gebhart/patrepeval huggingface dataset:
Nanochannel Array Glass (1992)

The fabrication and characterization of a glass containing a regular parallel array of submicrometer channels or capillaries are described. The capillaries are arranged in a two-dimensional hexagonal close packing configuration with channel diameters as small as 33 nanometers and packing densities as high as 3 x 10(10) channels per square centimeter. The high-temperature stability of the nanochannel glass array is well suited as a host or template for the formation of quantum confined semiconductor structures or as a mask for massively parallel patterned lithographic applications.
Noncontact ultrasonic transportation of small objects in a circular trajectory in air by flexural vibrations of a circular disc (2010)

We have developed a noncontact ultrasonic technique for transporting small objects with a linear trajectory over long distances using a bending vibrating plate and a reflector. In this paper, noncontact transportation of small particles around a circular trajectory was investigated. A circular aluminum plate with a piezoelectric ring was employed as a vibrating plate. On the basis of finite element analysis (FEA) calculations, the electrodes of the piezoelectric ring were divided into 24 pieces to generate a flexural vibration mode with one nodal circle and four nodal lines at the resonance frequency of 47.8 kHz. A circular plate having the same dimensions as the vibrating plate was installed parallel to the vibrator. It was used as a reflector to generate an acoustic standing wave in the air between the two plates. The acoustic field between the vibrating plate and reflector was calculated by FEA and the distribution of the acoustic radiation force acting on a small rigid particle was calculated to predict the position of the trapped particle. Using a prototype of the vibrating plate, polystyrene particles with diameters of several millimeters could be trapped at regular intervals along the horizontal nodal line of the standing wave. The sound pressure distribution between the vibrating plate and reflector was measured by a fiber optic probe and the experimental and calculated results showed good agreement. By switching the driving conditions of the divided electrodes in the circumferential direction, the nodal lines of the vibrating plate could be rotated and the trapped particle could be manipulated with a circular trajectory in air.
Generalized Belief Propagation (2000)

Belief propagation (BP) was only supposed to work for tree-like networks but works surprisingly well in many applications involving networks with loops, including turbo codes. However, there has been little understanding of the algorithm or the nature of the solutions it finds for general graphs. We show that
C-fiber spontaneous discharge evoked by chronic inflammation is suppressed by a long-term infusion of lidocaine yielding nanogram per milliliter plasma levels (2008)

Nociceptors innervating inflamed tissue acquire an abnormal spontaneous discharge that is believed to be at least part of the reason for the persistent spontaneous pain, allodynia, and hyperalgesia that accompany inflammation. Recent studies suggest that patients with chronic inflammatory pain may obtain an analgesic effect with transdermal application of lidocaine that yields very low plasma levels (130-225 ng/ml). The aim of this study was to investigate whether a 7-day exposure to such low plasma levels of lidocaine had an effect on inflammation-evoked spontaneous discharge in the rat. Seven days after a hind-paw injection of Complete Freund's Adjuvant (CFA), we confirmed the presence of myositis, pain hypersensitivity, and a significant increase in the incidence of spontaneous discharge in A-fibers and C-fibers innervating both muscle and skin. We then compared the incidence of spontaneous discharge in muscle and cutaneous fibers in CFA-injected animals treated with a 7-day infusion of saline or lidocaine. The lidocaine infusion yielded a plasma level of 210 ng/ml. The muscle C-fiber discharge was completely inhibited by the lidocaine infusion and the cutaneous C-fiber discharge was suppressed by 50%. Lidocaine infusion had no effect on the incidence of spontaneous discharge in muscle or cutaneous A-fibers. Lidocaine infusion reduced mechano-hyperalgesia but had no effect on mechano-allodynia or heat-hyperalgesia. We conclude that the analgesic effects seen clinically with transdermal lidocaine administration yielding low plasma levels may be due to a systemic drug action on spontaneously active C-fibers.
Mobility resilience and overhead constrained adaptation in directional 60 GHz WLANs (2016)

High directivity of 60 GHz links introduces new link training and adaptation challenges due to both client and environmental mobility. In this paper, we design, implement and evaluate MOCA, a protocol for Mobility resilience and Overhead Constrained Adaptation for directional 60 GHz links. Since mobility-induced link blockage and misalignment cannot be countered with data rate adaptation alone, we introduce Beam Sounding as a mechanism invoked before each data transmission to estimate the link quality for selected beams, and identify and adapt to link impairments. We devise proactive techniques to restore broken directional links with low overhead and design a mechanism to jointly adapt beamwidth and data rate, targeting throughput maximization that incorporates data rate, overhead for beam alignment, and mobility resilience. We implement a programmable node and testbed using software defined radios with commercial 60 GHz transceivers, and conduct an extensive over-the-air measurement study to collect channel traces for various environments. Based on trace based emulations and the IEEE 802.11ad channel model, we evaluate MOCA under a variety of propagation environments and mobility scenarios. Our experiments show that MOCA achieves up to 2x throughput gains compared to a baseline WLAN scheme in a diverse set of operational conditions.
DFTB+, a Sparse Matrix-Based Implementation of the DFTB Method (2007)

A new Fortran 95 implementation of the DFTB (density functional-based tight binding) method has been developed, where the sparsity of the DFTB system of equations has been exploited. Conventional dense algebra is used only to evaluate the eigenproblems of the system and long-range Coulombic terms, but drop-in O(N) or O(N2) modules are planned to replace the small code sections that these entail. The developed sparse storage structure is discussed in detail, and a short overview of other features of the new code is given.
Characterization and clinical course of 1000 patients with coronavirus disease 2019 in New York: retrospective case series (2020)

Patients admitted to hospital with covid-19 at this medical center faced major morbidity and mortality, with high rates of acute kidney injury and inpatient dialysis, prolonged intubations, and a bimodal distribution of time to intubation from symptom onset.
ICOS+ Th cells produce distinct cytokines in different mucosal immune responses (2003)

T cell activation, differentiation and effector functions depend on signals delivered through the antigen-specific TCR and non-clonal costimulatory receptors on the T cell. Activated T cells express the inducible costimulator (ICOS). We examined the co-expression of ICOS with Th cytokines in mucosal immune responses. ICOS+CD4+ Th cells expressed strikingly different cytokines depending on the type of infection encountered and the cells' anatomical localization. In the Th2-dominated response to Schistosoma mansoni, ICOS expression of CD4+ cells isolated from the liver was strongly associated with the expression of IL-5, IL-10, IL-13, and T1/ST2, but not with the chemokine receptor CXCR5, a pattern consistent with Th2 effector cells. In the secondary lymphatic organs of schistosome-infected mice, ICOS expression was randomly correlated with Th2 effector-cytokines, but positively correlated with CXCR5 expression; a pattern consistent with follicular Th cells. In Th cells isolated from gut or liver of mice infected with Toxoplasma gondii, ICOS expression was positively correlated with IFN-gamma production. Finally, in the severe combined immunodeficiency transfer colitis model, ICOS expression was strongly positively associated with IFN-gamma and IL-2. Thus, ICOS appears to costimulate distinct effector functions in different immune responses, depending on factors such as the nature of the antigen encountered and localization and chronicity of the immune response.
Terminal Cross-linking of DNA Catalyzed by an Enzyme System Containing DNA Ligase, DNA Polymerase, and Exonuclease of Bacteriophage T7 (1974)

An enzymatic activity that terminally cross-links T7 DNA has been detected in extracts from phage T7-infected Escherichia coli cells. This activity required the functional products of gene 1.3 (T7 DNA ligase), gene 5 (T7 DNA polymerase), and gene 6 (T7 exonuclease) as well as Mg 2+ ions, the four deoxytriphosphates, and ATP. The cross-linking system could be reconstituted with purified ligase, polymerase, and exonuclease, and maximal activity required the presence of all three enzymes. The system was active on phage DNA which possessed unique termini but not on DNA with non-unique ends.
Structure of Polymer Brushes under Shear Flow in a Good Solvent (2000)

ADVERTISEMENT RETURN TO ISSUEPREVCommunication to the...Communication to the EditorNEXTStructure of Polymer Brushes under Shear Flow in a Good SolventS. M. Baker, G. S. Smith, D. L. Anastassopoulos, C. Toprakcioglu, A. A. Vradis, and D. G. BucknallView Author Information Harvey Mudd College, Claremont, California 91711; LANSCE, Los Alamos National Laboratory, New Mexico 87545, University of Patras, Patras GR 26 500 Greece, FORTH, P.O. Box 1527 GR 711 10, Heraklion, Crete, Greece, and ISIS Facility, CLRC Rutherford Appleton Laboratory, Chilton, Didcot, OX11 0QX, UK Cite this: Macromolecules 2000, 33, 4, 1120–1122Publication Date (Web):February 4, 2000Publication History Received31 August 1999Revised28 December 1999Published online4 February 2000Published inissue 1 February 2000https://pubs.acs.org/doi/10.1021/ma991499ohttps://doi.org/10.1021/ma991499orapid-communicationACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views610Altmetric-Citations53LEARN 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 SUBJECTS:Chemical structure,Desorption,Optical properties,Polymer brushes,Solvents Get e-Alerts
MRI reporter genes: applications for imaging of cell survival, proliferation, migration and differentiation (2012)

Molecular imaging strives to detect molecular events at the level of the whole organism. In some cases, the molecule of interest can be detected either directly or with targeted contrast media. However many genes and proteins and particularly those located in intracellular compartments are not accessible for targeted agents. The transcriptional regulation of these genes can nevertheless be detected, although indirectly, using reporter gene encoding for readily detectable proteins. Such reporter proteins can be expressed in the tissue of interest by genetically introducing the reporter gene in the target cells. Imaging of reporter genes has become a powerful tool in modern biomedical research. Typically, expression of fluorescent and bioluminescent proteins and the reaction product of expressed enzymes and exogenous substrates were examined using in vitro histological methods and in vivo whole body imaging methods. Recent advances in MRI reporter gene methods raised the possibility that MRI could become a powerful tool for concomitant high-resolution anatomical and functional imaging and for imaging of reporter gene activity. An immediate application of MRI reporter gene methods was by monitoring gene expression patterns in gene therapy and in vivo imaging of the survival, proliferation, migration and differentiation of pluripotent and multipotent cells used in cell-based regenerative therapies for cancer, myocardial infarction and neural degeneration. In this review, we characterized a variety of MRI reporter gene methods based on their applicability to report cell survival/proliferation, migration and differentiation. In particular, we discussed which methods were best suited for translation to clinical use in regenerative therapies.
Small Molecule Inhibitors of Signal Transducer and Activator of Transcription 3 (Stat3) Protein (2012)

ADVERTISEMENT RETURN TO ISSUEPerspectiveNEXTSmall Molecule Inhibitors of Signal Transducer and Activator of Transcription 3 (Stat3) ProteinBikash Debnath, Shili Xu, and Nouri Neamati*View Author Information Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, California 90089, United States*Telephone: 323-442-2341. Fax: 323-442-1390. E-mail: [email protected]Cite this: J. Med. Chem. 2012, 55, 15, 6645–6668Publication Date (Web):May 31, 2012Publication History Received15 February 2012Published online15 June 2012Published inissue 9 August 2012https://doi.org/10.1021/jm300207sCopyright © 2012 American Chemical SocietyRequest reuse permissionsArticle Views6015Altmetric-Citations158LEARN 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 InReddit Read OnlinePDF (6 MB) Get e-AlertscloseSUBJECTS:Cancer,Cells,Inhibitors,Peptides and proteins,Post-translational modification Get e-Alerts
Annual Report to the Nation on the Status of Cancer, 1975‐2012, featuring the increasing incidence of liver cancer (2016)

Overall, cancer incidence and mortality declined among men; and, although cancer incidence was stable among women, mortality declined. The burden of liver cancer is growing and is not equally distributed throughout the population. Efforts to vaccinate populations that are vulnerable to hepatitis B virus (HBV) infection and to identify and treat those living with HCV or HBV infection, metabolic conditions, alcoholic liver disease, or other causes of cirrhosis can be effective in reducing the incidence and mortality of liver cancer. Cancer 2016;122:1312-1337. © 2016 American Cancer Society.
The two-faced T cell epitope (2013)

Advances in the field of T cell immunology have contributed to the understanding that cross-reactivity is an intrinsic characteristic of the T cell receptor (TCR), and that each TCR can potentially interact with many different T cell epitopes. To better define the potential for TCR cross-reactivity between epitopes derived from the human genome, the human microbiome, and human pathogens, we developed a new immunoinformatics tool, JanusMatrix, that represents an extension of the validated T cell epitope mapping tool, EpiMatrix. Initial explorations, summarized in this synopsis, have uncovered what appear to be important differences in the TCR cross-reactivity of selected regulatory and effector T cell epitopes with other epitopes in the human genome, human microbiome, and selected human pathogens. In addition to exploring the T cell epitope relationships between human self, commensal and pathogen, JanusMatrix may also be useful to explore some aspects of heterologous immunity and to examine T cell epitope relatedness between pathogens to which humans are exposed (Dengue serotypes, or HCV and Influenza, for example). In Hand-Foot-Mouth disease (HFMD) for example, extensive enterovirus and human microbiome cross-reactivity (and limited cross-reactivity with the human genome) seemingly predicts immunodominance. In contrast, more extensive cross-reactivity with proteins contained in the human genome as compared to the human microbiome was observed for selected Treg epitopes. While it may be impossible to predict all immune response influences, the availability of sequence data from the human genome, the human microbiome, and an array of human pathogens and vaccines has made computationally-driven exploration of the effects of T cell epitope cross-reactivity now possible. This is the first description of JanusMatrix, an algorithm that assesses TCR cross-reactivity that may contribute to a means of predicting the phenotype of T cells responding to selected T cell epitopes. Whether used for explorations of T cell phenotype or for evaluating cross-conservation between related viral strains at the TCR face of viral epitopes, further JanusMatrix studies may contribute to developing safer, more effective vaccines.
Challenges in optically interconnecting electronics (1996)

The challenges associated with the development of free-space optically interconnected electronics are discussed. These include finding an application for which optics offers an improved performance, developing optical transceivers, and developing suitable optics and mechanics. The main focus of the paper is the discussion of some novel approaches that smart pixels offer to increase alignment tolerance.
Possible metabolic basis for the different immunodeficient states associated with genetic deficiencies of adenosine deaminase and purine nucleoside phosphorylase. (1982)

An inherited deficiency of adenosine deaminase (Ado deaminase; adenosine aminohydrolase, EC 3.5.4.4) causes severe combined immunodeficiency disease in humans. A similar deficiency in purine nucleoside phosphorylase (Puo phosphorylase; purine-nucleoside:orthophosphate ribosyltransferase, EC 2.4.2.1) engenders a selective cellular immune deficit. To elucidate the possible metabolic basis for the contrasting immunologic phenotypes, we compared the toxicity toward mature resting human lymphocytes of the Ado deaminase substrates deoxyadenosine and adenosine and the Puo phosphorylase substrate deoxyguanosine. When Ado deaminase was inhibited, micromolar concentrations of deoxyadenosine progressively killed nondividing helper and suppressor-cytotoxic T cells, but not B cells. The toxicity required phosphorylation, with subsequent dATP formation. The deoxyadenosine analogs 2-chlorodeoxyadenosine, 2-fluorodeoxyadenosine, and adenine arabinonucleoside also killed resting T cells. Cell death was unrelated to inhibition of adenosylhomocysteinase (EC 3.3.1.1) but was preceded by a gradual decline in ATP levels. As much as 1 mM deoxyguanosine did not impair resting lymphocyte viability, despite the synthesis of dGTP. The combination of 200 microM adenosine plus 500 microM homocysteine thiolactone killed dividing lymphocytes but had no discernible toxic effect toward resting T cells, which accumulated adenosylhomocysteine over a 4-hr period but thereafter excreted the nucleoside into the culture medium. The different clinical syndromes associated with genetic deficiencies of Ado deaminase and Puo phosphorylase may be explained by the ability of dATP to kill mature resting T lymphocytes by depleting ATP levels.
Application of Multilayer Perceptron with Automatic Relevance Determination on Weed Mapping Using UAV Multispectral Imagery (2017)

Remote sensing techniques are routinely used in plant species discrimination and of weed mapping. In the presented work, successful <i>Silybum marianum</i> detection and mapping using multilayer neural networks is demonstrated. A multispectral camera (green-red-near infrared) attached on a fixed wing unmanned aerial vehicle (UAV) was utilized for the acquisition of high-resolution images (0.1 m resolution). The Multilayer Perceptron with Automatic Relevance Determination (MLP-ARD) was used to identify the <i>S. marianum</i> among other vegetation, mostly <i>Avena sterilis</i> L. The three spectral bands of Red, Green, Near Infrared (NIR) and the texture layer resulting from local variance were used as input. The <i>S. marianum</i> identification rates using MLP-ARD reached an accuracy of 99.54%. Τhe study had an one year duration, meaning that the results are specific, although the accuracy shows the interesting potential of <i>S. marianum</i> mapping with MLP-ARD on multispectral UAV imagery.
Direct Binding of Syndecan-4 Cytoplasmic Domain to the Catalytic Domain of Protein Kinase Cα (PKCα) Increases Focal Adhesion Localization of PKCα (2003)

Syndecan-4 is a transmembrane heparan sulfate proteoglycan that acts as a coreceptor with integrins in focal adhesion formation. The central region of syndecan-4 cytoplasmic domain (4V; LGKKPIYKK) binds phosphatidylinositol 4,5-bisphosphate, and together they regulate protein kinase C alpha (PKC alpha) activity. Syndecan 4V peptide directly potentiates PKC alpha activity, leading to "superactivation" of the enzyme, apparently through an interaction with its catalytic domain. We now have performed yeast two-hybrid and in vitro binding assays to determine the interaction sites between 4V and PKC alpha. Full-length PKC alpha weakly interacted with 4V by yeast two-hybrid assays, but PKC alpha constructs that lack the pseudosubstrate region or constructs of the whole catalytic domain interacted more strongly. A mutated 4V sequence (4V(YF): LGKKPIFKK) did not interact with PKC alpha, indicating that tyrosine 192 in the syndecan-4 cytoplasmic domain might be critical for this interaction. Further assays identified a novel interaction site in the C terminus of the catalytic domain of PKC alpha (amino acid sequence 513-672). This encompasses the autophosphorylation sites, which are implicated in activation and stability. Yeast two-hybrid data were confirmed by in vitro binding and coimmunoprecipitation assays. The interaction of syndecan-4 with PKC alpha appears unique since PKC delta and epsilon did not interact with 4V in yeast two-hybrid assays or coimmunoprecipitate with syndecan-4. Finally, overexpression of syndecan-4 in rat embryo fibroblast cells, but not expression of the YF mutant, increased PKC alpha localization to focal adhesions. The data support a mechanism where syndecan-4 binds PKC alpha and localizes it to focal adhesions, whose assembly may be regulated by the kinase.