gebhart/patrepeval huggingface dataset:
Learning Human-like Knowledge by Singular Value Decomposition: A Progress Report (1997)

Singular value decomposition (SVD) can be viewed as a method for unsupervised training of a network that associates two classes of events reciprocally by linear connections through a single hidden layer. SVD was used to learn and represent relations among very large numbers of words (20k-60k) and very large numbers of natural text passages (1k70k) in which they occurred. The result was 100-350 dimensional &amp;quot;semantic spaces&amp;quot; in which any trained or newly added word or passage could be represented as a vector, and similarities were measured by the cosine of the contained angle between vectors. Good accuracy in simulating human judgments and behaviors has been demonstrated by performance on multiple-choice vocabulary and domain knowledge tests, emulation of expert essay evaluations, and in several other ways. Examples are also given of how the kind of knowledge extracted by this method can be applied.
Improving Access to Intestinal Stem Cells as a Step Toward Intestinal Gene Transfer (1994)

In previous studies exploring the intestinal epithelium as a potential site for somatic gene therapy, we concluded that the mucus lining the intestine constitutes a significant barrier to any attempts at gene transfer via the lumenal route. The mucus problem is aggravated by the fact that the epithelial stem cells, which are the logical target for gene transfer, are located deep in the intestinal crypts. The goals of the current study were to develop procedures that would improve accessibility to the intestinal stem cells and which would effect in vivo mucus removal without damaging the underlying epithelium. Initial experiments involved evaluation of the use of distension to improve accessibility to the intestinal crypts and the use of the mucolytic agents dithiothreitol (DTT) and N-acetyl-cysteine (NAC) versus a control solution of phosphate-buffered saline (PBS) for mucus removal. Catheters were inserted in each end of 3-cm terminal ileal segments in anesthetized rats. Two milliliters of agent was instilled into the clamped segment for 2 min, removed, and repeated. Lumenal distension resulted in shortened villi with wider intervillus spacing, thereby improving crypt access. Both NAC and DTT washes removed significant mucus between the villi but failed to reach the crypt lumen. To enhance mucus release from the crypt lumen, pilocarpine was selected due to its cholinergic properties and preferential binding to muscarinic receptors on crypt goblet cells. Pilocarpine given intraperitoneally 30 min prior to the mucolytic or PBS wash resulted in significant eradication of mucus down into the crypt lumen. This effect was still evident 3-4 hr later provided the intestine remained undisturbed.
Cloning and nucleotide sequence analysis of psaA, the Streptococcus pneumoniae gene encoding a 37-kilodalton protein homologous to previously reported Streptococcus sp. adhesins (1994)

Gene psaA, which encodes the Streptococcus pneumoniae 37-kDa protein, was cloned in Escherichia coli, and its complete nucleotide sequence was determined. Analysis of the sequence of the 2.4-kb cloned fragment revealed three open reading frames (ORFs). ORF2, which is 933 bp long, was identified as psaA. The two other ORFs identified flank psaA. ORF1, located upstream of psaA, is 836 nucleotides long and encodes a protein with a calculated molecular mass of 29,843 Da. The sequence for ORF3, located downstream of psaA, was only partially determined. Northern (RNA) blot analysis of pneumococcal RNA suggests that psaA is transcribed as part of a polycistronic message. Analysis of the primary structure of the protein encoded by this gene indicated significant similarity to two previously reported streptococcal proteins, SsaB (80% similarity) and FimA (92.3% similarity), from S. sanguis and S. parasanguis, respectively. These two homologous proteins have been shown to be associated with bacterial adhesion, and the possibility of a similar role for PsaA is hypothesized.
Lysyl Oxidase-Like 2 Level and Glaucoma Surgical Outcomes (2014)

The TGF-β and lysyl oxidase-like 2 levels at the time of surgery were significantly correlated with 1-year outcomes of glaucoma surgery. The level of lysyl oxidase-like 2 was significantly correlated with that of TGF-β, suggesting induction by TGF-β. Modulation of lysyl oxidase-like 2 levels may have important applications in glaucoma surgery.
Transcription of the mouse dihydrofolate reductase gene proceeds unabated through seven polyadenylation sites and terminates near a region of repeated DNA. (1984)

We observed equimolar transcription throughout the 35-kilobase mouse dihydrofolate reductase structural gene. Transcription termination occurred within a discrete region (900 base pairs) located 1 kilobase beyond the last of seven functional polyadenylation sites and near a repetitive DNA sequence element. The results imply that a distinct genetic signal may be associated with the process of transcription termination.
Cloning, sequence analysis, expression, and inactivation of the Corynebacterium glutamicum icd gene encoding isocitrate dehydrogenase and biochemical characterization of the enzyme (1995)

NADP(+)-dependent isocitrate dehydrogenase (ICD) is an important enzyme of the intermediary metabolism, as it controls the carbon flux within the citric acid cycle and supplies the cell with 2-oxoglutarate and NADPH for biosynthetic purposes. In the amino acid-producing organism Corynebacterium glutamicum, the specific activity of ICD was independent of the growth substrate and of the growth phase at approximately 1 U/mg, indicating that this enzyme is constitutively formed. The ICD gene, icd, was isolated, subcloned on a plasmid, and introduced into C. glutamicum. Compared with the wild type, the recombinant strains showed up to 10-fold-higher specific ICD activities. The nucleotide sequence of a 3,595-bp DNA fragment containing the icd gene was determined. The predicted gene product of icd consists of 739 amino acids (M(r) = 80.091) and showed 58.5% identity with the monomeric ICD isozyme II from Vibrio sp. strain ABE-1 but no similarity to any known ICD of the dimeric type. Inactivation of the chromosomal icd gene led to glutamate auxotrophy and to the absence of any detectable ICD activity, suggesting that only a single ICD is present in C. glutamicum. From an icd-overexpressing C. glutamicum strain, ICD was purified and biochemically characterized. The native ICD was found to be a monomer; to be specific for NADP+; to be weakly inhibited by oxaloacetate, 2-oxoglutarate, and citrate; and to be severely inhibited by oxaloacetate plus glyoxylate. The data indicate that ICD from C. glutamicum is structurally similar to ICDs from bacteria of the genera Vibrio, Rhodomicrobium, and Azotobacter but different from all other known procaryotic and eucaryotic ICDs.
Gender differences in routine treatment of depressed outpatients with the selective serotonin reuptake inhibitor sertraline (2004)

Gender is known to have an influence on medical treatment and the prescribing and outcome of drug treatment. This has also been suggested for selective serotonin reuptake inhibitors (SSRIs). To examine sex differences in the treatment with the SSRI sertraline in routine treatment of depression, data from a 6-month prospective drug utilization observation study on 3,858 women and 1,594 men were analysed for gender differences. Compared to men, women were more often treated by a general practitioner, were somewhat older, had a later onset of illness, were more likely to suffer from a recurrent rather than a first episode of depression, had been treated for depression before, and showed more anxious and less neurasthenic or retarded syndromes. There was no difference regarding duration of the present episode or severity of illness. The mean prescribed dose of sertraline was marginally lower for females compared to males (45.5 versus 46.5 mg/day) with no difference in the rate of psychoactive concomitant medication (6.76% versus 6.80%). There was no difference in side-effects, treatment termination or treatment response.
A unified framework for Web link analysis (2003)

Web link analysis has been proved to significantly enhance the precision of Web searching in practice. Among existing approaches, Kleinberg's (1998) HITS and Google's PageRank are the two most representative algorithms that employ explicit hyperlink structure among Web pages to conduct link analysis, and DirectHit represents the other extreme that takes the user's access frequency as an implicit link to the Web page for assessing its importance. We propose a novel link analysis algorithm which puts both explicit and implicit link structures under a unified framework, and show that HITS and DirectHit are essentially two extreme instances of our proposed method. One important advantage of our method is its ability to analyze not only the hyperlinks between Web pages but also the interactions between users and the Web at the same time. The importance of Web pages and users can reinforce each other to improve Web link analysis. Compared with traditional HITS and DirectHit algorithms, our method further improves the search precision by 11.8% and 25.3%.
In vitro peptide binding to soluble empty class I major histocompatibility complex molecules isolated from transfected Drosophila melanogaster cells. (1992)

A soluble form of a mouse class I major histocompatibility antigen (H-2Kb) has been expressed in transfected Drosophila melanogaster cells. These molecules were efficiently secreted (up to 4 mg/liter) as noncovalent heterodimers and purified to homogeneity from cell supernatants. The isolated soluble Kb molecules were devoid of endogenous peptides. Using these molecules, we have characterized the Kb heavy chain-beta 2-microglobulin (beta 2m) assembly as well as peptide binding in vitro. In detergent-free solution the heavy chains readily re-assembled with beta 2m even in the absence of peptides. Kinetic analyses showed that the peptide binding is rapid and reversible and dependent on the heavy chains being assembled with beta 2m. Likewise, peptide dissociated from Kb molecules without the displacement of beta 2m. Equilibrium binding experiments using various peptides confirmed that octapeptides bind to Kb molecules with the highest affinity and form the most stable complexes. However, in contrast to earlier studies, the amino-terminal positioning of peptide to Kb molecules was more crucial than the carboxyl-terminal positioning and amidation of the peptide carboxylate did not affect the binding. Soluble Kb molecules could selectively bind allele-specific peptides among a mixture of randomly synthesized octapeptides in vitro; however, no dominant residue was observed at the carboxyl terminus of bound peptides. This suggests that the previously observed hydrophobic residues at the carboxyl terminus of peptides may reflect the specificity of enzyme(s) or protein(s) involved in peptide processing in vivo.
Falsely low results obtained with the Hybritech Tandem-R PSA assay. (1988)

Journal Article Falsely low results obtained with the Hybritech Tandem-R PSA assay. Get access H Alfthan, H Alfthan Dept. I of Obstetrics & Gynecology, Helsinki University Central Hospital, Finland Search for other works by this author on: Oxford Academic Google Scholar U H Stenman U H Stenman Dept. I of Obstetrics & Gynecology, Helsinki University Central Hospital, Finland Search for other works by this author on: Oxford Academic Google Scholar Clinical Chemistry, Volume 34, Issue 10, 1 October 1988, Page 2152, https://doi.org/10.1093/clinchem/34.10.2152 Published: 01 October 1988
Tyrosine Kinases Are Required for Interferon- -Stimulated Proliferation of Trypanosoma brucei brucei (1997)

The tyrosine kinase activity of Trypanosoma brucei brucei upon stimulation with interferon-gamma (IFN-gamma) was investigated. IFN-gamma induced a rapid and strong increase of tyrosine phosphorylation of several cellular proteins that reached maximum after 5 min and was followed by a decrease to control levels after 120 min. The tyrosine kinase-specific inhibitor tyrphostin A47 at a concentration of 10(-6) M reduced IFN-gamma-induced protein phosphorylation. In vitro application of 10(-6) M tyrphostin A47 to the trypanosome cultures caused a significant reduction of [3H]thymidine uptake by IFN-gamma-stimulated trypanosomes. In animals, 2 x 0.5 mg of tyrphostin A47 (injected intraperitoneally) caused a significant reduction of parasite growth compared with the vehicle dimethyl sulfoxide or the inactive compound tyrphostin A1. In conclusion, tyrosine kinases are strongly up-regulated in IFN-gamma-stimulated T. b. brucei, and specific tyrosine kinase inhibitors can prevent trypanosome growth in vitro and in vivo.
Identification of a complex congenital heart defect susceptibility locus by using DNA pooling and shared segment analysis (1997)

The identification of genetic loci involved in most forms of congenital heart disease has been hampered by the complex inheritance patterns of these disorders. Atrioventricular canal defects (AVCDs) are most commonly associated with Down syndrome, although non-syndromic cases also occur. Non-syndromic AVCDs have been attributed to multifactorial inheritance. However, the occurrence of a few kindreds with multiple affected individuals has suggested that a major genetic locus can account for the disorder in some families. We have used a combination of DNA pooling and shared segment analysis to perform a high density screen of the entire autosomal human genome in an extended kindred. In so doing, we have identified a genetic locus on chromosome 1 shared by all affected individuals. Our data demonstrate the existence of a congenital heart defect susceptibility gene, inherited as an autosomal dominant with incomplete penetrance, involved in AVCD. Furthermore, our data demonstrate the power of using key isolated kindreds in combination with high density genomic screens to identify loci involved in complex disorders such as congenital heart defects.
Requirement for an initial signal from the membrane-proximal region of the interleukin 2 receptor γ c chain for Janus kinase activation leading to T cell proliferation (1997)

The interleukin 2 receptor (IL-2R) generates proliferative signals in T lymphocytes by ligand-induced heterodimerization of two chains, IL-2Rbeta and gamma(c), which associate with the tyrosine kinases Jak1 and Jak3, respectively. Genetic and molecular studies have demonstrated that Jak3 is essential for mitogenic signaling by the gamma(c) chain; because it is also the only molecule known to associate with gamma(c), we speculated that Jak3 might be sufficient for signaling by this chain. Therefore, fusion proteins were constructed in which all or part of the cytoplasmic domain of gamma(c) was replaced by Jak3. Signaling was evaluated in the IL-2-dependent T cell line CTLL-2 using chimeric IL-2Rbeta and gamma(c) chains that bind and are activated by the cytokine granulocyte-macrophage colony-stimulating factor. Chimeric gamma(c) chains containing only Jak3 in the cytoplasmic domain failed to mediate proliferation of CTLL-2 cells, but addition of a conserved membrane-proximal (PROX) domain of gamma(c) in tandem with Jak3 fully reconstituted gamma(c) function. The requirement for the PROX domain reflected an essential role in the activation of Jak3 in vivo. Despite lacking defined catalytic motifs, PROX induced an early Jak-independent signal, including tyrosine phosphorylation of IL-2Rbeta and the tyrosine phosphatase SHP-2. The results define the minimal signaling components of gamma(c) and suggest a new mechanism by which the IL-2R initiates signaling in response to ligand.
Successful rescue therapy with darunabir (TMC114) in HIV-infected patients who have failed several ritonavir-boosted protease inhibitors (2006)

Darunabir, formerly TMC114, is a new protease inhibitor (PI) under clinical development designed to be active against HIV strains resistant to currently available PI. The virological and immunological response to ritonavir-boosted darunabir was assessed in four heavily antiretroviral-experienced patients who had failed enfuvirtide and two or more previous ritonavir-boosted PI regimens, including tipranavir in one instance. All four patients reached undetectable plasma HIV-RNA levels within 8 weeks of therapy and experienced significant CD4 cell count gains.
EFFECTS OF SHOCK PRESTRAIN ON THE DYNAMIC MECHANICAL BEHAVIOR OF TANTALUM (1991)

The effects of shock prestrain on the mechanical behavior, microstructure, and substructure of annealed tantalum have been examined. The test material was shocked to 15 GPa for 1 µs and soft-recovered such that deformation that occurred during this procedure was predominantly due to the shock loading. Mechanical characterization of the annealed and shock-recovered tantalum was performed over a wide range of strain rates (10-3 to 7000 s-l) in both tension and compression. Shock prestraining caused an increase in the quasi-static yield strength of tantalum but had virtually no influence on the dynamic stress-strain response. Consistent with this, the dynamic tensile behavior of both the annealed and shock-recovered materials were nearly identical. The effects of shock prestrain on the microstructure and substructure of the test material was examined using optical and transmission electron microscopy. The results of these examinations and how they correlate with the effects of shock prestrain on mechanical behavior are discussed.
Calcium-dependent development of secondary cytostatic factor (2°CSF) fromXenopus laevisoocytes and zygotes (1996)

Fresh cytosols extracted from unfertilised eggs of Xenopus laevis contain a cytostatic factor (CSF) which arrests the cell cycle at metaphase when microinjected into cleaving blastomeres. This CSF is sensitive to Ca2+ and is designated primary CSF (1 degrees CSF). During storage of Ca2(+)-containing cytosols at 2 degrees C, a stable CSF activity appears which is designated secondary CSF (2 degrees CSF). In the present study, we report that 2 degrees CSF activity can be induced in cytosols extracted from stage VI oocytes, unfertilised eggs, electrically activated eggs or blastulae, in the presence of Ca2+. Both the intensity and the rate of 2 degrees CSF development are dependent on the concentration of Ca2+ ions added to the cytosol. At Ca2+ concentrations of 5-10 mM, 2 degrees CSF activity reaches a maximum in about 7 days. Secondary CSF is relatively resistant to heat but loses all activity after 5 min at 70 degrees C. When stored at-80 degrees C, 2 degrees CSF activity remains detectable for about 6 weeks. Cytological observations show that blastomeres arrested by microinjection of 2 degrees CSF developed in cytosols of unfertilised eggs, activated eggs or blastulae contain metaphase chromosomes embedded in a bipolar spindle that has no asters developed at its poles. In contrast, blastomeres arrested by 2 degrees CSF in cytosols of stage VI oocytes contain condensed chromosomes but no spindle is formed. The mechanisms of the development of 2 degrees CSF in Ca2(+)-containing cytosols and its mode of action are discussed.
Reaction Mechanisms of Dry Ca-Based Sorbents with Gaseous HCl (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReaction Mechanisms of Dry Ca-Based Sorbents with Gaseous HClWojciech Jozewicz and Brian K. GullettCite this: Ind. Eng. Chem. Res. 1995, 34, 2, 607–612Publication Date (Print):February 1, 1995Publication History Published online1 May 2002Published inissue 1 February 1995https://doi.org/10.1021/ie00041a022RIGHTS & PERMISSIONSArticle Views434Altmetric-Citations63LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (793 KB) Get e-Alerts Get e-Alerts
Granulocyte Macrophage Colony-Stimulating Factor–Secreting Allogeneic Cellular Immunotherapy for Hormone-Refractory Prostate Cancer (2007)

These results suggest that this GM-CSF-secreting, allogeneic cellular immunotherapy is well tolerated and may have clinical activity in patients with metastatic HRPC. Phase 3 trials to confirm these results are under way.
Visualization of novel virulence activities of the Xanthomonas type III effectors AvrBs1, AvrBs3 and AvrBs4 (2008)

Xanthomonas campestris pv. vesicatoria secretes at least 20 effector proteins through the type III secretion system directly into plant cells. In this study, we uncovered virulence activities of the effector proteins AvrBs1, AvrBs3 and AvrBs4 using Agrobacterium-mediated transient expression of the corresponding genes in Nicotiana benthamiana, followed by microscopic analyses. We showed that, in addition to the nuclear-localized AvrBs3, the effector AvrBs1, which localizes to the plant cell cytoplasm, also induces a morphological change in mesophyll cells. Comparative analyses revealed that avrBs3-expressing plant cells contain highly active nuclei. Furthermore, plant cells expressing avrBs3 or avrBs1 show a decrease in the starch content in chloroplasts and an increased number of vesicles, indicating an enlargement of the central vacuole and the cell wall. Both AvrBs1 and AvrBs3 cause an increased ion efflux when expressed in N. benthamiana. By contrast, expression of the avrBs3 homologue avrBs4 leads to large catalase crystals in peroxisomes, suggesting a possible virulence function of AvrBs4 in the suppression of the plant defence responses. Taken together, our data show that microscopic inspection can uncover subtle and novel virulence activities of type III effector proteins.
A psychophysical technique for measuring cone photopigment bleaching. (1987)

A new, clinically applicable test has been developed to measure the bleaching of the foveal cone photopigments. This noninvasive test is called steady-state color matching. Steady-state color matching is based on the dependence of a color match on the optical density of the cone photopigments. By measuring the color match as a function of retinal illuminance, it is possible to compute the optical density of the cone photopigments at each illuminance. Thus, abnormalities of photopigment bleaching can be detected. This study demonstrates that the technique is readily performed by a clinical population. Patients with central serous retinopathy and retinitis pigmentosa are shown to have low effective optical densities.
Sonography of the Cervical Vagus Nerve (2001)

Sonography can reveal the vagus nerve in healthy conditions and correctly reveal the vagal origin of some tumors in the parapharyngeal spaces.