gebhart/patrepeval huggingface dataset:
Application of molecular dynamics simulations in molecular property prediction II: Diffusion coefficient (2011)

In this work, we have evaluated how well the general assisted model building with energy refinement (AMBER) force field performs in studying the dynamic properties of liquids. Diffusion coefficients (D) have been predicted for 17 solvents, five organic compounds in aqueous solutions, four proteins in aqueous solutions, and nine organic compounds in nonaqueous solutions. An efficient sampling strategy has been proposed and tested in the calculation of the diffusion coefficients of solutes in solutions. There are two major findings of this study. First of all, the diffusion coefficients of organic solutes in aqueous solution can be well predicted: the average unsigned errors and the root mean square errors are 0.137 and 0.171 × 10(-5) cm(-2) s(-1), respectively. Second, although the absolute values of D cannot be predicted, good correlations have been achieved for eight organic solvents with experimental data (R(2) = 0.784), four proteins in aqueous solutions (R(2) = 0.996), and nine organic compounds in nonaqueous solutions (R(2) = 0.834). The temperature dependent behaviors of three solvents, namely, TIP3P water, dimethyl sulfoxide, and cyclohexane have been studied. The major molecular dynamics (MD) settings, such as the sizes of simulation boxes and with/without wrapping the coordinates of MD snapshots into the primary simulation boxes have been explored. We have concluded that our sampling strategy that averaging the mean square displacement collected in multiple short-MD simulations is efficient in predicting diffusion coefficients of solutes at infinite dilution.
Depth map-based human activity tracking and recognition using body joints features and Self-Organized Map (2014)

In this paper, we implement human activity tracking and recognition system utilizing body joints features using depth maps. During HAR settings, depth maps are processed to track human silhouettes by considering temporal continuity constraints of human motion information and compute centroids for each activity based on contour generation. In body joints features, depth silhouettes are computed first through geodesic distance to identify anatomical landmarks which produce joint points information from specific body parts. Then, body joints are processed to produce centroid distance features and key joints distance features. Finally, Self-Organized Map (SOM) is employed to train and recognize different human activities from the features. Experimental results show that body joints features achieved high recognition rate over the conventional features. The proposed system should be applicable as e-healthcare systems for monitoring elderly people, surveillance systems for observing pedestrian traffic areas and indoor environment systems which recognize activities of multiple users.
Mechanisms of Nuclear Signalling by Vitamin D3. Interplay with Retinoid and Thyroid Hormone Signalling (1995)

Hormones that act through nuclear receptors contribute to vertebrate development and homeostasis by serving as biological signals to control cellular growth and differentiation. Their response pathways must meet two requirements, which can be contradictory: they must be highly specific for a given signal, but at the same time they have to be flexible, allowing different responses under different physiological conditions. The current model for nuclear signalling of vitamin D3 (calcitriol), thyroid hormone and retinoic acid seems to be too simple to solve the specificity puzzle. Therefore, an advanced model is proposed that combines recent findings on the structure of hormone response elements, the promiscuous dimerization of the receptors for vitamin D3, thyroid hormone and retinoids and the heterodimer polarity. Special attention is taken on the mechanism of vitamin D3 signalling, where at least 14 different pathways are differentiated.
Eigenmode Analysis of a Two Element Segmented Capped Monopole Antenna (2009)

The behavior of a two element segmented capped monopole antenna is described in terms of three natural resonances of the antenna structure. A numerical eigenmode solver is used to derive the resonant frequency and <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Q</i> -factor of the natural resonances, as well as the impedance properties of these modes when excited individually. The impedance of the antenna is described as a lumped element network, where the component values of the network are determined from the impedance parameters of the resonant modes and the static properties of the antenna structure. The model is applied to predict the behavior of the antenna when a lumped element inductor is used to connect the two segments. The inductor tunes the properties of one of the three resonances, enabling the impedance bandwidth to be optimized. The analysis is then extended to predict the behavior of the antenna when the two vertical elements have different radii, a configuration that enables wide bandwidth operation without the use of an inductor. The modal analysis accurately predicts the impedance and far-field properties of the antennas. Analyzing the antenna in terms of its natural resonant modes provides physical insights into both its behavior and the fundamental limitations of its performance.
Analysis and evaluation of the TCP/IP protocol stack of LINUX (2002)

With the rapid progress of high-speed network technology, the communication speed between hosts will reach Gbit/s. So it is important to investigate the traditional TCP/IP protocol stack to find out whether it is suitable for high-speed communication and can provide QoS or not. Based on this consideration, the LINUX TCP/IP stack's structure, the buffer management, the procedures for sending and receiving data, and the interaction with the OS are analyzed in this paper. A probing node method is proposed to investigate the internal structure of the stack. With this method, the throughput of the stack, the time consuming of each layer and the queuing of the IP layer at high speed are tested. Our experiments show that the throughput of the TCP/IP stack of LINUX can reach 360 Mbit/s at the sending side and 150 Mbit/s when the local host device is used for bi-directional operation, the protocol stack can he improved to support higher speed; the percentages of the various costs of the TCP/IP protocol suite have changed greatly, zero-copy and zero-scan techniques cannot improve the performance dramatically; there is no queuing at the receiving side of the IP layer, so FCFS (first come first served scheduler) is enough, but a more sophisticated packet scheduler such as WFQ (weighted fair queuing) is needed at the sending layer of the IP layer to provide QoS in the future.
Factors That Influence the Activity of 2,4-Dihydroxy-7-methoxy-2<i>H</i>-1,4-benzoxazin-3(4<i>H</i>)-one on <i>Erwinia</i> Species in Growth Assays (1978)

Factors affecting the inhibitory activity of 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one (DIMBOA) against Erwinia carotovora, a nonpathogen of Zea mays L., and against a maize pathovar of Erwinia chrysanthemi (ECZ) were examined. Most experiments were performed with DIMBOA dissolved in a bacterial growth medium containing 10 g/liter of sucrose, inorganic salts, and 1 g/liter of casamino acids at pH 6.75. When temperature and pH were held constant, inhibition of E. carotovora varied linearly with the logarithm of the initial cell population. By altering temperatures, assays with constant pH and initial cell populations were performed under conditions of varying DIMBOA stability. When E. carotovora was grown at 24, 28, 32, and 36 C in the presence of 0.1 to 0.5 mm DIMBOA, the inhibition of bacterial growth was maintained long after DIMBOA had decomposed in the medium to levels which, if added initially, would not have been inhibitory. When assays were performed at pH 5.5, the pH of aqueous maize extracts, E. carotovora was more inhibited than at pH 6.75; however, ECZ was substantially less inhibited at the lower pH.
Non-radioactive gene-specific probes (1984)

Conference Article| April 01 1984 Non-radioactive gene-specific probes J. LESLEY WOODHEAD; J. LESLEY WOODHEAD 1Department of Biochemistry, St. Mary's Hospital Medical School, University of London, Norfolk Place, London W2 1PG, U.K. Search for other works by this author on: This Site PubMed Google Scholar ALAN D. B. MALCOLM ALAN D. B. MALCOLM 1Department of Biochemistry, St. Mary's Hospital Medical School, University of London, Norfolk Place, London W2 1PG, U.K. Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1984) 12 (2): 279. https://doi.org/10.1042/bst0120279 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation J. LESLEY WOODHEAD, ALAN D. B. MALCOLM; Non-radioactive gene-specific probes. Biochem Soc Trans 1 April 1984; 12 (2): 279. doi: https://doi.org/10.1042/bst0120279 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search This content is only available as a PDF. © 1984 Biochemical Society1984 Article PDF first page preview Close Modal You do not currently have access to this content.
Heat shock factor-independent heat control of transcription of the CTT1 gene encoding the cytosolic catalase T of Saccharomyces cerevisiae (1991)

Transcription of the Saccharomyces cerevisiae CTT1 gene encoding the cytosolic catalase T has been previously shown to be derepressed by nutrient stress. To investigate whether expression of this gene is also affected by other types of stress, the influence of heat shock on CTT1 expression was studied. The results obtained show that expression of the gene is low at 23 degrees C and is induced rapidly at 37 degrees C. By deletion analysis, a promoter element necessary for high level induction by heat shock was located between base pairs -340 and -364 upstream of the translation start codon. This region was demonstrated to be sufficient for heat shock control by placing it upstream of a S. cerevisiae LEU2-lacZ fusion gene. Mutagenesis of the region showed that the response to heat shock is not mediated by a sequence similar to canonical heat shock elements, but by DNA elements also involved in nutrient control of transcription. Catalase T appears to have a function in protecting yeast cells against oxidative damage under stress conditions. Catalase T-containing strains are less sensitive to exposure to 50 degrees C ("lethal heat shock") than isogenic catalase T-deficient mutants, and catalase T-containing strains pretreated by incubation at 37 degrees C are less sensitive to H2O2 than pretreated catalase-deficient mutants.
Annealing control primer system for identification of differentially expressed genes on agarose gels (2004)

We developed GeneFishing technology, an improved method for the identification of differentially expressed genes (DEGs) using our novel annealing control primer (ACP) system. Because of high annealing specificity during PCR using the ACP system, the application of the ACP to DEG discovery generates reproducible, authentic, and long (100 bp to 2 kb) PCR products that are detectable on agarose gels. To demonstrate this method for gene expression profiling, Gene-Fishing technology was used to detect genes that are differentially expressed during development using total RNAs isolated from mouse conceptus tissues at 4.5-18.5 days of gestation. Ten DEGs (DEG1-10) were isolated and confirmed by Northern blot hybridization. The sequence analysis of these DEGs showed that DEG6 and DEG10 are unknown genes.
Proprotein conversion is determined by a multiplicity of factors including convertase processing, substrate specificity, and intracellular environment. Cell type-specific processing of human prorenin by the convertase PC1. (1992)

Proprotein and prohormone processing at pairs of basic residues is generally thought to be both tissue- and precursor-specific and to be developmentally regulated. Furin, PC1 (also called PC3), and PC2 represent three recently discovered subtilisin-like proteinases which cleave a number of precursors at the same pairs of basic residues normally processed in vivo. Using human prorenin as a model, we show that PC1 can process it to active renin in cells containing secretory granules, such as the somatomammotroph cell line GH4, but not in cells which lack granules, such as the Chinese hamster ovary or African green monkey kidney epithelial (BSC-40) cell lines. In contrast, in both cell types, human prorenin is not activated by either PC2 or furin. Using the vaccinia virus expression system, biosynthetic labeling experiments demonstrated that PC1 and PC2 are themselves cleaved intracellularly at pairs of basic residues and that these two proenzymes are processed to different extents independent of whether the cell line contains dense core secretory granules. Furthermore, we also show that the cells mostly secrete the cleaved forms of PC1 and PC2, and that intracellularly the pro- form of PC2 predominates. Our data demonstrate that propeptide removal from these enzymes, possibly leading to their activation, is not the only criterion which governs precursor processing.
THE FAST FOURIER TRANSFORM (2015)

Fast Fourier transform (FFT) is a fast algorithm to compute the discrete Fourier transform in O(N logN) operations for an array of size N = 2J . It is based on the nice property of the principal root of xN = 1. In addition to the recursive implementation, a non-recursive and in-place implementation, known as butterfly algorithm, is also provided. Fourier series can be written as
Jodeinbringungsgeschwindigkeit verschieden konzentrierter Röntgenkontrastmittel bei schneller intravenöser Injektion (2004)

Very high iodinated contrast agent concentrations do not increase the iodine delivery rate of rapid peripheral intravenous injections, since the high viscosity of such agents causes the injection pressure to increase more than the higher iodine concentration would compensate for. With lower injection velocities, the higher viscosity of highly concentrated contrast agents may remain without practical consequences.
The future of e-learning: a shift to knowledge networking and social software (2007)

The main aim of Knowledge Management (KM) is to connect people to quality knowledge as well as people to people in order to peak performance. This is also the primary goal of Learning Management (LM). In fact, in the world of e-learning, it is more widely recognised that how learning content is used and distributed by learners might be more important than how it is designed. In the last few years, there has been an increasing focus on social software applications and services as a result of the rapid development of Web 2.0 concepts. In this paper, we argue that LM and KM can be viewed as two sides of the same coin, and explore how Web 2.0 technologies can leverage knowledge sharing and learning and enhance individual performance whereas previous models of LM and KM have failed, and present a social software driven approach to LM and KM.
Loss of Sex and Age Driven Differences in the Gut Microbiome Characterize Arthritis-Susceptible *0401 Mice but Not Arthritis-Resistant *0402 Mice (2012)

We have demonstrated for the first time that HLA genes in association with the gut microbiome may determine the immune environment and that the gut microbiome might be a potential biomarker as well as contributor for susceptibility to arthritis. Identification of pathogenic commensal bacteria would provide new understanding of disease pathogenesis, thereby leading to novel approaches for therapy.
Papua New Guinea (2010)

On 12 November 2004 the Constitution of the Autonomous Region of Bougainville was adopted. Bougainville remained a constituent part of the Independent State of Papua New Guinea (PNG, the country's full name), but an Autonomous Bougainville Government (ABG), with a charter to develop and promote Bougainville's autonomy, was established. The ABG is to a large extent, or will be when the processes are complete, effectively an independent government. Bougainville has gained significant autonomy and PNG avoided losing completely a large and potentially wealthy region.
Beneficial effects of CD39/ecto-nucleoside triphosphate diphosphohydrolase-1 in murine intestinal ischemia-reperfusion injury (2004)

CD39 (ecto-nucleoside triphosphate diphosphohydrolase-1; E-NTPDase-1), is highly expressed on quiescent vascular endothelial cells and efficiently hydrolyzes extracellular ATP and ADP to AMP and ultimately adenosine. This action blocks extracellular nucleotide-dependent platelet aggregation and abrogates endothelial cell activation. However, CD39 enzymatic activity is rapidly lost following exposure to oxidant stress. Modulation of extracellular nucleotide levels may therefore play an important role in the pathogenesis of vascular injury. Acute ischemic injury of the bowel is a serious medical condition characterized by high mortality rates with limited therapeutic options. Here we evaluate the effects of cd39-deletion in mutant mice and the use of supplemental NTPDase or adenosine in influencing the outcomes of intestinal ischemia-reperfusion. Wild-type, cd39-null, or hemizygous cd39-deficient mice were subjected to intestinal ischemia. In selected animals, 0.2 U/g apyrase (soluble NTPDase) was administered prior to re-establishment of blood-flow. In parallel experiments adenosine/amrinone was infused over 60 min during reperfusion periods. Survival rates were determined, serum and tissue samples were taken. Intravital videomicroscopy and studies of vascular permeability were used to study platelet-endothelial cell interactions and determine capillary leakage. In wild-type animals, ischemia reperfusion injury resulted in 60% mortality within 48 hours. In mutant mice null or deficient for cd39, ischemia reperfusion-related death occurred in 80% of animals. Apyrase supplementation protected all wild-type animals from death due to intestinal ischemia but did not fully protect cd39-null and cd39-hemizygote mice. Adenosine/amrinone treatment failed to improve survival figures. In wild type mice, platelet adherence to postcapillary venules was significantly decreased and vascular integrity was well preserved following apyrase administration. In cd39-null mice, ischemia-reperfusion induced marked albumin leakage indicative of heightened vascular permaeability when compared to wild-type animals (p=0.04). Treatment with NTPDase or adenosine supplementation abrogated the increased vascular permeability in ischemic jejunal specimens of both wild-type mice and cd39-null. CD39 activity modulates platelet activation and vascular leak during intestinal ischemia reperfusion injury in vivo. The potential of NTPDases to maintain vascular integrity suggests potential pharmacological benefit of these agents in mesenteric ischemic injury.
Esters of β-Alkylaminoethanols (1945)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEsters of β-AlkylaminoethanolsJulian R. Reasenberg and Samuel D. GoldbergCite this: J. Am. Chem. Soc. 1945, 67, 6, 933–939Publication Date (Print):June 1, 1945Publication History Published online1 May 2002Published inissue 1 June 1945https://pubs.acs.org/doi/10.1021/ja01222a017https://doi.org/10.1021/ja01222a017research-articleACS PublicationsRequest reuse permissionsArticle Views178Altmetric-Citations14LEARN 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
Study on retinal dopamine transporter in form deprivation myopia using the radiopharmaceutical tracer 99mTc-TRODAT-1 (2010)

Tc-TRODAT-1 can be used to trace the distributions and changes in DAT in the retina. DATs in the myopic retinas were lower than that in the fellow and normal control eyes. Radionuclide tracing may provide a new approach in vivo for further studies on the dopamine system in myopia.
Optimal probes for withdrawal of uncontaminated fluid samples (2005)

Withdrawal of fluid by a composite probe pushed against the face z=0 of a porous half-space z&gt;0 is modeled assuming incompressible Darcy flow. The probe is circular, of radius a, with an inner sampling section of radius αa and a concentric outer guard probe αa&lt;r&lt;a. The porous rock in 0⩽z⩽βa is saturated with fluid 1, and the region z&gt;βa is saturated with fluid 2; the two fluids have the same viscosity. It is assumed that the interface between the two fluids is sharp and remains so as it moves through the rock. The pressure in the probe is lower than that of the pore fluid in the rock, so that the fluid interface is convected with the fluids towards the probe. This idealized axisymmetric problem is solved numerically, and it is shown that an analysis based on far-field spherical flow towards a point sink is a good approximation when the nondimensional depth of fluid 1 is large, i.e., β⪢1. The inner sampling probe eventually produces pure fluid 2, and this technique has been proposed for sampling pore fluids in rock surrounding an oil well [A. Hrametz, C. Gardner, M. Wais, and M. Proett, U.S. Patent No. 6,301,959 B1 (16 October 2001)]. Fluid 1 is drilling fluid filtrate, which has displaced the original pore fluid (fluid 2), a pure sample of which is required. The time required to collect an uncontaminated sample of original pore fluid can be minimized by a suitable choice of the probe geometry α [J. Sherwood, J. Fitzgerald and B. Hill, U.S. Patent No. 6,719,049 B2 (13 April 2004)]. It is shown that the optimal choice of α depends on the depth of filtrate invasion β and the volume of sample required.