gebhart/patrepeval huggingface dataset:
Silicon nanowire based Pirani sensor for vacuum measurements (2012)

Nano-Pirani vacuum gauges based on the physical properties of suspended silicon nanowires have been fabricated and characterized. With a 160 × 260 nm2 rectangular section and a 5.2 μm length, they are 50 times smaller than the smallest silicon based vacuum sensor and they exhibits much lower power consumption. The nano-Pirani constructed are capable of measuring pressures from 50 to 105 Pa. Moreover, their fabrication is compatible with microelectronic and micromachining fabrication techniques making them suitable for in-situ monitoring of micro and nano systems vacuum packaging.
GPCRdb in 2021: integrating GPCR sequence, structure and function (2020)

G protein-coupled receptors (GPCRs) form both the largest family of membrane proteins and drug targets, mediating the action of one-third of medicines. The GPCR database, GPCRdb serves >4 000 researchers every month and offers reference data, analysis of own or literature data, experiment design and dissemination of published datasets. Here, we describe new and updated GPCRdb resources with a particular focus on integration of sequence, structure and function. GPCRdb contains all human non-olfactory GPCRs (and >27 000 orthologs), G-proteins and arrestins. It includes over 2 000 drug and in-trial agents and nearly 200 000 ligands with activity and availability data. GPCRdb annotates all published GPCR structures (updated monthly), which are also offered in a refined version (with re-modeled missing/distorted regions and reverted mutations) and provides structure models of all human non-olfactory receptors in inactive, intermediate and active states. Mutagenesis data in the GPCRdb spans natural genetic variants, GPCR-G protein interfaces, ligand sites and thermostabilising mutations. A new sequence signature tool for identification of functional residue determinants has been added and two data driven tools to design ligand site mutations and constructs for structure determination have been updated extending their coverage of receptors and modifications. The GPCRdb is available at https://gpcrdb.org.
Time-borrowing multi-cycle on-chip interconnects for delay variation tolerance (2006)

Insertion of time-borrowing (TB) flip-flops in multi-cycle repeater-based on-chip interconnects enables significant improvements in mean performance and energy by averaging systematic and random within-die (WID) delay variations across multiple interconnect segments. A statistically-based analytical model is derived to design a TB N-cycle interconnect with optimal delay variation tolerance. The model elucidates the dependency of the transparency window required to achieve data delay averaging on the delay variation mismatch between interconnect segments. Statistical circuit simulations and analyses in a 65nm process technology demonstrate that TB multi-cycle interconnects enable a 4-6% mean maximum clock frequency (FMAX) improvement and a corresponding 10% average energy savings over optimally designed multi-cycle interconnects with conventional master-slave flip-flops. The maximum mean FMAX benefit ranges from 4.0-7.5%, corresponding to approximately a bin-split shift in the FMAX distribution. For 1.41X larger WID delay variations, the maximum mean FMAX gain rises to 5-10%.
Experimental Validations of a Low Boom Aircraft Design (2013)

A two-phase study is described that designs and validates a supersonic airliner feasible for entry into service in the 2018 to 2020 timeframe (NASA N+2 generation). A Mach 1.6 to 1.8 low sonic-boom aircraft configuration is developed that meets aggressive sonic-boom and performance goals. The concept and the tools utilized for its design are validated through a series of wind-tunnel tests at the NASA Ames 9 ft x 7 ft Supersonic Wind Tunnel, NASA Ames 11 ft Transonic Wind Tunnel, and NASA Glenn 8 ft x 6 ft Supersonic Wind Tunnel. Comparisons between CFD and wind-tunnel near-field pressure distributions are made. Sonic-boom test techniques are described and investigated. Results from spatial-averaging show the best agreement with CFD.
Microbial conversion of β‐ionone by immobilized Aspergillus niger in the presence of an organic solvent (1989)

Aspergillus niger JTS191 was capable of the conversion of beta-ionone to a mixture of its derivatives that is utilized to an essential oil of tobacco. The authors attempted this microbial conversion in the presence of an organic solvent to improve its reaction rate. The addition of isooctane accelerated the microbial conversion of beta-ionone. It took three days to complete the reaction whereas without isooctane it took more than six days. The addition of isooctane also improved the resistance of A. niger to the antifungal property of beta-ionone. A. niger pellets were immobilized in hydrophobic polymer, PU-3, and applied for the microbial conversion of beta-ionone. Further improvement of the resistance to the antifungal property of beta-ionone was achieved by immobilization. PU-3 immobilized A. niger was repeatedly used for microbial conversion of beta-ionone in the presence of isooctane for more than 480 hours.
Distinct Interstitial Immune Cell Interactions in Human Kidney Allografts With Antibody-Mediated Rejection. (2014)

The intragraft role of B cells in allograft rejection is controversial. We recently developed a novel cell distance mapping (CDM) technique that utilizes four-color immunofluorescent confocal microscopy and allows automated distance measurements between hundreds of pairs of T follicular helper (Tfh) cells (CD4+/ICOS+) and CD20+ B cells in a rapid and robust manner. When the distance between the nuclei of Tfh and B cells is less than 2 pixels (0.54 μm), these conjugates are presumed to be interacting. Images of human kidney transplant biopsies with T cell-mediated rejection (TCMR) only (n=7, using 59 high power fields) and both TCMR and antibody-mediated rejection (AMR), termed mixed rejection (MR, n=8, using 29 high power fields) were captured at 600X original magnification and converted for image analysis. Focusing on areas of co-localization, Tfh cell densities between groups were similar. However, the Tfh:B cell conjugate rate in biopsies of TCMR and MR was significantly different - 15% versus >80%, respectively (p=<0.0001). Notably, interstitial plasma cell aggregates were often present in MR but not TCMR biopsies. Measuring inter-B cell and inter-T cell distances found no values of less than 2 pixels, consistent with lack of T-T and B-B interactions in both groups. Nested qPCR of laser capture-microdissected ICOS+ Tfh cells (N=40 to 60) from a subset of biopsies with MR versus TCMR revealed an approximately 800-fold and 100-fold increase for bcl6 and IL-21, respectively, compared to normalized normal kidney controls. Both bcl6 and IL-21 are important for Tfh cell differentiation. The average time from transplantation for MR and TCMR biopsies was 52 and 48 months, respectively; however, 3 biopsies in the MR and TCMR groups occurred within 5 months of kidney transplantation. Thus allograft age alone did not account for this difference in Tfh:B cell interaction. In conclusion, a higher frequency of Tfh:B cell interactions in the inflammatory infiltrate of MR biopsies suggests a distinct immunophenotype of rejection from TCMR. Given that type II and type III allograft rejection can be T cell- or antibody-mediated, our data suggests that a subset of type I rejection may include a “B cell and antibody-mediated” process.
Downregulation of microRNA expression in the lungs of rats exposed to cigarette smoke (2008)

Although microRNAs have been investigated extensively in cancer research, little is known regarding their response to noxious agents in apparently healthy tissues. We analyzed the expression of 484 miRNAs in the lungs of rats exposed to environmental cigarette smoke (ECS) for 28 days. ECS down-regulated 126 miRNAs (26.0%) at least 2-fold and 24 miRNAs more than 3-fold. We previously demonstrated that 107 of 4858 genes (2.9%) and 50 of 518 proteins (9.7%) were up-regulated by ECS in the same tissue, which is consistent with the role of microRNAs as negative regulators of gene expression. The most remarkably down-regulated microRNAs belonged to the families of let-7, miR-10, miR-26, miR-30, miR-34, miR-99, miR-122, miR-123, miR-124, miR-125, miR-140, miR-145, miR-146, miR-191, miR-192, miR-219, miR-222, and miR-223, which regulate stress response, apoptosis, proliferation, angiogenesis, and expression of genes. In contrast, miR-294, an inhibitor of transcriptional repressor genes, was up-regulated by ECS. There was a strong parallelism in dysregulation of rodent microRNAs and their human homologues, which are often transcribed from genes localized in fragile sites deleted in lung cancer. Five ECS-down-regulated microRNAs are known to be affected by single nucleotide polymorphisms. Thus, changes in microRNA expression are an early event following exposure to cigarette smoke.
Functional Mapping of Hepatitis C Virus Envelope-Heparan Sulfate Interaction (2005)

Hepatitis C virus (HCV) is a major cause of chronic hepatitis world-wide. Although a detailed analysis of its genomic organization has led to the identification of various genetic elements, knowledge of receptor-mediated viral attachment and entry is still limited. Glycosaminoglycan (GAG) chains on cell surface proteoglycans provide initial docking sites for the binding of viruses to target cells. Recently, we have shown that cellular binding of HCV envelope glycoprotein E2 requires heparan sulfate (HS) (Barth et al. 2003, J. Biol. Chem. 278: 41003). In this study, we aimed to (i) assess the role of E1 for viral envelope-HS interaction, (ii) define the structural requirements of HS-envelope binding and (iii) further determine the functional role of HS for viral binding and entry. Using soluble GAGs and FACS analysis, we demonstrate a HS-dependent binding of E1 to HuH–7 cells. HS-dependent cellular E1 binding was confirmed by surface plasmon resonance analysis demonstrating an interaction of E1 with heparin–a homologue of highly sulfated HS (KD E1: 7.5×10–7 M). Binding of envelope glycoproteins to HuH–7 cells and human hepatocytes was strongly inhibited by fully sulfated heparin, de–2-O- and de–6-O-sulfated heparin but not de-N-sulfated heparin indicating that N-sulfation of cell surface HS plays a crucial role in HCV envelope-target cell interaction. Using HS oligosaccharides in inhibition of E1/E2 binding studies, we demonstrate that a 14 saccharide subunit represents the minimal oligosaccharide required for envelope-HS interaction. Using retroviral HCV pseudotyped particles (HCVpp) as a model for viral binding and entry, we demonstrate that HCVpp binding to HuH–7 cells is strongly inhibited by pre-incubation of HCVpp with heparin, whereas temperature-dependent HCVpp entry is only partially inhibited by heparin. In conclusion, our data indicate that highly sulfated HS represents an important cell surface molecule mediating tissue-specific attachment of the viral envelope to hepatocytes. Envelope-HS interaction is mediated by both E1 and E2 envelope glycoproteins and a specific HS configuration that includes N-sulfate and a minimum of 14 saccharide subunits.
Enhanced activation in the extrastriate body area by goal‐directed actions (2008)

EBA might contribute to understanding others' actions by representing the dynamic aspects of human motions.
Correction to "Achieving the Welch Bound With Difference Sets" (2006)

In the above titled paper (ibid., vol. 51, no. 5, pp. 1900-1907, May 05), changes were made to equations on p. 1905.
Mutational analysis of the HIV-1 auxiliary protein Vif identifies independent domains important for the physical and functional interaction with HIV-1 reverse transcriptase (2009)

The HIV-1 accessory protein Vif plays a dual role: it counteracts the natural restriction factors APOBEC3G and 3F and ensures efficient retrotranscription of the HIV-1 RNA genome. We have previously shown that Vif can act as an auxiliary factor for HIV-1 reverse transcriptase (RT), increasing its rate of association to RNA or DNA templates. Here, by using seven different Vif mutants, we provide in vitro evidences that Vif stimulates HIV-1 RT through direct protein-protein interaction, which is mediated by its C-terminal domain. Physical interaction appears to require the proline-rich region comprised between amino acid (aa) 161 and 164 of Vif, whereas the RT stimulatory activity requires, in addition, the extreme C-terminal region (aa 169-192) of the Vif protein. Neither the RNA interaction domain, nor the Zn(++)-binding domain of Vif are required for its interaction with the viral RT. Pseudotyped HIV-1 lentiviral vectors bearing Vif mutants deleted in the RNA- or RT-binding domains show defects in retrotranscription/integration processes in both permissive and nonpermissive cells. Our results broaden our knowledge on how three important functions of Vif (RNA binding, RT binding and stimulation and Zn(++) binding), are coordinated by different domains.
HTS and Rational Drug Design to Generate a Class of 5‐HT2C‐Selective Ligands for Possible Use in Schizophrenia. (2010)

Treating neurological conditions: Optimization of a previously identified lead 5-HT2C agonist (left) led to the discovery of a highly selective 5-HT2C agonist (right). Importantly, this compound is a 5-HT2B receptor antagonist. Because of its selective 5-HT2C receptor activity, the compound was further evaluated in the phencyclidine model of disrupted prepulse inhibition, and found to exhibit normalizing effects comparable to those shown by the 5-HT2C agonist vabicaserin, a drug currently in phase II clinical studies for schizophrenia.
Evolution of the Toxoglossa Venom Apparatus as Inferred by Molecular Phylogeny of the Terebridae (2008)

Toxoglossate marine gastropods, traditionally assigned to the families Conidae, Terebridae, and Turridae, are one of the most populous animal groups that use venom to capture their prey. These marine animals are generally characterized by a venom apparatus that consists of a muscular venom bulb and a tubular venom gland. The toxoglossan radula, often compared with a hypodermic needle for its use as a conduit to inject toxins into prey, is considered a major anatomical breakthrough that assisted in the successful initial radiation of these animals in the Cretaceous and early Tertiary. The pharmacological success of toxins from cone snails has made this group a star among biochemists and neuroscientists, but very little is known about toxins from the other Toxoglossa, and the phylogeny of these families is largely in doubt. Here we report the first molecular phylogeny for the Terebridae and use the results to infer the evolution of the venom apparatus for this group. Our findings indicate that most of the genera of terebrids are polyphyletic, and one species ("Terebra" (s.l.) jungi) is the sister group to all other terebrids. Molecular analyses combined with mapping of venom apparatus morphology indicate that the Terebridae have lost the venom apparatus at least twice during their evolution. Species in the genera Terebra and Hastula have the typical venom apparatus found in most toxoglossate gastropods, but all other terebrid species do not. For venomous organisms, the dual analysis of molecular phylogeny and toxin function is an instructive combination for unraveling the larger questions of phylogeny and speciation. The results presented here suggest a paradigm shift in the current understanding of terebrid evolution, while presenting a road map for discovering novel terebrid toxins, a largely unexplored resource for biomedical research and potential therapeutic drug development.
Hierarchical Bayesian Modelling of Variability and Uncertainty in Synthetic Action Potential Traces (2016)

There are many sources of uncertainty in the recording and modelling of membrane action potentials (APs) from cardiomyocytes. For example, there are measurement, parameter, and model uncertainties. There is also extrinsic variability between cells, and intrinsic beat-to-beat variability within a single cell. These combined uncertainties and variability make it very difficult to extrapolate predictions from these models, since current AP models have single parameter values and thus produce a single AP trace. We aim to re-parameterise existing AP models to fit experimental data, and to quantify uncertainty associated with ion current densities when measuring and modelling these APs. We then wish to propagate this uncertainty into model predictions, such as ion channel block effected by a pharmaceutical compound. We perform an in silico study using synthetic data generated from different sets of parameters. We then 'forget' these parameter values and re-infer their distributions using hierarchical Markov chain Monte Carlo methods. We find that we can successfully infer the 'correct' distributions for most ion current densities for each AP trace, along with an approximation to the higher-level distribution from which these parameter values were sampled. There is, however, some level of unidentifiability amongst some of the current densities.
<title>Multiscale geometric image processing</title> (2003)

Since their introduction a little more than 10 years ago, wavelets have revolutionized image processing. Wavelet based algorithms define the state-of-the-art for applications including image coding (JPEG2000), restoration, and segmentation. Despite their success, wavelets have significant shortcomings in their treatment of edges. Wavelets do not parsimoniously capture even the simplest geometrical structure in images, and wavelet based processing algorithms often produce images with ringing around the edges. As a first step towards accounting for this structure, we will show how to explicitly capture the geometric regularity of contours in cartoon images using the wedgelet representation and a multiscale geometry model. The wedgelet representation builds up an image out of simple piecewise constant functions with linear discontinuities. We will show how the geometry model, by putting a joint distribution on the orientations of the linear discontinuities, allows us to weigh several factors when choosing the wedgelet representation: the error between the representation and the original image, the parsimony of the representation, and whether the wedgelets in the representation form "natural" geometrical structures. Finally, we will analyze a simple wedgelet coder based on these principles, and show that it has optimal asymptotic performance for simple cartoon images.
Optimum classification in subband coding of images (2002)

This paper investigates the classification technique, applied to subband coding of images, as a way of exploiting the non-stationary nature of image subbands. An algorithm for maximizing the classification gain, is presented. Each subband is optimally classified and the classification map is sent as side information. After optimum rate allocation, the classes are encoded using arithmetic and trellis coded quantization (ACTCQ) system. We compare this approach with other approaches for classification proposed in the literature. We propose a method for reducing the side rate which exploits the dependence between subbands as well as the within band dependence.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Application of Multilayer Testing and Analysis: A Field Case (1986)

ABSTRACT Recently developed well testing and analysis techniques for multilayered reservoirs to estimate individual-layer permeabilities, skin factors, and pressure are discussed with regard to their applications to a two-layered reservoir. The multilayer testing technique consists of a number of sequential flow tests with downhole flow rate and pressure measurements at the top of each layer using the production logging tool. The analysis techniques are based on convolution and the use of nonlinear regression to fit the measured downhole flow rate or pressure data with a layered reservoir model. This paper presents a field example that is used to estimate layer parameters. The results are compared to those from conventional analyses.
Helping Horton Hear His Whos (2019)

ADVERTISEMENT RETURN TO ISSUEEditorialNEXTHelping Horton Hear His WhosMichael J. SailorMichael J. SailorUniversity of California, San Diego, California, United StatesMore by Michael J. Sailorhttp://orcid.org/0000-0002-4809-9826Cite this: ACS Sens. 2019, 4, 2, 265–266Publication Date (Web):February 22, 2019Publication History Received3 February 2019Published online22 February 2019Published inissue 22 February 2019https://pubs.acs.org/doi/10.1021/acssensors.9b00255https://doi.org/10.1021/acssensors.9b00255editorialACS PublicationsCopyright © 2019 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views1264Altmetric-Citations-LEARN 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 PDF (416 KB) Get e-AlertscloseSUBJECTS:Biotechnology,Electrochemical cells,Fluorescence,Molecules,Sensors Get e-Alerts
Cognitive Enhancers (Nootropics). Part 2: Drugs Interacting with Enzymes. Update 2014 (2014)

Scientists working in the field of Alzheimer's disease and, in particular, cognitive enhancers are very productive. The review on Drugs interacting with Enzymes was accepted in August 2012. However, this field is very dynamic. New potential targets for the treatment of Alzheimer's disease were identified. This update describes drugs interacting with 60 enzymes versus 43 enzymes in the first paper. Some compounds progressed in their development, while many others were discontinued. The present review covers the evolution of research in this field through April 2014.