gebhart/patrepeval huggingface dataset:
Hyperbaric oxygen therapy and cancer—a review (2012)

Hypoxia is a critical hallmark of solid tumors and involves enhanced cell survival, angiogenesis, glycolytic metabolism, and metastasis. Hyperbaric oxygen (HBO) treatment has for centuries been used to improve or cure disorders involving hypoxia and ischemia, by enhancing the amount of dissolved oxygen in the plasma and thereby increasing O(2) delivery to the tissue. Studies on HBO and cancer have up to recently focused on whether enhanced oxygen acts as a cancer promoter or not. As oxygen is believed to be required for all the major processes of wound healing, one feared that the effects of HBO would be applicable to cancer tissue as well and promote cancer growth. Furthermore, one also feared that exposing patients who had been treated for cancer, to HBO, would lead to recurrence. Nevertheless, two systematic reviews on HBO and cancer have concluded that the use of HBO in patients with malignancies is considered safe. To supplement the previous reviews, we have summarized the work performed on HBO and cancer in the period 2004-2012. Based on the present as well as previous reviews, there is no evidence indicating that HBO neither acts as a stimulator of tumor growth nor as an enhancer of recurrence. On the other hand, there is evidence that implies that HBO might have tumor-inhibitory effects in certain cancer subtypes, and we thus strongly believe that we need to expand our knowledge on the effect and the mechanisms behind tumor oxygenation.
Stream Traffic Communication in Packet Switched Networks: Destination Buffering Considerations (1982)

In this paper we consider the problem of sending a stream of data (speech, for example) through a packet-switched network which introduces variable source-to-destination delays for different packets of the stream. Ideally, this delay difference should be smoothed so as to preserve the continuity of the stream. We investigate an adaptive destination buffering scheme which may be used to achieve the smoothing of the output stream. The scheme uses delay information, measured for previous streams, in order to compute destination buffering information. Specifically, of the last <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</tex> packet delays, one discards the largest <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">k</tex> and then the range of this partial sample is used for the destination wait time <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</tex> . We obtain a rule of thumb for choosing <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</tex> and <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">k</tex> , and demonstrate its applicability on some empirical delay distributions from ARPANET measurements. It is, in general, necessary to deal with discontinuities which occur even after smoothing. To this end, we consider two possible playback schemes: method <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">E</tex> (time expanded in order to preserve information) and method <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">I</tex> (late data ignored in order to preserve timing). The two methods are at opposite ends of a continuum of possible playback schemes. We study the implication of methods <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">E</tex> and <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">I</tex> on the choice of smoothing parameters and establish a foundation for evaluating all schemes in this continuum.
Second-order nonlinear-optical processes in orientationally ordered materials: relationship between molecular and macroscopic properties (1987)

Liquid crystals and polymer glasses can be formed into orientationally ordered materials by raising the temperature of the material to a temperature at which molecular motion is greatly enhanced, applying an external aligning field, and then cooling with the field applied. The resulting material exhibits second-order nonlinear-optical effects. In this paper, the relationship between the molecular hyperpolarizability and the macroscopic susceptibility is presented. The susceptibility is seen to depend on the microscopic order parameters commonly associated with liquid crystals and is discussed in the limits of one-dimensional molecules and poled polymer glasses. Agreement is found between the theory and second-harmonic-generation measurements of polymer glasses. Results of electro-optic measurements are compared with second-harmonic-generation measurements that suggest that the electro-optic effect is mostly electronic in origin.
Regulated phosphorylation and dephosphorylation of tau protein: effects on microtubule interaction, intracellular trafficking and neurodegeneration (1997)

This review attempts to summarize what is known about tau phosphorylation in the context of both normal cellular function and dysfunction. However, conceptions of tau function continue to evolve, and it is likely that the regulation of tau distribution and metabolism is complex. The roles of microtubule-associated kinases and phosphatases have yet to be fully described, but may afford insight into how tau phosphorylation at the distal end of the axon regulates cytoskeletal-membrane interactions. Finally, lipid and glycosaminoglycan modification of tau structure affords yet more complexity for regulation and aggregation. Continued work will help to determine what is causal and what is coincidental in Alzheimer's disease, and may lead to identification of therapeutic targets for halting the progression of paired helical filament formation.
Social Determinants of Child Health in Colombia: Can Community Education Moderate the Effect of Family Characteristics? (2013)

Contextual effects on child health have been investigated extensively in previous research. However, few studies have considered the interplay between community characteristics and individual-level variables. This study examines the influence of community education and family socioeconomic characteristics on child health (as measured by height and weight-for-age Z-scores), as well as their interactions. We adapted the Commission on Social Determinants of Health (CSDH) framework to the context of child health. Using data from the 2010 Colombian Demographic and Health Survey (DHS), weighted multilevel models are fitted since the data are not selfweighting. The results show a positive impact of the level of education of other women in the community on child health, even after controlling for individual and family socioeconomic characteristics. Different pathways through which community education can substitute for the effect of family characteristics on child nutrition are found. The interaction terms highlight the importance of community education as a moderator of the impact of the mother’s own education and autonomy, on child health. In addition, the results reveal differences between height and weight-for-age indicators in their responsiveness to individual and contextual factors. Our findings suggest that community intervention programmes may have differential effects on child health. Therefore, their identification can contribute to a better targeting of child care policies.
Human Aspartyl (Asparaginyl) β-Hydroxylase Monoclonal Antibodies: Potential Biomarkers for Pancreatic Carcinoma (2002)

These results suggest that the FB50 and SF25 MoAbs represent excellent potential biomarkers of pancreatic adenocarcinoma and could be configured in an immunoassay for detecting pancreatic adenocarcinoma cells in biologic fluids.
Femtosecond-resolution pulse-front distortion measurement by time-of-flight interferometry (1989)

The pulse-front distortion occurring in lenses and lens systems has been measured by a Michelson interferometer. In this technique the plane pulse front from one arm of the interferometer is used as a temporal reference level to map contour lines of equal propagation time on the pulse-front surface. The experimental arrangement is capable of detecting pulse-front distortion with a resolution of 20 fsec, and this can be improved to approximately 1 fsec. The measured value of pulse-front distortion in a telescope (1.1 psec) is in good agreement with the calculated data.
Identifying biological themes within lists of genes with EASE (2003)

EASE is a customizable software application for rapid biological interpretation of gene lists that result from the analysis of microarray, proteomics, SAGE and other high-throughput genomic data. The biological themes returned by EASE recapitulate manually determined themes in previously published gene lists and are robust to varying methods of normalization, intensity calculation and statistical selection of genes. EASE is a powerful tool for rapidly converting the results of functional genomics studies from 'genes' to 'themes'.
Steering Endogenous Butyrate Production in the Intestinal Tract of Broilers as a Tool to Improve Gut Health (2015)

The ban on antimicrobial growth promoters and efforts to reduce therapeutic antibiotic usage has led to major problems of gastrointestinal dysbiosis in livestock production in Europe. Control of dysbiosis without the use of antibiotics requires a thorough understanding of the interaction between the microbiota and the host mucosa. The gut microbiota of the healthy chicken is highly diverse, producing various metabolic end products, including gases and fermentation acids. The distal gut knows an abundance of bacteria from within the Firmicutes Clostridium clusters IV and XIVa that produce butyric acid, which is one of the metabolites that are sensed by the host as a signal. The host responds by strengthening the epithelial barrier, reducing inflammation, and increasing the production of mucins and antimicrobial peptides. Stimulating the colonization and growth of butyrate-producing bacteria thus may help optimizing gut health. Various strategies are available to stimulate butyrate production in the distal gut. These include delivery of prebiotic substrates that are broken down by bacteria into smaller molecules which are then used by butyrate producers, a concept called cross-feeding. Xylo-oligosaccharides (XOS) are such compounds as they can be converted to lactate, which is further metabolized to butyrate. Probiotic lactic acid producers can be supplied to support the cross-feeding reactions. Direct feeding of butyrate-producing Clostridium cluster IV and XIVa strains are a future tool provided that large scale production of strictly anaerobic bacteria can be optimized. Current results of strategies that promote butyrate production in the gut are promising. Nevertheless, our current understanding of the intestinal ecosystem is still insufficient, and further research efforts are needed to fully exploit the capacity of these strategies.
Why is the partial oxygen pressure of human tissues a crucial parameter? Small molecules and hypoxia (2011)

Oxygen supply and diffusion into tissues are necessary for survival. The oxygen partial pressure (pO(2)), which is a key component of the physiological state of an organ, results from the balance between oxygen delivery and its consumption. In mammals, oxygen is transported by red blood cells circulating in a well-organized vasculature. Oxygen delivery is dependent on the metabolic requirements and functional status of each organ. Consequently, in a physiological condition, organ and tissue are characterized by their own unique 'tissue normoxia' or 'physioxia' status. Tissue oxygenation is severely disturbed during pathological conditions such as cancer, diabetes, coronary heart disease, stroke, etc., which are associated with decrease in pO(2), i.e. 'hypoxia'. In this review, we present an array of methods currently used for assessing tissue oxygenation. We show that hypoxia is marked during tumour development and has strong consequences for oxygenation and its influence upon chemotherapy efficiency. Then we compare this to physiological pO(2) values of human organs. Finally we evaluate consequences of physioxia on cell activity and its molecular modulations. More importantly we emphasize the discrepancy between in vivo and in vitro tissue and cells oxygen status which can have detrimental effects on experimental outcome. It appears that the values corresponding to the physioxia are ranging between 11% and 1% O(2) whereas current in vitro experimentations are usually performed in 19.95% O(2), an artificial context as far as oxygen balance is concerned. It is important to realize that most of the experiments performed in so-called normoxia might be dangerously misleading.
Nonencapsulated Variant of Cryptococcus neoformans I. Virulence Studies and Characterization of Soluble Polysaccharide (1971)

A weakly virulent nonencapsulated variant of Cryptococcus neoformans is described. The chemical structure and antigenicity of the soluble polysaccharides produced by the variant strain and a typical virulent strain were compared. The soluble polysaccharides produced by both strains were composed of the same constituent monosaccharides; however, the virulent strain produced a polysaccharide having a greater uronic acid content and a larger molecular size than that of the variant strain. Soluble polysaccharides from the two strains are not closely related immunologically. Soluble polysaccharide obtained from the virulent strain did not affect persistence of the variant strain in mice.
Recent developments in thermoelectric materials (2003)

Efficient solid state energy conversion based on the Peltier effect for cooling and the Seebeck effect for power generation calls for materials with high electrical conductivity σ, high Seebeck coefficient S, and low thermal conductivity k. Identifying materials with a high thermoelectric figure of merit Z(= S2σ/k) has proven to be an extremely challenging task. After 30 years of slow progress, thermoelectric materials research experienced a resurgence, inspired by the developments of new concepts and theories to engineer electron and phonon transport in both nanostructures and bulk materials. This review provides a critical summary of some recent developments of new concepts and new materials. In nanostructures, quantum and classical size effects provide opportunities to tailor the electron and phonon transport through structural engineering. Quantum wells, superlattices, quantum wires, and quantum dots have been employed to change the band structure, energy levels, and density of states of electrons, and have led to improved energy conversion capability of charged carriers compared to those of their bulk counterparts. Interface reflection and the scattering of phonons in these nanostructures have been utilised to reduce the heat conduction loss. Increases in the thermoelectric figure of merit based on size effects for either electrons or phonons have been demonstrated. In bulk materials, new synthetic routes have led to engineered complex crystal structures with the desired phonon-glass electron-crystal behaviour. Recent studies on new materials have shown that dimensionless figure of merit (Z ×temperature) values close to 1·5 could be obtained at elevated temperatures. These results have led to intensified scientific efforts to identify, design, engineer and characterise novel materials with a high potential for achieving ZT much greater than 1 near room temperature.
Cyclooxygenases: structural and functional insights (2008)

Cyclooxygenase (COX; prostaglandin G/H synthase, EC 1.14.99.1) catalyzes the first two steps in the biosynthesis of prostaglandins (PGs). The two COX isoforms COX-1 and COX-2 are the targets of the widely used nonsteroidal anti-inflammatory drugs, indicating a role for these enzymes in pain, fever, inflammation, and tumorigenesis. The ubiquitous constitutive expression of COX-1 and inducible expression of COX-2 have led to the widely held belief that COX-1 produces homeostatic PGs, while PGs produced by COX-2 are primarily pathophysiological. However, recent discoveries call this paradigm into question and reveal as yet underappreciated functions for both enzymes. This review focuses on some of these new insights.
Multilevel phase-change memory (2010)

Phase-change memory (PCM) has emerged in recent years as one among the most attractive technologies for future non-volatile solid-state memory. PCM relies on the reversible phase transition in chalcogenide materials between different states, i.e., amorphous and poly-crystalline, which are characterized by very different electrical properties. Multilevel storage, namely storage of multiple bits in a memory cell, is a key factor for the competitiveness of PCM technology in the nonvolatile memory market. This paper presents experimental characterization of multilevel PCM devices and addresses the feasibility and reliability issues of multilevel storage using adaptive program-and-verify schemes.
A Clone of Methicillin-ResistantStaphylococcus aureusamong Professional Football Players (2005)

We describe a highly conserved, community-associated MRSA clone that caused abscesses among professional football players and that was indistinguishable from isolates from various other regions of the United States.
NeuroML: A Language for Describing Data Driven Models of Neurons and Networks with a High Degree of Biological Detail (2010)

Biologically detailed single neuron and network models are important for understanding how ion channels, synapses and anatomical connectivity underlie the complex electrical behavior of the brain. While neuronal simulators such as NEURON, GENESIS, MOOSE, NEST, and PSICS facilitate the development of these data-driven neuronal models, the specialized languages they employ are generally not interoperable, limiting model accessibility and preventing reuse of model components and cross-simulator validation. To overcome these problems we have used an Open Source software approach to develop NeuroML, a neuronal model description language based on XML (Extensible Markup Language). This enables these detailed models and their components to be defined in a standalone form, allowing them to be used across multiple simulators and archived in a standardized format. Here we describe the structure of NeuroML and demonstrate its scope by converting into NeuroML models of a number of different voltage- and ligand-gated conductances, models of electrical coupling, synaptic transmission and short-term plasticity, together with morphologically detailed models of individual neurons. We have also used these NeuroML-based components to develop an highly detailed cortical network model. NeuroML-based model descriptions were validated by demonstrating similar model behavior across five independently developed simulators. Although our results confirm that simulations run on different simulators converge, they reveal limits to model interoperability, by showing that for some models convergence only occurs at high levels of spatial and temporal discretisation, when the computational overhead is high. Our development of NeuroML as a common description language for biophysically detailed neuronal and network models enables interoperability across multiple simulation environments, thereby improving model transparency, accessibility and reuse in computational neuroscience.
A translational rheostat for RFLAT-1 regulates RANTES expression in T lymphocytes (2002)

Activation of T lymphocytes by specific antigen triggers a 3- to 7-day maturation process. Terminal differentiation begins late after T cell activation and involves expression of effector genes, including the chemokine RANTES and its major transcriptional regulator, RANTES factor of late-activated T lymphocytes-1 (RFLAT-1). In this article we demonstrate that RFLAT-1 expression is translationally regulated through its 5'-UTR and in a cell type-specific manner. Overexpression of the translation initiation factor eIF4E increases RFLAT-1 protein, while inhibition of Mnk1, which phosphorylates eIF4E, reduces RFLAT-1 production, indicating cap-dependent translational regulation. These events are regulated by ERK-1/2 and p38 MAP kinases and allow T cells to rapidly adjust RANTES expression in response to changes in the cellular environment, such as stress and/or growth factors. These findings provide a molecular mechanism for a rheostat effect of increasing or decreasing RANTES expression at sites of inflammation. Memory T cells, already poised to make RANTES, are finely regulated by translational control of the major transcription factor regulating RANTES expression. This is the first example of such a mechanism regulating a chemokine, but it seems likely that this will prove to be a general way for cells to rapidly respond to stress, cytokines, and other proinflammatory factors in their local environment.
Engineered CH2 domains (nanoantibodies) (2009)

Currently, almost all FDA approved therapeutic antibodies (except ReoPro, Lucentis and Cimzia which are Fabs), and the vast majority of those in clinical trials are full-size antibodies mostly in IgG1 format of about 150 kDa size. A fundamental problem for such large molecules is their poor penetration into tissues (e.g., solid tumors) and poor or absent binding to regions on the surface of some molecules (e.g., on the HIV envelope glycoprotein) which are fully accessible only by molecules of smaller size. Therefore, much work especially during the last decade has been aimed at developing novel scaffolds of much smaller size and high stability. Here I briefly describe a proposition to use the immunoglobulin (Ig) constant CH2 domain (CH3 for IgE and IgM) as a scaffold. CH2 is critical for the Ig effector functions. Isolated CH2 is stable monomer in contrast to all other constant domains and most of the variable domains. CH2 and engineered CH2 domains with improved stability can be used as scaffolds for construction of libraries containing diverse binders to various antigens. Such binders based on a CH2 scaffold could also confer some effector functions. Because the CH2 domains are the smallest independently folded antibody domains that can be engineered to contain simultaneously antigen-binding sites and binding sites mediating effector and stability functions, and to distinguish them from domain antibodies which are used to denote engineered VH or VL domains or nanobodies which are used to denote camelid VHH, I termed them nanoantibodies (nAbs).
Neural Stem Cells, Neural Progenitors, and Neurotrophic Factors (2007)

Neural stem cells (NSCs) have been proposed as a promising cellular source for the treatment of diseases in nervous systems. NSCs can self-renew and generate major cell types of the mammalian central nervous system throughout adulthood. NSCs exist not only in the embryo, but also in the adult brain neurogenic region: the subventricular zone (SVZ) of the lateral ventricle. Embryonic stem (ES) cells acquire NSC identity with a default mechanism. Under the regulations of leukemia inhibitory factor (LIF) and fibroblast growth factors, the NSCs then become neural progenitors. Neurotrophic and differentiation factors that regulate gene expression for controlling neural cell fate and function determine the differentiation of neural progenitors in the developing mammalian brain. For clinical application of NSCs in neurodegenerative disorders and damaged neurons, there are several critical problems that remain to be resolved: 1) how to obtain enough NSCs from reliable sources for autologous transplantation; 2) how to regulate neural plasticity of different adult stem cells; 3) how to control differentiation of NSCs in the adult nervous system. In order to understand the mechanisms that control NSC differentiation and behavior, we review the ontogeny of NSCs and other stem cell plasticity of neuronal differentiation. The role of NSCs and their regulation by neurotrophic factors in CNS development are also reviewed.