gebhart/patrepeval huggingface dataset:
Identification of specific residues of human interleukin 2 that affect binding to the 70-kDa subunit (p70) of the interleukin 2 receptor. (1988)

Analogs of interleukin 2 containing defined amino acid substitutions and deletions were assayed for bioactivity and for competitive binding to the high-affinity human interleukin 2 receptor complex and its two component subunits, a 55-kDa subunit (p55 or TAC) and a 70-kDa subunit (p70). Substitution of Asp20 or deletion of Phe124 resulted in inactive analog proteins that were unable to interact with the high-affinity p55/p70 complex or the intermediate-affinity p70 subunit of the interleukin 2 receptor. These analogs, however, retained the capacity to compete for binding to the low-affinity p55 subunit. The presence of the carboxylic acid in the side chain of Asp20 was necessary for effective binding to the p70 protein. In contrast, substitution of Trp121 and Leu17 created analogs that were inactive in the bioassay and all three binding assays. The effects of these mutations on protein conformation were assessed by circular dichroism. These results demonstrate that specific residues in the NH2 and COOH termini of interleukin 2 are crucial for its structure and activity.
Assessing Advising Style: Student Perceptions of Academic Advisors (2001)

In this large, geographically diverse population, A(H1N1)pdm09 infection increased the risk for hospitalization during pregnancy. Late initiation of antiviral treatment was also associated with an increased risk for hospitalization.
Restoration of NET formation by gene therapy in CGD controls aspergillosis (2009)

Chronic granulomatous disease (CGD) patients have impaired nicotinamide adenine dinucleotide phosphate (NADPH) oxidase function, resulting in poor antimicrobial activity of neutrophils, including the inability to generate neutrophil extracellular traps (NETs). Invasive aspergillosis is the leading cause of death in patients with CGD; it is unclear how neutrophils control Aspergillus species in healthy persons. The aim of this study was to determine whether gene therapy restores NET formation in CGD by complementation of NADPH oxidase function, and whether NETs have antimicrobial activity against Aspergillus nidulans. Here we show that reconstitution of NET formation by gene therapy in a patient with CGD restores neutrophil elimination of A nidulans conidia and hyphae and is associated with rapid cure of preexisting therapy refractory invasive pulmonary aspergillosis, underlining the role of functional NADPH oxidase in NET formation and antifungal activity.
Long-Term Prognosis of Different Forms of Coronary Heart Disease: The Reykjavik Study (1995)

Different categories of CHD had different risk factor profiles and the long-term prognosis resulted from a complex interplay between those factors and the diagnostic category of CHD. The risk factors maintained their detrimental effects on prognosis in the presence of CHD and after accounting for the comprehensive risk factor score marked differences persisted in the long-term prognosis, being worst for those having suffered a myocardial infarction, either symptomatic or silent.
An IF CMOS signal component separator chip for LINC transmitters (2002)

The LINC transmitter provides linear amplification using highly nonlinear but power efficient amplifiers. The signal component separator (SCS) is a crucial function of LINC. This paper presents an IF SCS chip implemented in a 0.35 /spl mu/m CMOS process using a design based on voltage-translinear circuits. The experimental LINC transmitter, built with the chip and nonlinear amplifiers, had output spurious levels some -55 dBc and -48 dBc for a NADC signal and an IS-95 signal, respectively. This implies a high degree of linearity.
The Study of Porous Media Reconstruction Using a 2D Micro-CT Image and MPS (2009)

A new method named multiple-point geostatistics (MPS) which originated from geoscience allows extracting the characteristics and structures from training images and anchoring them to the simulated regions. The 3D reconstruction of porous media is quite significant to the study of mechanisms of fluid flow in porous media. Therefore, a method using a real 2D micro-CT image and MPS to reconstruct the 3D structures of porous media is proposed. A cross-section of porous media, with the resolution of 10 microns, obtained by micro-CT scanning is used as an original training image. By using MPS and extracted sample points from each former regenerated training image, each newly reconstructed image is taken as a new training image to reconstruct its next layer. Then, the stochastic 3D images of porous media are generated by stacking all the reconstructed layers successively. The permeabilities of the reconstructed images and the target image composed of real sandstone volume data were computed by using lattice Boltzmann method (LBM) for comparison. The experimental results show that although the structures of porous media reconstructed through this method are stochastic, all the reconstructed results have the similar structures, which are close to those of real volume data obtained by micro-CT scanning, demonstrating better reconstructed results than what two-point geostatistics does.
Expression and Regulation of Normal and Polymorphic Epithelial Sodium Channel by Human Lymphocytes (2001)

Gene expression, protein expression, and function of amiloride-sensitive sodium channels were examined in human lymphocytes from normal individuals and individuals with Liddle's disease. Using reverse transcriptase polymerase chain reactions, expression of all three cloned epithelial sodium channel (ENaC) subunits was detected in lymphocytes. Polyclonal antibodies to bovine alpha-ENaC bound to the plasma membrane of normal and Liddle's lymphocytes. A quantitative analysis of fluorescence-tagged ENaC antibodies indicated a 2.5-fold greater surface binding of the antibodies to Liddle's lymphocytes compared with normal lymphocytes. The relative binding intensity increased significantly (25%; p < 0.001) for both normal and Liddle's cells after treatment with 40 microM 8-CPT-cAMP. Amiloride-sensitive whole cell currents were recorded under basal and cAMP-treated conditions for both cell types. Liddle's cells had a 4.5-fold larger inward sodium conductance compared with normal cells. A specific 25% increase in the inward sodium current was observed in normal cells in response to cAMP treatment. Outside-out patches from both cell types under both treatment conditions revealed no obvious differences in the single channel conductance. The P(open) was 4.2 +/- 3.9% for patches from non-Liddle's cells, and 27.7 +/- 5.4% in patches from Liddle's lymphocytes. Biochemical purification of a protein complex, using the same antibodies used for the immunohistochemistry, yielded a functional sodium channel complex that was inhibited by amiloride when reconstituted into lipid vesicles and incorporated into planar lipid bilayers. These four independent methodologies yielded findings consistent with the hypotheses that human lymphocytes express functional, regulatable ENaC and that the mutation responsible for Liddle's disease induces excessive channel expression.
Maintaining interactivity while exploring massive time series (2008)

The speed of data retrieval qualitatively affects how analysts visually explore and analyze their data. To ensure smooth interactions in massive time series datasets, one needs to address the challenges of computing ad hoc queries, distributing query load, and hiding system latency. In this paper, we present ATLAS, a visualization tool for temporal data that addresses these issues using a combination of high performance database technology, predictive caching, and level of detail management. We demonstrate ATLAS using commodity hardware on a network traffic dataset of more than a billion records.
Conditional gene targeted deletion by Cre recombinase demonstrates the requirement for the double-strand break repair Mre11 protein in murine embryonic stem cells (1997)

Repair of DNA damage resulting in double-strand breaks (DSBs) is controlled by gene products executing homologous recombination or end-joining pathways. The MRE11 gene has previously been implicated in DSB repair in the yeast Saccharomyces cerevisiae . Here we have developed a methodology to study the roles of the murine Mre11 homolog in pluripotent embryonic stem cells. Using a gene targeting approach, a triple LoxP site cassette was inserted into a region of MRE11 genomic DNA flanking conserved phosphodiesterase motifs. The addition of Cre recombinase activity promotes deletions of three types that can be scored. We find that deletion at phosphodiesterase motif III encoded in the N-terminus of Mre11 is acheived in the presence of a wild-type MRE11 allele. However, when the wild-type MRE11 allele is inactivated by gene targeted insertion of a neo marker, only Cre recombination events that allow expression of wild-type Mre11 protein are observed. Therefore, Mre11 is required for normal cell proliferation. This methodology introduces a means to study important regions of essential genes in cell culture models.
Grapefruit juice–felodipine interaction: Mechanism, predictability, and effect of naringin (1993)

Grapefruit juice produces a marked and variable increase in felodipine bioavailability. The pharmacokinetics of felodipine and its single primary oxidative metabolite, dehydrofelodipine, were studied after drug administration with 200 ml water, grapefruit juice, or naringin in water at the same concentration as the juice in a randomized crossover trial of nine healthy men. With grapefruit juice, mean +/- SEM felodipine area under the plasma concentration-time curve (AUC) and peak plasma concentration (Cmax) were 206% +/- 23% (range, 123% to 330%, p < 0.01) and 170% +/- 24% (range, 127% to 310%, p < 0.02), respectively, compared with water. Dehydrofelodipine/felodipine ratios for AUC (1.5 +/- 0.2 versus 2.2 +/- 0.2, p < 0.001) and felodipine Cmax (1.5 +/- 0.2 versus 2.2 +/- 0.2, p < 0.001) were reduced, consistent with inhibition of presystemic felodipine metabolism. Intersubject changes in felodipine and dehydrofelodipine AUC supported inhibition of both primary and secondary metabolic steps as a mechanism. The interaction could not be predicted from baseline pharmacokinetics with water and did not result in more consistent bioavailability among individuals. Naringin solution produced much less of an interaction, showing that other factors were important.
Type- and subtype-specific detection of influenza viruses in clinical specimens by rapid culture assay (1995)

A rapid culture assay which allows for the simultaneous typing and subtyping of currently circulating influenza A(H1N1), A(H3N2), and B viruses in clinical specimens was developed. Pools of monoclonal antibodies (MAbs) against influenza A and B viruses and MAbs HA1-71 and HA2-76, obtained by immunizing mice with the denatured hemagglutinin subfragments HA1 and HA2 of influenza virus A/Victoria/3/75, were used for immunoperoxidase staining of antigens in infected MDCK cells. MAb HA1-71 reacted exclusively with influenza A viruses of the H3 subtype, while MAb HA2-76 reacted with subtypes H1, H3, H4, H6, H8, H9, H10, H11, and H12, as determined with 78 human, 4 swine, and 10 avian influenza virus reference strains subtyped by the hemagglutination inhibition test. To determine if the technique can be used as a rapid diagnostic test, 263 known influenza virus-positive frozen nasal or throat swabs were inoculated into MDCK cells. After an overnight incubation, the cells were fixed and viral antigens were detected by immunoperoxidase staining. Influenza A viruses of the H1 and H3 subtypes were detected in 31 and 113 specimens, respectively. The subtypes of 10 influenza A virus-positive specimens could not be determined because they contained too little virus. Influenza B viruses were detected in 84 specimens, and 25 specimens were negative. We conclude that this assay is a rapid, convenient, non-labor-intensive, and relatively inexpensive test for detecting, typing, and subtyping influenza viruses in clinical specimens.
Probing the mechanism and improving the rate of substrate-assisted catalysis in subtilisin BPN' (1991)

A mutant of the serine protease, subtilisin BPN', in which the catalytic His64 is replaced by Ala (H64A), is very specific for substrates containing a histidine, presumably by the substrate-bound histidine assisting in catalysis [Carter, P., & Wells, J.A. (1987) Science (Washington, D.C.) 237, 394-399]. Here we probe the catalytic mechanism of H64A subtilisin for cleaving His and non-His substrates. We show that the ratio of aminolysis to hydrolysis is the same for ester and amide substrates as catalyzed by the H64A subtilisin. This is consistent with formation of a common acyl-enzyme intermediate for H64A subtilisin, analogous to the mechanism of the wild-type enzyme. However, the catalytic efficiencies (kcat/KM) for amidase and esterase activities with His-containing substrates are reduced by 5000-fold and 14-fold, respectively, relative to wild-type subtilisin BPN, suggesting that acylation is more compromised than deacylation in the H64A mutant. High concentrations of imidazole are much less effective than His substrates in promoting hydrolysis by the H64A variant, suggesting that the His residue on the bound (not free) substrate is involved in catalysis. The reduction in catalytic efficiency kcat/KM for hydrolysis of the amide substrate upon replacement of the oxyanion stabilizing asparagine (N155G) is only 7-fold greater for wild-type than H64A subtilisin. In contrast, the reductions in kcat/KM upon replacement of the catalytic serine (S221A) or aspartate (D32A) are about 3000-fold greater for wild-type than H64A subtilisin, suggesting that the functional interactions between the Asp32 and Ser221 with the substrate histidine are more compromised in substrate-assisted catalysis.(ABSTRACT TRUNCATED AT 250 WORDS)
Surface Free Energy of Alloy Nitride Coatings Deposited Using Closed Field Unbalanced Magnetron Sputter Ion Plating (2006)

The sticking of product material to injection molding tools is a serious problem, which reduces productivity and reliability. Depositing alloy nitride coatings (TiN, ZrN, CrN, and TiAlCrN) using closed field unbalanced magnetron sputter ion plating and electrodeposition of chromium, and characterizing their surface free energies in the temperature range 20–120°C have led to the development of a non-sticking (with a low surface free energy) coating system for semiconductor IC packaging molding dies. The contact angles of water, diiodomethane and ethylene glycol on the coated surfaces were measured at temperatures in the range 20–120°C using a Dataphysics OCA-20 contact angle analyzer. The surface free energy of the coatings and their components (dispersion and polar) were calculated using the Owens-Wendt geometric mean approach. The surface roughness of these coatings were investigated by atomic force microscopy (AFM). The adhesion force of these coatings were measured using direct tensile pull-off test apparatus. The experimental results revealed that TiAlCrN, CrN and ZrN coatings outperformed Hard-Cr and TiN coatings in terms of anti-adhesion, and thus have the potential as working layers for injection molding industrial equipment, especially in semiconductor IC packaging molding applications.
Ubiquitous Transgenic Expression of the IL-23 Subunit p19 Induces Multiorgan Inflammation, Runting, Infertility, and Premature Death (2001)

p19, a molecule structurally related to IL-6, G-CSF, and the p35 subunit of IL-12, is a subunit of the recently discovered cytokine IL-23. Here we show that expression of p19 in multiple tissues of transgenic mice induced a striking phenotype characterized by runting, systemic inflammation, infertility, and death before 3 mo of age. Founder animals had infiltrates of lymphocytes and macrophages in skin, lung, liver, pancreas, and the digestive tract and were anemic. The serum concentrations of the proinflammatory cytokines TNF-alpha and IL-1 were elevated, and the number of circulating neutrophils was increased. In addition, ubiquitous expression of p19 resulted in constitutive expression of acute phase proteins in the liver. Surprisingly, liver-specific expression of p19 failed to reproduce any of these abnormalities, suggesting specific requirements for production of biologically active p19. Bone marrow transfer experiments showed that expression of p19 by hemopoietic cells alone recapitulated the phenotype induced by its widespread expression, pointing to hemopoietic cells as the source of biologically active p19. These findings indicate that p19 shares biological properties with IL-6, IL-12, and G-CSF and that cell-specific expression is required for its biological activity.
Design and evaluation of lightweight IEEE 802.11p-based TDMA MAC method for road side-to-vehicle communications (2010)

Wireless vehicular communications (WVC) has been identified as a key technology for intelligent transportation systems (ITS) for a few years ago. IEEE 802.11p is the proposed standard for physical and MAC layer of WVC devices. The main objective of the standard is to change the frame format and increase delay spread tolerance introduced by vehicle mobility, in which the channel bandwidth is scaled from 20 MHz i.e.802.11a to 10 MHz i.e. 802.11p. This paper proposes TDMA technique with fixed time slots and guard band between slots to ensure interoperability between wireless devices communicate in rapidly changing environment where transactions must be completed in small timeframe. The new TDMA sub-layer is proposed to be on-top of the conventional 802.11p MAC. The simulation results present the performance analysis and validate the efficiency of the proposed scheme.
Genome-wide methylation profiling of the different stages of hepatitis B virus-related hepatocellular carcinoma development in plasma cell-free DNA reveals potential biomarkers for early detection and high-risk monitoring of hepatocellular carcinoma (2014)

Our data revealed highly dynamic cfDNA methylation profiles in support of HBV-related HCC development. We have identified a panel of DMGs that are predictive for the early, middle and late stages of HCC development, and these are potential markers for the early detection of HCC as well as the screening of high-risk populations.
Study of the ground bounce caused by power plane resonances (1998)

We describe Delta-I noise caused by power plane resonances in multilayer boards. First, we study the effect of power plane resonances on the ground bounce of the system by performing finite-difference time-domain (FDTD) simulations. We simulate the voltage fluctuations at one point of the printed circuit board (PCB) due to a current surge between the power planes in a different point. Next, two methods to prevent this ground bounce effect are investigated. The first method consists of adding lumped capacitances to the design. The effect of one large capacitor is compared to the effect of adding a "wall" of smaller capacitors. A second approach is to isolate the chips by etching a slot around the sensitive integrated circuits (ICs) and connecting both sides by a small inductor. Both methods provide excellent protection against power plane resonances.
Distribution of Diacetyl and Acetylmethylcarbinol between Fat and Water, with Special Reference to Butter (1942)

In butter made with butter culture, diacetyl and acetylmethylcarbinol are derived largely from the culture added to the cream and from the fermentation of citric acid during holding or ripening of the cream. Only small portions of these compounds present in the cream at churning appear in the finished butter. They are carried out in the buttermilk
Thienyl analog of 1-(3-methoxycarbonyl)propyl-1-phenyl-[6,6]-methanofullerene for bulk heterojunction photovoltaic devices in combination with polythiophenes (2006)

An analog of 1-(3-methoxycarbonyl)propyl-1-phenyl-[6,6]-methanofullerene (PCBM) was designed with the aim of improving miscibility with polythiophene donors, especially poly(3-hexyl thiophene) (P3HT). In the title compound the phenyl group from PCBM is replaced by a thienyl group, it is named 1-(3-methoxycarbonyl)propyl-1-thienyl-[6,6]-methanofullerene (ThCBM). In this letter, experimental studies of the morphology, charge transport, and solar cell performance in blends of P3HT:ThCBM are reported. This may open a route for the design of more specific fullerene based acceptor materials, which may optimize the morphology of bulk heterojunction photovoltaic devices with respect to their transport.
A novel fluorescence-activated cell sorter-based screen for yeast endocytosis mutants identifies a yeast homologue of mammalian eps15. (1996)

A complete understanding of the molecular mechanisms of endocytosis requires the discovery and characterization of the protein machinery that mediates this aspect of membrane trafficking. A novel genetic screen was used to identify yeast mutants defective in internalization of bulk lipid. The fluorescent lipophilic styryl dye FM4-64 was used in conjunction with FACS to enrich for yeast mutants that exhibit internalization defects. Detailed characterization of two of these mutants, dim1-1 and dim2-1, revealed defects in the endocytic pathway. Like other yeast endocytosis mutants, the temperature-sensitive dim mutant were unable to endocytose FM4-64 or radiolabeled alpha-factor as efficiently as wild-type cells. In addition, double mutants with either dim1-delta or dim2-1 and the endocytosis mutants end4-1 or act1-1 displayed synthetic growth defects, indicating that the DIM gene products function in a common or parallel endocytic pathway. Complementation cloning of the DIM genes revealed identity of DIM1 to SHE4 and DIM2 to PAN1. Pan1p shares homology with the mammalian clathrin adaptor-associated protein, eps15. Both proteins contain multiple EH (eps15 homology) domains, a motif proposed to mediate protein-protein interactions. Phalloidin labeling of filamentous actin revealed profound defects in the actin cytoskeleton in both dim mutants. EM analysis revealed that the dim mutants accumulate vesicles and tubulo-vesicular structures reminiscent of mammalian early endosomes. In addition, the accumulation of novel plasma membrane invaginations where endocytosis is likely to occur were visualized in the mutants by electron microscopy using cationized ferritin as a marker for the endocytic pathway. This new screening strategy demonstrates a role for She4p and Pan1p in endocytosis, and provides a new general method for the identification of additional endocytosis mutants.
Expression and Function of Formyl Peptide Receptors on Human Fibroblast Cells (2003)

The migration of polymorphonuclear leukocytes from the blood to sites of infection in tissues is a hallmark of the innate immune response. Formylated peptides produced as a byproduct of bacterial protein synthesis are powerful chemoattractants for leukocytes. Formyl peptides bind to two different G protein-coupled receptors (formyl peptide receptor (FPR) and the low affinity formyl peptide receptor-like-1 (FPRL1)) to initiate a signal transduction cascade leading to cell activation and migration. Our analysis of expressed sequences from many cDNA libraries draws attention to the fact that FPRs are widely expressed in nonlymphoid tissues. Here we demonstrate that FPRs are expressed by normal human lung and skin fibroblasts and the human fibrosarcoma cell line HT-1080. The expression on fibroblasts of receptors for bacteria-derived peptides raises questions about the possible function of these receptors in nonleukocyte cells. We studied the function of FPRs on fibroblasts and find that stimulation with fMLP triggers dose-dependent migration of these cells. Furthermore, fMLP induces signal transduction including intracellular calcium flux and a transient increase in F-actin. The fMLP-induced adhesion and motility of fibroblasts on fibronectin require functional protein kinase C and phosphatidylinositol 3-kinase. This first report of a functional formyl peptide receptor in cells of fibroblast origin opens new possibilities for the role of fibroblasts in innate immune responses.