gebhart/patrepeval huggingface dataset:
<sup>19</sup>F Nuclear Magnetic Resonance and Crystallographic Studies of 5-Fluorotryptophan-Labeled Anthrax Protective Antigen and Effects of the Receptor on Stability (2014)

The anthrax protective antigen (PA) is an 83 kDa protein that is one of three protein components of the anthrax toxin, an AB toxin secreted by Bacillus anthracis. PA is capable of undergoing several structural changes, including oligomerization to either a heptameric or octameric structure called the prepore, and at acidic pH a major conformational change to form a membrane-spanning pore. To follow these structural changes at a residue-specific level, we have conducted initial studies in which we have biosynthetically incorporated 5-fluorotryptophan (5-FTrp) into PA, and we have studied the influence of 5-FTrp labeling on the structural stability of PA and on binding to the host receptor capillary morphogenesis protein 2 (CMG2) using (19)F nuclear magnetic resonance (NMR). There are seven tryptophans in PA, but of the four domains in PA, only two contain tryptophans: domain 1 (Trp65, -90, -136, -206, and -226) and domain 2 (Trp346 and -477). Trp346 is of particular interest because of its proximity to the CMG2 binding interface, and because it forms part of the membrane-spanning pore. We show that the (19)F resonance of Trp346 is sensitive to changes in pH, consistent with crystallographic studies, and that receptor binding significantly stabilizes Trp346 to both pH and temperature. In addition, we provide evidence that suggests that resonances from tryptophans distant from the binding interface are also stabilized by the receptor. Our studies highlight the positive impact of receptor binding on protein stability and the use of (19)F NMR in gaining insight into structural changes in a high-molecular weight protein.
Cell wall glycoproteins of Candida albicans as released by different methods (1991)

Different methods of extraction frequently used in other studies were used to release glycoproteins from both intact cells and isolated cell walls of yeast and hyphal forms of Candida albicans. Extracts were obtained from whole cells by treatment (i) with 2-mercaptoethanol (beta ME) at pH 8.6 and 37 C degrees and (ii) with zymolyase after treatment with beta ME. Extracts were obtained from isolated and washed cell walls (i) by boiling with beta ME and sodium dodecyl sulphate (SDS), (ii) by boiling with SDS and (iii) by treatment with zymolyase after SDS. The extracts were separated by SDS-polyacrylamide gel electrophoresis and analysed by Western blotting with four reagents. Analysis with concanavalin A (ConA) revealed different glycoprotein populations depending on the treatment. Three possible germ-tube-specific constituents were observed; and 80 kDa component released by beta ME from both intact cells and cell walls, and 47 kDa and 43 kDa moieties released by zymolyase only from intact cells. MAb 4C12, specific for the protein portion of a large germ tube constituent, recognized polydisperse material which just entered the gel in beta ME extracts and in the region extending up from 200 kDa to near the top of the gel in zymolyase extracts. MAb 24.17, specific for a carbohydrate determinant of yeast phase cells, reacted with disperse material in the region from the top of the gel to one-third to two-thirds the distance to the 220 kDa mass marker. Antiserum specific for the serotype A determinant of mannan reacted with large disperse component(s) migrating in the region from the top of the gel to about two-thirds the distance to the 220 kDa mass marker and with a 180 kDa component. The components recognized by MAb 4C12, but not those recognised by MAb 24.17 and serotype A antiserum, were effected by treatment with endo-beta-N-acetylglucosamidase H. The various analyses revealed that the method of extraction affected the composition and size of the constituents recognized by the reagents.
A simulation based learning meachanism for scheduling systems with continuous control and update structure (2005)

A simulation based learning mechanism is proposed in this study. The system learns in the manufacturing environment by constructing a learning tree and selects a dispatching rule from the tree for each scheduling period. The system utilizes the process control charts to monitor the performance of the learning tree which is automatically updated whenever necessary. Therefore, the system adapts itself for the changes in the manufacturing environment and works well over time. Extensive simulation experiments are conducted for the system parameters such as monitoring (MPL) and scheduling period lengths (SPL) on a job shop problem with objective of minimizing average tardiness. Simulation results show that the performance of the proposed system is considerably better than the simulation-based single-pass and multi-pass scheduling algorithms available in the literature.
Platelet polyphosphates: The nexus of primary and secondary hemostasis (2011)

For decades it has been known that activated platelets promote plasma clotting and that the fibrin forming activity of activated platelets is dependent on blood coagulation factor XII. However, because factor XII deficiency is not associated with any bleeding disorder, platelet-driven factor XII activation was believed to be an in vitro artefact with no importance for coagulation in vivo. Using arterial and venous thrombosis models in factor XII deficient mice we recently demonstrated that factor XII is essential for thrombosis in vivo. However it was not known how factor XII is activated by procoagulant platelets within the growing thrombus. Here, we review our studies of the last 5 years that led to the identification of the endogenous factor XII activator. We found that platelets release polyphosphates, linear inorganic polymers of 60-100 phosphate residues that directly bound to and activated factor XII. Platelet polyphosphates potently initiate fibrin formation via the factor XII-driven intrinsic pathway. Inhibition of factor XII or polyphosphates protected mice from lethal thrombotic disease and strongly reduced clot stability in patients. Our data identify polyphosphates as the endogenous factor XII activator in vivo linking platelet activation (primary hemostasis) and fibrin production (secondary hemostasis). Targeting polyphosphate-mediated factor XII activation offers the exciting possibility for a safe anticoagulation with minimal therapy-associated bleeding.
The Biogenesis of Nascent Circular RNAs (2016)

Steady-state circular RNAs (circRNAs) have been mapped to thousands of genomic loci in mammals. We studied circRNA processing using metabolic tagging of nascent RNAs with 4-thiouridine (4sU). Strikingly, the efficiency of circRNA processing from pre-mRNA is extremely low endogenously. Additional studies revealed that back-splicing outcomes correlate with fast RNA Polymerase II elongation rate and are tightly controlled by cis-elements in vivo. Additionally, prolonged 4sU labeling in cells shows that circRNAs are largely processed post-transcriptionally and that circRNAs are stable. Circular RNAs that are abundant at a steady-state level tend to accumulate. This is particularly true in cells, such as neurons, that have slow division rates. This study uncovers features of circRNA biogenesis by investigating the link between nascent circRNA processing and transcription.
Slot Time Synchronization for TDMA-Based Ad Hoc Networks (2008)

Time synchronization is very important for a Time Division Multiple Access (TDMA) Ad Hoc Network. In this paper, we proposed Slot Time Synchronization protocol to synchronize all the nodes in a TDMA network. We compute the receive time from Absolute Slot Number (ASN) and use linear regression to eliminate the clock drift. We have carried out our method in real ad hoc networks and achieved the tolerable precision and improved network stability.
A versatile low-pressure ozone source (1991)

A low-pressure source for pure ozone has been developed and successfully tested in the growth of oxide superconductor thin films. Ozone is selectively adsorbed on silica gel at a temperature of −77 °C from an O3/O2 gas mixture stream containing 8 wt% O3, produced by a commercial ozone generator. Since only O3 is trapped, no further purification steps are required. Ozone/gel loading factors below 10% (wt/wt) ensure the safe storage of O3 over prolonged periods. Pure O3 is extracted from the silica gel trap, in which the O3 vapor pressure is maintained at around 10 mTorr, by applying a dynamic vacuum. Films of Ba2YCu3O7−δ with Tc above 86 K have been grown in situ by molecular beam epitaxy techniques using this ozone source.
Dynamic recruitment of the adaptor protein LAT: LAT exists in two distinct intracellular pools and controls its own recruitment (2004)

The integral membrane adaptor protein linker for activation of T cells (LAT) couples the T-cell receptor (TCR) with downstream signalling and is essential for T-cell development and activation. Here, we investigate the dynamic distribution of LAT-GFP fusion proteins by time-lapse video imaging of live T lymphocytes interacting with antigen-presenting cells. We show that LAT forms two distinct cellular pools, one at the plasma membrane and one that co-distributes with transferrin-labelled intracellular compartments also containing the TCR/CD3-associated zeta chain. The distribution of LAT between these two pools is dependent on LAT intracytoplasmic residues. Whereas plasma membrane-associated LAT is recruited to immune synapses after a few seconds of cell conjugate formation, the intracellular pool is first polarized and then recruited after a few minutes. We further show that LAT intracytoplasmic amino acid residues, particularly the Tyr136, 175, 195 and 235 residues, are required for its own recruitment to the immune synapse and that a herein-identified juxtamembrane LAT region (amino acids 32-104) is involved in the localization of LAT in intracellular pools and in T-cell signalling. Altogether, our results demonstrate that LAT controls its own recruitment at the immune synapse, where it is required as a scaffold protein for the signalling machinery. The results also suggest that the intracellular pool of LAT might be required for T-cell activation.
A fast algorithm and practical considerations for passive macromodeling of measured/simulated data (2003)

Passive macromodeling of high-speed package and interconnect modules characterized by simulated/measured data has generated immense interest during the recent years. This paper presents a fast algorithm for generating passive macro-models for simulated/measured data, based on linear formulation. New constraints are proposed to quickly generate passive macromodels. Examples are presented to demonstrate the validity and efficiency of the proposed algorithm.
Human Neutrophil Elastase-Mediated Cleavage Sites of MMP-9 and TIMP-1: Implications to Cystic Fibrosis Proteolytic Dysfunction (2010)

Cystic fibrosis (CF) is a lethal genetic disorder characterized by airway remodeling and inflammation, leading to premature death. Recent evidence suggests the importance of protease activity in CF pathogenesis. One prominent protease, matrix metalloprotease (MMP)-9, demonstrates increased activity in CF individuals undergoing acute pulmonary exacerbation. This is thought to be mediated by both direct MMP-9 activation and the degradation of its natural inhibitor, tissue inhibitor of metalloprotease-1 (TIMP-1). To examine if this relationship exists in nonexacerbating CF individuals, we examined protease activity in sputum from these individuals compared with nondisease controls. We demonstrated increased gelatinolytic activity in CF sputum. These samples had elevated human neutrophil elastase (HNE) levels which correlated with an increased MMP-9/TIMP-1 ratio. To determine if HNE could discretely cleave and activate MMP-9, these enzymes were coincubated and two specific cleavage sites, between Valine(38) and Alanine(39), and between Alanine (39) and glutamic acid(40) were observed. These sites corresponded with appropriate molecular weight for the activated MMP-9 isoform in CF sputum. Using N-terminal sequencing of cleavage fragments obtained with TIMP-1 incubation with HNE, we confirmed the TIMP-1 cleavage site for HNE is at Valine(69)-Cysteine(70). We also show for the first time that human neutrophils were capable of degrading TIMP-1 ex vivo and that a 16 kDa TIMP-1 fragment was identified in CF sputum, consistent with the expected cleavage of TIMP-1 by HNE. These results demonstrate increased MMP-9 activity in stable CF lung disease, and the presence of specific protease products in CF sputum highlights that HNE-mediated activity plays a role in this dysregulation.
Introduction to Probability and Statistics (1974)

Introduction to probability and statistics , Introduction to probability and statistics , مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی
Electrochromic Devices For Transmissive And Reflective Light Control (1986)

Fundamental properties of the transmissive electrochromic device are described. The device comprises of a semi-solid electrolyte and a WO3 film sandwiched by a pair of transparent electroconductive sheet glasses. The transmittance of the device can be arbitrarily controlled within the range from 80% to 10%. The response time was found to be greatly depended on the size. The life time for the repetitive operations is more than 105 cycles. Fairly good durability against the outdoor conditions has been clarified. This device is capable of controlling reflectance of mirror when a reflective layer is coated on the either surface of outer glass. Outline of this reflective device is also described. The reflectance of the mirror of the size of 25cm x 6.5cm can be changed from 72% to 20% within 4sec at 1.5VDC. This device is suitable for anti-dazzling mirror of motor cars.
Sex Differences in Longevity and in Responses to Anti-Aging Interventions: A Mini-Review (2015)

A robust, often underappreciated, feature of human biology is that women live longer than men not just in technologically advanced, low-mortality countries such as those in Europe or North America, but across low- and high-mortality countries of the modern world as well as through history. Women's survival advantage is not due to protection from one or a few diseases. Women die at lower rates than men from virtually all the top causes of death with the notable exception of Alzheimer's disease, to which women are particularly prone. Yet, despite this robust survival advantage, women across countries of the world suffer worse health throughout life. The biological mechanisms underlying either longer female survival or poorer female health remain elusive and understudied. Mechanisms of mammalian biology, particularly with respect to aging and disease, are most easily studied in laboratory mice. Although there are no consistent differences in longevity between mouse sexes even within single genotypes, there are often substantial differences in individual studies, sometimes favoring females, other times males. Investigating the environmental causes of this puzzling variation in longevity differences could prove illuminating. Sex differences in response to life-extending genetic or pharmacological interventions appear surprisingly often in mice. Longevity enhancement due to reduced signaling through IGF-1 or mTOR signaling typically favors females, whereas enhancement via a range of pharmacological treatments favors males. These patterns could be due to interactions of the interventions with sex steroids, with adiponectin or leptin levels, or with the sex differences in immune function or the regional distribution of body fat. Clearly, generalizations from one sex cannot be extended to the other, and inclusion of both sexes in biomedical studies of human or other animals is worth the effort and expense.
Biological Dosimetry by Automated Dicentric Scoring in a Simulated Emergency (2013)

Dicentric chromosome analysis remains the most widely used method in biodosimetry. It has a lower detection limit of about 0.1 Gy, and allows one to distinguish between whole- and partial-body exposures. A drawback of the dicentric analysis is that it is a time consuming method and maybe difficult to implement in a mass casualty event. To try to increase the analysis capacity, automatic dicentric scoring (ADS) using image analysis software is being incorporated in several laboratories. Here we present the results obtained in an emergency exercise simulating 50 victims. The ability to distinguish different radiations scenarios is evaluated. To simulate whole-body exposures peripheral blood samples were irradiated at doses between 0-4.7 Gy, and to simulate partial-body exposures irradiated and nonirradiated blood were mixed in different proportions. With the data obtained from the first slide analyzed (with about 300-400 cells), 32 of 34 simulated whole-body exposures were correctly classified according to radiation exposure levels. For simulated partial-body irradiations, it was possible to detect them as partial exposures at the end of the first slide analyzed but only at the highest doses. In all cases the classification was updated every time the analysis of one additional slide was finished. The comparison between our present results and those reported in the literature for manual scoring shows that for triage purposes the ADS based on 300-400 cells is similar in efficiency to classifying the cases based on manual scoring of 50 cells. However, if one accounts for the associated uncertainties and the time needed for ADS, we suggest that ADS triage scoring should be based on about 1,000 cells. For final dose estimations the number of cells to score will depend on the initial estimated dose, and on the information contributed from physical dose-reconstruction or clinical symptoms. At doses higher than 1 Gy, we propose analysis of 1,500 and for lower doses or suspected partial-body exposures, the number of cells to score should be 3,000.
A novel three-layered tablet for extended release with various layer formulations and<i>in vitro</i>release profiles (2011)

A novel three-layered tablet consisting of a water-soluble mid-layer and two barrier layers with swellable polymers was investigated to develop a preferable once-a-day formulation containing terazosin HCl as a hydrophilic model drug. When the tablet was exposed to a release medium, the medium quickly permeated to the mid-layer and the two barrier layers swelled surrounding the mid-layer rapidly. It facilitated the tablet to absorb a lot of water compared with monolithic matrix. Moreover, formation of a lot of pores in the tablet during dissolution could be observed, suggesting significant water absorption in the inner matrix and swollen polymers of the tablet. Barrier layers influenced drug release profiles significantly, potentially due to differences in viscosity after swelling that produce different diffusion coefficients and mechanical strength. The drug in the mid-layer showed the sigmoid type of release pattern because a period of time might be needed to release the drug from the mid-layer through the barrier layers, but the drug in barrier layers showed the typical release pattern of monolithic matrix. As the amount of water-soluble excipient in the mid-layer increased, the degree of swelling also increased, suggesting that its amount in the layer may affect the overall swelling properties of the tablet. It was also shown that more hydrophilic mid-layer caused faster erosion rate, which was related to the results of swelling property. The three-layered tablets showed more consistent release kinetics than the matrix tablets. These results can give good information for the development of sustained drug delivery systems, especially once-a-day administration.
Voltammetric pH measurements with surface-modified electrodes and a voltammetric internal reference (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTVoltammetric pH measurements with surface-modified electrodes and a voltammetric internal referenceIsrael. RubinsteinCite this: Anal. Chem. 1984, 56, 7, 1135–1137Publication Date (Print):June 1, 1984Publication History Published online1 May 2002Published inissue 1 June 1984https://pubs.acs.org/doi/10.1021/ac00271a018https://doi.org/10.1021/ac00271a018research-articleACS PublicationsRequest reuse permissionsArticle Views281Altmetric-Citations47LEARN 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
Effects of Heterogeneity and Wetting on Relative Permeability Using Pore Level Modeling (1997)

Abstract We present a three-dimensional, capillary equilibrium based, pore level network model that computes relative permeability and capillary pressure for drainage and imbibition cycles. The model accounts for wetting layers in crevices of the pore space, cooperative pore filling and different contact angles. Arbitrary distributions of pore size with different spatial correlations are studied. We show that relative permeabilities for unconsolidated media can be represented in the model using spatially uncorrelated distributions of pore size, but that curves typical of consolidated rock can only be explained by allowing spatial correlation in the pore structure. We also study the effects of flow in wetting layers and different types of cooperative pore filling. This represents changes in contact angle from a completely water-wet system to a neutrally-wet rock. Relative permeability can be extremely sensitive to small changes in contact angle. In general, the residual non-wetting phase saturation decreases as the system becomes less strongly water-wet.