gebhart/patrepeval huggingface dataset:
A Novel Human tRNA-Dihydrouridine Synthase Involved in Pulmonary Carcinogenesis (2005)

An increased level of dihydrouridine in tRNA(Phe) was found in human malignant tissues nearly three decades ago, but its biological significance in carcinogenesis has remained unclear. Through analysis of genome-wide gene-expression profiles among non-small cell lung carcinomas (NSCLC), we identified overexpression of a novel human gene, termed hDUS2, encoding a protein that shared structural features with tRNA-dihydrouridine synthases (DUS). The deduced 493-amino-acid sequence showed 39% homology to the dihydrouridine synthase 2 enzyme (Dus2) of Saccharomyces cerevisiae and contained a conserved double-strand RNA-binding motif (DSRM). We found that hDUS2 protein had tRNA-DUS activity and that it physically interacted with EPRS, a glutamyl-prolyl tRNA synthetase, and was likely to enhance translational efficiencies. A small interfering RNA against hDUS2 transfected into NSCLC cells suppressed expression of the gene, reduced the amount of dihydrouridine in tRNA molecules, and suppressed growth. Immunohistochemical analysis showed significant association between higher levels of hDUS2 in tumors and poorer prognosis of lung cancer patients. Our data imply that up-regulation of hDUS2 is a relatively common feature of pulmonary carcinogenesis and that selective suppression of hDUS2 enzyme activity and/or inhibition of formation of the hDUS2-tRNA synthetase complex could be a promising therapeutic strategy for treatment of many lung cancers.
Electronic Decay Constant of Carotenoid Polyenes from Single-Molecule Measurements (2005)

The conductance of carotenoid polyenes chemically bound at each end to gold contacts has been measured for single molecules containing 5, 7, 9, and 11 carbon-carbon double bonds in conjugation. The electronic decay constant, beta, is determined to be 0.22 +/- 0.04 A-1, in close agreement with the value obtained from first principles simulations (0.22 +/- 0.01 A-1). The absolute values of the molecular conductance are within a factor of 3 of those calculated from first principles. The small value of beta demonstrates that conductivity drops off only slowly with chain length, confirming that carotenoid conjugated chains are relatively good molecular "wires".
Epitaxial growth of Y2O3 films on Si(100) without an interfacial oxide layer (1997)

Heteroepitaxial Y2O3 films were grown on Si(100) substrates by the technique of reactive ionized cluster beam deposition. The crystallinity of the films was investigated with reflection high energy electron diffraction (RHEED), glancing angle x-ray diffraction (GXRD), and the interface was examined by high resolution transmission electron microscopy (HRTEM). Under the condition of 5 kV acceleration voltage at the substrate temperature of 800 °C, the Y2O3 film grows epitaxially on the Si(100) substrate. RHEED and GXRD results revealed that the epitaxial relationship between Y2O3 and Si(100) is Y2O3(110)//Si(100), and HRTEM observation showed a sharp interface without an amorphous layer.
Learning During Stressful Times (2004)

Stressful life events can have profound effects on our cognitive and motor abilities, from those that could be construed as adaptive to those not so. In this review, I discuss the general notion that acute stressful experience necessarily impairs our abilities to learn and remember. The effects of stress on operant conditioning, that is, learned helplessness, as well as those on classical conditioning procedures are discussed in the context of performance and adaptation. Studies indicating sex differences in learning during stressful times are discussed, as are those attributing different responses to the existence of multiple memory systems and nonlinear relationships. The intent of this review is to highlight the apparent plasticity of the stress response, how it might have evolved to affect both performance and learning processes, and the potential problems with interpreting stress effects on learning as either good or bad. An appreciation for its plasticity may provide new avenues for investigating its underlying neuronal mechanisms.
Perceptual attention focus prediction for multiple viewers in case of multimedia perceptual compression with feedback delay (2006)

Human eyes have limited perception capabilities. Only 2 degrees of our 180 degree vision field provide the highest quality of perception. Due to this fact the idea of perceptual attention focus emerged to allow a visual content to be changed in a way that only part of the visual field where a human attention is directed to is encoded with a high quality. The image quality in the periphery can be reduced without a viewer noticing it. This compression approach allows a significant decrease in bit-rate for a video stream, and in the case of the 3D stream rendering, it decreases the computational burden. A number of previous researchers have investigated the topic of real-time perceptual attention focus but only for a single viewer. In this paper we investigate a dynamically changing multi-viewer scenario. In this type of scenario a number of people are watching the same visual content at the same time. Each person is using eye-tracking equipment. The visual content (video, 3D stream) is sent through a network with a large transmission delay. The area of the perceptual attention focus is predicted for the viewers to compensate for the delay value and identify the area of the image which requires highest quality coding.
Association of apolipoprotein E allele ϵ4 with late‐onset familial and sporadic Alzheimer's disease (1993)

Apolipoprotein E, type epsilon 4 allele (APOE epsilon 4), is associated with late-onset familial Alzheimer's disease (AD). There is high avidity and specific binding of amyloid beta-peptide with the protein ApoE. To test the hypothesis that late-onset familial AD may represent the clustering of sporadic AD in families large enough to be studied, we extended the analyses of APOE alleles to several series of sporadic AD patients. APOE epsilon 4 is significantly associated with a series of probable sporadic AD patients (0.36 +/- 0.042, AD, versus 0.16 +/- 0.027, controls [allele frequency estimate +/- standard error], p = 0.00031). Spouse controls did not differ from CEPH grandparent controls from the Centre d'Etude du Polymorphisme Humain (CEPH) or from literature controls. A large combined series of autopsy-documented sporadic AD patients also demonstrated highly significant association with the APOE epsilon 4 allele (0.40 +/- 0.026, p < or = 0.00001). These data support the involvement of ApoE epsilon 4 in the pathogenesis of late-onset familial and sporadic AD. ApoE isoforms may play an important role in the metabolism of beta-peptide, and APOE epsilon 4 may operate as a susceptibility gene (risk factor) for the clinical expression of AD.
Immunization of mice against tetanus with fragments of tetanus toxin synthesized in Escherichia coli (1987)

Two recombinant plasmids, pTet11 and pTet18, which express nontoxic protein fragments of tetanus toxin in Escherichia coli, were constructed. pTet11 protein (86 kilodaltons) is a fusion between part of the E. coli trpE protein and 441 amino acids of tetanus fragment C, and pTet18 (63 kilodaltons) consists of part of fragment B and all of fragment C of tetanus toxin. The synthesis of these proteins was induced in E. coli cultures, and the proteins were partially purified. Mice were immunized with these proteins, and dose-dependent titers of anti-tetanus toxoid antibodies were obtained. The proteins were able to induce neutralizing antibodies in mice, as demonstrated by the ability of mice immunized with 1 microgram or more of protein to survive challenge with 10 50% lethal doses of tetanus toxin.
Intravesical Heparin and Peripheral Neuromodulation on Interstitial Cystitis (2005)

Intravesical heparin and peripheral neuromodulation combination seems to be an alternative for patients with interstitial cystitis not responsive to other treatments.
Optical fiber two way FM video signal transmission for video conferencing applications (1994)

This paper describes an optical fiber transmission system to transmit two-way multi-channel FM video signals for video conferencing applications. A two-way optical fiber signal transmission system is built using a pair of optical distributors and a single optical fiber of 1 km for bidirectional communications. A pair of LEDs were used as light sources at 1.3 /spl mu/m and the bandwidth of the optical fiber transmission system was 300 MHz.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Mutations of KRAS and BRAF in Primary and Matched Metastatic Sites of Colorectal Cancer (2008)

These results demonstrate that both pain interference score and pain intensity are significant predictors of overall survival in men with castrate-refractory prostate cancer. Furthermore, pain interference score and pain intensity are statistically significant predictors of overall survival even when adjusting for established prognostic factors. It is known that high levels of alkaline phosphatase, PSA, and lactate dehydrogenase; low levels of hemoglobin; and high Gleason scores are indicators of advanced progression and death. Thus, these findings support the hypothesis that pain intensity and pain interference score are validated measures of advanced disease in men with prostate cancer. We agree with Klepstad and Kaasa in that investigating the relationship between pain and clinical outcomes in cancer patients is a fruitful area of research.
International financial reporting standards: A cautionary note for emerging economies (2011)

Long before the present economic crisis unfolded, the Financial Accounting Standards Board (FASB) and the International Accounting Standards Board (IASB) had been working to achieve harmonization in accounting and financial reporting standards across the globe. Now that the world economic community has become more integrated, cross border flow of capital has gained unprecedented momentum and steps are underway to achieve this goal as early as possible. Initial efforts to harmonize local accounting principles and practices with those followed in developed economies were generally aimed at facilitating foreign multinationals operating in other countries. The desired goal of harmonization now ought to be formulation of accounting standards that would facilitate optimal resource allocation for economic growth and prosperity and proper training of accountants with an informed professional outlook. Harmonization of accounting practices and procedures in emerging economies, therefore, should not be viewed as simply a process of complying with externally imposed standards. Rather, the process should involve exchange of ideas among all the participants. For such exchange of ideas to be meaningful, a critical examination of the factors that contributed to standards of reporting financial information is necessary. Discourse on such a vast topic requires an extensive work, which is beyond the scope of this paper. However, since United States of America has been at the forefront of codifying accounting principles, this paper is selectively focused on some contentious financial reporting issues and controversies that have impeded the development of a cohesive theory governing accounting standards for measurement and reporting of enterprise performance.
Primed stimulation of isolated perfused rabbit lung by endotoxin and platelet activating factor induces enhanced production of thromboxane and lung injury. (1990)

Bacterial sepsis often precedes the development of the adult respiratory distress syndrome (ARDS) and bacterial endotoxin (LPS) produces a syndrome similar to ARDS when infused into experimental animals. We determined in isolated, buffer-perfused rabbit lungs, free of plasma and circulating blood cells that LPS synergized with platelet activating factor (PAF) to injure the lung. In lungs perfused for 2 h with LPS-free buffer (less than 100 pg/ml), stimulation with 1, 10, or 100 nM PAF produced transient pulmonary hypertension and minimal edema. Lungs perfused for 2 h with buffer containing 100 ng/ml of Escherichia coli 0111:B4 LPS had slight elevation of pulmonary artery pressure (PAP) and did not develop edema. In contrast, lungs exposed to 100 ng/ml of LPS for 2 h had marked increases in PAP and developed significant edema when stimulated with PAF. LPS treatment increased capillary filtration coefficient, suggesting that capillary leak contributed to pulmonary edema. LPS-primed, PAF-stimulated lungs had enhanced production of thromboxane B2 (TXB) and 6-keto-prostaglandin F1 alpha (6KPF). Indomethacin completely inhibited PAF-stimulated production of TXB and 6KPF in control and LPS-primed preparations, did not inhibit the rise in PAP produced by PAF in control lungs, but blocked the exaggerated rise in PAP and edema seen in LPS-primed, PAF-stimulated lungs. The thromboxane synthetase inhibitor dazoxiben, and the thromboxane receptor antagonist, SQ 29,548, similarly inhibited LPS-primed pulmonary hypertension and edema after PAF-stimulation. These studies indicate that LPS primes the lung for enhanced injury in response to the physiologic mediator PAF by amplifying the synthesis and release of thromboxane in lung tissue.
From cellulose to cell (1999)

ABSTRACT The cell wall is often pictured as a more-or-less random feltwork of cellulose microfibrils in association with other polysaccharide and protein complexes. There is evidence from morphology, morphogenesis and mechanics that the structures in the cell wall are far more regular and that their interactions are driven by their chemical and morphological properties. In particular, a model based on liquid crystal structures has more than morphological implications.
Transition Metal-Catalyzed Nonoxidative Decarboxylation Reactions (2006)

Decarboxylases typically utilize an organic cofactor or a transition metal coupled with dioxygen to activate their substrates. The recent characterization of alpha-amino-beta-carboxymuconate-epsilon-semialdehyde decarboxylase (ACMSD) has revealed that this enzyme adopts a TIM-barrel (beta/alpha)(8) fold and employs a mononuclear transition metal center to decarboxylate the substrate in an oxidant-independent fashion. Thus, ACMSD represents a type of decarboxylation reaction that has been so far uncharacterized in biological systems. Several close homologues of ACMSD were analyzed, including isoorotate decarboxylase (IDCase), 5-carboxyvanillic acid decarboxylase (5-CVD), gamma-resorcylate decarboxylase (gamma-RSD), and 4-oxalomesaconate hydratase (OMAH). These enzymes are involved in the catabolism of tryptophan and vanillate, the biodegradation of hydroxylbenzoates, and the thymidine salvage pathways in certain organisms. They possess the signature sequence motifs of the amidohydrolase superfamily and likely share the same structural and mechanistic characteristics as that of ACMSD. Analysis of the sequence conservation and evolutionary relationship of ACMSD-related proteins suggests an emerging ACMSD protein family that includes ACMSD and ACMSD-like decarboxylases and hydratases with diverse substrate specificities, many of which are poorly understood in regard to their functions and mechanisms. Progress in the biochemical and structural characterization of ACMSD not only sheds light on the active site of this protein family but also promises the elucidation of the detailed catalytic mechanism of these novel transition metal-dependent nonoxidative decarboxylation reactions.
Planar GaAs IC technology: Applications for digital LSI (1978)

This technology utilizes multiple localized ion implantations directly into semi-insulating GaAs substrates, with unimplanted areas providing isolation between circuit elements. This approach allows for high yield, high density circuits, with optimization of various types of devices (e.g., GaAs MESFETs, high-speed Schottky-barrier diodes, etc.) made possible by optimizing the implantation profile for each type of device. The application of this fabrication technology for high-speed, ultra low power digital integrated circuits using a new circuit approach called Schottky diode-FET logic (SDFL) is described. Experimental GaAS SDFL logic ICs with LSI/VLSI compatible power levels (200-500 /spl mu/W/gate) and circuit densities (<10/SUP -3/ mm/SUP 2//gate) have been fabricated.
Design of a Molecular Beacon DNA Probe with Two Fluorophores (2001)

Fluorescence resonance energy transfer between two fluorophores (F<sub>1</sub> and F<sub>2</sub> ) attached to the two ends of a molecular beacon DNA probe containing a hairpin structure can be used for quantitative DNA/RNA studies. Concentrations of target-DNA as low as 1.7×10<sup>-10</sup> M could be determined with a commercial spectrometer by using coumarin and 6-carboxyfluorescein as the fluorophores. Measurements on the Förster energy transfer distance for the donor/acceptor pair can also be carried out using these DNA probes.
A novel combinatorial cancer immunotherapy (2014)

A non-antigen specific immunotherapy consisting of repeated co-administration of poly-IC and blocking antibodies targeting the programmed cell death-1 (PD-1) pathway dramatically inhibits tumor development in several mouse models of cancer. Tumor-reactive CD8<sup>+</sup> T cells mediate the antitumor effects mediated by PD-1 blockade. This therapeutic avenue can be readily translated to cancer patient treatment regimens.
CXCL10 Is Critical for the Progression and Maintenance of Depigmentation in a Mouse Model of Vitiligo (2014)

Vitiligo is an autoimmune disease of the skin that results in disfiguring white spots. There are no U.S. Food and Drug Administration-approved treatments for vitiligo, and most off-label treatments yield unsatisfactory results. Vitiligo patients have increased numbers of autoreactive, melanocyte-specific CD8(+) T cells in the skin and blood, which are directly responsible for melanocyte destruction. We report that gene expression in lesional skin from vitiligo patients revealed an interferon-γ (IFN-γ)-specific signature, including the chemokine CXCL10. CXCL10 was elevated in both vitiligo patient skin and serum, and CXCR3, its receptor, was expressed on pathogenic T cells. To address the function of CXCL10 in vitiligo, we used a mouse model of disease that also exhibited an IFN-γ-specific gene signature, expression of CXCL10 in the skin, and up-regulation of CXCR3 on antigen-specific T cells. Mice that received Cxcr3(-/-) T cells developed minimal depigmentation, as did mice lacking Cxcl10 or treated with CXCL10-neutralizing antibody. CXCL9 promoted autoreactive T cell global recruitment to the skin but not effector function, whereas CXCL10 was required for effector function and localization within the skin. Surprisingly, CXCL10 neutralization in mice with established, widespread depigmentation induces reversal of disease, evidenced by repigmentation. These data identify a critical role for CXCL10 in both the progression and maintenance of vitiligo and thereby support inhibiting CXCL10 as a targeted treatment strategy.
Genomic organization of the human TIMP-1 gene. Investigation of a causative role in the pathogenesis of X-linked retinitis pigmentosa 2. (1997)

The results of this study exclude mutations in the TIMP-1 coding sequence, splice sites, and the 5' upstream region as a cause of retinal degeneration in x-linked retinitis pigmentosa 2. However, an as yet unidentified regulatory element that lies outside these intervals may be implicated. The role of this tightly regulated protein in the normal functioning of the retina has yet to be determined.
Human monoclonal antibodies derived from lymph nodes of a patient with breast carcinoma react with MuMTV polypeptides (1987)

Nine human hybridoma cell lines were established from a fusion of axillary lymph node lymphocytes of a patient with breast ductal carcinoma with a human lymphoblastoid cell line. The human hybridoma nature of the fusion products was confirmed by chromosomal analysis and HLA typing. The hybridomas are stable over a year of growth, and can be frozen, thawed and regrown. The carcinoma cells of the patient harbor mouse mammary tumor virus (MuMTV) cross-reacting antigens. The patient's serum and the purified monoclonal antibodies reacted with MuMTV polypeptides. Radioimmunoprecipitation studies using labeled MuMTV confirmed the binding of the patient's serum to the viral proteins. None of the control immunoglobulins reacted with the virus. No binding of the hybridoma immunoglobulins was observed with two other retroviruses (avian myeloblastosis virus and simian sarcoma virus). The ligand binding characteristics of the monoclonal antibodies suggest binding to epitopes on the various structural virus polypeptides. These monoclonal antibodies may serve as a probe to analyze the MuMTV-human breast carcinoma relationship.
Prognostic Factors in Breast Cancer (2000)

Abstract Background. —Under the auspices of the College of American Pathologists, a multidisciplinary group of clinicians, pathologists, and statisticians considered prognostic and predictive factors in breast cancer and stratified them into categories reflecting the strength of published evidence. Materials and Methods. —Factors were ranked according to previously established College of American Pathologists categorical rankings: category I, factors proven to be of prognostic import and useful in clinical patient management; category II, factors that had been extensively studied biologically and clinically, but whose import remains to be validated in statistically robust studies; and category III, all other factors not sufficiently studied to demonstrate their prognostic value. Factors in categories I and II were considered with respect to variations in methods of analysis, interpretation of findings, reporting of data, and statistical evaluation. For each factor, detailed recommendations for improvement were made. Recommendations were based on the following aims: (1) increasing uniformity and completeness of pathologic evaluation of tumor specimens, (2) enhancing the quality of data collected about existing prognostic factors, and (3) improving patient care. Results and Conclusions. —Factors ranked in category I included TNM staging information, histologic grade, histologic type, mitotic figure counts, and hormone receptor status. Category II factors included c- erb B-2 (Her2- neu ), proliferation markers, lymphatic and vascular channel invasion, and p53. Factors in category III included DNA ploidy analysis, microvessel density, epidermal growth factor receptor, transforming growth factor-α, bcl-2, pS2, and cathepsin D. This report constitutes a detailed outline of the findings and recommendations of the consensus conference group, organized according to structural guidelines as defined.