary angle (fixture tilt), and the angular intensity profile (radiation pattern) of the LED luminary. To achieve this, we propose two mathematical representations to model the sophisticated intensity profiles of LED luminaries. Furthermore, we model the light utilization efficiency, illumination uniformity, and veiling luminance of glare due to one or several LED streetlamps.
Interleaving (1994)

There is an increasing trend to use commodity microprocessors as the compute engines in large-scale multiprocessors. However, given that the majority of the microprocessors are sold in the workstation market, not in the multiprocessor market, it is only natural that architectural features that benefit only multiprocessors are less likely to be adopted in commodity microprocessors. In this paper, we explore multiple-context processors, an architectural technique proposed to hide the large memory latency in multiprocessors. We show that while current multiple-context designs work reasonably well for multiprocessors, they are ineffective in hiding the much shorter uniprocessor latencies using the limited parallelism found in workstation environments. We propose an alternative design that combines the best features of two existing approaches, and present simulation results that show it yields better performance for both multiprogrammed workloads on a workstation and parallel applications on a multiprocessor. By addressing the needs of the workstation environment, our proposal makes multiple contexts more attractive for commodity microprocessors.
Analysis of Integrin α7 Mutations in Prostate Cancer, Liver Cancer, Glioblastoma Multiforme, and Leiomyosarcoma (2007)

Integrin alpha7 appears to be a tumor suppressor that operates by suppressing tumor growth and retarding migration.
The M184V Mutation Reduces the Selective Excision of Zidovudine 5′-Monophosphate (AZTMP) by the Reverse Transcriptase of Human Immunodeficiency Virus Type 1 (2002)

The M184V mutation in human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) causes resistance to lamivudine, but it also increases the sensitivity of the virus to zidovudine (3'-azido-3'-deoxythymidine; AZT). This sensitization to AZT is seen both in the presence and the absence of the mutations that confer resistance to AZT. AZT resistance is due to enhanced excision of AZT 5'-monophosphate (AZTMP) from the end of the primer by the RT of the resistant virus. Published data suggest that the excision reaction involves pyrophosphorolysis but that the likely in vivo pyrophosphate donor is not pyrophosphate but ATP. The mutations that lead to AZT resistance enhance ATP binding and, in so doing, enhance pyrophosphorolysis. The excision reaction is specific for AZT because HIV-1 RT, which can form a closed complex with a dideoxy-terminated primer and an incoming deoxynucleoside triphosphate (dNTP), does not form the closed complex with an AZTMP-terminated primer and an incoming dNTP. This means that an AZTMP-terminated primer has better access to the site where it can be excised. The M184V mutation alters the polymerase active site in a fashion that specifically interferes with ATP-mediated excision of AZTMP from the end of the primer strand. The M184V mutation does not affect the incorporation of AZT 5'-triphosphate (AZTTP), either in the presence or the absence of mutations that enhance AZTMP excision. However, in the presence of ATP, the M184V mutation does decrease the ability of HIV-1 RT to carry out AZTMP excision. Based on these results, and on the results of other excision experiments, we present a model to explain how the M184V mutation affects AZTMP excision.
Expansion and drug elution model of a coronary stent (2007)

The present study illustrates a possible methodology to investigate drug elution from an expanded coronary stent. Models based on finite element method have been built including the presence of the atherosclerotic plaque, the artery and the coronary stent. These models take into account the mechanical effects of the stent expansion as well as the effect of drug transport from the expanded stent into the arterial wall. Results allow to quantify the stress field in the vascular wall, the tissue prolapse within the stent struts, as well as the drug concentration at any location and time inside the arterial wall, together with several related quantities as the drug dose and the drug residence times.
Cell-based therapy for insulin-dependent diabetes mellitus (1998)

Insulin-secreting pancreatic beta-cell lines represent a promising approach for treatment of insulin-dependent diabetes mellitus. Such cell lines can provide an abundant and reproducible source of beta-cell material for transplantation. A number of highly differentiated beta-cell lines have been developed using transgenic mice. These cells produce insulin amounts comparable to normal pancreatic islets and release it in response to physiological insulin secretagogues. Our laboratory has employed a reversible transformation approach to tightly regulate cell replication in these beta-cell lines, both in culture and in vivo. Beta-cell lines can be modulated by gene transfer to improve their function and survival. We have utilized adenovirus genes, which downregulate antigen presentation and increase cell resistance to cytokines, to facilitate transplantation of mouse beta cells across allogeneic barriers. These approaches could be applied to the development of human beta-cell lines by genetic engineering of isolated human islets.
Photonic-crystal slab for terahertz-wave integrated circuits (2012)

This paper focuses on a two-dimensional (2D) photonic-crystal semiconductor slab, which has a 2D periodic variation of the refractive index on a length scale comparable with the wavelength, as the interconnection of a THz-wave IC. This is because ultralow-loss manipulation of a light wave in the photonic crystal has been demonstrated in planar and ultrasmall structure.
Application of thin-film optical filters to the temperature compensation of optical fiber grating-based devices (1997)

A major problem currently affecting the implementation of in-fiber refractive-index grating-based optical fiber devices is the drift in wavelength modulation due to the change in the ambient temperature. For accurate and reliable long-term operation of these devices, suitable temperature compensation techniques are a necessity. This paper presents a novel temperature compensation technique for in-fiber refractive index grating-based devices and components. The proposed technique is based on the temperature-dependent spectral characteristics of a dielectric multilayer thin-film interference filter fabricated on the endface of refractive-index grating impressed optical fiber. Temperature compensation is achieved by comparing the reflected intensities at the grating-reflected and the interference filter-reflected wavelengths. The proposed scheme also compensates for light source fluctuations and lead-in fiber bending losses.
Suppression of lethal autoimmunity by regulatory T cells with a single TCR specificity (2017)

The regulatory T cell (T reg cell) T cell receptor (TCR) repertoire is highly diverse and skewed toward recognition of self-antigens. TCR expression by T reg cells is continuously required for maintenance of immune tolerance and for a major part of their characteristic gene expression signature; however, it remains unknown to what degree diverse TCR-mediated interactions with cognate self-antigens are required for these processes. In this study, by experimentally switching the T reg cell TCR repertoire to a single T reg cell TCR, we demonstrate that T reg cell function and gene expression can be partially uncoupled from TCR diversity. An induced switch of the T reg cell TCR repertoire to a random repertoire also preserved, albeit to a limited degree, the ability to suppress lymphadenopathy and T helper cell type 2 activation. At the same time, these perturbations of the T reg cell TCR repertoire led to marked immune cell activation, tissue inflammation, and an ultimately severe autoimmunity, indicating the importance of diversity and specificity for optimal T reg cell function.
Survivable storage systems (2002)

Survivable storage systems must maintain data and access to it in the face of malicious and accidental problems with storage servers, interconnection networks, client systems and user accounts. These four component types can be grouped into two classes: server-side problems and client-side problems. The PASIS architecture addresses server-side problems, including the connections to those servers, by encoding data with threshold schemes and distributing trust amongst sets of storage servers. Self-securing storage addresses client and user account problems by transparently auditing accesses and versioning data within each storage server. Thus, PASIS clients use threshold schemes to protect themselves from compromised servers, and self-securing servers use full access auditing to protect their data from compromised clients. Together, these techniques can provide truly survivable storage systems.
Low power optoelectronic modules for high performance switching applications (1997)

Low power optoelectronic modules are being developed for high speed switching applications. In this paper, we will summarize the motivation for utilizing photonics within micro-volume switching networks. Specific hardware issues will also be addressed for the individual components: vertical cavity surface emitting lasers (VCSELs), diffractive optical interconnect elements (DOIEs), and GaAs and Si smart pixel arrays, which consist of monolithic receivers, amplifiers, digital memories, etc. Finally, we will discuss the application and algorithm basis for optoelectronic modules in high speed switching/communication systems.