gebhart/patrepeval huggingface dataset:
Accelerating the secondary immune response by inactivating CD4+CD25+ T regulatory cells prior to BCG vaccination does not enhance protection against tuberculosis (2008)

CD4(+)CD25(+) natural T regulatory cells (Tregs) have been shown to suppress protective immune responses in several different vaccination models. Since the effect of Tregs on vaccination against tuberculosis (Tb) was unknown, we used a murine model to investigate whether natural Tregs suppress the development of protective immunity following Mycobacterium bovis bacille Calmette-Guérin (BCG) vaccination. Using a monoclonal antibody against CD25, natural Tregs were inactivated prior to vaccination with BCG. The primary immune response was evaluated after BCG vaccination and the secondary immune response was assessed after an intranasal BCG challenge 42 days after vaccination. Inactivation of natural Tregs prior to vaccination led to an increased immune response 14 days after vaccination, increased numbers of antigen-responsive lymphocytes immediately prior to secondary challenge and the earlier appearance of IFN-gamma-producing CD4(+) and CD8(+) lymphocytes in the draining lymph nodes and lungs after challenge. Despite this, protection from virulent Mycobacterium tuberculosis or M. bovis aerosol challenge was unaffected by natural Treg inactivation prior to BCG vaccination. This suggests that increasing the primary and accelerating the secondary immune responses by inactivating natural Tregs at the time of vaccination, does not affect the development of protective immunity to Tb.
Fast Variable Block Size Motion Estimation for H.264 Using Likelihood and Correlation of Motion Field (2006)

Variable block size motion compensation has been adopted by the emerging video coding standard H.264. It can represent the motion characteristic in a macroblock more accurately and, therefore, reduces the prediction error to achieve high compression gains. On the other hand, it causes high computational complexity in motion estimation at the encoder. The motion estimation exhaustively performed over all modes to find the best mode for inter coding is slow and computationally involved. In order to reduce the complexity, we proposed a fast inter mode decision algorithm for H.264 encoder. The proposed method efficiently determines a suitable block mode according to the motion field distribution and correlation within a macroblock. The experimental results show that the proposed method reduces a considerable amount of complexity at encoder, while the rate-distortion performance of the proposed method is comparable to that of full mode search
ETS Family Proteins Activate Transcription from HIV-1 Long Terminal Repeat (1993)

ets is a multigene family and its members share a common ETS DNA-binding domain. ETS proteins activate transcription via binding to a purine-rich GGAA core sequence located in promoters/enhancers of various genes, including several that are transcriptionally active in T cells. The ETS1, ETS2, and ERBG/Hu-FLI-1 gene expression pattern also suggests a role for these genes in cells of hematopoietic lineage. The HIV-1 LTR core enhancer contains two 10-base pair direct repeat sequences (left and right) that are required for regulation of HIV-1 mRNA expression by host transcription factors, including NF kappa B. Two ETS-binding sites are present in the core enhancer of all the HIV-1 isolates reported so far. In our studies, we utilized HIV-1 HXB2 and HIV-1 Z2Z6 core enhancers because the Z2Z6 strain has a single point mutation flanking the right ETS-binding site. We demonstrate that the ETS1, ETS2, and ERGB/Hu-FLI-1 proteins can trans-activate transcription from both the HXB2 and Z2Z6 core enhancer when linked to a reporter (cat) gene. In addition, we show that the DNA binding and trans-activation with the Z2Z6 core enhancer is at least 40-fold higher than that observed with the HXB2 core enhancer. Further, we provide evidence that the marked increase in binding and trans-activation with Z2Z6 core enhancer sequences is due to the substitution of a flanking T residue in HXB2 TGGAA) by a C residue in Z2Z6 (CGGAA) isolate, thus generating an optimal ETS-binding core (CGGAA) sequence.
Pseudomonas aeruginosa Reveals High Intrinsic Resistance to Penem Antibiotics: Penem Resistance Mechanisms and Their Interplay (2001)

Pseudomonas aeruginosa exhibits high intrinsic resistance to penem antibiotics such as faropenem, ritipenem, AMA3176, sulopenem, Sch29482, and Sch34343. To investigate the mechanisms contributing to penem resistance, we used the laboratory strain PAO1 to construct a series of isogenic mutants with an impaired multidrug efflux system MexAB-OprM and/or impaired chromosomal AmpC beta-lactamase. The outer membrane barrier of PAO1 was partially eliminated by inducing the expression of the plasmid-encoded Escherichia coli major porin OmpF. Susceptibility tests using the mutants and the OmpF expression plasmid showed that MexAB-OprM and the outer membrane barrier, but not AmpC beta-lactamase, are the main mechanisms involved in the high intrinsic penem resistance of PAO1. However, reducing the high intrinsic penem resistance of PAO1 to the same level as that of penem-susceptible gram-negative bacteria such as E. coli required the loss of either both MexAB-OprM and AmpC beta-lactamase or both MexAB-OprM and the outer membrane barrier. Competition experiments for penicillin-binding proteins (PBPs) revealed that the affinity of PBP 1b and PBP 2 for faropenem were about 1.8- and 1.5-fold lower, than the respective affinity for imipenem. Loss of the outer membrane barrier, MexAB, and AmpC beta-lactamase increased the susceptibility of PAO1 to almost all penems tested compared to the susceptibility of the AmpC-deficient PAO1 mutants to imipenem. Thus, it is suggested that the high intrinsic penem resistance of P. aeruginosa is generated from the interplay among the outer membrane barrier, the active efflux system, and AmpC beta-lactamase but not from the lower affinity of PBPs for penems.
A Technical Evaluation of Lidar‐Based Measurement of River Water Levels (2020)

Abstract Measuring river water level (stage) is key for a variety of applications including discharge estimation and flood prediction. Although a variety of in situ and noncontact methods are available, there is an urgent need for new and more cost‐efficient methods. Rapid technological progress has accelerated the use of noncontact methods and development of time‐of‐flight distance sensors. Among available techniques, the use of lidar for distance measurement is promising because of its low cost, high energy efficiency, and small measurement footprint. However, lidar has rarely been used to measure water levels. Here we test a near‐infrared (905 nm) lidar sensor to determine its suitability for stage measurements under a range of environmental conditions. Using different laboratory and field setups, we assess sensor performance as a function of measurement distance, surface roughness, air temperature, water turbidity, and measurement angle. Despite the low reflectivity of water for infrared radiation, we find that the tested sensor is able to take measurements under all tested conditions, up to an incidence angle of ∼40°. The accuracy of the sensor is within the technical specifications of the device and is characterized by a relative error of around 0.1%. We find a strong dependence of the accuracy on sensor temperature, which we attribute to suboptimal internal compensation of the electronics. The precision of the sensor decreases with increasing measured distance and increases with surface roughness of the water body. We did not find any significant impact of water turbidity on the measurements.
Fluorinated Coatings and Films: Motivation and Significance (2001)

Fluorinated surfaces are sought for a number of technologies requiring low surface energy, low adhesion, chemical robustness, among other desired properties. Bulk fluorinated materials (e.g., polymers) can be used, but their relative expense and difficult processing problems preclude widespread application. Small molecule perfluorinated precursors are popular film-forming materials but, without crosslinking or stabilization in situ, lack the durability of higher molecular weight materials. Methods to fabricate perfluorinated coatings and films to impart the desirable properties of perfluorocarbons where they are most needed, without the disadvantages of handling and applying bulk perfluorinated materials are described in this volume. This chapter attempts to introduce the reader to the issues and general strategies described in detail in the following chapters.
Reporting of medical errors: An intensive care unit experience (2004)

Medical errors appear to be common among patients requiring intensive care. Medical events resulting in an error can result in the need for additional life-sustaining treatments and, in some circumstances, can contribute to patient death. Patient healthcare providers appear to be in a unique position to identify medical errors. Institutions should develop formalized methods for the reporting and analysis of medical errors to improve patient care.
Severe combined immunodeficient mice engrafted with human splenocytes have functional human T cells and reject human allografts. (1994)

Previous studies have shown that human hemopoietic cells can be adoptively transferred into immunodeficient C.B-17 scid/scid (SCID) mice that lack autologous T and B lymphocytes, to generate chimeric animals. The future development of novel immunomodulatory drugs in transplantation will depend increasingly on experimental animal models to investigate the properties of the agents on human cells before starting clinical trials. However, in previous models of SCID mice engrafted with human PBLs, human T cells have been found either to be in an unresponsive state, unable to respond to mitogenic stimulations in vitro, or to mediate skin graft rejection only when HLA-primed in vivo before their adoptive transfer into SCID mice. In addition, T cells and other leukocyte subsets engraft quite poorly in the lymphoid tissues of the animals. In an attempt to develop a useful model for transplantation research, we have inoculated SCID mice with fresh human splenocytes from cadaveric organ donors (hu-Spl-SCID mice). In this model, various leukocyte subsets engraft effectively in different lymphoid compartments. In addition, human T cells retain their proliferative responses to mitogens and to alloantigens when tested 3 wk after engraftment into SCID mice. Finally, mice engrafted with unprimed human spleen cells acutely reject human foreskin allografts. Treatment of hu-Spl-SCID mice with OKT3, an immunosuppressive mAb directed against the human CD3 complex associated with the TCR, prevents the rejection of most human skin allografts, indicating a major role for human T cells in this phenomenon. Thus, this hu-Spl-SCID model may be useful for the study of immunosuppressive therapies in a preclinical in vivo setting.
Corrosion Control Using Polyelectrolyte Multilayers (2002)

The corrosion of stainless steel under anodic conditions in salt solutions was strongly suppressed by an ultrathin layer of polyelectrolyte complex, applied using the layer-by-layer deposition method. Voltammetric scans over a wide potential region, as well as constant potential measurements in the metastable pitting regime, reveal the surprising effectiveness of polyelectrolyte multilayers, both hydrophilic and hydrophobic, at corrosion control, despite the significant water content and ion permeability of the thin film.
Characterization of the receptor to vasculotropin on bovine adrenal cortex-derived capillary endothelial cells. (1990)

Recently a new growth factor was purified to homogeneity, and its bioactivity seemed to be restricted to vascular endothelial derived cells. As it was also angiogenic in vivo, it was provisionally named vasculotropin (VAS). As an iodination procedure used to label VAS did not damage the molecule, it was possible to undertake binding studies. The binding of iodinated vasculotropin to bovine adrenal cortex-derived capillary endothelial cells was saturable at 250 pM, and half-maximal binding occurred at 47 pM. Scatchard's analysis of the data demonstrated two apparent classes of binding sites with apparent dissociation constants of 2 and 82 pM displaying 280 and 3400 binding sites, respectively. The binding was specific; half-displacement was observed with a 2-fold excess of unlabeled VAS. The structurally related platelet-derived growth factor did not compete in a radioreceptor assay. 125I-VAS was displaced by suramin and not by heparin. 125I-VAS was covalently cross-linked to its cell surface receptor on intact bovine adrenal cortex-derived capillary endothelial cells using the homobifunctional agents ethylene glycol bis(succinimidyl succinate) or disuccinimidyl tartarate. A major macromolecular species with an apparent molecular mass of 230,000 Da was labeled under reducing and nonreducing conditions. These data demonstrate the existence of a specific binding protein for VAS and an estimation of the size at 185,000 Da.
Monitoring response to convection-enhanced taxol delivery in brain tumor patients using diffusion-weighted magnetic resonance imaging. (2001)

Convection-enhanced drug delivery (CEDD) is a novel approach to enhance the delivery of drugs directly into brain tumors. We have used diffusion-weighted MRI (DWMRI) to monitor the effects of intratumoral CEDD in three brain tumor patients treated with Taxol. Clear changes in the images and the water diffusion parameters were observed shortly after the initiation of treatment. Initially, a bright area corresponding to decreased diffusion appeared, followed by the appearance of a dark area of increased diffusion within the bright area. The time to appearance of the dark area varied among the patients, suggesting different response rates. In this work, we have demonstrated the feasibility of using DWMRI as a noninvasive tool to achieve unique early tissue characterization not attainable by other conventional imaging methods.
Expression of an epitope by surface glycoproteins ofCandida albicans. Variability among species, strains and yeast cells of the genusCandida (1990)

Expression of an antigenic epitope reactive with an IgM monoclonal antibody was studied in 253 Candida isolates by direct agglutination. Isolates of Candida albicans reacted significantly more often with the antibody than did isolates of other species. The agglutination scores for C. albicans isolates from sources associated with possible deep-seated Candida infection were significantly higher than for those from other sources. However, there was considerable overlap of scores between these two groups so that the functional significance of the association is uncertain. There were no associations between agglutination score and C. albicans biotype: multiple isolates from individual patients gave similar agglutination scores. Expression of the epitope within colonies of cloned strains was studied by autoradiography of colony blots on nitrocellulose and by immunoperoxidase staining of colonies in situ. It was found that the epitope was expressed variably by portions of colonies of both agglutination-positive and agglutination-negative strains. Indirect immunofluorescence revealed that expression of the epitope at the surface of C. albicans germ tubes and their associated buds was variable from cell to cell. It was not directly related to morphology or stage of growth of the cells.
Expression of Gastrointestinal Glutathione Peroxidase Is Inversely Correlated to the Presence of Hepatitis C Virus Subgenomic RNA in Human Liver Cells (2004)

There is great medical need to develop novel therapies for treatment of human hepatitis C virus (HCV). By gene expression analysis of three HCV-subgenomic RNA replicon cell lines, we identified cellular proteins whose expression is affected by the presence of HCV and therefore may serve as drug targets. Data from cDNA array filter hybridization, as well as from Northern and Western blotting, revealed that the gastrointestinal-glutathione peroxidase (GI-GPx) was drastically down-regulated (up to 20-fold) in all replicon cell lines tested. Concomitantly, total cellular glutathione peroxidase activity was drastically reduced, which rendered these human liver cells more susceptible toward oxidative stress. Interferon alpha caused down-regulation of the HCV-replicon followed by recovery of GI-GPx expression to nearly normal levels. Furthermore, expression of GI-GPx in replicon cells by gene transduction caused down-regulation of HCV RNA in a dose-dependent manner. Moreover, activating the endogenous gene coding for GI-GPx by all-trans-retinoic acid (RA) was sufficient to cause down-regulation of the HCV replicon. A small interfering RNA duplex abrogated GI-GPx up-regulation by RA and concomitantly suppression of HCV. The RA effect was dependent on the presence of sodium selenite, was reversible, and was independent of RNA-activated protein kinase. Taken together, these results show that HCV inhibits the expression of GI-GPx in replicon cells to promote its intracellular propagation. Modulation of GI-GPx activity may open new avenues of treatment for HCV patients.
Isolation and gene expression analysis of Phospholipase C in response to abiotic stresses from Vigna radiata (L.) Wilczek. (2015)

Phosphatidylinositol (PtdIns) is a major phospholipid in eukaryotic cells. Many studies have revealed that the phosphoinositide (PI) signaling pathway plays an important role in plant growth and development. Phospholipase C (PLC) is reported to have a crucial role in the PI pathway. This work focuses on the isolation and investigation of PLC in response to abiotic stress factors in green gram. The PLC cDNA, designated VrPLC, encoding a protein of 591 amino acids was cloned and expressed in E. coli. The predicted isoelectric point (pI) and molecular weight were 5.96 and 67.3 kDa, respectively. The tertiary structure of the PLC was also predicted and found to be mainly composed of random coils. In addition, VrPLC expression analysis was performed under environmental stress and the results showed that the expression of VrPLC was rapidly induced in an abscisic acid independent manner in response to drought and salt stress. PLC expression was found to be up-regulated by SA and down-regulated by wound in leaf tissues; however, there was no significant difference in the expression of PLC in plants subjected to high temperature and H2O2. Our results suggest that a close link/relationship between PLC expression and stress responses in green gram.
Direct detection of verotoxin-producing Escherichia coli in stool samples by PCR (1995)

A method for the rapid detection of verotoxin-producing Escherichia coli in stool samples by PCR was evaluated. Verotoxin-1 and verotoxin-2 genes in DNA extracted directly from stool samples were amplified with oligonucleotide primers. Stools spiked with control organisms, E. coli C600 (H19B) (verotoxin-1) or E. coli C600 (933W) (verotoxin-2), demonstrated that verotoxin-1-containing organisms could be detected at 10(2) CFU per 0.1 g of stool and verotoxin-2-containing organisms could be detected at 10(7) CFU per 0.1 g of stool. Testing of stool samples from patients with diarrhea showed a high concordance between PCR positivity and the presence of verotoxin-producing E. coli, determined by isolation of serotype O157:H7 on sorbitol-MacConkey medium (34 of 35 stool samples) or by colony blots with gene probes (19 of 21 stool samples). Conversely, only 1 of 20 (5.0%) stool samples that were O157:H7 culture negative and colony blot negative and that contained free verotoxin only was positive by PCR. As well, only 4 of 145 (2.8%) stool samples that were negative for serotype O157:H7 or free verotoxin were PCR positive. PCR of DNA extracted directly from stool samples provides a rapid method for the detection of stool samples containing verotoxin-producing E. coli compared with colony blot testing.
A 76-amino acid disulfide loop in the Yersinia pseudotuberculosis invasin protein is required for integrin receptor recognition. (1993)

The Yersinia pseudotuberculosis invasin protein is a 986-amino acid protein that promotes bacterial penetration into mammalian cells by avidly binding multiple beta 1-chain integrins. A 192-amino acid carboxyl-terminal domain of invasin was previously shown to be sufficient for binding. Evidence is presented here that a 76-amino acid disulfide loop in the integrin binding domain of invasin is required for invasin-mediated cell binding and entry. Bacterial mutants that were altered at either of 2 cysteine residues in the binding domain of invasin were completely defective for entry. Purified invasin protein derivatives altered at either of these cysteines, in contrast to the wild-type invasin, did not promote either cell binding or penetration. Analysis of proteolytic products of invasin in the presence or absence of reducing agent provided evidence of an intra-chain disulfide bond near the carboxyl terminus of the protein. Alkylation of invasin derivatives with [3H]iodoacetate indicated that these 2 cysteines were normally disulfide-bonded. A treatment that resulted in the maximal reduction of the disulfide bond also resulted in maximal loss of cell attachment activity. These results indicate that the 76-amino acid disulfide loop at the carboxyl terminus of invasin is required for recognition by integrins.
High molecular weight caldesmon positive stromal cells in the capsule of thyroid follicular tumours and tumour-like lesions (2002)

The presence of HCD+ cells in the capsule is characteristic of thyroid follicular tumours and tumour-like lesions. The stromal cells in the capsule of thyroid follicular tumours and tumour-like lesions are different from those of encapsulated papillary carcinoma.
Automated 2D‐3D registration of a radiograph and a cone beam CT using line‐segment enhancementa) (2006)

The objective of this study was to develop a fully automated two-dimensional (2D)-three-dimensional (3D) registration framework to quantify setup deviations in prostate radiation therapy from cone beam CT (CBCT) data and a single AP radiograph. A kilovoltage CBCT image and kilovoltage AP radiograph of an anthropomorphic phantom of the pelvis were acquired at 14 accurately known positions. The shifts in the phantom position were subsequently estimated by registering digitally reconstructed radiographs (DRRs) from the 3D CBCT scan to the AP radiographs through the correlation of enhanced linear image features mainly representing bony ridges. Linear features were enhanced by filtering the images with "sticks," short line segments which are varied in orientation to achieve the maximum projection value at every pixel in the image. The mean (and standard deviations) of the absolute errors in estimating translations along the three orthogonal axes in millimeters were 0.134 (0.096) AP(out-of-plane), 0.021 (0.023) ML and 0.020 (0.020) SI. The corresponding errors for rotations in degrees were 0.011 (0.009) AP, 0.029 (0.016) ML (out-of-plane), and 0.030 (0.028) SI (out-of-plane). Preliminary results with megavoltage patient data have also been reported. The results suggest that it may be possible to enhance anatomic features that are common to DRRs from a CBCT image and a single AP radiography of the pelvis for use in a completely automated and accurate 2D-3D registration framework for setup verification in prostate radiotherapy. This technique is theoretically applicable to other rigid bony structures such as the cranial vault or skull base and piecewise rigid structures such as the spine.