gebhart/patrepeval huggingface dataset:
Protein interactions ofhsp27. (1999)

Heat shock protein (hsp) 27 is a member of the small heat shock protein family. The amount of hsp27 in cells correlates with the ability of cells to survive toxic or stressful conditions. The protective effect of hsp27 is believed to occur as a result of hsp27 stabilizing microfilaments, assisting in re-folding of denatured proteins, or by modulating the redox status of cells. Hsp27 exists in cells as oligomers and its activities have been shown to depend on the size of oligomers. Observations have also suggested that hsp27 may interact with other proteins. Thus, how hsp27 forms oligomers is a subject of interest to biologists. This thesis project has focused on the protein-protein interactions of hsp27, both with itself and with other proteins. Using the yeast two-hybrid system, I have shown that hsp27 binds to itself via a 30-amino acid region within the conserved domain shared by the small hsp family. Interaction of hsp27 with itself or with another small hsp, alphaB-crystallin, does not require the N-terminal half or the C-terminal tail of hsp27. These results indicate that hsp27 forms dimers from which larger oligomers then assemble. To identify others proteins with which hsp27 interacts, the yeast two-hybrid system was also used to screen a cDNA library prepared from rat Sertoli cells. A novel hsp27 binding protein was identified from the Sertoli cell library and has been named PASS1 (<italic>p</italic>rotein <italic> a</italic>ssociated with <italic>s</italic>mall <italic> s</italic>tress proteins 1). PASS1 was confirmed to bind to hsp27 by GST pull-down assay and by co-immunoprecipitation, primarily via a 100-amino acid region near its N-terminal terminus. PASS1 was demonstrated by Northern hybridization and Western blot to be expressed most abundantly in Sertoli cells and in kidney. Expression of PASS1 in cultured cells was shown to inhibit the ability of hsp27 to protect the cells from heat shock. This result indicates that PASS1 is unlikely a component of the cell protective mechanism of hsp27 and suggests that PASS1 may affect the oligomer structure of hsp27 by its binding to hsp27 and thus may have regulatory effects on hsp27 <italic>in vivo</italic>.
Real-word spelling correction using Google web 1Tn-gram data set (2009)

We present a method for correcting real-word spelling errors using the Google Web 1T n-gram data set and a normalized and modified version of the Longest Common Subsequence (LCS) string matching algorithm. Our method is focused mainly on how to improve the correction recall (the fraction of errors corrected) while keeping the correction precision (the fraction of suggestions that are correct) as high as possible. Evaluation results on a standard data set show that our method performs very well.
Simulating Soft Shadows with Graphics Hardware (1997)

This paper describes an algorithm for simulating soft shadows at interactive rates using graphics hardware. On current graphics workstations, the technique can calculate the soft shadows cast by moving, complex objects onto multiple planar surfaces in about a second. In a static, diffuse scene, these high quality shadows can then be displayed at 30 Hz, independent of the number and size of the light sources. For a diffuse scene, the method precomputes a radiance texture that captures the shadows and other brightness variations on each polygon. The texture for each polygon is computed by creating registered projections of the scene onto the polygon from multiple sample points on each light source, and averaging the resulting hard shadow images to compute a soft shadow image. After this precomputation, soft shadows in a static scene can be displayed in real-time with simple texture mapping of the radiance textures. All pixel operations employed by the algorithm are supported in hardware by existing graphics workstations. The technique can be generalized for the simulation of shadows on specular surfaces.
New Stereoselective β-C-Glycosidation by Uncatalyzed 1,4-Addition of Organolithium Reagents to a Glycal-Derived Vinyl Oxirane (2003)

[reaction: see text] Epoxide 4 is generated in situ from d-glucal-derived hydroxy mesylate 3. Reaction of epoxide 4 with a series of alkyl- and aryllithium reagents affords 2,3-unsaturated beta-C-glycosides with excellent 1,4-regioselectivity and complete stereoselectivity for the beta-glycoside. Other organometallic reagents demonstrate more complex behavior in their reactions with epoxide 4.
A traceless aryl-triazene linker for DNA-directed chemistry (2013)

DNA-directed synthesis of encoded combinatorial libraries of small organic compounds most often involves transfer of organic building blocks from one DNA strand to another. This requires cleavable linkers to enable cleavage of the link to the original DNA strand from which the building block is transferred. Relatively few cleavable linkers are available for DNA-directed synthesis and most often they leave an amino group at the organic molecule. Here we have extended the application of aryltriazenes as traceless linkers for DNA-directed synthesis. After reaction of one building block with a building block at another DNA strand the triazene linker is cleaved and reduced with hypophosphorous acid in high yield to leave the aryl group with a hydrogen in place of the triazene i.e. without a functional group trace. It was also demonstrated that alternatively the triazene could be converted to an azide, which was used in a cycloaddition reaction. The linker is generally stable at pH > 7 and could be stored for several months in a freezer without significant degradation.
Demyelination and axonal degeneration in Lewis rat experimental allergic neuritis depend on the myelin dosage. (1988)

We describe the clinical and pathologic features of experimental allergic neuritis in Lewis rats inoculated with varying doses of myelin, ranging from 0.5 to 20 mg. The clinical scores were assessed daily. On days 18 and 19 or 28 postimmunization, the rats were perfused with fixative and samples of cervical and lumbar roots and sciatic nerves were processed and embedded in Epon. Tissues were examined by light and electron microscopy and the degree of edema, inflammation, demyelination, and axonal degeneration was assessed quantitatively. We found that the severity of clinical and pathologic experimental allergic neuritis correlated positively with the dose of myelin used for immunization. High dose tolerance was not observed. Demyelination prevailed in nerve roots and increased with higher doses of antigen. Accompanying axonal degeneration was seen only with high doses of myelin. The pathology of sciatic nerves differed. Sciatic nerves of rats immunized with 0.5 and 1 mg of myelin were either normal or showed perivenular lymphocytic infiltrates and demyelination, but nerves from rats with higher immunizing doses of myelin showed increasingly severe axonal degeneration. The axonal degeneration in nerve roots paralleled the degree of inflammation and demyelination and may have been a nonspecific product of the inflammatory reaction. However, the much more severe axonal destruction seen in sciatic nerves with high myelin doses was probably due to other pathogenetic mechanisms.
Isolation and Characterization of Human Placenta Fibronectin1 (1984)

Fibronectin was isolated from human placenta tissues and compared with human plasma fibronectin. Placenta and plasma fibronectins had similar amino acid compositions, immunological properties, and cell attachment-promoting activities, but differed in apparent molecular weight on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, which could be accounted for at least partly by the difference in carbohydrate composition. Unlike plasma fibronectin, placenta fibronectin failed to form a precipitin line with concanavalin A in a double diffusion system. The non- or low-reactivity of placenta fibronectin with this lectin was also demonstrated by affinity chromatography with concanavalin A-agarose, in which more than 90% of the radiolabeled glycopeptides derived from placenta fibronectin was not retained on the gel. The two fibronectins also differed in the reactivity with Lens culinaris agglutinin of their glycopeptide fractions. These data indicate that placenta and plasma fibronectins are different in their carbohydrate structures and, therefore, suggest the presence of a tissue- or cell-specific mechanism for processing the carbohydrates of this glycoprotein.
A Targeted Gene Knockout in Drosophila (2001)

We previously described a method for targeted homologous recombination at the yellow gene of Drosophila melanogaster. Because only a single gene was targeted, further work was required to show whether the method could be extended to become generally useful for gene modification in Drosophila. We have now used this method to produce a knockout of the autosomal pugilist gene by homologous recombination between the endogenous locus and a 2.5-kb DNA fragment. This was accomplished solely by tracking the altered genetic linkage of an arbitrary marker gene as the targeting DNA moved from chromosome X or 2 to chromosome 3. The results indicate that this method of homologous recombination is likely to be generally useful for Drosophila gene targeting.
MP3 Robust Audio Watermarking (1999)

This paper presents methods for audio watermarking in the frequency domain. It will consider desired properties and possible applications of watermarking algorithms. Special attention is given to statistical methods relying on the so-called patchwork techniques. It will present a solution of robust watermarking of audio data and reflect the security properties of the technique. Experimental results show good robustness of the approach against MP3 compression and other common signal processing manipulations. Enhancements of the presented methods are discussed.
Growth and metabolism in somatotropin-treated steers: III. Protein synthesis and tissue energy expenditures (1990)

Rates of in vivo protein synthesis in intercostal, sartorius and semitendinosus muscle and in the heart, liver, kidneys, rumen and jejunum were determined in 20 growing Hereford steers treated for 112 d with daily subcutaneous injections of either saline (S) or recombinantly derived bovine somatotropin (rBST; 20.6 mg/d). In vitro rates of protein synthesis and energy expenditures associated with Na+, K+ transport also were determined in external intercostal muscle, liver, kidneys and jejunum. Neither in vivo nor in vitro tissue protein fractional synthetic rates (mg/[g protein.d]), using either the plasma (P) or intracellular fluid (ICF) phenylalanine specific radioactivity for the precursor pool, were affected by rBST treatments. Energy expended on Na+, K+ transport was greater (P less than .1) in the livers of rBST-treated steers, which would increase the maintenance energy expenditures of these steers. Protein accretion rates in the liver, kidneys, stomach, hide, and head, feet and tail of rBST-treated steers were greater (P less than .05) than in S steers. Tissue amino acid profiles were not affected by rBST treatments except in the rumen, where profiles suggested that less collagen was present in rumen wall tissue protein of rBST steers. Plasma phenylalanine entry rates also were not affected by rBST treatment; muscle protein synthesis accounted for a minimum of 20% of this entry rate.
Analytical and Clinical Evaluation of the Bayer ADVIA Centaur Automated B-Type Natriuretic Peptide Assay in Patients with Heart Failure: A Multisite Study (2004)

The ADVIA Centaur is the first commercially available BNP assay for use on an automated immunochemistry platform. This assay has good analytical and clinical performance characteristics for diagnosing HF.
Quantitation of factor VII in the plasma of normal and warfarin-treated individuals by radioimmunoassay (1983)

Highly purified single-chain factor VII was isolated from plasma and used to generate monospecific antibodies. A double-antibody equilibrium radioimmunoassay was constructed. The assay was tested for and met all the criteria required for a specific, sensitive, and accurate determination of factor VII in plasma. The range of sensitivity of the assay was between 1 and 500 ng factor VII/ml, and the coefficient of variation was 1%-3% within assay and 12%-16% between assays. Pure factor VII and plasmic factor VII from normal, warfarin-treated, and hereditary deficient individuals inhibited competition assays with parallel slopes, indicating the expression of similar epitopes by these molecules and validating the measurement of this protein in plasma. The concentration of factor VII in normal plasma (n = 41) was 470 +/- 112 ng/ml, and the measurement of factor VII antigen correlated with activity (r = 0.82). Factor VII concentration in the plasma of individuals on warfarin therapy (n = 24) was 238 +/- 73 ng/ml. Factor VII activity was about 38% of normal and correlated less well with factor VII antigen (r = 0.53). The specific activity of these molecules was 78% of normal (p less than 0.01), suggesting the presence of nonfunctional or partially functional molecules in the circulation of individuals undergoing drug therapy. Analysis of two hereditary deficient patients revealed that, while there were significant levels of factor VII protein, the procoagulant activity was less than 2%, indicating a discordant relationship of these parameters in individuals expressing the deficient factor VII phenotype.
The serum resistome of a globally disseminated multidrug resistant uropathogenic Escherichia coli Clone (2013)

Escherichia coli ST131 is a globally disseminated, multidrug resistant clone responsible for a high proportion of urinary tract and bloodstream infections. The rapid emergence and successful spread of E. coli ST131 is strongly associated with antibiotic resistance; however, this phenotype alone is unlikely to explain its dominance amongst multidrug resistant uropathogens circulating worldwide in hospitals and the community. Thus, a greater understanding of the molecular mechanisms that underpin the fitness of E. coli ST131 is required. In this study, we employed hyper-saturated transposon mutagenesis in combination with multiplexed transposon directed insertion-site sequencing to define the essential genes required for in vitro growth and the serum resistome (i.e. genes required for resistance to human serum) of E. coli EC958, a representative of the predominant E. coli ST131 clonal lineage. We identified 315 essential genes in E. coli EC958, 231 (73%) of which were also essential in E. coli K-12. The serum resistome comprised 56 genes, the majority of which encode membrane proteins or factors involved in lipopolysaccharide (LPS) biosynthesis. Targeted mutagenesis confirmed a role in serum resistance for 46 (82%) of these genes. The murein lipoprotein Lpp, along with two lipid A-core biosynthesis enzymes WaaP and WaaG, were most strongly associated with serum resistance. While LPS was the main resistance mechanism defined for E. coli EC958 in serum, the enterobacterial common antigen and colanic acid also impacted on this phenotype. Our analysis also identified a novel function for two genes, hyxA and hyxR, as minor regulators of O-antigen chain length. This study offers novel insight into the genetic make-up of E. coli ST131, and provides a framework for future research on E. coli and other Gram-negative pathogens to define their essential gene repertoire and to dissect the molecular mechanisms that enable them to survive in the bloodstream and cause disease.
A Distinct G 1 Step Required to Specify the Chinese Hamster DHFR Replication Origin (1996)

Nuclei isolated from Chinese hamster ovary (CHO) cells at various times during the G1 phase of the cell cycle were stimulated to enter S phase by incubation in Xenopus egg cytosol. Replication of DNA initiated within the dihydrofolate reductase (DHFR) origin locus in nuclei isolated late in G1, but at random sites in nuclei isolated early in G1. A discrete transition point occurred 3 to 4 hours after metaphase. Neither replication licensing nor nuclear assembly was sufficient for origin recognition. Thus, a distinct cell cycle-regulated event in the nucleus restricts the initiation of replication to specific sites downstream of the DHFR gene.
Expression of SALL4 in acute myeloid leukemia and its potential clinical significance (2009)

Objective To detect the expression of SALL4 in patients with acute myeloid leukemia (AML) and analyze its potential clinical significance. Methods Reverse transcription polymerase chain reaction and Real-time fluorescence quantitative reverse transcription polymerase chain reaction (FQ-RT-PCR) was used to examine SALLA expression in peripheral blood mononuclear cells (PBMCs) of 68 cases of AML including 36 cases in acute phase and 32 cases in remission phase, 30 healthy controls, Kasumi-1 cells and THP-1 cells. Then, flow cytometry, bone marrow smear and automated hematology analyzer were used to analyze the relationship between the SALL4 expression and blast cell counts in the bone marrow, peripheral white blood cell (WBC) counts, peripheral large unstained cell (LUC), CD34 in blast cells. Further, the change of SALL4 level during pre-chemotherapy, chemotherapy (2nd w to 3rd w) and remission were investigated in 5 AML cases. Results The level of SALL4 expression in patients with AML in acute phase [69.01 (17.20-120.28)] was 26-fold and 61-fold high compared with that in remission phase [2.64(1.35-5.41)] and in healthy control [1.14(0.50-1.62)] (Z=-6.48,-6.83,P<0.01). The level of SALL4 expression in remission phase was 2.3-fold high compared with that in healthy control (Z=-3.61 ,P<0.01). The expression level of SALL4 was decreased along with efficient chemotherapy in 5 AML cases in which SALL4 expression level was 79.74 (33.76-89.09), 7.19 (5.97-20.21) and 3.40 (1.44-15.53) during pre-chemotherapy, chemotherapy (2nd w to 3rd w) and remission, respectively. In groups of abnormal increased counts of blast cell, peripheral LUC% and CD34%, expression of SALL4 [33.82 (16.00-144.01), 30.70(23.75-72.50) and 56.25(23.79-153.81), respectively] were higher than that in groups of normal counts [2.74 (1.59-5.13), 5.71 (2.52-22.40) and 20.82 (14.03-55.12), respectively ] (Z=-4.64,-2.18,-3.66,P<0.01 or P<0.05). The expression of SALL4 in the group of increased WBC counts [89.26(23.75-154.34)] was higher than that in the group of normal WBC counts [3.86(2.03-6.01)] and the group of decreased WBC counts [6.66(2.51-17.06)] (Z=-4.91,-4.21,P<0.01). The level of SALL4 expression was positively correlated with blast cell counts in bone marrow and peripheral WBC counts (r=0.45,0.40,P<0.01). Conclusions FQ-RT-PCR method can be used successfully to detect the expression of SALL4,and the expression of SALLA may be useful to predict disease progression of AML.

Key words: 
Leukemia,myeloid,acute;  Transcription factors;  Polymerase chain reaction
Comparison of Inhibitory and Bactericidal Activity of Antipseudomonal Antibiotics against <i>Pseudomonas aeruginosa</i> Isolates from Cystic Fibrosis Patients (1990)

Using a broth microtiter dilution method, the minimum inhibitory (MIC) and minimum bactericidal concentrations (MBC) of so-called antipseudomonal antibiotics were determined against 79 Pseudomonas aeruginosa isolates from cystic fibrosis patients. On the basis of the MIC values and using DIN breakpoints, the percentual susceptibilities led to the following rank order: imipenem (91%), ciprofloxacin (90%), tobramycin (87%), amikacin (87%), ceftazidime (82%), cefsulodin (76%), piperacillin (71%), azlocillin (62%), followed by gentamicin, ceftriaxone, mezlocillin, netilmicin, and cefotaxime (less than 50%). However, evaluating MBC values according to DIN breakpoints, only ciprofloxacin (82%), tobramycin (77%), amikacin (58%), and imipenem (57%) showed a pronounced antipseudomonal effectiveness. The data indicate that MBC determinations are necessary to evaluate the antibiotic susceptibility of P. aeruginosa rather than MIC determinations, at least in patients with impaired defence mechanisms which require bactericidal therapy.
Selective Greedy Equivalence Search: Finding Optimal Bayesian Networks Using a Polynomial Number of Score Evaluations (2015)

We introduce Selective Greedy Equivalence Search (SGES), a restricted version of Greedy Equivalence Search (GES). SGES retains the asymptotic correctness of GES but, unlike GES, has polynomial performance guarantees. In particular, we show that when data are sampled independently from a distribution that is perfect with respect to a DAG ${\cal G}$ defined over the observable variables then, in the limit of large data, SGES will identify ${\cal G}$'s equivalence class after a number of score evaluations that is (1) polynomial in the number of nodes and (2) exponential in various complexity measures including maximum-number-of-parents, maximum-clique-size, and a new measure called {\em v-width} that is at least as small as---and potentially much smaller than---the other two. More generally, we show that for any hereditary and equivalence-invariant property $Π$ known to hold in ${\cal G}$, we retain the large-sample optimality guarantees of GES even if we ignore any GES deletion operator during the backward phase that results in a state for which $Π$ does not hold in the common-descendants subgraph.
Effects of glucagon-like peptide-1 on endothelial function in type 2 diabetes patients with stable coronary artery disease (2004)

GLP-1 stimulates insulin secretion, suppresses glucagon secretion, delays gastric emptying, and inhibits small bowel motility, all actions contributing to the anti-diabetogenic peptide effect. Endothelial dysfunction is strongly associated with insulin resistance and type 2 diabetes mellitus and may cause the angiopathy typifying this debilitating disease. Therefore, interventions affecting both endothelial dysfunction and insulin resistance may prove useful in improving survival in type 2 diabetes patients. We investigated GLP-1's effect on endothelial function and insulin sensitivity (S(I)) in two groups: 1) 12 type 2 diabetes patients with stable coronary artery disease and 2) 10 healthy subjects with normal endothelial function and S(I). Subjects underwent infusion of recombinant GLP-1 or saline in a random crossover study. Endothelial function was measured by postischemic FMD of brachial artery, using ultrasonography. S(I) [in (10(-4) dl.kg(-1).min(-1))/(muU/ml)] was measured by hyperinsulinemic isoglycemic clamp technique. In type 2 diabetic subjects, GLP-1 infusion significantly increased relative changes in brachial artery diameter from baseline FMD(%) (3.1 +/- 0.6 vs. 6.6 +/- 1.0%, P < 0.05), with no significant effects on S(I) (4.5 +/- 0.8 vs. 5.2 +/- 0.9, P = NS). In healthy subjects, GLP-1 infusion affected neither FMD(%) (11.9 +/- 0.9 vs. 10.3 +/- 1.0%, P = NS) nor S(I) (14.8 +/- 1.8 vs. 11.6 +/- 2.0, P = NS). We conclude that GLP-1 improves endothelial dysfunction but not insulin resistance in type 2 diabetic patients with coronary heart disease. This beneficial vascular effect of GLP-1 adds yet another salutary property of the peptide useful in diabetes treatment.
Application of Single Molecule Detection to Dna Sequencing (1997)

Abstract A flow cytometric, single molecule approach to DNA sequencing is described. A single, fluorescently labeled DNA fragment is suspended in a flow stream. An exonuclease is added to sequentially cleave the end base into the flow stream where it is detected and identified by laser-induced fluorescence.
Psychosurgery: a retrospective. (1991)

Of the 56 patients within the Yakovlev collection who had undergone psychosurgery 11 (20%) improved, 18 (32%) were either worse or without improvement, and 27 (48%) were without any clinical follow-up. Thus, in retrospect, psychosurgery was perhaps not as successful as once envisioned.