gebhart/patrepeval huggingface dataset:
Antibiotics in Yersinia enterocolitica infections (1987)

A prospective study was undertaken to evaluate the incidence, course, effects of treatment and outcome of patients with Yersinia enterocolitica infections. A total of 189 patients were followed: 62.5% had enteric forms of illness, 20.6% extramesenteric forms, 23.2% arthritis and erythema nodosum. Lymphadenopathy with high fever and weight loss, a septic syndrome and hepatitis were predominant manifestations of the extramesenteric form. Ten per cent of the isolates (135) were susceptible to amoxycillin (4 mg/l), 38% to cephradine (8 mg/l), 82% to doxycycline (4 mg/l), 83% to chloramphenicol (4 mg/l), 85% to trimethoprim (1 mg/l), 87% to cefuroxime (8 mg/l), 92% to piperacillin (16 mg/l), 99% to gentamicin (1 mg/l) and 100% to cefotaxime (4 mg/l), pefloxacin (0.12 mg/l), ofloxacin (0.06 mg/l) and ciprofloxacin (0.016 mg/l). The majority of the patients with enteritis recovered without antibiotic therapy. The duration of enteritis was not significantly influenced by antibiotic treatment. Eighty five patients, 46 with enteric and 39 with extramesenteric forms were treated. The clinical response to co-trimoxazole was 71%, and to doxycycline 75%. Cefuroxime, ceftazidime, cefoperazone, piperacillin and gentamicin failed in seven of eight courses. Three patients treated with ciprofloxacin responded well. The role of quinolones in yersiniosis needs further attention.
X-ray Structure of Novamyl, the Five-Domain “Maltogenic” α-Amylase from Bacillus stearothermophilus:  Maltose and Acarbose Complexes at 1.7 Å Resolution, (1999)

The three-dimensional structure of the Bacillus stearothermophilus "maltogenic" alpha-amylase, Novamyl, has been determined by X-ray crystallography at a resolution of 1.7 A. Unlike conventional alpha-amylases from glycoside hydrolase family 13, Novamyl exhibits the five-domain structure more usually associated with cyclodextrin glycosyltransferase. Complexes of the enzyme with both maltose and the inhibitor acarbose have been characterized. In the maltose complex, two molecules of maltose are found in the -1 to -2 and +2 to +3 subsites of the active site, with two more on the C and E domains. The C-domain maltose occupies a position identical to one previously observed in the Bacillus circulans CGTase structure [Lawson, C. L., et al. (1994) J. Mol. Biol. 236, 590-600], suggesting that the C-domain plays a genuine biological role in saccharide binding. In the acarbose-maltose complex, the tetrasaccharide inhibitor acarbose is found as an extended hexasaccharide species, bound in the -3 to +3 subsites. The transition state mimicking pseudosaccharide is bound in the -1 subsite of the enzyme in a 2H3 half-chair conformation, as expected. The active site of Novamyl lies in an open gully, fully consistent with its ability to perform internal cleavage via an endo as opposed to an exo activity.
Mitogen-activated Protein Kinase Activation Requires Two Signal Inputs from the Human Anaphylatoxin C5a Receptor (1995)

The anaphylatoxin C5a receptor activates the Ras/Raf/mitogen-activated protein (MAP) kinase pathway in human neutrophils. The signal pathways involved in Ras/Raf/MAP kinase activation in response to C5a and other chemoattractant receptors is poorly understood. Stimulation of the C5a receptor expressed in HEK293 cells results in modest MAP kinase activation, which is inhibited by pertussis toxin-catalyzed ADP-ribosylation of G(i). Coexpression of the C5a receptor and the G16 alpha subunit (alpha 16) results in the G16-mediated activation of phospholipase C beta and a robust MAP kinase activation. Pertussis toxin treatment of C5a receptor/alpha 16-cotransfected cells inhibits C5a stimulation of MAP kinase activity approximately 60% relative to the control response. Similarly, the protein kinase C inhibitor, GF109203X inhibits activation of MAP kinase activation in C5a receptor/alpha 16-cotransfected cells by 60%; the protein kinase C inhibitor does not affect the modest C5a receptor response in the absence of alpha 16 expression. These results demonstrate that two independent signals are required for the maximal activation of MAP kinase by G protein-coupled receptors.
Methylation Profiling Defines an Extensive Field Defect in Histologically Normal Prostate Tissues Associated with Prostate Cancer (2013)

Prostate cancer (PCa) is typically found as a multifocal disease suggesting the potential for molecular defects within the morphologically normal tissue. The frequency and spatial extent of DNA methylation changes encompassing a potential field defect are unknown. A comparison of non-tumor-associated (NTA) prostate to histologically indistinguishable tumor-associated (TA) prostate tissues detected a distinct profile of DNA methylation alterations (0.2%) using genome-wide DNA arrays based on the Encyclopedia of DNA Elements 18 sequence that tile both gene-rich and poor regions. Hypomethylation (87%) occurred more frequently than hypermethylation (13%). Several of the most significantly altered loci (CAV1, EVX1, MCF2L, and FGF1) were then used as probes to map the extent of these DNA methylation changes in normal tissues from prostates containing cancer. In TA tissues, the extent of methylation was similar both adjacent (2 mm) and at a distance (>1 cm) from tumor foci. These loci were also able to distinguish NTA from TA tissues in a validation set of patient samples. These mapping studies indicate that a spatially widespread epigenetic defect occurs in the peripheral prostate tissues of men who have PCa that may be useful in the detection of this disease.
The relationship of pretreatment serum hemoglobin level to the survival of epithelial ovarian carcinoma patients (1998)

BACKGROUND Tumor anemia is a common symptom in cancer patients. This study assessed the prognostic relationship of pretreatment serum hemoglobin levels to survival in a retrospective sample of 206 patients with epithelial ovarian carcinoma. METHODS Survival analysis was evaluated by univariate (Kaplan-Meier product limit method and log rank test) and multivariate (Cox proportional hazards model) analysis. Mean values were compared by the Kruskal-Wallis test. Serum hemoglobin levels were determined in each patient 24-48 hours before surgery. Anemia was defined as a serum hemoglobin value below 12 g/dL. RESULTS Tumor anemia was present in 32% of the patients before primary surgery. Hemoglobin levels were significantly lower in patients with residual tumor than in those with no detectable residual tumor after initial surgery (P = 0.008). Although statistically not significant, we found a trend toward lower hemoglobin levels with advanced stage of disease. For 5 years, overall survival probability was 38.5% and 52.3% for patients with pretreatment hemoglobin levels P = 0.008). In multivariate analysis, the relative risk of death was significantly associated with decreasing serum hemoglobin levels. No interaction was found between the grade of anemia and chemotherapy or radiation therapy with respect to its influence on overall survival. CONCLUSIONS After adjustment for established prognostic factors, tumor anemia was found to have an independent relationship to the overall survival of patients with ovarian carcinoma. Because no significant interaction could be found between the grade of anemia and chemotherapy, marked tumor anemia was considered an indicator of the presence of biologically aggressive tumor cell clones. Cancer 1998;83:726-731. © 1998 American Cancer Society.
Monoclonal antibody 7G3 recognizes the N-terminal domain of the human interleukin-3 (IL-3) receptor alpha-chain and functions as a specific IL-3 receptor antagonist (1996)

The human interleukin-3 receptor (IL-3R) is expressed on myeloid, lymphoid, and vascular endothelial cells, where it transduces IL-3-dependent signals leading to cell activation. Although IL-3R activation may play a role in hematopoiesis and immunity, its aberrant expression or excessive stimulation may contribute to pathologic conditions such as leukemia, lymphoma, and allergic reactions. We describe here the generation and characterization of a monoclonal antibody (MoAb), 7G3, which specifically binds to the IL-3R alpha-chain and completely abolishes its function. MoAb 7G3 immunoprecipitated and recognized in Western blots the IL-3R alpha-chain expressed by transfected cells and bound to primary cells expressing IL-3R alpha. MoAb 7G3 bound the IL-3R alpha-chain with a kd of 900 pmol/L and inhibited 125I-IL-3 binding to high- and low-affinity receptors in a dose-dependent manner. Conversely, IL-3 but not granulocyte-macrophage colony-stimulating factor (GM-CSF) inhibited 125I-7G3 binding to high- and low-affinity IL-3Rs, indicating that MoAb 7G3 and IL-3 bind to common or adjacent sites. In keeping with the inhibition of IL-3 binding, MoAb 7G3 antagonized IL-3 biologic activities, namely stimulation of TF-1 cell proliferation, basophil histamine release, and IL-6 and IL-8 secretion from human endothelial cells. Two other anti-IL-3R alpha-chain MoAbs failed to inhibit IL-3 binding or function. Epitope mapping experiments using truncated IL-3R alpha-chain mutants and IL-3R alpha/GM-CSFR alpha chimeras revealed that 31 amino acids in the N-terminus of IL-3R alpha were required for MoAb 7G3 binding. MoAb 7G3 may be of clinical significance for antagonizing IL-3 in pathologic conditions such as some myeloid leukemias, follicular B-cell lymphoma, and allergy. Furthermore, these results implicate the N-terminal domain of IL-3R alpha in IL-3 binding. Since this domain is unique to the IL-3/GM-CSF/IL-5 receptor subfamily, it may represent a novel and common binding feature in these receptors.
Expression of uncoupling protein‐3 and mitochondrial activity in the transition from hypothyroid to hyperthyroid state in rat skeletal muscle (1999)

We sought a correlation between rat skeletal muscle triiodothyronine (T3)-mediated regulation of uncoupling protein-3 (UCP3) expression and mitochondrial activity. UCP3 mRNA expression increased strongly during the hypothyroid-hyperthyroid transition. The rank order of mitochondrial State 3 and State 4 respiration rates was hypothyroid < euthyroid < hyperthyroid. The State 4 increase may have been due to the increased UCP3 expression, as the proton leak kinetic was stimulated in the hypothyroid-hyperthyroid transition and a good correlation exists between the State 4 and UCP3 mRNA level. As a significant proportion of an organism's resting oxygen consumption is dedicated to opposing the proton leak, skeletal muscle mitochondrial UCP3 may mediate part of T3's effect on energy metabolism.
High-performance hollow sulfur nanostructured battery cathode through a scalable, room temperature, one-step, bottom-up approach (2013)

Sulfur is an exciting cathode material with high specific capacity of 1,673 mAh/g, more than five times the theoretical limits of its transition metal oxides counterpart. However, successful applications of sulfur cathode have been impeded by rapid capacity fading caused by multiple mechanisms, including large volume expansion during lithiation, dissolution of intermediate polysulfides, and low ionic/electronic conductivity. Tackling the sulfur cathode problems requires a multifaceted approach, which can simultaneously address the challenges mentioned above. Herein, we present a scalable, room temperature, one-step, bottom-up approach to fabricate monodisperse polymer (polyvinylpyrrolidone)-encapsulated hollow sulfur nanospheres for sulfur cathode, allowing unprecedented control over electrode design from nanoscale to macroscale. We demonstrate high specific discharge capacities at different current rates (1,179, 1,018, and 990 mAh/g at C/10, C/5, and C/2, respectively) and excellent capacity retention of 77.6% (at C/5) and 73.4% (at C/2) after 300 and 500 cycles, respectively. Over a long-term cycling of 1,000 cycles at C/2, a capacity decay as low as 0.046% per cycle and an average coulombic efficiency of 98.5% was achieved. In addition, a simple modification on the sulfur nanosphere surface with a layer of conducting polymer, poly(3,4-ethylenedioxythiophene), allows the sulfur cathode to achieve excellent high-rate capability, showing a high reversible capacity of 849 and 610 mAh/g at 2C and 4C, respectively.
Enhanced light transmission through a single subwavelength aperture (2001)

The optical transmission through a subwavelength aperture in a metal film is strongly enhanced when the incident light is resonant with surface plasmons at the corrugated metal surface surrounding the aperture. Conversely, the aperture acts as a novel probe of the surface plasmons, yielding useful insights for optimizing the transmission enhancement. For the optimal corrugation geometry, a set of concentric circular grooves, three times more light is transmitted through the central subwavelength aperture than directly impinges upon it. This effect is useful in the fabrication of near-field optical devices with extremely high optical throughput.
Poly(dimethylsiloxane)-Based Polyurethane with Chemically Attached Antifoulants for Durable Marine Antibiofouling (2015)

Marine biofouling is a problem for marine industry and maritime activities. We have prepared polyurethane with poly(dimethylsiloxane) (PDMS) main chains and N-(2,4,6-trichlorophenyl) maleimide (TCM) pendant groups via a combination of a thiol-ene click reaction and a condensation reaction and studied its properties. The polymer has low surface energy and a high water contact angle. When TCM content in bulk is high enough, sufficient antifoulant groups can be exposed on the surface. Our study reveals that such polymeric surface can effectively inhibit the adhesion and colonization of marine organisms such as bacteria (Micrococcus luteus), diatom Navicula, and barnacle cyprids. Particularly, marine field tests demonstrate that the polymer has excellent antibiofouling performance in 110 days.
High mobility solution processed 6,13-bis(triisopropyl-silylethynyl) pentacene organic thin film transistors (2007)

Using the small molecule organic semiconductor 6,13-bis(triisopropyl-silylethynyl) pentacene (TIPS-pentacene), the authors have fabricated the solution-processed organic thin film transistors (OTFTs) with carrier mobility &amp;gt;1cm2∕Vs, current on/off ratio greater than 107, and subthreshold slope &amp;lt;0.3V/decade. The high mobility TIPS-pentacene solution-processed films are deposited from high boiling point solvents and show strong molecular ordering including molecular terracing. Film ordering varies substantially for different solvents and film deposition techniques and OTFT mobility correlates well with film ordering.
Triamcinolone Stimulates bFGF Production and Inhibits TGF–β1 Production by Human Dermal Fibroblasts (2002)

We conclude from these results that triamcinolone acetonide increases the production of bFGF and decreases production of TGF-beta1 by human dermal fibroblasts.
[The asthmatic child]. (1992)

Asthma is the most frequent chronic pediatric disease. Management is based on assessment of severity and should normalize lifestyle as well as pulmonary function. Mild asthma is treated with intermittent beta-2-agonists. Moderate asthma should receive non-steroids prophylactic anti-inflammatory drugs. Immunotherapy should be considered. Severe asthma requires inhaled steroids. At each stage inhaled medications should be preferred. Therefore inhalation delivery system must be adapted for children of different ages and degree of dyspnea. The importance of environment control is well recognized. Establishing a partnership with the child and its family and with the medical staff and with the child's school is always necessary.
Role of splanchnic venous system in overall cardiovascular homeostasis. (1983)

A blood reservoir is an organ or region containing a significant portion of the blood volume that can be mobilized by the sympathetic nervous system to subserve overall cardiovascular homeostasis. To be effective, the reservoir must be as insensitive as possible to the passive effects of changes in flows or external pressures. Evidence is presented that the splanchnic venous bed fulfills these criteria. Hepatic venous resistance maintains portal pressure and intrinsic hepatic arterial mechanisms maintain total hepatic flow. These mechanisms minimize passive effects of portal flow changes on splanchnic blood volume, whereas enclosure of the liver in the peritoneal cavity minimizes effects of external pressures. Up to 27% of total blood volume can be mobilized from the splanchnic venous bed by sympathetic stimulation. Maintenance of cardiac preload depends on the ability of the central nervous system to control venous compliance and hence to redistribute blood volume between peripheral organs and the cardiopulmonary compartment. Three examples of the role of the splanchnic blood reservoir in overall homeostasis are discussed: hemorrhage, splanchnic nerve stimulation, and responses to epinephrine. Reflex and central control of the splanchnic blood reservoir are discussed but available information is fragmentary.
Identification of Peptide Ligands for Targeting to the Blood-Brain Barrier (2010)

These results indicate that two new peptide ligands have been identified that may be used for specific targeting of drugs to the blood-brain barrier.
Regulation of the cell cycle machinery by oncogenic ras. (1996)

The ras proto-oncogene has been implicated during the formation of tumors in vivo as well as the transformation of cell lines in culture. Conditional expression of an activated ras mutant in Balb/c-3T3 fibroblasts failed to stimulate S phase entry in the absence of plasma-derived progression factors, but did shorten the G1 interval from 12 to 6 h and abrogate the normal proliferative requirement for platelet-derived growth factor. Ras-dependent alteration of the 3T3 cell cycle was accompanied by a dramatic increase in the expression of the G1 regulatory protein, cyclin D1, while expression of cyclin E and cyclin A proteins were only weakly induced. Cyclin/cdk complexes assembled in response to ectopic ras expression in the absence of growth factor stimulation bound the cdk inhibitory factor, Kip1, and were inactive. However, plasma-stimulated regulatory pathways functioned co-operatively with the oncogenic ras molecule to decrease Kip1 levels, induce the kinase activities associated with cyclins D, E and A, and trigger the initiation of DNA replication. Our results suggest that a ras-activated signal transduction pathway may link environmental mitogenic stimuli to the cell cycle machinery via modulation of G1 cyclin expression.
Cell Wall Architecture in Yeast: New Structure and New Challenges (1998)

The chemical composition of many fungal cell walls is known, but we have not understood the interactions of the various macromolecules nor the assembly processes. The biochemistry and molecular genetics of biosynthesis have been comprehensively reviewed ([9][1], [42][2]), but recent results obtained
Estimating the Return-on-Investment From Changes in Employee Health Risks on The Dow Chemical Companyʼs Health Care Costs (2005)

Findings from this study were incorporated into other components of a business case for health and productivity management, and these supported continued investments in health improvement programs designed to achieve risk reduction and cost savings.
Mather Sets for Twist Maps and Geodesics on Tori (1988)

The title refers to a theory which is based on independent research in three different fields—differential geometry, dynamical systems and solid state physics—and which has attracted growing interest and research activity in the last few years. The objects of this theory are respectively: (1) Geodesics on a 2-dimensional torus with Riemannian (or symmetric Finsler) metric. (2) The dynamics of monotone twist maps of an annulus. (3) The discrete Frenkel-Kontorova model.
Stuff I've Seen (2016)

Most information retrieval technologies are designed to facilitate information discovery. However, much knowledge work involves finding and re-using previously seen information. We describe the design and evaluation of a system, called Stuff I've Seen (SIS), that facilitates information re-use. This is accomplished in two ways. First, the system provides a unified index of information that a person has seen, whether it was seen as email, web page, document, appointment, etc. Second, because the information has been seen before, rich contextual cues can be used in the search interface. The system has been used internally by more than 230 employees. We report on both qualitative and quantitative aspects of system use. Initial findings show that time and people are important retrieval cues. Users find information more easily using SIS, and use other search tools less frequently after installation.
Genome Survey and Characterization of Endophytic Bacteria Exhibiting a Beneficial Effect on Growth and Development of Poplar Trees (2008)

The association of endophytic bacteria with their plant hosts has a beneficial effect for many different plant species. Our goal is to identify endophytic bacteria that improve the biomass production and the carbon sequestration potential of poplar trees (Populus spp.) when grown in marginal soil and to gain an insight in the mechanisms underlying plant growth promotion. Members of the Gammaproteobacteria dominated a collection of 78 bacterial endophytes isolated from poplar and willow trees. As representatives for the dominant genera of endophytic gammaproteobacteria, we selected Enterobacter sp. strain 638, Stenotrophomonas maltophilia R551-3, Pseudomonas putida W619, and Serratia proteamaculans 568 for genome sequencing and analysis of their plant growth-promoting effects, including root development. Derivatives of these endophytes, labeled with gfp, were also used to study the colonization of their poplar hosts. In greenhouse studies, poplar cuttings (Populus deltoides x Populus nigra DN-34) inoculated with Enterobacter sp. strain 638 repeatedly showed the highest increase in biomass production compared to cuttings of noninoculated control plants. Sequence data combined with the analysis of their metabolic properties resulted in the identification of many putative mechanisms, including carbon source utilization, that help these endophytes to thrive within a plant environment and to potentially affect the growth and development of their plant hosts. Understanding the interactions between endophytic bacteria and their host plants should ultimately result in the design of strategies for improved poplar biomass production on marginal soils as a feedstock for biofuels.
Pyridoxal phosphate binding to wild type, W330F, and C298S mutants of Escherichia coli apotryptophanase: unraveling the cold inactivation (1998)

The mechanism of pyridoxal phosphate (PLP) binding to apotryptophanase was investigated using stopped-flow kinetics with wild type (WT), W330F and C298S mutants. Based on the dependence of the rate constants on PLP concentrations for the fast and slow phases detected, two mechanistic schemes were proposed. For the WT and C298S mutant, the slow process is due to an isomerization of the aldimine complex after its formation, and not to the binding to an alternative conformation of the apoenzyme, which is the case proposed for the W330F mutant. It is suggested that during the cold inactivation process a conformational change precedes the aldimine bond cleavage. For the W330F apotryptophanase, another conformational change occurs subsequent to the aldimine bond cleavage.