gebhart/patrepeval huggingface dataset:
Effects of a synthetic peptide of a parathyroid hormone-related protein on calcium homeostasis, renal tubular calcium reabsorption, and bone metabolism in vivo and in vitro in rodents. (1988)

A synthetic peptide corresponding to the first 34 amino acids of the parathyroid hormone-related protein (PTH-rP) produced by a human tumor associated with hypercalcemia was examined for skeletal and renal effects on calcium metabolism in vivo and in vitro. These effects were compared with those of human parathyroid hormone (1-34), hPTH (1-34). Equal doses of PTH-rP(1-34) and hPTH(1-34) produced equivalent stimulation of adenylate cyclase in vitro in bone cells and kidney cells and tubules. Subcutaneous injection of PTH-rP(1-34) in mice caused a significant dose-related increase in blood ionized calcium similar to that seen with hPTH(1-34) at equivalent doses. Repeated injections of equal doses of both peptides caused sustained hypercalcemia which was significantly greater in PTH-rP(1-34)-treated mice, although each induced comparable increases in histomorphometric indices of osteoclastic bone resorption. PTH-rP(1-34) and hPTH(1-34) also caused similar increases in bone resorption when incubated with fetal rat long bones in organ culture. Infusion of either peptide into thyroparathyroidectomized rats suppressed urinary calcium excretion and increased urinary excretion of cyclic AMP. PTH-rP appears to have similar effects to those of PTH on the skeleton, the kidney, and overall calcium homeostasis.
Early On–Cardiopulmonary Bypass Hypotension and Other Factors Associated With Vasoplegic Syndrome (2009)

The results of this investigation suggest that it is possible to predict vasoplegia intraoperatively before separation from CPB and that the presence of a clinically significant area above the mean arterial blood pressure curve serves as a predictor of poor clinical outcome.
Relief of amplification inhibition in PCR with bovine serum albumin or T4 gene 32 protein (1996)

The benefits of adding bovine serum albumin (BSA) or T4 gene 32 protein (gp32) to PCR were evaluated with reaction mixtures containing substances that inhibit amplification. Whereas 10- to 1,000-fold more FeCl3, hemin, fulvic acids, humic acids, tannic acids, or extracts from feces, freshwater, or marine water were accommodated in PCR when either 400 ng of BSA per microl or 150 ng of gp32 per microl was included in the reactions, neither BSA nor gp32 relieved interference significantly when minimum inhibitory levels of bile salts, bilirubin, EDTA, NaCl, sodium dodecyl sulfate, or Triton X-100 were present. Use of BSA and gp32 together offered no more relief of inhibition than either alone at its optimal level, and neither protein had any noticeable effect on amplification in the absence of inhibitors.
Classifying Patients for Breast Cancer by Detection of Autoantibodies against a Panel of Conformation-Carrying Antigens (2014)

Patients with breast cancer elicit an autoantibody response against cancer proteins, which reflects and amplifies the cellular changes associated with tumorigenesis. Detection of autoantibodies in plasma may provide a minimally invasive mechanism for early detection of breast cancer. To identify cancer proteins that elicit a humoral response, we generated a cDNA library enriched for breast cancer genes that encode membrane and secreted proteins, which are more likely to induce an antibody response compared with intracellular proteins. To generate conformation-carrying antigens that are efficiently recognized by patients' antibodies, a eukaryotic expression strategy was established. Plasma from 200 patients with breast cancer and 200 age-matched healthy controls were measured for autoantibody activity against 20 different antigens designed to have conformational epitopes using ELISA. A conditional logistic regression model was used to select a combination of autoantibody responses against the 20 different antigens to classify patients with breast cancer from healthy controls. The best combination included ANGPTL4, DKK1, GAL1, MUC1, GFRA1, GRN, and LRRC15; however, autoantibody responses against GFRA1, GRN, and LRRC15 were inversely correlated with breast cancer. When the autoantibody responses against the 7 antigens were added to the base model, including age, BMI, race and current smoking status, the assay had the following diagnostic capabilities: c-stat (95% CI), 0.82 (0.78-0.86); sensitivity, 73%; specificity, 76%; and positive likelihood ratio (95% CI), 3.04 (2.34-3.94). The model was calibrated across risk deciles (Hosmer-Lemeshow, P = 0.13) and performed well in specific subtypes of breast cancer including estrogen receptor positive, HER-2 positive, invasive, in situ and tumor sizes >1 cm.
Stereomutation in Trigonal‐Bipyramidal Systems: A Unified Picture (2011)

Same difference: Berry pseutorotation (BPR) and Ugi turnstile rotation, which are generally treated as two distinctly different mechanisms for rearrangement of trigonal-bipyramidal structures, have been shown to be equivalent. Alternative mechanisms consist of sequences of pseudorotations proceeding in a single step.
Sample + Seek (2016)

Data volumes are growing exponentially for our decision-support systems making it challenging to ensure interactive response time for ad-hoc queries without increasing cost of hardware. Aggregation queries with Group By that produce an aggregate value for every combination of values in the grouping columns are the most important class of ad-hoc queries. As small errors are usually tolerable for such queries, approximate query processing (AQP) has the potential to answer them over very large datasets much faster.
Evaluation of the CFP-substrate-YFP system for protease studies: advantages and limitations (2004)

A protease can be defined as an enzyme capable of hydrolyzing peptide bonds. Thus, characterization of a protease involves identification of target peptide sequences, measurement of activities toward these sequences, and determination of kinetic parameters. Biological protease substrates based on fluorescent protein pairs, which allow for use of fluorescence resonance energy transfer (FRET), have been recently developed for in vivo protease activity detection and represent a very interesting alternative to chemical substrates for in vitro protease characterization. Here, we analyze a FRET system consisting of cyan and yellow fluorescent proteins (CFP and YFP, respectively), which are fused by a peptide linker serving as protease substrate. Conditions for CFP-YFP fusion protein production in Escherichia coli and purification of proteins were optimized. FRET between CFP and YFP was found to be optimum at a pH between 5.5 and 10.0, at low concentrations of salt and a temperature superior to 25 degrees C. For efficient FRET to occur, the peptide linker between CFP and YFP can measure up to 25 amino acids. The CFP-substrate-YFP system demonstrated a high degree of resistance to nonspecific proteolysis, making it suitable for enzyme kinetic analysis. As with chemical substrates, substrate specificity of CFP-substrate-YFP proteins was tested towards different proteases and kcat/Km values were calculated.
Effects of Uracil Incorporation, DNA Mismatches, and Abasic Sites on Cleavage and Religation Activities of Mammalian Topoisomerase I (1997)

Abasic sites and deamination of cytosine to uracil are probably the most common types of endogenous DNA damage. The effects of such lesions on DNA topoisomerase I (top1) activity were examined in oligonucleotides containing a unique top1 cleavage site. The presence of uracils and abasic sites within the first 4 bases immediately 5' to the cleavage site suppressed normal top1 cleavage and induced new top1 cleavage sites. Uracils immediately 3' to the cleavage site increased cleavage and produced a camptothecin mimicking effect. A mismatch with a bulge or abasic sites immediately 3' to the top1 cleavage site irreversibly trapped top1 cleavable complexes in the absence of camptothecin and produced a suicide cleavage complex. These results demonstrate that top1 activity is sensitive to physiological, environmental, and pharmacological DNA modifications and that top1 can act as a specific mismatch- and abasic site-nicking enzyme.
A Human Domain Antibody and LewisbGlycoconjugate That Inhibit Binding ofHelicobacter pylorito LewisbReceptor and Adhesion to Human Gastric Epithelium (2009)

Increasing antibiotic resistance has prompted development of alternative approaches to antimicrobial therapy, including blocking microbial adhesion to host receptors. The BabA adhesin of Helicobacter pylori binds to fucosylated blood group antigens, such as the Lewis(b) antigens in human primate gastric mucosa. We have isolated a human domain antibody specific for BabA that inhibits binding of BabA to Lewis(b) and prevents adhesion of H. pylori to human gastric epithelium. In addition, Lewis(b) oligosaccharides covalently linked to poly-D-lysine inhibited BabA binding to Le(b). The poly-D-lysine-Le(b) hexasaccharide and an Le(b) human serum albumin conjugate not only inhibited adherence of H. pylori to gastric epithelium but also displaced adherent bacteria when added to human stomach sections. Combinations of Le(b) and sialyl Le(x) or domain antibody 25 and sialyl Le(x) acted synergistically. Domain antibody 25 inhibitor may have potential for prophylactic use and, in combination with Le(b) glycoconjugates, therapeutic use in treatment of drug-resistant H. pylori infection.
RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination (2017)

Our results suggest that many other proteins with the PRY/SPRY domain could have yet uncharacterized RNA-binding potential. Together, our data reveal new insights into the molecular roles and characteristics of RNA-binding E3 ubiquitin ligases and demonstrate that RNA could be an essential factor in their enzymatic activity.
Anti-HIV Cyclotides from the Chinese Medicinal Herb Viola yedoensis (2007)

Cyclotides are macrocyclic plant peptides characterized by a knotted arrangement of three disulfide bonds. They display a range of interesting bioactivities, including anti-HIV and insecticidal activities. More than 100 different cyclotides have been isolated from two phylogenetically distant plant families, the Rubiaceae and Violaceae. In this study we have characterized the cyclotides from Viola yedoensis, an important Chinese herb from the Violaceae family that has been reported to contain potential anti-HIV agents. From V. yedoensis five new and three known cyclotides were identified and shown to have anti-HIV activity. The most active of these is cycloviolacin Y5, which is one of the most potent of all cyclotides tested so far using in vitro XTT-based anti-HIV assays. Cycloviolacin Y5 is the most hydrophobic of the cyclotides from V. yedoensis. We show that there is a positive correlation between the hydrophobicity and the anti-HIV activity of the new cyclotides and that this trend tracks with their ability to disrupt membranes, as judged from hemolytic assays on human erythrocytes.
Emerging treatment for chronic migraine and refractory chronic migraine (2012)

Medication overuse headache (MOH) is now recognized to be a major factor in many cases of both chronic and refractory chronic migraine. MOH must be addressed prior to evaluating the effectiveness of new preventative and prophylactic treatment approaches. Innovative new drugs and electrical neuromodulation are promising CM treatments. Future studies must carefully screen patients and acquire data that can lead to personalized, tailored treatment strategies.
Getting Started with GIS (1999)

&lt;p&gt;This best-selling non-technical, reader-friendly introduction to GIS makes the complexity of this rapidly growing high-tech field accessible to beginners. It uses a “learn-by-seeing” approach that features clear, simple explanations, an abundance of illustrations and photos, and generic practice labs for use with any GIS software. What Is a GIS? GIS's Roots in Cartography. Maps as Numbers. Getting the Map into the Computer. What Is Where? Why Is It There? Making Maps with GIS. How to Pick a GIS. GIS in Action. The Future of GIS. For anyone interested in a hands-on introduction to Geographic Information Systems. &lt;/p&gt;
Liposuction of the Legs and Ankles: A Review of the Literature (2004)

Weniger, Frederick G. M.D., M.B.A.; Calvert, Jay W. M.D.; Newton, E. Douglas M.D. Author Information
Inhibition of the activity of poly(ADP ribose) synthetase reduces ischemia–reperfusion injury in the heart and skeletal muscle (1997)

Reperfusion of the ischemic myocardium results in the generation of oxygen-derived free radicals, NO, and presumably peroxynitrite. These, in turn, may cause strand breaks in DNA, which activate the nuclear enzyme poly(ADP ribose) synthetase (PARS). This results in a rapid depletion of intracellular NAD and ATP. When this reaction is excessive, there is ultimately cell death. Here we demonstrate that 3-aminobenzamide (and several other, chemically distinct, inhibitors of PARS activity) reduces the infarct size caused by ischemia and reperfusion of the heart or skeletal muscle of the rabbit. Inhibition of PARS activity also attenuates the myocardial dysfunction caused by global ischemia and reperfusion in the isolated, perfused heart of the rabbit. In skeletal muscle, inhibition of the activity of neuronal NO synthase reduces infarct size, indicating that the formation of NO contributes to the activation of PARS there. There is no significant neuronal NO synthase activity in the heart, and hence NO synthase inhibitors did not reduce myocardial infarct size. Thus, activation of PARS contributes to the cell death caused by ischemia-reperfusion, and PARS inhibitors may constitute a novel therapy for ischemia-reperfusion injury.
Analysis of Respiratory Syncytial Virus Preclinical and Clinical Variants Resistant to Neutralization by Monoclonal Antibodies Palivizumab and/or Motavizumab (2011)

Resistant RSV variants were detected in a small subset (∼ 5%) of RSV breakthrough cases. The fitness of these variants was impaired, compared to wild-type RSV.
Cloning and sequence analysis of human pituitary cDNA encoding the novel polypeptide 7B2 (1988)

Application of a differential hybridization technique led to the isolation of a human pituitary cDNA clone encoding the complete structure of the polypeptide 7B2. This protein of unknown function, which is sorted to secretory granules, appears to be present selectively in neurons and endocrine cells. The polypeptide chain of human 7B2, preceded by a cleaved signal peptide, comprises 185 amino acids (a calculated Mr of 20,793). Interesting features of the highly-conserved 7B2 structure include (i) a serine phosphorylation consensus sequence, (ii) the occurrence of three pairs of dibasic amino acids representing potential proteolytic cleavage sites and, in particular, (iii) the presence of three regions homologous to GTP-binding domains giving 7B2 structural characteristics of a GTP-binding protein.
<title>Mapping perceived depth to regions of interest in stereoscopic images</title> (2004)

The usable perceived depth range of a stereoscopic 3D display is limited by human factors considerations to a defined range around the screen plane. There is therefore a need in stereoscopic image creation to map depth from the scene to a target display without exceeding these limits. Recent image capture methods provide precise control over this depth mapping but map a single range of scene depth as a whole and are unable to give preferential stereoscopic representation to a particular region of interest in the scene. A new approach to stereoscopic image creation is described that allows a defined region of interest in scene depth to have an improved perceived depth representation compared to other regions of the scene. For example in a game this may be the region of depth around a game character, or in a scientific visualization the region around a particular feature of interest. To realize this approach we present a novel algorithm for stereoscopic image capture and describe an implementation for the widely used ray-tracing package POV-Ray. Results demonstrate how this approach provides content creators with improved control over perceived depth representation in stereoscopic images.
Studies on a family with combined functional deficiencies of vitamin K-dependent coagulation factors. (1982)

Two siblings with m ild hemorrhagic symptoms had combined functional deficiencies of vitamin K-dependent clotting factors. Prothrombin (0.18-0.20 U/ml) and Stuart factor (Factor X, 0.18-0.20 U/ml) and Stuart factor (Factor X, 0.18-0.20 U/ml) were most severely affected. Antigenic amounts of affected coagulation factors were normal and normal generation of thrombin activity occurred in the patients' plasmas after treatment with nonophysiologic activators that do not require calcium for prothrombin activation. Hepatobilary disease, malabsorptive disorders, and plasma warfarin were not present. Both parents had normal levels of all coagulation factors. The patients' plasmas contained prothrombin that reacted both with antibody directed against des-gamma-carboxyprothrombin and native prothrombin. Crossed immunoelectrophoresis of patients' plasmas and studies of partially purified patient prothrombin suggested the presence of a relatively homogeneous species of dysfunctional prothrombin, distinct from the heterologous species found in the plasma of warfarin-treated persons. These studies are most consistent with a posttranslational defect in hepatic carboxylation of vitamin K-dependent factors. This kindred uniquely possesses an autosomal recessive disorder of vitamin K-dependent factor formation that causes production of an apparently homogeneous species of dysfunctional prothrombin; the functional deficiencies in clotting factors are totally corrected by oral or parenteral administration of vitamin K1.
Direct‐Write Assembly of 3D Silk/Hydroxyapatite Scaffolds for Bone Co‐Cultures (2012)

3D silk/HA microperiodic scaffolds for bone tissue engineering and angiogenesis are fabricated by direct-write assembly. This approach can be used to control filament and spacing size in the scaffold to allow investigation of the effect of scaffold architecture on osteogenesis and vessel-like structure formation from stem cells and endothelial cells.
Eosinophil activation and T lymphocyte infiltration in allergen-induced late phase skin reactions and classical delayed-type hypersensitivity (1991)

T lymphocyte infiltration is a well documented feature of classical delayed-type hypersensitivity (DTH) reactions. Recently, we have shown that T lymphocytes and activated (EG2+) eosinophils accumulate in the allergen-induced late phase skin reaction (LPR). To compare the kinetics and phenotypic composition of these T lymphocyte responses, LPR and DTH reactions of comparable induration size were induced in atopic subjects. In addition, DTH and LPR were compared between atopic and nonatopic subjects. In atopic individuals, allergen challenge elicited a perivascular influx of T lymphocytes that was predominantly CD4+. Eosinophil accumulation and activation were also prominent. There was no cellular response to allergen challenge in the nonatropic group. In both groups, DTH responses showed an intense T cell infiltrate which was more dense and dispersed than in the LPR. CD4+ T cells predominated but at 48 h CD8+ numbers were also significantly increased. In DTH, total leukocyte numbers (CD45+) were increasing at 48 h, whereas in the LPR, cell numbers reached a plateau between 24 and 48 h. T cell activation (shown by expression of IL-2R) was more prominent in DTH. Endothelial expression of HLA-DR was increased in both LPR and DTH, implying the local release of inflammatory cytokines in both reactions. Small but significant numbers of activated eosinophils (EG2+) were detected in atopics and non-atopics at 24 h in DTH but not at 48 h. These findings suggest that the allergen-induced LPR induced in atopic subjects is, at least in part, a form of cell-mediated hypersensitivity but with T cell kinetics that differ from classical DTH.
A tightly associated serine/threonine protein kinase regulates phosphoinositide 3-kinase activity. (1993)

We identified a serine/threonine protein kinase that is associated with and phosphorylates phosphoinositide 3-kinase (PtdIns 3-kinase). The serine kinase phosphorylates both the 85- and 110-kDa subunits of PtdIns 3-kinase and purifies with it from rat liver and immunoprecipitates with antibodies raised to the 85-kDa subunit. Tryptic phosphopeptide maps indicate that p85 from polyomavirus middle T-transformed cells is phosphorylated in vivo at three sites phosphorylated in vitro by the associated serine kinase. The 85-kDa subunit of PtdIns 3-kinase is phosphorylated in vitro on serine at a stoichiometry of approximately 1 mol of phosphate per mol of p85. This phosphorylation results in a three- to sevenfold decrease in PtdIns 3-kinase activity. Dephosphorylation with protein phosphatase 2A reverses the inhibition. This suggests that the association of protein phosphatase 2A with middle T antigen may function to activate PtdIns 3-kinase.
What drives the translocation of proteins? (1992)

We propose that protein translocation across membranes is driven by biased random thermal motion. This "Brownian ratchet" mechanism depends on chemical asymmetries between the cis and trans sides of the membrane. Several mechanisms could contribute to rectifying the thermal motion of the protein, such as binding and dissociation of chaperonins to the translocating chain, chain coiling induced by pH and/or ionic gradients, glycosylation, and disulfide bond formation. This helps explain the robustness and promiscuity of these transport systems.
Highly Regio- and Stereocontrolled Synthesis of Vinyl Sulfides via Transition-Metal-Catalyzed Hydrothiolation of Alkynes with Thiols (1999)

Regio- and stereoselectivity in the hydrothiolation of alkynes with thiols in the presence of a variety of transition-metal catalysts is investigated in detail. Among the catalysts employed, RhCl(PPh3)3 exhibits excellent catalytic ability toward the anti-Markovnikov addition of thiols (ArSH) to alkynes (RC⋮CH), which affords the corresponding vinylic sulfides (trans-RCHCHSAr) regio- and stereoselectively. The reaction may proceed by the formation of hydrorhodium sulfide species (H−[Rh]−SAr) and probably via the subsequent hydrorhodation of alkynes to provide vinylrhodium intermediates (RCHCH−[Rh]−SAr). In contrast, PdCl2(PhCN)2-catalyzed hydrothiolation of aromatic alkynes (ArC⋮CH) takes place to give the corresponding Markovnikov adducts (R(ArS)CCH2) with excellent regioselectivity, probably via thiopalladation of alkynes by palladium sulfide species (ArS−[Pd]−Cl), which may be formed by ligand-exchange reaction between PdCl2(PhCN)2 and ArSH. Furthermore, in the case of alkynes bearing propargylic protons (R‘CH2C⋮CH), a sequential addition/isomerization reaction occurs to provide the internal vinylic sulfides (R‘CHC(SAr)CH3) regioselectively. From the same starting materials (alkyne and thiol), therefore, the regioselectivity of hydrothiolation can be attained simply by changing the catalysts, i.e., RhCl(PPh3)3 and PdCl2(PhCN)2.
Optical gain in InAs/InGaAs quantum-dot structures: Experiments and theoretical model (2000)

The dependence of the mode optical gain on current in InAs/InGaAs quantum-dot structures grown by the method of molecular-beam epitaxy is obtained from the experimental study of ultra-low-threshold laser diodes. The record lowest inversion threshold at room temperature was about 13 A cm-2. A theoretical model is proposed that relates the optical gain to the ground-state transitions in quantum dots. The effective gain cross section is estimated to be ~7 × 10-15 cm-2.