gebhart/patrepeval huggingface dataset:
Guest Encapsulation within Self‐Assembled Molecular Containers (2007)

Molecular hospitality: Self-assembled molecular containers provide a very specific geometric as well as chemical environment for a bound guest, which allows for selective guest binding or the stabilization of unstable molecules or unstable conformations within the capsule (see scheme). The geometric constraints imposed by the container can even change the outcome of a chemical reaction.
SAP90, a rat presynaptic protein related to the product of the Drosophila tumor suppressor gene dlg-A. (1993)

A novel synapse-associated protein, SAP90, accumulates around the axon hillock of Purkinje cells in rat cerebellum. By immuno-electron microscopy, SAP90 has been localized to the presynaptic termini of basket cells forming inhibitory, gamma-aminobutyric acid (GABA)ergic synapses onto Purkinje cell axon hillocks. The amino acid sequence for SAP90 has been deduced from the nucleotide sequence of a series of overlapping cDNA clones. SAP90 is related to the gene product encoded by the Drosophila tumor suppressor gene dlg-A. SAP90 and the dlg-A product share an overall sequence identity of 54%. Three distinct domains can be identified: (i) a potential cytoskeletal region consisting of three repeats of 90 amino acids in length, (ii) a domain with similarity to SH3, a putative regulatory motif found in the src family of non-receptor protein tyrosine kinases and several proteins associated with the cortical cytoskeleton, and (iii) a carboxyl-terminal domain homologous to yeast guanylate kinase. These features suggest a possible role for SAP90 in a guanine nucleotide-mediated signal transduction pathway at a subset of GABAergic synapses in the rat cerebellum.
Tiny Drosophila intestinal stem cells, big power (2022)

The signaling pathways are highly conserved between Drosophila and mammals concerning intestinal development, regeneration, and disease. The powerful genetic tools of Drosophila make it a valuable and convenient alternative to answer basic biological questions that can not be addressed using mammalian models. In this review, we discuss recent advances in how we use fly midgut to answer the following key questions: (1) How intestine stem cell niches are established; (2) which factors control asymmetric division of stem cells; (3) how intestinal cells interact with environmental factors, such as tissue damage, microbiota, and diet; (4) how to screen aging/cancer-related factors or drugs by fly intestine stem cells.
Intermittent Antibiotic Therapy for Recurrent Nodular Bronchiectatic Mycobacterium avium Complex Lung Disease (2017)

Intermittent, three-times-weekly oral antibiotic therapy is recommended for the initial treatment of noncavitary nodular bronchiectatic (NB) <i>Mycobacterium avium</i> complex (MAC) lung disease. However, intermittent therapy is not recommended for patients who have been previously treated. We evaluated 53 patients with recurrent noncavitary NB MAC lung disease who underwent antibiotic treatment for ≥12 months with daily therapy (<i>n</i> = 26) or intermittent therapy (<i>n</i> = 27) between January 2008 and December 2015. Baseline characteristics were comparable between daily therapy and intermittent therapy groups. Sputum culture conversion rates did not differ between daily therapy (21/26, 81%) and intermittent therapy (22/27, 82%) groups. Compared to the etiologic organism at the time of previous treatment, recurrent MAC lung disease was caused by the same MAC species in 38 patients (72%) and by a different MAC species in 15 patients (28%). Genotype analysis in patients with sequenced paired isolates revealed that 86% (12/14) of cases with same species recurrence were due to reinfection with a new MAC genotype. In conclusion, most recurrent noncavitary NB MAC lung disease cases were caused by reinfection rather than relapse. Intermittent antibiotic therapy is a reasonable treatment strategy for recurrent noncavitary NB MAC lung disease.
Quantitative Evaluation of Transtemporal and Facial Translocation Approaches to Infratemporal Fossa (2008)

Based on the results, we propose a clinical algorithm for selecting a surgical approach based on the position and extent of an infratemporal or petrotemporal lesion.
Reduced prostaglandin levels in the semen of men with very high sperm concentrations (1979)

The prostaglandin levels have been measured in a group of men with sperm concentrations greater than 300 X 10(6)/ml and compared with the levels in men with sperm concentrations of 50 to 150 X 10(6)/ml. The distribution of the PG levels in all groups was highly skewed but the data could be transformed to a normal distribution by taking logarithms. Comparison of the PG levels showed a highly significant lowering of the PG levels in the polyzoospermic group when compared wieth either of the groups with normal sperm concentrations.
Synthesis of α-Deoxymono and Difluorohexopyranosyl 1-Phosphates and Kinetic Evaluation with Thymidylyl- and Guanidylyltransferases (2016)

Eight fluorinated isosteric α-d-glucopyranosyl 1-phosphate (Glc 1P) analogues have been synthesized. A promiscuity investigation of the thymidylyltransferase Cps2L and the guanidylyltansferase GDP-ManPP with these analogues showed that all were accepted by either enzyme, with the exception of 1,6-diphosphate 6. Kinetic parameters were determined for these analogues using a continuous coupled assay. These data demonstrated the broad substrate promiscuity of Cps2L, with k<sub>cat</sub>/K<sub>m</sub> changes for monofluoro substitution at C-2, C-4, and C-6 and difluoro substitution at C-2 within two orders of magnitude. In contrast, the kinetic analysis of GDP-ManPP was only possible with three out of eight analogues. The pKa<sub>2</sub> values of analogues (1-3) were determined by proton decoupled <sup>31</sup>P and <sup>19</sup>F NMR titration experiments. Counterintuitively, the axial fluoro substituent in 3 did not change chemical shift upon titration, and there was no significant increase in acidity for the difluoro analogue over the monofluoro analogues. No strong Brønsted linear free-energy correlations were observed among all five substrates (1-3, Glc 1P, and Man 1P) for either enzyme-catalyzed reactions. However, Brønsted correlations were observed among selected substrates, indicating that the acidity of the nucleophilic phosphate and the configuration of the hexose each plays a significant role in determining the substrate specificity.
Thermoelectric power of bismuth nanowires (1999)

We report here measurements of the thermoelectric power and longitudinal magneto-Seebeck coefficient of 200 nm diameter single-crystal bismuth nanowires. Nanowires of pure Bi and of n-type-doped Bi (with Te at about $5\ifmmode\times\else\texttimes\fi{}{10}^{18}{\mathrm{cm}}^{\mathrm{\ensuremath{-}}3})$ were measured. The wires are imbedded in porous anodic alumina. The data are taken on arrays of wires connected in parallel, at temperatures from 8 to 300 K, and, between 10 and 80 K, in magnetic fields from 0 to 5 Tesla. It has been theoretically calculated that bismuth nanowires should have a strongly increased thermoelectric figure of merit over bulk Bi, when the diameter is decreased below about 10 nm. The nanowires in this study were selected because they are easier to prepare and handle. The temperature-dependent thermopower data are consistent with the partial electron and hole thermopower values calculated using the carrier Fermi energies obtained from Shubnikov--de Haas oscillations on the same samples.
Mechanical design of the VIRUS2 instrument (2020)

VIRUS2 is a new NSF-funded facility instrument on the McDonald Observatory Harlan J Smith 2.7m Telescope. The instrument is a fiber-fed multiplexed integral field spectrograph consisting of 6 units, each with 4 spectral channels, to provide large on-sky area coverage coupled with broad spectral coverage. A novel beam switch module is implemented in the fiber feed which separates light into the pass bands of the four spectral channels. This paper details the mechanical design of the spectrograph, cryostat, and the beam switch module. A unique method for precise six degree of freedom positioning of the CCD detectors is presented, along with process for determination of required adjustments. Results from prototype testing and first article production is included.
Two-pupil synthesis of optical transfer functions (1978)

Incoherent optical spatial filtering systems have a number of advantages over their coherent counterparts; however, they are limited in their conventional form to operating with nonnegative-real input, output, and pointspread distributions. Most serious is the limitation to nonnegative-real impulse responses. A broad class of hybrid methods is investigated that employs two pupils in the synthesis of bipolar-real impulse responses. The mathematical structure of these syntheses is presented along with limitations in the presence of various constraints. Minimization of image plane bias is considered. Methods for implementation are described and categorized.
Population‐specific frequencies for LRRK2 susceptibility variants in the genetic epidemiology of Parkinson's disease (GEO‐PD) consortium (2013)

ABSTRACT Background Variants within the leucine‐rich repeat kinase 2 gene are recognized as the most frequent genetic cause of Parkinson's disease. Leucine‐rich repeat kinase 2 variation related to disease susceptibility displays many features that reflect the nature of complex, late‐onset sporadic disorders like Parkinson's disease. Methods The Genetic Epidemiology of Parkinson's Disease Consortium recently performed the largest genetic association study for variants in the leucine‐rich repeat kinase 2 gene across 23 different sites in 15 countries. Results Herein, we detail the allele frequencies for the novel risk factors (p.A419V and p.M1646T) and the protective haplotype (p.N551K‐R1398H‐K1423K) nominated in the original publication. Simple population allele frequencies not only can provide insight into the clinical relevance of specific variants but also can help genetically define patient groups. Conclusions Establishing individual patient‐based genomic susceptibility profiles that incorporate both risk factors and protective factors will determine future diagnostic and treatment strategies. © 2013 International Parkinson and Movement Disorder Society
Non-Anticoagulant Heparin Increases Endothelial Nitric Oxide Synthase Activity: Role of Inhibitory Guanine Nucleotide Proteins (1998)

Heparin, which is widely used clinically, has recently been shown to have specific properties affecting the vascular endothelium. We hypothesized that heparin stimulates endothelial nitric oxide synthase (eNOS) activity by a mechanism independent of its anticoagulant properties and dependent on an inhibitory guanine nucleotide regulatory protein (Gi). We determined the effect of both heparin and N-acetyl heparin (Non-Hep), a heparin derivative without anticoagulant properties, on eNOS activity in cultured bovine aortic endothelial cells and on endothelium-dependent relaxation in isolated vascular rings. The eNOS activity was determined by measuring both citrulline and nitric oxide (NO) metabolite formation. Heparin and Non-Hep dose-dependently increased basal eNOS activity (ED50 1.0 microgram/ml or 0.15 U/ml), an effect that was significantly inhibited by pertussis toxin (100 ng/ml), a Gi-protein inhibitor. Agonist-stimulated (acetylcholine, 10 microM) eNOS activity was potentiated following pre-treatment with both heparin and Non-Hep and reversed by pertussis toxin. Heparin and Non-Hep induced a dose-dependent relaxation in preconstricted thoracic aortic rings, an effect that was significantly inhibited by pertussis toxin, endothelial inactivation (following treatment with sodium deoxycholate) and NG-nitro-L-arginine-methyl ester (L-NAME). We conclude that heparin and non-anticoagulant heparin induce endothelium-dependent relaxation following activation of eNOS by a mechanism involving a Gi-protein. Administration of heparin derivatives without anticoagulant properties may have therapeutic implications for the preservation of eNOS in conditions characterized by endothelial dysfunction.
Protection From Type 1 Diabetes in the Face of High Levels of Activated Autoaggressive Lymphocytes in a Viral Transgenic Mouse Model Crossed to the SV129 Strain (2001)

In comparing the incidence of virally induced type 1 diabetes in F(1) crosses of RIP-LCMV mice to three different mouse strains identical at the major histocompatibility complex H-2D(b) locus, we surprisingly found that disease development was reduced by 80% in F(1) crosses to the SV129 genetic background and by 60% after eight backcrosses to the original C57BL/6 RIP-LCMV mice. In this model, diabetes is strongly dependent on a virally induced H-2D(b)-restricted cytotoxic T-cell (CTL) response. Importantly, numbers and effector functions of autoaggressive CD4 and CD8 lymphocytes were not decreased in the protected mice, and CTLs were still able to kill syngeneic islet cells in vitro with equal efficacy compared with CTLs from the original RIP-LCMV strain. Furthermore, CTLs were able to extravasate into islets in vivo, and no evidence for induction of regulatory cells was observed. However, regeneration of beta-cells in islets under "attack" occurred only in the protected SV129-crossed animals, whereas it was not evident at any time in any mice that developed diabetes. Thus, genetic factors can "override" the diabetogenic potential of high numbers of autoaggressive lymphocytes through, for example, increased islet regeneration. This finding has important implications for interpreting numbers and pathogenicity of autoreactive lymphocytes in prediabetic patients of genetically diverse backgrounds.
Interband and Intraband Optical Gain in Colloidal Nanoplatelets (2022)

Two-dimensional nanoplatelets, or colloidal quantum wells, display large gain coefficients and low threshold amplified spontaneous emission and lasing thresholds spanning visible energies. In addition to interband gain via biexcitons, thresholdless intraband gain is observed with interband excitation in a quantum fountain-like population inversion.
Characterization of GaAs thin films grown by molecular beam epitaxy on Si-on-insulator (1991)

The direct growth of GaAs by molecular-beam epitaxy (MBE) on silicon-on-insulator (SOI) structure is presented. Rutherford backscattering and channeling (RBS/C), transmission electron microscope (TEM), and infrared (IR) reflection measurements have been employed to characterize the GaAs thin films. RBS/C results show that there is considerable lattice disorder at the GaAs-Si interface, but the crystal quality of the GaAs thin films improves remarkably toward GaAs surface for thicker films where the minimum channeling yield drops to 10% IR reflection spectra in the wavenumber range 1500 - 5000 cm-1 were measured for GaAs thin films on SOI. Interference fringes observed in IR reflection spectra also prove that the crystalline GaAs thin films have been deposited on SOI substrates. By computer simulation of the IR reflection interference spectra refractive index profiles of the GaAs/SOI structures were obtained.
Serotherapy of primary rat mammary carcinoma: inhibition by ethylenedinitrilotetraacetic acid but not by [ethylenebis(oxyethylenenitrilo)]tetraacetic acid. (1986)

We reported inhibition of growth of primary rat mammary carcinomas after infusions of tumor-bearer plasma absorbed with Protein A-Sepharose or inactivated CNBr Sepharose. Absorbed plasmas were depleted of the third component of complement (C3) (other complement components defined similarly) and C5 but not C1, C4, or C2. These results suggested that activation of the alternative pathway of complement might be involved in the observed antitumor effects. To test this concept sera were treated with ethylenedinitrilotetraacetic acid or [ethylenebis(oxyethylenenitrilo)]tetraacetic acid before absorption with Protein A-Sepharose. Ethylenedinitrilotetraacetic acid, by chelating calcium and magnesium, prevents activation of both the alternative and classical complement pathways. [Ethylenebis(oxyethylenenitrilo)]tetraacetic acid, by chelating calcium but not magnesium, permits activation of the alternative pathway but inhibits activation of the classical complement pathway. Sera in the presence or absence of chelating agent were absorbed with Protein A-Sepharose twice at room temperature. After absorption calcium was added to the sera. Rats were treated by i.v. injection of sera twice a week for 2 weeks. Measurements of tumor size were made weekly for 5-7 weeks and then tumor weight was determined. Groups were compared both for size of index and total tumors. The results can be summarized as follows: tumor-bearer sera before absorption did not inhibit the growth of rat primary mammary carcinomas; tumor-bearer sera after absorption with Protein A-Sepharose showed significant consumption of C3 and did inhibit tumor growth; tumor-bearer sera absorbed in the presence of ethylenedinitrilotetraacetic acid did not show a decrease in C3 functional activity and did not inhibit tumor growth; tumor-bearer sera absorbed in the presence of [ethylenebis(oxyethylenenitrilo)]tetraacetic acid did show a decrease in C3 functional activity and did inhibit tumor growth; sera from normal adult female rats after absorption with Protein A-Sepharose did inhibit tumor growth. The results are consistent with a role for the alternative pathway of complement in the inhibition of growth of rat primary mammary carcinomas observed after treatment with absorbed sera.
<title>Accelerated modeling of light transport in heterogeneous tissues using superposition of virtual sources</title> (1995)

We present a perturbation theory for diffusive light transport in turbid media, which allows us to model the light distribution around inhomogeneities of complex geometries. The diffusion equation for an inhomogeneous medium is transformed into an equivalent integral equation that can be solved with a fast iterative numerical algorithm. This method models three dimensional geometries considerably faster than standard methods. Furthermore, the integral formulation supports an intuitive understanding of the physical processes.
Mechanism of Decomposition of the Human Defense Factor Hypothiocyanite Near Physiological pH (2011)

Relatively little is known about the reaction chemistry of the human defense factor hypothiocyanite (OSCN(-)) and its conjugate acid hypothiocyanous acid (HOSCN), in part because of their instability in aqueous solutions. Herein we report that HOSCN/OSCN(-) can engage in a cascade of pH- and concentration-dependent comproportionation, disproportionation, and hydrolysis reactions that control its stability in water. On the basis of reaction kinetic, spectroscopic, and chromatographic methods, a detailed mechanism is proposed for the decomposition of HOSCN/OSCN(-) in the range of pH 4-7 to eventually give simple inorganic anions including CN(-), OCN(-), SCN(-), SO(3)(2-), and SO(4)(2-). Thiocyanogen ((SCN)(2)) is proposed to be a key intermediate in the hydrolysis; and the facile reaction of (SCN)(2) with OSCN(-) to give NCS(═O)SCN, a previously unknown reactive sulfur species, has been independently investigated. The mechanism of the aqueous decomposition of (SCN)(2) around pH 4 is also reported. The resulting mechanistic models for the decomposition of HOSCN and (SCN)(2) address previous empirical observations, including the facts that the presence of SCN(-) and/or (SCN)(2) decreases the stability of HOSCN/OSCN(-), that radioisotopic labeling provided evidence that under physiological conditions decomposing OSCN(-) is not in equilibrium with (SCN)(2) and SCN(-), and that the hydrolysis of (SCN)(2) near neutral pH does not produce OSCN(-). Accordingly, we demonstrate that, during the human peroxidase-catalyzed oxidation of SCN(-), (SCN)(2) cannot be the precursor of the OSCN(-) that is produced.
Premature ventricular contractions activate vagal afferents and alter autonomic tone: implications for premature ventricular contraction-induced cardiomyopathy (2019)

Mechanisms behind development of premature ventricular contraction (PVC)-induced cardiomyopathy remain unclear. PVCs may adversely modulate the autonomic nervous system to promote development of heart failure. Afferent neurons in the inferior vagal (nodose) ganglia transduce cardiac activity and modulate parasympathetic output. Effects of PVCs on cardiac parasympathetic efferent and vagal afferent neurotransmission are unknown. The purpose of this study was to evaluate effects of PVCs on vagal afferent neurotransmission and compare these effects with a known powerful autonomic modulator, myocardial ischemia. In 16 pigs, effects of variably coupled PVCs on heart rate variability (HRV) and vagal afferent neurotransmission were evaluated. Direct nodose neuronal recordings were obtained in vivo, and cardiac-related afferent neurons were identified based on their response to cardiovascular interventions, including ventricular chemical and mechanical stimuli, left anterior descending (LAD) coronary artery occlusion, and variably coupled PVCs. On HRV analysis before versus after PVCs, parasympathetic tone decreased (normalized high frequency: 83.6 ± 2.8 to 72.5 ± 5.3; <i>P</i> < 0.05). PVCs had a powerful impact on activity of cardiac-related afferent neurons, altering activity of 51% of neurons versus 31% for LAD occlusion (<i>P</i> < 0.05 vs. LAD occlusion and all other cardiac interventions). Both chemosensitive and mechanosensitive neurons were activated by PVCs, and their activity remained elevated even after cessation of PVCs. Cardiac afferent neural responses to PVCs were greater than any other intervention, including ischemia of similar duration. These data suggest that even brief periods of PVCs powerfully modulate vagal afferent neurotransmission, reflexly decreasing parasympathetic efferent tone.<b>NEW & NOTEWORTHY</b> Premature ventricular contractions (PVCs) are common in many patients and, at an increased burden, are known to cause heart failure. This study determined that PVCs powerfully modulate cardiac vagal afferent neurotransmission (exerting even greater effects than ventricular ischemia) and reduce parasympathetic efferent outflow to the heart. PVCs activated both mechano- and chemosensory neurons in the nodose ganglia. These peripheral neurons demonstrated adaptation in response to PVCs. This study provides additional data on the potential role of the autonomic nervous system in PVC-induced cardiomyopathy.
Parallel architectures and algorithms for image understanding. Final technical report, 1 November 1988-30 September 1989 (1990)

Several issues in using parallel processing for image understanding are addressed. First, efficient schemes for parallel image array access are developed. New class of latin squares called perfect latin squares are defined. Several construction methods are shown and some useful properties of such squares are identified. A generic parallel model of computation employing electro optical devices is developed. Parallel techniques for image computations are developed on this model. Finally, processor time optimal solutions to several low and intermediate level image understanding tasks are designed on orthogonal access parallel architectures.