gebhart/patrepeval huggingface dataset:
ArrayExpress--a public repository for microarray gene expression data at the EBI (2003)

ArrayExpress is a new public database of microarray gene expression data at the EBI, which is a generic gene expression database designed to hold data from all microarray platforms. ArrayExpress uses the annotation standard Minimum Information About a Microarray Experiment (MIAME) and the associated XML data exchange format Microarray Gene Expression Markup Language (MAGE-ML) and it is designed to store well annotated data in a structured way. The ArrayExpress infrastructure consists of the database itself, data submissions in MAGE-ML format or via an online submission tool MIAMExpress, online database query interface, and the Expression Profiler online analysis tool. ArrayExpress accepts three types of submission, arrays, experiments and protocols, each of these is assigned an accession number. Help on data submission and annotation is provided by the curation team. The database can be queried on parameters such as author, laboratory, organism, experiment or array types. With an increasing number of organisations adopting MAGE-ML standard, the volume of submissions to ArrayExpress is increasing rapidly. The database can be accessed at http://www.ebi.ac.uk/arrayexpress.
Antimicrobial peptides of leukocytes (1997)

Leukocytes use an array of antimicrobial peptides and proteins to help them destroy invading microorganisms. These endogenous antibiotic molecules are remarkable for their structural variety, rapid evolutionary divergence, intraspecies variation, and complex yet subtle interactions with their targets. This arsenal has been studied most extensively in neutrophils, where its members include lactoferrin, secretory phospholipase A2, lysozyme, and the cathelicidins in the secretory granule compartment; defensins, bactericidal permeability inducing protein, serprocidins, and (again) lysozyme in the azurophil granule compartment; and calprotectin in the cytosolic compartment. That antimicrobial peptides and proteins are not limited to neutrophils and other phagocytes was made clear by the recent discovery of a microbicidal protein, NK lysin, in porcine natural killer cells and cytotoxic T lymphocytes. The structural homology of NK-lysin to amebapore, an antimicrobial cytolytic peptide of the parasitic protozoan Entamoeba histolytica, provides remarkable support for a long-suspected evolutionary connection between the leukocytes of higher animals and their unicellular, protozoan ancestors.
Nanoparticles that do not adhere to mucus provide uniform and long-lasting drug delivery to airways following inhalation (2017)

Mucoadhesive particles (MAP) have been widely explored for pulmonary drug delivery because of their perceived benefits in improving particle residence in the lungs. However, retention of particles adhesively trapped in airway mucus may be limited by physiologic mucus clearance mechanisms. In contrast, particles that avoid mucoadhesion and have diameters smaller than mucus mesh spacings rapidly penetrate mucus layers [mucus-penetrating particles (MPP)], which we hypothesized would provide prolonged lung retention compared to MAP. We compared in vivo behaviors of variously sized, polystyrene-based MAP and MPP in the lungs following inhalation. MAP, regardless of particle size, were aggregated and poorly distributed throughout the airways, leading to rapid clearance from the lungs. Conversely, MPP as large as 300 nm exhibited uniform distribution and markedly enhanced retention compared to size-matched MAP. On the basis of these findings, we formulated biodegradable MPP (b-MPP) with an average diameter of <300 nm and examined their behavior following inhalation relative to similarly sized biodegradable MAP (b-MAP). Although b-MPP diffused rapidly through human airway mucus ex vivo, b-MAP did not. Rapid b-MPP movements in mucus ex vivo correlated to a more uniform distribution within the airways and enhanced lung retention time as compared to b-MAP. Furthermore, inhalation of b-MPP loaded with dexamethasone sodium phosphate (DP) significantly reduced inflammation in a mouse model of acute lung inflammation compared to both carrier-free DP and DP-loaded MAP. These studies provide a careful head-to-head comparison of MAP versus MPP following inhalation and challenge a long-standing dogma that favored the use of MAP for pulmonary drug delivery.
Introduction To Electrosurgery (1981)

Electrosurgery is effective in the operating room, saving both time and surgical trauma to the patient. Many hospitals have demonstrated that it can be used without injury to either the patient or the staff. This article presents an introduction to the concepts used in electrosurgery and covers the theory of operation, applications, and safety considerations. A description of the surgical effects of desiccation, cutting and fulguration is presented.
Nutra-ergonomics: influence of nutrition on physical employment standards and the health of workers (2016)

The importance of ergonomics across several scientific domains, including biomechanics, psychology, sociology, and physiology, have been extensively explored. However, the role of other factors that may influence the health and productivity of workers, such as nutrition, is generally overlooked. Nutra-ergonomics describes the interface between workers, their work environment, and performance in relation to their nutritional status. It considers nutrition to be an integral part of a safe and productive workplace that encompasses physical and mental health as well as the long-term wellbeing of workers. This review explores the knowledge, awareness, and common practices of nutrition, hydration, stimulants, and fortified product use employed prior to physical employment standards testing and within the workplace. The influence of these nutra-ergonomic strategies on physical employment standards, worker safety, and performance will be examined. Further, the roles, responsibilities, and implications for the applicant, worker, and the employer will be discussed within the context of nutra-ergonomics, with reference to the provision and sustainability of an environment conducive to optimize worker health and wellbeing. Beyond physical employment standards, workplace productivity, and performance, the influence of extended or chronic desynchronization (irregular or shift work) in the work schedule on metabolism and long-term health, including risk of developing chronic and complex diseases, is discussed. Finally, practical nutra-ergonomic strategies and recommendations for the applicant, worker, and employer alike will be provided to enhance the short- and long-term safety, performance, health, and wellbeing of workers.
Access versus Ownership: How Real an Alternative Is It? (1996)

Le postulat selon lequel la politique actuelle est de preferer l'acces a l'information a la possession des documents necessite un examen approfondi. L'acces a la documentation ne permet ni le butinage ni les decouvertes inattendues. Il se concoit mieux pour les periodiques que pour les monographies, pour la plus grande rapidite, la fiabilite et la facilite d'utilisation qu'il offre ; mais la communication sur place est de toute facon preferable. Si l'on considere le seul critere du cout, les couts actuels sont en faveur de l'acces, mais ils pourront changer considerablement au fur et a mesure que l'acces deviendra numerique. Les nouvelles formes de controle et de publication des documents de recherche ont leurs avantages et leurs inconvenients. La possession des ouvrages a ses limites : elle ne peut jamais atteindre l'exhaustivite. On devrait pouvoir associer la possession d'un large eventail de documents recents en libre acces a l'acces a des documents plus anciens. L'importance croissante de l'autoapprentissage pourrait aider a defendre un budget d'acquisitions plus developpe.
Multimodal Attribute Extraction (2017)

The broad goal of information extraction is to derive structured information from unstructured data. However, most existing methods focus solely on text, ignoring other types of unstructured data such as images, video and audio which comprise an increasing portion of the information on the web. To address this shortcoming, we propose the task of multimodal attribute extraction. Given a collection of unstructured and semi-structured contextual information about an entity (such as a textual description, or visual depictions) the task is to extract the entity's underlying attributes. In this paper, we provide a dataset containing mixed-media data for over 2 million product items along with 7 million attribute-value pairs describing the items which can be used to train attribute extractors in a weakly supervised manner. We provide a variety of baselines which demonstrate the relative effectiveness of the individual modes of information towards solving the task, as well as study human performance.
Human UDP-galactose 4-Epimerase (2001)

UDP-galactose 4-epimerase catalyzes the interconversion of UDP-galactose and UDP-glucose during normal galactose metabolism. One of the key structural features in the proposed reaction mechanism for the enzyme is the rotation of a 4'-ketopyranose intermediate within the active site pocket. Recently, the three-dimensional structure of the human enzyme with bound NADH and UDP-glucose was determined. Unlike that observed for the protein isolated from Escherichia coli, the human enzyme can also turn over UDP-GlcNAc to UDP-GalNAc and vice versa. Here we describe the three-dimensional structure of human epimerase complexed with NADH and UDP-GlcNAc. To accommodate the additional N-acetyl group at the C2 position of the sugar, the side chain of Asn-207 rotates toward the interior of the protein and interacts with Glu-199. Strikingly, in the human enzyme, the structural equivalent of Tyr-299 in the E. coli protein is replaced with a cysteine residue (Cys-307) and the active site volume for the human protein is calculated to be approximately 15% larger than that observed for the bacterial epimerase. This combination of a larger active site cavity and amino acid residue replacement most likely accounts for the inability of the E. coli enzyme to interconvert UDP-GlcNAc and UDP-GalNAc.
Stable nuclear transformation of Chlamydomonas using the Chlamydomonas gene for nitrate reductase. (1989)

We have developed a nuclear transformation system for Chlamydomonas reinhardtii, using micro-projectile bombardment to introduce the gene encoding nitrate reductase into a nit1 mutant strain which lacks nitrate reductase activity. By using either supercoiled or linear plasmid DNA, transformants were recovered consistently at a low efficiency, on the order of 15 transformants per microgram of plasmid DNA. In all cases the transforming DNA was integrated into the nuclear genome, usually in multiple copies. Most of the introduced copies were genetically linked to each other, and they were unlinked to the original nit1 locus. The transforming DNA and nit+ phenotype were stable through mitosis and meiosis, even in the absence of selection. nit1 transcripts of various sizes were expressed at levels equal to or greater than those in wild-type nit+ strains. In most transformants, nitrate reductase enzyme activity was expressed at approximately wild-type levels. In all transformants, nit1 mRNA and nitrate reductase enzyme activity were repressed in cells grown on ammonium medium, showing that expression of the integrated nit1 genes was regulated normally. When a second plasmid with a nonselectable gene was bombarded into the cells along with the nit1 gene, transformants carrying DNA from both plasmids were recovered. In some cases, expression of the unselected gene could be detected. With the advent of nuclear transformation in Chlamydomonas, it becomes the first photosynthetic organism in which both the nuclear and chloroplast compartments can be transformed.
Entity categorization over large document collections (2008)

Extracting entities (such as people, movies) from documents and identifying the categories (such as painter, writer) they belong to enable structured querying and data analysis over unstructured document collections. In this paper, we focus on the problem of categorizing extracted entities. Most prior approaches developed for this task only analyzed the local document context within which entities occur. In this paper, we significantly improve the accuracy of entity categorization by (i) considering an entity's context across multiple documents containing it, and (ii) exploiting existing large lists of related entities (e.g., lists of actors, directors, books). These approaches introduce computational challenges because (a) the context of entities has to be aggregated across several documents and (b) the lists of related entities may be very large. We develop techniques to address these challenges. We present a thorough experimental study on real data sets that demonstrates the increase in accuracy and the scalability of our approaches.
Production of single-stranded DNA templates by exonuclease digestion following the polymerase chain reaction (1989)

Journal Article Production of single-stranded DNA templates by exonuclease digestion following the polymerase chain reaction Get access Russell G. Higuchi, Russell G. Higuchi Search for other works by this author on: Oxford Academic PubMed Google Scholar Howard Ochman Howard Ochman 1Department of Human Genetics, Washington University School of MedicineSt Louis, MO 63110, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 17, Issue 14, 25 July 1989, Page 5865, https://doi.org/10.1093/nar/17.14.5865 Published: 25 July 1989
Effects of serum, transforming growth factor type beta, or 12-O-tetradecanoyl-phorbol-13-acetate on ionized cytosolic calcium concentration in normal and transformed human bronchial epithelial cells. (1989)

Fluctuations in ionized cytosolic calcium ([Ca2+]i) are considered important signals for induction of growth or differentiation in mammalian cells. The resting concentrations of [Ca2+]i in normal and adenovirus 12-SV40 hybrid virus-transformed (BEAS-2B) human bronchial epithelial cells were 63 +/- 15 nM (SD) and 44 +/- 15 nM, respectively. Eight % calcium-free fetal bovine serum rapidly caused a significant increase in [Ca2+]i, while causing both cell types to undergo squamous differentiation. When treated with 8% calcium-free fetal bovine serum, a serum-sensitive subclone of BEAS-2B cells exhibited a higher elevation of [Ca2+]i than a serum-resistant (i.e., not stimulated to differentiate by serum) subclone. However, a serum component involved in the induction of squamous differentiation, transforming growth factor type beta, did not increase [Ca2+]i in either normal cells or BEAS-2B cells. 12-O-Tetradecanoyl-phorbol-13-acetate, an exogenous inducer of squamous differentiation and activator of protein kinase C, did not increase [Ca2+]i, but did attenuate serum-induced elevation of [Ca2+]i. These results suggest that while an increase in [Ca2+]i is associated with serum-induced squamous differentiation, a cytosolic ionized calcium signal is not required for the initiation of the squamous differentiation pathway induced by either transforming growth factor type beta or 12-O-tetradecanoylphorbol-13-acetate.
Dual-frequency microstrip reflectarray (2002)

Microstrip antennas are known to have a narrow bandwidth. However, they exhibit many other advantages that make them suitable for mobile and satellite communications. While narrow in bandwidth, microstrip antennas are well-suited for dual-frequency operation. Developments in microstrip reflectarrays have further demonstrated the viability of printed-circuit technology for space communications. Combining the novel characteristics of microstrip reflectarrays with the concept of dual-frequency operation, we examine the feasibility of a stacked dual-frequency microstrip reflectarray. Our results show that accurate CAD tools are essential in the design of dual-frequency microstrip reflectarray.
Short-term Administration of Glucagon-like Peptide-2. Effects on Bone Mineral Density and Markers of Bone Turnover in Short-Bowel Patients with No Colon (2002)

A 5-week GLP-2 administration significantly increased spinal BMD in short-bowel patients with no colon. The mechanism by which GLP-2 affects bone metabolism remains unclear, but may be related to an increased mineralization of bone resulting from an improved intestinal calcium absorption.
Bit rate reduction algorithm for a digital VCR (1991)

The authors describe a bit rate reduction algorithm for use in digital VCRs, based on block scrambling and the two-dimensional adaptive discrete cosine transform. This method satisfies many of the demands unique to digital VCRs. Before the encoding process, the input image is divided into 8*8 pixel blocks and then scrambled on a block-by-block basis to achieve efficient bit distribution in a frame and to simplify buffer control strategy. In addition to block scrambling, a simple yet efficient variable length coding method is proposed. Simulation results are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Effective combination of chemotherapy and dendritic cell administration for the treatment of advanced-stage experimental breast cancer. (2003)

The combination of DC administration with repeated cycles of chemotherapy and dexamethasone (conditions similar to real clinical practice) resulted in the induction of antitumor response despite the immunosuppression induced by such treatment.
The Caenorhabditis elegans sel-1 Gene, a Negative Regulator of lin-12 and glp-1, Encodes a Predicted Extracellular Protein (1996)

The Caenorhabditis elegans lin-12 and glp-1 genes encode members of the LIN-12/NOTCH family of receptors. The sel-1 gene was identified as an extragenic suppressor of a lin-12 hypomorphic mutant. We show in this report that the sel-1 null phenotype is wild type, except for an apparent elevation in lin-12 and glp-1 activity in sensitized genetic backgrounds, and that this genetic interaction seems to be lin-12 and glp-1 specific. We also find that sel-1 encodes a predicted extracellular protein, with a domain sharing sequence similarity to predicted proteins from humans and yeast. SEL-1 may interact with the LIN-12 and GLP-1 receptors and/or their respective ligands to down-regulate signaling.
The relative contribution of affinity and efficacy to agonist activity: organ selectivity of noradrenaline and oxymetazoline with reference to the classification of drug receptors (1984)

Oxymetazoline demonstrated a pronounced organ selectivity, when compared to noradrenaline, by being a potent full agonist in rat anococcygeus muscle and a partial agonist in rat vas deferens. Responses of rat anococcygeus muscles to oxymetazoline were relatively more sensitive to antagonism by phenoxybenzamine (Pbz) an alkylating alpha-adrenoceptor antagonist. Therefore, although oxymetazoline was more potent than noradrenaline in this tissue, after Pbz (0.3 microM for 10 min), the responses to oxymetazoline were completely inhibited while those to noradrenaline were only partially inhibited. Schild analysis with phentolamine, corynanthine, prazosin and yohimbine indicated no alpha-adrenoceptor heterogeneity within the rat anococcygeus muscle or between this tissue and rat vas deferens. Measurement of agonist Kd values and Schild analysis of oxymetazoline antagonism of responses to noradrenaline (after alkylation) confirmed the homogeneity of alpha-adrenoceptors with respect to these two agonists. The above profiles of activity would be predicted if oxymetazoline had a higher affinity but lower efficacy than noradrenaline. Experimentally this was confirmed when it was found that oxymetazoline had 5 times the affinity but 0.2 to 0.3 times the efficacy of noradrenaline. These results serve as a caveat to the use of selective receptor desensitization and/or selective receptor alkylation (or protection from alkylation) as means of differentiating drug receptors. Theoretical modelling and these experimental results indicate that high affinity/low efficacy agonists are much more sensitive to receptor coupling. The implications for therapeutic selectivity could be important in that high affinity/low efficacy agonists theoretically have a much greater potential for organ selectivity.
Geldanamycin, a Ligand of Heat Shock Protein 90, Inhibits the Replication of Herpes Simplex Virus Type 1 In Vitro (2004)

Geldanamycin (GA) is an antibiotic targeting the ADP/ATP binding site of heat shock protein 90 (Hsp90). In screening for anti-herpes simplex virus type 1 (HSV-1) candidates, we found GA active against HSV-1. HSV-1 replication in vitro was significantly inhibited by GA with an 50% inhibitory concentration of 0.093 microM and a concentration that inhibited cellular growth 50% in comparison with the results seen with untreated controls of 350 microM. The therapeutic index of GA was over 3700 (comparable to the results seen with acyclovir). GA did not inhibit HSV-1 thymidine kinase. Cells infected with HSV-1 demonstrated cell cycle arrest at the G(1)/S transition; however, treatment with GA resulted in a cell cycle distribution pattern identical to that of untreated cells, indicating a restoration of cell growth in HSV-1-infected cells by GA treatment. Accordingly, HSV-1 DNA synthesis was suppressed in HSV-1(+) cells treated with GA. The antiviral mechanism of GA appears to be associated with Hsp90 inactivation and cell cycle restoration, which indicates that GA exhibits broad-spectrum antiviral activity. Indeed, GA exhibited activities in vitro against other viruses, including severe acute respiratory syndrome coronavirus. Since GA inhibits HSV-1 through a cellular mechanism unique among HSV-1 agents, we consider it a new candidate agent for HSV-1.
Quantum communication and the creation of maximally entangled pairs of atoms over a noisy channel (1998)

We show how to create maximally entangled EPR pairs between spatially distant atoms, each of them inside a high–Q optical cavity, by sending photons through a general, noisy channel, such as a standard optical fiber. An error correction scheme that uses few auxiliary atoms in each cavity effectively eliminates photoabsorption and other transmission errors. This realizes the ‘absorption free channel’. A concatenation protocol using the absorption free channel allows for quantum communication with single qubits over distances much larger than the coherence length of the channel.