gebhart/patrepeval huggingface dataset:
VIPERdb: A Tool for Virus Research (2018)

The VIrus Particle ExploreR database (VIPERdb) ( http://viperdb.scripps.edu ) is a database and web portal for primarily icosahedral virus capsid structures that integrates structure-derived information with visualization and analysis tools accessed through a set of web interfaces. Our aim in developing VIPERdb is to provide comprehensive structure-derived information on viruses comprising simple to detailed attributes such as size (diameter), architecture ( T number), genome type, taxonomy, intersubunit association energies, and surface-accessible residues. In addition, a number of web-based tools are provided to enable users to interact with the structures and compare and contrast structure-derived properties between different viruses. Recently, we have constructed a series of data visualizations using modern JavaScript charting libraries such as Google Charts that allow users to explore trends and gain insights based on the various data available in the database. Furthermore, we now include helical viruses and nonicosahedral capsids by implementing modified procedures for data curation and analysis. This article provides an up-to-date overview of VIPERdb, describing various data and tools that are currently available and how to use them to facilitate structure-based bioinformatics analysis of virus capsids.
Radioimmunoassays for type III procollagen amino-terminal peptides in humans. (1985)

Use of radioimmunoassay for the amino-terminal propeptide of type III procollagen for monitoring fibrotic processes in humans has been frustrating because of the nonparallel relation between results for the standard bovine antigen and human serum samples. In the radioimmunoassays I developed for this propeptide and its monomeric Col 1 domain, based on use of antigens from humans, serum samples generated less-steep inhibition curves than did the standard antigen in the propeptide assay; in the Col 1 assay, however, serum and urine samples both generated inhibition curves having the same slope as that generated with the standard Col 1 peptide. Concentrations of human fragment Col 1 in serum samples as measured with the Col 1 assay were usually double those obtained with the human propeptide assay, which in turn were two- to threefold those obtained with the bovine antigen assay. In control subjects and alcoholic cirrhotics the concentrations of antigen in urine and the daily excretion rates as measured with the assay for human Col 1 exceeded those reported previously. The presence of different antigen forms was demonstrated with both assays by gel-filtration analysis of serum and urine samples. The assay for human Col 1 should be suitable for routine clinical chemical use.
Implementation of artificial neural networks using current mode analogue circuit techniques (1989)

The logistic function is a close approximation to the biological neuron's dendritic input (graded response) versus the output activation (number of action potentials/second). It also has some useful mathematical characteristics and the resulting output is a unipolar signal. An artificial neural network is constructed by cascading these simple neurons in structures consisting of one or more layers.
Functional phenotype of phosphoinositide 3-kinase p85 -null platelets characterized by an impaired response to GP VI stimulation (2003)

Phosphoinositide 3-kinases (PI3Ks), a family of lipid kinases comprising 3 classes with multiple isoforms, have been shown to participate in different phases of platelet signaling. To investigate the roles that enzymes play in platelet function in vivo and determine which isoforms are important for particular signaling events, we analyzed platelet function of gene knockout mice deficient in the p85alpha regulatory subunit of heterodimeric class IA PI3K. The kinase activity of p85alpha-/- platelets was only 5% of the activity of platelets from wild-type littermates. Platelet aggregation induced by adenosine diphosphate (ADP), thrombin, U46619, phorbol 12-myristate 13-acetate (PMA), or botrocetin was not defective in p85alpha-/- mice, compared with wild-type animals. In contrast, aggregation induced by collagen and collagen-related peptide (CRP) was partially but readily impaired in p85alpha-/- mice. Both P-selectin expression and fibrinogen binding in response to CRP were also decreased to a similar extent in p85alpha-/- platelets. Platelets from p85alpha-/- mice appeared to spread poorly over a CRP-coated surface with intact filopodial protrusions. Significant attenuation of CRP-induced tyrosine phosphorylation in known PI3K effectors such as Btk, Tec, PKB/Akt, and phospholipase Cgamma2 were observed with p85alpha-/- platelets, whereas no alteration was noted in upstream molecules of Syk, LAT, and SLP-76. Considered as a whole, these results provide the first genetic evidence that PI3K p85alpha plays a significant role in platelet function, almost exclusively in the glycoprotein (GP) VI/Fc receptor gamma chain complex-mediated signaling pathway.
Thermodynamic description of the competition between quantum dots and quantum dashes during metalorganic vapor phase epitaxy in the In As ∕ In P ( 001 ) system: Experiment and theory (2006)

International audience
Jasmonate-Based Wound Signal Transduction Requires Activation of WIPK, a Tobacco Mitogen-Activated Protein Kinase (1999)

A gene encoding a tobacco mitogen-activated protein kinase (WIPK) is transcriptionally activated in response to wounding. Transgenic tobacco plants, in which expression of endogenous wipk was suppressed, did not accumulate jasmonic acid or its methyl ester when wounded, suggesting that WIPK is involved in jasmonate-mediated wound signal transduction. Here, we demonstrate that activation of WIPK is required for triggering the jasmonate-mediated signal transduction cascade that occurs when wild-type tobacco plants are wounded. We also show that when plants are wounded, WIPK is rapidly and transiently activated, whereas the quantity of WIPK protein is maintained at a constant level. A transgenic tobacco plant in which the wipk gene was constitutively expressed at a high level showed constitutive enzymatic activation of WIPK and exhibited three- to fourfold higher levels of jasmonate than did its wild-type counterpart. This plant also showed constitutive accumulation of jasmonate-inducible proteinase inhibitor II transcripts. These results show that WIPK is activated in response to wounding, which subsequently causes an increase in jasmonate synthesis.
Differential Processing of Colony-Stimulating Factor 1 Precursors Encoded by Two Human cDNAs (1988)

The biosynthesis of macrophage colony-stimulating factor 1 (CSF-1) was examined in mouse NIH-3T3 fibroblasts transfected with a retroviral vector expressing the 554-amino-acid product of a human 4-kilobase (kb) CSF-1 cDNA. Similar to results previously obtained with a 1.6-kb human cDNA that codes for a 256-amino-acid CSF-1 precursor, the results of the present study showed that NIH-3T3 cells expressing the product of the 4-kb clone produced biologically active human CSF-1 and were transformed by an autocrine mechanism when cotransfected with a vector containing a human c-fms (CSF-1 receptor) cDNA. The 4-kb CSF-1 cDNA product was synthesized as an integral transmembrane glycoprotein that was assembled into disulfide-linked dimers and rapidly underwent proteolytic cleavage to generate a soluble growth factor. Although the smaller CSF-1 precursor specified by the 1.6-kb human cDNA was stably expressed as a membrane-bound glycoprotein at the cell surface and was slowly cleaved to release the extracellular growth factor, the cell-associated product of the 4-kb clone was efficiently processed to the secreted form and was not detected on the plasma membrane. Digestion with glycosidic enzymes indicated that soluble CSF-1 encoded by the 4-kb cDNA contained both asparagine(N)-linked and O-linked carbohydrate chains, whereas the product of the 1.6-kb clone had only N-linked oligosaccharides. Removal of the carbohydrate indicated that the polypeptide chain of the secreted 4-kb cDNA product was longer than that of the corresponding form encoded by the smaller clone. These differences in posttranslational processing may reflect diverse physiological roles for the products of the two CSF-1 precursors in vivo.
Extending a Run-time Resource Management framework to support OpenCL and Heterogeneous Systems (2014)

From Mobile to High-Performance Computing (HPC) systems, performance and energy efficiency are becoming always more challenging requirements. In this regard, heterogeneous systems, made by a general-purpose processor and one or more hardware accelerators, are emerging as affordable solutions. However, the effective exploitation of such platforms requires specific programming languages, like for instance OpenCL, and suitable run-time software layers. This work illustrates the extension of a run-time resource management (RTRM) framework, to support the execution of OpenCL applications on systems featuring a multi-core CPU and multiple GPUs. Early results show how this solution leads to benefits both for the applications, in terms of performance, and for the system, in terms of resource utilization, i.e. load balancing and thermal leveling over the computing devices.
Thin-film interference effects on the efficiency of a normal-incidence grating in the 100–350-Å wavelength region (1999)

Thin-film interference effects were observed in the normal-incidence efficiency of a 2400-groove/mm replica grating. The efficiency was measured in the 100-350-A wavelength range and had an oscillatory behavior that resulted from the presence of a thin SiO(2) coating. The thicknesses of the SiO(2) and the underlying oxidized aluminum layers were inferred from computer modeling of the zero-order efficiency. The efficiencies in the diffracted orders were calculated with the modified integral approach and accounting for the multilayer coating and the groove profile derived from atomic force microscopy. The calculated and measured efficiencies were in good agreement.
Synthesis of Novel Indazole-Derived Ionic Liquids (2015)

A very simple, convenient, two-step halide-free method for the synthesis of a novel homologous series of 36 room-temperature indazolium ionic liquids is reported, in which the indazolium moiety is substituted with different <i>n</i>-alkyl chains, and coupled with a tetrafluoroborate anion. As an example, the newly designed indazolium ionic liquid, 1-ethyl-2-pentyl-2<i>H</i>-indazol-2-ium tetrafluoroborate ([EPentIn]BF<sub>4</sub>) is employed as an ionic solvent to demonstrate its efficiency as a green solvent in a crossed aldol condensation reaction.
COUP-TF and Sp1 Interact and Cooperate in the Transcriptional Activation of the Human Immunodeficiency Virus Type 1 Long Terminal Repeat in Human Microglial Cells (1997)

We have recently reported that chicken ovalbumin upstream promoter transcription factor (COUP-TF) activates human immunodeficiency virus type 1 (HIV-1) gene transcription in glial and neuronal cells. Here, we have examined the role of COUP-TF in microglial cells, the major target cells for HIV-1 infection in brain. We show that COUP-TF activates gene expression from both the lymphotropic LAI and the macrophage-tropic JR-FL HIV-1 strains. Although COUP-TF binds to the -352/-320 nuclear receptor responsive element of the long terminal repeat, it functions as a transcriptional activator by acting on the -68/+29 minimal promoter. This region is a direct target of transcription factors Sp1 and Sp3. We report the discovery and features of a physical and functional interplay between COUP-TF and Sp1. Our cotransfection experiments provide evidence for a functional synergism between Sp1 and COUP-TF leading to enhanced transcriptional activity of the HIV-1 long terminal repeat through the Sp1 element. In contrast, Sp3 functions as a repressor of Sp1- or COUP-TF-induced activation. We further demonstrate that COUP-TF and Sp1 are capable of physically interacting, via the DNA-binding domain of COUP-TF, in vitro and in the cell. These findings reveal how the novel interplay of Sp1 and COUP-TF families of transcription factors regulate HIV-1 gene expression.
Identification of DNA-PKcs as a primary resistance factor of TIC10 in hepatocellular carcinoma cells (2017)

The current study tested the anti-hepatocellular carcinoma (HCC) cell activity of TIC10, a first-in-class small-molecule tumor necrosis (TNF)-related apoptosis-inducing ligand (TRAIL) inducer. TIC10 exerted potent anti-proliferative and pro-apoptotic actions in primary and established human HCC cells. TIC10 blocked Akt-Erk activation, leading to Foxo3a nuclear translocation, as well as TRAIL and death receptor-5 (DR5) transcription in HCC cells. We propose that DNA-PKcs is a major resistance factor of TIC10 possibly via inhibiting Foxo3a nuclear translocation. DNA-PKcs inhibition, knockdown or mutation facilitated TIC10-induced Foxo3a nuclear translocation, TRAIL/DR5 expression and cell apoptosis. Reversely, exogenous DNA-PKcs over-expression inhibited above actions by TIC10. In vivo, oral administration of TIC10 significantly inhibited HepG2 tumor growth in nude mice, which was further potentiated with Nu7026 co-administration. Thus, TIC10 shows promising anti-HCC activity, alone or together with DNA-PKcs inhibitors.
CD38 expression enhances sensitivity of lymphoma T and B cell lines to biochemical and receptor‐mediated apoptosis (2006)

CD38 has been widely characterised both as an ectoenzyme and as a receptor. In the present paper, we investigated the role of CD38 as possible modulator of apoptosis. CD38-positive (CD38(+)) and negative (CD38(-)) fractions, obtained by sorting CD38(+) cells from lymphoma T (Jurkat) and lymphoma B (Raji) and by transfecting lymphoma LG14 and myeloid leukemia K562 cell lines, were used. Cellular subpopulations were exposed to different triggers (H(2)O(2), UV-B, alpha-TOS and hrTRAIL) and the extent of apoptosis was determined by Annexin V-FITC/PI assay. Our data showed that, in lymphoma cells, propensity to apoptosis was significantly linked to CD38 expression and that, remarkably, such response was independent of the nature of the trigger used. Inhibition of CD38 expression by antisense oligonucleotides treatment resulted in CD38-silenced fractions which were as prone to apoptosis as CD38(-) ones. Notably, susceptibility of K562 to apoptosis-inducing challenges was not affected by CD38 expression.
Glucagon-like peptide-1 receptor agonists as neuroprotective agents for ischemic stroke: a systematic scoping review (2020)

Stroke mortality and morbidity is expected to rise. Despite considerable recent advances within acute ischemic stroke treatment, scope remains for development of widely applicable neuroprotective agents. Glucagon-like peptide-1 receptor agonists (GLP-1RAs), originally licensed for the management of Type 2 Diabetes Mellitus, have demonstrated pre-clinical neuroprotective efficacy in a range of neurodegenerative conditions. This systematic scoping review reports the pre-clinical basis of GLP-1RAs as neuroprotective agents in acute ischemic stroke and their translation into clinical trials. We included 35 pre-clinical studies, 11 retrospective database studies, 7 cardiovascular outcome trials and 4 prospective clinical studies. Pre-clinical neuroprotection was demonstrated in normoglycemic models when administration was delayed by up to 24 h following stroke induction. Outcomes included reduced infarct volume, apoptosis, oxidative stress and inflammation alongside increased neurogenesis, angiogenesis and cerebral blood flow. Improved neurological function and a trend towards increased survival were also reported. Cardiovascular outcomes trials reported a significant reduction in stroke incidence with semaglutide and dulaglutide. Retrospective database studies show a trend towards neuroprotection. Prospective interventional clinical trials are on-going, but initial indicators of safety and tolerability are favourable. Ultimately, we propose that repurposing GLP-1RAs is potentially advantageous but appropriately designed trials are needed to determine clinical efficacy and cost-effectiveness.
Characterization of Si(100) Surface after High Density HBr/Cl2/O2 Plasma Etching (2000)

The nature of deposited film on unmasked Si(100) surface after high density HBr/Cl 2 /O 2 plasma etching has been investigated. The as-etched surface was treated sequentially with HF for different duration and monitored with atomic force microscopy (AFM) and X-ray photoelectron spectroscopy (XPS). It was found that microscopic Si pillars are formed on the etched surface and might be attributed to the formation of micromasks. XPS surface analysis indicated the passivation film consists mainly of silicon oxides and oxybromides. Ab initio calculations using Si 4 cluster model suggested the direct attack of oxyhalide species on the surface as the energetically most favored process. It is also shown that HF treatment for 40 s was effective in the complete removal of the residual film.
Fatigue, Tiredness, Lack of Energy, and Sleepiness in Multiple Sclerosis Patients Referred for Clinical Polysomnography (2012)

Objectives. To assess the relationship between nocturnal polysomnographic (PSG) findings and a group of key self-reported symptoms-fatigue, tiredness, lack of energy, and sleepiness-among sleep-laboratory referred patients with and without multiple sclerosis (MS). Methods. PSG and questionnaire data from n = 30 MS patients and n = 30 matched controls were analyzed retrospectively. Associations between symptoms of fatigue, tiredness, lack of energy, sleepiness, and PSG variables of interest were examined among MS patients and controls. Results. More MS patients than controls reported fatigue, tiredness, and lack of energy to occur often or almost always (Chi-square P < 0.0001 for each), but sleepiness was reported similarly by both groups (P = 0.3409). Among MS patients, tiredness correlated with sleepiness (Spearman correlation P = 0.005), and a trend emerged toward correlation between fatigue and sleepiness (Spearman correlation P = 0.076). Decreased sleep efficiency on PSGs correlated with fatigue, tiredness, and lack of energy in MS patients (Spearman correlation P = 0.002, 0.029, and 0.048, resp.), but not sleepiness or any symptom among controls. Conclusion. In comparison to controls, MS patients report more fatigue, tiredness, and lack energy, but not sleepiness. Fatigue and related symptoms may arise from MS itself or in relation to reduced sleep efficiency.
Spatial evaluation of the accessibility of public service facilities in Shanghai: A community differentiation perspective (2022)

Following the 'people-oriented' concept, increased attention should be paid to the heterogeneity of community residents when configuring public service facilities. Taking Shanghai as an example, this study analyzed the spatial pattern of urban and rural community differentiation and evaluated spatial differences in the level of accessibility to four types of public service facilities based on the shortest travel distance. There were significant differences between community types in Shanghai, with a clear circular structure in the urban and rural spaces. Here, facility accessibility decreased from the core to the periphery. Population density, income level, and the shortest walking distance to facilities revealed a significant negative correlation. Age level, household registration, and the shortest walking distance to facilities were partially weakly correlated or uncorrelated. The spatial matching of population density and facility accessibility simultaneously presented a circular pattern and heterogeneity, while planned new towns in suburbs and mid-suburbs presented a double-medium-sized match of the same community type. From the perspective of community differentiation, mechanisms behind the formation of the spatial pattern of facility accessibility included urban-rural pattern continuity and differences in allocation specifications, the continuity of population agglomeration and the accumulation of facility construction, and urban planning guidance and population agglomeration.
Western Blots from A Sox2:miR-486-5p Axis Regulates Survival of GBM Cells by Inhibiting Tumor Suppressor Networks (2023)

&lt;p&gt;File contains full blots used for immunoblotting analysis.&lt;/p&gt;
Focusing of Sound in a 3D Phononic Crystal (2004)

We present a combined experimental and theoretical study of phonon focusing phenomena in a pass band above the complete band gap in a 3D phononic crystal. Wave propagation was found to depend dramatically on both frequency and incident direction. This propagation anisotropy leads to very large negative refraction, which can be used to focus a diverging ultrasonic beam into a narrow focal spot with a large focal depth. The experimental field patterns are well explained using a Fourier imaging technique, based on the 3D equifrequency surfaces calculated from multiple scattering theory.
Nanographene‐Constructed Hollow Carbon Spheres and Their Favorable Electroactivity with Respect to Lithium Storage (2009)

Nanographene-constructed hollow carbon spheres (NGHCs) are fabricated using discotic nanographene as a building block and a silica/space/mesoporous silica sphere as a template. The resultant NGHCs exhibit uniform size and consist of dual walls. In the exterior walls of the NGHCs, nanochannels arrange perpendicularly to the surface, which is favorable for lithium ion diffusion from different orientations, while the interior graphitic solid walls can facilitate the collection and transport of electrons. The NGHCs show excellent electrochemical performance when used as anode material for lithium ion batteries. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
The glycoasparagines in urine of a patient with aspartylglycosaminuria (1974)

The isolation and analysis of 2-acetamido-N-(4'-l-aspartyl)-2-deoxy-beta-d- glucopyranosylamine and 13 higher-molecular-weight derivatives from the urine of a patient with aspartylglycosaminuria is described. Some structural information is presented for nine of these compounds.
The “switching on” of mammalian spermatozoa: Molecular events involved in promotion and regulation of capacitation (2009)

Following the discovery of mammalian sperm capacitation and its fundamental importance for the acquisition of fertilizing potential, it has gradually become possible to identify some specific molecules and molecular events that play pivotal roles in the "switching on" of spermatozoa. These are discussed in the context of the promotion and regulation of capacitation, emphasizing differences between commonly used conditions in vitro and the environment in vivo where spermatozoa normally undergo capacitation. Although typical culture media used in vitro do support capacitation, they do not prevent capacitated cells from undergoing spontaneous acrosome reactions and so losing fertilizing potential. This is not a problem in vitro, but could be in vivo where few spermatozoa reach the site of fertilization. Several small molecules, known to be present in vivo, have been shown in vitro to bind to spermatozoa and to regulate capacitation, first accelerating capacitation and then inhibiting spontaneous acrosome reactions, by regulating cAMP production. Since spermatozoa would contact these molecules during and after ejaculation, it is plausible that they serve a similar function in vivo. The mechanisms whereby the presence or absence of decapacitation factors might alter plasma membrane architecture and so alter functionality of a number of membrane-associated enzymes involved in capacitation are also considered. Finally, several unresolved issues relating to events during capacitation are discussed.