gebhart/patrepeval huggingface dataset:
Multiple source surveillance incidence and aetiology of out-of-hospital sudden cardiac death in a rural population in the West of Ireland (2008)

The burden of SCD in the West of Ireland is considerable. The vast majority of cases occur in the home. Survival rates in this rural population cohort remain low.
Novel rhodopsin mutations Gly114Val and Gln184Pro in dominant retinitis pigmentosa. (2000)

Summation of the results of cases in this study with those of 272 unrelated cases of ADRP previously evaluated by our group shows that 90 of 363 (25%) of cases were caused by rhodopsin mutations.
Folding and activity of circularly permuted forms of a polytopic membrane protein (2000)

The transmembrane subunit of the Glc transporter (IICB(Glc)), which mediates uptake and concomitant phosphorylation of glucose, spans the membrane eight times. Variants of IICB(Glc) with the native N and C termini joined and new N and C termini in the periplasmic and cytoplasmic surface loops were expressed in Escherichia coli. In vivo transport/in vitro phosphotransferase activities of the circularly permuted variants with the termini in the periplasmic loops 1 to 4 were 35/58, 32/37, 0/3, and 0/0% of wild type, respectively. The activities of the variants with the termini in the cytoplasmic loops 1 to 3 were 0/25, 0/4 and 24/70, respectively. Fusion of alkaline phosphatase to the periplasmic C termini stabilized membrane integration and increased uptake and/or phosphorylation activities. These results suggest that internal signal anchor and stop transfer sequences can function as N-terminal signal sequences in a circularly permuted alpha-helical bundle protein and that the orientation of transmembrane segments is determined by the amino acid sequence and not by the sequential appearance during translation. Of the four IICB(Glc) variants with new termini in periplasmic loops, only the one with the discontinuity in loop 4 is inactive. The sequences of loop 4 and of the adjacent TM7 and TM8 are conserved in all phosphoenolpyruvate-dependent carbohydrate:phosphotransferase system transporters of the glucose family.
Development and functional characterization of human bone marrow mesenchymal cells immortalized by enforced expression of telomerase (2003)

To create immortal mesenchymal cell lines, we transduced primary human bone marrow mesenchymal cells with telomerase reverse transcriptase (TERT). TERT+ mesenchymal cells continued to grow for > 2 years; parallel TERT- cultures underwent senescence after 15 weeks. TERT+ mesenchymal cells did not form foci in soft agar, had a normal karyotype and could differentiate into osteoblasts and chondrocytes. Their capacity to support leukaemic lymphoblasts and normal CD34+ haematopoietic cells was equal to or greater than that of primary cells; 42 TERT+ mesenchymal cell clones varied in their supporting capacity. Immortalized mesenchymal cells offer a promising tool for identifying molecules that regulate human haematopoiesis.
The clinical study on the effect of depression on the antiplatelet effect of clopidogrel in patients with USP treated with elective PCI (2010)

Objective To evaluate the significance of depression on the effect of depression on the antiplatelet effect of clopidogrel in patients with USP treated with elective PCI.Methods The study group consisted of 240 patients with USP treated with elective PCI that was divided into two groups:Group A-117 patients with depression,including 81 persistently depressed patients and 36 remittent depressed patients,group B-123 persistently nondepressed patients,and the control group consisted of 20 healthy subjects.An ADP-induced lighttransmittance aggregometry( Chronolog Corp,USA)was used to measure the antiplatelet effect of clopidogrel,and the activated platelets CD62P was studied by flow cytometry.All of them were measured at baseline and at 1 day,5day and 1 month after PCI respectively.Results Preprocedural platelet aggregation and CD62P were higher in patients with depression than those in patients without depression.Post-procedural levels at day 1 and 5day showed a more decrease in patients without depression than in depression patients compared with preprocedural levels.The Patients with depression showed more clopidogrel resistance than patients without depression at 1 day and 5day after PCI.Furthermore,clopidogrel resistance was still found significantly higher in persistently depressed patients at 1 month after PCI.Conclusion Patients with USP suffering from depression show enhanced intravascular platelet activation,increased clopidogrel resistance.

Key words: 
Unstable Angina Pectoris; Percutaneous Coronary Intervention; PAG; CD62P; Depression
Stereoselective synthesis of alcohols, XL. Stereoselective cyclization of 7‐oxo‐2‐heptenylboronates (1991)

Abstract Intramolecular allylboration reaction of 7‐oxo‐2‐heptenyl boronates leads to 2‐vinylcyclopentanols. The cyclization proceeds in a stereospecific manner, such that the ( E )‐allylboronate 8 is converted into trans ‐2‐vinylcyclopentanol ( 2 ) and the ( Z )‐allylboronate 10 into cis ‐2‐vinylcyclopentanol ( 3 ). Asymmetric induction originating from stereogenic centers placed between the boronate and the aldehyde function has been found to be low.
Isolation of 1,3-distearoyl-glycero-2-phosphocholine (beta-lecithin) from commercial 1,2-distearoyl-sn-glycero-3-phosphocholine. (1980)

Different batches of 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) had varying amounts of contaminants which appeared to affect systematic biological studies. This contaminant was separated by silica gel column chromatography followed by high performance liquid chromatography and identified as 1,3-distearoyl-glycerol-2-phosphocholine (beta-lecithin.
An IBM second generation RISC processor architecture (2002)

A second-generation reduced-instruction-set-computer (RISC) architecture designed to support superscalar implementations which can execute multiple instructions every cycle is described. The architecture provides compound-function instructions that allow application path lengths to be less than would be required on many complex-instruction-set computers. This new RISC architecture also exploits advances in optimizing compiler and operating system technology. The processor architecture is based on a logical view of the processor consisting of three independent functional units: a branch processor, a fixed-point processor, and a floating-point processor. The key feature of these functional units is that they are designed for maximum concurrency among the units.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Catheter‐based coronary bypass: A development update (2003)

Catheter-based coronary bypass has evolved since its origin in 1995. We present a status update of one version of catheter-based bypass, percutaneous in situ coronary venous arterialization (PICVA), its successes and failures, and the many questions and challenges that remain. Initial clinical experience with PICVA demonstrated promising mitigation of angina in no-option patients, but was complicated by a relatively low procedural completion rate and a high incidence of MACE. A great deal was learned in these initial cases. The system of devices is currently undergoing significant modification, and further clinical study is underway.
Comparative Study of Cellulases Associated with Adventitious Root Initiation, Apical Buds, and Leaf, Flower, and Pod Abscission Zones in Soybean (1994)

Cellulase activity was measured in soybean (Glycine max) leaf abscission zones, flower abscission zones, pod abscission zones, apical buds, and adventitious rooting hypocotyls. Immunoprecipitation data showed that a cellulase immunologically similar to the bean abscission cellulase (isoelectric point 9.5) is present in soybean leaf, flower, and pod abscission zones, but is not present in soybean apical buds or rooting hypocotyls. cDNA and genomic clones for two different soybean genes were identified and show sequence similarity with the bean abscission cellulase clone pBAC10. The cDNA clone pSAC1, isolated from a soybean abscission cDNA library, hybridized to transcripts in soybean leaf, flower, and pod abscission zones. Although ethylene has been shown to play a role in the increase in cellulase activity associated with both abscission and adventitious root initiation, no signal was seen for hybridization of the soybean abscission cellulase clone, pSAC1, to RNA from soybean adventitious rooting hypocotyls. In addition, no soybean abscission cellulase transcripts were detected in apical buds. Transcripts for a second soybean cellulase gene (SC2) were not detected in any of the tissues surveyed.
Comparative Evaluation of Automatic Age Progression Methodologies (2008)

Automatic age-progression is the process of modifying an image showing the face of a person in order to predict his/her future facial appearance. In this paper, we compare the performance of two age-progression methodologies reported in the literature against two novel approaches to the problem. In particular, we compare the performance of a method based on age prototypes, a method based on aging functions defined in a low-dimensional parametric model space, and two methods based on the distributions of samples belonging to different individuals and different age groups. Quantitative comparative results reported in the paper are based on dedicated performance evaluation metrics that assess the ability of each method to produce accurate predictions of the future/previous facial appearance of subjects. The framework proposed in this paper promotes the idea of a standardized performance evaluation protocol for age-progression methodologies, using images from a publicly available image database.
Nanostructured materials for applications in drug delivery and tissue engineering (2007)

Research in the areas of drug delivery and tissue engineering has witnessed tremendous progress in recent years due to their unlimited potential to improve human health. Meanwhile, the development of nanotechnology provides opportunities to characterize, manipulate and organize matter systematically at the nanometer scale. Biomaterials with nano-scale organizations have been used as controlled release reservoirs for drug delivery and artificial matrices for tissue engineering. Drug-delivery systems can be synthesized with controlled composition, shape, size and morphology. Their surface properties can be manipulated to increase solubility, immunocompatibility and cellular uptake. The limitations of current drug delivery systems include suboptimal bioavailability, limited effective targeting and potential cytotoxicity. Promising and versatile nano-scale drug-delivery systems include nanoparticles, nanocapsules, nanotubes, nanogels and dendrimers. They can be used to deliver both small-molecule drugs and various classes of biomacromolecules, such as peptides, proteins, plasmid DNA and synthetic oligodeoxynucleotides. Whereas traditional tissue-engineering scaffolds were based on hydrolytically degradable macroporous materials, current approaches emphasize the control over cell behaviors and tissue formation by nano-scale topography that closely mimics the natural extracellular matrix (ECM). The understanding that the natural ECM is a multifunctional nanocomposite motivated researchers to develop nanofibrous scaffolds through electrospinning or self-assembly. Nanocomposites containing nanocrystals have been shown to elicit active bone growth. Drug delivery and tissue engineering are closely related fields. In fact, tissue engineering can be viewed as a special case of drug delivery where the goal is to accomplish controlled delivery of mammalian cells. Controlled release of therapeutic factors in turn will enhance the efficacy of tissue engineering. From a materials point of view, both the drug-delivery vehicles and tissue-engineering scaffolds need to be biocompatible and biodegradable. The biological functions of encapsulated drugs and cells can be dramatically enhanced by designing biomaterials with controlled organizations at the nanometer scale. This review summarizes the most recent development in utilizing nanostructured materials for applications in drug delivery and tissue engineering.
Expression of the Arp protein, a member of the M protein family, is not sufficient to inhibit phagocytosis of Streptococcus pyogenes (1995)

Many Streptococcus pyogenes immunoglobulin-binding proteins have structural similarities to the antiphagocytic M protein, including the well-known C repeats. One of these molecules is the immunoglobulin A-binding protein Arp, which is expressed by a serotype 4 strain for which no antiphagocytic M protein has yet been described. We expressed Arp4 in an S. pyogenes strain from which the structural gene for the M protein has been deleted and found that Arp4 is not sufficient to inhibit phagocytosis.
Churchill: an ultra-fast, deterministic, highly scalable and balanced parallelization strategy for the discovery of human genetic variation in clinical and population-scale genomics (2015)

While advances in genome sequencing technology make population-scale genomics a possibility, current approaches for analysis of these data rely upon parallelization strategies that have limited scalability, complex implementation and lack reproducibility. Churchill, a balanced regional parallelization strategy, overcomes these challenges, fully automating the multiple steps required to go from raw sequencing reads to variant discovery. Through implementation of novel deterministic parallelization techniques, Churchill allows computationally efficient analysis of a high-depth whole genome sample in less than two hours. The method is highly scalable, enabling full analysis of the 1000 Genomes raw sequence dataset in a week using cloud resources. http://churchill.nchri.org/.
V-MycAlters the Response of a Cloned Mouse Mammary Epithelial Cell Line to Lactogenic Hormones (1988)

Several oncogenes have now been implicated in mammary carcinogenesis. We investigated the phenotypic effects of expressing three representative oncogenes in mammary epithelial cells. v-myc (coding for a nuclear protein), v-Ha-ras (a G-protein homologue) and v-fgr (a tyrosine kinase) genes were introduced into the nontumorigenic clone 14 of the mouse mammary epithelial cell line COMMA-1D. Their effects upon growth and differentiation were determined. Anchorage-independent growth was induced by all three oncogenes with low efficiency. v-Ha-ras and v-fgr induced tumorigenicity in nude mice. The effect of oncogenes upon parameters unique to mammary epithelial cells in vitro was assayed. Both v-myc and v-fgr abolished the ability of clone 14 to grow as three-dimensional branching structures in hydrated collagen gel. v-fgr completely and v-myc partially inhibited the expression of the epithelium specific cytokeratins. Clone 14 can be induced to produce the beta-casein milk protein by the combination of the lactogenic hormones, dexamethasone, insulin, and PRL. Introduction of v-myc into clone 14 cells resulted in an estimated 50-fold increased induction of beta-casein protein and at least a 60-fold increase in beta-casein mRNA. The number of cells stained with anti-beta casein antibodies also showed a 10-fold increase after v-myc introduction. This still required the synergistic action of all three lactogenic hormones. Thus v-myc can alter the normal response of mammary epithelial cells to lactogenic hormones.
Hypothermia for neuroprotection in adults after cardiopulmonary resuscitation (2009)

Conventional cooling methods to induce mild therapeutic hypothermia seem to improve survival and neurologic outcome after cardiac arrest. Our review supports the current best medical practice as recommended by the International Resuscitation Guidelines.
INTERLEUKIN‐8 AND INDUCIBLE NITRIC OXIDE SYNTHASE mRNA LEVELS IN INFLAMMATORY BOWEL DISEASE AT FIRST PRESENTATION (1997)

Interleukin-8 (IL-8) and nitric oxide (NO) may be important mediators in the pathogenesis of chronic idiopathic inflammatory bowel disease (CIIBD), but their roles in disease activity in ulcerative colitis (UC) and Crohn's disease (CD) are uncertain. The aim of this study was to measure mRNA for IL-8 and inducible NO synthase (iNOS) in small mucosal biopsies from untreated patients at first presentation and to relate these measurements to the histological levels of polymorph infiltration graded on a ten-point scale. For this purpose, a sensitive enzyme-linked oligonucleotide chemiluminescent assay (ELOCA) was developed to quantitate reverse transcription-polymerase chain reaction (RT-PCR) products amplified from RNA from paired biopsy samples. The levels of IL-8 and iNOS mRNAs were calculated as ratios of the RT-PCR products to glyceraldehyde-3-phosphate dehydrogenase (GAPDH) RT-PCR product. In UC patients, median values of IL-8/GAPDH and iNOS/GAPDH were significantly elevated compared with controls and CD. However, in both UC and CD, the IL-8/GAPDH and iNOS/GAPDH ratios correlated significantly with polymorph infiltration. ELOCA enabled quantitation of multiple mRNAs in small mucosal biopsies from untreated patients with CIIBD and supported a role for IL-8 and iNOS in acute inflammation in both UC and CD. © 1997 by John Wiley & Sons, Ltd.
Direct uptake and degradation of DNA by lysosomes (2013)

Lysosomes contain various hydrolases that can degrade proteins, lipids, nucleic acids and carbohydrates. We recently discovered "RNautophagy," an autophagic pathway in which RNA is directly taken up by lysosomes and degraded. A lysosomal membrane protein, LAMP2C, a splice variant of LAMP2, binds to RNA and acts as a receptor for this pathway. In the present study, we show that DNA is also directly taken up by lysosomes and degraded. Like RNautophagy, this autophagic pathway, which we term "DNautophagy," is dependent on ATP. The cytosolic sequence of LAMP2C also directly interacts with DNA, and LAMP2C functions as a receptor for DNautophagy, in addition to RNautophagy. Similarly to RNA, DNA binds to the cytosolic sequences of fly and nematode LAMP orthologs. Together with the findings of our previous study, our present findings suggest that RNautophagy and DNautophagy are evolutionarily conserved systems in Metazoa.
Structural comparison of two serine proteinase-protein inhibitor complexes: Eglin-C-subtilisin Carlsberg and CI-2-subtilisin Novo (1988)

The crystal structures of the molecular complexes between two serine proteinases and two of their protein inhibitors have been determined: subtilisin Carlsberg with the recombinant form of eglin-c from the leech Hirudo medicinalis and subtilisin Novo with chymotrypsin inhibitor 2 from barley seeds. The structures have been fully refined by restrained-parameter least-squares methods to crystallographic R factors (sigma[[Fo[ - [Fc[[/sigma[Fo[) of 0.136 at 1.8-A resolution and 0.154 at 2.1-A resolution, respectively. The 274 equivalent alpha-carbon atoms of the enzymes superpose with an rms deviation of 0.53 A. Sequence changes between the enzymes result in localized structural adjustments. Functional groups in the active sites superpose with an rms deviation of 0.19 A for 161 equivalent atoms; this close similarity in the conformation of active-site residues provides no obvious reason for known differences in catalytic activity between Carlsberg and Novo. Conformational changes in the active-site region indicate a small induced fit of enzyme and inhibitor. Some conformational differences are observed between equivalent active-site residues of subtilisin Carlsberg and alpha-chymotrypsin. Despite differences in tertiary architecture, most enzyme-substrate (inhibitor) interactions are maintained. Subtilisin Carlsberg has a rare cis-peptide bond preceding Thr211 (Gly211 in Novo). Both enzymes contain tightly bound Ca2+ ions. Site 1 is heptacoordinate with the oxygen atoms at the vertices of a pentagonal bipyramid. Site 2 in Carlsberg is probably occupied by a K+ ion in Novo. Conserved water molecules appear to play important structural roles in the enzyme interior, in the inhibitor beta-sheet, and at the enzyme-inhibitor interface. The 62 equivalent alpha-carbon atoms of the inhibitors superpose with an rms deviation of 1.68 A. Sequence changes result in somewhat different packing of the alpha-helix, beta-sheet, and reactive-site loop relative to each other. Hydrogen bonds and electrostatic interactions supporting the conformation of the reactive-site loop are conserved. The 24 main-chain plus C beta atoms of P4 to P1' overlap with an rms deviation of 0.19 A. Features contributing to the inhibitory nature of eglin-c and CI-2 are discussed.
Amplification by nucleic acid-templated reactions (2014)

Nucleic acid-templated reactions enable the design of conditional reaction systems, in which bond formation occurs only when a particular DNA or RNA molecule is present. Such reaction systems are currently being explored for applications in DNA/RNA diagnosis, drug screening and as a means to design gene expression specific therapy. However, biological nucleic acid templates usually have low abundance. Therefore, either the targeted nucleic acid template has to be multiplied by means of an amplification step or the template itself has to act as a catalyst which amplifies product formation. This critical review highlights the recent advancements in nucleic acid-templated reactions that proceed with turnover in template and thereby provide a means of amplification. Improvements in reaction engineering and the development of new chemistries have pushed the limits from 10(1) to 10(2)-10(3) turnovers. This includes reaction systems that lead to the ligation of oligonucleotides or to the interconversion of appended functional groups beyond ligation as well as templated chemistries that enable the activation of catalysts for subsequent triggering of reactions between non-nucleotidic substrates. The present limitations and future opportunities are discussed.
Molecular pathogenesis of neuroinflammation (2003)

The past few years have seen significant progress towards understanding the mechanisms of immune surveillance and inflammation in the nervous system. In this review, the milestones of scientific discovery in this field are discussed, and the strengths and limitations of the different ways of examining the molecular pathogenesis of neuro-inflammation examined. The review is limited to the inflammatory reactions of the central nervous system that occur in multiple sclerosis and experimental autoimmune encephalomyelitis.
The Krakatoa Chronicle: An Interactive Personalized Newspaper on the Web (1995)

This paper describes The Krakatoa Chronicle, a highly interactive, personalized newspaper on the World Wide Web (WWW). It is intended for Java-savvy WWW browsers such as HotJava, and is architecturally quite different from conventional Web-based newspapers. Its high interactivity and powerful personalization are the result of sending an interactive agent along with the text of the newspaper to operate within the user's Web-browser. The agent keeps a network connection open to the WWW server site to fetch resources dynamically, and for updating the user's personal profile as it garners relevance feedback. Users are provided a variety of article browsing options such as scrolling, maximizing, resizing, and the ability to "peek." These operations not only enhance the reading experience in ways conventional newspapers cannot, but also transparently provide information to our agent about the user's locus of interest. Ours is the first Web newspaper to attempt a realistic rendering of a newspaper, with a multicolumn format and embedded custom widgets for easy browsing. We provide dynamic layout control mechanisms that let the user specify how personal and community interests should be interpreted by the agent in designing the layout.