gebhart/patrepeval huggingface dataset:
Characterization of the Epstein-Barr virus-inducible gene encoding the human leukocyte adhesion and activation antigen BLAST-1 (CD48). (1991)

BLAST-1 (CD48) (previously referred to as BCM-1 by the Human Gene Nomenclature Committee) is an early-activation-associated membrane glycoprotein expressed on the surface of human leukocytes and induced to a high level following infection of B cells by the Epstein-Barr virus. It is a member of the immunoglobulin superfamily, mediates cell adhesion, and has significant sequence homology to two other adhesion molecules, CD2 and LFA3. Here we report the isolation and characterization of the BLAST-1 gene. The gene is at least 28.6 kb in length, is split into 4 exons, and contains a restriction fragment-length polymorphism. The overall genomic organization is consistent with other members of the immunoglobulin superfamily, in which extracellular immunoglobulinlike domains are encoded by discrete exons. Transcription is initiated at a series of major and minor sites in both normal and tumor-derived lymphoid cells. Appropriately located TATA and CCAAT box sequences were not detected. These characteristics have also been demonstrated for the recently described B-cell-specific genes B29 and CD20. The expression of these genes in B cells may involve the use of multiple promoters and novel transcription initiator-binding proteins. A 1.58-kb genomic DNA fragment, consisting of the 5'-flanking region located immediately upstream of the ATG initiation codon, was able to drive the expression of a reporter gene in an orientation-dependent and tissue-restricted manner.
Single-Walled Carbon Nanotube Networks Decorated with Silver Nanoparticles:  A Novel Graded SERS Substrate (2007)

We report on investigations of surface-enhanced Raman scattering (SERS) from a nanostructure of single-walled carbon nanotubes (SWNTs) decorated with Ag nanoparticles. Ag is electrochemically deposited on a two-dimensional network of SWNTs, forming nanoparticles of graded density and size away from the contact electrode. The morphology of the Ag nanoparticles on the SWNTs is correlated to their optical properties and the degree of enhancement of the Raman spectra. A strong correlation between localized surface plasmon resonance wavelength, particle size and density, laser excitation wavelength, and SWNT Raman scattering intensity is found. This knowledge is used to increase the degree of enhancement by adjusting the nanoparticle size and density. These results demonstrate a tunable approach to controlling the enhancement of Raman scattering from SWNTs, enabling high sensitivity SERS measurements. Furthermore, the nanostructure produced has considerable potential as a generic SERS substrate for the study of a variety of target molecules in air and under solution.
Control of Cell Behavior During Vertebrate Development by <i>Slug</i> , a Zinc Finger Gene (1994)

Slug, a vertebrate gene encoding a zinc finger protein of the Snail family, is expressed in the neural crest and in mesodermal cells emigrating from the primitive streak. Early chick embryos were incubated with antisense oligonucleotides to chick Slug. These oligonucleotides specifically inhibit the normal change in cell behavior that occurs at the two sites in the emerging body plan in which the gene is expressed. This change, which is the transition from epithelial to mesenchymal character, occurs at the formation of mesoderm during gastrulation and on emigration of the neutral crest from the neural tube.
IDO2 Is a Critical Mediator of Autoantibody Production and Inflammatory Pathogenesis in a Mouse Model of Autoimmune Arthritis (2014)

Rheumatoid arthritis and other autoimmune disorders are associated with altered activity of the immunomodulatory enzyme IDO. However, the precise contributions of IDO function to autoimmunity remain unclear. In this article, we examine the effect of two different IDO enzymes, IDO1 and IDO2, on the development of autoimmune arthritis in the KRN preclinical model of rheumatoid arthritis. We find that IDO2, not IDO1, is critical for arthritis development, providing direct evidence of separate in vivo functions for IDO1 and IDO2. Mice null for Ido2 display decreased joint inflammation relative to wild-type mice owing to a reduction in pathogenic autoantibodies and Ab-secreting cells. Notably, IDO2 appears to specifically mediate autoreactive responses, but not normal B cell responses, as total serum Ig levels are not altered and IDO2 knockout mice are able to mount productive Ab responses to model Ags in vitro and in vivo. Reciprocal adoptive transfer studies confirm that autoantibody production and arthritis are modulated by IDO2 expression in a cell type extrinsic to the T cell. Taken together, our results, provide important insights into IDO2 function by defining its pathogenic contributions to autoantibody-mediated autoimmunity.
High-Gain SIW Filtering Antenna With Low H-Plane Cross Polarization and Controllable Radiation Nulls (2020)

In this communication, a high-gain substrate-integrated waveguide (SIW) filtering patch antenna with low H-plane cross-polarization (cross-pol) and controllable radiation nulls is proposed. The antenna is composed of a radiation patch integrated with three pairs of shorting pins and a single layer SIW cavity with two transverse slots. The shorting pins loaded on the patch can improve the gain and reduce the H-plane cross-pol of the antenna. The long slot on the middle layer can not only split the TE <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">110</sub> -mode resonator into two half-mode resonators but also generate magnetic coupling between half-mode resonators and the patch. Another short slot achieves mixed electric and magnetic coupling between the left half-mode resonator and the patch that introducing controllable radiation nulls to improve the selectivity. By adjusting the parameters of the short slot, the positions of two radiation nulls can be easily controlled. Finally, one prototype filtering antenna is fabricated and measured for demonstration. Experimental results show that the proposed SIW filtering antenna achieves a high gain of 9 dBi with only one radiator and has the merit of high-frequency selectivity as well as low H-plane cross-pol of lower than -43 dB.
First-principles calculation of the electric-field gradient in hcp metals (1988)

The electric-field gradient (EFG) for all hcp metals from Be to Cd is obtained from energy-band calculations using the full-potential linearized-augmented-plane-wave (LAPW) method. Our first-principles method, which does not rely on any Sternheimer antishielding factor, yields EFG's in good agreement with experiment and predicts also the sign of the EFG's. The EFG was found to be determined mainly by the nonspherical distribution of the valence-electron density close to the nucleus. In general, contributions to the EFG originating from p states dominate. This is the case even for transition metals, where the d anisotropy is large.
An Overview of Evolutionary Algorithms for Parameter Optimization (1993)

Three main streams of evolutionary algorithms (EAs), probabilistic optimization algorithms based on the model of natural evolution, are compared in this article: evolution strategies (ESs), evolutionary programming (EP), and genetic algorithms (GAs). The comparison is performed with respect to certain characteristic components of EAs: the representation scheme of object variables, mutation, recombination, and the selection operator. Furthermore, each algorithm is formulated in a high-level notation as an instance of the general, unifying basic algorithm, and the fundamental theoretical results on the algorithms are presented. Finally, after presenting experimental results for three test functions representing a unimodal and a multimodal case as well as a step function with discontinuities, similarities and differences of the algorithms are elaborated, and some hints to open research questions are sketched.
Opportunities For Near-Infrared Thermal Ablation of Colorectal Metastases By Guanylyl Cyclase C-Targeted Gold Nanoshells (2006)

Colorectal cancer is the third most common malignancy and the second most common cause of cancer-related mortality worldwide. While surgery remains the mainstay of therapy, approximately 50% of patients who undergo resection develop parenchymal metastatic disease. Unfortunately, current therapeutic regimens offer little improvement to the survival of patients with parenchymal metastases in the liver and lung. In that context, there is a significant unrealized opportunity at the intersection of engineering and biology for the development of novel targeted therapeutic approaches to colorectal cancer metastases. This opportunity exploits the discovery that an intestinal receptor, guanylyl cyclase C, which mediates diarrhea induced by bacterial heat-stable enterotoxins (STs), is over-expressed by metastatic colorectal tumors only. Moreover, it leverages recent advances in the fabrication of metal nanoshells with defined thicknesses absorb near-infrared (NIR) light, resulting in resonance and transfer of thermal energies of more than 40 degrees C. Thus, the conjugation of ST to gold nanoshells, which can undergo resonance excitation by NIR light and emit heat, represents a previously unrecognized approach for the targeted therapy of parenchymal colorectal cancer metastases, specifically to the liver and lung. This article discusses the potential of ST-targeted nanoshells for NIR thermal ablation of metastatic colorectal tumors and highlights the significant challenges and solutions linked to the translation of this emerging technology to patient care.
On the Performance of Synchronous Multiprocessors (1985)

In this correspondence, we study the performance of a multiprocessor in which a crossbar is employed to interconnect p processors to m commonly shared memory modules. A set of nonuniformly distributed probabilities including a probability P(0) which denotes the probability of a processor not generating any request is also employed to illustrate the program behavior, but no distinction is made between processors. Several relations between the average request completion time, the average processor utilization, and the effective memory bandwidth are obtained. One approximation method based on the idea of aggregation is proposed. Its solutions are compared to the exact solution.
Regulation of ACE2 in cardiac myocytes and fibroblasts (2008)

Angiotensin-converting enzyme 2 (ACE2) preferentially forms angiotensin-(1-7) [ANG-(1-7)] from ANG II. We showed that cardiac ACE2 is elevated following treatment of coronary artery-ligated rats with AT1 receptor blockers (ARBs). Cardiac myocytes and fibroblasts were isolated from neonatal rats to determine the molecular mechanisms for the ACE2 upregulation by ARB treatment. ANG II significantly reduced ACE2 activity and downregulated ACE2 mRNA in cardiac myocytes, effects blocked by the ARB losartan, indicating that ANG II regulates ACE2. ANG II also reduced ACE2 mRNA in cardiac fibroblasts; however, no enzyme activity was detected, reflecting the limited expression of ACE2 in these cells. Endothelin-1 (ET-1) also significantly reduced myocyte ACE2 mRNA. The reduction in ACE2 mRNA by ANG II or ET-1 was blocked by inhibitors of mitogen-activated protein kinase kinase 1, suggesting that ANG II or ET-1 activates extracellular signal-regulated kinase (ERK) 1/ERK2 to reduce ACE2. Although ACE2 mRNA was not affected by ANG-(1-7), both the ANG II- and ET-1-mediated reductions in ACE2 mRNA were blocked by the heptapeptide. The ANG-(1-7) modulatory effect was prevented by the ANG-(1-7) receptor antagonist [D-Ala7]-ANG-(1-7), indicating that the ANG-(1-7) response was mediated by a specific AT(1-7) receptor. Myocyte treatment with atrial natriuretic peptide (ANP) also reversed the ACE2 mRNA downregulation by ANG II or ET-1, whereas treatment with ANP alone was ineffective. These results indicate that multiple hypertrophic and anti-hypertropic peptides regulate ACE2 production in myocytes, suggesting that ACE2 expression in the heart is dependent upon the compliment and concentration of regulatory molecules.
Comparison of Heavy Labeled (SIL) Peptide versus SILAC Protein Internal Standards for LC-MS/MS Quantification of Hepatic Drug Transporters (2014)

We studied the precision of quantification of organic anion-transporting polypeptide 1B1 (OATP1B1), OATP1B3, OATP2B1, and P-glycoprotein (P-gp) in human livers by surrogate peptide based LC-MS/MS approach using two different internal standards: stable isotope labeled peptide (SIL) versus stable isotope labeled protein (SILAC). The SIL peptides were procured commercially and the SILAC proteins were generated in-house by labeling arginine and/or lysine residues in cells expressing these transporters. Liver tissue (n = 20) was homogenized and the membrane fraction was isolated. The membranes were trypsin digested and the peptides were analyzed using LC-MS/MS under optimized conditions. The precision in the quantification of proteins in three independently trypsin digested samples from each liver was calculated as the standard deviation of the log transformed protein concentration. The precision of the SIL internal standard method was either slightly (P < 0.05, paired t-test) better than that of the SILAC method (OATP1B1, OATP1B3, and P-gp) or not different (OATP2B1). Trypsin digestion, as measured by the response of the labeled peptide derived from the SILAC protein, was consistent across liver samples. These results indicate that when maximum trypsin digestion is ensured, the SIL internal standard method can be used with confidence for quantification of drug transporters.
Role of Tumor Necrosis Factor-α and TRAIL in High-Dose Radiation–Induced Bystander Signaling in Lung Adenocarcinoma (2007)

In the present study, ionizing radiation (IR)-induced bystander effects were investigated in two lung cancer cell lines. A549 cells were found to be more resistant to radiation-conditioned medium (RCM) obtained from A549 cells when compared with the H460 exposed to RCM procured from H460 cells. Significant release of tumor necrosis factor-alpha (TNF-alpha) was observed in A549 cells after IR/RCM exposure, and the survival was reversed with neutralizing antibody against TNF-alpha. In H460 cells, significant release of TNF-related apoptosis-inducing ligand (TRAIL), but not TNF-alpha, was observed in response to IR, RCM exposure, or RCM + 2Gy, and neutralizing antibody against TRAIL diminished clonogenic inhibition. Mechanistically, TNF-alpha present in RCM of A549 was found to mediate nuclear factor-kappaB (NF-kappaB) translocation to nucleus, whereas the soluble TRAIL present in RCM of H460 cells mobilized the nuclear translocation of PAR-4 (a proapoptotic protein). Analysis of IR-inducible early growth response-1 (EGR-1) function showed that EGR-1 was functional in A549 cells but not in H460 cells. A significant decrease in RCM-mediated apoptosis was observed in both A549 cells stably expressing small interfering RNA EGR-1 and EGR-1(-/-) mouse embryonic fibroblast cells. Thus, the high-dose IR-induced bystander responses in A549 may be dependent on the EGR-1 function and its target gene TNF-alpha. These findings show that the reduced bystander response in A549 cells is due to activation of NF-kappaB signaling by TNF-alpha, whereas enhanced response to IR-induced bystander signaling in H460 cells was due to release of TRAIL associated with nuclear translocation of PAR-4.
Diffusion maps for high-dimensional single-cell analysis of differentiation data (2015)

Supplementary data are available at Bioinformatics online.
Effects of Dopamine Antagonists Injected Through Vortex Veins on Intraocular Pressure (1989)

In order to avoid the factors of the corneal barrier and tearing washout on absorption of eye drops, dopamine and antagonists were injected into rabbit eyeballs through vortex veins. Many dopamine antagonists, such as haloperidol, moperone, metoclopramide, trifluperidol, lenperone, and fluoropipamide, lowered the intraocular pressure (IOP), whereas a few of them, such as chlofluperol and trifluoperazine, raised the IOP. Furthermore, it was found that dopamine agonists also could either increase or decrease the IOP. The ocular hypertensive effect of dopamine was blocked by haloperidol as expected. However, when the hypotension-inducing dopamine agonist, bromocriptine, and antagonist, haloperidol, were combined, the IOP remained unchanged. It was concluded that dopamine agonists and antagonists act at different sites and changes in IOP resulted from a combined summary of these complex effects. As a result, dopamine agonists and antagonists, while they may both lower the IOP when given alone, can antagonize each other through different sites and produce no net change in IOP.
SYNTHESIS OF 6-(6'-ARYLPYRIDIN-2'-YL) AND 6-(4',6'-DIARYLPYRIDIN-2'-YL)-3(4H)-OXO-1,4-BENZOTHIAZINES UNDER MICROWAVE IRRADIATION CONDITIONS (2006)

Article SYNTHESIS OF 6-(6'-ARYLPYRIDIN-2'-YL) AND 6-(4',6'-DIARYLPYRIDIN-2'-YL)-3(4H)-OXO-1,4-BENZOTHIAZINES UNDER MICROWAVE IRRADIATION CONDITIONS was published on August 1, 2006 in the journal Heterocyclic Communications (volume 12, issue 3-4).
Chimeric Polyomavirus-Derived Virus-Like Particles: The Immunogenicity of an Inserted Peptide Applied without Adjuvant to Mice Depends on Its Insertion Site and Its Flanking Linker Sequence (2007)

We inserted the sequence of the carcinoembryonic antigen-derived T cell epitope CAP-1-6D (CEA) into different positions of the hamster polyomavirus major capsid protein VP1. Independently from additional flanking linkers, yeast-expressed VP1 proteins harboring the CEA insertion between VP1 amino acid residues 80 and 89 (site 1) or 288 and 295 (site 4) or simultaneously at both positions assembled to chimeric virus-like particles (VLPs). BALB/c mice immunized with adjuvant-free VLPs developed VP1- and epitope-specific antibodies. The level of the CEA-specific antibody response was determined by the insertion site, the number of inserts, and the flanking linker. The strongest CEA-specific antibody response was observed in mice immunized with VP1 proteins harboring the CEA insert at site 1. Moreover, the CEA-specific antibodies in these mice were still detectable 6 mo after the final booster immunization. Our results indicate that hamster polyomavirus-derived VLPs represent a highly immunogenic carrier for foreign insertions that might be useful for clinical and therapeutic applications.
<title>Introduction to Bayesian image analysis</title> (1993)

The basic concepts in the application of Bayesian methods to image analysis are introduced. The Bayesian approach has benefits in image analysis and interpretation because it permits the use of prior knowledge concerning the situation under study. The fundamental ideas are illustrated with a number of examples ranging from a problem in one and two dimensions to large problems in image reconstruction that make use of sophisticated prior information.
Physiological Analysis of Growth and Yield of Watermelon (Citrullus ianatus Thunb Musf) in Relation to Irrigation and Nitrogen Fertilization (1988)

Abstract Analysis of growth and yield of watermelon in relation to irrigation and N fertilization carried out at the Indian Institute of Horticultural Research, Bangalore, during 1983–84 and 1984–85 indicated that frequent irrigations when the soil matric potential at 15 cm depth reached ‐25 kPa resulted in maximum dry matter accumulation and distribution, leaf area index (LAI), leaf area duration (LAD), net assimilation rate (NAR) and crop growth rate (CGR) leading to higher fruit yield as compared to irrigations at ‐50 and ‐75 kPa. Imposing a stress of ‐75 kPa either during pre‐flowering or flowering or fruit development phase adversely affected various growth parameters resulting in reduced yield as compared to that irrigated uniformly at ‐25 kPa. Increasing levels of N fertilization increased the dry matter accumulation and distribution through higher LAI, LAD and CGR and contributed larger proportion of the dry matter to fruits resulting in higher fruit yield.
Substitution of Bi for Sb and its Role in the Thermoelectric Properties and Nanostructuring in Ag<sub>1−<i>x</i></sub>Pb<sub>18</sub>MTe<sub>20</sub> (M = Bi, Sb) (<i>x</i> = 0, 0.14, 0.3) (2008)

We have performed a comparative investigation of the Ag1−xPb18MTe20 (M = Bi, Sb) (x = 0, 0.14, 0.3) system to assess the roles of Sb and Bi on the thermoelectric properties. Detailed charge transport data including electrical conductivity, the Seebeck coefficient, the Hall coefficient, and thermal conductivity are presented. Optical reflectivity data support the conclusions of the transport studies. For comparable nominal compositions, the carrier concentrations are lower in the Sb analogs and the mobilities are higher. The Seebeck coefficient decreases dramatically in going from Sb to Bi. High resolution transmission electron microscopy (TEM) images of both samples reveal that all systems contain compositional fluctuations at the nanoscopic level and are nanostructured. Compared to PbTe, the lattice thermal conductivity of AgPb18BiTe20 is substantially reduced. The lattice thermal conductivity of the Bi analog is, however, higher than the Sb analog, and this correlates with the decrease in the degree of mass fluctuation between the nanostructures and the matrix (for the Bi analog). As a result the dimensionless figure of merit ZT of Ag1−xPb18BiTe20 is found to be substantially smaller than that of Ag1−xPb18SbTe20. Electronic structure calculations performed within the density functional theory and generalized gradient approximation show marked differences in the band structure near the Fermi level between the two analogs providing useful insights on the carrier transport in these systems.
Production of Bioactive, Post-Translationally Modified, Heterotrimeric, Human Recombinant Type-I Collagen in Transgenic Tobacco (2009)

Collagen's biocompatibility, biodegradability and low immunogenicity render it advantageous for extensive application in pharmaceutical or biotechnological disciplines. However, typical collagen extraction from animal or cadaver sources harbors risks including allergenicity and potential sample contamination with pathogens. In this work, two human genes encoding recombinant heterotrimeric collagen type I (rhCOL1) were successfully coexpressed in tobacco plants with the human prolyl-4-hydroxylase (P4H) and lysyl hydroxylase 3 (LH3) enzymes, responsible for key posttranslational modifications of collagen. Plants coexpressing all five vacuole-targeted proteins generated intact procollagen yields of approximately 2% of the extracted total soluble proteins. Plant-extracted rhCOL1 formed thermally stable triple helical structures and demonstrated biofunctionality similar to human tissue-derived collagen supporting binding and proliferation of adult peripheral blood-derived endothelial progenitor-like cells. Through a simple, safe and scalable method of rhCOL1 production and purification from tobacco plants, this work broadens the potential applications of human recombinant collagen in regenerative medicine.
The Impact of the Space Radiation Environment on Micro Electro Mechanical Systems (MEMS) and Microstructures (2005)

Micro electro mechanical system (MEMS) and microstructures yield great promise for future space applications and the requirements to understand their relationship to the uniqueness of space. A key enabler for inserting MEMS in critical flight applications is an understanding of the environmental impacts including radiation effects. MEMS devices used in space missions are exposed to many different types of environments. These environments include manufacturing, assembly, test and qualification at the part, board and assembly levels. Subsystem and system level environments include pre-launch, launch, and mission. Each of these environments contributes unique stress factors. An overview of these stress factors is given along with a discussion of the environments with an emphasis on the radiation environment.