gebhart/patrepeval huggingface dataset:
Antibacterial Action of Extracellular Mammalian Group IIA Phospholipase A2 against Grossly Clumped Staphylococcus aureus (1999)

Fibrinogen-dependent interactions of Staphylococcus aureus are believed to contribute to bacterial virulence by promoting bacterial attachment to fibrinogen-coated surfaces and inducing the formation of bacterial clumps that are likely resistant to phagocytosis. Although S. aureus produces several fibrinogen-binding proteins, the cell wall-associated protein clumping factor (encoded by clfA) appears to be most important in bacterial interactions with immobilized or soluble purified fibrinogen. We have compared bacterial clumping in several strains of S. aureus, including isogenic ClfA+ and ClfA- Newman strains, in the presence of purified rabbit fibrinogen, human plasma, and inflammatory fluid and examined the effect of clumping on bacterial sensitivity to mammalian group IIA phospholipase A2 (PLA2). This enzyme is the major extracellular bactericidal agent in inflammatory fluid active against S. aureus. Both ClfA-dependent and ClfA-independent bacterial clumping was observed, depending on the source and fibrinogen content of the biological fluid. In each case, clumping only partially reduced the antibacterial activity of PLA2, suggesting that this extracellular enzyme can substantially penetrate dense bacterial clumps. Bacterial clumps could be dispersed by added proteases, restoring full antibacterial activity to PLA2. Thus, the extracellular mobilization of group IIA PLA2 during inflammation may provide a mechanism by which the host can control the proliferation and survival of S. aureus even after bacterial clumping.
Fourteen-and Ninety-Day Oral Toxicity Studies of Methyl Tertiary-Butyl Ether in Sprague-Dawley Rats (1990)

Male and female Sprague-Dawley rats were gavaged with methyl tertiary-butyl ether (MtBE) for 14 or 90 days to evaluate subacute and subchronic toxicity. Five daily dose levels ranged from 0 to 1428 mg/kg body weight for the 14 day study and 0 to 1200 mg/kg body weight for the 90-day exposure. Controls received the corn oil vehicle. At or above dose levels of 1200 mg/kg, MtBE-induced anesthesia lasted about 2 h, followed by uneventful recovery. Diarrhea was common in all treatment groups, but no deaths were attributed to MtBE toxicity. In the subacute study, lung weights were reduced in high-dose females. Trends in the 14-day exposure also included increased cholesterol in both females and males and decreased blood-urea nitrogen (BUN) and creatinine in females. In the 90-day study, females exhibited elevated cholesterol and decreased BUN, while creatinine was decreased in high-dose males. Microscopic findings in most organs were unremarkable, except for high-dose males where renal changes were compatible with alpha 2 -globulin nephropathy and were considered to have little toxicologic significance for humans. Both studies indicated that dose levels below those which induce anesthesia (1200 mg/kg) do not result in significant pathophysiologic changes.
Significant decrease of the lattice thermal conductivity due to phonon confinement in a free-standing semiconductor quantum well (1998)

Lattice thermal conductivity of a quantum well limited by umklapp, impurity, and boundary scattering was investigated theoretically by taking into account dispersion of confined acoustic-phonon modes. We show that strong modification of phonon group velocities due to spatial confinement leads to a significant increase in the phonon relaxation rates. From the numerical calculations, we predict a decrease by an order of magnitude of the lattice thermal conductivity in a 100-\AA{}-wide free-standing quantum well. Our theoretical results are consistent with recent experimental investigations of the lateral thermal conductivity of nitride/silicon/oxide membranes conducted in our group.
Thyroid-Stimulating Hormone and Thyroid-Stimulating Hormone Receptor Structure-Function Relationships (2002)

This review focuses on recent advances in the structure-function relationships of thyroid-stimulating hormone (TSH) and its receptor. TSH is a member of the glycoprotein hormone family constituting a subset of the cystine-knot growth factor superfamily. TSH is produced by the pituitary thyrotrophs and released to the circulation in a pulsatile manner. It stimulates thyroid functions using specific membrane TSH receptor (TSHR) that belongs to the superfamily of G protein-coupled receptors (GPCRs). New insights into the structure-function relationships of TSH permitted better understanding of the role of specific protein and carbohydrate domains in the synthesis, bioactivity, and clearance of this hormone. Recent progress in studies on TSHR as well as studies on the other GPCRs provided new clues regarding the molecular mechanisms of receptor activation. Such advances are a result of extensive site-directed mutagenesis, peptide and antibody approaches, detailed sequence analyses, and molecular modeling as well as studies on naturally occurring gain- and loss-of-function mutations. This review integrates expanding information on TSH and TSHR structure-function relationships and summarizes current concepts on ligand-dependent and -independent TSHR activation. Special emphasis has been placed on TSH domains involved in receptor recognition, constitutive activity of TSHR, new insights into the evolution of TSH bioactivity, and the development of high-affinity TSH analogs. Such structural, physiological, pathophysiological, evolutionary, and therapeutic implications of TSH-TSHR structure-function studies are frequently discussed in relation to concomitant progress made in studies on gonadotropins and their receptors.
Biochemical composition of amniotic fluid and extraembryonic coelomic fluid in the first trimester of pregnancy (1992)

Amniotic fluid and extraembryonic coelomic fluid have a widely differing biochemical composition. The biological significance of these differences remains unexplained.
Bone Marrow-Derived Mesenchymal Stem Cells: Isolation, Expansion, Characterization, Viral Transduction, and Production of Conditioned Medium (2008)

Mesenchymal stem cells (MSCs) are defined as self-renewing and multipotent cells capable of differentiating into multiple cell types, including osteocytes, chondrocytes, adipocytes, hepatocytes, myocytes, neurons, and cardiomyocytes. MSCs were originally isolated from the bone marrow stroma but they have recently been identified also in other tissues, such as fat, epidermis, and cord blood. Several methods have been used for MSC isolation. The most common method is based on the ability of the MSCs to selectively adhere to plastic surfaces. Phenotypic characterization of MSCs is usually carried out using immunocytochemical detection or fluorescence-activated cell sorting (FACS) analysis of cell surface molecule expression. However, the lack of specific markers renders the characterization of MSCs difficult and sometimes ambiguous. MSCs posses remarkable expansion potential in culture and are highly amenable to genetic modification with various viral vectors rendering them optimal vehicles for cell-based gene therapy. Most importantly, MSC plasticity and the possibility to use them as autologous cells render MSCs suitable for cell therapy and tissue engineering. Furthermore, it is known that MSCs produce and secrete a great variety of cytokines and chemokines that play beneficial paracrine actions when MSCs are used for tissue repair. In this chapter, we describe methods for isolation, ex vivo expansion, phenotypic characterization, and viral infection of MSCs from mouse bone marrow. We also describe a method for preparation of conditioned and concentrated conditioned medium from MSCs. The conditioned medium can be easily tested both in vitro and in vivo when a particular paracrine effect (i.e., cytoprotection) is hypothesized to be an important mechanism of action of the MSCs and/or screened to identify a target paracrine/autocrine mediator.
Tacholess Envelope Order Analysis and Its Application to Fault Detection of Rolling Element Bearings with Varying Speeds (2013)

Vibration analysis is an effective tool for the condition monitoring and fault diagnosis of rolling element bearings. Conventional diagnostic methods are based on the stationary assumption, thus they are not applicable to the diagnosis of bearings working under varying speed. This constraint limits the bearing diagnosis to the industrial application significantly. In order to extend the conventional diagnostic methods to speed variation cases, a tacholess envelope order analysis technique is proposed in this paper. In the proposed technique, a tacholess order tracking (TLOT) method is first introduced to extract the tachometer information from the vibration signal itself. On this basis, an envelope order spectrum (EOS) is utilized to recover the bearing characteristic frequencies in the order domain. By combining the advantages of TLOT and EOS, the proposed technique is capable of detecting bearing faults under varying speeds, even without the use of a tachometer. The effectiveness of the proposed method is demonstrated by both simulated signals and real vibration signals collected from locomotive roller bearings with faults on inner race, outer race and rollers, respectively. Analyzed results show that the proposed method could identify different bearing faults effectively and accurately under speed varying conditions.
The role of Seprafilm™ bioresorbable membrane in the prevention and therapy of endometrial synechiae (2002)

This randomized controlled blind prospective study is undertaken to evaluate the safety and efficacy of Seprafilm--a novel bioresorbable membrane of chemically modified hyaluronic acid and carboxymethylcellulose--in prevention and reduction of postoperative endometrial and endocervical synechiae formation after general suction evacuation or curettage for incomplete, missed, and recurrent abortion. In total, 150 patients with incomplete or missed abortion participated in the clinical study. The study population was divided into two main groups. In the treatment (Seprafilm) group (n=50), application of Seprafilm membrane in the endometrial cavity and the cervical canal was used after the suction evacuation and/or the curettage. In the control group (n=100), nothing was inserted in the uterus. Both groups were divided into two subgroups: patients who had no previous suction or curettage, (with no previous D&C) (n=88), and patients who had at least one previous suction or curettage (with one or more previous D&C) (n=62). In the treatment (Seprafilm) group, 32 patients had no previous D&C and 18 patients had one or more previous D&C. In the control group, 56 patients had no previous D&C and 44 patients had one or more previous D&C. Further fertility was estimated by pregnancy success in all groups. Endometrial synechiae formation was evaluated with the use of hysterosalpingography (HSG) in patients of all groups without pregnancy success 8 months after the intervention. Registering any adverse reaction and performing ultrasound controls assessed the safety of Seprafilm use. From the subgroup with no previous D&C, all 32 patients (100%) who received Seprafilm had a pregnancy in the following 8 months; in the controls, pregnancy occurred only in 54%. It was also demonstrated with hysterosalpingography (HSG) that patients with one or more previous interventions and no pregnancy 8 months later were adhesion free in 90% of the patients where Seprafilm was used, and only 50% in the untreated group. The membrane was tested on the endometrial area of the uterus and did not produce any adverse reaction. Ultrasound controls did not show any abnormal echoes. Intrauterine insertion of Seprafilm is safe, prevents the appearance of endocervical adhesions or endometrial synechiae after curettage, and reduces the area of the endometrial cavity occupied by them in a large percent of cases. It also seems that its use improves the possibility of a new pregnancy and fertility.
Evaluation of sit-stand workstations in an office setting: a randomised controlled trial (2015)

ClinicalTrials.gov NCT02496507 .
Involvement of Double-strand Chromosomal Breaks for Mating-type Switching in Saccharomyces cerevisiae (1984)

The yeast S. cerevisiae switches a and alpha cell types by a transposition mechanism that replaces genetic information residing at the mating-type locus (MAT) with information copied from either of the two donor loci, HML and HMR. The donor HML and HMR loci contain the same genetic information as the MATa and MAT alpha alleles, yet they do not switch. Additionally, Strathern et al. (1982) have described an in vivo double-strand DNA break found at subgenomic levels (approximately 2% of MAT DNA) within the MAT locus but not within HML and HMR. We have examined the role of this double-strand DNA break in the switching process. Cell lineage studies show that strains containing deletions of the donor HML and HMR loci produce lethal progeny in the exact pattern described for MAT switching in standard strains. Our interpretation is that the double-strand MAT break in the deletion strains cannot be repaired because of the lack of the donor loci, resulting in cell death. We suggest that the double-strand DNA break is an initiating event for switching and that this event is lethal in the absence of the donor loci. MAT mutants isolated as survivors from this "pedigree of death" define a site required for switching where the double-strand break occurs. We have also examined marl mutant strains in which the donor loci are expressed and observed to switch (Klar et al. 1981a). The double-strand DNA cut appears at the HM loci in these strains. Thus, there is a strong correlation between the presence or absence of the double-strand break at each cassette and its ability or inability to switch as observed at the single cell level.
Small-Molecule Inhibitors of PKR Improve Glucose Homeostasis in Obese Diabetic Mice (2013)

Obesity and metabolic diseases appear as clusters, often featuring high risk for insulin resistance and type 2 diabetes, and constitute a major global health problem with limited treatment options. Previous studies have shown that double-stranded RNA-dependent kinase, PKR, plays an important role in the nutrient/pathogen-sensing interface, and acts as a key modulator of chronic metabolic inflammation, insulin sensitivity, and glucose homeostasis in obesity. Recently, pathological PKR activation was also demonstrated in obese humans, strengthening its prospects as a potential drug target. Here, we investigate the use of two structurally distinct small-molecule inhibitors of PKR in the treatment of insulin resistance and type 2 diabetes in cells and in a mouse model of severe obesity and insulin resistance. Inhibition of PKR reduced stress-induced Jun NH2-terminal kinase activation and insulin receptor substrate 1 serine phosphorylation in vitro and in vivo. In addition, treatment with both PKR inhibitors reduced adipose tissue inflammation, improved insulin sensitivity, and improved glucose intolerance in mice after the establishment of obesity and insulin resistance. Our findings suggest that pharmacologically targeting PKR may be an effective therapeutic strategy for the treatment of insulin resistance and type 2 diabetes.
Aluminum- and Boron-Mediated C-Glycoside Synthesis from 1,2-Anhydroglycosides (2000)

[reaction: see text]This letter describes a single flask strategy to the synthesis of alpha-C-glycosides from glycals. This protocol couples a glycal epoxidation reaction with a C-2 alkoxy-directed carbon-carbon bond-forming reaction.
Whole-Body Hypothermia for Neonates with Hypoxic–Ischemic Encephalopathy (2005)

Whole-body hypothermia reduces the risk of death or disability in infants with moderate or severe hypoxic-ischemic encephalopathy.
Establishment of SV40-tsA58 Transgenic Rats as a Source of Conditionally Immortalized Cell Lines. (1999)

To isolate a variety of rat cell lines with differentiated functions, we established transgenic rat lines expressing the temperature-sensitive large T-antigen of simian virus 40 (SV40) tsA58 mutant under the control of the SV40 large T-antigen itself. We microinjected the DNA into 564 eggs of Wistar rat and 23 independent transgenic candidates were obtained. Ten pups died before weaning and eight transgenic rats could not transmit the transgene to the progeny. Finally, five lines of the transgenic rat were established. Although one line (#1511-6) had low reproductivity, the other four lines reproduced normally. Three out of the four lines (#1507-2, #1509-7, #1519-8) appeared normal but the other line had tumors in the brain and subcutaneous tissue at 3 weeks of age (#1511-6), and in the kidneys and subcutaneous tissue at 18 to 19-weeks of age (#1507-5). Fibroblast cells prepared from transgenic fetuses of lines #1507-5 and #1519-8 expressed the transgene and exhibited temperature-dependent growth. Both of the lines (#1507-5 and #1519-8) were successfully generated to be homozygous by sibling mating of transgenic offspring. These transgenic rat lines have bred through many generations and have been established to be a ready source of novel conditionally immortalized cell lines.
Engineering of Adenovirus Vectors Containing Heterologous Peptide Sequences in the C Terminus of Capsid Protein IX (2002)

The utility of the present generation of adenovirus (Ad) vectors for gene therapy applications could be improved by restricting native viral tropism to selected cell types. In order to achieve modification of Ad tropism, we proposed to exploit a minor component of viral capsid, protein IX (pIX), for genetic incorporation of targeting ligands. Based on the proposed structure of pIX, we hypothesized that its C terminus could be used as a site for incorporation of heterologous peptide sequences. We engineered recombinant Ad vectors containing modified pIX carrying a carboxy-terminal Flag epitope along with a heparan sulfate binding motif consisting of either eight consecutive lysines or a polylysine sequence. Using an anti-Flag antibody, we have shown that modified pIXs are incorporated into virions and display Flag-containing C-terminal sequences on the capsid surface. In addition, both lysine octapeptide and polylysine ligands were accessible for binding to heparin-coated beads. In contrast to virus bearing lysine octapeptide, Ad vector displaying a polylysine was capable of recognizing cellular heparan sulfate receptors. We have demonstrated that incorporation of a polylysine motif into the pIX ectodomain results in a significant augmentation of Ad fiber knob-independent infection of CAR-deficient cell types. Our data suggest that the pIX ectodomain can serve as an alternative to the fiber knob, penton base, and hexon proteins for incorporation of targeting ligands for the purpose of Ad tropism modification.
Paclitaxel in the treatment of metastatic breast cancer: M.D. Anderson Cancer Center experience. (1995)

Paclitaxel (Taxol; Bristol-Myers Squibb Company, Princeton, NJ) 250 mg/m2 by 24-hour infusion at 21-day intervals was evaluated at M.D. Anderson Cancer Center as a single agent in patients who had received one prior chemotherapy regimen either as adjuvant therapy or for metastatic disease. Of 25 patients treated, 12% had a complete remission and 44% had a partial response. The median time to progression was 9 months (range, 1 to 20 months). In the next phase of development, a phase I trial evaluated sequentially administered paclitaxel and doxorubicin as initial therapy for metastatic disease. Granulocyte colony-stimulating factor also was administered in each cycle. The dose-limiting toxicity was either stomatitis or neutropenic fever. The maximum tolerated dose (MTD) was 125 mg/m2 for paclitaxel and 48 mg/m2 for doxorubicin. Because of much lower than anticipated MTDs of both drugs in this schedule, it was hypothesized that there may be a schedule-dependent toxicity; therefore, in the second phase I study the schedule of administration was reversed (ie, doxorubicin followed by paclitaxel infusion). The MTDs of this schedule were 60 mg/m2 and 150 mg/m2 for doxorubicin and paclitaxel, respectively. Pharmacokinetic studies subsequently have confirmed that administration of paclitaxel before doxorubicin impairs the elimination of doxorubicin by some unknown mechanism. In an ongoing phase II study, paclitaxel is being evaluated in patients who have received three or more treatments with chemotherapy. Paclitaxel is administered at doses of 135 and 150 mg/m2 (for poor- and good-risk patients, respectively) without granulocyte colony-stimulating factor. Six patients (19%) have shown objective partial responses. Our initial phase II study showed significant antitumor activity for paclitaxel in patients who had received limited prior chemotherapy. Our phase I studies established that initial administration of paclitaxel alters the pharmacokinetics of doxorubicin and increases morbidity. The reverse sequence of administration was associated with better tolerance and a higher MTD. In heavily treated patients this drug also has significant antitumor activity.
Tumor Cell and Endothelial Cell Therapy of Oral Cancer by Dual Tyrosine Kinase Receptor Blockade (2004)

Expression of the epidermal growth factor (EGF) and activation of its receptor (EGFR), a tyrosine kinase, are associated with progressive growth of head and neck cancer. Expression of the vascular endothelial growth factor (VEGF) is associated with angiogenesis and progressive growth of tumor. The tyrosine kinase inhibitor NVP-AEE788 (AEE788) blocks the EGF and VEGF signaling pathways. We examined the effects of AEE788 administered alone, or with paclitaxel (Taxol), on the progression of human head and neck cancer implanted orthotopically into nude mice. Cells of two different human oral cancer lines, JMAR and MDA1986, were injected into the tongues of nude mice. Mice with established tumors were randomized to receive three times per week oral AEE788, once weekly injected paclitaxel, AEE788 plus paclitaxel, or placebo. Oral tumors were resected at necropsy. Kinase activity, cell proliferation, apoptosis, and mean vessel density were determined by immunohistochemical immunofluorescent staining. AEE788 inhibited cell growth, induced apoptosis, and reduced the phosphorylation of EGFR, VEGFR-2, AKT, and mitogen-activated protein kinase in both cell lines. Mice treated with AEE788 and AEE788 plus paclitaxel had decreased microvessel density, decreased proliferative index, and increased apoptosis. Hence, AEE788 inhibited tumor vascularization and growth and prolonged survival. Inhibition of EGFR and VEGFR phosphorylation by AEE788 effectively inhibits cellular proliferation of squamous cell carcinoma of the head and neck, induces apoptosis of tumor endothelial cells and tumor cells, and is well tolerated in mice. These data recommend the consideration of patients with head and neck cancer for inclusion in clinical trials of AEE788.
3-(2-Carboxyindol-3-yl)propionic acid-based antagonists of the NMDA (N-methyl-D-aspartic acid) receptor associated glycine binding site (1992)

A series of substituted 3-(2-carboxyindol-3-yl)propionic acids was synthesized and tested as antagonists for the strychnine-insensitive glycine binding site of the NMDA receptor. Chlorine, and other small electron-withdrawing substituents in the 4- and 6-positions of the indole ring, greatly enhanced binding and selectivity for the glycine site over the glutamate site of the NMDA receptor; one of the most potent compounds is 3-(4,6-dichloro-2-carboxyindol-3-yl)propionic acid (IC50 = 170 nM; greater than 2100-fold selective for glycine). The importance of a heteroatom NH and the enhancing effect of the propionic acid side chain were demonstrated and are consistent with previous results which suggest the presence of a pocket on the receptor which can accept an acidic side chain. Substitution of a sulfur at C3 led to the most potent compound 3-[(carboxymethyl)thio]-2-carboxy-4,6-dichloroindole (IC50 = 100 nM).