gebhart/patrepeval huggingface dataset:
The Coronavirus Spike Protein Is a Class I Virus Fusion Protein: Structural and Functional Characterization of the Fusion Core Complex (2003)

Coronavirus entry is mediated by the viral spike (S) glycoprotein. The 180-kDa oligomeric S protein of the murine coronavirus mouse hepatitis virus strain A59 is posttranslationally cleaved into an S1 receptor binding unit and an S2 membrane fusion unit. The latter is thought to contain an internal fusion peptide and has two 4,3 hydrophobic (heptad) repeat regions designated HR1 and HR2. HR2 is located close to the membrane anchor, and HR1 is some 170 amino acids (aa) upstream of it. Heptad repeat (HR) regions are found in fusion proteins of many different viruses and form an important characteristic of class I viral fusion proteins. We investigated the role of these regions in coronavirus membrane fusion. Peptides HR1 (96 aa) and HR2 (39 aa), corresponding to the HR1 and HR2 regions, were produced in Escherichia coli. When mixed together, the two peptides were found to assemble into an extremely stable oligomeric complex. Both on their own and within the complex, the peptides were highly alpha helical. Electron microscopic analysis of the complex revealed a rod-like structure approximately 14.5 nm in length. Limited proteolysis in combination with mass spectrometry indicated that HR1 and HR2 occur in the complex in an antiparallel fashion. In the native protein, such a conformation would bring the proposed fusion peptide, located in the N-terminal domain of HR1, and the transmembrane anchor into close proximity. Using biological assays, the HR2 peptide was shown to be a potent inhibitor of virus entry into the cell, as well as of cell-cell fusion. Both biochemical and functional data show that the coronavirus spike protein is a class I viral fusion protein.
Cell cycle–dependent expression of CXC chemokine receptor 3 by endothelial cells mediates angiostatic activity (2001)

Endothelial cell receptors for the angiostatic chemokines IFN-gamma-inducible protein of 10 kDa (IP-10) and monokine induced by IFN-gamma (Mig) have not yet been identified, and the mechanisms responsible for the effects of these chemokines on angiogenesis are still unclear. IP-10 and Mig share a common functional receptor on activated T lymphocytes, named CXC chemokine receptor 3 (CXCR3). Using in situ hybridization and immunohistochemistry, we show that CXCR3 is expressed by a small percentage of microvascular endothelial cells in several human normal and pathological tissues. Primary cultures of human microvascular endothelial cells (HMVECs) likewise express CXCR3, although this expression is limited to the S/G2-M phase of their cell cycle. Both IP-10 and Mig, as well as the IFN-gamma-inducible T-cell alpha chemoattractant (I-TAC), which all share high-affinity binding for CXCR3, block HMVEC proliferation in vitro, an effect that can be inhibited by an anti-CXCR3 antibody. These data provide definitive evidence of CXCR3 expression by HMVEC and open new avenues for therapeutic interventions in all conditions in which an angiostatic effect may be beneficial.
A systematic review of the role of human papillomavirus testing within a cervical screening programme. (1999)

T he overall aim of the NHS R&D Health Technology Assessment (HTA) programme is to ensure that high-quality research information on the costs, effectiveness and broader impact of health technologies is produced in the most efficient way for those who use, manage and work in the NHS. Research is undertaken in those areas where the evidence will lead to the greatest benefits to patients, either through improved patient outcomes or the most efficient use of NHS resources.
The future of research at the Department of Veterans Affairs (1992)

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On sparse reconstruction from Fourier and Gaussian measurements (2007)

Abstract This paper improves upon best‐known guarantees for exact reconstruction of a sparse signal f from a small universal sample of Fourier measurements. The method for reconstruction that has recently gained momentum in the sparse approximation theory is to relax this highly nonconvex problem to a convex problem and then solve it as a linear program. We show that there exists a set of frequencies Ω such that one can exactly reconstruct every r ‐sparse signal f of length n from its frequencies in Ω, using the convex relaxation, and Ω has size A random set Ω satisfies this with high probability. This estimate is optimal within the log log n and log 3 r factors. We also give a relatively short argument for a similar problem with k ( r, n ) ≈ r [12 + 8 log( n / r )] Gaussian measurements. We use methods of geometric functional analysis and probability theory in Banach spaces, which makes our arguments quite short. © 2007 Wiley Periodicals, Inc.
Methylation-Controlled J Protein Promotes c-Jun Degradation To Prevent ABCB1 Transporter Expression (2007)

Methylation-controlled J protein (MCJ) is a newly identified member of the DnaJ family of cochaperones. Hypermethylation-mediated transcriptional silencing of the MCJ gene has been associated with increased chemotherapeutic resistance in ovarian cancer. However, the biology and function of MCJ remain unknown. Here we show that MCJ is a type II transmembrane cochaperone localized in the Golgi network and present only in vertebrates. MCJ is expressed in drug-sensitive breast cancer cells but not in multidrug-resistant cells. The inhibition of MCJ expression increases resistance to specific drugs by inducing expression of the ABCB1 drug transporter that prevents intracellular drug accumulation. The induction of ABCB1 gene expression is mediated by increased levels of c-Jun due to an impaired degradation of this transcription factor in the absence of MCJ. Thus, MCJ is required in these cells to prevent c-Jun-mediated expression of ABCB1 and maintain drug response.
Growth Hormone in Vivo Potentiates the Stimulatory Effect of Insulin-Like Growth Factor-1 in Vitro on Colony Formation of Epiphyseal Chondrocytes Isolated from Hypophysectomized Rats* (1987)

The effect of GH pretreatment in vivo on the colony formation of epiphyseal chondrocytes from hypophysectomized rats and the subsequent responsiveness to insulin-like growth factor (IGF-I) was studied in vitro. Chondrocytes from epiphyseal growth plates of the proximal tibia of 36-day-old hypophysectomized rats were enzymatically isolated and cultured in suspension, stabilized with agarose (0.5%) in Ham's F-12 medium and serum supplement. After 14 days the cultures were terminated and screened for cloning efficiency (number of colonies with a diameter greater than 56 microns/1000 seeded cells) and for distribution of cloning efficiency as a function of colony size. Pretreatment with human GH in vivo for 24 h (10 micrograms X 3) increased the cloning efficiency during the subsequent culture period (control, 1.5 +/- 0.1; human GH, 4.4 +/- 0.3). Addition of IGF-I to the chondrocyte cultures from control rats caused a slight increase in cloning efficiency (control, 1.5 +/- 0.1; IGF-I, 2.2 +/- 0.3) but caused a marked increase in chondrocyte cultures from GH-pretreated rats (control, 4.4 +/- 0.4; IGF-I, 8.2 +/- 0.9). The cloning efficiency was increased 12 and 24 h, but not 4 h, after start of GH-treatment in vivo. The increased responsiveness to IGF-I in vivo showed a similar time course after GH pretreatment. The distribution of cloning efficiency was altered in cultures of chondrocytes isolated from the GH-pretreated rats; large colonies were overrepresented in the GH-treated group. Colonies with a diameter exceeding 180 microns were only seen in cultures of chondrocytes isolated from the GH-pretreated animals. Addition of IGF-I in vitro did not alter the distribution of cloning efficiency, but increased the mean colony size of all colonies. Pretreatment of the rats with two different doses of IGF-I in vivo for 24 h (5 micrograms X 3 or 50 micrograms X 3) had a slight stimulatory effect on subsequent colony formation, but no potentiation of IGF-I in vitro was demonstrated. The results of the present study show that pretreatment of hypophysectomized rats with GH, but not with IGF-I, promotes the formation of chondrocyte colonies and make the chondrocytes susceptible to IGF-I in vitro. The results suggest that GH induces colony formation by IGF-I-independent mechanisms and that IGF-I is a second effector in GH action as previously shown for cultured 3T3-preadipose cells.(ABSTRACT TRUNCATED AT 400 WORDS)
Characteristics of a small planar loop antenna (1997)

Small planar-type loop antennas used in pagers have fixed directivity patterns. As a result, the received signal strength depends on the orientation of the antenna. A new type of small planar loop antenna (PLA) is, therefore, proposed. The position of the conductor posts can be changed and MOSFETs are adopted for switching the conductor posts. If the positions of the posts can be switched at will, then the dependence of the received signal on the orientation of the antenna can be minimized. Fundamental experiments were performed in order to investigate the characteristics of polarization switching. Polarization directivity was measured while switching each conductor alternately. The receiving characteristics are affected by a cable connected to the receiver. Therefore, the transmission characteristics are measured by using an internal oscillator. As a result, meaningful results were obtained and the possibility of polarization diversity was shown.
Mouse models for human hair loss disorders (2003)

The outer surface of the hand, limb and body is covered by the epidermis, which is elaborated into a number of specialized appendages, evolved not only to protect and reinforce the skin but also for social signalling. The most prominent of these appendages is the hair follicle. Hair follicles are remarkable because of their prolific growth characteristics and their complexity of differentiation. After initial embryonic morphogenesis, the hair follicle undergoes repeated cycles of regression and regeneration throughout the lifetime of the organism. Studies of mouse mutants with hair loss phenotypes have suggested that the mechanisms controlling the hair cycle probably involve many of the major signalling molecules used elsewhere in development, although the complete pathway of hair follicle growth control is not yet understood. Mouse studies have also led to the discovery of genes underlying several human disorders. Future studies of mouse hair-loss mutants are likely to benefit the understanding of human hair loss as well as increasing our knowledge of mechanisms controlling morphogenesis and tumorigenesis.
Extracellular Matrices and Polypeptide Growth Factors as Mediators of Functions of Cells of the Periodontium (1987)

This is a review of the interactions between cells and their extracellular matrices and polypeptide growth factors. The review not only attempts to provide a basic understanding of the functions of extracellular matrices and polypeptide growth factors but, in addition, suggests the role these biological molecules may play in periodontal regeneration. It is conceivable that future periodontal therapy will include the treatment of a scaled root with biological response modifiers to predictably attain a true new connective tissue attachment.
Mycobacterium tuberculosis LprG ( Rv1411c ): A Novel TLR-2 Ligand That Inhibits Human Macrophage Class II MHC Antigen Processing (2004)

MHC class II (MHC-II)-restricted CD4(+) T cells are essential for control of Mycobacterium tuberculosis infection. This report describes the identification and purification of LprG (Rv1411c) as an inhibitor of primary human macrophage MHC-II Ag processing. LprG is a 24-kDa lipoprotein found in the M. tuberculosis cell wall. Prolonged exposure (>16 h) of human macrophages to LprG resulted in marked inhibition of MHC-II Ag processing. Inhibition of MHC-II Ag processing was dependent on TLR-2. Short-term exposure (<6 h) to LprG stimulated TLR-2-dependent TNF-alpha production. Thus, LprG can exploit TLR-2 signaling to inhibit MHC-II Ag processing in human macrophages. Inhibition of MHC-II Ag processing by mycobacterial lipoproteins may allow M. tuberculosis, within infected macrophages, to avoid recognition by CD4(+) T cells.
Rat alpha-lactalbumin has a 17-residue-long COOH-terminal hydrophobic extension as judged by sequence analysis of the cDNA clones. (1981)

cDNA for rat alpha-lactalbumin has been cloned in bacterial plasmid, and its sequence has been analyzed. The DNA sequence analysis shows that rat alpha-lactalbumin has 17 extra residues beyond the COOH terminus of the alpha-lactalbumin isolated and sequenced to date from other species. The predicted COOH-terminal sequence is hydrophobic and proline rich and bears some resemblance to beta-casein sequences.
Determining Soil Water Flux and Pore Water Velocity by a Heat Pulse Technique (2000)

A method is presented for measuring soil water flux density ( J ) with a thermo‐TDR (time domain reflectometry) probe. Constant heat input during a small time interval (15 s) is used to emit a heat pulse from a line heat source. Asymmetry in the thermal field near the heat source is quantified by computing the maximum dimensionless temperature difference (MDTD) between upstream and downstream locations. Heat transfer theory was used to relate MDTD to J A thermo‐TDR probe was used to obtain measurements of MDTD in water‐saturated soil materials of different textures (sand, sandy loam, and clay loam) with imposed water flux densities ranging from 1.16 × 10 −5 to 6.31 × 10 −5 m 3 m −2 s −1 A nearly linear relationship between measured MDTDs and fluxes was observed for all soil materials. Measured and predicted MDTDs agreed well for flow experiments in sand. Greater discrepancies were observed for flow experiments in sandy loam and clay loam. Despite the lack of universal agreement between measured and predicted MDTDs, the experimental results indicate that the proposed method may provide a useful means of measuring J The method presented herein improves upon earlier methods by reducing distortion of the water flow field and minimizing heat‐induced soil water redistribution. Because the thermo‐TDR probe can be used to make TDR‐based measurements of volumetric water content (θ), the proposed method also may permit measurement of pore water velocity ( J /θ).
PCR candidate region mismatch scanning: adaptation to quantitative, high-throughput genotyping (2001)

Linkage and association analyses were performed to identify loci affecting disease susceptibility by scoring previously characterized sequence variations such as microsatellites and single nucleotide polymorphisms. Lack of markers in regions of interest, as well as difficulty in adapting various methods to high-throughput settings, often limits the effectiveness of the analyses. We have adapted the Escherichia coli mismatch detection system, employing the factors MutS, MutL and MutH, for use in PCR-based, automated, high-throughput genotyping and mutation detection of genomic DNA. Optimal sensitivity and signal-to-noise ratios were obtained in a straightforward fashion because the detection reaction proved to be principally dependent upon monovalent cation concentration and MutL concentration. Quantitative relationships of the optimal values of these parameters with length of the DNA test fragment were demonstrated, in support of the translocation model for the mechanism of action of these enzymes, rather than the molecular switch model. Thus, rapid, sequence-independent optimization was possible for each new genomic target region. Other factors potentially limiting the flexibility of mismatch scanning, such as positioning of dam recognition sites within the target fragment, have also been investigated. We developed several strategies, which can be easily adapted to automation, for limiting the analysis to intersample heteroduplexes. Thus, the principal barriers to the use of this methodology, which we have designated PCR candidate region mismatch scanning, in cost-effective, high-throughput settings have been removed.
Advances in target design for heavy ion fusion (2005)

Over the past few years, the emphasis in heavy ion target design has moved from the distributed radiator target to the 'hybrid' target because the hybrid target allows a larger beam focal spot than the distributed radiator ({approx} 5 mm radius rather than {approx} 2 mm radius). The larger spot relaxes some of the requirements on the driver, but introduces some new target physics issues. Most notable is the use of shine shields and shims in the hohlraum to achieve symmetry rather than achieving symmetry by beam placement. The shim is a thin layer of material placed on or near the capsule surface to block a small amount of excess radiation. While we have been developing this technique for the heavy ion hybrid target, the technique can be used in any indirect drive target. We have begun testing the concept of a shim to improve symmetry using a double-ended z-pinch hohlraum on the Sandia Z-machine. Experiments using shimmed thin wall capsules have shown that we can reverse the sign of a P{sub 2} asymmetry and significantly reduce the size of a P{sub 4} asymmetry. These initial experiments demonstrate the concept of a shim as another method for controlling early time asymmetries in ICF capsules.
Milk sialyllactose influences colitis in mice through selective intestinal bacterial colonization (2010)

Milk oligosaccharides contribute to the development of the intestinal environment by acting as decoy receptors for pathogens and as prebiotics, which promote the colonization of commensal bacteria. Here, using α2,3- and α2,6-sialyltransferase-deficient mice, we investigated the role of the sialylated milk oligosaccharides sialyl(α2,3)lactose and sialyl(α2,6)lactose on mucosal immunity. The exposure of newborn mice to milk containing or deficient in sialyllactose had no impact on the development of mucosal leukocyte populations. However, when challenged by dextran sulfate sodium (DSS) in drinking water, adult mice that had been fostered on sialyl(α2,3)lactose-deficient milk were more resistant to colitis compared with mice fostered on normal milk or sialyl(α2,6)lactose-deficient milk. Analysis of intestinal microbiota showed different colonization patterns depending on the presence or absence of sialyl(α2,3)lactose in the milk. Germ-free mice reconstituted with intestinal microbiota isolated from mice fed on sialyl(α2,3)lactose-deficient milk were more resistant to DSS-induced colitis than germ-free mice reconstituted with standard intestinal microbiota. Thus, exposure to sialyllactose during infancy affects bacterial colonization of the intestine, which influences the susceptibility to DSS-induced colitis in adult mice.
Digital terrestrial television broadcasting with OFDM - a study on the performance of single frequency networks (1996)

OFDM is expected to be a suitable modulation method for digital terrestrial broadcasting systems. One of the reasons is that it makes it possible to construct a single frequency network (SFN) and to make effective use of the frequency bands. In a SFN environment, however, some receivers will obtain their signals from more than one transmitter. This causes two effects, intersymbol interference and degradation of frequency characteristics due to echoes. This paper describes a theoretical study on the latter effect in a variety of signal numbers, D/U ratios and delays arriving at the receiving antenna and the BER (bit error rate) distribution within the coverage area of SFNs in a variety of the transmitter numbers with computer simulations on a virtual plain. Finally we suggest a method to improve the quality in a coverage area.
Efficacy of Two Sputum Collection Techniques in Patients with Air Flow Obstruction (1999)

Sputum collection is equally efficacious by the induced method and the home collection method. A learning effect was responsible for the increased yield of sputum abnormalities in the second collection session. Sputum collection at home may facilitate the amount of dysplasic and neoplastic bronchial epithelial changes in heavy smokers with COPD.
Low temperature direct bonding of silicon and silicon dioxide by the surface activation method (2002)

Low temperature bonding of Si and SiO/sub 2/ by the surface modification in a vacuum was examined. For the bonding of Si wafers, surface cleaning by Ar beam etching was effective to improve the bonding prepared in the vacuum at room temperature. The strength was equivalent to that of conventional wafer bonding with high temperature annealing. For the bonding of SiO/sub 2/ both Ar beam and H/sub 2/O beam treatment were applied. SiO/sub 2/ bonding strength was about a half of Si bonding. The influence of surface oxidation was also examined by exposing etched Si surface to residual gas in a vacuum chamber. Long time exposure before bonding caused the reduction of bonding strength. These results mean that oxidized surface has less bonding ability than clean surface etched by Ar beam at the room temperature.
Mobile monitoring with wearable photoplethysmographic biosensors (2003)

We address both technical and clinical issues of wearable biosensors (WBS). First, design concepts of a WBS are presented, with emphasis on the ring sensor developed by the author's group at MIT. The ring sensor is an ambulatory, telemetric, continuous health-monitoring device. This WBS combines miniaturized data acquisition features with advanced photoplethysmographic (PPG) techniques to acquire data related to the patient's cardiovascular state using a method that is far superior to existing fingertip PPG sensors. In particular, the ring sensor is capable of reliably monitoring a patient's heart rate, oxygen saturation, and heart rate variability. Technical issues, including motion artifact, interference with blood circulation, and battery power issues, are addressed, and effective engineering solutions to alleviate these problems are presented. Second, based on the ring sensor technology the clinical potentials of WBS monitoring are addressed.
Molecular basis of valine resistance in Escherichia coli K-12. (1981)

The relationship of valine resistance to the expression of the ilvGEDA operon of Escherichia coli K-12 has been determined. DNA sequence and in vivo protein analyses indicate that in wild-type E. coli K-12 there is a frameshift site within the gene (ilvG) for valine resistance. The ilvG+2096 (formerly designated ilv02096) mutation displaces this frameshift site, resulting in the expression of ilvG and the relief of transcriptional polarity on the distal genes of this operon. Thus, the "ilv0" mutation, which concomitantly confers valine resistance and increased expression of the ilvEDA genes, is, in fact, the "reversion" of a polar site within the first structural gene of the ilvGEDA operon.