gebhart/patrepeval huggingface dataset:
ConsensusPathDB—a database for integrating human functional interaction networks (2008)

ConsensusPathDB is a database system for the integration of human functional interactions. Current knowledge of these interactions is dispersed in more than 200 databases, each having a specific focus and data format. ConsensusPathDB currently integrates the content of 12 different interaction databases with heterogeneous foci comprising a total of 26,133 distinct physical entities and 74,289 distinct functional interactions (protein-protein interactions, biochemical reactions, gene regulatory interactions), and covering 1738 pathways. We describe the database schema and the methods used for data integration. Furthermore, we describe the functionality of the ConsensusPathDB web interface, where users can search and visualize interaction networks, upload, modify and expand networks in BioPAX, SBML or PSI-MI format, or carry out over-representation analysis with uploaded identifier lists with respect to substructures derived from the integrated interaction network. The ConsensusPathDB database is available at: http://cpdb.molgen.mpg.de.
Smart meeting systems (2010)

Smart meeting systems, which record meetings and analyze the generated audio--visual content for future viewing, have been a topic of great interest in recent years. A successful smart meeting system relies on various technologies, ranging from devices and algorithms to architecture. This article presents a condensed survey of existing research and technologies, including smart meeting system architecture, meeting capture, meeting recognition, semantic processing, and evaluation methods. It aims at providing an overview of underlying technologies to help understand the key design issues of such systems. This article also describes various open issues as possible ways to extend the capabilities of current smart meeting systems.
High activity ethylene polymerisation catalysts based on chelating diamide ligands (1998)

Treatment of Zr(NMe2)4 with RNH(SiPh2)NHR and RNH(Me2SiCH2CH2SiMe2)NHR (R = 2,6-Me2C6H3) affords the four- and seven-membered chelate complexes {Zr[RN(SiPh2)NR](NMe2)2(HNMe2)} and {Zr[RN(Me2SiCH2CH2SiMe2)NR](NMe2)2} respectively; a dramatic effect of chelate ring size on ethylene polymerisation activity and kinetic profile is found.
Methoxycarbonyl-etomidate (2009)

MOC-etomidate is an etomidate analogue that retains etomidate's important favorable pharmacological properties. However, it is rapidly metabolized, ultra-short-acting, and does not produce prolonged adrenocortical suppression after bolus administration.
95 GHz millimeter wave signal generation using an arrayed waveguide grating dual wavelength semiconductor laser (2012)

We report the generation of a 95 GHz carrier frequency by optical heterodyning of two wavelengths from adjacent channels from an arrayed waveguide grating-based multiwavelength laser. The extended cavity structure of the device provides low phase noise and narrow optical linewidth, further enhanced by the intracavity filter effect of the arrayed waveguide grating. We demonstrate that the generated RF beat note, at 95 GHz, has a -3 dB linewidth of 250 kHz. To the best of our knowledge, this is the narrowest RF linewidth generated from a free-running dual-wavelength semiconductor laser. The device is realized as a photonic integrated circuit using active-passive integration technology, and fabricated on a multiproject wafer run, constituting a novel approach for a compact, low-cost dual-wavelength heterodyne source.
Evaluation of nanopores as candidates for electronic analyte detection (2002)

In an effort to increase throughput and decrease the cost of electrophoretic separation of DNA and proteins, various groups are developing highly parallel, miniaturized separation devices based on capillaries etched into silicon, glass or plastic substrates. To date, these miniaturized devices have relied on optical detectors, thus placing a lower limit on instrument size, and complicating the incorporation of an entire DNA analyzer instrument on a chip. To address this limitation, we are evaluating nanopores as candidate Coulter counters for purely electronic detection of analytes in miniaturized electrophoresis and similar separation devices. To establish feasibility of this detection scheme, we have investigated the detection sensitivity of a nanopore sensor through experiments with the alpha-hemolysin (alpha-HL) ion channel, and through a Monte Carlo (MC) model of polymer capture rate with a cylindrical nanopore under an applied voltage. Experimental and model results are extrapolated to predict the capture rate of synthetic pores operating at higher voltages than presently achievable with protein pores.
T Cell Regulation of Bacteroides fragilis–Induced Intraabdominal Abscesses (1990)

Intraabdominal abscesses (IAA) caused by Bacteroides fragilis are a major sequela to colonic spillage into the peritoneum. The development of an animal model that closely reproduces the disease observed in humans permitted careful inspection of the cellular and/or humoral contributions to the development and control of this disease. The results obtained thus far describe an immunoregulatory T cell circuit that governs both the development of and the immunity against these abscesses. T cells of CD4+8+ phenotype induce the development of IAA in response to B. fragilis. CD8+ T cells generated in response to immunization with the B. fragilis capsular polysaccharide confer protection against the development of IAA. These cells elaborate an antigen-specific factor that mediates the observed protection by these cells. Moreover, a third type of T cell, a CD8+ cell that is also present in nonimmune individuals, is required for the immune T cell or its factor to confer protection. Thus, in the specific disease process of IAA induced by the encapsulated microorganism B. fragilis, immunity proceeds by cellular and not humoral mechanisms.
Simultaneous isolation and preconcentration of exosomes by ion concentration polarization (2018)

Exosomes carry microRNA biomarkers, occur in higher abundance in cancerous patients than in healthy ones, and because they are present in most biofluids, including blood and urine, these can be obtained noninvasively. Standard laboratory techniques to isolate exosomes are expensive, time consuming, provide poor purity, and recover on the order of 25% of the available exosomes. We present a new microfluidic technique to simultaneously isolate exosomes and preconcentrate them by electrophoresis using a high transverse local electric field generated by ion-depleting ion-selective membrane. We use pressure-driven flow to deliver an exosome sample to a microfluidic chip such that the transverse electric field forces them out of the cross flow and into an agarose gel which filters out unwanted cellular debris while the ion-selective membrane concentrates the exosomes through an enrichment effect. We efficiently isolated exosomes from 1× PBS buffer, cell culture media, and blood serum. Using flow rates from 150 to 200 μL/h and field strengths of 100 V/cm, we consistently captured between 60 and 80% of exosomes from buffer, cell culture media, and blood serum as confirmed by both fluorescence spectroscopy and nanoparticle tracking analysis. Our microfluidic chip maintained this recovery rate for more than 20 min with a concentration factor of 15 for 10 min of isolation.
Histamine H3receptor antagonists (2000)

AbstractThe histamine H3 receptor provides a negative feedback mechanism for the release and synthesis of histamine. On non-histaminergic neurones the H3 receptor regulates the release of many other neurotransmitters. Blockade of stimulated H3 receptors results in the release of endogenous neurotransmitters. Possible indications for a histamine H3 receptor antagonist include attention-deficit hyperactivity disorder (ADHD), epilepsy, Alzheimer’s disease, narcolepsy, epilepsy, obesity, schizophrenia and respiratory diseases such as allergic rhinitis. Current H3 receptor antagonists fall into two classes, imidazole-containing and non-imidazole compounds, with there being far more examples of the former. The development of imidazole antagonists has produced the compound GT-2331 (Perceptin™, Gliatech), which has successfully passed early stage clinical trials. The search for non-imidazole antagonists is a burgeoning area, which may profit from the recent cloning of a human H3 receptor.Keywordsallergic rhinitisAlzheimer’s diseaseattention-deficit hyperactivity disorderepilepsyGT-2331histamine H3 antagonisthistamineimidazolenarcolepsyobesityschizophrenia
Hypoxia-Inducible Factor-1α and the Glycolytic Phenotype in Tumors (2005)

Metastatic tumors generally exhibit aerobic glycolysis (the Warburg effect). The advent of [18F]fluorodeoxyglucose positron emission tomography imaging, coupled with recent findings linking hypoxia-inducible factor (HIF-1alpha) overexpression to aggressive cancers, has rekindled an interest in this aspect of tumor metabolism. These studies explore the role of HIF-1alpha in human breast cancer lines and its relationship to glycolytic regulation. Here we demonstrate that, under normal oxygen conditions, nonmetastatic cells consume less glucose and express low HIF-1alpha, whereas metastatic cells constitutively express high glycolysis and HIF-1alpha, suggesting that dysregulation of HIF-1alpha may induce the Warburg effect. This hypothesis was tested by renormalizing HIF-1alpha levels in renal carcinoma cells, leading to inhibition of aerobic glycolysis.
Campylobacter-like omega intracellular antigen in proliferative colitis of ferrets. (1988)

Proliferative colitis in the ferret consistently displays, along with marked proliferation of mucosal cells, intracytoplasmic campylobacter-like organisms within the apical portion of the epithelial cells. Fluorescent antibody to "omega" campylobacter antigen present in porcine intestinal adenomatosis and hamster proliferative ileitis was demonstrated at the site of bacterial colonization within hyperplastic epithelial cells of six colons from ferrets affected with proliferative colitis.
Poloxamer 188 Volumetrically Decreases Neuronal Loss in the Rat in a Time-dependent Manner (2004)

Intrathecal P-188 reduces neuronal loss after excitotoxic injury in the rat only when delivered immediately after the toxin. This observation confirms the potential of surfactant molecules as neuroprotectants but predicts that their usefulness is best realized by early and potentially ongoing treatment.
Tumor Necrosis Factor-Dependent Adhesions as a Major Protective Mechanism Early in Septic Peritonitis in Mice (2001)

The occurrence of peritoneal adhesions in surgical patients is positively correlated with tumor necrosis factor (TNF) levels. In a model of septic peritonitis-cecal ligation and puncture-TNF neutralization prevented formation of peritoneal adhesions and increased mortality, most likely because localization of the septic focus was prevented. To discriminate between the coagulation-independent protective TNF effect and a potential protective procoagulant TNF effect, formation of peritoneal adhesions after CLP was inhibited with heparin, hirudin, or urokinase. Each treatment increased mortality and increased the number of bacteria in the peritoneal lavage fluid, kidney, and liver to various degrees. Under these experimental conditions, antibiotics prevented death. In coagulation-compromised mice, lethality was further enhanced by additional TNF neutralization. These findings demonstrate that peritoneal adhesions early in septic peritonitis are an important mechanism of innate immunity that prevents increased spread of bacteria and reduces mortality.
<title>Lithographic simulation: a review</title> (2001)

A review of the current state of the art in optical and electron beam lithography simulation is presented. Basic physical models are described and examples are given. In addition, rigorous electromagnetic simulation for mask topography is shown and the use of statistical modeling to predict feature size distributions in manufacturing is described. Finally, numerous examples of the use of lithography simulation and its impact on the semiconductor industry are offered.
Application of massive parallel sequencing to whole genome SNP discovery in the porcine genome (2009)

Background: Although the Illumina 1 G Genome Analyzer generates billions of base pairs of sequence data, challenges arise in sequence selection due to the varying sequence quality. Therefore, in the framework of the International Porcine SNP Chip Consortium, this pilot study aimed to evaluate the impact of the quality level of the sequenced bases on mapping quality and identification of true SNPs on a large scale.
Similar Efficacy with Omalizumab in Chronic Idiopathic/Spontaneous Urticaria Despite Different Background Therapy (2015)

Omalizumab 300 mg was safe and effective in reducing CIU/CSU symptoms regardless of background therapy.
Photoconduction Properties in Aligned Assemblies of Colloidal CdSe/CdS Nanorods (2010)

We report on photoconduction and optical properties of aligned assemblies of core-shell CdSe/CdS nanorods prepared by a seeded growth approach. We fabricate oriented layers of nanorods by drop casting the nanorods from a solution on substrates with prepatterned, micrometer-spaced electrodes and obtain nanorod alignment due to the coffee stain effect. The photoconductivity of the nanorod layers can be improved significantly by an annealing process under vacuum conditions. The spectral response of the photocurrent shows distinct features that can be assigned to the electronic level structure of the core-shell nanorods and that relate well to the spectra obtained by absorption measurements. We study assemblies of nanorods oriented parallel and perpendicular to the applied electric field by the combined use of photocurrent and photoluminescence spectroscopy. We obtain consistent results which show that charge carrier separation and transport are more efficient for nanorods oriented parallel to the electric field. We also investigate the light polarization sensitivity of the photocurrent for the oriented nanorod layers and observe higher conductivity in the case of perpendicular polarization with respect to the long axis of the nanorods.
Syndecan‐2 can promote clearance of T‐cell receptor/CD3 from the cell surface (2012)

T cells express the heparan sulphate proteoglycans syndecan-2 and syndecan-4. Syndecan-4 plays a T-cell inhibitory role; however, the function of syndecan-2 is unknown. In an attempt to examine this function, syndecan-2 was expressed constitutively in Jurkat T cells. Interestingly, the expression of syndecan-2 decreased the surface levels of T-cell receptor (TCR)/CD3 complex, concomitant with intracellular retention of CD3ε and partial degradation of the TCR-ζ chain. Immunofluorescence microscopy revealed that intracellular CD3ε co-located with Rab-4 endosomes. However, the intracellular pool of CD3ε did not recycle to the cell surface. The lower TCR/CD3 surface levels caused by syndecan-2 led to reduced TCR/CD3 responsiveness. We show that the cytosolic PDZ-binding domain of syndecan-2 is not necessary to elicit TCR/CD3 down-regulation. These results identify a previously unrecognized means of controlling surface TCR/CD3 expression by syndecan-2.
Next‐Generation o‐Nitrobenzyl Photolabile Groups for Light‐Directed Chemistry and Microarray Synthesis (2015)

Light as an external trigger is a valuable and easily controllable tool for directing chemical reactions with high spatial and temporal accuracy. Two o-nitrobenzyl derivatives, benzoyl- and thiophenyl-NPPOC, undergo photo-deprotection with significantly improved efficiency over that of the commonly used NPPOC group. The two- and twelvefold increase in photo-deprotection efficiency was proven using photolithograph synthesis of microarrays.
Analysis of transgene-specific immune responses that limit the in vivo persistence of adoptively transferred HSV-TK–modified donor T cells after allogeneic hematopoietic cell transplantation (2005)

The introduction of an inducible suicide gene such as the herpes simplex virus thymidine kinase (HSV-TK) might allow exploitation of the antitumor activity of donor T cells after allogeneic hematopoietic cell transplantation (HCT) without graft versus host disease. However, HSV-TK is foreign, and immune responses to gene-modified T cells could lead to their premature elimination. We show that after the infusion of HSV-TK-modified donor T cells to HCT recipients, CD8+ and CD4+ T-cell responses to HSV-TK are rapidly induced and coincide with the disappearance of transferred cells. Cytokine flow cytometry using an overlapping panel of HSV-TK peptides allowed rapid detection and quantitation of HSV-TK-specific T cells in the blood and identified multiple immunogenic epitopes. Repeated infusion of modified T cells boosted the induced HSV-TK-specific T cells, which persisted as memory cells. These studies demonstrate the need for nonimmunogenic suicide genes and identify a strategy for detection of CD4+ and CD8+ T-cell responses to transgene products that should be generally applicable to monitoring patients on gene therapy trials. The potency of gene-modified T cells to elicit robust and durable immune responses imply this approach might be used for vaccination to elicit T-cell responses to viral or tumor antigens.
Pharmacokinetics of Rytary®, An Extended-Release Capsule Formulation of Carbidopa–Levodopa (2017)

Parkinson's disease (PD) is a chronic progressive neurological disorder characterized by resting tremor, rigidity, bradykinesia, gait disturbance, and postural instability. Levodopa, the precursor to dopamine, coadministered with carbidopa or benserazide, aromatic amino acid decarboxylase inhibitors, is the most effective and widely used therapeutic agent in the treatment of PD. With continued levodopa treatment, a majority of patients develop motor complications such as dyskinesia and motor 'on-off' fluctuations, which are, in part, related to the fluctuations in plasma concentrations of levodopa. A new extended-release (ER) carbidopa-levodopa capsule product (also referred to as IPX066) was developed and approved in the US as Rytary<sup>®</sup> and in the EU as Numient<sup>®</sup>. The capsule formulation is designed to provide an initial rapid absorption of levodopa comparable to immediate-release (IR) carbidopa-levodopa, and to subsequently provide stable levodopa concentrations with reduced peak-to-trough excursions in plasma concentrations in order to reduce motor fluctuations associated with pulsatile stimulation of dopamine receptors and to minimize dyskinesia. Phase III studies of this ER carbidopa-levodopa capsule formulation in patients with PD have shown a significant reduction in 'off' time compared with IR carbidopa-levodopa and carbidopa-levodopa-entacapone. We present a review of the clinical pharmacokinetics and pharmacodynamics of this ER product of carbidopa-levodopa in healthy subjects and in patients with PD.
Rapid visual information processing as a cognitive endophenotype of attention deficit hyperactivity disorder (2013)

Our findings suggest that attention performance assessed by the RVP task, but not the RTI or MTS tasks, of the CANTAB may be a useful cognitive endophenotype for ADHD genetic studies.
Intravenous or Epidural Clonidine for Intra- and Postoperative Analgesia (1993)

Epidural clonidine reduces the intra- and early postoperative analgesic requirements when compared with the same dose given by the intravenous route. The side effects were similar with the two routes of administration.
Characterization of A2A adenosine receptors in human lymphocyte membranes by [3H]‐SCH 58261 binding (1997)

1. The present study describes for the first time the characterization of the adenosine A2A receptor in human lymphocyte membranes with the new potent and selective antagonist radioligand, [3H]-5-amino-7-(2-phenylethyl)-2-(2-furyl)-pyrazolo [4,3-e]-1,2,4 triazolo [1,5-c] pyrimidine, ([3H]-SCH 58261). In addition, both receptor affinity and potency of reference adenosine receptor agonists and antagonists were determined in binding and adenylyl cyclase studies. 2. Saturation experiments revealed a single class of binding sites with Kd and Bmax values of 0.85 nM and 35 fmol mg-1 protein, respectively. A series of adenosine receptor ligands were found to compete for the binding of 0.8 nM [3H]-SCH 58261 to human lymphocyte membranes with a rank order of potency consistent with that typically found for interactions with the A2A-adenosine receptor. In the adenylyl cyclase assay the same compounds exhibited a rank order of potency similar to that observed in binding experiments. 3. Thermodynamic data indicate that [3H]-SCH 58261 binding to human lymphocytes is entropy and enthalpy-driven, a finding in agreement with the thermodynamic behaviour of antagonists for rat striatal A2A-adenosine receptors. 4. It is concluded that in human lymphocyte membranes [3H]-SCH 58261 directly labels binding sites showing the characteristic properties of the adenosine A2A-receptor. The presence of A2A-receptors in peripheral tissue such as human lymphocytes strongly suggests an important role for adenosine in modulating immune and inflammatory responses.
Engineered oryzacystatin‐I expressed in transgenic hairy roots confers resistance to Globodera pallida (1995)

The cysteine proteinase inhibitor, oryzacystatin-I (Oc-I), and several engineered Oc-I variants have been tested for efficacy in inhibiting growth and development of both the free-living nematode, Caenorhabditis elegans, and the plant parasitic nematode Globodera pallida. To assist in the design of protein engineering experiments to improve the efficacy of Oc-I, an alignment of 28 cystatins and a molecular model of Oc-I were generated. Inhibitory activities (Ki) of wild-type and variant forms of Oc-I against both papain and the C. elegans cysteine proteinase, gcp-1, were measured. For one variant, in which residue Asp86 was deleted (Oc-I deltaD86), the Ki was reduced by 13- to 14-fold. LD50 studies to test the effect of Oc-I and Oc-I delta D86 against C. elegans showed the relative median potency of Oc-I delta D86 to be 0.76 that of wild-type Oc-I. When expressed in tomato hairy roots both Oc-I and Oc-I delta D86 had a detrimental effect on growth and development of G. pallida. This effect was significantly greater on Oc-I deltaD86-expressing roots leading to a reduction in size of G. pallida females to a level at which fecundity is profoundly affected.