gebhart/patrepeval huggingface dataset:
Isolation of Antigenic Components from the Lyme Disease Spirochete: Their Role in Early Diagnosis (1987)

Patients with early Lyme disease produce IgM antibodies to a 41,000-dalton polypeptide of Borrelia burgdorferi. With advancing disease, IgG antibodies recognize a larger number of spirochetal polypeptides. Sodium dodecyl sulfate treatment of spirochetes at a concentration of 0.03% resulted in an outer envelope (OE) fraction in the supernatant and a protoplasmic cylinder (PC) flagellar fraction in the pellet. Shearing of the PC pellet followed by ultrafiltration and dialysis resulted in a flagellin-enriched fraction. From the OE and flagellin-rich fractions, individual polypeptides with Mr of 66,000, 41,000, and 31,000/34,000 daltons were eluted in microgram quantities after electrophoresis. The flagellin-enriched fraction as well as the eluted polypeptides were used as antigens in the ELISA. The flagellin-enriched fraction was superior to the standard ELISA antigen. The 41-kilodalton (kDa) flagellin antigen was not useful. Antigens of 66 kDa and 31/34 kDa were confirmed to be part of the late antibody response.
Safety of Intrathecal Sodium Nitroprusside for the Treatment and Prevention of Refractory Cerebral Vasospasm and Ischemia in Humans (1999)

These results suggest that ITSNP is a safe and potentially effective treatment for established DCV and cerebral ischemia refractory to conventional treatment. The preliminary results of prophylactic treatment are also favorable with regard to safety.
Ischemic Acute Renal Failure (1998)

Acute renal failure (ARF) is a clinical syndrome characterized by a deterioration of renal function over hours to days, with associated failure of the kidney to excrete nitrogenous waste products and to maintain fluid and electrolyte homeostasis. This clinical entity was defined in the seminal works of Bywaters, who characterized it in victims of aerial bombings during World War II. Bywaters described tubular cell necrosis and intratubular pigmented casts in the kidneys of these patients.
Maladaptive Role of IL-6 in Ischemic Acute Renal Failure (2005)

The role of IL-6 was investigated in murine ischemic acute renal failure. The renal pedicles were clamped for 17 min, and the mice were studied at various times after reperfusion. We found that serum IL-6 increased after murine ischemic renal injury. This increase was associated with increased IL-6 mRNA in the ischemic kidney but not in the contralateral kidney or the liver. Maximal IL-6 production occurred at 4 to 8 h and decreased to baseline by 24 h. Reperfusion of the kidney was required for IL-6 production. In situ hybridization and immunohistochemistry showed that macrophages infiltrated areas adjacent to the vascular bundles in the outer medulla within hours of reperfusion and showed that these macrophages produced IL-6 mRNA. For understanding how macrophages were stimulated to produce IL-6, an in vitro model in which S3 proximal tubular cells were injured by reactive oxygen species was set up. These injured cells released molecules that activated macrophages to produce IL-6 in vitro. IL-6 that was produced in response to renal ischemia was maladaptive because transgenic knockout of IL-6 ameliorated renal injury as measured by serum creatinine and histology. IL-6 transgenic knockout mice were lethally irradiated, and their bone marrow was reconstituted with wild-type IL-6 cells. Such bone marrow transfers abolished the protective effects of transgenic IL-6 knockout. It is concluded that macrophages infiltrate the area of the vascular bundles of the outer medulla, these macrophages produce IL-6, and this IL-6 exacerbates ischemic murine acute renal failure.
Suspension Plasma Spraying of Nano-Ceramics Using an Axial Injection Torch (2005)

Abstract Nanostructured coatings of Al2O3 and ZrO2 (1.5% Y2O5) are produced by suspension plasma spraying, introducing the liquid feedstock internally into the central part of three converging plasma jets of a Mettech Axial III torch (Northwest Mettech Corp.). Spraying nanosized ceramic powders in a liquid carrier can yield thinner coatings with more refined microstructures than conventional plasma spraying. In-flight particle states are measured for a number of plasma conditions of varying torch current, gas flow rates and compositions (Ar, H2, N2), and related to the resulting microstructure and phase composition in the coatings, as determined by EDS, SEM and XRD. Results show that particle velocities up to 600 m/sec can be reached, yielding high impact velocities and cooling rates. Some comparison is made to previous work performed using external injection of a suspension droplet stream into a conventional dc plasma flame. At optimized conditions, dense γ-Al2O3 deposits with an average crystallite size below 30 nm are obtained at deposition efficiency above 80%, which was not previously attainable. Eutectic alumina-zirconia composite coatings with a finely layered lamellar structure are also realized. The laminates have potential advantages as thermal barrier coatings with beneficial properties arising from nano-composite components.
Histology and Pathology of the Human Intervertebral Disc (2006)

The intervertebral disc is a highly organized matrix laid down by relatively few cells in a specific manner. The central gelatinous nucleus pulposus is contained within the more collagenous anulus fibrosus laterally and the cartilage end plates inferiorly and superiorly. The anulus consists of concentric rings or lamellae, with fibers in the outer lamellae continuing into the longitudinal ligaments and vertebral bodies. This arrangement allows the discs to facilitate movement and flexibility within what would be an otherwise rigid spine. At birth, the human disc has some vascular supply within both the cartilage end plates and the anulus fibrosus, but these vessels soon recede, leaving the disc with little direct blood supply in the healthy adult. With increasing age, water is lost from the matrix, and the proteoglycan content also changes and diminishes. The disc-particularly the nucleus-becomes less gelatinous and more fibrous, and cracks and fissures eventually form. More blood vessels begin to grow into the disc from the outer areas of the anulus. There is an increase in cell proliferation and formation of cell clusters as well as an increase in cell death. The cartilage end plate undergoes thinning, altered cell density, formation of fissures, and sclerosis of the subchondral bone. These changes are similar to those seen in degenerative disc disease, causing discussion as to whether aging and degeneration are separate processes or the same process occurring over a different timescale. Additional disorders involving the intervertebral disc can demonstrate other changes in morphology. Discs from patients with spinal deformities such as scoliosis have ectopic calcification in the cartilage end plate and sometimes in the disc itself. Cells in these discs and cells from patients with spondylolisthesis have been found to have very long cell processes. Cells in herniated discs appear to have a higher degree of cellular senescence than cells in nonherniated discs and produce a greater abundance of matrix metalloproteinases. The role that abnormalities play in the etiopathogenesis of different disorders is not always clear. Disorders may be caused by a genetic predisposition or a tissue response to an insult or altered mechanical environment. Whatever the initial cause, a change in the morphology of the tissue is likely to alter the physiologic and mechanical functioning of the tissue.
The Lactulose Hydrogen Breath Test as a Diagnostic Test for Small-Bowel Bacterial Overgrowth (1979)

The lactulose hydrogen breath test has been evaluated as a diagnostic test for small-bowel bacterial overgrowth using the 14C-glycocholate breath test for comparison. Twenty-seven patients with suspected bacterial overgrowth and 37 control patients were studied. The lactulose test was positive in 8 out of 9 patients with Subsequently proven bacterial overgrowth, all of whom had positive 14C-glycocholate tests. However, 6 patients with ileal disease or resection had positive 14C-glycocholate tests but negative lactulose tests. subsequent bacteriological study of duodenal juice from these patients was negative. Negative results were obtained by both tests in the remaining 12 patients, none of whom were subsequently shown to have bacterial overgrowth. All 37 control subjects had negative lactulose tests. The lactulose breath test is a simple and promising diagnostic test for the detection of small-bowel bacterial overgrowth and, unlike the 14C-glycocholate test, has the advantage of being able to distinguish bacterial overgrowth from ileal disease.
Bioconversion of Fumaric Acid to Succinic Acid by Recombinant E. coli (1998)

Succinic acid was produced efficiently from fumaric acid by a recombinant E. coli strain DH5α/pGC1002 containing multicopy fumarate reductase genes. The effects of initial fumaric acid and glucose concentration on the production of succinic acid were investigated. Succinic acid reached 41 to over 60 g/L in 48.5 h starting with 50 to 64 g/L fumaric acid. Significant substrate inhibition was observed at initial fumaric acid concentration of 90 g/L. l-Malic acid became the major fermentation product under these conditions. Provision of glucose (5–30 g/L) to the fermentation medium stimulated the initial succinic acid production rate over two folds.
Modeling of species distributions with Maxent: new extensions and a comprehensive evaluation (2008)

Accurate modeling of geographic distributions of species is crucial to various applications in ecology and conservation. The best performing techniques often require some parameter tuning, which may be prohibitively time‐consuming to do separately for each species, or unreliable for small or biased datasets. Additionally, even with the abundance of good quality data, users interested in the application of species models need not have the statistical knowledge required for detailed tuning. In such cases, it is desirable to use “default settings”, tuned and validated on diverse datasets. Maxent is a recently introduced modeling technique, achieving high predictive accuracy and enjoying several additional attractive properties. The performance of Maxent is influenced by a moderate number of parameters. The first contribution of this paper is the empirical tuning of these parameters. Since many datasets lack information about species absence, we present a tuning method that uses presence‐only data. We evaluate our method on independently collected high‐quality presence‐absence data. In addition to tuning, we introduce several concepts that improve the predictive accuracy and running time of Maxent. We introduce “hinge features” that model more complex relationships in the training data; we describe a new logistic output format that gives an estimate of probability of presence; finally we explore “background sampling” strategies that cope with sample selection bias and decrease model‐building time. Our evaluation, based on a diverse dataset of 226 species from 6 regions, shows: 1) default settings tuned on presence‐only data achieve performance which is almost as good as if they had been tuned on the evaluation data itself; 2) hinge features substantially improve model performance; 3) logistic output improves model calibration, so that large differences in output values correspond better to large differences in suitability; 4) “target‐group” background sampling can give much better predictive performance than random background sampling; 5) random background sampling results in a dramatic decrease in running time, with no decrease in model performance.
Dynamic partitioning: a mechanism for shared memory management (1999)

We propose a novel buffer management scheme in order to regulate the individual queue lengths in a shared-memory switch. The primary motivations of our scheme are: (i) provide differentiated allocations to the queues sharing the memory, where the allocations are directly derived from the call admission control (CAC) parameters; (ii) allow for the co-existence of regulated and best-effort traffic achieving high buffer utilization without violating the guaranteed buffer allocations of the regulated connections; (iii) protect well-behaving connections that conform to their allocations from any misbehaviour in other traffic; and (iv) handle deviations in incoming traffic patterns, from the ones assumed by CAC, by distributing unavoidable losses in an equitable manner. The new scheme, which we call dynamic partitioning, achieves all these objectives, and constitutes a first example of a scheme that is highly efficient, derives its parameters directly from CAC, and is also very robust against misbehaviour. The scheme is simple to implement, and therefore amenable for deployment in current high-speed switches. We present the scheme in the context of ATM switches, together with cell level simulations for its validation.
CaT1 and the Calcium Release-activated Calcium Channel Manifest Distinct Pore Properties (2001)

The calcium release-activated calcium channel (CRAC) is a highly Ca(2+)-selective ion channel that is activated on depletion of inositol triphosphate (IP(3))-sensitive intracellular Ca(2+) stores. It was recently reported that CaT1, a member of the TRP family of cation channels, exhibits the unique biophysical properties of CRAC, which led to the conclusion that CaT1 comprises all or part of the CRAC pore (Yue, L., Peng, J. B., Hediger, M. A., and Clapham, D. E. (2001) Nature 410, 705-709). Here, we directly compare endogenous CRAC with heterologously expressed CaT1 and show that they manifest several clearly distinct properties. CaT1 can be distinguished from CRAC in the following features: sensitivity to store-depleting agents; inward rectification in the absence of divalent cations; relative permeability to Na(+) and Cs(+); effect of 2-aminoethoxydiphenyl borate (2-APB). Moreover, CaT1 displays a mode of voltage-dependent gating that is fully absent in CRAC and originates from the voltage-dependent binding/unbinding of Mg(2+) inside the channel pore. Our results imply that the pores of CaT1 and CRAC are not identical and indicate that CaT1 is a Mg(2+)-gated channel not directly related to CRAC.
Hypoxia Impairs Vasodilation in the Lung (1981)

Alveolar hypoxia causes pulmonary vasoconstriction; we investigated whether hypoxia could also impair pulmonary vasodilation. We found in the isolated perfused rat lung a delay in vasodilation following agonist-induced vasoconstriction. The delay was not due to erythrocyte or plasma factors, or to alterations in base-line lung perfusion pressure. Pretreating lungs with arachidonic acid abolished hypoxic vasoconstriction, but did not influence the hypoxia-induced impairment of vasodilation after angiotensin II, bradykinin, or serotonin pressor responses. Progressive slowing of vasodilation followed angiotensin II-induced constriction as the lung oxygen tension fell progressively below 60 Torr. KCl, which is not metabolized by the lung, caused vasoconstriction; the subsequent vasodilation time was delayed during hypoxia. However, catecholamine depletion in the lungs abolished this hypoxic vasodilation delay after KCl-induced vasoconstriction. In lungs from high altitude rats, the hypoxia-induced vasodilation impairment after an angiotensin II pressor response was markedly less than it was in lungs from low altitude rats. We conclude from these studies that (a) hypoxia impairs vasodilation of rat lung vessels following constriction induced by angiotensin II, serotonin, bradykinin, or KCl, (b) hypoxia slows vasodilation following KCl-induced vasoconstriction probably by altering lung handling of norepinephrine, (c) the effect of hypoxia on vasodilation is not dependent on its constricting effect on lung vessels, (d) high altitude acclimation moderates the effect of acute hypoxia on vasodilation, and (e) the hypoxic impairment of vasodilation is possibly the result of an altered rate of dissociation of agonists from their membrane receptors on the vascular smooth muscle.
L-658,310, a new injectable cephalosporin. I. In vitro antibacterial properties. (1989)

The in vitro antibacterial spectrum of L-658,310, a new semisynthetic cephalosporin, was compared with ceftazidime, aztreonam and piperacillin against a wide variety of randomly selected human clinical isolates. The compound was found to be a broad spectrum bactericidal agent that was more potent than any of the comparison drugs against glucose nonfermenting bacteria. It has especially potent activity against Pseudomonas aeruginosa including multiply-resistant strains. The superior activity of L-658,310 against this group of organisms is attributed to the presence of the dihydroxy substituents on the 2-methylisoindoline moiety of the compound. L-658,310 is not cross-resistant with either imipenem, ceftazidime or piperacillin (representatives of three different classes of beta-lactam compounds) against P. aeruginosa. The lack of cross-resistance with ceftazidime extends to other glucose nonfermenters and several strains of Enterobacteriaceae as well. The compound is active against bacteria known to possess either R-plasmid- or chromosomally-mediated beta-lactamases.
Equilibrium dissociation and unfolding of the arc repressor dimer (1989)

The equilibrium unfolding reaction of Arc repressor, a dimeric DNA binding protein encoded by bacteriophage P22, can be monitored by fluorescence or circular dichroism changes. The stability of Arc is concentration dependent, and the unfolding reaction is well described as a two-state transition from folded dimer to unfolded monomer. The stability of the protein is decreased at low pH and increased by high salt concentration. The salt dependence suggests that two ions bind preferentially to the folded protein. In 10 mM potassium phosphate (pH 7.3) and 100 mM KCl, the unfolding free energy reaches a maximum near room temperature. The results suggest that at the low protein concentrations where operator DNA binding is normally measured, Arc is predominantly monomeric and unfolded.
C-terminal Extension of Truncated Recombinant Proteins in Escherichia coli with a 10Sa RNA Decapeptide (1995)

When murine interleukin-6 is overexpressed in Escherichia coli, a small population of molecules exhibits a novel C-terminal modification. Peptide mapping, electrospray ionization-mass spectrometry, and automated N- and C-terminal sequencing identified a peptide ("tag" peptide), -Ala-Ala-Asn-Asp-Glu-Asn-Tyr-Ala-Leu-Ala-Ala-COOH, encoded by a small metabolically stable RNA of E. coli (10Sa RNA) attached to truncated C termini of the recombinant protein. A mutant strain of E. coli in which the chromosomal 10Sa RNA gene (ssrA) is disrupted does not produce this C-terminal modification, confirming that the tag peptide originates from the ssrA gene.
4-Anilino-3-quinolinecarbonitriles: An Emerging Class of Kinase Inhibitors - An Update (2004)

In 2000, Wyeth disclosed that 4-(3-bromoanilino)-6,7-dimethoxy-3-quinolinecarbonitrile was a potent and selective EGFR kinase inhibitor. Subsequent reports showed that variation of the substituents on the 4-anilino group of the 3-quinolinecarbonitrile core changed the kinase specificity from EGFR to either Src or MEK. This article is an update of a 2002 review that summarized Wyeths efforts in the area of 4-anilino-3-quinolinecarbonitrile kinase inhibitors. Since then, Wyeth has reported the SAR of EKB-569, an irreversible EGFR inhibitor currently in clinical trials. Variation of the 4-anilino group of EKB-569 provided HKI-272, a dual inhibitor of EGFR and HER-2. In addition, the 3- quinolinecarbonitrile analogs of known quinazoline EGFR inhibitors were prepared. SKI-606, initially reported to be a Src inhibitor, was found to also inhibit Abl kinase and therefore could be a potential alternative treatment to Gleevec. SKI-606 was also efficacious in a rat model of stroke. Additional Src kinase inhibitors, including some tricyclic analogs, were obtained by variation of the substituent at C-7. Finally, 3-quinolinecarbonitrile MEK inhibitors with potent cell activity were identified.
Structural Basis of Neutralization by a Human Anti-severe Acute Respiratory Syndrome Spike Protein Antibody, 80R (2006)

Severe acute respiratory syndrome (SARS) is a newly emerged infectious disease that caused pandemic spread in 2003. The etiological agent of SARS is a novel coronavirus (SARS-CoV). The coronaviral surface spike protein S is a type I transmembrane glycoprotein that mediates initial host binding via the cell surface receptor angiotensin-converting enzyme 2 (ACE2), as well as the subsequent membrane fusion events required for cell entry. Here we report the crystal structure of the S1 receptor binding domain (RBD) in complex with a neutralizing antibody, 80R, at 2.3 A resolution, as well as the structure of the uncomplexed S1 RBD at 2.2 A resolution. We show that the 80R-binding epitope on the S1 RBD overlaps very closely with the ACE2-binding site, providing a rationale for the strong binding and broad neutralizing ability of the antibody. We provide a structural basis for the differential effects of certain mutations in the spike protein on 80R versus ACE2 binding, including escape mutants, which should facilitate the design of immunotherapeutics to treat a future SARS outbreak. We further show that the RBD of S1 forms dimers via an extensive interface that is disrupted in receptor- and antibody-bound crystal structures, and we propose a role for the dimer in virus stability and infectivity.
Multiple progesterone receptor assays in human breast cancer. (1984)

A review of assay results from more than 5500 patients revealed 283 patients in whom multiple breast cancer specimens were analyzed for progesterone receptor (PGR). All assays were performed in a single laboratory between 1975 and 1982 using the sucrose gradient technique. We considered only the 8S fraction of PGR. Simultaneous assays in 109 patients yielded 14% discordance [one assay with greater than 10 fmol/mg cytosol protein (PGR+) and one assay with less than 5 fmol/mg protein (PGR-)]. Among 161 sequential assays, there was an overall discordance of 19%: 8% (nine of 106) when the initial assay was PGR-, but 44% (24 of 55) when the initial assay was PGR+. Among PGR+ patients initially assayed at the time of diagnosis, there was a tendency to greater receptor loss in patients with positive axillary lymph nodes (44 versus 11%). The length of time between biopsies did not increase the discordance, but endocrine therapy within this interval did increase it (56% of initially PGR+ patients who received interim endocrine therapy were PGR- at second biopsy). to evaluate the significance of interval loss of PGR, we compared survival from first biopsy in initially PGR+ patients who subsequently lost their receptor versus those whose receptor persisted. The latter group experienced a significantly longer survival (p less than 0.02). In summary, we observed an ominous loss of PGR in sequential biopsies, particularly with intervening endocrine therapy, and those patients whose tumor cells lost PGR experienced poorer survival than did patients retaining PGR. Therefore, patients with PGR+ primary tumors require repeat biopsy for PGR upon disease recurrence for optimal treatment planning.