gebhart/patrepeval huggingface dataset:
Molecular Pathways: Hypoxia Response in Immune Cells Fighting or Promoting Cancer (2011)

Both malignant and stromal components in tumors are influenced by the physiologic conditions of the microenvironment. Hypoxia is a prominent feature of solid tumors as a result of defective vascularization and intense metabolic activity. The gene-expression control mechanisms that adapt tissues to hypoxia are exploited by tumors to promote angiogenesis and vasculogenesis. The functions of infiltrating immune cells (macrophages and lymphocytes) and other stromal components are also influenced by a limited O(2) supply. Hypoxia-inducible factors (HIF) are the main molecular transcriptional mediators in the hypoxia response. The degradation and activity of HIF-1α and HIF-2α are tightly controlled by the fine-tuned action of oxygen-sensing prolyl and asparaginyl hydroxylase enzymes. Recent evidence indicates that hypoxia can modulate the differentiation and function of T lymphocytes and myeloid cells, skewing their cytokine-production profiles and modifying the expression of costimulatory receptors. This conceivably includes tumor-infiltrating lymphocytes. Hypoxia not only directly affects tumor-infiltrating leukocytes but also exerts effects on tumor cells and vascular cells that indirectly cause selective chemokine-mediated recruitment of suppressive and proangiogenic T-cell subsets. This review focuses on changes induced by hypoxia in immune cells infiltrating solid malignancies. Such changes may either promote or fight cancer, and thus are important for immunotherapy.
Inactivation of Multiple Bacterial Histidine Kinases by Targeting the ATP-Binding Domain (2014)

Antibacterial agents that exploit new targets will be required to combat the perpetual rise of bacterial resistance to current antibiotics. We are exploring the inhibition of histidine kinases, constituents of two-component systems. Two-component systems are the primary signaling pathways that bacteria utilize to respond to their environment. They are ubiquitous in bacteria and trigger various pathogenic mechanisms. To attenuate these signaling pathways, we sought to broadly target the histidine kinase family by focusing on their highly conserved ATP-binding domain. Development of a fluorescence polarization displacement assay facilitated high-throughput screening of ∼53 000 diverse small molecules for binding to the ATP-binding pocket. Of these compounds, nine inhibited the catalytic activity of two or more histidine kinases. These scaffolds could provide valuable starting points for the design of broadly effective HK inhibitors, global reduction of bacterial signaling, and ultimately, a class of antibiotics that function by a new mechanism of action.
Cold Stress Response in Patients with Severe Burns After ?? -Blockade (1992)

Adrenergic receptor blockade has been shown to be of benefit in the treatment of adverse cardiovascular changes in patients with burns during the hypermetabolic phase. This article examines the stress response to cold exposure in adults and children with 33% to 95% total body surface area burns with and without beta-blockade. Resting energy expenditures were measured by indirect calorimetry; the test subjects were exposed to mean temperatures of 27.5 degrees C (room temperature) or 24.6 degrees C (cold). The mean resting energy expenditure at ambient room temperature in patients with burns without beta-blockade was 1411 +/- 70 kcal/m2/day (mean +/- SEM). This value was 142% of that predicted for normal control subjects without burns. When placed in a cold temperature, patients with burns significantly increased their resting energy expenditures by 160% of predicted values, whereas patients with similar burns and beta-blockade increased their resting energy expenditures by 156%. Adults with septic burns had a mean resting energy expenditure 198% of the predicted value. These patients did not significantly increase their resting energy expenditures when they were exposed to cold either with or without beta-blockade. Data suggest that patients with septic burns already have a maximal metabolic response and that cold stress does not further increase this response. Males, ages 17 to 54 years, were found to increase their resting energy expenditures by 11.4 kcal/m2/day for each percent total body surface area burn. We conclude that beta-blockade with propranolol in therapeutic doses may be used in patients with burns without adversely affecting the cold stress response.
Early and Persistent Bone Marrow Hematopoiesis Defect in Simian/Human Immunodeficiency Virus-Infected Macaques despite Efficient Reduction of Viremia by Highly Active Antiretroviral Therapy during Primary Infection (2001)

The hematological abnormalities observed in human immunodeficiency virus (HIV)-infected patients appear to be mainly due to bone marrow dysfunction. A macaque models of AIDS could greatly facilitate an in vivo approach to the pathogenesis of such dysfunction. Here, we evaluated in this model the impact of infection with a pathogenic simian/human immunodeficiency virus (SHIV) on bone marrow hematopoiesis. Three groups of macaques were inoculated with 50 50% median infective doses of pathogenic SHIV 89.P, which expresses env of dual-tropic HIV type 1 (HIV-1) 89.6 primary isolate. During the primary phase of infection, animals were treated with either a placebo or highly active antiretroviral therapy (HAART) combining zidovudine, lamivudine, and indinavir, initiated 4 or 72 h postinfection (p.i.) and administered twice a day until day 28 p.i. In both placebo-treated and HAART-treated animals, bone marrow colony-forming cells (CFC) progressively decreased quite early, during the first month p.i. One year p.i., both placebo- and HAART-treated animals displayed decreases in CFC to about 56% of preinfection values. At the same time, a dramatic decrease (greater than 77%) of bone marrow CD34(+) long-term culture-initiating cells was noted in all animals were found. No statistically significant differences between placebo- and HAART-treated monkeys were found. These data argue for an early and profound alteration of myelopoiesis at the level of the most primitive CD34(+) progenitor cells during SHIV infection, independently of the level of viremia, circulating CD4(+) cell counts, or antiviral treatment.
14.1: <i>Invited Paper</i>: Heavy Metal‐Free Quantum Dots for Display Applications (2015)

Due to their superior colour quality, quantum dot‐containing displays have started to appear on the consumer market. However, cadmium presents a serious threat to environmental and human health. We report a liquid crystal display backlight unit comprising heavy metal‐free quantum dots, offering a consumer‐friendly alternative to cadmium‐based quantum dot displays.
Structural Basis for DNA Damage–Dependent Poly(ADP-ribosyl)ation by Human PARP-1 (2012)

Poly(ADP-ribose) polymerase-1 (PARP-1) (ADP, adenosine diphosphate) has a modular domain architecture that couples DNA damage detection to poly(ADP-ribosyl)ation activity through a poorly understood mechanism. Here, we report the crystal structure of a DNA double-strand break in complex with human PARP-1 domains essential for activation (Zn1, Zn3, WGR-CAT). PARP-1 engages DNA as a monomer, and the interaction with DNA damage organizes PARP-1 domains into a collapsed conformation that can explain the strong preference for automodification. The Zn1, Zn3, and WGR domains collectively bind to DNA, forming a network of interdomain contacts that links the DNA damage interface to the catalytic domain (CAT). The DNA damage-induced conformation of PARP-1 results in structural distortions that destabilize the CAT. Our results suggest that an increase in CAT protein dynamics underlies the DNA-dependent activation mechanism of PARP-1.
High-Voltage-Tolerant Analog Circuits Design in Deep-Submicrometer CMOS Technologies (2007)

Electrical stress-relieved analog circuit design techniques using only baseline devices are presented, 1-to-2 logic level shifter, optional diode insertion, and adaptive biasing scheme are introduced to meet a reliability guideline that ensures sufficient lifetime. The proposed idea was successfully demonstrated with 12-bit <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">I/Q</i> digital-to-analog converter (DAC) and an operational amplifier having a Classs-AB output stage in 65-nm n-well CMOS technology and a high temperature operating life (HTOL) test was performed to evaluate the reliability of the design.
Synthesis and properties of alkoxy- and acyloxysilanes (1966)

Abstract
An adaptive information retrieval system using a probabilistic user model (2001)

We propose a user model which enables an individual user to customize a probabilistic document retrieval system using the maximum entropy principle. A user can retrieve documents adaptively and more appropriately by using this model. Without using this model, there is a problem that a retrieval system outputs too many retrieval results for insufficient numbers of keywords, but our new models has solved this problem by supplementing keywords from a user model.
Isoelectric focusing technology quantifies protein signaling in 25 cells (2006)

A previously undescribed isoelectric focusing technology allows cell signaling to be quantitatively assessed in <25 cells. High-resolution capillary isoelectric focusing allows isoforms and individual phosphorylation forms to be resolved, often to baseline, in a 400-nl capillary. Key to the method is photochemical capture of the resolved protein forms. Once immobilized, the proteins can be probed with specific antibodies flowed through the capillary. Antibodies bound to their targets are detected by chemiluminescence. Because chemiluminescent substrates are flowed through the capillary during detection, localized substrate depletion is overcome, giving excellent linearity of response across several orders of magnitude. By analyzing pan-specific antibody signals from individual resolved forms of a protein, each of these can be quantified, without the problems associated with using multiple antibodies with different binding avidities to detect individual protein forms.
JAK inhibitor tofacitinib for treating rheumatoid arthritis: from basic to clinical (2012)

Rheumatoid arthritis (RA) is a representative autoimmune disease characterized by chronic and destructive inflammatory synovitis. The multiple cytokines play pivotal roles in RA pathogenesis by inducing intracellular signaling, and members of the Janus kinase (JAK) family are essential for such signal transduction. An orally available JAK3 inhibitor, tofacitinib, has been applied for RA, with satisfactory effects and acceptable safety in multiple clinical examinations. From phase 2 dose-finding studies, tofacitinib 5 mg and 10 mg twice a day appear suitable for further evaluation. Subsequently, multiple phase 3 studies were carried out, and tofacitinib with or without methotrexate (MTX) is efficacious and has a manageable safety profile in active RA patients who are MTX naïve or show inadequate response to methotrexate (MTX-IR), disease-modifying antirheumatic drugs (DMARD)-IR, or tumor necrosis factor (TNF)-inhibitor-IR. The common adverse events were infections, such as nasopharyngitis; increases in cholesterol, transaminase, and creatinine; and decreases in neutrophil counts. Although the mode of action of tofacitinib remains unclear, we clarified that the inhibitory effects of tofacitinib could be mediated through suppression of interleukin (IL)-17 and interferon (IFN)-γ production and proliferation of CD4(+) T cells in the inflamed synovium. Taken together, an orally available kinase inhibitor tofacitinib targeting JAK-mediated signals would be expected to be a new option for RA treatment.
Improvement of Czochralski Silicon Wafers By High‐Temperature Annealing (1995)

High‐temperature annealing in hydrogen, argon, and oxygen ambients improves the electrical performance of Czochralski Si wafers considerably. The gate oxide integrity of such wafers can approach values close to 100% yield after annealing for 1 to 2 h at 1200°C in argon and hydrogen ambient which is related to a significant reduction of near‐surface crystal defects as compared to nonannealed polished wafers. The perfection of epitaxial wafers is, however, not obtained. The high‐temperature treatment deteriorates the surface of polished wafers depending on the ambient used. A protective oxide layer grown during annealing in an oxygen ambient prevents roughening due to desorption of . A more pronounced roughening occurs by annealing in hydrogen or argon which is tightly connected to the chemical composition of the surface. A hydrogen terminated reconstructed Si (100) surface is observed after annealing in hydrogen. An oxygen‐denuded zone is formed close to the surface during high‐temperature annealing preventing oxygen precipitation in this region of the wafer. The oxygen precipitation in the bulk of the wafers depends significantly on the details of the annealing process. A precipitation behavior similar to nonannealed Si wafers can be obtained by appropriate process parameters.
Sorption of aromatic organic compounds by montmorillonite. Part 1.—Orientation studies (1955)

R. Greene-Kelly, Trans. Faraday Soc., 1955, 51, 412 DOI: 10.1039/TF9555100412
Cuatro personajes en imágenes−texto del Códice Dresde (2007)

Cuatro paginas del Dresde hasta ahora consideradas como una ceremonia del ano nuevo maya nos permiten incursionar en el complejo analisis de las imagenes y de sus recursos de comunicacion. En la busqueda de significados e interpretaciones de estas formas de mensaje, hemos venido desarrollando una tecnica de desarticulacion de elementos visuales que nos permitan identificar objetos, conceptos y significados para establecer su posible correspondencia con formulas rituales extraidas de los documentos coloniales. La aplicacion de esta tecnica es una propuesta hacia nuevas formas de analisis y de lectura de textos mayas
Build-to-last (2014)

The emergence of low-cost 3D printers steers the investigation of new geometric problems that control the quality of the fabricated object. In this paper, we present a method to reduce the material cost and weight of a given object while providing a durable printed model that is resistant to impact and external forces. We introduce a hollowing optimization algorithm based on the concept of honeycomb-cells structure. Honeycombs structures are known to be of minimal material cost while providing strength in tension. We utilize the Voronoi diagram to compute irregular honeycomb-like volume tessellations which define the inner structure. We formulate our problem as a strength--to--weight optimization and cast it as mutually finding an optimal interior tessellation and its maximal hollowing subject to relieve the interior stress. Thus, our system allows to build-to-last 3D printed objects with large control over their strength-to-weight ratio and easily model various interior structures. We demonstrate our method on a collection of 3D objects from different categories. Furthermore, we evaluate our method by printing our hollowed models and measure their stress and weights.
Enhancement of electroluminescence through a two-dimensional corrugated metal film by grating-induced surface-plasmon cross coupling (2005)

We report enhancement of electroluminescence through opaque-topped metal cathodes in organic light-emitting devices (OLEDs), which are periodically corrugated in two dimensions. The enhancement is caused by grating-induced cross coupling and outcoupling of surface plasmons. The emission intensity observed at normal direction is enhanced by a factor of 4 compared with that of OLEDs with one-dimensionally corrugated metal cathodes and is higher than that observed from the transparent substrate side in uncorrugated OLEDs. We attribute the enhancement to the fact that the surface plasmons propagating in all lateral directions are coupled out into free space by the two-dimensional corrugated structure of the OLEDs. In addition, the emission from the transparent substrate side is also much enhanced owing to the efficient coupling out of the waveguide modes trapped in the emissive layer.
MedIEQ-Quality labelling of medical web content using multilingual information extraction. (2006)

Quality of Internet health information is essential because it has the potential to benefit or harm a large number of people and it is therefore essential to provide consumers with some tools to aid them in assessing the nature of the information they are accessing and how they should use it without jeopardizing their relationship with their doctor. Organizations around the world are working on establishing standards of quality in the accreditation of health-related web content. For the full success of these initiatives, they must be equipped with technologies that enable the automation of the rating process and allow the continuous monitoring of labelled web sites alerting the labelling agency. In this paper we describe the European project MedIEQ (Quality Labelling of Medical Web Content Using Multilingual Information Extraction) that integrates the efforts of relevant organizations on medical quality labelling, multilingual information retrieval and extraction and semantic resources, from six different European countries (Spain, Germany, Greece, Finland, Czech Republic and Switzerland). The main objectives of MedIEQ are: first, to develop a scheme for the quality labelling of medical web content and provide the tools supporting the creation, maintenance and access of labelling data according to this scheme and second, to specify a methodology for the content analysis of medical web sites according to the MedIEQ scheme and develop the tools that will implement it.
Integrated precision medicine: the role of electronic health records in delivering personalized treatment (2017)

Precision Medicine involves the delivery of a targeted, personalized treatment for a given patient. By harnessing the power of electronic health records (EHRs), we are increasingly able to practice precision medicine to improve patient outcomes. In this article, we introduce the scientific community at large to important building blocks for personalized treatment, such as terminology standards that are the foundation of the EHR and allow for exchange of health information across systems. We briefly review different types of clinical decision support (CDS) and present the current state of CDS, which is already improving the care patients receive with genetic profile-based tailored recommendations regarding diagnostic and treatment plans. We also report on limitations of current systems, which are slowly beginning to integrate new genomic data into patient records but still present many challenges. Finally, we discuss future directions and how the EHR can evolve to increase the capacity of the healthcare system in delivering Precision Medicine at the point of care. WIREs Syst Biol Med 2017, 9:e1378. doi: 10.1002/wsbm.1378 For further resources related to this article, please visit the WIREs website.
COMPARATIVE PHYSIOLOGY AND BIOCHEMISTRY AND TAXONOMIC ASSIGNMENT OF THE <i>CHLORELLA</i> (CHLOROPHYCEAE) STRAINS OF THE CULTURE COLLECTION OF THE UNIVERSITY OF TEXAS AT AUSTIN<sup>1</sup> (1992)

ABSTRACT The species of the genus Chlorella exhibit considerable biochemical and physiological differences. Therefore, it is important to select for and utilize in research or biotechnology correctly identified strains of the species having the most favorable properties for the respective project. We examined the Chlorella strains of the University of Texas collection at Austin, Texas, according to species‐specific chemotaxonomic characters and assigned 58 strains to 10 well‐established species (only 17 of these strains were correctly named before).
Studies on Lipase from Candida cylindracea (1966)

Lipase from Candida cylindracea has been purified by ammonium sulfate precipitation, sodium deoxycholate treatment, ethanol-ether precipitation and chromatography on SE-Sephadex and Sephadex G-100 columns. The purification of the enzyme was 33.4-fold with a yeild of 18.0% on the basis of activity per weight of protein. The purified enzyme was homogeneous on ultracentrifugation and electrophoresis. Optimum pH for the hydrolysis of olive oil was 7.2 by the assay method using a polyvinylalcohol-emulsified system and 5.2 by the assay method using a shaken system without a macromolecular emulsifier. Optimum temperature was 45°C. The enzyme was stable up to 15°C and in the range of pH from 2.0 to 8.5. Sodium taurocholate showed either an activating or an inhibiting effect at pH 7.0, depending on the sodium taurocholate concentration and on the assay system.
Wireless Power Transmission With Self-Regulated Output Voltage for Biomedical Implant (2013)

This paper presents a wireless power transfer (WPT) system for powering implantable biomedical devices; the system is configured to achieve high efficiency even with CMOS switches and printed-circuit-board pattern coils and to maintain constant output voltage against coupling and loading variations without any additional blocks. It is shown that the parallel-resonant transmitter (TX) and receiver (RX) topology is advantageous for high efficiency even with lossy but compact components. In addition, the output voltage of the topology is insensitive to coupling and/or loading variations if the operating frequency is automatically adjusted according to coupling variations. A parallel-resonant class-D oscillator TX is developed to track the optimum operating frequency for the constant output voltage. The operating distance for the constant output voltage is also extended using a novel resonator structure, which contains two resonating coils. These proposed schemes allow a compact, efficient, and robust wireless power system. Maximum power of 174 mW can be transmitted with 63% overall efficiency.
Insect growth regulators and insect control: a critical appraisal. (1976)

Insect growth regulators (IGRs) of the juvenile hormone type alter physiological processes essential to insect development and appear to act specifically on insects. Three natural juvenile hormones have been found in insects but not in other organisms. Future use of antagonists or inhibitors of hormone synthesis may be technically possible as an advantageous extension of pest control by IGRs. A documented survey of the properties, metabolism, toxicology, and uses of the most commercially advanced chemical, methoprene, shows it to be environmentally acceptable and toxicologically innocuous. Derivation of its current use patterns is discussed and limitations on these are noted. Residue levels and their measurement in the ppb region have allowed exemption from the requirement of tolerances in the EPA registered use of methoprene for mosquito control. Tolerances for foods accompany its fully approved use for control of manure breeding flies through a cattle feed supplement. The human health effects of using this chemical appear to be purely beneficial, but further advances through new IGR chemicals appear unlikely without major changes in regulatory and legislative policy.