gebhart/patrepeval huggingface dataset:
MORPHOLOGICAL, BIOCHEMICAL, AND PHYSIOLOGICAL CHARACTERISTICS OF SPORE-FORMING LACTIC ACID BACTERIA (1987)

One hundred and eighteen strains of spore-forming lactic acid bacteria, and one strain of Lactobacillus plantarum were investigated with regard to morphological, biochemical, and physiological characteristics. These characteristics were analyzed numerically. The strains were separated into three clusters. Cluster 1 consists of 44 strains including Sporolactobacillus inulinus (2 strains), "Sporolactobacillus laevas" (15 strains), "Sporolactobacillus laevas var. intermedius" (7 strains), "Sporolactobacillus racemicus" (7 strains), "Bacillus laevolacticus" (12 strains), and "Bacillus racemilacticus" (1 strain). Cluster 2 consists of 70 strains: "B. laevolacticus" (57 strains), "B. racemilacticus" (2 strains), "S. racemicus" (8 strains), "S. laevas" (2 strains), and "S. laevas var. intermedius" (1 strain). Cluster 3 comprises 3 strains including the type strain of Bacillus coagulans and one strain each of "B. laevolacticus" and "B. racemilacticus." One strain of "S. racemicus" and the type strain of Lactobacillus plantarum were not included in the above clusters. The clusters are considered to correspond respectively to the taxa Sporolactobacillus, "Bacillus laevolacticus, " and Bacillus coagulans. Catalase activity and production of acid from lactose and melibiose were useful in differentiating the three clusters.
In vivo neutralization of P-selectin protects feline heart and endothelium in myocardial ischemia and reperfusion injury. (1993)

The cardioprotective effects of an mAb to P-selectin designated mAb PB1.3 was examined in a feline model of myocardial ischemia (MI) and reperfusion. PB1.3 (1 mg/kg), administered after 80 min of ischemia (i.e., 10 min before reperfusion), significantly attenuated myocardial necrosis compared to a non-blocking mAb (NBP1.6) for P-selectin (15 +/- 3 vs 35 +/- 3% of area at risk, P < 0.01). Moreover, endothelial release of endothelium derived relaxing factor, as assessed by relaxation to acetylcholine, was also significantly preserved in ischemic-reperfused coronary arteries isolated from cats treated with mAb PB1.3 compared to mAb NBP1.6 (67 +/- 6 vs 11 +/- 3, P < 0.01). This endothelial preservation was directly related to reduced endothelial adherence of PMNs in ischemic-reperfused coronary arteries. Immunohistochemical localization of P-selectin was significantly upregulated in the cytoplasm of endothelial cells that lined coronary arteries and veins after 90 min of ischemia and 20 min of reperfusion. The principal site of intracytoplasmic expression was in venous vessels. mAb PB1.3 significantly decreased (P < 0.01) adherence of unstimulated PMNs to thrombin and histamine stimulated endothelial cells in a concentration-dependent manner in vitro. These results demonstrate that PMN adherence to endothelium by P-selectin is an important early consequence of reperfusion injury, and a specific monoclonal antibody to P-selectin exerts significant endothelial preservation and cardioprotection in myocardial ischemia and reperfusion.
DNA Fingerprinting: State of the Science (1993)

DNA fingerprinting had a well-defined birthday. In the March 7, 1985 issue of Nature, Alec Jeffreys and coworkers described the first develop ment ofmu1tilocus probes capable of simultaneously reveali
An Application of the On-line Respiratory Mass Spectrometer to the Detection of Helicobacter pylori Infection Using 13C-Labeled Urea. (1999)

In recent studies, it has been revealed that Helicobacter pylori (HP) causes stomach cancer, stomach ulcers, duodenal ulcers and chronic gastritis. The 13C-urea breath test (UBT) is one of the diagnostic methods for HP infection. A new UBT method with the respiratory mass spectrometer developed by authors continuously measures with on-line the amount of decomposed 13C-urea in the stomach after the administration of 13C-urea. Trial examinations by the new method were carried out with two subjects; one was diagnosed positive of HP infection and the other was negative by clinical examinations. Significant difference was found in the amount of decomposed 13C-urea between both subjects. The results presented in this paper demonstrate that the new UBT method is applicable to the clinical use in the diagnosis of HP infection.
Review: Control of IRF-3 Activation by Phosphorylation (2002)

Interferon (IFN) regulatory factor-3 (IRF-3) is a unique member of the IRF family. Its transcriptional activity is regulated solely by posttranslational modifications. We review current knowledge of the mechanism of IRF-3 activation: signalling triggered by infections including viruses and bacteria, phosphorylation of IRF-3 on certain serine residues, homodimer formation, and active holocomplex formation with coactivator CBP/p300.
Ceramic-Based Multisite Electrode Arrays for Chronic Single-Neuron Recording (2004)

A method is described for the manufacture of a microelectrode array for chronic, multichannel, single neuron recording. The ceramic-based, multisite electrode array has four recording sites patterned onto a ceramic shaft the size of a single typical microwire electrode. The sites and connecting wires are applied to the ceramic substrate using a reverse photolithographic procedure. Recording sites (22 x 80 microm) are separated by 200 microm along the shaft. A layer of alumina insulation is applied over the whole array (exclusive of recording sites) by ion-beam assisted deposition. These arrays were capable of recording single neuron activity from each of their recording sites for at least three weeks during chronic implantation in the somatosensory cortex of rats, and several sites had recordings that lasted for more than 8 weeks. The vertical arrangement of the recording sites on these electrodes is ideal for simultaneously recording across the different layers of brain areas such as the cerebral cortex and hippocampus in chronic preparations.
Repression of the IgH Enhancer in Teratocarcinoma Cells Associated with a Novel Octamer Factor (1989)

Embryonal carcinoma (EC) cell lines are models for early cells in mouse embryogenesis. A 300-base pair fragment of the heavy chain enhancer was inactive in F9 EC cells, unlike in other nonlymphoid cells where it has significant activity. Alterations of the octamer motif increased enhancer activity. Nuclear extracts from F9 cells contained an octamer binding protein (NF-A3) that was unique to EC cells; the amount of NF-A3 decreased upon differentiation. It is proposed that NF-A3 represses specific regulatory sequences that contain the octamer motif. Thus, the same DNA sequence mediates either negative or positive transcriptional effects, depending on the cell type.
Essential role for proteinase-activated receptor-2 in arthritis (2003)

Using physiological, pharmacological, and gene disruption approaches, we demonstrate that proteinase-activated receptor-2 (PAR-2) plays a pivotal role in mediating chronic inflammation.Using an adjuvant monoarthritis model of chronic inflammation, joint swelling was substantially inhibited in PAR-2-deficient mice, being reduced by more than fourfold compared with wild-type mice, with virtually no histological evidence of joint damage.Mice heterozygous for PAR-2 gene disruption showed an intermediate phenotype.PAR-2 expression, normally limited to endothelial cells in small arterioles, was substantially upregulated 2 weeks after induction of inflammation, both in synovium and in other periarticular tissues.PAR-2 agonists showed potent proinflammatory effects as intraarticular injection of ASKH95, a novel synthetic PAR-2 agonist, induced prolonged joint swelling and synovial hyperemia.Given the absence of the chronic inflammatory response in the PAR-2-deficient mice, our findings demonstrate a key role for PAR-2 in mediating chronic inflammation, thereby identifying a novel and important therapeutic target for the management of chronic inflammatory diseases such as rheumatoid arthritis.
The genetic basis of tetrathionate respiration in Salmonella typhimurium (1999)

A range of bacteria are able to use tetrathionate as a terminal respiratory electron acceptor. Here we report the identification and characterization of the ttrRSBCA locus required for tetrathionate respiration in Salmonella typhimurium LT2a. The ttr genes are located within Salmonella pathogenicity island 2 at centisome 30.5. ttrA, ttrB and ttrC are the tetrathionate reductase structural genes. Sequence analysis suggests that TtrA contains a molybdopterin guanine dinucleotide cofactor and a [4Fe-4S] cluster, that TtrB binds four [4Fe-4S] clusters, and that TtrC is an integral membrane protein containing a quinol oxidation site. TtrA and TtrB are predicted to be anchored by TtrC to the periplasmic face of the cytoplasmic membrane implying a periplasmic site for tetrathionate reduction. It is inferred that the tetrathionate reductase, together with thiosulphate and polysulphide reductases, make up a previously unrecognized class of molybdopterin-dependent enzymes that carry out the reductive cleavage of sulphur-sulphur bonds. Cys-256 in TtrA is proposed to be the amino acid ligand to the molybdopterin cofactor. TtrS and TtrR are the sensor and response regulator components of a two-component regulatory system that is absolutely required for transcription of the ttrBCA operon. Expression of an active tetrathionate reduction system also requires the anoxia-responsive global transcriptional regulator Fnr. The ttrRSBCA gene cluster confers on Escherichia coli the ability to respire with tetrathionate as electron acceptor.
Expression and characterization of a cDNA for rat kidney biliverdin reductase. Evidence suggesting the liver and kidney enzymes are the same transcript product. (1992)

Biliverdin reductase is a unique dual cofactor- and pH-dependent enzyme that converts biliverdin to bilirubin and displays extensive inter-organ pI and molecular weight microheterogeneity. Presently we have explored the molecular basis for these properties. The amino acid composition and the sequences of NH2 termini plus five tryptic fragments of purified rat liver and kidney enzymes were obtained. A 62-nucleotide DNA probe was designed and in combination with antibody was used to screen a rat kidney cDNA library. A cDNA sequence of 1108 base pairs (bp) containing an 885-bp open reading frame was generated. The cloned cDNA probe detected a single mRNA of approximately 1500 bp in liver and kidney. The open reading frame encodes a 295 amino acid protein. Methionine and aspartic acid residues at positions 1 and 2 of the deduced protein are removed during processing. The deduced amino acid composition of the mature protein closely matched that of the purified rat liver and kidney enzymes. All liver peptides were found in the deduced amino acid sequence of kidney enzyme and the NH2 termini of both enzymes were identical. The expressed protein co-migrated with purified reductase and was recognized by antiserum to the enzyme. The expressed reductase displayed two distinct pH optima using a different cofactor at each pH: NADH at the lower pH 6.7-6.9 range and NADPH at pH 8.5-8.7. The findings suggest that the liver and kidney enzymes are the products of the same transcript(s) and that their microheterogeneity may reflect tissue-specific post-translational modifications.
Cotunneling in pairs of coupled flux qubits (2010)

We report measurements of macroscopic resonant tunneling between the two lowest energy states of a pair of magnetically coupled rf-superconducting quantum interference device flux qubits. This technique provides both a direct means of measuring the energy gap of the two-qubit system and a method for probing of the environment coupled to the pair of qubits. Measurements of the tunneling rate as a function of qubit flux bias show a Gaussian line shape that is well matched to theoretical predictions. Moreover, the peak widths indicate that each qubit is coupled to a local environment whose fluctuations are uncorrelated with that of the other qubit.
Micromethod for assaying reverse transcriptase of human T-cell lymphotropic virus type III/lymphadenopathy-associated virus (1987)

A micromethod for assaying the reverse transcriptase enzyme of human T-cell lymphotropic virus type III/lymphadenopathy-associated virus in cocultures of clinical specimens for viral isolation was developed and compared with the macromethod in use. Ultracentrifuged, pelleted, and solubilized viral culture supernatants were transferred into either tubes (macromethod) or microtiter plates (micromethod) and incubated with tritiated enzyme substrate. Trichloroacetic acid-precipitated DNA was collected on individual filter papers with a Millipore filtration manifold (macromethod) or on filter sheets using a semiautomated cell harvester (micromethod). Filters were then placed in scintillation fluid and counted on a beta scintillation counter. Results of the micromethod significantly correlated to those of the macromethod, with a linear relationship between the two. The cutoffs for positivity based on the mean + 2 standard deviations for a set of known negative specimens (n = 19) was 4,973 cpm for the micromethod compared with 5,336 for the macromethod. The intrarun and interrun variations were comparable for both methods. There was a 67% increase in the maximal daily number of specimens which could be run (100 versus 60) as well as a reduction in reagent use. In summary, the micromethod utilizing a semiautomated cell harvester is comparable to the existing macromethod in accuracy and is an improvement due to savings in time and reagents.
n -Type Conducting CdSe Nanocrystal Solids (2003)

A bottleneck limiting the widespread application of semiconductor nanocrystal solids is their poor conductivity. We report that the conductivity of thin films of n-type CdSe nanocrystals increases by many orders of magnitude as the occupation of the first two electronic shells, 1Se and 1Pe, increases, either by potassium or electrochemical doping. Around half-filling of the 1Se shell, a peak in the conductivity is observed, indicating shell-to-shell transport. Introducing conjugated ligands between nanocrystals increases the conductivities of these states to approximately 10(-2) siemens per centimeter.
Activation of MET via Diverse Exon 14 Splicing Alterations Occurs in Multiple Tumor Types and Confers Clinical Sensitivity to MET Inhibitors (2015)

Here we report the identification of diverse exon 14 splice site alterations in MET that result in constitutive activity of this receptor and oncogenic transformation in vitro. Patients whose tumors harbored these alterations derived meaningful clinical benefit from MET inhibitors. Collectively, these data support the role of METex14 alterations as drivers of tumorigenesis, and identify a unique subset of patients likely to derive benefit from MET inhibitors.
A Herpesvirus Ribosome-Associated, RNA-Binding Protein Confers a Growth Advantage upon Mutants Deficient in a GADD34-Related Function (1999)

The herpes simplex virus type 1 gamma34.5 gene product and the cellular GADD34 protein both contain similar domains that can regulate the activity of eukaryotic initiation factor 2 (eIF2), a critical translation initiation factor. Viral mutants that lack the GADD34-related function grow poorly on a variety of malignant human cells, as activation of the cellular PKR kinase leads to the accumulation of inactive, phosphorylated eIF2 at late times postinfection. Termination of translation prior to the completion of the viral reproductive cycle leads to impaired growth. Extragenic suppressors that regain the ability to synthesize proteins efficiently in the absence of the viral GADD34-related function have been isolated. These suppressor alleles are dominant in trans and affect the steady-state accumulation of several viral mRNA species. We demonstrate that deregulated expression of Us11, a virus-encoded RNA-binding, ribosome-associated protein is necessary and sufficient to confer a growth advantage upon viral mutants that lack a GADD34-related function. Ectopic expression of Us11 reduces the accumulation of the activated cellular PKR kinase and allows for sustained protein synthesis. Thus, an RNA-binding, ribosome-associated protein (Us11) and a GADD34-related protein (gamma34.5) both function in a signal pathway that regulates translation by modulating eIF2 phosphorylation.
RAD51 Interacts with the Evolutionarily Conserved BRC Motifs in the Human Breast Cancer Susceptibility Gene brca2 (1997)

Recent work has shown that the murine BRCA2 tumor suppressor protein interacts with the murine RAD51 protein. This interaction suggests that BRCA2 participates in DNA repair. Residues 3196-3232 of the murine BRCA2 protein were shown to be involved in this interaction. Here, we report the detailed mapping of additional domains that are involved in interactions between the human homologs of these two proteins. Through yeast two-hybrid and biochemical assays, we demonstrate that the RAD51 protein interacts specifically with the eight evolutionarily conserved BRC motifs encoded in exon 11 of brca2 and with a similar motif found in a Caenorhabditis elegans hypothetical protein. Deletion analysis demonstrates that residues 98-339 of human RAD51 interact with the 59-residue minimal region that is conserved in all BRC motifs. These data suggest that the BRC repeats function to bind RAD51.
Use of T Cell Epitopes for Vaccine Development (2001)

T lymphocytes play a major role in the recognition and subsequent elimination of tumors and intracellular pathogens. Induction of epitope-specific T cell responses can help in the clearance of diseases for which no conventional vaccines exist. However, the lack of simple methods to identify relevant T cell epitopes, the high mutation rate of many pathogens, and HLA polymorphism have made the development of efficient T cell epitope-based, or "epitope-driven" vaccines difficult to achieve. Our research over the past several years has applied bioinformatics tools in conjunction with T cell assays to identify naturally processed putative T cell epitopes from several pathogens. This strategy will accelerate the development of new generation T cell epitope-based vaccines against various pathogens including viruses such as HIV and WNV, bacteria such as M.tb., and parasites such as plasmodium. This chapter will review the use of a bioinformatics-based approach to identify putative T cell epitopes. It will summarize the current state of knowledge regarding T cell-epitope-based vaccines and discuss several ways to improve their efficacy.
SYNTHESIS OF SOME BIOLOGICALLY ACTIVE HETEROCYCLES. REACTIONS OF THE HYDRAZIDE OF 2′-THIENOYL ANTHRANILIC ACID AND ITS 3,5-DIBROMO DERIVATIVE (1992)

Abstract The hydrazide of 2′-thienoyl anthranilic acid and its 3,5-dibromo derivative (1a and b) were condensed with carbon disulphide to give 1–3′-quinazolin-2-thione 5–2′′-aminophenyl-1,3,4-triazoles (2a, b). When treated with acetyl chloride 3-N-acetamidoquinazolin-4-ones (3a, b), with aromatic aldehydes the schiff bases 4 and 5(a, b). Potassium thiocyanate and phenyl isothiocyanate gave the semicarbazide derivatives (6a, b) while ammonium thiocyanate afforded the triazol-thiones (7a, b). Reaction with ethyl acetoacetate and acetylacetone gave the pyrazole derivatives 8 and 9 respectively; Biological activities of some of these compounds are tested.
Cluster analysis of long time-series medical datasets (2004)

This paper presents a comparative study about the characteristics of clustering methods for inhomogeneous time-series medical datasets. Using various combinations of comparison methods and grouping methods, we performed clustering experiments of the hepatitis data set and evaluated validity of the results. The results suggested that (1) complete-linkage (CL) criterion in agglomerative hierarchical clustering (AHC) outperformed average-linkage (AL) criterion in terms of the interpretability of a dendrogram and clustering results, (2) combination of dynamic time warping (DTW) and CL-AHC constantly produced interpretable results, (3) combination of DTW and rough clustering (RC) would be used to find the core sequences of the clusters, (4) multiscale matching may suffer from the treatment of 'no-match' pairs, however, the problem may be eluded by using RC as a subsequent grouping method.
Evaluation of the Tru-Trax cervical mucus penetration test in predicting fertilization and pregnancy rates in in-vitro fertilization. (1995)

To evaluate the role of the Tru-Trax cervical mucus penetration testing of prognosis of patient performance in in-vitro fertilization (IVF) and to examine its use as a possible screening test prior to IVF, 133 couples presenting with infertility prospectively underwent in-vitro cervical mucus penetration testing. Of these, 66 couples subsequently underwent IVF. The penetration distance of the vanguard spermatozoa in both human and bovine mucus was compared to the fertilization and pregnancy rates during IVF. The fertilization rates in couples with normal human mucus penetration (n = 42, 80.6%) were higher than those with abnormal scores (n = 24, 49.6%; P < 0.001). Similarly, the fertilization rates in those couples with normal bovine mucus penetration (n = 50, 77.5%) were higher than those with abnormal results (n = 16, 40.0%; P < 0.001). Fertilization rates and penetration scores were highly correlated for both human (r = 0.66; P < 0.0001) and bovine (r = 0.66; P < 0.0001) mucus. However, the predictive value of an abnormal result for failed fertilization was poor for both human and bovine penetration, since 83.33 and 81.25% fertilized respectively. Pregnancy rates did not differ among couples with normal and abnormal penetrations. In conclusion, in-vitro cervical mucus penetration testing was highly correlated with fertilization rates in IVF. However, the poor predictive value of an abnormal result may limit the value of this test for generalized pretreatment screening.
The file system research based on the volume holographic data storage (2005)

The Volume Holographic Data Storage (VHDS) is an optical technology that allows one million bits of data to be written and read out in single flashes of light. To accommodate the characteristics of VHDS, this paper presents the following strategies in designing the file system based on VHDS: (1) Construct the virtual storage layer on the Holographic Storage media, which turns the storage-on-pages into the storage-on-blocks. (2) Use the two-layer structure of the directory table and the index node, and the data stored in the immediate area of the index node. This method can access the index node and the content (partial or all) of the file with an accessing operation. (3) Adopt the allocating method of the page priority in storing data--allocate the whole page to a file while the length of the file exceeds the page. In the meantime, a page is partitioned into many zones to enhance the storing utilities of VHDS. (4) To meet the three-dimension storage's need, the two-dimension Logical Block Address (LBA) is to be used, and makes the more continuity between data blocks--allocate the continuous data blocks in vertical and horizontal direction while storing data. The simulation test shows that the file system can be compatible with the existing file system, and has better stability.