gebhart/patrepeval huggingface dataset:
Identification of Prognostic Biomarkers for Prostate Cancer (2008)

The process described here identified genes that add information not available from current clinical measures and can improve the prognosis of prostate cancer.
Synthesis of hydroxy pyrrolidines and piperidines via free-radical cyclisations (1998)

The tin hydride-mediated cyclisation of a variety of α- and β-amino aldehydes to form substituted pyrrolidines and piperidines under mild, neutral reaction conditions has been investigated. The amino aldehyde precursors, prepared from the corresponding amino ester or alcohol, are purified or immediately reacted with Bu3SnH–AIBN in boiling benzene. The method is shown to be general and cyclisation of the intermediate O-stannyl ketyl is observed using a variety of (electron poor or rich) acceptor carbon–carbon double bonds to afford hydroxy-pyrrolidines or -piperidines after work-up. Related cyclisations using an alkyne or α,β-unsaturated amide radical acceptor are shown to be problematic and low-yielding. Radical cyclisation of allylic O-stannyl ketyls, generated from reaction of α,β-unsaturated ketones with tin hydride, are also shown to have application in pyrrolidine/piperidine synthesis. A dilution study suggests that the cyclisation onto a cinnamyl double bond is irreversible.
Rising Cellular Immune Response after Injection of pVax/iutA: A Genetic DNA Cassette as Candidate Vaccine against Urinary Tract Infection. (2016)

Cellular immune response has a main protective role against UTI. Raising this kind of immune response is important to preventing of recurrent infection. Moreover, the current DNA cassette will be valuable for more trying to prepare a new vaccine against UTI.
Declining Severity of First Attack of Rheumatic Fever (1963)

A decline in the incidence and severity of rheumatic fever has been reported from several centers in the past 2 decades.<sup>1-11</sup>It is the purpose of this report to document this trend as it has occurred on the Children's Cardiac Service at Bellevue Hospital over a 24-year period from 1935 through 1958. <h3>Case Material and Methods</h3> A total of 792 initial attacks of acute rheumatic fever form the basis for this study. The patients, ranging in age from 2 to 15 years, fulfill the following requirements: (1) They were hospitalized at Bellevue during their first attack, and (2) a definite diagnosis of acute rheumatic fever was made in each. Cases in which the diagnosis of acute rheumatic fever was considered to be questionable at the time of review for the study were not included. A definite diagnosis required at least one of the major criteria of Jones<sup>12,13</sup>(arthritis,
Organic Depth Profiling of a Nanostructured Delta Layer Reference Material Using Large Argon Cluster Ions (2009)

Cluster ion beams have revolutionized the analysis of organic surfaces in time-of-flight secondary ion mass spectrometry and opened up new capabilities for organic depth profiling. Much effort has been devoted to understanding the capabilities and improving the performance of SF(5)(+) and C(60)(n+), which are successful for many, but not all, organic materials. Here, we explore the potential of organic depth profiling using novel argon cluster ions, Ar(500)(+) to Ar(1000)(+). We present results for an organic delta layer reference sample, consisting of ultrathin "delta" layers of Irganox 3114 (approximately 2.4 nm) embedded between thick layers of Irganox 1010 (approximately 46 or 91 nm). This indicates that, for the reference material, major benefits can be obtained with Ar cluster ions, including a constant high sputtering yield throughout a depth of approximately 390 nm, and an extremely low sputter-induced roughness of <5 nm. Although the depth resolution is currently limited by an instrumental artifact, and may not be the best attainable, these initial results strongly indicate the potential to achieve high depth resolution and suggest that Ar cluster ions may have a major role to play in the depth profiling of organic materials.
The human EBNA-2 coactivator p100: multidomain organization and relationship to the staphylococcal nuclease fold and to the tudor protein involved in Drosophila melanogaster development (1997)

The human p100 protein was recently identified as a coactivator of the Epstein-Barr virus nuclear antigen 2. On the basis of sequence analysis with the hydrophobic cluster analysis method, we predict that this protein consists of a repeat of four similar domains. Their fold can be related to the staphylococcal nuclease structure whose first subdomain belongs to the large oligonucleotide/oligosaccharide-binding (OB)-fold superfamily. The catalytic amino acids present in nucleases are missing, however, suggesting that these repeated motifs could only serve to bind DNA without catalytic activity, as in many other OB-folds. A highly modified fifth domain follows the four nuclease-like domains, conserving the second subdomain of the nuclease structure but not the first one (the OB-fold), which is replaced by an original domain found in multiple copies in the tudor protein, a Drosophila melanogaster protein required during oogenesis for establishment of a functional posterior organizing centre. We named this heretofore undescribed domain the 'tudor domain' and highlight within it five invariant residues which could be involved in one of the essential roles played by these proteins.
Sister chromatids are preferred over homologs as substrates for recombinational repair in Saccharomyces cerevisiae. (1992)

A diploid Saccharomyces cerevisiae strain was constructed in which the products of both homolog recombination and unequal sister chromatid recombination events could be selected. This strain was synchronized in G1 or in G2, irradiated with X-rays to induce DNA damage, and monitored for levels of recombination. Cells irradiated in G1 were found to repair recombinogenic damage primarily by homolog recombination, whereas those irradiated in G2 repaired such damage preferentially by sister chromatid recombination. We found, as have others, that G1 diploids were much more sensitive to the lethal effects of X-ray damage than were G2 diploids, especially at higher doses of irradiation. The following possible explanations for this observation were tested: G2 cells have more potential templates for repair than G1 cells; G2 cells are protected by the RAD9-mediated delay in G2 following DNA damage; sister chromatids may share more homology than homologous chromosomes. All these possibilities were ruled out by appropriate tests. We propose that, due to a special relationship they share, sister chromatids are not only preferred over homologous chromatids as substrates for recombinational repair, but have the capacity to repair more DNA damage than do homologs.
Role of heating and current-induced forces in the stability of atomic wires (2005)

We investigate the role of local heating and forces on ions in the stability of current-carrying aluminum wires. For a given bias, we find that heating increases with wire length due to a redshift of the frequency spectrum. Nevertheless, the local temperature of the wire is relatively low for a wide range of biases provided good thermal contact exists between the wire and the bulk electrodes. On the contrary, current-induced forces increase substantially as a function of bias and reach bond-breaking values at about 1 V. These results suggest that local heating promotes low-bias instabilities if dissipation into the bulk electrodes is not efficient, while current-induced forces are mainly responsible for the wire breakup at large biases. We compare these results to experimental observations.
Intracellular serine protease of Bacillus subtilis: sequence homology with extracellular subtilisins (1978)

Intracellular serine protease was isolated from stationary-grown Bacillus subtilis A-50 cells and purified to homogeneity. The molecular weight of the enzyme is 31,000 +/- 1,000, with an isoelectric point of 4.3. Its amino acid composition is characteristically enriched in glutamic acid content, differing from that of extra-cellular subtilisins. The enzyme is completely inhibited with phenylmethylsulfonyl fluoride and ethylenediaminetetraacetic acid. Intracellular protease possesses negligible activity towards bovine serum albumin and hemoglobin, but has 5- to 20-fold higher specific activity against p-nitroanilides of benzyloxycarbonyl tripeptides than subtilisin BPN'. Esterolytic activity of the enzyme is also higher than that of subtilisin BPN'. The enzyme is sequence homologous with secretory subtilisins throughout 50 determined NH2-terminal residues, indicating the presence of duplicated structural genes for serine proteases in the B. subtilis genome. The occurrence of two homologous genes in the cell might accelerate the evolution of serine protease not only by the loosening of selective constrainst, but also by creation of sequence variants by means of intragenic recombination. Three molecular forms of intracellular protease were found, two of them with NH2-terminal glutamic acid and one minor form, three residues longer, with asparagine as NH2 terminus. These data indicate the possible presence of an enzyme precursor proteolytically modified during cell growth.
Fabrication of a hollow needle structure by dicing, wet etching and metal deposition (2006)

We previously proposed a novel fabrication process, which combined mechanical dicing and anisotropic wet etching, to reduce the cost of micro-electro-mechanical system devices, and fabricated various solid-type microneedle structures using this process for trans-dermal drug delivery systems. The current research involved us enhancing our previous processes by applying metal plating and using a minimum number of photolithography steps, and we fabricated a hollow-type micro-needle structure, in which a flow channel was formed at the center of the needle projection, for supplying medical solutions from the area behind the needle. We fabricated two different shaped needle structures, pyramidal and flattened needles. The height and pitch of both needle types were 120–250 µm and 230–280 µm, respectively. The developed process is useful for producing disposable microneedles for bio-medical applications.
Induction of a Multiple Sclerosis-Like Disease in Mice with an Immunodominant Epitope of Myelin Oligodendrocyte Glycoprotein (1998)

Myelin oligodendrocyte glycoprotein (MOG) is postulated to be a target autoantigen in multiple sclerosis (MS). Here we investigated the encephalitogenicity of an immunodominant epitope of MOG, peptide 35-55, in various strains of mice. An MS-like disease was induced in NOD/Lt mice (H-2g7) and C57BL/6 mice (H-2b) by a single injection of MOG35-55 in CFA. The disease followed a relapsing-remitting course in NOD/Lt mice, whereas C57BL/6 mice developed a chronic paralytic disease. Histologically, the disease in both strains was characterized by cellular infiltration and multifocal demyelination in the CNS. Significant DTH type reactions to MOG35-55 were only seen in MOG-susceptible animals, with the NOD/Lt mice showing the strongest responses. Susceptible mice also showed specific antibody responses to MOG35-55 but not to a panel of other MOG peptides. These results provide further evidence for the role of MOG as a highly autoantigenic molecule capable of inducing severe demyelinating disease.
Palladium‐Catalyzed Synthesis of Propellanes with Hexaarylethane Structure (1997)

Abstract Areno‐anellated [3.3. n ]propellanes with n = 2, 3, and 4 are easily accesible by palladium‐catalyzed domino coupling processes of the pentalene system 8 with various aryl iodides. The X‐ray structure investigations reveled a noteworthy elongation of the central CC single bond of these propellanes to ca. 162 pm.
Effects of solvent on the maximum charge state and charge state distribution of protein ions produced by electrospray ionization (2000)

The effects of solvent composition on both the maximum charge states and charge state distributions of analyte ions formed by electrospray ionization were investigated using a quadrupole mass spectrometer. The charge state distributions of cytochrome c and myoglobin, formed from 47%/50%/3% water/solvent/acetic acid solutions, shift to lower charge (higher m/z) when the 50% solvent fraction is changed from water to methanol, to acetonitrile, to isopropanol. This is also the order of increasing gas-phase basicities of these solvents, although other physical properties of these solvents may also play a role. The effect is relatively small for these solvents, possibly due to their limited concentration inside the electrospray interface. In contrast, the addition of even small amounts of diethylamine (<0.4%) results in dramatic shifts to lower charge, presumably due to preferential proton transfer from the higher charge state ions to diethylamine. These results clearly show that the maximum charge states and charge state distributions of ions formed by electrospray ionization are influenced by solvents that are more volatile than water. Addition of even small amounts of two solvents that are less volatile than water, ethylene glycol and 2-methoxyethanol, also results in preferential deprotonation of higher charge state ions of small peptides, but these solvents actually produce an enhancement in the higher charge state ions for both cytochrome c and myoglobin. For instruments that have capabilities that improve with lower m/z, this effect could be taken advantage of to improve the performance of an analysis.
Perhexiline Maleate-Associated Hepatic Injury Prevalence and Characteristics (1980)

In order to assess the prevalence and characteristics of perhexiline maleate (PM)-associated hepatic injury, we have conducted a study in 46 patients on PM therapy (100-400 mg/day) for angina pectoris. Hepatomegaly was found in 6 patients. The prevalence of abnormal liver function tests were: (1) fractional clearance of BSP, 74%; (2) fasting total serum bile acids, 57% and (3) serum transaminases, 30%. The other tests were abnormal in less than 10% of the patients. A significant increase in BSP clearance was observed 3-6 months after PM withdrawal. Conversely, while treatment continued unchanged BSP clearance significantly decreased. A pathological and histochemical study of the liver was performed in 11 patients with an abnormal BSP clearance. Diffuse micro- and macrovacuolar fatty change and hepatocellular hyperplasia were found in all the specimens. In addition to an excess of triglycerides, the histochemical study revealed an abnormal amount of phospholipids and/or gangliosides in some liver specimens. This study shows that PM induces liver injury in a high proportion of patients receiving the drug. This liver injury is: (1) usually clinically latent; (2) characterized by an impairment of the hepatic transport of BSP or bile acids and by the presence of an abnormal amount of various classes of lipids in the liver, and (3) progressive while PM therapy continues.
[Correlation between OPN and P21 in non-small cell lung cancer]. (2007)

The abnormal expression of OPN and P21 in NSCLC may act in a synergistic way. Immunopositivity of OPN may suggest a potential risk of metastasis in NSCLC.
Sphingosine 1-phosphate signalling in mammalian cells (2000)

Sphingosine 1-phosphate is formed in cells in response to diverse stimuli, including growth factors, cytokines, G-protein-coupled receptor agonists, antigen, etc. Its production is catalysed by sphingosine kinase, while degradation is either via cleavage to produce palmitaldehyde and phosphoethanolamine or by dephosphorylation. In this review we discuss the most recent advances in our understanding of the role of the enzymes involved in metabolism of this lysolipid. Sphingosine 1-phoshate can also bind to members of the endothelial differentiation gene (EDG) G-protein-coupled receptor family [namely EDG1, EDG3, EDG5 (also known as H218 or AGR16), EDG6 and EDG8] to elicit biological responses. These receptors are coupled differentially via Gi, Gq, G12/13 and Rho to multiple effector systems, including adenylate cyclase, phospholipases C and D, extracellular-signal-regulated kinase, c-Jun N-terminal kinase, p38 mitogen-activated protein kinase and non-receptor tyrosine kinases. These signalling pathways are linked to transcription factor activation, cytoskeletal proteins, adhesion molecule expression, caspase activities, etc. Therefore sphingosine 1-phosphate can affect diverse biological responses, including mitogenesis, differentiation, migration and apoptosis, via receptor-dependent mechanisms. Additionally, sphingosine 1-phosphate has been proposed to play an intracellular role, for example in Ca2+ mobilization, activation of non-receptor tyrosine kinases, inhibition of caspases, etc. We review the evidence for both intracellular and extracellular actions, and extensively discuss future approaches that will ultimately resolve the question of dual action. Certainly, sphingosine 1-phosphate will prove to be unique if it elicits both extra- and intra-cellular actions. Finally, we review the evidence that implicates sphingosine 1-phosphate in pathophysiological disease states, such as cancer, angiogenesis and inflammation. Thus there is a need for the development of new therapeutic compounds, such as receptor antagonists. However, identification of the most suitable targets for drug intervention requires a full understanding of the signalling and action profile of this lysosphingolipid. This article describes where the research field is in relation to achieving this aim.
Identifying Substrate Motifs of Protein Kinases by a Random Library Approach (1994)

Protein phosphorylation is an important posttranslational modification process that plays a crucial role in signal transduction. There are many protein kinases involved in cell signaling. However, substrate motifs of many protein kinases in signal transduction are not well-known. Traditional methodologies for identifying these motifs are often difficult and inefficient. In the present study, we developed a novel approach for discovering linear substrate motifs of protein kinases. This method is based on the screening of random synthetic combinatorial peptide libraries on beads where each bead expresses only one peptide entity [Lam et al. (1991) Nature 354, 82-84]. We chose cyclic AMP-dependent protein kinase (cAPK) as a model system in the present study since it is a well-studied enzyme. Random pentapeptide and heptapeptide libraries were screened with the addition of [gamma-32P]ATP and cAPK. 32P-Labeled peptide-beads were then isolated for microsequencing. The identified peptide motif for cAPK was RRXS and is identical to that reported in the literature. Kinetic studies of the best three peptides indicate that they are efficient substrates for cAPK discovered from random synthetic combinatorial peptide libraries. Our results also suggest that this method is potentially useful for identifying substrate motifs of various protein kinases with high sensitivity and specificity. In addition, this method can also be used as a general method for identifying linear substrate motifs for various posttranslational modifications.
Finite-element full-vectorial propagation analysis for three-dimensional z-varying optical waveguides (1998)

A finite-element-based full-vectorial beam propagation method (BPM) for the analysis of the electromagnetic field evolution in three-dimensional (3-D) dielectric waveguides is presented. The approach has been derived in order to be suitable for the numerical discretization through finite elements and to fully account for the vectorial nature of the electromagnetic field. To this aim the problem related to the permittivity derivative at dielectric interface has been addressed and overcome. The advantages and the potentialities of the finite elements usage are discussed. The precision and the correctness of the proposed approach is demonstrated through numerical examples. Typical integrated optics structures, as a tapered waveguide and a Y-junction, are analyzed to assess the applicability of the method.
Rapid and automated detection of salmonella by electrical measurements (1985)

A rapid method for determining the presence of salmonella in food is described. It consists of pre-enrichment in buffered peptone water modified by the addition of dulcitol and trimethylamine oxide, followed by selective enrichment in a selenite-cystine broth with similar modifications. Changes in the conductance of the selective enrichment broth are monitored continuously using a suitable impediometric instrument. Most of the Salmonella spp. tested gave a fast (approximately 100 microS/h) and large (greater than 600 microS) change in conductance, other enteric bacteria much less or no change. The assay is usually complete within 24 h. Samples of foodstuffs, naturally and artificially contaminated with Salmonella spp., were all correctly classified. Some strains of Citrobacter freundii produced a false positive conductance response, and they could not be selectively eliminated using antibiotics or cyanide. The conductance method is simple and easy to use, gives rapid results and involves less media and subculturing than is required for traditional methods.
Understanding the Inflammatory Cytokine Response in Pneumonia and Sepsis (2007)

The circulating cytokine response to pneumonia is heterogeneous and continues for more than a week after presentation, with considerable overlap between those who do and do not develop severe sepsis. Unbalanced activation is uncommon, and mortality is highest when both proinflammatory and anti-inflammatory cytokine levels are high.
Determination of ocular torsion by means of automatic pattern recognition (1996)

A new, automatic method for determination of human ocular torsion (OT) was developed based on the tracking of iris patterns in digitized video images. Instead of quantifying OT by means of cross-correlation of circular iris samples, a procedure commonly applied, this new method automatically selects and recovers a set of 36 significant patterns in the iris by the technique of template matching as described by In den Haak et al. Each relocated landmark results in a single estimate of the torsion angle. A robust algorithm estimates OT from this total set of individually determined torsion angles, thereby largely correcting for errors which may arise due to misjudgement of the rotation center. The new method reproduced OT in a prepared set of images of an artificial eye with an accuracy of 0.1 degree. In a sample of 256 images of human eyes, a practical reliability of 0.25 degrees was achieved. To illustrate the method's usefulness, an experiment is described in which ocular torsion was measured during two dynamic conditions of whole-body roll, namely during sinusoidally pendular motion about either an earth horizontal or earth vertical axis (that is "with" and "without" otolith stimulation, respectively).
Phase I Trial of Intramuscular Injection of a Recombinant Adeno-Associated Virus Alpha 1-Antitrypsin (rAAV2-CB-hAAT) Gene Vector to AAT-Deficient Adults (2004)

A recombinant virus vector constructed from adeno-associated virus (AAV) that has been altered to carry the human alpha1-antitrypsin (hAAT) gene expressed from a hybrid chicken beta-actin promoter with a cytomegalovirus enhancer has been developed. The construct has been shown to initiate the production of hAAT in animal models closely matching the proposed human trial. The proposed clinical trial is an open-label, phase I study administering recombinant adeno-associated virus alpha1-antitrypsin (rAAV2-CB-hAAT) gene vector intramuscularly to AAT-deficient human subjects where gene expression can be measured directly in blood samples to assess safety. Safety parameters will be measurement of changes in serum chemistries and hematology, urinalysis, pulmonary function testing, semen assay for vector genomes, immunologic response to AAT, and AAV, as well as reported subject history of any symptoms.