gebhart/patrepeval huggingface dataset:
Recombinant Gamma Interferon Stimulates Signal Transduction and Gene Expression in Alveolar Macrophages In Vitro and in Tuberculosis Patients (2003)

Tuberculosis is the seventh leading cause of morbidity and mortality in the world, with eight million cases per year. Animal and human studies demonstrate an enrichment of CD4 cells at sites of disease, with a more favorable clinical course when there is a Th1 response with the presence of gamma interferon (IFN-gamma). We previously treated patients who had multidrug-resistant tuberculosis with recombinant IFN-gamma (rIFN-gamma) in aerosol form and were able to convert smear-positive cases to smear negative with 12 treatments over 1 month. We hypothesized that rIFN-gamma would induce signal transducer and activator of transcription (STAT) and interferon regulatory factor (IRF) binding activity in alveolar macrophages (AM). AM treated in vitro showed clear upregulation of STAT-1 and IRF-1 by rIFN-gamma. STAT-1 was not activated and IRF-1 was only weakly induced after 1 day of infection by Mycobacterium tuberculosis TN913. In bronchoalveolar lavage (BAL) cells obtained from 10 of 10 tuberculosis patients 10 +/- 2 days post-antituberculosis treatment, there was no detectable STAT-1 or IRF-1 DNA-binding activity. After 4 weeks of treatment with rIFN-gamma aerosol in addition to the antituberculosis drugs, 10 of 10 patients had increased STAT-1, IRF-1, and/or IRF-9 DNA-binding activity in BAL cells from lung segments shown radiographically to be involved and in those shown to be uninvolved. Symptoms and chest radiographs improved, and amounts of macrophage inflammatory cytokines and human immunodeficiency virus type 1 (HIV-1) viral loads (in five of five HIV-1-coinfected patients) declined in the second BAL specimens. rIFN-gamma aerosol induces signal transduction and gene expression in BAL cells and should be evaluated for efficacy in a randomized, controlled clinical trial.
Formation and release of arrestin domain-containing protein 1-mediated microvesicles (ARMMs) at plasma membrane by recruitment of TSG101 protein (2012)

Mammalian cells are capable of delivering multiple types of membrane capsules extracellularly. The limiting membrane of late endosomes can fuse with the plasma membrane, leading to the extracellular release of multivesicular bodies (MVBs), initially contained within the endosomes, as exosomes. Budding viruses exploit the TSG101 protein and endosomal sorting complex required for transport (ESCRT) machinery used for MVB formation to mediate the egress of viral particles from host cells. Here we report the discovery of a virus-independent cellular process that generates microvesicles that are distinct from exosomes and which, like budding viruses, are produced by direct plasma membrane budding. Such budding is driven by a specific interaction of TSG101 with a tetrapeptide PSAP motif of an accessory protein, arrestin domain-containing protein 1 (ARRDC1), which we show is localized to the plasma membrane through its arrestin domain. This interaction results in relocation of TSG101 from endosomes to the plasma membrane and mediates the release of microvesicles that contain TSG101, ARRDC1, and other cellular proteins. Unlike exosomes, which are derived from MVBs, ARRDC1-mediated microvesicles (ARMMs) lack known late endosomal markers. ARMMs formation requires VPS4 ATPase and is enhanced by the E3 ligase WWP2, which interacts with and ubiquitinates ARRDC1. ARRDC1 protein discharged into ARMMs was observed in co-cultured cells, suggesting a role for ARMMs in intercellular communication. Our findings reveal an intrinsic cellular mechanism that results in direct budding of microvesicles from the plasma membrane, providing a formal paradigm for the evolutionary recruitment of ESCRT proteins in the release of budding viruses.
Network control method and human-machine interface design for ISDN multimedia terminals (1990)

A human-machine interface has been created for an integrated services digital network (ISDN) network control unit (I-NUU). I-NUI is a sophisticated terminal device that allows a voice communication channel and two data channels to be connected through an ISDN I-series interface. ISDN communication functions and network control operations were analyzed to determine the required characteristics of I-NCU. I-NCU features the minimum number of control buttons and a liquid crystal display. Visual and audible information are used to keep the operator fully informed about the state of the communication channels.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Two homologous regulatory genes, lin-12 and glp-1, have overlapping functions (1991)

Two homologous genes, lin-12 and glp-1, encode transmembrane proteins required for regulatory cell interactions during C. elegans development. Based on their single mutant phenotypes, each gene has been thought to govern a distinct set of cell fates. We show here that lin-12 and glp-1 are functionally redundant during embryogenesis: Unlike either single mutant, the lin-12 glp-1 double mutant dies soon after hatching. Numerous cellular defects can be observed in these Lag (for lin-12 and glp-1) double mutants. Furthermore, we have identified two genes, lag-1 and lag-2, that appear to be required for both lin-12 and glp-1-mediated cell interactions. Strong loss-of-function lag mutants are phenotypically indistinguishable from the lin-12 glp-1 double; weak lag mutants have phenotypes typical of lin-12 and glp-1 single mutants. We speculate that the lin-12 and glp-1 proteins are biochemically interchangeable and that their divergent roles in development may rely largely on differences in gene expression.
Salt-Resistant Alpha-Helical Cationic Antimicrobial Peptides (1999)

Analogues based on the insect cecropin-bee melittin hybrid peptide (CEME) were studied and analyzed for activity and salt resistance. The new variants were designed to have an increase in amphipathic alpha-helical content (CP29 and CP26) and in overall positive charge (CP26). The alpha-helicity of these peptides was demonstrated by circular dichroism spectroscopy in the presence of liposomes. CP29 was shown to have activity against gram-negative bacteria that was similar to or better than those of the parent peptides, and CP26 had similar activity. CP29 had cytoplasmic membrane permeabilization activity, as assessed by the unmasking of cytoplasmic beta-galactosidase, similar to that of CEME and its more positively charged derivative named CEMA, whereas CP26 was substantially less effective. The activity of the peptides was not greatly attenuated by an uncoupler of membrane potential, carbonyl cyanide-m-chlorophenylhydrazone. The tryptophan residue in position 2 was shown to be necessary for interaction with cell membranes, as demonstrated by a complete lack of activity in the peptide CP208. Peptides CP29, CEME, and CEMA were resistant to antagonism by 0.1 to 0.3 M NaCl; however, CP26 was resistant to antagonism only by up to 160 mM NaCl. The peptides were generally more antagonized by 3 and 5 mM Mg2+ and by the polyanion alginate. It appeared that the positively charged C terminus in CP26 altered its ability to permeabilize the cytoplasmic membrane of Escherichia coli, although CP26 maintained its ability to kill gram-negative bacteria. These peptides are potential candidates for future therapeutic drugs.
CLINICAL SIGNIFICANCE OF GLUCOCORTICOID PHARMACODYNAMICS ASSESSED BY ANTILYMPHOCYTE ACTION IN KIDNEY TRANSPLANTATION (1994)

A number of studies have demonstrated the impact of glucocorticoid response of peripheral lymphocytes on kidney allograft survival, suggesting that the better the glucocorticoid selection, the better the clinical outcome. However, individual differences in pharmacodynamics of clinically important glucocorticoids have not been taken into account. Four glucocorticoids (hydrocortisone, prednisolone, methylprednisolone, and dexamethasone) were examined for their ability to suppress in vitro blastogenesis of mitogen-stimulated PBL obtained from 122 chronic renal failure (CRF) patients waiting for renal transplantation and 98 healthy volunteers. Concentrations of steroids that gave 50% inhibition of lymphocyte blastogenesis (IC50) were determined individually in order to compare steroids and subject groups. Graft outcomes in 36 kidney transplant recipients treated with prednisolone were compared retrospectively with the prednisolone pretransplant IC50 values. Lymphocyte response to each glucocorticoid showed wide deviations among the subjects. Prednisolone IC50 values of the CRF patients showed the largest deviation, ranging from 1.0 to 10,000 micrograms/L. Thus, a significantly large population of the CRF patients (26.2%), when compared with the healthy subjects (4.1%) showed a marked decrease in lymphocyte response to prednisolone (P < 0.01). The binding capacity and affinity of lymphocyte glucocorticoid receptors did not differ significantly between the responders and nonresponders, suggesting that steroid resistance is a post-receptor event. The antilymphocyte potency of prednisolone assessed by IC50 of the steroid was less than that of hydrocortisone, whereas methylprednisolone was > 12-fold superior to prednisolone. After kidney transplantation, CRF patients who showed impaired preoperative lymphocyte response to prednisolone had a significantly high incidence of acute allograft rejection under prednisolone/CsA therapy (P < 0.01). It is concluded from these results that methylprednisolone could be of benefit to prednisolone-resistant recipients, who can be identified by the preoperative lymphocyte culture.
Regional assignment of the steroid sulfatase—X-linked ichthyosis locus: Implications for a noninactivated region on the short arm of human X chromosome (1979)

The expression of steroid sulfatase (SS; sterol-sulfatase; sterol-sulfate sulfohydrolase, EC 3.1.6.2), a microsomal enzyme that catalyzes the hydrolysis of a variety of 3beta-hydroxysteroid sulfates, was evaluated in mouse-human hybrid clones. The mouse parental line, A9, was found to have little SS as determined by activity measurements. Human SS can be separated from mouse SS by electrophoresis. Two human fibroblast lines, one carrying an X/13 translocation [46,X,t(X;13)(p22;q12)] and the other carrying an X/20 translocation [46,X,t(X;20)(Xp20q;Xq20p)] were used as the human parental lines. Several independently derived hybrid clones from each of the two fusion experiments were analyzed for the expression of human SS by activity measurements and electrophoresis. Cytogenetic analyses were done on these hybrid clones at the same passage level. The results showed that the expression of human SS in these cell hybrids was concordant only with the presence of the distal half (p22-->pter) of the short arm of the human X chromosome, thus assigning the locus for SS to Xp22-->Xpter. Earlier studies have shown that the deficiency of SS is the basis for the dermatologic condition X-linked ichthyosis, the gene for which is known to be located approximately 10 centimorgans from the Xg blood group locus. The localization of SS on the X chromosome indicates that Xg locus may be on the short arm of X and possibly on its distal half. The Xg locus is thought to escape X-inactivation in man, and recent investigations suggest that the SS locus also escapes X-inactivation. Our results thus provide evidence for the location of an apparently noninactivated site on the distal half of the short arm of the human X-chromosome that contains the locus for SS and possibly the Xg locus.
Corrections: Recombinant Vesicular Stomatitis Viruses from DNA (1995)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Polymerase Θ is a key driver of genome evolution and of CRISPR/Cas9-mediated mutagenesis (2015)

Cells are protected from toxic DNA double-stranded breaks (DSBs) by a number of DNA repair mechanisms, including some that are intrinsically error prone, thus resulting in mutations. To what extent these mechanisms contribute to evolutionary diversification remains unknown. Here, we demonstrate that the A-family polymerase theta (POLQ) is a major driver of inheritable genomic alterations in Caenorhabditis elegans. Unlike somatic cells, which use non-homologous end joining (NHEJ) to repair DNA transposon-induced DSBs, germ cells use polymerase theta-mediated end joining, a conceptually simple repair mechanism requiring only one nucleotide as a template for repair. Also CRISPR/Cas9-induced genomic changes are exclusively generated through polymerase theta-mediated end joining, refuting a previously assumed requirement for NHEJ in their formation. Finally, through whole-genome sequencing of propagated populations, we show that only POLQ-proficient animals accumulate genomic scars that are abundantly present in genomes of wild C. elegans, pointing towards POLQ as a major driver of genome diversification.
MicroRNAs and cancer: Profile, profile, profile (2007)

MicroRNAs (miRNAs) represent a new class of small noncoding RNAs (ncRNAs, RNAs that do not codify for proteins) that can regulate gene expression by targeting messenger RNAs of protein coding genes and other ncRNA transcripts. miRNAs were recently found to be involved in the pathophysiology of all types of analyzed human cancers mainly by aberrant gene expression. This is characterized by abnormal levels of expression for mature and/or precursor miRNA transcripts in comparison to the corresponding normal tissues. miRNA profiling has allowed the identification of signatures associated with diagnosis, prognosis and response to treatment of human tumors. Therefore, miRNAs fingerprinting represents a new addition to the tools to be used by medical oncologists.
Effect of cortisol on energy expenditure and amino acid metabolism in humans (1995)

Hydrocortisone was infused overnight into nine normal healthy adults on three occasions at 0, 80, and 200 micrograms.kg-1.h-1, producing plasma cortisol concentrations of 10.6 +/- 1.2, 34.0 +/- 2.0, and 64.9 +/- 4.3 micrograms/dl, respectively. L-[1-13C]leucine, L-[phenyl-2H5]phenylalanine, and L-[2-15N]glutamine were infused during the last 7 h of hypercortisolemia to measure amino acid kinetics. During the last 3.5 h, somatostatin, glucagon, and insulin were infused to reduce the cortisol-induced elevation in plasma insulin to basal. Hypercortisolemia increased plasma glucose, free fatty acid (FFA), and insulin concentrations. Institution of the somatostatin clamp returned insulin to basal but increased glucose and FFA. Acute hypercortisolemia increased protein breakdown 5-20%, as measured by increases in leucine and phenylalanine appearance rates. Normalizing insulin during hypercortisolemia did not alter phenylalanine flux but enhanced leucine appearance rate, the latter result indicating that insulin was affecting leucine metabolism during hypercortisolemia. The fraction of the leucine flux that was oxidized was not significantly increased with hypercortisolemia, but disposal by the nonoxidative route of leucine uptake for protein synthesis was increased. Hypercortisolemia increased cycling of amino acids by increasing protein breakdown and synthesis, but the increase in this process could have increased resting energy expenditure (REE) only 1-2%. Hypercortisolemia increased glutamine flux in a dose-dependent fashion through an increase in de novo synthesis, which presumably reflects increased release from skeletal muscle. Hypercortisolemia increased REE 9-15% at the 80 and 200 micrograms.kg-1.h-1 infusion rates. Respiratory quotient did not rise with cortisol infusion but tended to decrease, suggesting that the increase in REE was fueled by increased oxidation of fat. These data demonstrate that hypercortisolemia increases metabolic rate and may be in part responsible for the hypermetabolic state in injury.
Liquid-chromatographic separation and determination of coproporphyrins I and III in urine. (1983)

We describe a method of determining coproporphyrin I, III, and I plus III in urine by "high-performance" liquid chromatography. Urine is simply injected after dilution with an equal volume of glacial acetic acid. Some urinary coproporphyrin apparently binds zinc without acetic acid treatment. The working linear range of coproporphyrin concentrations is 10 to 2000 micrograms/L of urine. The sensitivity of the method is sufficient to detect as little as 10 micrograms of coproporphyrins per liter of urine. Analytical recoveries for both coproporphyrins were 96.7-106%. Results by the present method and those by an extraction method (Br J Ind Med 31:72-74, 1974) correlate well (r = 0.975). Mean (and range) coproporphyrin I, III, and I plus III concentrations in urine from normal subjects are 33.7 (7-75), 28.6 (0-130), and 62.2 (7-174) micrograms/L, respectively.
Plasmid analysis of Borrelia burgdorferi, the Lyme disease agent (1988)

A simple procedure for extraction of plasmid-enriched DNA from borreliae was used in a plasmid analysis of 13 strains of the Lyme disease agent, Borrelia burgdorferi. The extracted DNA was subjected to low-percentage agarose gel electrophoresis and examined either directly by ethidium bromide staining or after hybridization of the plasmids in situ with a DNA probe for the gene encoding the major outer membrane protein OspA. Each isolate had four to seven discernible plasmids of various sizes. Only 2 of the 13 strains had the same plasmid profile. The ospA gene probe hybridized to large plasmids to strains from both North America and Europe. A strain which had been passaged many times was found to have lost two of the six plasmids originally present. These findings indicate the potential usefulness of plasmid analysis as a strain-typing procedure and for identifying possible plasmid-conferred virulence factors.
High‐frequency and adaptive‐like dynamics of human CD1 self‐reactive T cells (2010)

CD1 molecules present lipid antigens to T cells. An intriguing subset of human T cells recognize CD1-expressing cells without deliberately added lipids. Frequency, subset distribution, clonal composition, naïve-to-memory dynamic transition of these CD1 self-reactive T cells remain largely unknown. By screening libraries of T-cell clones, generated from CD4(+) or CD4(-) CD8(-) double negative (DN) T cells sorted from the same donors, and by limiting dilution analysis, we find that the frequency of CD1 self-reactive T cells is unexpectedly high in both T-cell subsets, in the range of 1/10-1/300 circulating T cells. These T cells predominantly recognize CD1a and CD1c and express diverse TCRs. Frequency comparisons of T-cell clones from sorted naïve and memory compartments of umbilical cord and adult blood show that CD1 self-reactive T cells are naïve at birth and undergo an age-dependent increase in the memory compartment, suggesting a naïve/memory adaptive-like population dynamics. CD1 self-reactive clones exhibit mostly Th1 and Th0 functional activities, depending on the subset and on the CD1 isotype restriction. These findings unveil the unanticipated relevance of self-lipid T-cell response in humans and clarify the basic parameters of the lipid-specific T-cell physiology.
Characterizing Application Runtime Behavior from System Logs and Metrics (2011)

Large-scale systems are heavily shared resource environments where a mix of applications are launched concurrently competing for network and storage resources. It is essential to characterize the runtime behavior of these applications for provisioning system resources and understanding the impact of application s performance when competing for resources. In this paper, we study the use of zero- and low-overhead system logs and other system metric data for characterizing the runtime behavior of several applications. We present our preliminary work on estimating individual application s I/O demands by observing file system usage pattern over multiple runs, and interpreting application s network utilization characteristics by observing link-layer error logs. We also present preliminary findings on using such information in making context-sensitive scheduling decisions that minimize potentially negative interactions between applications competing for shared resources. Our analysis is based on four months of system log data collected on one of the world s largest supercomputing facilities, the Jaguar XT5 petaflop system at Oak Ridge National Laboratory.
Downregulation of Wnt Signaling by Increased Expression of Dickkopf-1 and -2 is a Prerequisite for Late-Stage Osteoblast Differentiation of KS483 Cells (2005)

Our data suggest that Wnt signaling in maturing osteoblasts needs to be downregulated to enable the formation of a mineralized bone matrix. Furthermore, they suggest that Dkk-1 and Dkk-2 may have distinct functions in osteoblast differentiation.
Marinobufagenin, an endogenous ligand of alpha-1 sodium pump, is a marker of congestive heart failure severity (2002)

In CHF, MBG exhibits progressive increases similar to ANP, varies with CHF severity and correlates with LV systolic function. We hypothesize, that, in CHF, the concurrent production of these two natriuretic hormones, a vasorelaxant, ANP, and a vasoconstrictor, MBG, potentiate each other's natriuretic effects, but may offset their vasoactive actions.
Active site of triosephosphate isomerase: in vitro mutagenesis and characterization of an altered enzyme. (1985)

We have replaced the glutamic acid-165 at the active site of chicken triosephosphate isomerase with an aspartic acid residue using site-directed mutagenesis. Expression of the mutant protein in a strain of Escherichia coli that lacks the bacterial isomerase results in a complementation phenotype that is intermediate between strains that have no isomerase and strains that produce either the wild-type chicken enzyme or the native E. coli isomerase. The value of kcat for the purified mutant enzyme when glyceraldehyde 3-phosphate is the substrate is 1/1500th that of the wild-type enzyme, and the Km is decreased by a factor of 3.6. With dihydroxyacetone phosphate as substrate, the kcat value is 1/240th that of the wild-type enzyme, and Km is 2 times higher. The value of Ki for a competitive inhibitor, phosphoglycolate, is the same for the mutant and wild-type enzymes, at 2 X 10(-5) M. By treating the enzyme-catalyzed isomerization as a simple three step process and assuming that substrate binding is diffusion limited, it is evident that the mutation of glutamic acid-165 to aspartic acid principally affects the free energy of the transition state(s) for the catalytic reaction itself.
The Essential Cofactor TRRAP Recruits the Histone Acetyltransferase hGCN5 to c-Myc (2000)

The c-Myc protein functions as a transcription factor to facilitate oncogenic transformation; however, the biochemical and genetic pathways leading to transformation remain undefined. We demonstrate here that the recently described c-Myc cofactor TRRAP recruits histone acetylase activity, which is catalyzed by the human GCN5 protein. Since c-Myc function is inhibited by recruitment of histone deacetylase activity through Mad family proteins, these opposing biochemical activities are likely to be responsible for the antagonistic biological effects of c-Myc and Mad on target genes and ultimately on cellular transformation.