gebhart/patrepeval huggingface dataset:
Effect of Ancillary Ligands and Solvents on H/D Exchange Reactions Catalyzed by Cp*Ir Complexes (2010)

A series of complexes of the form Cp*Ir(NHC)(X)n and [Cp*Ir(NHC)(L)2][OTf]2, where NHC = 1,3,4,5-tetramethylimidazol-2-ylidene (n = 2, X = Cl− (1-Cl), NO3− (1-NO3), −OC(O)CF3 (=TFA, 1-TFA); n = 1, X = SO42− (1-SO4); L = H2O (1-H2O), CH3CN (1-CH3CN), OTf = trifluoromethanesulfonato), were prepared. X-ray crystal structures of 1-OH2, 1-SO4, and 1-NO3 and the dimeric complex [(Cp*Ir(NHC)Cl)2][OTf]2 (2) were obtained. In solution, the complex 1-TFA was found to exist in equilibrium with [Cp*Ir(NHC)(OH2)2][OCOCF3]2 (1-aqua-TFA), where the aqua ligands are strongly hydrogen bound to the −OCOCF3 counterion. A van’t Hoff plot from −10 to 30 °C yielded values for the reaction enthalpy and entropy of ΔH° = −7.6 ± 0.7 kcal/mol and ΔS° = −30.6 ± 2.4 eu, respectively. These data are consistent with the observation that at higher temperatures the complex 1-TFA is favored. An X-ray crystal structure of 1-aqua-TFA was obtained. Catalytic H/D exchange reactions between benzene and various deuterium sources (CD3OD, CF3COOD, CD3COCD3, and D2O) were performed and assessed by GC-MS. The best deuterium sources for this reaction were found to be CD3OD or CD3OD/D2O (1:1) mixtures. The highest turnover numbers (TONs) were observed for the H/D exchange reactions catalyzed by Cp*Ir(NHC) complexes with labile ligands. These results suggest that the dissociation of the ancillary ligand to form an unsaturated 16-electron intermediate is an important step prior to C−H activation in the catalytic cycle, which is consistent with the Shilov electrophilic C−H activation mechanism. In contrast, the most effective deuterium source for H/D exchange with the aqua complex [Cp*Ir(OH)3][OTf2] (3) was the acidic solvent CF3COOD. Thus, the σ-donating NHC ligand serves to attenuate the electrophilicity of the metal center so that milder reaction conditions are required for the C−H activation reactions.
Relative Entropy Based Method for Global and Regional Sensitivity Analysis in Probabilistic Design (2004)

To overcome the limitations of existing variance-based methods for Probabilistic Sensitivity Analysis (PSA) in design under uncertainty, a new PSA approach based on the concept of relative entropy is proposed. The relative entropy based method evaluates the impact of a random variable by measuring the divergence between two probability density functions of a response. The method can be applied both globally over the whole distribution of a performance response (called global response probabilistic sensitivity analysis–GRPSA) and in any regional range of a response distribution (called regional response probabilistic sensitivity analysis–RRPSA). The former is the most useful for studying variable impact on robust design objective, while the latter provides insight into reliability constraints. The proposed method is applicable to both the prior-design and post-design stages, for variable screening and uncertainty reduction, respectively. The proposed method is verified by numerical examples and industrial design cases.
Inhibition of Carbonic Anhydrase-II by Sulfamate and Sulfamide Groups:  An Investigation Involving Direct Thermodynamic Binding Measurements (2006)

This paper examines the relative effectiveness of bioisosteric sulfamate and sulfamide derivatives for inhibition of human carbonic anhydrase-II (CA-II) by using a direct binding assay based on the ThermoFluor method (Matulis et al. Biochemistry 2005, 44, 5258). Compounds 1-10, which represent five cognate sulfamate/sulfamide pairs, were studied by ThermoFluor to obtain binding affinities (K(a) values). The corresponding dissociation constants, K(d), provide an independent measure of CA-II activity relative to commonly used K(i) values from enzyme kinetics studies. There was a sizable difference in potency between the sulfamates and sulfamides, with the sulfamides being much less potent, by factors ranging from 25 (7/8) to 1,200 (3/4). These results are consistent with our recent report that sulfamides tend to be much weaker inhibitors of CA-II than their corresponding sulfamates (Maryanoff et al. J. Med. Chem. 2005, 48, 1941). Additionally, for arylsulfamides 10-12 the K(d) values determined by ThermoFluor and the K(i) values determined from enzyme kinetics are consistent. It appears that the sulfamide group is less suitable than the sulfamate group for obtaining potent inhibition of CA-II.
Corneal Storage Medium Preservation with Defensins (1992)

We used a synthetic defensin (rabbit neutrophil peptide-1; NP-1) as a microbicide in a corneal storage medium, Optisol without antimicrobial compounds. We established growth curves in Optisol for Staphylococcus aureus, Streptococcus pneumoniae, and Pseudomonas aeruginosa. Each organism was evaluated separately at 4 degrees C, 23 degrees C, and 37 degrees C in Optisol with NP-1 at each of four different concentrations including 1, 10, 100, and 200 micrograms/ml. When the three organisms were evaluated in Optisol containing NP-1, we found that a concentration of 200 micrograms/ml of NP-1 successfully killed 99.9% (the limits of our assay) of all three organisms at all temperatures tested. We conclude that NP-1 exhibits promise as a nonantibiotic preservative agent in corneal storage media, since it was effective in killing organisms at all temperatures, including 4 degrees C.
Serological detection of Gram-positive bacterial infection around prostheses (2000)

Coagulase-negative staphylococci produce an exocellular glycolipid antigen which has potential as a serological marker of infection in bone. The value of this newly detected antigen was investigated by enzyme-linked immunosorbent assay (ELISA) in 15 patients with culture-proven infection of prostheses caused by Gram-positive bacteria. The antigen was purified by gel-permeation chromatography from the culture supernatants of coagulase-negative staphylococci grown in a chemically defined medium. There were significant differences (p &lt; 0.0001) between the serum IgG and IgM levels in patients with infection due to Gram-positive staphylococci and those of a control group of 32 patients with no infection. The ELISA test, which has potential for the diagnosis of infection, may be valuable in distinguishing between staphylococcal infection around prostheses and aseptic loosening.
Thinking with image making in supervision (2003)

Abstract The authors describe how regular discussions about their supervisory work with art therapy students highlighted an interest in the role of the image in art therapy supervision. This is explored through their experience of using image making in supervision groups. The nature of the supervision process and the role of image making in supervision is discussed with reference to the literature. The aims and composition of the supervision groups are described in the context of the training. The effects of incorporating aesthetic experience into the groups, and its effect on thinking are explored. The authors conclude by discussing the uniqueness of image making and its evolving position within the profession.
Role of tumor necrosis factor-alpha in lipopolysaccharide-induced pathologic alterations. (1990)

Tumor necrosis factor-alpha (TNF) has been implicated strongly as a principal mediator in the pathogenesis of septic shock. The authors investigated the in vivo production of TNF in CBA/J and CD-1 mice that had been primed by an intraperitoneal injection of complete Freund's adjuvant followed 2 weeks later by an intraperitoneal injection of lipopolysaccharide (LPS). TNF bioactivity peaked in both the ascites and plasma one hour after challenge, and TNF mRNA expression in the ascites cells peaked 30 minutes after LPS. After the induction of bioactivity, an interstitial pulmonary neutrophilic infiltrate occurred that was quantitated both morphometrically and by a myeloperoxidase (MPO) assay. Peripheral blood neutrophilia and lymphopenia developed after the LPS injection (PMNs: control, 46 +/- 2%; LPS, 65 +/- 3%; Lymphs control, 53 +/- 2%; LPS, 37 +/- 3%). Treatment with dexamethasone (Dex) completely inhibited the pulmonary neutrophilic infiltrate as measured by the (MPO) assay. Because Dex will inhibit the production of several cytokines, anti-TNF antiserum was given to mice at the same time as the LPS challenge to assess specifically the role of TNF in inducing these changes. This antiserum partially blocked the pulmonary neutrophil infiltrate, and completely blocked the peripheral blood changes at one hour after LPS. These data demonstrate that TNF plays an important role in the early pathophysiologic alterations that occur after systemic exposure to LPS.
Basic ingredients of free energy calculations: A review (2009)

Methods to compute free energy differences between different states of a molecular system are reviewed with the aim of identifying their basic ingredients and their utility when applied in practice to biomolecular systems. A free energy calculation is comprised of three basic components: (i) a suitable model or Hamiltonian, (ii) a sampling protocol with which one can generate a representative ensemble of molecular configurations, and (iii) an estimator of the free energy difference itself. Alternative sampling protocols can be distinguished according to whether one or more states are to be sampled. In cases where only a single state is considered, six alternative techniques could be distinguished: (i) changing the dynamics, (ii) deforming the energy surface, (iii) extending the dimensionality, (iv) perturbing the forces, (v) reducing the number of degrees of freedom, and (vi) multi-copy approaches. In cases where multiple states are to be sampled, the three primary techniques are staging, importance sampling, and adiabatic decoupling. Estimators of the free energy can be classified as global methods that either count the number of times a given state is sampled or use energy differences. Or, they can be classified as local methods that either make use of the force or are based on transition probabilities. Finally, this overview of the available techniques and how they can be best used in a practical context is aimed at helping the reader choose the most appropriate combination of approaches for the biomolecular system, Hamiltonian and free energy difference of interest.
Platelets: Inflammatory Firebugs of Vascular Walls (2008)

Atherosclerosis is an inflammatory disease. Platelets can "inflame" the vascular wall by various mechanisms and thereby initiate and support the development of atherosclerosis. Platelet interaction with leukocytes, endothelial cells, and circulating progenitor cells triggers autocrine and paracrine activation processes, leading to inflammatory and atherogenic cascades at the vascular wall. This review highlights the molecular key components and pathways used by platelets to trigger and accelerate inflammation at the vascular wall and, thereby, atherosclerosis.
Early onset of inflammation and later involvement of TGFβ in Duchenne muscular dystrophy (2005)

Our data show stage-specific remodeling of human dystrophin-deficient muscle, with inflammatory pathways predominating in the presymptomatic stages and acute activation of TGFbeta and failure of metabolic pathways later in the disease.
Healthy lifestyles in Europe: prevention of obesity and type II diabetes by diet and physical activity (2001)

The prevalence of obesity is increasing rapidly in all age groups in most EU-countries and is one of the fastest growing epidemics, now affecting 10-40% of the adult population. Obesity increases the risk of serious co-morbidities such as type 2 diabetes, cardiovascular disease, certain cancers and reduced life expectancy, and these complications may account for 5-10% of all health costs in EU countries. The risk of diabetes is particularly increased by obesity, and 80-95% of the increase in diabetes can be attributed to obesity and overweight with abdominal fat distribution. There is robust evidence from cross-sectional and longitudinal studies to support that an energy-dense, high fat diet and physical inactivity are independent risk factors for weight gain and obesity. Furthermore, interaction between dietary fat and physical fitness determine fat balance, so that the obesity promoting effect of a high fat diet is enhanced in susceptible subjects, particularly in sedentary individuals with a genetic predisposition to obesity. Ad libitum consumption of diets low in fat and high in protein and complex carbohydrates, with a low glycaemic index, contributes to the prevention of weight gain in normal weight subjects. It also causes a spontaneous weight loss of 3-4 kg in overweight subjects, and has beneficial effects on risk factors for diabetes and CVD. To prevent obesity and diabetes there are grounds for recommending the combination of increasing daily physical activity level to a PAL-value of at least 1.8 and reducing dietary fat content to 20-25 energy-% in sedentary subjects, and to 25-35% in more physically active individuals.
Hematopoietic stem cell deficiencies in mice lacking c-Mpl, the receptor for thrombopoietin (1998)

Thrombopoietin (TPO) acts as a lineage-specific late-acting factor to stimulate megakaryocyte and platelet formation. However, analysis of mice lacking either the cytokine or its receptor, c-Mpl, also revealed deficiencies in progenitor cells of multiple hematopoietic lineages, suggesting that TPO signaling may play an important role in the regulation of the hematopoietic stem cell compartment. To investigate this hypothesis, we determined preprogenitor and colony forming unit-spleen (CFU-S) numbers and analyzed the long-term hematopoietic repopulating capacity of bone marrow cells from mpl-/- mice. mpl-/- mice had 4- to 12-fold fewer preprogenitor cells than wild-type mice. In irradiated normal recipients, mpl-/- bone marrow generated 8- to 10-fold fewer spleen colonies than wild-type marrow at both 8 and 12 days after transplantation. This defect was intrinsic to the transplanted hematopoietic cells, as the microenvironment of mpl-/- recipients supported similar CFU-S growth to that observed in wild-type recipients. In definitive assays of stem cell function, bone marrow cells from mpl-/- mice failed to compete effectively with normal cells for long-term reconstitution of the hematopoietic organs of irradiated recipients, even when transplanted in 10-fold excess. Serial transplantation studies further suggested that stem cell self-renewal also may be compromised in mpl-/- mice. These data imply that TPO, signaling through c-Mpl, plays a vital physiological role in the regulation of hematopoietic stem cell production and function.
A multichannel neural probe for selective chemical delivery at the cellular level (1997)

A bulk-micromachined multichannel silicon probe capable of selectively delivering chemicals at the cellular level as well as electrically recording from and stimulating neurons in vivo has been developed. The process buries multiple flow channels in the probe substrate, resulting in a hollow-core device. Microchannel formation requires only one mask in addition to those normally used for probe fabrication and is compatible with on-chip signal-processing circuitry. Flow in these microchannels has been studied theoretically and experimentally. For an effective channel diameter of 10 microns, a channel length of 4 mm, and water as the injected fluid, the flow velocity at 11 torr is about 1.3 mm/s, delivering 100 pl in 1 s. Intermixing of chemicals with the tissue fluid due to natural diffusion through the outlet orifice becomes significant for dwell times in excess of about 30 min, and a shutter is proposed for chronic use. The probe has been used for acute monitoring of the neural responses to various chemical stimuli in guinea pig superior and inferior colliculus.
Anti-Salmonella lacatic acid bacteria from porcine intestinal sources (2003)

The aim of this study was to isolate lactic acid bacteria (LAB) with anti-Salmonella activity from the porcine gastrointestinal tract (GIT) and to characterise these for potentially probiotic properties using in vitro assays. Porcine caecal and faecal samples were screened for the presence of anti-Salmonella LAB; the ten most promising isolates belonged to the genera Lactobacillus and Pediococcus. The LAB exhibited large variation in their ability to survive in simulated gastric juice at pH 1.85. While Lactobacillus acidophilus species survived at up to 80% for 30 min, Lb. pentosus species declined to less than 0.001%. All isolates tolerated porcine bile at a concentration of 0.3%, with some capable of growth in the presence of up to 5% bile. The ability of the LAB isolates to prevent Salmonella invasion of intestinal epithelial cells varied, with reductions of 55% (Lb. acidophilus spp.) to 82% (Lb. salivarius spp.) observed. The data demonstrates that some porcine intestinal LAB isolates may offer potential as probiotics for the reduction of Salmonella carriage in pigs.
A systematic review of quality of life and weight gain-related issues in patients treated for severe and persistent mental disorders: focus on aripiprazole (2009)

Aripiprazole is a relatively novel second-generation antipsychotic belonging to the chemical class of benzisoxazole derivatives and is characterized by a unique pharmacological profile which suggests that the drug acts as a dopamine-serotonin system stabilizer. Whereas all previously available antipsychotics are antagonists at D(2) receptors, aripiprazole is the only available partial agonist at these receptors. Thus, it has been suggested that aripiprazole could be associated with a relatively neutral impact on bodyweight, possibly reducing risks of a detrimental impact on the quality of life that often complicates management for a large number of patients diagnosed with severe and persistent mental disorders (SPMDs) treated chronically with antipsychotic medications. However, data from short- and long-term reviewed studies indicate that the prevalence rate of clinically relevant weight gain during therapy with this drug is similar to that occurring during treatments with other antipsychotic agents, either typical or atypical. Moreover, information on the impact of aripiprazole therapy on the quality of life of patients diagnosed with SPMDs is scarce and characterized by conflicting results. Given these results, further, large, well-designed studies are needed before confirming potential advantages of aripiprazole over first-generation antipsychotics and other SGAs.
Scaling laws for pulsed electrohydrodynamic drop formation (2006)

A pulsed electrohydrodynamic jet can produce on-demand drops much smaller than the delivery nozzle. This letter describes an experimentally validated model for electrically pulsed jets. Viscous drag in a thin nozzle limits the flow rate and leads to intrinsic pulsations of the cone jet. A scale analysis for intrinsic cone-jet pulsations is derived to establish the operating regime for drop deployment. The scaling laws are applicable to similar electrohydrodynamic processes in miniaturized electrospraying systems.
Etanercept for the treatment of psoriasis and psoriatic arthritis (2004)

Etanercept is a fully human soluble recombinant p75 TNF receptor that blocks the binding of TNF to cell surface receptors, thereby neutralizing its biologic activity. Data supporting the FDA's approval of etanercept for controlling signs and symptoms and for inhibiting XRAY progression of psoriatic arthritis will be presented. Data supporting the FDA filing of etanercept for the treatment of moderate to severe psoriasis will also be presented. Long term safety data of etanercept in the over 231,000 adults and children with rheumatoid arthritis who have been treated worldwide will be briefly summarized.
Routine Limulus amoebocyte lysate (LAL) test for endotoxin determination in milk using a Toxinometer ET-201 (1993)

A rapid method of performing the Limulus amoebocyte lysate (LAL) test in milk is proposed using the Toxinometer ET-201. This instrument measured the increase in turbidity due to the interaction between the endotoxins of the Gram-negative bacteria and the LAL reagent, monitored the ratio Rt of the sequential to the initial transmission at 12 s intervals and quantified endotoxins by determination of the reaction time Tr required to obtain a 5% decrease in Rt. There was a good correlation between the toxinometrically determined endotoxin concentrations and the number of Gram-negative bacteria (SD, 0.18 log(plate count units)), and the repeatability (CV, 6-10%) was high. The assay may be useful for screening raw materials for UHT milk production, as the endotoxin content of the raw material is related to the rest proteinase activity in the UHT milk.
Wilms' Tumor Gene 1 (WT1)--loaded dendritic cell immunotherapy in patients with uterine tumors: a phase I/II clinical trial. (2013)

A first series of six patients with uterine cancer treated with WT1 mRNA-electroporated DCs is presented herein. Oncological and immunological responses were observed and are supportive for further research.
Titration of the Infectivity of Hepatitis D Virus in Chimpanzees (1987)

The infectivity of hepatitis D virus (HDV) was evaluated by intravenous inoculation of chimpanzees. HDV was present in the inoculum at a titer of 10(11) chimpanzee infectious doses (CID). In contrast, the titer of hepatitis B virus (HBV) in the same inoculum was 10(6) CID. All HBV-infected chimpanzees inoculated with less than or equal to 10(-11) dilutions of the HDV-positive plasma were superinfected; an animal receiving a 10(-12) dilution did not develop markers of HDV replication in serum or liver. All HDV-infected chimpanzees had marked elevations of serum alanine aminotransferase activities. The incubation period from exposure to development of hepatitis was inversely related to the dose of HDV inoculum, although the severity and duration of hepatitis were independent of it. All animals recovered and rapidly developed antibody to hepatitis D antigen.
Tissue Doppler Echocardiographic Evidence of Reverse Remodeling and Improved Synchronicity by Simultaneously Delaying Regional Contraction After Biventricular Pacing Therapy in Heart Failure (2002)

Biventricular pacing reverses LV remodeling and improves cardiac function. Improvement of LV mechanical synchrony seems to be the predominant mechanism.
Characterization of bacteriophage T7 DNA polymerase purified to homogeneity by antithioredoxin immunoadsorbent chromatography. (1981)

DNA polymerase of bacteriophage T7 is composed of two subunits, the gene 5 protein of the phage and the host-coded thioredoxin. We have purified T7 DNA polymerase to homogeneity from T7-infected Escherichia coli B cells with a novel technique based on immunoadsorbent affinity chromatography. The enzyme binds quantitatively to a column of anti-thioredoxin Sepharose 4B and remains as an active complex in the immobilized state. It is eluted in fully active and highly purified form by a pulse of buffer at pH 12. After a final phosphocellulose chromatography, T7 DNA polymerase of better than 99% purity, as estimated from sodium dodecyl sulfate polyacrylamide gel electrophoresis, is obtained. Determination of the molecular weight by sedimentation equilibrium centrifugation gives a value of 112,000. Denaturing gels showed that the enzyme is composed of gene 5 protein (Mr = 87,000 +/- 3,000) and thioredoxin (Mr = 12,000) in a 1:1 stoichiometry. The amino acid composition of the enzyme and its spectrum was determined. The DNA polymerase activity is dependent on sulfhydryl compounds, sensitive to salt, and shows a comparatively high Km value for the four deoxyribonucleotides. The enzyme preparation has an inherent 3' leads to 5' exonuclease activity, attacking both native and denatured T7 DNA; it is free from detectable endonuclease activity.
WebGuard: Web based adult content detection and filtering system (2004)

@inproceedings{CI-CHAHIR-2003, author = {Hammami, M. and Chahir, Y. and Chen, L.}, title = {WebGuard: Web-Based Adult Content Detection and Filtering System}, booktitle = {IEEE/WIC International Conference on Web Intelligence (WI'03)}, pages = {574-578}, year = {2003}, address = {Halifax, Canada}, month = {October} }