gebhart/patrepeval huggingface dataset:
Apolipoprotein E ∈4 Associated With Chronic Traumatic Brain Injury in Boxing (1997)

<h3>Context.</h3> —Given the similarities between Alzheimer disease and dementia pugilistica, we evaluated the relationship between apolipoprotein E (<i>APOE</i>) genotype and chronic traumatic brain injury (CTBI) in boxers to determine whether there is a genetic susceptibility to the effects of head trauma. <h3>Objective.</h3> —To assess the relationship between CTBI and<i>APOE</i>genotype in boxers. <h3>Design and Setting.</h3> —Clinical characterization of 24 volunteer and 6 referred boxers in an outpatient setting. <h3>Participants.</h3> —Thirty professional boxers aged 23 to 76 years underwent neurologic and behavioral assessment in conjunction with<i>APOE</i>genotyping. <h3>Main Outcome Measures.</h3> —Apolipoprotein E genotype was examined in relationship to measures of CTBI. A10-point clinical rating scale (0-9), the Chronic Brain Injury (CBI) scale, was devised to assess the severity of traumatic encephalopathy associated with boxing. Boxers with abnormal CTBI scores were further classified on the basis of whether their impairments were possibly or probably related to boxing. Scores were analyzed in relation to boxing exposure (number of bouts) and<i>APOE</i>genotype. <h3>Results.</h3> —Among the 30 boxers, 11 were found to be normal (CBI score=0), 12 showed mild deficits (CBI score=1-2), 4 were moderately impaired (CBI score=3-4), and 3 showed signs of severe impairment (CBI score &gt;4). High-exposure boxers (ie, those with ≥12 professional bouts) had significantly higher CBI scores (mean [SD], 2.6 [1.9]) than low-exposure boxers (mean [SD], 0.3 [0.7]) (<i>P</i>&lt;.001), indicating that neurologic impairment as measured by the CBI scale seems related to boxing exposure. The<i>APOE</i>genotype frequencies of the study population were approximately the same as those found in the general population. Boxers with low exposure had mean CBI scores of 0.33, irrespective of<i>APOE</i>genotype. However, high-exposure boxers with an<i>APOE</i>∈4 allele had significantly greater CBI scores (mean [SD], 3.9 [2.3]) than high-exposure boxers without<i>APOE</i>∈4 (mean [SD], 1.8 [1.2]) (<i>P</i>=.04). All boxers with severe impairment possessed at least 1<i>APOE</i>∈4 allele. The tendency for greater CTBI among those with both high exposure and an ∈4 allele was statistically significant at the<i>P</i>&lt;.001 level. <h3>Conclusions.</h3> —These preliminary findings suggest that possession of an<i>APOE</i>∈4 allele may be associated with increased severity of chronic neurologic deficits in high-exposure boxers.
Evaluation of Benign vs Malignant Hepatic Lesions With Positron Emission Tomography (1998)

The PET technique using FDG static imaging was useful to differentiate malignant from benign lesions in the liver. Limitations include false-positive results in a minority of abscesses and false-negative results in a minority of hepatocellular carcinoma. The PET technique was useful in tumor staging and detection of recurrence, as well as monitoring response to therapy for all adenocarcinomas and sarcomas and most hepatocellular carcinomas. Therefore, pretherapy PET imaging is recommended to help assess new hepatic lesions.
SAR of 9-Amino-1,2,3,4-tetrahydroacridine-Based Acetylcholinesterase Inhibitors:  Synthesis, Enzyme Inhibitory Activity, QSAR, and Structure-Based CoMFA of Tacrine Analogues (2000)

In this study, we attempted to derive a comprehensive SAR picture for the class of acetylcholinesterase (AChE) inhibitors related to tacrine, a drug currently in use for the treatment of the Alzheimer's disease. To this aim, we synthesized and tested a series of 9-amino-1,2,3,4-tetrahydroacridine derivatives substituted in the positions 6 and 7 of the acridine nucleus and bearing selected groups on the 9-amino function. By means of the Hansch approach, QSAR equations were obtained, quantitatively accounting for both the detrimental steric effect of substituents in position 7 and the favorable electron-attracting effect exerted by substituents in positions 6 and 7 of the 9-amino-1,2,3,4-tetrahydroacridine derivatives. The three-dimensional (3D) properties of the inhibitors were taken into consideration by performing a CoMFA analysis on the series of AChE inhibitors made by 12 9-amino-1,2,3, 4-tetrahydroacridines and 13 11H-indeno[1,2-b]quinolin-10-ylamines previously developed in our laboratory. The alignment of the molecules to be submitted to the CoMFA procedure was carried out by taking advantage of docking models calculated for the interactions of both the unsubstituted 9-amino-1,2,3,4-tetrahydroacridine and 11H-indeno[1,2-b]quinolin-10-ylamine with the target enzyme. A highly significant CoMFA model was obtained using the steric field alone, and the features of such a 3D QSAR model were compared with the classical QSAR equations previously calculated. The two models appeared consistent, the main aspects they had in common being (a) the individuation of the strongly negative contribution of the substituents in position 7 of tacrine and (b) a tentative assignment of the hydrophobic character to the favorable effect exerted by the substituents in position 6. Finally, a new previously unreported tacrine derivative designed on the basis of both the classical and the 3D QSAR equations was synthesized and kinetically evaluated, to test the predictive ability of the QSAR models. The 6-bromo-9-amino-1,2,3,4-tetrahydroacridine was predicted to have a pIC(50) value of 7.31 by the classical QSAR model and 7.40 by the CoMFA model, while its experimental IC(50) value was equal to 0.066 (+/-0.009) microM, corresponding to a pIC(50) of 7.18, showing a reasonable agreement between predicted and observed AChE inhibition data.
Towards automatically generating summary comments for Java methods (2010)

Studies have shown that good comments can help programmers quickly understand what a method does, aiding program comprehension and software maintenance. Unfortunately, few software projects adequately comment the code. One way to overcome the lack of human-written summary comments, and guard against obsolete comments, is to automatically generate them. In this paper, we present a novel technique to automatically generate descriptive summary comments for Java methods. Given the signature and body of a method, our automatic comment generator identifies the content for the summary and generates natural language text that summarizes the method's overall actions. According to programmers who judged our generated comments, the summaries are accurate, do not miss important content, and are reasonably concise.
Selective Sparing of a Class of Striatal Neurons in Huntington's Disease (1985)

A distinct subpopulation of striatal aspiny neurons, containing the enzyme nicotinamide adenine dinucleotide phosphate diaphorase, is preserved in the caudate nucleus in Huntington's disease. Biochemical assays confirmed a significant increase in the activity of this enzyme in both the caudate nucleus and putamen in postmortem brain tissue from patients with this disease. The resistance of these neurons suggests that the gene defect in Huntington's disease may be modifiable by the local biochemical environment. This finding may provide insight into the nature of the genetically programmed cell death that is a characteristic of the disease.
Structure-Based Design, Synthesis, and Biological Evaluation of Irreversible Human Rhinovirus 3C Protease Inhibitors. 1. Michael Acceptor Structure−Activity Studies (1998)

The structure-based design, chemical synthesis, and biological evaluation of peptide-derived human rhinovirus (HRV) 3C protease (3CP) inhibitors are described. These compounds incorporate various Michael acceptor moieties and are shown to irreversibly bind to HRV serotype 14 3CP with inhibition activities (kobs/[I]) ranging from 100 to 600 000 M-1 s-1. These inhibitors are also shown to exhibit antiviral activity when tested against HRV-14-infected H1-HeLa cells with EC50's approaching 0.50 μM. Extensive structure−activity relationships developed by Michael acceptor alteration are reported along with the evaluation of several compounds against HRV serotypes other than 14. A 2.0 Å crystal structure of a peptide-derived inhibitor complexed with HRV-2 3CP is also detailed.
In Situ Spectroscopic Examination of a Low Overpotential Pathway for Carbon Dioxide Conversion to Carbon Monoxide (2012)

Lowering the overpotential for the electrochemical conversion of CO2 to useful products is one of the grand challenges in the Department Of Energy report, “Catalysis for Energy”. In a previous paper, we showed that CO2 conversion occurs at low overpotential on a 1-ethyl-3-methylimidazolium tetrafluoroborate (EMIM-BF4)-coated silver catalyst in an aqueous solution of EMIM-BF4. One of the surprises in the previous paper was that the selectivity to CO was better than 96% on silver, compared with ∼80% in the absence of ionic liquid. In this article, we use sum frequency generation (SFG) to explore the mechanism of the enhancement of selectivity. The study used platinum rather than silver because previous workers had found that platinum is almost inactive for CO production from CO2. The results show that EMIM-BF4 has two effects: it suppresses hydrogen formation and enhances CO2 conversion. SFG shows that there is a layer of EMIM on the platinum surface that inhibits hydrogen formation. CO2, however, can react with the EMIM layer to form a complex such as CO2-EMIM at potentials more negative than −0.1 V with respect to a standard hydrogen electrode (SHE). That complex is converted to adsorbed CO at cathodic potentials of −0.25 V with respect to SHE. These results demonstrate that adsorbed monolayers can substantially lower the barrier for CO2 conversion on platinum and inhibit hydrogen formation, opening the possibility of a new series of metal/organic catalysts for this reaction.
First evidences for a third sulfatase maturation system in prokaryotes from E. coli aslB and ydeM deletion mutants (2007)

To be active all known arylsulfatases undergo a unique post-translational modification leading to the conversion of an active site residue (serine or cysteine) into a C(alpha)-formylglycine. Although deprived of sulfatase activity, Escherichia coli K12 can efficiently mature heterologous Cys-type sulfatases. Three potential enzymes (AslB, YdeM and YidF) belonging to the anaerobic sulfatase maturating enzyme family (an SME) are present in its genome. Here we show that E. coli could mature Cys-type sulfatases only in aerobic conditions and that knocking-out of aslB, ydeM and yidF does not impair Cys-type sulfatase maturation. These findings demonstrate that these putative anSME are not involved in Cys-type sulfatase maturation and strongly support the existence of a second, oxygen-dependent and Cys-type specific sulfatase maturation system among prokaryotes.
Stochastic Particle Barcoding for Single-Cell Tracking and Multiparametric Analysis (2014)

This study presents stochastic particle barcoding (SPB), a method for tracking cell identity across bioanalytical platforms. In this approach, single cells or small collections of cells are co-encapsulated within an enzymatically-degradable hydrogel block along with a random collection of fluorescent beads, whose number, color, and position encode the identity of the cell, enabling samples to be transferred in bulk between single-cell assay platforms without losing the identity of individual cells. The application of SPB is demonstrated for transferring cells from a subnanoliter protein secretion/phenotyping array platform into a microtiter plate, with re-identification accuracies in the plate assay of 96±2%. Encapsulated cells are recovered by digesting the hydrogel, allowing subsequent genotyping and phenotyping of cell lysates. Finally, a model scaling is developed to illustrate how different parameters affect the accuracy of SPB and to motivate scaling of the method to thousands of unique blocks.
Automated generation of DSP program development tools using a machine description formalism (1993)

The authors introduce a retargetable microcode generator for application specific digital signal processors (ASDSPs). The primary goal is to provide quickly system architects with the set of tools necessary for program development (assemblers, instruction set simulators, debuggers, and compilers), particularly when the processor architecture is refined simultaneously with the algorithm. After a modification of the architecture, only the machine description written in the language nML must be altered; the tools are then produced automatically. The machine description need not explicitly list every possible instruction in full length. Instead, a derivation tree is described. Through the extensive use of inheritance and sharing of properties, this description can be very compact. Based on the latter, the recognition of critical data paths and the analysis of machine inherent parallelism is solely performed by the tool generator.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Enhanced Light Output in Double Roughened GaN Light-Emitting Diodes via Various Texturing Treatments of Undoped-GaN Layer (2006)

An InGaN–GaN light-emitting diodes (LEDs) with double roughened (p-GaN and undoped-GaN) surfaces were successfully fabricated by surface-roughening, wafer-bonding and laser lift-off technologies. The effect of the roughness of the undoped-GaN layer on the performance of double roughened LEDs was investigated. It was found that the rms roughness of the undoped-GaN layer increased from 18.6 to 146.7 nm, the output power increased from 7.2 to 10.2 mW, and view angle decreased from 133.6 to 116°.
Bioinformatics analysis of alternative splicing (2005)

Over the past few years, the analysis of alternative splicing using bioinformatics has emerged as an important new field, and has significantly changed our view of genome function. One exciting front has been the analysis of microarray data to measure alternative splicing genome-wide. Pioneering studies of both human and mouse data have produced algorithms for discerning evidence of alternative splicing and clustering genes and samples by their alternative splicing patterns. Moreover, these data indicate the presence of alternative splice forms in up to 80 per cent of human genes. Comparative genomics studies in both mammals and insects have demonstrated that alternative splicing can in some cases be predicted directly from comparisons of genome sequences, based on heightened sequence conservation and exon length. Such studies have also provided new insights into the connection between alternative splicing and a variety of evolutionary processes such as Alu-based exonisation, exon creation and loss. A number of groups have used a combination of bioinformatics, comparative genomics and experimental validation to identify new motifs for splice regulatory factors, analyse the balance of factors that regulate alternative splicing, and propose a new mechanism for regulation based on the interaction of alternative splicing and nonsense-mediated decay. Bioinformatics studies of the functional impact of alternative splicing have revealed a wide range of regulatory mechanisms, from NAGNAG sites that add a single amino acid; to short peptide segments that can play surprisingly complex roles in switching protein conformation and function (as in the Piccolo C2A domain); to events that entirely remove a specific protein interaction domain or membrane anchoring domain. Common to many bioinformatics studies is a new emphasis on graph representations of alternative splicing structures, which have many advantages for analysis.
Embryonic and adult expression patterns of the Tec tyrosine kinase gene suggest a role in megakaryocytopoiesis, blood vessel development, and melanogenesis. (1997)

The Tec cytoplasmic tyrosine kinase is a member of a family of src-like proteins that are thought to play important roles in hematopoiesis. Here we describe the temporal and spatial expression of the Tec gene during embryogenesis and in the adult. Our data demonstrate that embryonic Tec expression is restricted to distinct hematopoietic cells as well as structures and cell types that share a common feature of containing fluid in an enclosed cavity, e.g., endothelial cells. In addition, Tec is expressed in melanocytes late in gestation. The observed developmental expression pattern of Tec suggests a role for this gene in several aspects of hematopoiesis and/or blood vessel development as well as in late stages of melanogenesis.
The UCSC Table Browser data retrieval tool (2003)

The University of California Santa Cruz (UCSC) Table Browser (http://genome.ucsc.edu/cgi-bin/hgText) provides text-based access to a large collection of genome assemblies and annotation data stored in the Genome Browser Database. A flexible alternative to the graphical-based Genome Browser, this tool offers an enhanced level of query support that includes restrictions based on field values, free-form SQL queries and combined queries on multiple tables. Output can be filtered to restrict the fields and lines returned, and may be organized into one of several formats, including a simple tab- delimited file that can be loaded into a spreadsheet or database as well as advanced formats that may be uploaded into the Genome Browser as custom annotation tracks. The Table Browser User's Guide located on the UCSC website provides instructions and detailed examples for constructing queries and configuring output.
Negative Regulation of LRP6 Function by Casein Kinase I ϵ Phosphorylation (2006)

Wnt signaling acts in part through the low density lipoprotein receptor-related transmembrane proteins LRP5 and LRP6 to regulate embryonic development and stem cell proliferation. Up-regulated signaling is associated with many forms of cancer. Casein kinase I epsilon (CKIepsilon) is a known component of the Wnt-beta-catenin signaling pathway. We find that CKIepsilon binds to LRP5 and LRP6 in vitro and in vivo and identify three CKIepsilon-specific phosphorylation sites in LRP6. Two of the identified phosphorylation sites, Ser1420 and Ser1430, influence Wnt signaling in vivo, since LRP6 with mutation of these sites is a more potent activator of both beta-catenin accumulation and Lef-1 reporter activity. Whereas Wnt3a regulates CKIepsilon kinase activity, LRP6 does not, placing CKIepsilon upstream of LRP6. Mutation of LRP6 Ser1420 and Ser1430 to alanine strengthens its interaction with axin, suggesting a mechanism by which CKIepsilon may negatively regulate Wnt signaling. The role of CKIepsilon is therefore more complex than was previously appreciated. Generation of active CKIepsilon may induce a negative feedback loop by phosphorylation of sites on LRP5/6 that modulate axin binding and hence beta-catenin degradation.
Immunotherapy of Multiple Myeloma With a Monoclonal Antibody Directed Against a Plasma Cell-Specific Antigen, HM1.24 (1997)

Multiple myeloma remains an incurable malignancy because of marked resistance of tumor cells to conventional chemotherapeutic agents. Alternative strategies are needed to solve these problems. To develop a new strategy, we have generated a monoclonal antibody (MoAb), which detects a human plasma cell-specific antigen, HM1.24. In this report, we evaluated the in vivo antitumor effect of unconjugated anti-HM1.24 MoAb on human myeloma xenografts implanted into severe combined immunodeficiency (SCID) mice. Two models of disseminated or localized tumors were established in SCID mice by either intravenous or subcutaneous injection of human myeloma cell lines, ARH-77 and RPMI 8226. When mice were treated with a single intraperitoneal injection of anti-HM1.24 MoAb 1 day after tumor inoculation, the development of disseminated myeloma was completely inhibited. In mice bearing advanced tumors, multiple injections of anti-HM1.24 MoAb reduced the tumor size and significantly prolonged survival, including tumor cure, in a dose-dependent manner. The proliferation of cultured human myeloma cells was inhibited in vitro by anti-HM1.24 IgG-mediated complement-dependent cytotoxicity, but not by the antibody alone. Moreover, spleen cells from SCID mice mediated antibody-dependent cell cytotoxicity against RPMI 8226 cells. These results indicate that anti-HM1.24 MoAb can be used for immunotherapy of multiple myeloma and related plasma cell dyscrasias.
COX-2, a synaptically induced enzyme, is expressed by excitatory neurons at postsynaptic sites in rat cerebral cortex. (1996)

Postnatal development and adult function of the central nervous system are dependent on the capacity of neurons to effect long-term changes of specific properties in response to neural activity. This neuronal response has been demonstrated to be tightly correlated with the expression of a set of regulatory genes which include transcription factors as well as molecules that can directly modify cellular signaling. It is hypothesized that these proteins play a role in activity-dependent response. Previously, we described the expression and regulation in brain of an inducible form of prostaglandin synthase/cyclooxygenase, termed COX-2. COX-2 is a rate-limiting enzyme in prostanoid synthesis and its expression is rapidly regulated in developing and adult forebrain by physiological synaptic activity. Here we demonstrate that COX-2 immunoreactivity is selectively expressed in a subpopulation of excitatory neurons in neo-and allocortices, hippocampus, and amygdala and is compartmentalized to dendritic arborizations. Moreover, COX-2 immunoreactivity is present in dendritic spines, which are specialized structures involved in synaptic signaling. The developmental profile of COX-2 expression in dendrites follows well known histogenetic gradients and coincides with the critical period for activity-dependent synaptic remodeling. These results suggest that COX-2, and its diffusible prostanoid products, may play a role in postsynaptic signaling of excitatory neurons in cortex and associated structures.
Detecting early glaucoma by assessment of retinal nerve fiber layer thickness and visual function. (2001)

In general, areas under the ROC curve were largest (although not always significantly so) for OCT parameters, followed by FDT, SLP, and SWAP, regardless of the definition of glaucoma used. The most sensitive OCT and FDT parameters tended to be more sensitive than the most sensitive SWAP and SLP parameters at the specificities investigated, regardless of diagnostic criteria.