gebhart/patrepeval huggingface dataset:
Identification of a novel protein D3UPCA from <b><i>Halobacterium salinarum</i></b> and prediction of its function (2004)

Halobacterium salinarum is an extremely halophilic archaea, which is able to live in highly saline environments. In a recent study, several halophilic archaea were found to have the ability to biodegrade organic hydrocarbon pollutants, but protein information regarding hydrocarbon degradation and tolerance in halophilic archaea has been relatively rare. In this study, the protein expression profile of H. salinarum cultured under different diesel concentrations (0, 2 and 4%) was investigated by two-dimensional gel electrophoresis. Proteins which increased their expression levels in diesel media were identified using matrix-assisted laser desorption/ionization-time of flight and electrospray ionization-tandem mass spectrometry analysis. Among these, a protein spot (named D3UPCA) which was up-regulated about nine-fold and found to have COG3388, an uncharacterized protein conserved in archaea, was selected in order to further characterize its functions. The D3UPCA coding gene (named d3upca) was cloned and expressed in Escherichia coli, and purified by the glutathione-S-transferase-fusion method. The function of the protein was estimated using various bioinformatics tools and was predicted to be related to the regulation of transcription and/or translation of genes needed to tolerate stresses associated within the presence of diesel oil.
Overexpression of protease‐activated receptors‐1,‐2, and‐4 (PAR‐1, ‐2, and ‐4) in prostate cancer (2007)

PARs are overexpressed in prostate cancer and may serve as potential predictors of recurrence. The data suggest potential role of PARs in autocrine and paracrine mechanisms of prostate cancer.
Reduction of Vinyl Chloride in Metallic Iron−Water Systems (1999)

Batch experiments examining the kinetics and mechanism of vinyl chloride (VC) reduction by metallic iron in aqueous systems were performed. The effects of various iron loadings, VC concentrations, pH conditions, temperatures, and Fe(II)/Fe(III) chelating agents (1,10-phenanthroline, 2,2‘-dipyridyl, and nitrilotriacetic acid) on reduction kinetics were examined. Ethylene was the major carbon-containing product of VC reduction under all conditions examined, indicating hydrogenolysis. The reaction was pseudo-first-order with respect to aqueous VC concentration. The amount of VC adsorption on iron surfaces was estimated from the rapid initial loss of VC from solution, and the resultant sorption isotherm was linear over the concentration range examined. The first-order kinetics and the linear sorption for VC suggest that the portion of VC sorption to surface reactive sites relative to nonreactive sorption sites is constant, unlike the behavior observed for the higher chlorinated ethenes. The activation energy of the reaction was measured to be 41.6 ± 2.0 kJ/mol, sufficiently large to indicate that the chemical reaction at the surface, rather than aqueous phase diffusion to the surface, controls the overall rate of the reaction. Experiments with the chelating agents suggest that the effect of available Fe(II) on VC reduction is not significant.
Effects of phosphorus on stress of multi-stacked polysilicon film and single crystalline silicon (1999)

In multi-stacked polysilicon films, the stress was examined in terms of dopant distribution and the polysilicon/polysilicon interface at which phosphorus and oxygen atoms were piled up. The phosphorus dopant introduced the compressive stress in the films. The thin oxidized layer formed at the interface was an important factor governing the stress gradient in the multi-stacked film. This interface effect could be minimized using symmetrical stacking of polysilicon films and resulted in a low stress gradient of -0.15 MPa µm-1 for a 5.3 µm thick polysilicon layer. In single crystalline silicon, the phosphorus dopant induced the tensile stress. The lattice dilation coefficient of 4.5 × 10-24 cm3 for phosphorus was measured using a high-resolution x-ray rocking curve. A stress model was introduced on the basis of the lattice dilation theory to calculate the stress and stress gradient induced by the dopant.
Head and Neck Arteriovenous Malformations: Results of Ethanol Sclerotherapy (2012)

Ethanol sclerotherapy has potential for complete eradication of head and neck AVM with low recurrence within the first year after completion of treatment. Complete eradication may require several treatment sessions during which complications should be minimized with careful techniques.
Bivalent β-Carbolines as Potential Multitarget Anti-Alzheimer Agents (2010)

Alzheimer's disease (AD) is a prevalent neurodegenerative disorder with multifactorial causes that requires multitargeted treatment. Inhibitors of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) improve cholinergic signaling in the central nervous system and thus AChE inhibitors are well established in the therapy of AD to improve memory disturbances and other cognitive symptoms. On the other hand, AD patients benefit from reduction of pathologic glutamate-induced, Ca(2+)-mediated excitotoxicity by the N-methyl-d-aspartate receptor (NR) antagonist memantine. New drugs that simultaneously affect both cholinergic transmission and glutamate-induced excitotoxicity may further improve AD treatment. While connecting beta-carboline units by alkylene spacers in two different series of compounds and subsequent evaluation of their AChE/BChE-inhibitory potential, we found that several of these bivalent beta-carbolines were potent NR blockers. The most promising compound was a N(9)-homobivalent beta-carboline with a nonylene spacer, which displayed IC(50) values of 0.5 nM for AChE, 5.7 nM for BChE, and 1.4 microM for NR, respectively.
Computer-Aided Design (CAD) of Synzymes:  Use of Molecular Mechanics (MM) for the Rational Design of Superoxide Dismutase Mimics (1999)

Mn(II) complexes of C-substituted macrocyclic 1,4,7,10,13-pentaazacyclopentadecane ligands have been shown to be excellent functional mimics (Synzymes) of the native enzyme manganese superoxide dismutase (Mn SOD). To better understand the profound effects that substituents exert on the SOD catalytic activity, we have utilized molecular mechanics (MM) calculations employing the CAChe system. Such a conformational analysis has made it possible to develop a consistent model that correlates catalytic rate with the ability of the ligand to adopt a folded geometry about the high-spin d(5) spherically symmetrical Mn(II) ion, thus affording a six-coordinate pseudo-octahedral geometry (the geometry required by Mn(III)). This conformational analysis is consistent with the model that one of the nitrogen donors of the pentaaza crown ligand folds to occupy a pseudo-axial coordination position of an octahedron. The DeltaE between the lowest energy folded ligand structure about Mn(II) and its corresponding Mn(III) structure correlates with catalytic activity; i.e., for a large series of complexes an excellent correlation is obtained for both the inner-sphere and outer-sphere rate constants for oxidation of Mn(II)-the rate-determining step in the catalytic cycle for these SOD mimics. From single-crystal X-ray structure determinations on several different members of this class of 7-coordinate dichloro(pentaaza crown) Mn(II) complexes, we have observed that the arrangement of NH's of the secondary amine donors is such that they alternate in their relative orientation to the plane generated by the five nitrogens and the Mn; i.e., the NH's are arranged in an up-down-up-down-up stereochemistry. Thus, one side of the plane of the macrocyclic ring possesses two nonadjacent NH's, while the opposite side has three NH's. Two unique folding motifs generated from MM calculations are found to correlate with the two pathways for Mn(II) oxidation: (1) the inner-sphere path correlates with an NH from the side of the two NH's folding into the axial octahedral coordination site, and (2) the outer-sphere path correlates with an NH from the side of the three NH's folded into an axial O(h) site. MM calculations allow one to probe the effect that substituents on the macrocyclic ring carbons have on the relative energies of the Mn(II) and Mn(III) complexes with these ligands in the various potential folded geometries. The details of this modeling paradigm and the results of MM calculations utilizing the folding motif for a large number complexes are described. Of particular significance is the ability of the MM tool to predict correctly that certain substituent patterns and substituents enhance or reduce the contribution of one or the other pathway to the overall catalytic rate. The syntheses of several new complexes are reported and the rate constants for the two pathways of Mn(II) oxidation have been measured and found to correlate with the predictions arising from the energetics of folding as calculated by MM calculations.
YAP/TAZ initiate and maintain Schwann cell myelination (2017)

Nuclear exclusion of the transcriptional regulators and potent oncoproteins, YAP/TAZ, is considered necessary for adult tissue homeostasis. Here we show that nuclear YAP/TAZ are essential regulators of peripheral nerve development and myelin maintenance. To proliferate, developing Schwann cells (SCs) require YAP/TAZ to enter S-phase and, without them, fail to generate sufficient SCs for timely axon sorting. To differentiate, SCs require YAP/TAZ to upregulate Krox20 and, without them, completely fail to myelinate, resulting in severe peripheral neuropathy. Remarkably, in adulthood, nuclear YAP/TAZ are selectively expressed by myelinating SCs, and conditional ablation results in severe peripheral demyelination and mouse death. YAP/TAZ regulate both developmental and adult myelination by driving TEAD1 to activate Krox20. Therefore, YAP/TAZ are crucial for SCs to myelinate developing nerve and to maintain myelinated nerve in adulthood. Our study also provides a new insight into the role of nuclear YAP/TAZ in homeostatic maintenance of an adult tissue.
Embryonic epithelial membrane transporters (2000)

Embryonic epithelial membrane transporters are organized into transporter families that are functional in several epithelial organs, namely, in kidney, lung, pancreas, intestine, and salivary gland. Family members (subtypes) are developmentally expressed in plasma membranes in temporospatial patterns that are 1) similar for one subtype within different organs, like aquaporin-1 (AQP1) in lung and kidney; 2) different between subtypes within the same organ, like the amiloride-sensitive epithelial sodium channel (ENaC) in lung; and 3) apparently matched among members of different transporter families, as alpha-ENaC with AQP1 and -4 in lung and with AQP2 in kidney. Finally, comparison of temporal expression patterns in early embryonic development of transporters from different families [e.g., cystic fibrosis transmembrane conductance regulator (CFTR), ENaC, and outer medullary potassium channel] suggests regulatory activating or inactivating interactions in defined morphogenic periods. This review focuses on embryonic patterns, at the mRNA and immunoprotein level, of the following transporter entities expressed in epithelial cell plasma membranes: ENaC; the chloride transporters CFTR, ClC-2, bumetanide-sensitive Na-K-Cl cotransporter, Cl/OH, and Cl/HCO(3); the sodium glucose transporter-glucose transporter; the sodium/hydrogen exchanger; the sodium-phosphate cotransporter; the ATPases; and AQP. The purpose of this article is to relate temporal and spatial expression patterns in embryonic and in early postnatal epithelia to developmental changes in organ structure and function.
An interline transfer CCD for a single sensor 2/3" color camera (1980)

A 492(V) × 400(H) interline transfer CCD imager was designed and fabricated for a single sensor 2/3" color camera use. One unit cell consists of a PN junction photodiode, a buried channel vertical CCD and an overflow drain. In spite of the complicated structure having various functional parts packed in a small area, a high aperture ratio of 35% is still maintained. This was realized by designing the vertical CCD as small as possible, taking the narrow channel effect into consideration. The vertical CCD is driven by four phase clocked pulses during signal charge transfer and by single phase clocked pulses during the blanking period to sweep out leakage photo-carriers for anti-smearing. Other features employed in this device are double poly-Si electrode structures, assuring better production yields, and P/N epitaxial wafers, reducing color signal mixture and blooming effects. Color pictures are obtained by a special hybrid color filter, in which blue parts are made of a dichroic filter giving a good sensitivity and a high reliability.
Gut microbiota and probiotics in colon tumorigenesis (2020)

The human gastrointestinal tract harbors a complex and abundant microbial community reaching as high as 1013–1014 microorganisms in the colon. This endogenous microbiota forms a symbiotic relationship with their eukaryotic host and this close partnership helps maintain homeostasis by performing essential and non-redundant tasks (e.g. nutrition/energy and, immune system balance, pathogen exclusion). Although this relationship is essential and beneficial to the host, various events (e.g. infection, diet, stress, inflammation) may impact microbial composition, leading to the formation of a dysbiotic microbiota, further impacting on health and disease states. For example, Crohn’s disease and ulcerative colitis, collectively termed inflammatory bowel diseases (IBD), have been associated with the establishment of a dysbiotic microbiota. In addition, extra-intestinal disorders such as obesity and metabolic syndrome are also associated with the development of a dysbiotic microbiota. Consequently, there is an increasing interest in harnessing the power of the microbiome and modulating its composition as a means to alleviate intestinal pathologies/disorders and maintain health status. In this review we will discuss the emerging relationship between the microbiota and development of colorectal cancer as well as present evidence that microbial manipulation (probiotic, prebiotic) impacts disease development.
Resistance of the medicinal plant Jiwhang (Rehmannia glutinosa) on paraquat (1992)

Response of medicinal plants(58 species in 28 families) cultivated or naturally grown in Korea on paraquat (1,1'-dimethyl-4,4'-bipyridinium ion) was determined. All the plants, except for Jiwhang(Rehmannia glutinosa Liboch.) were killed by paraquat at 0. 8kg . Jiwhang showed a great resistance to paraquat. The phytotoxic effect did not occur in Jiwhang with paraquat applied at 3.2kg . Only 10% growth inhibition of Jiwhang was obtained at 4.8kg . Normal growth of Jiwhang also occurred when at 0.8kg of paraquat different application dates from 2 leaf stage(LS) to 8 LS and/or five-repeated applications at 20-day intervals starting from 3 LS were employed. However, Jiwhang was completely killed by glyphosate[N-(phosphonomethyl) glycine], 2,4-D[2,4-dichlorophenoxy) acetic acid], and dicamba[3,6-dichloro-2-methoxy benzoic acid]+2, 4-D at the respective recommended rates.
Peptide models for membrane channels (1996)

Peptides may be synthesized with sequences corresponding to putative transmembrane domains and/or pore-lining regions that are deduced from the primary structures of ion channel proteins. These can then be incorporated into lipid bilayer membranes for structural and functional studies. In addition to the ability to invoke ion channel activity, critical issues are the secondary structures adopted and the mode of assembly of these short transmembrane peptides in the reconstituted systems. The present review concentrates on results obtained with peptides from ligand-gated and voltage-gated ion channels, as well as proton-conducting channels. These are considered within the context of current molecular models and the limited data available on the structure of native ion channels and natural channel-forming peptides.
Systematic Review: Cardiac Resynchronization in Patients with Symptomatic Heart Failure (2004)

In selected patients with heart failure, cardiac resynchronization therapy improves functional and hemodynamic status, reduces heart failure hospitalizations, and reduces all-cause mortality.
Metabolic engineering of cyanobacteria for the production of hydrogen from water (2013)

Requirements concerning the construction of a minimal photosynthetic design cell with direct coupling of water-splitting photosynthesis and H2 production are discussed in the present paper. Starting from a cyanobacterial model cell, Synechocystis PCC 6803, potentials and possible limitations are outlined and realization strategies are presented. In extension, the limits of efficiency of all major biological components can be approached in a semi-artificial system consisting of two electrochemically coupled half-cells without the physiological constraints of a living cell.
Application of preceramic polymers in powder metallurgy: their use as low-loss binders and for the in situ formation of dispersed ceramic phases in the metal matrix (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTApplication of preceramic polymers in powder metallurgy: their use as low-loss binders and for the in situ formation of dispersed ceramic phases in the metal matrixDietmar Seyferth and Pawel CzubarowCite this: Chem. Mater. 1994, 6, 1, 10–12Publication Date (Print):January 1, 1994Publication History Published online1 May 2002Published inissue 1 January 1994https://pubs.acs.org/doi/10.1021/cm00037a003https://doi.org/10.1021/cm00037a003research-articleACS PublicationsRequest reuse permissionsArticle Views250Altmetric-Citations20LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Enzyme replacement therapy from birth in a feline model of mucopolysaccharidosis type VI. (1997)

We report evidence of a dose responsive effect of enzyme replacement therapy in mucopolysaccharidosis type VI cats from birth, at the clinical, biochemical, and histopathological level. Cats treated with weekly, intravenous recombinant human N-acetylgalactosamine-4-sulfatase at 1 and 5 mg/kg, were heavier, more flexible, had greatly reduced or no spinal cord compression, and had almost normal urinary glycosaminoglycan levels. There was near normalization or complete reversal of lysosomal storage in heart valve, aorta, skin, dura, liver, and brain perivascular cells. No reduction in lysosomal vacuolation was observed in cartilage or cornea; however, articular cartilage was thinner and external ear pinnae were larger in some treated cats. Degenerative joint changes were not obviously delayed in treated cats. Skeletal pathology was reduced, with more normalized bone dimensions and with more uniform bone density and trabecular pattern clearly visible on radiographs by 5 to 6 mo; however, differences between 1 and 5 mg/kg dose rates were not clearly distinguishable. At a dose of 0.2 mg/kg, disease was not significantly altered in the majority of parameters examined. Lysosomal storage was present in all tissues examined in the midterm mucopolysaccharidosis type VI fetus and increased rapidly in extent and severity from birth.
A Prehistory of the Mangaian Chiefdom (2010)

This essay examines the history of the Mangaian polity drawing on the fields of archaeology and indigenous history. Both disciplines are concerned with explaining the past, but they operate at different scales, and their methods, sources and forms of representation are different. We argue that the strength of a multi-disciplinary approach to understanding Mangaia's history lies in recognising disciplinary differences rather than cross-checking one against the other, or using the paradigms of one to interpret the other. When read together the two discourses provide a more nuanced, multi-layered representation of Mangaia's political history than either does on its own.
Deep Generative Learning via Variational Gradient Flow (2019)

We propose a general framework to learn deep generative models via \textbf{V}ariational \textbf{Gr}adient Fl\textbf{ow} (VGrow) on probability spaces. The evolving distribution that asymptotically converges to the target distribution is governed by a vector field, which is the negative gradient of the first variation of the $f$-divergence between them. We prove that the evolving distribution coincides with the pushforward distribution through the infinitesimal time composition of residual maps that are perturbations of the identity map along the vector field. The vector field depends on the density ratio of the pushforward distribution and the target distribution, which can be consistently learned from a binary classification problem. Connections of our proposed VGrow method with other popular methods, such as VAE, GAN and flow-based methods, have been established in this framework, gaining new insights of deep generative learning. We also evaluated several commonly used divergences, including Kullback-Leibler, Jensen-Shannon, Jeffrey divergences as well as our newly discovered `logD' divergence which serves as the objective function of the logD-trick GAN. Experimental results on benchmark datasets demonstrate that VGrow can generate high-fidelity images in a stable and efficient manner, achieving competitive performance with state-of-the-art GANs.
A Generalized Predictive Control for Management of an Intelligent Well's Downhole, Interval Control Valves—Design and Practical Implementation (2009)

Abstract This paper presents an advanced control method for online regulation of downhole Interval Control Valves (ICVs) to achieve optimal production via choke performance management. A Generalized Predictive Controller (GPC) has been shown to be capable of automatically controlling the area open to flow of multiple ICVs to achieve a specified production rate. A black box model was established using real-time, downhole, instrument data as a predictive model for the controller. The model parameters were updated in real-time using the Decay Recursive Least Squares (DRLS) method. A case study in which a multi-zone horizontal intelligent well was located in complex reservoir showed that the GPC operation is highly effective. The robustness of the technique was illustrated by its ability to operate effectively in the complex reservoir environment when the signal is perturbed by outliers or by random noise levels up to the control error limits. The value of these control error limits must be increased as the step size of each valve operation becomes larger.