gebhart/patrepeval huggingface dataset:
Polarization-induced charge and electron mobility in AlGaN/GaN heterostructures grown by plasma-assisted molecular-beam epitaxy (1999)

The formation of the two-dimensional electron gas (2DEG) in unintentionally doped AlxGa1−xN/GaN (x⩽0.31) heterostructures grown by rf plasma-assisted molecular-beam epitaxy is investigated. Low-temperature electrical-transport measurements revealed that the two-dimensional electron gas density strongly depends on both the thickness of the AlGaN layer and alloy composition. The experimental results agree very well with the theoretical estimates of the polarization-induced 2DEG concentrations. Low-temperature electron mobility was found to be much higher in the structures with lower electron sheet densities. Interface roughness scattering or alloy disorder scattering are proposed to be responsible for this trend. A maximum mobility of 51 700 cm2/V s (T=13 K) was obtained in the Al0.09Ga0.91N/GaN structure with a two-dimensional electron gas density of 2.23×1012 cm−2.
Amyloid β-peptide spin trapping I (1995)

Synthetic beta-amyloid peptides (A betas) demonstrate lot-to-lot variation in toxicity that has not been adequately explained. Studies from our laboratory have shown that A beta toxicity may result from the ability of the peptide to promote oxidation reactions. Both A beta(1-40) and A beta(25-35) inactivate the oxidation-sensitive enzyme glutamine synthetase (GS) and generate electron paramagnetic resonance (EPR)-detectable products upon reaction with the spin trap phenyl-tert-butylnitrone (PBN). We now report that samples of synthetic A beta(1-40) and A beta(25-35) with attenuated toxicity with respect to peptide-induced GS inactivation, produce qualitatively different EPR spectra when the peptides are incubated with PBN. The results suggest an interpretation of conflicting observations regarding the toxicity of synthetic A betas, and that investigators must be careful to assess the reactivity state of A beta being studied.
Axe–Txe, a broad‐spectrum proteic toxin–antitoxin system specified by a multidrug‐resistant, clinical isolate of Enterococcus faecium (2003)

Enterococcal species of bacteria are now acknowledged as leading causes of bacteraemia and other serious nosocomial infections. However, surprisingly little is known about the molecular mechanisms that promote the segregational stability of antibiotic resistance and other plasmids in these bacteria. Plasmid pRUM (24 873 bp) is a multidrug resistance plasmid identified in a clinical isolate of Enterococcus faecium. A novel proteic-based toxin-antitoxin cassette identified on pRUM was demonstrated to be a functional segregational stability module in both its native host and evolutionarily diverse bacterial species. Induced expression of the toxin protein (Txe) of this system resulted in growth inhibition in Escherichia coli. The toxic effect of Txe was alleviated by co-expression of the antitoxin protein, Axe. Homologues of the axe and txe genes are present in the genomes of a diversity of Eubacteria. These homologues (yefM-yoeB) present in the E. coli chromosome function as a toxin-antitoxin mechanism, although the Axe and YefM antitoxin components demonstrate specificity for their cognate toxin proteins in vivo. Axe-Txe is one of the first functional proteic toxin-antitoxin systems to be accurately described for Gram-positive bacteria.
Increased therapeutic potential of an experimental anti-mitotic inhibitor SB715992 by genistein in PC-3 human prostate cancer cell line (2006)

Our results clearly show that SB715992 is a potent anti-tumor agent whose therapeutic effects could be enhanced by genistein. Hence, we believe that SB715992 could be a novel agent for the treatment of prostate cancer with greater success when combined with a non-toxic natural agent like genistein.
Effect of mastitis and related-germ on milk yield and composition during naturally-occurring udder infections in dairy cows (2002)

The effect of mastitis and related-germs on milk chemical composition (protein and lactose contents) and milk somatic cell count (SCC) was investigated in 501 milk quarter samples during two consecutive years in cows from three experimental herds. Each infected quarter was matched by a healthy one in the same udder, as a control. Milk protein and mineral assays were performed in a subsample of 128 milks. Staphylococci were the most frequently isolated germs (Staphylococcus aureus: 27%, coagulase-negative Staphylococci: 26%, Streptococci: 21%). Major milk pathogens (Staphylococcus aureus, Streptococcus uberis or Escherichia coli) associated with clinical signs of mastitis were accompanied by higher SCC (+1.6 logmL -1 , P < 0.01), lower lactose concentration (-7.6 gkg -1 , P < 0.01), higher protein concentration (+3.3 gkg -1 , P < 0.01) and higher soluble protein concentrations (IgG and BSA), hence a sharp decrease in the casein/protein ratio (-10 percentage points, P < 0.01). Changes were more marked when Escherichia coli was present. Corynebacterium bovis did not alter milk chemical composition whereas coagulase-negative Staphylococci slightly reduced lactose concentration (-1.8 gkg -1 ) and increased SCC (+0.37 logmL -1 ). Calcium and phosphorus milk contents were hardly modified by the presence of microorganisms. The decrease in milk yield during clinical mastitis varied from 1.6 kgd -1 in the presence of Staphylococcus aureus to 15 kgd -1 in the presence of Escherichia coli.
Vilse, a conserved Rac/Cdc42 GAP mediating Robo repulsion in tracheal cells and axons (2004)

Slit proteins steer the migration of many cell types through their binding to Robo receptors, but how Robo controls cell motility is not clear. We describe the functional analysis of vilse, a Drosophila gene required for Robo repulsion in epithelial cells and axons. Vilse defines a conserved family of RhoGAPs (Rho GTPase-activating proteins), with representatives in flies and vertebrates. The phenotypes of vilse mutants resemble the tracheal and axonal phenotypes of Slit and Robo mutants at the CNS midline. Dosage-sensitive genetic interactions between vilse, slit, and robo mutants suggest that vilse is a component of robo signaling. Moreover, overexpression of Vilse in the trachea of robo mutants ameliorates the phenotypes of robo, indicating that Vilse acts downstream of Robo to mediate midline repulsion. Vilse and its human homolog bind directly to the intracellular domains of the corresponding Robo receptors and promote the hydrolysis of RacGTP and, less efficiently, of Cdc42GTP. These results together with genetic interaction experiments with robo, vilse, and rac mutants suggest a mechanism whereby Robo repulsion is mediated by the localized inactivation of Rac through Vilse.
Bovine Hemoglobin as a Basis for Artificial Oxygen Carriers (1988)

Under physiological conditions of pH and [Cl-] ions the oxygen affinity of bovine hemoglobin is lower than that of human hemoglobin. The difference tends to disappear at low ionic strength, while it increases at high ionic strength. In the presence of Cl- ions bovine hemoglobin is not sensitive to 2,3-DPG, while in the absence of Cl- ions human and bovine hemoglobin respond to 2,3-DPG in a similar way. This is due to a high preferential binding of halogens by the deoxy-conformation in the bovine system. Reaction of deoxy-bovine hemoglobin with 2,3-dibromo-salycyl-fumarate results in a decreased oxygen affinity. Compounds can be purified by anion exchange chromatography which have the sedimentation velocity of tetrameric hemoglobins. They fail to dissociate into dimers at acid pH because of the presence of intramolecular crosslinks. Reverse phase chromatography shows that both kind of subunits are modified by the reaction. The half time of retention in rats of these tetramers is near 5 h. Bovine red cells do not contain 2,3-DPG, therefore they can be stored in the cold in saline for at least 2 months without significant modifications of their oxygen affinity. The oxygen affinity of bovine red cells can be modulated by addition and subtraction of Cl- ions from and by changing the pH of the media.
Introduction (2004)

A workshop on current and emerging research opportunities in probability was recently held at the American National Science Foundation (NSF 2002). One of the principal reasons for holding this meeting was to acknowledge the fact that the probabilistic approach to scientific investigation has now become an indispensable tool in many important scientific disciplines. Several areas of research were highlighted by invited speakers and in what follows we briefly mention a few of these. Below we quote directly from NSF (2002) on some areas of particular interest to applied mathematicians. For the full report the reader is referred to the original article and to an abbreviated article in SIAM News (Protter & Waymire 2002).
Uncoupling of stem cell inhibition from monocyte chemoattraction in MIP-1alpha by mutagenesis of the proteoglycan binding site. (1996)

We have studied the role of proteoglycans in the function of Macrophage Inflammatory Protein-1 alpha (MIP-1alpha), a member of the proteoglycan binding chemokine family. Sequence and peptide analysis has identified a basic region within MIP-1alpha which appears to be the major determinant of proteoglycan binding and we have now produced a mutant of MIP-1alpha lacking the basic charges on two of the amino acids within this proteoglycan binding site. This mutant (Hep Mut) appears to have lost the ability to bind to proteoglycans. Bioassay of Hep Mut indicates that it has retained stem cell inhibitory properties but has a compromised activity as a monocyte chemoattractant, thus suggesting uncoupling of these two properties of MIP-1alpha. Receptor studies have indicated that the inactivity of Hep Mut on human monocytes correlates with its inability to bind to CCR1, a cloned human MIP-1alpha receptor. In addition, studies using proteoglycan deficient cells transfected with CCR1 have indicated that the proteoglycan binding site in MIP-1alpha is a site that is also involved in the docking of MIP-1alpha to the monocyte receptor. The site for interaction with the stem cell receptor must therefore be distinct, suggesting that MIP-1alpha utilizes different receptors for these two different biological processes.
Probing the Pareto Frontier for Basis Pursuit Solutions (2008)

The basis pursuit problem seeks a minimum one-norm solution of an underdetermined least-squares problem. Basis pursuit denoise (BPDN) fits the least-squares problem only approximately, and a single parameter determines a curve that traces the optimal trade-off between the least-squares fit and the one-norm of the solution. We prove that this curve is convex and continuously differentiable over all points of interest, and show that it gives an explicit relationship to two other optimization problems closely related to BPDN. We describe a root-finding algorithm for finding arbitrary points on this curve; the algorithm is suitable for problems that are large scale and for those that are in the complex domain. At each iteration, a spectral gradient-projection method approximately minimizes a least-squares problem with an explicit one-norm constraint. Only matrix-vector operations are required. The primal-dual solution of this problem gives function and derivative information needed for the root-finding method. Numerical experiments on a comprehensive set of test problems demonstrate that the method scales well to large problems.
Input shaped control of a planar gantry crane with hoisting (1997)

The dynamic behavior of a planar gantry crane with hoisting of the load is investigated. The feedforward technique of input shaping is proposed for reduction of the residual vibration. Several versions of input shaping are evaluated and compared with time-optimal rigid-body commands over a wide range of parameters. Input shaping offers significant reduction in both, the residual and transient oscillation.
Respiration in the yeast and mycelial phases of Histoplasma capsulatum (1979)

Respiration in the yeast and mycelial phases of Histoplasma capsulatum proceeds via a cytochrome system and an alternate oxidase, both present constitutively. The mycelial cytochrome system is distinguished by an additional partial shunt around the antimycin-sensitive site.
Autophosphorylation of the focal adhesion kinase, pp125FAK, directs SH2-dependent binding of pp60src. (1994)

The phosphorylation of protein tyrosine kinases (PTKs) on tyrosine residues is a critical regulatory event that modulates catalytic activity and triggers the physical association of PTKs with Src homology 2 (SH2)-containing proteins. The integrin-linked focal adhesion kinase, pp125FAK, exhibits extracellular matrix-dependent phosphorylation on tyrosine and physically associates with two nonreceptor PTKs, pp60src and pp59fyn, via their SH2 domains. Herein, we identify Tyr-397 as the major site of tyrosine phosphorylation on pp125FAK both in vivo and in vitro. Tyrosine 397 is located at the juncture of the N-terminal and catalytic domains, a novel site for PTK autophosphorylation. Mutation of Tyr-397 to a nonphosphorylatable residue dramatically impairs the phosphorylation of pp125FAK on tyrosine in vivo and in vitro. The mutation of Tyr-397 to Phe also inhibits the formation of stable complexes with pp60src in cells expressing Src and FAK397F, suggesting that autophosphorylation of pp125FAK may regulate the association of pp125FAK with Src family kinases in vivo. The identification of Tyr-397 as a major site for FAK autophosphorylation provides one of the first examples of a cellular protein containing a high-affinity binding site for a Src family kinase SH2 domain. This finding has implications for models describing the mechanisms of action of pp125FAK, the regulation of the Src family of PTKs, and signal transduction through the integrins.
The head involution defective gene of Drosophila melanogaster functions in programmed cell death. (1995)

Deletions of chromosomal region, 75C1,2 block virtually all programmed cell death (PCD) in the Drosophila embryo. We have identified a gene previously in this interval, reaper (rpr), which encodes an important regulator of PCD. Here we report the isolation of a second gene in this region, head involution defective (hid), which plays a similar role in PCD. hid mutant embryos have decreased levels of cell death and contain extra cells in the head. We have cloned the hid gene and find that its expression is sufficient to induce PCD in cell death defective mutants. The hid gene appears to encode a novel 410-amino-acid protein, and its mRNA is expressed in regions of the embryo where cell death occurs. Ectopic expression of hid in the Drosophila retina results in eye ablation. This phenotype can be suppressed completely by expression of the anti-apoptotic p35 protein from baculovirus, indicating that p35 may act genetically downstream from hid.
Relative hyperlactatemia and hospital mortality in critically ill patients: a retrospective multi-centre study (2010)

In critically ill patients, relative hyperlactataemia is independently associated with increased hospital mortality. Blood lactate concentrations > 0.75 mmol.L-1 can be used by clinicians to identify patients at higher risk of death. The current reference range for lactate in the critically ill may need to be re-assessed.
Light on the Tip of a Needle: Plasmonic Nanofocusing for Spectroscopy on the Nanoscale (2012)

The efficiency of plasmonic nanostructures as optical antennas to concentrate optical fields to the nanoscale has been limited by intrinsically short dephasing times and small absorption cross sections. We discuss a new optical antenna concept based on surface plasmon polariton (SPP) nanofocusing on conical noble metal tips to achieve efficient far- to near-field transformation of light from the micro- to the nanoscale. The spatial separation of the launching of propagating SPPs from their subsequent apex confinement with high energy concentration enables background-free near-field imaging, tip-enhanced Raman scattering, and nonlinear nanospectroscopy. The broad bandwidth and spectral tunability of the nanofocusing mechanism in combination with frequency domain pulse shaping uniquely allow for the spatial confinement of ultrashort laser pulses and few-femtosecond spatiotemporal optical control on the nanoscale. This technique not only extends powerful nonlinear and ultrafast spectroscopies to the nanoscale but can also generate fields of sufficient intensity for electron emission and higher harmonic generation.
HUMAN PAPILLOMAVIRUSES (1994)

During the past 17 years 73 genotypes of human pathogenic papillomaviruses (HPV) have been identified. Most of them are found in benign proliferations; however, several have been discovered in malignant tumors. Specifically, cancer of the cervix, other anogenital cancers, but also some cancers of the skin, the oral and nasal cavity, and the rare periungual carcinomas have been linked to specific HPV infections. The pathogenesis of cancer of the cervix has been particularly well studied. Specific viral genes (E6 and E7) of high risk HPVs (types 16, 18, and others) act as oncogenes. Their expression emerges as necessary but not sufficient factors for malignant conversion. Besides stimulating cell proliferation, they are responsible for the genetic instability of the infected cells. Their transcriptional and functional activity is regulated by host cell genes. Mutational modifications of the latter appear to be required for malignant progression.
A human T lymphocyte differentiation marker defined by monoclonal antibodies that block E-rosette formation. (1981)

A new human T cell surface antigen, Leu-5, has been defined using a set of monoclonal antibodies that block rosette formation between T lymphocytes and sheep erythrocytes (SRBC). Four antibodies obtained from 2 different fusions using 2 immunized mouse strains all reacted with the same antigen. All these antibodies gave identical quantitative immunofluorescence (FACS) profiles, all gave the same staining profiles and intensities when used singly or in combinations, and all precipitated the same molecule. The antigen is a single polypeptide chain, 40,000 to 50,000 Mr, and is found on all thymocytes, peripheral T cells, and some null cells, but not on B cells. Leu-5 is a differentiation antigen that decreases in density as thymocytes mature to peripheral T lymphocytes. Thus, the Leu-5+ subpopulations ranked in order of decreasing Leu-5 density are: a subpopulation of subcapsular thymocytes greater than cortical and medullary thymocytes greater than peripheral T cells (cytotoxic/suppressor subset) greater than peripheral T cells (helper/inducer subset). The density distribution pattern of Leu-5 parallels the relative affinity of thymocytes and peripheral T lymphocytes for SRBC. We suggest that Leu-5 is either identical to or closely associated with the human T lymphocyte receptor for SRBC.
How many joints in the hands and wrists should be included in a score of radiologic abnormalities used to assess rheumatoid arthritis? (1985)

Numerous methods for reading abnormalities of rheumatoid arthritis in hand and wrist radiographs have been proposed over the past several decades. There are many differences among these methods, one of the more striking of which is the variation in the number of joints that are scored. In this study, we tested the number of joints that need to be read in order to represent abnormalities accurately and reproducibly, using the scores of multiple observers. Thirteen rheumatologists and radiologists each read a set of 41 hand and wrist films from patients with rheumatoid arthritis. Ten of 13 readers scored 27 joints in each hand and wrist; the other 3 readers scored fewer areas. Fourteen combinations of joints were selected based on the frequency of involvement and the technical adequacy of routine films in assessing a given area. After testing these 14 different combinations, 1 scheme, which included 17 areas read for erosions and 18 areas read for joint space narrowing, was tested further. The correlation coefficients for 10 intraobserver scores derived from this modified scheme compared with the original scores were between 0.981 and 0.997. Seventy-one of 78 interobserver comparisons were better using the new scheme than using the original scheme. These data indicate that the simplified scheme, using a combination of 17 joints to score erosions and 18 to score joint space narrowing, more accurately reflects the extent of abnormalities perceived by a panel of experts than does the original scheme. This abbreviated number of joints shortens the amount of time required to read a set of films and simplifies the scoring of films, since a number of areas that are difficult to read are eliminated from radiographic assessment.
The Extracellular Domain of Herpes Simplex Virus gE Is Sufficient for Accumulation at Cell Junctions but Not for Cell-to-Cell Spread (2000)

Herpes simplex virus (HSV) expresses a number of membrane glycoproteins, including gB, gD, and gH/gL, that function in both entry of virus particles and movement of virus from an infected cell to an uninfected cell (cell-to-cell spread). However, a complex of HSV glycoproteins gE and gI (gE/gI) is required for efficient cell-to-cell spread, especially between cells that form extensive cell junctions, yet it is not necessary for entry of extracellular virions. We previously showed that gE/gI has the capacity to localize specifically to cell junctions; the glycoprotein complex was found at lateral surfaces of cells in contact with other cells but not at those lateral surfaces not forming junctions or at apical surfaces. By virtue of these properties, gE/gI is an important molecular handle on the poorly understood process of cell-to-cell spread. Here, we show that the cytoplasmic domain of gE is important for the proper delivery of gE/gI to lateral surfaces of cells. Without this domain, gE/gI is found on the apical surface of epithelial cells, and more uniformly in the cytoplasm, although incorporation into the virion envelope is unaffected. However, even without proper trafficking signals, a substantial fraction of gE/gI retained the capacity to accumulate at cell junctions. Therefore, the extracellular domain of gE can mediate accumulation of gE/gI at cell junctions, if the glycoprotein can be delivered there, probably through interactions with ligands on the opposing cell. The role of phosphorylation of the cytoplasmic domain of gE was also studied. A second mutant HSV type 1 was constructed in which three serine residues that form a casein kinase II phosphorylation site were changed to alanine residues, reducing phosphorylation by 70 to 80%. This mutation did not affect accumulation at cell junctions or cell-to-cell spread.
Multiband characteristics of two fractal antennas (1999)

Experimental results show a multiband behavior for the Sierpinski gasket fractal antenna and the tree-like fractal antenna. Such behavior has been explained by the fractal structures of the antennas. We show that the matched frequencies possess a log-periodic behavior. ©1999 John Wiley & Sons, Inc. Microwave Opt Technol Lett 23: 242–245, 1999.