gebhart/patrepeval huggingface dataset:
G Proteins and Regulation of Adenylate Cyclase (Nobel Lecture) (1995)

How is the hormone‐activated synthesis of the second messenger cyclic AMP regulated? Or, in more general terms, how does the interaction of an extracellular agonist with a receptor lead to intracellular enzyme activity when receptor and enzyme are not distinct macromolecules? The mediators are membrane‐bound, guanine nucleotide binding regulatory proteins (G proteins). When the receptor is activated, G proteins dissociate into their subunits. These in turn activate or inhibit enzymes such as adenylate cyclases, which catalyze the synthesis of cyclic AMP. In these signal transmission processes G proteins act as molecular switches and amplifiers.
Direct Sequencing and Characterization of a Clinical Isolate of Epstein-Barr Virus from Nasopharyngeal Carcinoma Tissue by Using Next-Generation Sequencing Technology (2011)

Epstein-Barr virus (EBV)-encoded molecules have been detected in the tumor tissues of several cancers, including nasopharyngeal carcinoma (NPC), suggesting that EBV plays an important role in tumorigenesis. However, the nature of EBV with respect to genome width in vivo and whether EBV undergoes clonal expansion in the tumor tissues are still poorly understood. In this study, next-generation sequencing (NGS) was used to sequence DNA extracted directly from the tumor tissue of a patient with NPC. Apart from the human sequences, a clinically isolated EBV genome 164.7 kb in size was successfully assembled and named GD2 (GenBank accession number HQ020558). Sequence and phylogenetic analyses showed that GD2 was closely related to GD1, a previously assembled variant derived from a patient with NPC. GD2 contains the most prevalent EBV variants reported in Cantonese patients with NPC, suggesting that it might be the prevalent strain in this population. Furthermore, GD2 could be grouped into a single subtype according to common classification criteria and contains only 6 heterozygous point mutations, suggesting the monoclonal expansion of GD2 in NPC. This study represents the first genome-wide analysis of a clinical isolate of EBV directly extracted from NPC tissue. Our study reveals that NGS allows the characterization of genome-wide variations of EBV in clinical tumors and provides evidence of monoclonal expansion of EBV in vivo. The pipeline could also be applied to the study of other pathogen-related malignancies. With additional NGS studies of NPC, it might be possible to uncover the potential causative EBV variant involved in NPC.
Destroying RNA as a Therapeutic Approach (2006)

The ability to target RNA, mRNA and viral RNA in particular, for degradation is a powerful approach in molecular biology and pharmacology. Such approaches can be used in the study of gene function as in functional genomics, in the identification of disease-associated genes, and for the treatment of human diseases. This review provides a comprehensive up-to-date look at all the current available technologies used for the destruction of RNA, with a focus on their therapeutic potential. This includes approaches that utilize the activity of protein ribonucleases such as antisense oligonucleotide, small interfering RNA, RNase P-associated external guide sequence, onconase and bovine seminal RNase. Sequence-specific approaches that do not utilize activity of protein ribonucleases, such as ribozyme and DNazyme, are also reviewed and discussed. This review should provide a useful starting framework for researchers interested in using the RNA-destruction methodologies on the bench and in the clinic, and serves as a stimulus for further development of novel and more potent RNA degradation technologies. This is particularly critical, given the anticipation of discoveries of new cellular RNA degradation machineries and human diseases that are associated with dysfunctional RNA molecules.
Demonstration of 0.75 Gbar planar shocks in x-ray driven colliding foils (1993)

We have directly observed 0.75\ifmmode\pm\else\textpm\fi{}0.2 Gbar planar shocks in gold target foils impacted by ablatively driven gold flyer foils. The x-ray drive for the flyer foils was produced in a gold Hohlraum by ten beams of the Nova laser. The dynamic pressure inferred by shock velocity measurements is more than a factor of 7 greater than previous dynamic shocks produced in the laboratory and over a surface area significantly larger than most previous ultrahigh pressure experiments. The technique allows the laboratory investigation of equations of state in the gigabar regime.
Computer-based image analysis in breast pathology (2016)

Whole slide imaging (WSI) has the potential to be utilized in telepathology, teleconsultation, quality assurance, clinical education, and digital image analysis to aid pathologists. In this paper, the potential added benefits of computer-assisted image analysis in breast pathology are reviewed and discussed. One of the major advantages of WSI systems is the possibility of doing computer-based image analysis on the digital slides. The purpose of computer-assisted analysis of breast virtual slides can be (i) segmentation of desired regions or objects such as diagnostically relevant areas, epithelial nuclei, lymphocyte cells, tubules, and mitotic figures, (ii) classification of breast slides based on breast cancer (BCa) grades, the invasive potential of tumors, or cancer subtypes, (iii) prognosis of BCa, or (iv) immunohistochemical quantification. While encouraging results have been achieved in this area, further progress is still required to make computer-based image analysis of breast virtual slides acceptable for clinical practice.
Therapeutic applications of guanylate cyclase-C receptor agonists. (2002)

Uroguanylin, guanylin, lymphoguanylin and bacterial enterotoxin ST are structurally related peptides that activate common guanylate cyclase signaling molecules and, via cyclic GMP (cGMP), regulate water and ion homeostasis in a variety of tissues and organs, including the gastrointestinal (GI) tract, kidneys, lung, prostate, etc. Any disruptions in water and ionic homeostasis due to reduced production of one or more of the guanylin family of peptides can potentially lead to carcinogenic and inflammatory stimuli. Recent findings that expression of uroguanylin and guanylin is dramatically reduced in polyps and colon carcinoma tissues further support the notion that these peptide hormones are important modulators or mediators of signaling pathways leading to the processes involved in carcinogenesis and inflammatory disorders. This review briefly discusses recent research findings suggesting the novel therapeutic applications of agonist peptides of guanylate cyclase-C receptor.
An experimental investigation of human mismatches in machining (1999)

Mismatches refer to incompatibilities, inappropriateness, unsuitabilities or inconsistencies in machine operators' actions which, if not addressed, would lead to errors. A fuller understanding of the rate at which mismatches occur and their causes would allow human aspects to be given proper consideration alongside hardware and technological issues in the design of new working environments, machines and tasks. This research highlights these human aspects of machining by examining mismatches in relation to various human characteristics. The human task-mismatch matching method was developed and applied in manual turning operations using experimental and questionnaire techniques on groups of 16 skilled and 12 unskilled operators. The skilled subjects were drawn from local industry and university technical staff. Unskilled subjects were engineering students, all of whom had some familiarity with machining through periods of industrial placement. Statistically significant relationships were established between mismatches and many of the human characteristics studied (skill, age, work experience, self-confidence and trust) when considering all the subjects as a single group, but for skilled operators alone, the only significant relationship was between self-confidence and trust. As a general conclusion, it can be confirmed that studying operators in their own workplace provides invaluable information for the design and operation of future workplaces, but that the relationships between performance and human characteristics remain difficult to establish formally.
Lateral light emitting n-i-p diodes in InSb∕AlxIn1−xSb quantum wells (2006)

Lateral light emitting diodes have been fabricated in InSb∕AlxIn1−xSb quantum wells using a simple bevel etching technique. The peak in emission was found to be in the range of 4–5μm, confirming that the emission was from the quantum well.
Tyrosine Phosphorylation of p130Cas and Cortactin Accompanies Integrin-mediated Cell Adhesion to Extracellular Matrix (1995)

We show in this report that two v-src substrate proteins, p130Cas and cortactin, become tyrosine-phosphorylated during integrin-mediated cell adhesion to extracellular matrix substrata and upon cell attachment onto immobilized anti-integrin antibodies. This tyrosine phosphorylation does not occur when cells attach to polylysine or through antibodies against major histocompatibility complex. It also does not take place when adhesion-mediated reorganization of the actin cytoskeleton is inhibited with cytochalasin D. Tyrosine phosphorylation of p130Cas and cortactin coincides with tyrosine phosphorylation of focal adhesion kinase during integrin-mediated cell adhesion but is independent of cell adhesion in v-src-transformed cells. The tyrosine-phosphorylated sites in p130Cas and cortactin may serve as binding sites for proteins containing Src homology 2 domains, as is the case with two other integrin-regulated docking proteins, focal adhesion kinase and paxillin. Thus, these results suggest that ligand binding of integrins regulates the tyrosine phosphorylation state of multiple docking proteins. These proteins may mediate anchorage dependence of growth; their misregulation in v-src-transformed and other tumorigenic cells may be responsible for the anchorage independence of such cells.
SEX DIFFERENCE IN THE EFFECTS OF SOCIOCULTURAL STATUS ON DIABETES AND CARDIOVASCULAR RISK FACTORS IN MEXICAN AMERICANS: THE SAN ANTONIO HEART STUDY (1984)

The authors postulated that as Mexican Americans became more affluent and/or acculturated to "mainstream" United States life-style they would progressively lose their "obesity-related" pattern of cardiovascular risk factors which were defined as: obesity, diabetes, hypertriglyceridemia and low levels of high density lipoprotein cholesterol. This hypothesis was tested in 1979-1982 in the San Antonio Heart Study, a population-based study on 1,288 Mexican Americans and 929 Anglos living in three San Antonio neighborhoods: a low-income barrio, a middle-income transitional neighborhood, and a high-income suburb. The study population comprised 25-65-year-old men and nonpregnant women. In Mexican American women, all of the "obesity-related" risk factors fell sharply with rising socioeconomic status. In Mexican American men, by contrast, diabetes was the only "obesity-related" risk factor which fell with rising socioeconomic status. Moreover, it fell less steeply, there being an approximately twofold difference in diabetes prevalence between the barrio and the suburbs in men compared to a fourfold difference in women. Also, total and low density lipoprotein cholesterol rose with rising socioeconomic status in Mexican American men, but not in Mexican American women. "Obesity-related" risk factors were generally higher in Mexican Americans of both sexes than in their Anglo neighbors who were of similar socioeconomic status. These results suggest that cultural factors exert a stronger influence on diabetes and cardiovascular risk factors in Mexican Americans than do purely socioeconomic factors.
Introduction of a high‐pressure cell for use with Raman microscopy (2006)

Abstract A high‐pressure cell for Raman spectroscopical applications has been developed. By using this cell, it is possible to investigate reactions between solids and gases, applying pressures up to 3000 bar. The cell has been successfully tested on the reaction between ferrocene and carbon monoxide. The results point towards a multi‐step reaction mechanism. Furthermore, first results are presented for the investigation of the reaction path of CO 2 with a zinc thiolate complex. Copyright © 2006 John Wiley &amp; Sons, Ltd.
MicroRNA-Mediated Transformation by the Kaposi's Sarcoma-Associated Herpesvirus Kaposin Locus (2014)

Kaposi's sarcoma-associated herpesvirus (KSHV) is a human tumor virus. The viral Kaposin locus has known oncogenic potential, which has previously been attributed to the encoded KapA protein. Here we show that the virally encoded miR-K10a miRNA, whose precursor overlaps the KapA-coding region, may account for the oncogenic properties of this locus. Our data suggest that miR-K10a mimics the cellular miRNA miR-142-3p and thereby represses several known inhibitors of oncogenic transformation. Our work demonstrates that functional properties attributed to a coding region may in fact be carried out by an embedded noncoding element and sheds light on the functions of viral miR-K10a.
Fabrication and electrical characteristics of carbon nanotube field emission microcathodes with an integrated gate electrode (2001)

We report on the fabrication of field emission microcathodes which use carbon nanotubes as the field emission source. The devices incorporated an integrated gate electrode in order to achieve truly low-voltage field emission. A single-mask, self-aligned technique was used to pattern the gate, insulator and catalyst for nanotube growth. Vertically-aligned carbon nanotubes were then grown inside the gated structure by plasma-enhanced chemical vapour deposition. Our self-aligned fabrication process ensured that the nanotubes were always centred with respect to the gate apertures (2 µm diameter) over the entire device. In order to obtain reproducible emission characteristics and to avoid degradation of the device, it was necessary to operate the gate in a pulsed voltage mode with a low duty cycle. The field emission device exhibited an initial turn-on voltage of 9 V. After the first measurements, the turn-on voltage shifted to 15 V, and a peak current density of 0.6 mA cm-2 at 40 V was achieved, using a duty cycle of 0.5%.
Benchmarks for testing community detection algorithms on directed and weighted graphs with overlapping communities (2009)

Many complex networks display a mesoscopic structure with groups of nodes sharing many links with the other nodes in their group and comparatively few with nodes of different groups. This feature is known as community structure and encodes precious information about the organization and the function of the nodes. Many algorithms have been proposed but it is not yet clear how they should be tested. Recently we have proposed a general class of undirected and unweighted benchmark graphs, with heterogeneous distributions of node degree and community size. An increasing attention has been recently devoted to develop algorithms able to consider the direction and the weight of the links, which require suitable benchmark graphs for testing. In this paper we extend the basic ideas behind our previous benchmark to generate directed and weighted networks with built-in community structure. We also consider the possibility that nodes belong to more communities, a feature occurring in real systems, such as social networks. As a practical application, we show how modularity optimization performs on our benchmark.
Ab initio folding of proteins using restraints derived from evolutionary information (1999)

We present our predictions in the ab initio structure prediction category of CASP3. Eleven targets were folded, using a method based on a Monte Carlo search driven by secondary and tertiary restraints derived from multiple sequence alignments. Our results can be qualitatively summarized as follows: The global fold can be considered "correct" for targets 65 and 74, "almost correct" for targets 64, 75, and 77, "half-correct" for target 79, and "wrong" for targets 52, 56, 59, and 63. Target 72 has not yet been solved experimentally. On average, for small helical and alpha/beta proteins (on the order of 110 residues or smaller), the method predicted low resolution structures with a reasonably good prediction of the global topology. Most encouraging is that in some situations, such as with target 75 and, particularly, target 77, the method can predict a substantial portion of a rare or even a novel fold. However, the current method still fails on some beta proteins, proteins over the 110-residue threshold, and sequences in which only a poor multiple sequence alignment can be built. On the other hand, for small proteins, the method gives results of quality at least similar to that of threading, with the advantage of not being restricted to known folds in the protein database. Overall, these results indicate that some progress has been made on the ab initio protein folding problem. Detailed information about our results can be obtained by connecting to http:/(/)www.bioinformatics.danforthcenter.org/+ ++CASP3.
Long-term efficacy of erenumab in patients with episodic migranie who have failed prior preventive migraine therapies (2019)

Objective: To assess the sustained efficacy of erenumab through 52 weeks of treatment in patients with episodic migraine who had failed prior preventive therapies (EM ).Background: Erenumab has demonstrated efficacy and safety in migraine prevention studies.Design/Methods: Patients were randomized (1:1:1; n=955) to placebo or erenumab 70mg or 140mg monthly during the 24-week, double-blind treatment phase (DBTP) of the STRIVE study (NCT02456740).At week 24, 845 patients were re-randomized (1:1) to erenumab 70mg or 140mg for the subsequent 28-week, dose-blinded active treatment phase (ATP).The EM subgroup was defined as patients who failed one prior preventive therapy due to lack of efficacy/tolerability.Change from baseline in monthly migraine days (MMD) and monthly acute migraine-specific medication treatment days (MSMD) were assessed at week 52, as well as the proportion of patients achieving 50%/75%/100% MMD reduction in the last month of ATP.Patients were analyzed by dose received during the ATP (70mg or 140mg) for efficacy and safety reporting, irrespective of DBTP treatment.Results: Of the 845 patients who completed the DBTP and were re-randomized into the ATP, 343 (41%) patients had failed one prior preventive therapy.In EM , baseline MMD was 8.7(0.1);mean (SE) change from baseline to week 52 was -3.4(0.4) and -4.2(0.3) for the 70mg and 140mg erenumab dose groups, respectively.Baseline MSMD was 4.9(0.2);mean (SE) change from baseline to week 52 in MSMD was -1.9(0.3) and -2.5(0.2) for 70mg and 140mg erenumab, respectively.In total, 52.3% of EM patients on erenumab 70mg and 55.0% of EM patients on erenumab 140mg achieved 50% reduction from baseline in MMD at Week 52; 29% and 33% achieved 75% reduction, and 12% and 16% achieved 100% reduction.Conclusions: Erenumab provided sustained efficacy through week 52 in patients with episodic migraine who had failed prior preventive migraine therapy.
The ideal light source for datanets (1998)

The appetite for ever increasing computing power and interconnection bandwidth could be sated by vertical-cavity, surface-emitting lasers (VCSEL) for optical data communication. Made inexpensively using IC processing techniques, they can be diced in planar or linear arrays, such as in the wavelength-division multiplexer. The author discusses the essentials of semiconductor light sources, epitaxial growth of the surface-emitting laser and its interior design. The characteristics and operation of the VCSEL are described.
Classification of Hybridomas to Respiratory Syncytial Virus Glycoproteins (1982)

We have classified 28 hybridomas to the RS virus glycoproteins, VP66, VP84, by virus neutralization, RIP, and RIA tests. Without resorting to RIP, a combination of neutralization tests and RIA on BCH4 and RS/HO cells could be used to classify 79% of the hybridomas antibodies correctly. VP66 contains major determinants for virus neutralization since 11/13 hybridoma antibodies to this protein neutralized RS virus while 0/15 hybridoma antibodies to VP84 neutralized the virus.
Raw starch-digestive glucoamylase productivity of protease-less mutant from Aspergillus awamori var. kawachi. (1981)

Mutation experiments were performed to decrease the protease productivity of Aspergillus awamori var. kawachi using ultraviolet light and N-methyl-N'-nitro-N-nitrosoguanidine. The selected mutant HF-15 showed reductions in protease productivity of 93%, 84% and 50% in solid wheat bran culture, shaking Medium B and wheat bran cultures, respectively, as compared with the parent. Protease-less mutant HF-15 failed to produce α-mannosidase, and N-acety1-β-Dglucosaminidase productivity decreased by 35%. Mutant HF-15 specifically produced a high amount of raw starch-adsorbable and raw starch-digestive glucoamylase similar to GAI under all tested cultural conditions. On the contrary, high protease-producing mutant HF-10 produced a glucoamylase with very limited adsorption and digestion capacity on raw corn starch, and lower hydrolysis toward gelatinized potato starch and glycogen that was similar to GA I'.
Circulating high-mobility group box 1 (HMGB1) concentrations are elevated in both uncomplicated pneumonia and pneumonia with severe sepsis* (2007)

HMGB1 is elevated in almost all CAP subjects, and higher circulating HMGB1 is associated with mortality. But immunodetectable HMGB1 levels were also persistently elevated in those patients who fared well. Thus, additional work is needed to understand the biological activities of serum HMGB1 in sepsis.
Floor Plan Generation and Room Labeling of Indoor Environments from Laser Range Data (2014)

Automatic generation of building floor plans is useful in many emerging applications, including indoor navigation, augmented and virtual reality, as well as building energy simulation software. These applications require watertight models with limited complexity. In this paper, we present an approach that produces 2.5D extruded watertight models of building interiors from either 2D particle filter grid maps or full 3D point-clouds captured by mobile mapping systems. Our approach is to triangulate a 2D sampling of wall positions and separate these triangles into interior and exterior sets. We partition the interior volume of the building model by rooms, then simplify the model to reduce noise. Such labels are useful for building energy simulations involving thermal models, as well as for ensuring geometric accuracy of the resulting 3D model. We experimentally verify the performance of our proposed approach on a wide variety of buildings. Our approach is efficient enough to be used in real-time in conjunction with Simultaneous Localization and Mapping (SLAM) applications.