gebhart/patrepeval huggingface dataset:
Binding of agonists, antagonists and inverse agonists to the human δ‐opioid receptor produces distinctly different conformational states distinguishable by plasmon‐waveguide resonance spectroscopy (2002)

Structural changes induced by the binding of agonists, antagonists and inverse agonists to the cloned delta-opioid receptor from human brain immobilized in a solid-supported lipid bilayer were monitored using plasmon-waveguide resonance (PWR) spectroscopy. Agonist (e.g. deltorphin II) binding causes an increase in membrane thickness because of receptor elongation, a mass density increase due to an influx of lipid molecules into the bilayer, and an increase in refractive index anisotropy due to transmembrane helix and fatty acyl chain ordering. In contrast, antagonist (e.g. TIPPpsi) binding produces no measurable change in either membrane thickness or mass density, and a significantly larger increase in refractive index anisotropy, the latter thought to be due to a greater extent of helix and acyl chain ordering within the membrane interior. These results are closely similar to those reported earlier for another agonist (DPDPE) and antagonist (naltrindol) [Salamon et al. (2000) Biophys. J.79, 2463-2474]. In addition, we now find that an inverse agonist (TMT-Tic) produces membrane thickness, mass density and refractive index anisotropy increases which are similar to, but considerably smaller than, those generated by agonists. Thus, a third conformational state is produced by this ligand, different from those formed by agonists and antagonists. These results shed new light on the mechanisms of ligand-induced G-protein-coupled receptor functioning. The potential utilization of this new biophysical method to examine structural changes both parallel and perpendicular to the membrane normal for GPCRs is emphasized.
SIMULATION OF WATER DEMAND FROM SIMANINDO DISTRICT AND REGIONAL WATER SUPPLY COMPANY (PDAM) IN TOBA LAKE (2018)

Water demand is its relentless rise over many years and projections of population growth over coming decades. Water availability is also increasing remains in a catchment area. Human activities gave impact for environmental degradation such as water quality. The volume of Toba lak?se water is getting decline. There is an indication of the decrease of water level from year to year, while the growth of the population living in the water body of Lake Toba has a low increase with an average of almost 3 percent (2009- 2017). It will give impact for water demand. Forest destruction around Lake Toba is bad enough where the forest area is only 15.8% of the catchment area. It leads to unstable lake water level and disrupts the utilization of the lake, especially the stability of water supply for PDAMs and people who take the source water from Lake Toba. The purpose of this study is to analyze and estimate water demand of Toba Lake and estimate the consumer and water demand of PDAMs user. The method calculated growth population and water demand using Super Vector Machine (SVM) and growth population model for next two years. The result of the research is a one-dimensional graph relating to community water demand in Toba and PDAMs user. Findings indicate that in 2020, some villages in Simanindo sub-district will experience a decrease population and some increase in population. It will give impact on the fluctuation of water demand for communities. People are experiencing a decline water deman in some sub-district. PDAMs users will experience an increase in customers and water demand in 2020.
Pericytes Stimulate Oligodendrocyte Progenitor Cell Differentiation during CNS Remyelination (2017)

The role of the neurovascular niche in CNS myelin regeneration is incompletely understood. Here, we show that, upon demyelination, CNS-resident pericytes (PCs) proliferate, and parenchymal non-vessel-associated PC-like cells (PLCs) rapidly develop. During remyelination, mature oligodendrocytes were found in close proximity to PCs. In Pdgfb<sup>ret/ret</sup> mice, which have reduced PC numbers, oligodendrocyte progenitor cell (OPC) differentiation was delayed, although remyelination proceeded to completion. PC-conditioned medium accelerated and enhanced OPC differentiation in vitro and increased the rate of remyelination in an ex vivo cerebellar slice model of demyelination. We identified Lama2 as a PC-derived factor that promotes OPC differentiation. Thus, the functional role of PCs is not restricted to vascular homeostasis but includes the modulation of adult CNS progenitor cells involved in regeneration.
Mitochondrial Proteomic Analysis and Characterization of the Intracellular Mechanisms of Bis(7)-tacrine in Protecting against Glutamate-Induced Excitotoxicity in Primary Cultured Neurons (2007)

Increasing evidence supports that the mitochondrial dysfunction, mainly caused by abnormal changes in mitochondrial proteins, plays a pivotal role in glutamate-induced excitotoxicity, which is closely associated with the pathogenesis of acute and chronic neurodegenerative disorders, such as stroke and Alzheimer's disease. In this study, post-treatment of cerebellar granule neurons with bis(7)-tacrine significantly reversed declines in mitochondrial membrane potential, ATP production, and neuronal cell death induced by glutamate. Moreover, this reversal was independent of NMDA antagonism, acetylcholinesterase inhibition, and cholinergic pathways. Using two-dimensional differential in-gel electrophoresis, we conducted a comparative analysis of mitochondrial protein patterns. In all, 29 proteins exhibiting significant differences in their abundances were identified in the glutamate-treated group when compared with the control. The expression patterns in 22 out of these proteins could be reversed by post-treatment with bis(7)-tacrine. Most of the differentially expressed proteins are involved in energy metabolism, oxidative stress, and apoptosis. In particular, the altered patterns of four of these proteins were further validated by Western blot analysis. Our findings suggest that multiple signaling pathways initiated by the altered mitochondrial proteins may mediate glutamate-induced excitotoxicity and also offer potentially useful intracellular targets for the neuroprotection provided by bis(7)-tacrine.
Functional Gold Nanoparticle-Based Antibacterial Agents for Nosocomial and Antibiotic-Resistant Bacteria (2016)

These results suggested that the proposed antibacterial AuNPs are effective antibacterial agents for Staphylococci, Enterococci and antibiotic-resistant bacterial strains. [Formula: see text].
Distributed control and resource marking using best-effort routers (2001)

We present a method for creating differential QoS where control is in the hands of the end system or user, and the network distributes congestion feedback information to users via packet marking at resources. Current proposals for creating differential QoS in the Internet often rely on classifying packets into a number of classes with routers treating different classes appropriately. The router plays a critical role in guaranteeing performance. In contrast, there is a growing body of work that seeks to place more of the control in the hands of the end system or user, with simple functionality in the router. This is the approach outlined in this tutorial article: using insights from economics and control theory we show how cooperation between end systems and the network can be encouraged using a simple packet marking scheme. The network distributes congestion feedback information to users via packet marking at resources, and users react accordingly to obtain differential QoS.
Correction: Corrigendum: Amino Acid Polymorphisms in Hepatitis C Virus Core Affect Infectious Virus Production and Major Histocompatibility Complex Class I Molecule Expression (2015)

Amino acid (aa) polymorphisms in the hepatitis C virus (HCV) genotype 1b core protein have been reported to be a potent predictor for poor response to interferon (IFN)-based therapy and a risk factor for hepatocarcinogenesis. We investigated the effects of these polymorphisms with genotype 1b/2a chimeric viruses that contained polymorphisms of Arg/Gln at aa 70 and Leu/Met at aa 91. We found that infectious virus production was reduced in cells transfected with chimeric virus RNA that had Gln at aa 70 (aa70Q) compared with RNA with Arg at aa 70 (aa70R). Using flow cytometry analysis, we confirmed that HCV core protein accumulated in aa70Q clone transfected cells, and it caused a reduction in cell-surface expression of major histocompatibility complex (MHC) class I molecules induced by IFN treatment through enhanced protein kinase R phosphorylation. We could not detect any effects due to the polymorphism at aa 91. In conclusion, the polymorphism at aa 70 was associated with efficiency of infectious virus production, and this deteriorated virus production in strains with aa70Q resulted in the intracellular accumulation of HCV proteins and attenuation of MHC class I molecule expression. These observations may explain the strain-associated resistance to IFN-based therapy and hepatocarcinogenesis of HCV.
An innovative transmission mechanism applicable to variable speed wind turbines (2017)

An innovative transmission mechanism, named as independently controllable transmission (ICT), is proposed inthis study. While being applied to the variable speed windturbines, the proposed ICT mechanism can transmit a steady-speed output, which is independently manipulated by acontroller and completely not affected by the fluctuant speed ofthe rotor, to the generator to generate the electric power withconstant frequency.The ICT mechanism is fundamentallycomposed of two sets of planetary gear trains and two sets oftransmission-connecting members. Two prototypes of the ICTmechanisms are assembled to examine their kinematicalcharacteristicsandtodemonstratetheirfeasibilityinengineering applications.
Optimal design of batch‐storage network with recycle streams (2003)

Abstract An effective methodology is reported for determining the optimal capacity (lot size) of batch processing and storage networks which include material recycle or reprocessing streams. It is assumed that any given storage unit can store one material type which can be purchased from suppliers, internally produced, and internally consumed and/or sold to customers. It is further assumed that a storage unit is connected to all processing stages that use or produce the material to which that storage unit is dedicated. Each processing stage transforms a set of feedstock materials or intermediates into a set of products with constant conversion factors. The objective for optimization is to minimize the total cost composed of raw material procurement, setup, and inventory holding costs, as well as the capital costs of processing stages and storage units. A novel production and inventory analysis formulation, the PSW model, provides useful expressions for the upper/lower bounds and average level of the storage inventory holdup. The expressions for the Kuhn‐Tucker conditions of the optimization problem can be reduced to two subproblems. The first yields analytical solutions for determining batch sizes, while the second is a separable concave minimization network flow subproblem whose solution yields the average material flow rates through the networks. For the special case in which the number of storage units is equal to the number of process stages and raw materials storage units, a complete analytical solution for average flow rates can be derived.
Faculty Opinions recommendation of Antitubercular triazines: optimization and intrabacterial metabolism. (2020)

The triazine antitubercular JSF-2019 was of interest due to its in vitro efficacy and the nitro group shared with the clinically relevant delamanid and pretomanid. JSF-2019 undergoes activation requiring F420H2 and one or more nitroreductases in addition to Ddn. An intrabacterial drug metabolism (IBDM) platform was leveraged to demonstrate the system kinetics, evidencing formation of NO⋅ and a des-nitro metabolite. Structure-activity relationship studies focused on improving the solubility and mouse pharmacokinetic profile of JSF-2019 and culminated in JSF-2513, relying on the key introduction of a morpholine. Mechanistic studies with JSF-2019, JSF-2513, and other triazines stressed the significance of achieving potent in vitro efficacy via release of intrabacterial NO⋅ along with inhibition of InhA and, more generally, the FAS-II pathway. This study highlights the importance of probing IBDM and its potential to clarify mechanism of action, which in this case is a combination of NO⋅ release and InhA inhibition.Copyright © 2019 Elsevier Ltd. All rights reserved. PMID: 31711854 Funding information This work was supported by: NIAID NIH HHS, United States Grant ID: U19 AI109713 NIAID NIH HHS, United States Grant ID: R41 AI122434
Rapid freezing of the mouse blastocyst: effects of cryoprotectants and of time and temperature of exposure to cryoprotectant before direct plunging into liquid nitrogen (1991)

This study investigates the effects of time and temperature of exposure to a high concentration (4.5 M) of dimethyl sulfoxide (DMSO), glycerol, 1,2-propanediol (PROH), or a mixture of DMSO and glycerol (DG) in a solution containing 0.25 M sucrose, on the survival and development of rapidly frozen mouse blastocysts. Embryos had significantly (P less than 0.01) higher rates of survival and development when exposed to cryoprotectant at 0 degree C compared with room temperature. The time of exposure to cryoprotectant at either 0 degree C or room temperature before being plunged into liquid nitrogen significantly (P less than 0.01) affected the survival and development of frozen-thawed embryos. Survival and development of blastocysts in vitro and in vivo was significantly (P less than 0.05) higher when exposed at 0 degree C for 10 min to DG, DMSO and glycerol than to PROH. It is concluded that, unlike early-cleavage stage embryos, blastocysts need to be equilibrated at a low temperature (0 degree C) with high concentrations of cryoprotectant before rapid freezing. Exposure of blastocysts to 4.5 M cryoprotectant and 0.25 M sucrose at room temperature either was toxic or else markedly reduced their viability after freezing and thawing, depending on the duration of the initial exposure.
Ordered Mesoporous Materials as Supports for Stable Iron Catalysts in the Fischer–Tropsch Synthesis of Lower Olefins (2016)

Abstract The Fe‐catalyzed Fischer–Tropsch to olefins (FTO) synthesis is a non‐oil‐based route for the production of C 2 –C 4 olefins. The understanding of the interplay between the catalytically active species, promoters, and support materials has improved over the last years, but the nanostructures of the various supports used are often not comparable. Several ordered mesoporous materials with a comparable pore size and pore symmetry are used as model supports for Fe‐based FTO catalysts. Ammonium iron citrate is used as the Fe source for all supports, and Na and S are added as promoters. The formation of catalytically active iron carbide species is suppressed within the strongly interacting mesoporous silica support, but the weakly interacting carbon and silicon carbide supports yield highly active FTO catalysts. Carbon‐supported catalysts show a high selectivity towards lower olefins, low methane production, and stable operation for up to 140 h under industrially relevant FTO conditions.
Unusual 1,4-Addition of 2-Pyridyl Carboxylates to Benzynes:  A Convenient Route to 1-(2-Acylphenyl)-2-pyridones (2001)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTUnusual 1,4-Addition of 2-Pyridyl Carboxylates to Benzynes: A Convenient Route to 1-(2-Acylphenyl)-2-pyridonesDinesh Kumar Rayabarapu, Kanak Kanti Majumdar, Thota Sambaiah, and Chien-Hong ChengView Author Information Department of Chemistry, Tsing Hua University, Hsinchu, Taiwan 300 [email protected]Cite this: J. Org. Chem. 2001, 66, 10, 3646–3649Publication Date (Web):April 26, 2001Publication History Received9 February 2001Published online26 April 2001Published inissue 1 May 2001https://pubs.acs.org/doi/10.1021/jo010162thttps://doi.org/10.1021/jo010162tbrief-reportACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views1234Altmetric-Citations27LEARN 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 SUBJECTS:Addition reactions,Aromatic compounds,Inorganic carbon compounds,Ketones,Organic compounds Get e-Alerts
Gels from Husk Proteins (2008)

Fibroin, which is the structural component of the silk, is renowned for its use in the field of biomedical engineering. However, it has been reported to be allergic in some patients. Hence, a hypoallergenic alternative is required to be explored. Here, we examine the chemical properties of possible analogs of silk from rice and compare these properties to the previous studies using bioinformatics tools. The new data significantly add to the foundation for examining the relation between sequences, predicted structures and the observed chemical properties, thereby outlining the potential applications.
Supplementary Methods and Materials from Integration of Genotypic and Phenotypic Screening Reveals Molecular Mediators of Melanoma–Stromal Interaction (2023)

Supplementary Methods and Materials from Integration of Genotypic and Phenotypic Screening Reveals Molecular Mediators of Melanoma–Stromal Interaction
Genome-Wide Identification of Genes Regulated by the Rcs Phosphorelay System in <i>Erwinia amylovora</i> (2011)

The exopolysaccharide amylovoran is one of the major pathogenicity factors in Erwinia amylovora, the causal agent of fire blight of apples and pears. We have previously demonstrated that the RcsBCD phosphorelay system is essential for virulence by controlling amylovoran biosynthesis. We have also found that the hybrid sensor kinase RcsC differentially regulates amylovoran production in vitro and in vivo. To further understand how the Rcs system regulates E. amylovora virulence gene expression, we conducted genome-wide microarray analyses to determine the regulons of RcsB and RcsC in liquid medium and on immature pear fruit. Array analyses identified a total of 648 genes differentially regulated by RcsCB in vitro and in vivo. Consistent with our previous findings, RcsB acts as a positive regulator in both conditions, while RcsC positively controls expression of amylovoran biosynthetic genes in vivo but negatively controls expression in vitro. Besides amylovoran biosynthesis and regulatory genes, cell-wall and cell-envelope (membrane) as well as regulatory genes were identified as the major components of the RcsBC regulon, including many novel genes. We have also demonstrated that transcripts of rcsA, rcsC, and rcsD genes but not the rcsB gene were up-regulated when bacterial cells were grown in minimal medium or following infection of pear fruits compared with those grown in Luria Bertani medium. Furthermore, using the genome of E. amylovora ATCC 49946, a hidden Markov model predicted 60 genes with a candidate RcsB binding site in the intergenic region, 28 of which were identified in the microarray assay. Based on these findings as well as previous reported data, a working model has been proposed to illustrate how the Rcs phosphorelay system regulates virulence gene expression in E. amylovora.
A Reconfigurable FACTS System for University Laboratories (2004)

To fully understand the dynamic performance of the multiple flexible ac transmission systems (FACTS) devices, a hardware setup is needed to complement software simulation for university research laboratories. This paper presents the schematic and basic controls of a reconfigurable FACTS system that can be used to realize the major voltage-sourced-converter FACTS topologies: the StatCom, the static synchronous series compensator (SSSC), and the unified power-flow controller (UPFC). Furthermore, the state models and control algorithms for the FACTS devices are proposed. The digital signal processor (DSP)-based control system enables new control methods to be rapidly implemented. The comparison of the experimental and simulation results is also provided to verify the proposed controls. The paper culminates in a list of suggested experiments appropriate for an elective/graduate course in electric power systems.
Tapered slot waveguide antenna for Ku-band phased array applications (2015)

The design of a rectangular WR62 waveguide fed finline (tapered slot) antenna is presented. The antenna utilizes a tapered E-plane ridge within the rectangular waveguide to provide a smooth matched transition. This type of antenna is targeted for high power phased array applications where dielectric materials are prohibitive. Simulation shows wideband characteristics from covering the full WR62 bandwidth. The antenna is comprised of an all aluminum construction. This type of antenna is advantageous for millimeter-wave antenna arrays where simple feed structures are preferred.
Measurement and Analysis of Deformation Behavior of Polyethylene Tube Subjected to Linear Loading and Unloading Stress Paths with Large Strain (2022)

A material testing apparatus for measuring the biaxial deformation behavior of a polymer tube has been developed to quantitatively evaluate the deformation behavior of polymeric materials. The testing apparatus can apply axial force and internal pressure to a tubular specimen. A noncontact strain measurement system was also developed, and the biaxial strain components and the radius of curvature in the axial direction of the bulging specimen are continuously measured to control the stress path applied to the specimen. Polyethylene tube with an outer diameter of 17 mm and a thickness of 2 mm are used as a test sample. The tubular specimens were subjected to linear stress paths with stress ratios of σ Φ : σ θ =1:0, 4:1, 2:1, 4:3, 1:1, 3:4, 1:2, 1:4, and 0:1, where σ Φ and σ θ are the axial and circumferential stress components, respectively, applied to the central area of the bulging specimen. Loading and unloading tests were performed to determine the biaxial true stress-logarithmic plastic strain curves. The strain rate was 1×10 -3 s -1 . From these test results, contours of plastic work and the directions of the plastic strain rates were measured to identify a proper material model for the test sample using the Yld2000-2d yield function (Barlat et al., 2003).