gebhart/patrepeval huggingface dataset:
A 10-Amino-Acid Sequence in the N-Terminal A/B Domain of Thyroid Hormone Receptor α Is Essential for Transcriptional Activation and Interaction with the General Transcription Factor TFIIB (1995)

The effects of the thyroid hormone (3,5,3'-triiodo-L-thyronine [T3]) on gene transcription are mediated by nuclear T3 receptors (T3Rs). alpha- and beta-isoform T3Rs (T3R alpha and -beta) are expressed from different genes and are members of a superfamily of ligand-dependent transcription factors that also includes the receptors for steroid hormones, vitamin D, and retinoids. Although T3 activates transcription by mediating a conformational change in the C-terminal approximately 220-amino-acid ligand-binding domain (LBD), the fundamental mechanisms of T3R-mediated transcriptional activation remain to be determined. We found that deletion of the 50-amino-acid N-terminal A/B domain of chicken T3R alpha (cT3R alpha) decreases T3-dependent stimulation of genes regulated by native thyroid hormone response elements about 10- to 20-fold. The requirement of the A/B region for transcriptional activation was mapped to amino acids 21 to 30, which contain a cluster of five basic amino acids. The A/B region of cT3R alpha is not required for T3 binding or for DNA binding of the receptor as a heterodimer with retinoid X receptor. In vitro binding studies indicate that the N-terminal region of cT3R alpha interacts efficiently with TFIIB and that this interaction requires amino acids 21 to 30 of the A/B region. In contrast, the LBD interacts poorly with TFIIB. The region of TFIIB primarily involved in the binding of cT3R alpha includes an amphipathic alpha helix contained within residues 178 to 201. Analysis using a fusion protein containing the DNA-binding domain of GAL4 and the entire A/B region of cT3R alpha suggests that this region does not contain an intrinsic activation domain. These and other studies indicate that cT3R alpha mediates at least some of its effects through TFIIB in vivo and that the N-terminal region of DNA-bound cT3R alpha acts to recruit and/or stabilize the binding of TFIIB to the transcription complex. T3 stimulation could then result from ligand-mediated changes in the LBD which may lead to the interaction of other factors with cT3R alpha, TFIIB, and/or other components involved in the initiation of transcription.
Overexpression of Translation Elongation Factor 1A Affects the Organization and Function of the Actin Cytoskeleton in Yeast (2001)

The translation elongation factor 1 complex (eEF1) plays a central role in protein synthesis, delivering aminoacyl-tRNAs to the elongating ribosome. The eEF1A subunit, a classic G-protein, also performs roles aside from protein synthesis. The overexpression of either eEF1A or eEF1B alpha, the catalytic subunit of the guanine nucleotide exchange factor, in Saccharomyces cerevisiae results in effects on cell growth. Here we demonstrate that overexpression of either factor does not affect the levels of the other subunit or the rate or accuracy of protein synthesis. Instead, the major effects in vivo appear to be at the level of cell morphology and budding. eEF1A overexpression results in dosage-dependent reduced budding and altered actin distribution and cellular morphology. In addition, the effects of excess eEF1A in actin mutant strains show synthetic growth defects, establishing a genetic connection between the two proteins. As the ability of eEF1A to bind and bundle actin is conserved in yeast, these results link the established ability of eEF1A to bind and bundle actin in vitro with nontranslational roles for the protein in vivo.
A modular microfluidic architecture for integrated biochemical analysis (2005)

Microfluidic laboratory-on-a-chip (LOC) systems based on a modular architecture are presented. The architecture is conceptualized on two levels: a single-chip level and a multiple-chip module (MCM) system level. At the individual chip level, a multilayer approach segregates components belonging to two fundamental categories: passive fluidic components (channels and reaction chambers) and active electromechanical control structures (sensors and actuators). This distinction is explicitly made to simplify the development process and minimize cost. Components belonging to these two categories are built separately on different physical layers and can communicate fluidically via cross-layer interconnects. The chip that hosts the electromechanical control structures is called the microfluidic breadboard (FBB). A single LOC module is constructed by attaching a chip comprised of a custom arrangement of fluid routing channels and reactors (passive chip) to the FBB. Many different LOC functions can be achieved by using different passive chips on an FBB with a standard resource configuration. Multiple modules can be interconnected to form a larger LOC system (MCM level). We demonstrated the utility of this architecture by developing systems for two separate biochemical applications: one for detection of protein markers of cancer and another for detection of metal ions. In the first case, free prostate-specific antigen was detected at 500 aM concentration by using a nanoparticle-based bio-bar-code protocol on a parallel MCM system. In the second case, we used a DNAzyme-based biosensor to identify the presence of Pb(2+) (lead) at a sensitivity of 500 nM in <1 nl of solution.
Comparison of the immunogenicity and safety ofCervarix™ andGardasil®human papillomavirus (HPV) cervical cancer vaccines in healthy women aged 18–45 years (2009)

This observer-blind study compared the prophylactic human papillomavirus (HPV) vaccines, Cervarix (GlaxoSmithKline) and Gardasil (Merck), by assessing immunogenicity and safety through one month after completion of the three-dose vaccination course. Women (n = 1106) were stratified by age (18-26, 27-35, 36-45 years) and randomized (1:1) to receive Cervarix (Months 0, 1, 6) or Gardasil (Months 0, 2, 6). At Month 7 after first vaccination, all women in the according-to-protocol cohort who were seronegative/DNA negative before vaccination for the HPV type analyzed had seroconverted for HPV-16 and HPV-18 serum neutralizing antibodies, as measured by pseudovirion-based neutralization assay (PBNA), except for two women aged 27-35 years in the Gardasil group who did not seroconvert for HPV-18 (98%). Geometric mean titers of serum neutralizing antibodies ranged from 2.3-4.8-fold higher for HPV-16 and 6.8-9.1-fold higher for HPV-18 after vaccination with Cervarix compared with Gardasil, across all age strata. In the total vaccinated cohort (all women who received at least one vaccine dose, regardless of their serological and DNA status prior to vaccination), Cervarix induced significantly higher serum neutralizing antibody titers in all age strata (p < 0.0001). Positivity rates for anti-HPV-16 and -18 neutralizing antibodies in cervicovaginal secretions and circulating HPV-16 and -18 specific memory B-cell frequencies were also higher after vaccination with Cervarix compared with Gardasil. Both vaccines were generally well tolerated. The incidence of unsolicited adverse events was comparable between vaccinated groups. The incidence of solicited symptoms was generally higher after Cervarix, injection site reactions being most common. However, compliance rates with the three-dose schedules were similarly high (>or= 84%) for both vaccines. Although the importance of differences in magnitude of immune response between these vaccines is unknown, they may represent determinants of duration of protection against HPV-16/18. Long-term studies evaluating duration of efficacy after vaccination are needed for both vaccines.
Disease stage variation in CD4+ and CD8+ T-cell reactivity to the receptor tyrosine kinase EphA2 in patients with renal cell carcinoma. (2003)

We have evaluated CD8+ and CD4+ T-cell responses against a new tumor-associated antigen, the receptor tyrosine kinase EphA2, which is broadly expressed in diverse cancer histologies and is frequently overexpressed in advanced stage/metastatic disease. We report herein that EphA2 is overexpressed in renal cell carcinoma (RCC) cell lines and clinical specimens of RCC, and find that the highest levels of EphA2 are consistently found in the most advanced stages of the disease. We identified and synthesized five putative HLA class I-binding and three class II-binding peptides derived from EphA2 that might serve as targets for immune reactivity. Each peptide induced specific, tumor-reactive CD8+ or CD4+T-cell responses as measured using IFN-gamma enzyme-linked immunospot assays. The EphA2 peptides elicited relatively weak responses from CD8+ T cells derived from normal healthy volunteers or from RCC patients with active disease. In marked contrast, immune reactivity to EphA2-derived epitopes was greatly enhanced in CD8+ T cells that had been isolated from patients who were rendered disease-free, after surgery. Furthermore, enzyme-linked immunospot analyses demonstrated prominent EphA2-restricted T-helper 1-type CD4+ T cell activity in patients with early stage disease, whereas T-helper 2-type and T regulatory-type responses predominated in patients with more advanced forms of RCC. These data suggest that the immune system of cancer patients actively monitors EphA2-derived epitopes, and that the magnitude and character of T-cell responses to EphA2 epitopes may convey much-needed predictive information about disease stage and outcome.
Determination of Glucose in a Biological Matrix by Multivariate Analysis of Multiple Band-Pass-Filtered Fourier Transform Near-Infrared Interferograms (1997)

A multivariate calibration method is described in which Fourier transform near-infrared interferogram data are used to determine clinically relevant levels of glucose in an aqueous matrix of bovine serum albumin (BSA) and triacetin. BSA and triacetin are used to model the protein and triglycerides in blood, respectively, and are present in levels spanning the normal human physiological range. A full factorial experimental design is constructed for the data collection, with glucose at 10 levels, BSA at 4 levels, and triacetin at 4 levels. Gaussian-shaped band-pass digital filters are applied to the interferogram data to extract frequencies associated with an absorption band of interest. Separate filters of various widths are positioned on the glucose band at 4400 cm-1, the BSA band at 4606 cm-1, and the triacetin band at 4446 cm-1. Each filter is applied to the raw interferogram, producing one, two, or three filtered interferograms, depending on the number of filters used. Segments of these filtered interferograms are used together in a partial least-squares regression analysis to build glucose calibration models. The optimal calibration model is realized by use of separate segments of interferograms filtered with three filters centered on the glucose, BSA, and triacetin bands. Over the physiological range of 1-20 mM glucose, this 17-term model exhibits values of R2, standard error of calibration, and standard error of prediction of 98.85%, 0.631 mM, and 0.677 mM, respectively. These results are comparable to those obtained in a conventional analysis of spectral data. The interferogram-based method operates without the use of a separate background measurement and employs only a short section of the interferogram.
Enhancing three-dimensional vision with three-dimensional sound (2004)

This course offers a thorough introduction to three-dimensional, multi-channel sound. Three-dimensional sound has been neglected in most VR and AR applications, even though it can significantly enhance their realism and immersion. This course explains the main concepts and the most important terms, and provides a detailed overview of the currently available hardware and software. It combines theoretical and practical knowledge on how to apply these technologies in VR and AR systems.
Endoglin regulates renal ischaemia–reperfusion injury (2006)

Endoglin is up-regulated in the post-ischaemic kidney and endoglin-haploinsufficient mice are protected from renal I-R injury. Endoglin may play a primary role in promoting inflammatory responses following renal I-R.
Phlogistic properties of peptidoglycan-polysaccharide polymers from cell walls of pathogenic and normal-flora bacteria which colonize humans (1993)

PG-PS polymers which can induce experimental chronic inflammation in joints and other tissues can be isolated from the cell walls of human pathogens, such as group A streptococci, as well as from certain indigenous bacterial species which colonize the human intestinal tract. The structural and biological properties that are required for cell wall fragments to express this remarkable activity are still not well defined, but polymer size, resistance to tissue enzymes, and capacity to sustain activation of complement, macrophages, neutrophils, and T cells are properties associated with the most active preparations. There is increasing evidence that PG-PS structures with arthropathogenic activity occur in the human intestinal lumen and that these polymers can be translocated systemically. These observations support the concept that PG-PS, derived from a variety of bacterial species, can be part of the etiology of rheumatoid arthritis and other chronic inflammatory diseases. Since the PG component provides a common element to which all individuals are exposed, it follows that susceptibility is related to efficiency of disposal of bacterial cell wall debris, as well as to cytokine networks and immune cell function (51).
1,25-Dihydroxyvitamin D3 receptor measurement in primary renal cell carcinomas and autologous normal kidney tissue. (1988)

Recently it was reported that 1-alpha,25-dihydroxyvitamin D3 [1,25-(OH)2D3] inhibited cell growth in a cell line derived from a metastasis from renal cell carcinoma. We have examined samples from 23 primary renal cell carcinomas for 1,25-(OH)2D3 receptor content, and compared it with the concentrations in autologous normal kidney tissue. Nineteen of 23 (83%) renal cell carcinomas had detectable (above 1 fmol/mg protein) 1,25-(OH)2D3 receptor levels, and 15 of 23 (65%) had levels above 5 fmol/mg protein. Mean value for the renal cell carcinomas was 8.2 fmol/mg protein (range, 0-28 fmol/mg protein), and the mean value for autologous normal kidney tissue was 23.1 fmol/mg protein (range, 6.6-53.7 fmol/mg protein). The 1,25-(OH)2D3 receptor levels in the renal cell carcinomas were significantly lower than in the autologous normal kidney tissue (P less than 0.001). The 1,25-(OH)2D3 receptor was characterized by sucrose gradient analysis and DNA-cellulose chromatography. The features found for renal cell carcinoma were similar to the 1,25-(OH)2D3 receptor in normal human tissue. No correlation of 1,25-(OH)2D3 receptor levels to clinical parameters was found. This study shows that carcinomas originating from the kidney, the major vitamin D regulating organ, usually contain the 1,25-(OH)2D3 receptor. The receptor may have a cellular function in the transformed cell.
Microfabricated glucose sensor based on single-walled carbon nanotubes (2004)

This paper describes a novel glucose sensor that uses the hydrogen-specific gas sensing capability of single walled carbon nanotubes (SWCNTs) assembled on microelectrodes. Highly specific glucose sensing was demonstrated using buffered sample solutions with clinically significant concentrations. The proposed approach enables a simple but powerful bio-sensor reliably operating with a completely new principle, and opens up novel device applications where functional nano-components are integrated into a bioMEMS device.
A switching circuit scheme for a satellite site diversity system (2003)

Problems connected with a satellite site diversity system (SDS) i.e., diversity synchronization, diversity switching control, and interconnection of two diversity antenna sites are discussed, and different solutions are considered. A preliminary baseline for the SDS includes circuit solutions for the alignment and switching equipment using elastic memories, the choice of beacon signal attenuation as a quality parameter, and the adoption of an error-free optical-fiber link between the two diversity stations. As an example, the implementation of the SDS relative to the experimental Olympus satellite is presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Dual Leucine Zipper-bearing Kinase (DLK) Activates p46SAPK and p38 but Not ERK2 (1996)

Because the catalytic domain of dual leucine zipper-bearing kinase (DLK) bears sequence similarity to members of the mitogen-activated protein (MAP) kinase kinase kinase subfamily, this protein kinase was investigated for its ability to activate MAP kinase pathways. When transiently transfected and overexpressed in either COS 7 cells or NIH3T3 cells, wild type DLK potently activated p46(SAPK) (SAPK/JNK) but had no detectable effect in activating p42/44(MAPK). DLK also activated p38(mapk) when overexpressed in NIH3T3 cells. A catalytically inactive point mutant of DLK had no effect in these experiments. Consistent with its specificity in activating SAPK, DLK activated Elk-1 but not Sap1a-mediated transcription. In NIH3T3 cells, activation of SAPK by v-Src was markedly attenuated by coexpression of K185A, a catalytically inactive mutant of DLK, suggesting that this mutant could function in a dominant negative fashion in a pathway that leads from v-Src to SAPKs. In a series of co-transfection experiments, activation of p46(SAPK) by DLK was not inhibited by dominant negative mutants of Rac1 and Cdc42Hs, PAK65-R, or PAK65-A, but was attenuated by MEKK1(K432M). DLK(K185A) did not inhibit the ability of constitutively active MEKK1 to activate SAPK. Moreover, K185A significantly inhibited the activation of SAPK by constitutively active V-12 Rac1 and V-12 Cdc42Hs. These results suggest that DLK lies distal to Rac1 and/or Cdc42Hs but proximal to MEKK1 in a pathway leading from v-Src to SAPKs activation.
Fondaparinux for the treatment of suspected heparin-induced thrombocytopenia: a propensity score–matched study (2014)

Current guidelines for heparin-induced thrombocytopenia (HIT) management recommend heparin cessation and switching to a nonheparin anticoagulant (ie, argatroban, danaparoid) upon clinical suspicion. Fondaparinux may be effective but information supporting its use is limited. We retrospectively evaluated 239 patients who received a nonheparin anticoagulant (fondaparinux = 133, danaparoid = 59, and argatroban = 47) for suspected or confirmed HIT. A propensity score was constructed based on age, gender, creatinine, 4T scores, and comorbidity index, and used to match 133 patients to 60 controls. Outcomes were thrombosis or thrombosis-related death and major bleeding. In the matched population there were 22 (16.5%) episodes of thromboses in the fondaparinux group and 13 (21.4%) in the control group (χ(2) P = .424). Bleeding was observed in 28 (21.1%) patients in the fondaparinux group compared with 12 (20%) in the control group (χ(2) P = .867). Survival analysis, and subgroup and unmatched analyses showed similar results. In the fondaparinux group, 60% of patients received prophylactic doses. Fondaparinux has similar effectiveness and safety as argatroban and danaparoid in patients with suspected HIT. Prophylactic fondaparinux doses seem to be effective if no indication for full anticoagulation exists.
Prostate-specific membrane antigen (PSMA) enzyme activity is elevated in prostate cancer cells (2000)

Prostate carcinogenesis is associated with an elevation in PSMA and PSMA' enzyme activity. In contrast, no such enhancement in PSMA activity is observed with benign neoplastic changes in BPH. Thus, the enhancement observed in prostate cancer is not simply related to a generalized prostatic hyperplasia, but is specific to its malignancy.
Organization of the murine and human interleukin-7 receptor genes: two mRNAs generated by differential splicing and presence of a type I-interferon-inducible promoter. (1991)

To better understand the regulation of interleukin-7 receptor (IL-7R) expression, we have pursued a detailed analysis of the structure of the murine and human IL-7R genes. The genes consist of eight exons, the sizes of which are conserved in mouse and human cells, spread out over 24 kbp (murine) and 19 kbp (human). A differential splicing event results in an mRNA encoding a secreted form of the human IL-7R gene. Primer extension and S1 nuclease analysis show a single transcriptional start site for the murine IL-7R gene. The 5'-flanking region of the murine IL-7R gene contains TATA- and CAAT-like sequences. The promoter region also contains a functional interferon regulatory element, to which the interferon-induced nuclear factors IRF-1 and IRF-2 are capable of binding and which is able to confer interferon-inducible expression on a heterologous gene. There are also potential binding sites for the transcription factors AP-1 and AP-2 as well as multiple glucocorticoid response elements. A fusion gene containing 2.5 kb of murine IL-7R 5' regulatory sequence linked to the bacterial chloramphenicol acetyltransferase gene directed expression of chloramphenicol acetyltransferase activity in murine pre-B-cell line 70Z/3 but not in the mouse fibroblast cell line NIH 3T3. Comparison of the murine and human IL-7R exon/intron boundaries with those of other hematopoietin receptor superfamily members whose exon/intron boundaries are also known reveals a conserved evolutionary structure.
Perilipin, a major hormonally regulated adipocyte-specific phosphoprotein associated with the periphery of lipid storage droplets (1991)

The lipid fraction ("fat cake") of rat epididymal adipocytes contains a prominent phosphoprotein (62 kDaapp by sodium dodecyl sulfate-polyacrylamide gel electrophoresis) that is multiply phosphorylated by cAMP-dependent protein kinase in vivo, at which point it migrates as a 65/67-kDaapp doublet by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and is by far the most heavily radiolabeled protein in the cell. Western blot analysis of various tissues with immunopurified antibodies purified from antisera raised against the 62-kDa species suggests that the protein is specific for adipocytes. This protein, which we term perilipin, is found in differentiated cultured 3T3-L1 adipocytes, but not in their precursor 3T3-L1 fibroblasts. Immunocytochemical studies with specific antiserum shows that the perilipin is closely associated with the periphery of lipid storage droplets in cultured adipocytes. Given its adipocyte specificity, acute regulation by hormones, and subcellular location, we speculate that perilipin plays a role in the specialized lipid storage function of adipocytes.
A Review of: “Bassam Tibi:Islam Between Culture and Politics, Second Edition” (2007)

Bassam Tibi's account of the politicization of Islam is a thoughtful attempt to bring clarity from a social science perspective to the different roles of culture, ideology, and religion in the Musl...
Modelling of high dynamic range logarithmic CMOS image sensors (2004)

The quality of the output images from high dynamic range logarithmic sensors is limited by fixed pattern noise (FPN) which is caused by device mismatches within pixels in an array. It leads to inferior image quality in comparison to image from other sensors of similar resolution. Previous design and post-chip attempts to correct this type of noise have been either impractical or resulted in other complexities. However, FPN correction can be attempted using an accurate model approach for the response of this type of pixel. A three parameter model, previously suggested for logarithmic pixels, has been tried for this purpose. In this paper a simple parameter extraction procedure is proposed using this model to calibrate and correct FPN. The result is a model that works well over six decades of illumination but fails at high photocurrents. It is shown that this is caused by a breakdown in an assumption used to create the three parameter models. Consequently, a new four parameter model is developed that fits the data over six decades, and is usable in FPN correction for many wide current range applications that require complete and accurate characterisation.