gebhart/patrepeval huggingface dataset:
Microbiota-Sourced Purines Support Wound Healing and Mucous Barrier Function (2020)

The intestinal mucosa requires high levels of nucleotides for energy procurement, proliferation, and innate immunity. This need for nucleotide substrates substantially increases during injury, infection, and wound healing. In the present studies, we profile potential sources of purine nucleotides in murine mucosal tissue. This work reveals the gut microbiota as a prominent source of exogenous purines and that such microbiota-sourced purines (MSPs) are available to the intestinal mucosa. The MSPs are utilized for nucleotide genesis and promote energy balance. Further analyses reveal that colitic tissues lacking MSPs are proliferatively stunted, with notable energetic and endoplasmic reticulum stress to the detriment of mucous barrier integrity. Purine reconstitution either directly or through colonization of germ-free/antibiotic-treated mice with MSP-sufficient E. coli alleviates such deficits, establishing MSP as a critical source of substrate for tissue metabolism, wound healing, and mucous barrier sterile integrity.
Addressing the Skills Gap: A Regional Analysis (2017)

In the current volatile economic climate, job requirements and corresponding skill sets are also changing. This is evidenced by the apparent contradiction that while real unemployment rates for certain occupations remain high, jobs are left unfilled due to a lack of applicants with the requisite qualifications to fill them. Moreover, changes in existing jobs pose challenges for modifying existing skill sets. In order to stay competitive, organizational leaders and managers need to utilize effectively their investments in human capital. Using the case of Northwest Indiana (NWI), this study examines the current skills gap and solutions for closing it.
The response of the zonally averaged circulation to stratospheric ozone reductions (1978)

The effects of various ozone density reductions on the zonally averaged circulation are evaluated with a numerical quasigeostrophic model. If the ozone perturbations are confined to the polar regions and are minuscule on a global basis as was characteristic of the August 1972 solar proton event, then our calculations indicate a negligible effect on the mean circulation. For global ozone perturbations by predicted halocarbon pollution, we calculate the difference between a 10% reduction in the zonal jet strength and less than a 5% change in global mean stratospheric temperature. Large, uniform ozone reductions ( 50%) produce significant effects on the mean circulation: a substantial collapse of the stratosphere due to cooler temperature and a weak polar night jet. The reflection and transmission of quasi-stationary planetary waves in the middle atmosphere are computed to be insensitive to solar activity as extreme as the August 1972 solar proton event. It thus seems improbable that planetary waves are a viable mechanism for solar-weather interactions that involve perturbations of the zonally averaged circulation by ozone density reductions. (Author)
Spatial-proteomics reveal in-vivo phospho-signaling dynamics at subcellular resolution (2021)

Abstract Dynamic change in subcellular localization of signaling proteins is a general concept that eukaryotic cells evolved for eliciting a coordinated response to stimuli. Mass spectrometry (MS)-based proteomics in combination with subcellular fractionation can provide comprehensive maps of spatio-temporal regulation of cells, but involves laborious workflows that does not cover the phospho-proteome level. Here we present a high-throughput workflow based on sequential cell fractionation to profile the global proteome and phospho-proteome dynamics across six distinct subcellular fractions. We benchmarked the workflow by studying spatio-temporal EGFR phospho-signaling dynamics in-vitro in HeLa cells and in-vivo in mouse tissues. Finally, we investigated the spatio-temporal stress signaling, revealing cellular relocation of ribosomal proteins in response to hypertonicity and muscle contraction. Proteomics data generated in this study can be explored through https://SpatialProteoDynamics.github.io .
Free-standing spectral purity filters for extreme ultraviolet lithography (2012)

Free-standing multilayer films consisting of Si, Zr, Mo and silicides of both metals have been fabricated and studied as spectral purity filters (SPF) for extreme ultraviolet (EUV) (13.5 nm) lithography tools. Comparative tests of multilayer SPF structures of various compositions have been performed at high power loads. It was found that a Mo/ZrSi2 structure with MoSi2 capping layers is featured with capability to withstand prolonged heating in vacuum (10−7 mbar) at 900-950°C. A technique of fabrication of large aperture free-standing multilayers was developed, and a pilot sample of the above film structure of 160 mm in diameter, 50 nm thick, with transparency at 13.5 nm above 70% was fabricated as a conceptual prototype of SPFs with large dimensions.
Nicotinamide coenzyme regeneration. The rates of some 1,4-dihydropyridine, pyridinium salt, and flavin mononucleotide hydrogen-transfer reactions (1976)

The rates of H-transfer between various 1,4-dihydropyridines and pyridinium salts (including NADH and NAD + ), and from 1,4-dihydropyridines to FMN, have been measured. The reactions are found to be sufficiently slow for H-transfer to be rate-determining to a significant extent when such Systems are applied for nicotinamide coenzyme recycling purposes. The rates of H-transfer parallel the magnitudes of the donor–acceptor redox potential differences (ΔE 0 ′); ΔE 0 ′ values may therefore be used as qualitative guides in formulating and selecting redox couples of NAD/H recycling value. On the basis of deuterium isotope effects, it is concluded that formation of a complex prior to H-transfer is not rate determining for 1,4-dihydropyridine–NAD + reactions. This behavior is in contrast to that of other model alcohol dehydrogenase Systems.
Evaluation of biofilm colonization on multi-part dental implants in a rat model (2021)

We developed a new rodent model for the preclinical evaluation of dental implant materials with a special focus on the early biofilm colonization including human-derived oral bacteria. Reliable biofilm quantification on the implant surface and the symptoms of peri-implant mucositis of the bacterially inoculated animals will serve as a readout for experimental evaluation of biofilm-reducing modifications of implant materials.
Cardiac conduction alterations in a French family with amyloidosis of the finnish type with the p.Asp187Tyr mutation in the GSN gene (2005)

Familial amyloidosis of the Finnish type (FAF) is a rare autosomal-dominant disorder caused by the accumulation of a 71-amino acid amyloidogenic fragment of mutant gelsolin, an actin-modulating protein. The main symptoms include corneal lattice dystrophy, progressive cranial and peripheral neuropathy, and skin changes. To date, only two mutations in the GSN gene have been described: the p.Asp187Asn mutation in most patients and the p.Asp187Tyr mutation in a Danish and Czech family. We report on the third family with the p.Asp187Tyr mutation and the first French FAF family. Severe cardiac conduction alterations in three patients were mainly caused by cardiac sympathetic denervation. These findings demonstrate the cardiological involvement of the FAF phenotype and suggest that cardiological follow-up is required in FAF patients.
Mobility of the Doped Holes and the Antiferromagnetic Correlations in Underdoped High-TcCuprates (2001)

The emergence and the evolution of the metallic charge transport in the La2-xSrxCuO4 system from lightly to optimally doped samples (x = 0.01-0.17) are studied. We demonstrate that in high-quality single crystals the in-plane resistivity shows a metallic behavior for all values of x at moderate temperatures and that the hole mobility at 300 K changes only by a factor of 3 from x = 0.01 to 0.17, where its x dependence is found to be intriguingly similar to that of the inverse antiferromagnetic correlation length. We discuss an incoherent-metal picture and a charged-stripe scenario as candidates to account for these peculiar features.
<title>Si-based microphone testing methodology and noise reduction</title> (2000)

In this paper two different packaging and testing approaches were studied for Si based microphone. Microphone performance was tested with Ceramic, Plastic and metal packages. Sensitivity testing of microphone is done when it is connected to an ASIC die. Testing was done with microphone and ASIC packaged separately and also in a single package. Substantial noise was generated when microphone and ASIC are tested separately in a PCB. Noise was detected after 150 Hz with the noise intensity reducing as it goes to higher frequencies. This was observed regardless of the packaging schemes. Different shielding methods were tried and found that copper foil shielding results in substantial noise reduction during frequency response testing and a flat response curve was observed with metal can package. Form this new testing methodology, it is demonstrated that same ASIC can be used repeatedly during microphone testing and hence some cost reduction can be expected.
Molecular Gene Expression Profiling to Predict the Tissue of Origin and Direct Site-Specific Therapy in Patients With Carcinoma of Unknown Primary Site: A Prospective Trial of the Sarah Cannon Research Institute (2012)

In this large prospective trial, molecular tumor profiling predicted a tissue of origin in most patients with CUP. The median survival time of 12.5 months for patients who received assay-directed site-specific therapy compares favorably with previous results using empiric CUP regimens. Patients with CUP predicted to have more responsive tumor types had longer survival compared with patients with less responsive tumor types. Molecular tumor profiling contributes to the management of patients with CUP and should be a part of their standard evaluation.
Single-particle analysis of full-length human poly(ADP-ribose) polymerase 1 (2019)

PolyADP-ribosylation (PARylation) is a posttranslational modification that is involved in the various cellular functions including DNA repair, genomic stability, and transcriptional regulation. PARylation is catalyzed by the poly(ADP-ribose) polymerase (PARP) family proteins, which mainly recognize damaged DNA and initiate repair processes. PARP inhibitors are expected to be novel anticancer drugs for breast and ovarian cancers having mutation in <i>BRCA</i> tumor suppressor genes. However the structure of intact (full-length) PARP is not yet known. We have produced and purified the full-length human PARP1 (h-PARP1), which is the major family member of PARPs, and analyzed it with single particle electron microscopy. The electron microscopic images and the reconstructed 3D density map revealed a dimeric configuration of the h-PARP1, in which two ring-shaped subunits are associated with two-fold symmetry. Although the PARP1 is hypothesized to form a dimer on damaged DNA, the quaternary structure of this protein is still controversial. The present result would provide the first structural evidence of the dimeric structure of PARP1.
Scaffoldin Conformation and Dynamics Revealed by a Ternary Complex from the Clostridium thermocellum Cellulosome (2012)

Cellulosomes are multienzyme complexes responsible for efficient degradation of plant cell wall polysaccharides. The nonenzymatic scaffoldin subunit provides a platform for cellulolytic enzyme binding that enhances the overall activity of the bound enzymes. Understanding the unique quaternary structural elements responsible for the enzymatic synergy of the cellulosome is hindered by the large size and inherent flexibility of these multiprotein complexes. Herein, we have used x-ray crystallography and small angle x-ray scattering to structurally characterize a ternary protein complex from the Clostridium thermocellum cellulosome that comprises a C-terminal trimodular fragment of the CipA scaffoldin bound to the SdbA type II cohesin module and the type I dockerin module from the Cel9D glycoside hydrolase. This complex represents the largest fragment of the cellulosome solved by x-ray crystallography to date and reveals two rigid domains formed by the type I cohesin·dockerin complex and by the X module-type II cohesin·dockerin complex, which are separated by a 13-residue linker in an extended conformation. The type I dockerin modules of the four structural models found in the asymmetric unit are in an alternate orientation to that previously observed that provides further direct support for the dual mode of binding. Conserved intermolecular contacts between symmetry-related complexes were also observed and may play a role in higher order cellulosome structure. SAXS analysis of the ternary complex revealed that the 13-residue intermodular linker of the scaffoldin subunit is highly dynamic in solution. These studies provide fundamental insights into modular positioning, linker flexibility, and higher order organization of the cellulosome.
Increased duration of pollen and mold exposure are linked to climate change (2021)

Pollen and molds are environmental allergens that are affected by climate change. As pollen and molds exhibit geographical variations, we sought to understand the impact of climate change (temperature, carbon dioxide (CO<sub>2</sub>), precipitation, smoke exposure) on common pollen and molds in the San Francisco Bay Area, one of the largest urban areas in the United States. When using time-series regression models between 2002 and 2019, the annual average number of weeks with pollen concentrations higher than zero increased over time. For tree pollens, the average increase in this duration was 0.47 weeks and 0.51 weeks for mold spores. Associations between mold, pollen and meteorological data (e.g., precipitation, temperature, atmospheric CO<sub>2</sub>, and area covered by wildfire smoke) were analyzed using the autoregressive integrated moving average model. We found that peak concentrations of weed and tree pollens were positively associated with temperature (p < 0.05 at lag 0-1, 0-4, and 0-12 weeks) and precipitation (p < 0.05 at lag 0-4, 0-12, and 0-24 weeks) changes, respectively. We did not find clear associations between pollen concentrations and CO<sub>2</sub> levels or wildfire smoke exposure. This study's findings suggest that spore and pollen activities are related to changes in observed climate change variables.
Enamine Chemistry. II. Reactions with Acetylenedicarboxylates1 (1963)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEnamine Chemistry. II. Reactions with Acetylenedicarboxylates1Kent C. Brannock, Robert D. Burpitt, V. Wilson Goodlett, and John G. ThweattCite this: J. Org. Chem. 1963, 28, 6, 1464–1468Publication Date (Print):June 1, 1963Publication History Published online1 May 2002Published inissue 1 June 1963https://pubs.acs.org/doi/10.1021/jo01041a006https://doi.org/10.1021/jo01041a006research-articleACS PublicationsRequest reuse permissionsArticle Views427Altmetric-Citations85LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
In vitro subacute cataractogenic study in rainbow trout lens. (1987)

Crystalline lens of rainbow trout can be incubated in H10 medium at 0 degrees C for 2.5 months without loss of transparency and change in cation level. Applicability of this lens incubation system to test for drug toxicity was investigated. Changes in cation and glutathione (GSH) levels and lactic acid production which occurred with opacification were examined when the lens was treated with diamide, p-chloromercuribenzoic acid (PCMB), N-ethylmaleimide (NEM), 1,2-naphthoquinone, ouabain and valinomycin. Among biochemical parameters, the increase in Na+-K+ ratio (Na+/K+) was most closely related to lens opacification, as in mammalian lenses. Lens opacification was observed macroscopically. Therefore, Na+/K+ was used as a lens toxicity parameter of the drug. Valinomycin was found to be the most effective drug as measured by the lowest concentration (1.0 X 10(-10) M) which gave an increase in Na+/K+. On the other hand, the lens treated with 2.5 X 10(-5) M NEM demonstrated neither change in Na+/K+ nor loss of transparency for 2.5 months. Lens toxicities due to diamide, PCMB, valinomycin and ouabain were detectable in the rainbow trout lens at 1000 times lower concentrations than those in the mouse lens. By using rainbow trout lenses incubated at 0 degrees C, drug toxicity can be characterized by well-defined biochemical parameters and can be observed at lower concentrations for long periods of time. The rainbow trout lens is, therefore, very useful for studying long-term drug toxicity and the lens opacification mechanism.
Electrical Modeling of STT-MRAM Defects (2018)

Spin-transfer-torque magnetic RAM (STT-MRAM) is one of the most promising emerging memory technologies. As various manufacturing vendors make significant efforts to push it to the market, appropriate STT-MRAM testing is of great importance. In this paper, we demonstrate that conventional STT-MRAM defect modeling, which is based on linear resistors, is too pessimistic in representing the real nature of physical defects. It may result in incorrect fault models, which in turn can lead to low-quality test solutions. In addition, we propose a generic defect modeling methodology which captures the nonlinear behavior of STT-MRAM defects accurately; a defect is modeled by adjusting the affected STT-MRAM technology parameters. The methodology is illustrated by two examples, namely a pinhole defect and a sidewall redeposition defect, which are simulated for accurate fault modeling. In case of a pinhole defect, the STT-MRAM suffers from a fast transition between magnetic tunnel junction (MTJ) states with increased write current, making the MTJ more vulnerable to breakdown. However, with the conventional linear resistor as defect model the memory shows a slow transition or even a transition failure. Similarly, a sidewall redeposition defect causes a fast transition without current elevation, which is not observed when using the conventional approach.
Anionic ring-opening polymerization of propylene oxide in the presence of phosphonium catalysts (2002)

Anionic ring-opening polymerization of propylene oxide in the presence of potassium alcoholate initiator was accelerated by addition of the bulky phosphonium salt tetrakis[cyclohexyl(methyl)amino]phosphonium-tetrafluoroborate. Dipropylene glycol (DPG) was partially deprotonated (5%) and used as an initiator for the polymerization performed at 100 °C at normal pressure. The delocalization of the positive charge over five atoms promoted the formation of a separated ion pair, thus enhancing nucleophilicity and reactivity. Compared with those of polyaminophosphazenes and tetrabutylphosphonium cation, the average propagation rates increased in the order of Bu4P+, K+, P, P, and tBuP4H+. DPn for the polymers was in the range of 20–64. Characterization of poly(propylene oxide)s by means of 1H NMR, size exclusion chromatography (SEC), and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) showed low polydispersities (Mw/Mn) without any byproducts or impurities. The Mw/Mn obtained was 1.03–1.09 (MALDI-TOF-MS) and 1.11–1.15 (SEC), respectively. Values calculated from titration of the hydroxyl groups showed good agreement. Determination of the total degree of unsaturation in the range of 13–60 mmol/kg indicated larger amounts with increasing polymerization rates. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 864–873, 2002; DOI 10.1002/pola.10163
Novel Carbon-Doped TiO2 Nanotube Arrays with High Aspect Ratios for Efficient Solar Water Splitting (2005)

The photocatalytic splitting of water into hydrogen and oxygen using solar light is a potentially clean and renewable source for hydrogen fuel.(1,2) There has been extensive investigation into metal-oxide semiconductors such as TiO(2), WO(3), and Fe(2)O(3), which can be used as photoanodes in thin-film form.(3-5) Of the materials being developed for photoanodes, TiO(2) remains one of the most promising because of its low cost, chemical inertness, and photostability.(6) However, the widespread technological use of TiO(2) is hindered by its low utilization of solar energy in the visible region. In this study, we report the preparation of vertically grown carbon-doped TiO(2) (TiO(2-x)C(x)) nanotube arrays with high aspect ratios for maximizing the photocleavage of water under white-light irradiation. The synthesized TiO(2-x)C(x) nanotube arrays showed much higher photocurrent densities and more efficient water splitting under visible-light illumination (> 420 nm) than pure TiO(2) nanotube arrays. The total photocurrent was more than 20 times higher than that with a P-25 nanoparticulate film under white-light illumination.
Yeast/Mold Morphogenesis in Mucor and Candida albicans (2020)

The phenomenon of yeast (Y)⇄ mold (M) dimorphism (morphogenesis) has been observed for many years, but research in this area has intensified over the past 10 years. There are at least two major reasons for the current surge of interest. First, the nuclear complement of genetic material in a haploid fungal nucleus, such as in Saccharomyces cerevisiae, may be only five times that of a typical prokaryote (Hartwell, 1974). The relatively small number of genes in these primitive eukaryotes, coupled with the fact that Y ⇄ M dimorphism can be controlled in the laboratory and is a reversible event, makes fungi one of the simplest morphogenetic models of eukaryotes. It is hoped that clues to regulation and control of morphogenesis in mammalian and plant systems will be uncovered through studies on fungi. Second, several fungi that are capable of causing disease in man undergo a morphogenetic change upon invasion of host tissues. Organisms such as Ajellomyces capsulatus (Histoplasma capsulatum), Ajellomyces {Blastomyces) dermatitidis, Paracoccidioides brasiliensis, and Sporothrix schenckii grow as fluffy molds at room temperature on usual media, but predominate as yeasts when in host tissues or when grown in an appropriate medium at 37°C. Candida species, and most notably Candida albicans, usually grow as yeasts on common laboratory media at 24 and 37°C, but grow as a mixture of yeasts and hyphae (hyphae and pseudohyphae) upon tissue invasion in a susceptible animal host. Because a Y⇄M transformation of these important disease-producing agents of man seems to be a criterion for infectivity, an understanding of dimorphic mechanisms may lead to improved methods of controlling diseases by these fungi.