gebhart/patrepeval huggingface dataset:
Identification of Staphylococcus aureus virulence genes in a murine model of bacteraemia using signature‐tagged mutagenesis (1997)

Signature-tagged mutagenesis with transposon Tn917 was used to identify genes of Staphylococcus aureus required for virulence in a murine model of bacteraemia. Screening 1248 mutant strains in pools of 96 resulted in the provisional identification of 50 mutants attenuated in virulence. Subsequent individual analysis of many of these mutants confirmed that they are attenuated in virulence. DNA sequence analysis of regions flanking their transposon insertion points revealed that approximately half of them represent genes with unknown function, while most of the remainder are involved in nutrient biosynthesis and cell surface metabolism. Three mutants were found with transposon insertions in different positions in femA, and one mutant had an insertion in femB. Both femA and femB are involved in the formation of cell wall peptidoglycan pentaglycine cross-bridges. A further mutation occurred in a previously unknown gene that shares significant similarity to femB. Mutations were also obtained in recA and lsp (encoding the S. aureus prolipoprotein signal peptidase). On the basis of sequence similarities to proteins of known function, the products of other genes are probably involved in the synthesis of diaminopimelic acid (a component of peptidoglycan), maintenance of surface adhesins and cell surface membrane transport, showing that many components of the S. aureus cell surface are critical for the survival and replication of this pathogen in blood.
Enzymatic Phosphorylation of Unnatural Nucleosides (2002)

In an effort to expand the genetic alphabet, a number of unnatural, predominantly hydrophobic, nucleoside analogues have been developed which pair selectively in duplex DNA and during enzymatic synthesis. Significant progress has been made toward the efficient in vitro replication of DNA containing these base pairs. However, the in vivo expansion of the genetic alphabet will require that the unnatural nucleoside triphosphates be available within the cell at sufficient concentrations for DNA replication. We report our initial efforts toward the development of an unnatural in vivo nucleoside phosphorylation pathway that is based on nucleoside salvage enzymes. The first step of this pathway is catalyzed by the D. melanogaster nucleoside kinase, which catalyzes the phosphorylation of nucleosides to the corresponding monophosphates. We demonstrate that each unnatural nucleoside is phosphorylated with a rate that should be sufficient for the in vivo replication of DNA.
Herpes Simplex Virus Type 1 in Alzheimer's Disease: The Enemy Within (2008)

Alzheimer's disease is a modern scourge and is likely to become increasingly so in the future, with increasing longevity. The disease has been investigated for over one hundred years yet its causes and that of the neuropathological characteristics seen in AD brain are still completely unknown. Evidence for a major causative role of a common virus, herpes simplex virus type 1 (HSV1), acting in combination with a genetic factor - the type 4 allele of the apolipoprotein gene, a known susceptibility factor - is presented here. The characteristics of the virus, some of which make it an especially likely candidate for this role, are described, as are the many precedents for the action of a genetic factor modulating outcome of infection. Various possible ways in which HSV1 might lead to development of AD, such as its up-regulation of various enzymes and in particular certain kinases, its effect on the cell cycle, on autophagy, and its inflammatory and oxidative effects are also discussed. It is concluded that there is strong evidence that the virus is indeed a major factor in AD and therefore there is a strong case for appropriate treatment, and possibly for prevention in the future.
CHEMOTAXIS OF MONONUCLEAR CELLS (1968)

Chemotaxis of rabbit mononuclear cells was studied by the micropore-filter technique. Mononuclear cells obtained from mineral oil-induced peritoneal exudates respond chemotactically to rabbit serum treated with immune complexes or with streptokinase and plasminogen, to soluble factors produced by bacteria, and to lysates obtained from rabbit neutrophils. The first chemotactic factor requires heat-labile factors in serum for its generation, but, once formed, the chemotactic factor is relatively heat stable. This factor has been compared with the complement-associated factor in serum, C'(5, 6, 7)a, that is chemotactic for neutrophils. The ability to generate the mononuclear cell chemotactic factor in serum that has been treated with potassium thiocyanate suggests that complement is not required. The position of the chemotactic factor in preparative electrophoresis and density-gradient ultracentrifugation indicates that on the basis of physical-chemical criteria, this factor is not C'(5, 6, 7)a. The mononuclear cell chemotactic factor present in lysates of neutrophils sediments slowly in the ultracentrifuge and may be related, at least in part, to cationic peptides of lysosomal granules. A study in the time course of the chemotactic response of mononuclear cells reveals that the response begins to level off after 4 or 5 hr. This is in sharp contrast to the time course for the chemotactic response of neutrophils, in which the reaction is complete within 1.5 hr. Rabbit mononuclear cells obtained from a starch-induced peritoneal exudate respond to serum treated with plasminogen and streptokinase and to the soluble factor produced by bacteria, but no chemotactic response is elicited to serum treated with immune complexes. This indicates a functional difference between two populations of mononuclear cells. Rabbit alveolar macrophages respond poorly to all agents tested, although a weak chemotactic response to bacterial factors was found. The requirement of a serine esterase in the mononuclear cell for the cell to respond chemotactically was defined by the use of organophosphorus inhibitors. Pretreatment of mononuclear cells with several series of phosphonates renders them unresponsive in the chemotactic system. The effect is similar for mononuclear cells responding chemotactically to activated serum and to the bacterial chemotactic factor. Several points of contrast with inhibition profiles obtained in the chemotactic system of the neutrophil suggest that, while the mononuclear cell requires a serine esterase for chemotactic responsiveness, this enzyme is different from the one previously defined in the neutrophil.
Nuclear localization of the C1 factor (host cell factor) in sensory neurons correlates with reactivation of herpes simplex virus from latency (1999)

After a primary infection, herpes simplex virus is maintained in a latent state in neurons of sensory ganglia until complex stimuli reactivate viral lytic replication. Although the mechanisms governing reactivation from the latent state remain unknown, the regulated expression of the viral immediate early genes represents a critical point in this process. These genes are controlled by transcription enhancer complexes whose assembly requires and is coordinated by the cellular C1 factor (host cell factor). In contrast to other tissues, the C1 factor is not detected in the nuclei of sensory neurons. Experimental conditions that induce the reactivation of herpes simplex virus in mouse model systems result in rapid nuclear localization of the protein, indicating that the C1 factor is sequestered in these cells until reactivation signals induce a redistribution of the protein. The regulated localization suggests that C1 is a critical switch determinant of the viral lytic-latent cycle.
Damping controller design for power system oscillations using global signals (1996)

This paper describes a new power system stabilizer (PSS) design for damping power system oscillations focusing on interarea modes. The input to the PSS consists of two signals. The first signal is mainly to damp the local mode in the area where PSS is located using the generator rotor speed as an input signal. The second is an additional global signal for damping interarea modes. Two global signals are suggested; the tie-line active power and speed difference signals. The choice of PSS location, input signals and tuning is based on modal analysis and frequency response information. These two signals can also be used to enhance damping of interarea modes using SVC located in the middle of the transmission circuit connecting the two oscillating groups. The effectiveness and robustness of the new design are tested on a 19-generator system having characteristics and structure similar to the Western North American grid.
Arrays of Bundles of Carbon Nanotubes as Field Emitters (2007)

Experiments have shown that with suitable choices of critical dimensions, planar arrays of bundles of carbon nanotubes (see figure) can serve as high-current-density field emitter (cold-cathode) electron sources. Whereas some hot-cathode electron sources must be operated at supply potentials of thousands of volts, these cold-cathode sources generate comparable current densities when operated at tens of volts. Consequently, arrays of bundles of carbon nanotubes might prove useful as cold-cathode sources in miniature, lightweight electron-beam devices (e.g., nanoklystrons) soon to be developed. Prior to the experiments, all reported efforts to develop carbon-nanotube-based field-emission sources had yielded low current densities from a few hundred microamperes to a few hundred milliamperes per square centimeter. An electrostatic screening effect, in which taller nanotubes screen the shorter ones from participating in field emission, was conjectured to be what restricts the emission of electrons to such low levels. It was further conjectured that the screening effect could be reduced and thus emission levels increased by increasing the spacing between nanotubes to at least by a factor of one to two times the height of the nanotubes. While this change might increase the emission from individual nanotubes, it would decrease the number of nanotubes per unit area and thereby reduce the total possible emission current. Therefore, to maximize the area-averaged current density, it would be necessary to find an optimum combination of nanotube spacing and nanotube height. The present concept of using an array of bundles of nanotubes arises partly from the concept of optimizing the spacing and height of field emitters. It also arises partly from the idea that single nanotubes may have short lifetimes as field emitters, whereas bundles of nanotubes could afford redundancy so that the loss of a single nanotube would not significantly reduce the overall field emission.
N-acetylcysteine in psychiatry: current therapeutic evidence and potential mechanisms of action (2011)

There is an expanding field of research investigating the benefits of alternatives to current pharmacological therapies in psychiatry. N-acetylcysteine (NAC) is emerging as a useful agent in the treatment of psychiatric disorders. Like many therapies, the clinical origins of NAC are far removed from its current use in psychiatry. Whereas the mechanisms of NAC are only beginning to be understood, it is likely that NAC is exerting benefits beyond being a precursor to the antioxidant, glutathione, modulating glutamatergic, neurotropic and inflammatory pathways. This review outlines the current literature regarding the use of NAC in disorders including addiction, compulsive and grooming disorders, schizophrenia and bipolar disorder. N-acetylcysteine has shown promising results in populations with these disorders, including those in whom treatment efficacy has previously been limited. The therapeutic potential of this acetylated amino acid is beginning to emerge in the field of psychiatric research.
Perpendicular transport and magnetic properties in patterned multilayer magnetic microstructures (invited) (1996)

Using micron-level photolithography, we have prepared a set of patterned multilayer samples which have the form [Co/Cu/NiFeCo/Cu]×10 and which permit perpendicular current transport through the structure. Based on vibrating sample magnetometry, the multilayer stacks show a loss of ≊2 Å of magnetic material at each interface. The magnetoresistance was measured as a function of temperature, magnetic layer thickness, and element size and the ΔR/R values range up to 8% at 300 K and 18% at 10 K. The thickness dependent data are modeled using an extension of existing methods and can be fit using comparable resistivity, interface resistance, and spin asymmetry parameters. The magnetic fringe fields of the elements have an important effect on the observed R vs H curves.
Automated Heart-Type Fatty Acid–Binding Protein Assay for the Early Diagnosis of Acute Myocardial Infarction (2010)

We compared an automated quantitative heart-type fatty acid-binding protein (H-FABP) assay with other cardiac-marker assays to examine its usefulness as an early diagnostic marker of acute myocardial infarction (AMI). Serum samples for cardiac troponin T (cTnT), creatine kinase-MB isozyme (CK-MB), myoglobin, and H-FABP were obtained from 64 patients with AMI and 53 patients with other conditions (control group). H-FABP was measured by using 2 immunoassays, the H-FABP enzyme-linked immunosorbent assay (ELISA; Biocheck, Foster City, CA) and the H-FABP latex turbidimetric immunoassay (LTIA; HBI, Anyang, Korea). Sensitivities of assays for cTnT, CK-MB, myoglobin, H-FABP (by ELISA), H-FABP (by LTIA), and electrocardiogram (ECG) for the diagnosis of AMI at hospital admission were 39.1%, 59.4%, 64.1%, 68.7%, 70.3%, and 54.7%, respectively. Specificities of cTnT, CK-MB, myoglobin, H-FABP (by ELISA), H-FABP (by LTIA), and ECG were 98.1%, 71.7%, 81.1%, 77.4%, 90.6%, and 92.5%, respectively. The automated H-FABP (by LTIA) is superior to cTnT, CK-MB, myoglobin, and H-FABP (by ELISA) tests for the diagnosis of AMI in patients admitted within 4 hours from the onset of chest pain.
Trypsin and α-chymotrypsin partitioning in polyethylene glycol/maltodextrin aqueous-two-phase systems (1994)

The partitioning of trypsin and α-chymotrypsin in six Polyethylene glycol: Maltodextrin aqueous-two-phase systems was studied to assess the utility of maltodextrin as an alternative bottom phase-forming polymer to dextran or salt. Systems comprising Polyethylene glycol 1000:Maltodextrin M100 and Polyethylene glycol 1000:Maltodextrin M180 gave the best results with partition coefficient of 5.1 for trypsin and up to 1.5 for α-chymotrypsin. The former system was also highly selective for trypsin recovery in the PEG phase. Equilibrium phase diagrams are reported for these phase systems. Attempts to generate a phase diagram using a higher molecular weight maltodextrin polymer were abandoned due to rapid gel formation. The phase diagrams displayed a depression of the binodal line to lower polymer concentrations as polymer molecular weight was increased, however, there was a concurrent decrease in K value. An optimum was observed for trypsin partitioning into the top phase with increasing Tie Line Length in systems containing the lower molecular weight polymer combinations, but was either independent or decreasing with respect to Tie Line Length in the higher molecular weight polymer systems. Partitioning was performed in the optimal system under various conditions of pH, salt type and concentration to further improve yield and selectivity. Experiments provided insight into the influence of protein molecular structural characteristics on partitioning behaviour. Yeast extract loading trials were conducted to determine the effect of increasing levels of biomass loading on enzyme partitioning behaviour in the optimal system. These results confirm that polyethylene glycol:Maltodextrin systems behave similarly to other aqueous-two-phase systems used for protein recovery.
Interactive computation of holograms using a look-up table (1993)

Several methods of increasing the speed and simplicity of the computation of off-axis transmission holograms are presented, with applications to the real-time display ofholographic images. The bipolar intensity approach allows for the real-valued linear summation of interference fringes, a factor of 2 speed increase, and the elimination of image noise caused by object self-interference. An order of magnitude speed increase is obtained through the use of a precomputed look-up table containing a large array of elemental interference patterns corresponding to point source contributions from each of the possible locations in image space. Results achieved using a data-parallelsupercomputer to compute horizontal-parallaxonly holographic patterns containing six megasamples indicate that an image comprised of 10,000 points with arbitrary brightness (gray scale) can be computed in under 1 s. Implemented on a common workstation, the look-up table approach increases computation speed by a factor of 43.
Glycemic Control Is Related to the Morphological Severity of Diabetic Sensorimotor Polyneuropathy (2001)

The severity of peripheral DSP expressed by morphological criteria was significantly related to glycemic control in type 1 and type 2 diabetic patients. Inconsistent with previously published electrophysiological data demonstrating a correlation between height and conduction velocity, increasing height is not associated with morphological severity. Based on the results of the present study, it might be hypothesized that improving glycemic control will lessen severity of DSP in terms of FD loss in subjects with diabetes.
The Prevalence of Diabetic Retinopathy Among Adults in the United States (2004)

Approximately 4.1 million US adults 40 years and older have diabetic retinopathy; 1 of every 12 persons with DM in this age group has advanced, vision-threatening retinopathy.
Principles of Competitive Binding Assays (Saturation Analyses). I. Equilibrium Techniques (1973)

Abstract The principles of competitive binding assays are reviewed, with emphasis on the differentiation of equilibrium vs. sequential saturation techniques. Three methods of equilibrium analysis are outlined that differ from each other in the relative concentrations of labeled ligand and binder used in the incubation system. The linearization of dose-response curves through the use of the logit plot is discussed. The importance of the knowledge of the effective affinity constant K for optimization of the assays is stressed, and two methods of estimating K are demonstrated with a digoxin-antidigoxin-antiserum system.
Complementary DNA Microarray Analysis in Acute Lung Injury Induced by Lipopolysaccharide and Diesel Exhaust Particles (2004)

We have recently shown that diesel exhaust particles (DEP) synergistically enhance acute lung injury related to lipopoly-saccharide (LPS) in mice. The present study used cDNA microarray to elucidate the effects of DEP on the global pattern of LPS-related gene expression in the murine lung. The number of genes upregulated >/=2-fold as compared with their expression levels in the vehicle group was greater in the LPS group than in other groups, but treatment with DEP and LPS dramatically increased the number of the genes upregulated >/=6-fold. In particular, gene expression of metallothionein-1 and -2, S100 calcium-binding protein A9, lipocalin 2, and small inducible cytokine B family member 10 was higher by >/=20-fold in the DEP + LPS group than in the vehicle group. These results were concomitant with those obtained by real-time reverse transcription-polymerase chain reaction analysis in the overall trend. Our findings suggest that intense, focused expression of genes such as S100 calcium-binding protein A9, lipocalin 2, and small inducible cytokine B family member 10 relates to the synergistic aggravation of acute lung injury by LPS and DEP rather than weak, broad expression of various genes by exposure of LPS alone.
Sleep Apnea Syndrome: A Possible Contributing Factor to Resistant Hypertension (2001)

Our results demonstrate that hypertensive patients with sleep apnea whose blood pressure responds beneficially to treatment have less severe sleep apnea than those patients whose blood pressure remains elevated despite anti-hypertensive therapy. Since neither obesity nor nocturnal hypoxemia appear to be important determinants of ineffective treatment, we suggest that resistant hypertension may be caused by frequent intermittent sympathetic stimulation.
Deposition and electrical characterisation of a MOS memory structure containing AU nanoparticles in a high-k dielectric layer (2006)

In this work, we use the MBE method in order to fabricate MOS memory devices with gold (Au) nanoparticles embedded on a SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> /HfO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> interface. We have chosen to work with Au nanoparticles due to the fact that Au has a large work function. The device shows a clear hysteresis behavior on C-V (capacitance-voltage) and G-V (conductance-voltage) measurements. These measurements demonstrate that in our device we have a charge storage effect. When we apply a positive voltage to the gate, electrons tunnel through the thin SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> layer and are stored in the metallic nanoparticles. This MOS device shows a clear memory effect
Multifunctional Fullerene-Mediated Assembly of Gold Nanoparticles (2005)

Functionalized fullerenes are used as a mediator to assemble citrate-capped gold nanoparticles in aqueous solution. This nanostructured assembly exploits the electrostatic interaction between the negatively charged nanoparticles and the positively charged fullerene.
Treatment of SLE with Anti-CD20 Monoclonal Antibody (2004)

Systemic lupus erythemaotsus (SLE) is an autoimmune disease involving multiple organ systems and characterized by anti-nuclear antibodies. While T cells and dendritic cells may play major roles in SLE, several lines of evidence strongly suggest a central role for B cells. This article will review the role of B cells in human SLE as well as the currently available data on the treatment of SLE by depleting B cells with anti-CD20 (rituximab).