gebhart/patrepeval huggingface dataset:
Sonographic evaluations in elite college baseball athletes (2005)

This study compared the thickness of the biceps and supraspinatus tendons, the widths of the subacromial space in the frontal and scapular planes, and abnormal sonographic findings in the shoulders of injured, and uninjured elite college baseball athletes and healthy controls. This study recruited two groups of 42 and 12 athletes, with and without histories of shoulder injuries, respectively, as well as one control group of 16 college students who were matched for physical characteristics but not involved in sports. The results showed that the thickness of the biceps and supraspinatus tendons and the subacromial space widths at 0 degrees and 90 degrees shoulder abduction in the frontal plane were significantly greater in the athletes than in the controls (P-values <0.004). The occurrences of the acromioclavicular joint bulging, bicep tendon degeneration, infraspinatus tendon degeneration and infraspinatus cortical irregularity differ significantly between the injured athlete and the group of uninjured athletes and controls (P-values <0.05). However, only infraspinatus tendon degeneration corresponded to the injury histories. There was a high similarity of sonographic spectrum of abnormal findings among the groups. Longitudinal follow-ups are required to determine the clinical importance of the sonographic spectrums and the occurrences of abnormal finding in asymptomatic athletes' shoulders.
Release of potassium, lipids, and proteins from nonionic detergent treated chicken red blood cells (1994)

Abstract The plasma membrane of erythrocytes, as of other cells, is thought to act as the barrier responsible for maintaining intracellular gradients of most ions and small molecular species between the cell and its environment. Controlled application of the nonionic detergent Brij 58 effectively opened the erythrocyte plasma membrane, as judged by electron microscopy and lipid mobilization, but the cytoplasm maintained much of its integrity for about 30 min. Release of K + correlated well with release of protein into the surrounding medium. The results demonstrate that permeabilization of the erythrocyte plasma membrane does not result in an instantaneous equilibration of small ions, such as K + , between the cell and its environment. A comparison was made between erythrocytes treated with Brij 58 and Triton X‐100. The lipid and protein solubilizing actions of Triton X‐100 were not as easily separable in time as those of Brij 58. The results of treatment of the erythrocytes with different types of nonionic detergents suggest that the membranolytic and cytoplasmic protein destabilizing actions of nonionic detergents correspond with their hydrophilic‐lipophilic balance numbers (HLB values). © 1994 wiley‐Liss, Inc.
Hierarchy of Supramolecular Synthons: Persistent Carboxylic Acid···Pyridine Hydrogen Bonds in Cocrystals That also Contain a Hydroxyl Moiety (2008)

A Cambridge Structural Database (CSD) analysis was conducted in order to evaluate the hierarchy of supramolecular heterosynthons that involve two of the most relevant functional groups in the context of active pharmaceutical ingredients, carboxylic acids and alcohols, in competitive environments. The study revealed that 34% of the 5690 molecular carboxylic acid entries and 26% of the 25 035 molecular alcohol entries form supramolecular homosynthons, whereas the remaining entries form supramolecular heterosynthons with other functional groups, in particular Narom, CONH2, C−O−C, C═O, and chloride anions. Further refinement of this raw data revealed the following: 98% occurrence of the COOH···Narom supramolecular heterosynthon in the 126 crystal structures that contain acid and pyridine moieties in the absence of other hydrogen bond donors or acceptors; and 78% occurrence of the OH···Narom supramolecular heterosynthon in 228 crystal structures that contain hydroxyl and pyridine moieties (excluding intramolecular hydrogen bonding). Such high frequencies indicate that these supramolecular heterosynthons are strongly favored over their respective COOH···COOH and OH···OH supramolecular homosynthons. However, the CSD does not contain enough information to evaluate the predictability of even common supramolecular heterosynthons in the presence of competing hydrogen bonding moieties; for example, there are only 15 entries when -COOH, -OH, and Narom moieties are present exclusively (no other hydrogen bond donors and acceptors groups) in a molecule. We have addressed the competition between the COOH···Narom and the OH···Narom supramolecular heterosynthons by analyzing these 15 entries in CSD and characterizing 15 new compounds (cocrystals 1−13; salts 14 and 15) that are composed of cocrystal formers which contain a permutation of -COOH, -OH and Narom functional groups. Analysis of this group of compounds reveals that supramolecular heterosynthons are favored over the respective supramolecular homosynthons. We also address the methodologies that can be used to prepare 1−15 in the context of solvent evaporation, solvent-drop grinding, and slurrying.
Organic electro-optics: Understanding material structure/function relationships and device fabrication issues (2009)

Realization of large electro-optic (EO) activity for dipolar organic chromophore-containing materials requires the simultaneous optimization of chromophore first hyperpolarizability (β), acentric order <cos3θ>, and number density (N). As these parameters are inter-related, correlated quantum and statistical mechanical calculations are required to understand the dependence of macroscopic electro-optic activity upon chromophore structure and intermolecular electrostatic interactions. Correlated time-dependent density functional theory (TD-DFT) and pseudo-atomistic Monte Carlo (PAMC) calculations are used in an attempt to understand the dependence of linear and nonlinear optical properties on dielectric permittivity, optical frequency, and a variety of spatially-anisotropic interactions that can be nano-engineered into the macroscopic material structure. Structure/function relationships are considered for three classes of organic electro-optic materials: (1) Chromophore/polymer composite materials; (2) chromophores covalently incorporated into passive organic host materials; (3) chromophores incorporated into chromophore-containing host materials—a new class of materials referred to as binary chromophore organic glasses (BCOGs). Issues associated with processing these materials into device structures, including those relevant to the integration with silicon photonics, are discussed. The purpose of this article is to address issues critical to ascertaining the viability of organic electro-optic (OEO) materials for next generation telecommunications, computing, and sensing applications.
Ribozyme-mediated repair of RNAs encoding mutant tumor suppressors. (1996)

The observation that a number of genetic mutations can result in neoplastic transformation has led many investigators to speculate that gene therapy may represent a useful approach to treat cancer. Conceptually, this application of gene therapy seems quite simple: to treat cancer, restore the correctly regulated expression of the needed tumor suppressor genes inside tumor cells and revert the transformed phenotype of such cells. However, such regulated expression has been difficult to achieve in practice. Here we describe recent efforts at such restoration via a novel approach to gene therapy that involves ribozyme-mediated repair of mutant RNA transcripts.
PDZ-domain-mediated interaction of the Eph-related receptor tyrosine kinase EphB3 and the ras-binding protein AF6 depends on the kinase activity of the receptor (1998)

Eph-related receptor tyrosine kinases (RTKs) have been implicated in intercellular communication during embryonic development. To elucidate their signal transduction pathways, we applied the yeast two-hybrid system. We could demonstrate that the carboxyl termini of the Eph-related RTKs EphA7, EphB2, EphB3, EphB5, and EphB6 interact with the PDZ domain of the ras-binding protein AF6. A mutational analysis revealed that six C-terminal residues of the receptors are involved in binding to the PDZ domain of AF6 in a sequence-specific fashion. Moreover, this PDZ domain also interacts with C-terminal sequences derived from other transmembrane receptors such as neurexins and the Notch ligand Jagged. In contrast to the association of EphB3 to the PDZ domain of AF6, the interaction with full-length AF6 clearly depends on the kinase activity of EphB3, suggesting a regulated mechanism for the PDZ-domain-mediated interaction. These data gave rise to the idea that the binding of AF6 to EphB3 occurs in a cooperative fashion because of synergistic effects involving different epitopes of both proteins. Moreover, in NIH 3T3 and NG108 cells endogenous AF6 is phosphorylated specifically by EphB3 and EphB2 in a ligand-dependent fashion. Our observations add the PDZ domain to the group of conserved protein modules such as Src-homology-2 (SH2) and phosphotyrosine-binding (PTB) domains that regulate signal transduction through their ability to mediate the interaction with RTKs.
Human sperm glutathione reductase activity in situ reveals limitation in the glutathione antioxidant defense system due to supply of NADPH (1998)

In order to characterize further the antilipoperoxidative enzyme system of human sperm, that part of the system designed to provide reducing equivalents for the reduction of highly reactive and potentially damaging lipid hydroperoxides to relatively inert hydroxylipids was examined. The substrate that provides the reducing equivalents directly to glutathione peroxidase (GPX) is reduced glutathione (GSH), which is in turn oxidized to glutathione disulfide (GSSG). The reducing equivalents needed for regeneration of GSH through the action of glutathione reductase (GRD) are provided by NADPH, produced by the action of glucose-6-phosphate dehydrogenase (G6P-DH) on substrates glucose-6-phosphate and NADP+. The kinetic properties of the enzymes GRD and G6P-DH were determined by standard enzyme activity assay at 24 and 37 degrees C. At 37 degrees C, the Vmax for GRD was found to be 36 nmol/min x 10(8) cells, with Km values for GSSG and NAPH of 150 microM and 16 microM, respectively; the Vmax for G6P-DH was 3.3 nmol/min x 10(8) cells with Km for NADP+ of 8 microM. This suggested that G6P-DH activity was limiting in this reductive pathway. The activity of GRD in situ in intact cells was estimated using the thiol-reactive fluorogenic probe ThioGlo-1, which is cell permeant and reacts rapidly with GSH to give a highly fluorescent adduct. Mixing a suspension of human sperm with the fluorogenic reagent at 37 degrees C gave an initial rapid increase in fluorescence, followed by a slower one. The rapid phase is due to reaction with intracellular GSH already present; the slow phase is due to reaction with GSH generated by the GRD-catalyzed reduction of GSSG. Both rates showed first-order kinetics. Calculation of the maximal rate as NADPH oxidation, attributable to in situ GRD activity, gave the value of 1.0 nmol/min x 10(8) cells, less than the maximum for NADPH production by the dehydrogenase. These results support the suggestion that NADPH production limits the capacity of the pathway leading to hydroperoxide reduction in human sperm. We propose that the antilipoperoxidative defense system of human sperm has just sufficient capacity to allow these cells to fulfill their function but is limited to allow their timely disposal from the female reproductive tract.
Macrophage Scavenger Receptor Class A (2000)

In atherogenesis, elevated plasma levels of low density lipoprotein (LDL) lead to the chronic presence of LDL in the arterial wall. There, LDL is modified (eg, oxidized), and these modified lipoproteins activate endothelial cells, which attract circulating monocytes. These monocytes enter the vessel wall, differentiate into macrophages, and subject the modified lipoproteins to endocytosis through scavenger receptor pathways. This unrestricted uptake, which is not limited by intracellular cholesterol levels, eventually leads to the formation of lipid-filled foam cells, the initial step in atherosclerosis. Macrophage scavenger receptor class A (SRA) is thought to be one of the main receptors involved in foam cell formation, mediating the influx of lipids into the macrophages. In addition to this role in modified lipoprotein uptake by macrophages, the SRA has been shown to be important in the inflammatory response in host defense, cellular activation, adhesion, and cell-cell interaction. Given the importance of these processes in atherogenesis, these latter functions may prove to make the SRA a multifunctional player in the atherosclerotic process.
Prostate Cancer: A Current Perspective (1991)

Journal Article Prostate Cancer: A Current Perspective Get access Abraham M. Y. Nomura, Abraham M. Y. Nomura 1Japan-Hawaii Cancer Study, Kuakini Medical CenterHonolulu, Hawaii2Epidemiology Program, Cancer Research Center of Hawaii, University of HawaiiHonolulu, Hawaii Dr. Abraham M. Y. Nomura, Japan-Hawaii Cancer Study, Kuakini Medical Center, 347 N. Kuakini Street, Honolulu, HI 96718 Search for other works by this author on: Oxford Academic PubMed Google Scholar Laurence N. Kolonel Laurence N. Kolonel 2Epidemiology Program, Cancer Research Center of Hawaii, University of HawaiiHonolulu, Hawaii Search for other works by this author on: Oxford Academic PubMed Google Scholar Epidemiologic Reviews, Volume 13, Issue 1, 1991, Pages 200–227, https://doi.org/10.1093/oxfordjournals.epirev.a036069 Published: 01 March 1991 Article history Received: 09 January 1991 Published: 01 March 1991 Revision received: 22 April 1991
Standardization of Steroid Hormone Assays: Why, How, and When? (2007)

Lack of standardization of high-quality steroid hormone assays is a major deficiency in epidemiologic studies. In postmenopausal women, reported levels of serum 17beta-estradiol (E(2)) are highly variable and median normal values differ by approximately a 6-fold factor. A particular problem is the use of E(2) assays for prediction of breast cancer risk and osteoporotic fractures, where assay sensitivity may be the most important factor. Identification of women in the lowest categories of E(2) levels will likely provide prognostic information that would not be available in a large group of women in whom E(2) levels are undetectable by less sensitive assays. Detailed and costly methods involving extraction and chromatography in conjunction with RIA provide generally acceptable E(2) results in postmenopausal serum, whereas less tedious, direct immunoassays suffer from inadequate specificity and sensitivity. Studies comparing the two types of methods generally report higher E(2) values with the direct methods as a result of cross-reactivity with other steroids and reduced correlation with biological variables such as body mass index. Similar problems exist with measurements of E(2) and estrone in men, and estrone and testosterone in women. Interest in mass spectrometry-based assays is increasing as potential gold standard methods with enhanced sensitivity and specificity; however, these assays require costly instrumentation and highly trained personnel. Taking all of these issues into consideration, we propose establishment of standard pools of premenopausal, postmenopausal, and male serum, and utilization of these for cross-comparison of various methods on an international basis. An oversight group could then establish standards based on these comparisons and set agreed upon confidence limits of various hormones in the pools. These criteria would allow validation of sensitivity, specificity, precision, and accuracy of current steroid hormone assay methodology and provide surrogates until a true gold standard can be developed.
Characterization of Factors Involved in Modulating Persistence of Transgene Expression from Recombinant Adenovirus in the Mouse Lung (1997)

One potential limitation of adenovirus (Ad)-based vectors for the gene therapy of cystic fibrosis (CF) and other genetic diseases is the transience of expression observed in most in vivo systems. In this study, the influence of various factors on persistence of transgene expression in the lung was investigated. In the absence of immune pressure, such as in the nude mouse, the genomic structure of the vector was found to be predominant in determining the persistence of expression; Ad vector constructs with an E1-E3+E4ORF6+ backbone encoding beta-galactosidase (beta-Gal) or the cystic fibrosis transmembrane conductance regulator (CFTR) produced declining levels of expression while an Ad/CMV beta Gal vector with an E1-E3+E4+ backbone gave rise to sustained, long-term reporter gene expression. The ability of the latter vector to persist was in turn limited in part by the presence of cytotoxic T lymphocytes (CTLs). Adoptive transfer experiments indicated that CTLs directed against either viral proteins or the beta-Gal reporter gene product were able to reduce expression in nude C57BL/6 mice stably expressing beta-Gal from the E4+ vector. Finally, the specificity and strength of the CTL response elicited by Ad vector was found to vary considerably depending on mouse strain haplotype. These results indicate that persistence of transgene expression in a given system is determined by the interplay between several factors including genomic structure of the vector, host background, and immune response.
Anorexia nervosa: Towards an integrative neuroscience model (2010)

We reviewed the evidence for emotion-related disturbances in anorexia nervosa (AN) from behavioural, cognitive, biological and genetic domains of study. These domains were brought together within the framework of an integrative neuroscience model that emphasizes the role of emotion and feeling and their regulation, in brain organization. PsychInfo and Medline searches were performed to identify published peer-reviewed papers on AN within each domain. This review revealed evidence for 'Emotion', 'Thinking and Feeling' and 'Self-regulation' disturbances in AN that span non-conscious to conscious processes. An integrative neuroscience framework was then applied to develop a model of AN, from which hypotheses for empirical investigation are generated. We propose that AN reflects a core disturbance in emotion at the earliest time stage of information processing with subsequent effects on the later stages of thinking, feeling and self-regulation.
Some General Properties of Magnetic Amplifiers (1951)

The magnetic amplifier is discussed in general terms as a carrier system in which there is a modulation gain and a small demodulation loss. Relations are given which show how a magnetic modulator may exhibit a gain. Some results of calculation and measurement on the type of circuit in which the modulator output consists of the even harmonics of the carrier source for dc signal input are given. It is shown that the ratio of dc gain to response rise time is a constant depending only on the carrier frequency, the losses in the nonlinear core, and its non-linearity. The conditions for self-oscillation at the carrier even harmonics are also given.
Inferring gene regulatory network for cell reprogramming (2012)

The remarkable discovery of induced pluripotent stem cells (iPSCs) demonstrates that cell can be reprogrammed from somatic cell to a pluripotent state by the enforced expression of defined transcriptional factors. However, the underlying mechanism for cell reprogramming remains unknown and the regulatory interactions within this biological process have not been worked out. In particular from the gene regulatory network perspective, it is not clear how the four factors initialize the reprogramming process, propagate the information in a fine tuned way, and finally lead to the dramatic phenotype changes. In this paper, we analyze the time course gene expression data during cell reprogramming in mouse. We propose a three-stage procedure to infer gene regulatory networks. Specifically, we identify the major players during cell reprogramming by selecting differentially expressed genes in the first stage. Then in the second stage we utilize a new method to reveal strong correlations among those selected genes from short time series data. Finally the gene regulatory relationships are modeled by ordinary differential equations (ODE), the correlations are filtered by applying strong regularization, and directed and signed gene regulatory network for cell reprogramming is reconstructed. Preliminary analysis of the inferred network shows that short time series data provide biological insights for the dynamical process during reprogramming.
Hybrid porous solids: past, present, future (2007)

This critical review will be of interest to the experts in porous solids (including catalysis), but also solid state chemists and physicists. It presents the state-of-the-art on hybrid porous solids, their advantages, their new routes of synthesis, the structural concepts useful for their 'design', aiming at reaching very large pores. Their dynamic properties and the possibility of predicting their structure are described. The large tunability of the pore size leads to unprecedented properties and applications. They concern adsorption of species, storage and delivery and the physical properties of the dense phases. (323 references)
Numerical Analysis of Modern and Fossil Pollen Data from the Tibetan Plateau (2008)

This study applies a number of multivariate numerical techniques in the analysis of modern and fossil pollen data for the purpose of paleovegetational reconstruction in the Tibetan Plateau. Modern pollen spectra from 227 sampling sites in the Tibetan Plateau were classified into groups using cluster analysis and detrended correspondence analysis. By comparing the quantitatively derived groups with local vegetation types at sampling locations, the modern pollen spectra were assigned into five major vegetation types—shrubland, forest, meadow, steppe, and desert. These were used as a priori groups for discriminant analysis. A set of discriminant functions was derived that correctly classifies 93.3 percent of the surface samples. These functions were then applied to a fossil pollen record from Yidun Glacial Lake near the Sichuan–Tibet border to reconstruct the major pattern of vegetational changes since the last glacial maximum. The results show that steppe and meadow prevailed around the site during the Late Glacial period (17.3–11.5 ka BP). Regional vegetation changed from meadow to forest during the transitional period of 11.5–9.2 ka BP. Forests have persisted in the Yidun area since 9.2 ka BP. A comparison of our reconstructed paleovegetation with other proxy data suggests that the transition to forest around 9.2 ka BP followed the early Holocene intensification of the southwest Asian monsoon. Our study also demonstrates that discriminant analysis is a useful technique for reliable reconstruction of paleovegetation in the Tibetan Plateau.