gebhart/patrepeval huggingface dataset:
The degree sequence of a scale‐free random graph process (2001)

Abstract Recently, Barabási and Albert [2] suggested modeling complex real‐world networks such as the worldwide web as follows: consider a random graph process in which vertices are added to the graph one at a time and joined to a fixed number of earlier vertices, selected with probabilities proportional to their degrees. In [2] and, with Jeong, in [3], Barabási and Albert suggested that after many steps the proportion P ( d ) of vertices with degree d should obey a power law P ( d )α d −γ . They obtained γ=2.9±0.1 by experiment and gave a simple heuristic argument suggesting that γ=3. Here we obtain P ( d ) asymptotically for all d ≤ n 1/15 , where n is the number of vertices, proving as a consequence that γ=3. © 2001 John Wiley &amp; Sons, Inc. Random Struct. Alg., 18, 279–290, 2001
Patterned Superhydrophobic Metallic Surfaces (2009)

This work shows that after creating certain dual scale roughness structures by femtosecond laser irradiation different metal alloys initially show superhydrophilic behavior with complete wetting of the structured surface. However, over time, these surfaces become nearly superhydrophobic with contact angles in the vicinity of 150 degrees and superhydrophobic with contact angles above 150 degrees. The contact angle hysteresis was found to lie between 2 and 6 degrees. The change in wetting behavior correlates with the amount of carbon on the structured surface. The explanation for the time dependency of the surface wettability lies in the combined effect of surface morphology and surface chemistry.
Analysis of the nucleotide sequence of DNA from the region of the thymidine kinase gene of infectious laryngotracheitis virus; potential evolutionary relationships between the herpesvirus subfamilies (1990)

We have sequenced a 5.4 kb region of the genome from the avian herpesvirus infectious laryngotracheitis virus (ILTV) and identified genes homologous to the thymidine kinase (TK) gene, the capsid p40 gene of herpes simplex virus type 1 (HSV-1), a gene encoding a protein antigenic in Epstein-Barr virus infections plus one other highly conserved gene encoding a protein implicated in cell fusion in HSV-1. Computer analysis of the TK gene and the upstream overlapping gene sequence is used to produce trees showing potential evolutionary relationships between the herpesvirus subfamilies.
Transistor structures for the study of scaling in carbon nanotubes (2003)

We report on the fabrication and electrical characterization of two uniquely structured carbon nanotube field-effect transistors (CNFETs). These devices have been designed to emphasize different aspects of their electrical switching behavior, so that we may learn more about their transport properties. In one structure, back-gate CNFETs were built to study the effects of vertical scaling by varying the thickness of an underlying high-quality gate dielectric. An unexpected dependence of the subthreshold slope and transconductance on the gate dielectric thickness was observed, and was attributed to Schottky barrier switching at the metal/nanotube contacts. A second structure incorporates a top gate electrode with multiple, individually addressable segments of different width. This design decouples the interior of the device from the contacts, thereby enabling the study of lateral scaling within the same physical device structure. Clear indications of bulk switching were observed in this device, with strong evidence of ballistic transport, suggesting that CNFETs do not follow conventional gate length scaling rules.
Zirconium and hafnium Salalen complexes in isospecific polymerisation of propylene (2013)

The activity of dibenzylzirconium and dibenzylhafnium Salalen complexes in polymerisation of propylene with MAO as a cocatalyst is described. Three Salalen ligand precursors combining a bulky alkyl group (1-adamantyl) on the imine-side phenol and electron withdrawing halo groups of different sizes on the amine-side phenol were explored. All metal complexes were obtained as single diastereomers. An X-ray crystallographic structure of a hafnium complex of an additional ligand carrying the combination of tert-butyl and chloro substituted phenolates, 4-Hf, revealed a fac-mer wrapping of the Salalen ligand around the metal centre. All complexes led to active catalysts in propylene polymerisation and to isotactic polypropylene of high regioregularity. The zirconium complexes led to polypropylene having molecular weights of Mw = 132,000-200,000 and isotacticities of [mmmm] = 65.7-75.0%. The hafnium complexes led to polypropylene of higher molecular weights of Mw = 375,000-520,000 and higher stereoregularities of [mmmm] = 80.6-89.3%, the highest isotacticity obtained with 3-Hf.
Plasma clearance of nonradioactive iohexol as a measure of glomerular filtration rate. (1995)

Renal clearance of inulin is the best available indicator of GFR but cannot be used routinely for clinical purposes and is also difficult to perform for clinical investigation when repeated measurements are required. The aim of this study was to find a reliable alternative to inulin clearance that would allow one to avoid the use of radioactivity and problems related to the continuous infusion of the marker. The plasma clearance of unlabeled iohexol, a nonionic contrast agent, was used. Forty-one patients (creatinine clearance 6 to 160 mL/min per 1.73 m2) underwent simultaneous measurements of renal clearance of inulin and plasma clearance of iohexol. Iohexol was given as a single iv dose, and blood samples were drawn up to 600 min after the administration. Iohexol concentrations (by HPLC) were analyzed by a two-compartment, open-model system. A highly significant correlation between the plasma clearance of iohexol and the renal clearance of inulin over a wide range of GFR values was found. By analyzing the data with a simplified method that uses a one-compartment model corrected with the Bröchner-Mortensen formula, an excellent correlation with the inulin clearance was also observed. When only patients with moderate to severe renal failure were considered, a significant correlation between the two methods was found. A further comparison between GFR determined with iohexol and iopromide, a new low-osmolarity, low-viscosity contrast medium, was also performed in a subgroup of patients.(ABSTRACT TRUNCATED AT 250 WORDS)
E7080, an oral multitargeted tyrosine kinase inhibitor, has direct anti-tumor efficacy via inhibition of KIT signaling in gastrointestinal stromal tumor (GIST) (2006)

Proc Amer Assoc Cancer Res, Volume 47, 2006

4038 

Most gastrointestinal stromal tumors (GIST) express constitutively active forms of the receptor tyrosine kinase KIT, derived from oncogenic mutation in the extracullular, juxtamembrane, or kinase domains. Constitutively activated KIT signaling induces tumor growth and the tumor malignant phenotype of GIST. Glivec (Imatinib mesylate, STI571) which inhibits the kinase activity of KIT, has been therapeutically effective in patients with GIST. E7080 is an oral multitargeted tyrosine kinase inhibitor against KDR (VEGFR-2), Flt-1 (VEGFR-1), FGFR1 and PDGFRbeta with IC50 values of 5 - 50 nM in cell free kinase assays. E7080 also inhibits KIT with an IC50 value of 100 nM. We evaluated the effect of E7080 on KIT activity in GIST cell line. Treatment of GIST882 with E7080 resulted in dose-dependent inhibition of cell proliferation, with an IC50 value of 35 nM. E7080 inhibited KIT tyrosine phosphorylation in GIST882 in a dose-dependent manner, with an IC50 values of ∼ 200 nM. E7080 also inhibited downstream events following KIT activation including ERK1/2 and Akt phosphorylation in a dose-dependent manner, with IC50 values consistent with that observed for the inhibition of KIT phosphorylation. Anti-tumor efficacy of E7080 in a GIST882 xenograft model also was evaluated. Oral administration of E7080 at doses of 30 or 100 mg/kg (BID, QD×28) caused tumor dormancy. E7080 at a dose of 100 mg/kg resulted in tumor shrinkage that measured approximately 40%, even when treatment was initiated following significant tumor growth. The status of KIT activation was examined in GIST882 tumors resected after 2 h treatment with E7080. E7080 clearly reduced phospho-KIT levels in GIST882 tumors. Soluble KIT (s-KIT) was evaluated as a potential biomarker of E7080 in the GIST882 xenograft model, because it has been reported that s-KIT in plasma samples could be used as a biomarker for therapeutic efficacy in patients with GIST in clinical trials. Detectable level of s-KIT (ng/ml) existed in the plasma of mice implanted with GIST882, although it was not detected in normal mice. The level of s-KIT was correlated with tumor weight in mice implanted with GIST882 (r=0.90 ∼ 0.95). Moreover treatment with E7080 at a dose of 100 mg/kg (BID, QD × 14) clearly reduced s-KIT level in plasma, compared with the plasma from mice after treatment with vehicle control. Our results suggested that E7080 has therapeutic potential in GIST mediated by direct anti-tumor efficacy via inhibition of KIT signaling, and s-KIT might be useful as a biomarker in patients with GIST.
[Topography of P300 in psychiatry--1. Cognitive P300 fields in psychoses]. (1988)

P300 is known as a wave which enables the evaluation of cognitive function in neuropsychology and psychiatry. The most reliable result in psychoses was an amplitude reduction. Since similar wave alteration occurred not only in psychoses but also in dementia, the P300 reduction was too unspecific to serve as criteria for differential diagnosis. By means of topographical procedures it could be found out that the well defined P300 fields underwent characteristic changes in psychoses which even allowed a differentiation between different subgroups in schizophrenia. In hebephrenics the frontal field was very low whereas the paranoid group showed a lateralized P300-pattern with lower amplitudes in the right parieto-temporal area. In depression the P300-pattern was identical to the fields known in geriatric controls. The results will be discussed regarding other structural and functional imaging procedures. By means of topographical display of P300 the specificity of cognitive waves can be augmented considerably with the possibility to differentiate between different types of psychoses.
Network performance and integrity enhancement with optical path layer technologies (1994)

Path layer technologies will play a key role in the development of a powerful and failure resilient B-ISDN. So far, they have been based on electrical technologies. This paper highlights WDM/FDM techniques and demonstrates that optical paths can greatly enhance the path layer capability and, therefore, the network performance. It is also shown that effective network failure restoration can be achieved with optical paths. The applicability of the wavelength path (WP) technique to global area networks is revealed by comparing different optical path realization techniques. WPs are applied to the national backbone network example to evaluate the required number of wavelengths, and to identify optical cross-connect node requirements. It then proposes a new optical path concept: the virtual wavelength path (VWP). In the VWP scheme, wavelengths are assigned on a link-by-link basis. In other words, the wavelength assigned to a wavelength path has only local significance. Significant benefits of the VWP such as the simplified path accommodation design within a transmission facility network and the reduced number of wavelengths needed, are elucidated. An optical cross-connect node architecture that enables the VWPs is also proposed. The architecture allows the VWP concept to be realized with commercially available optical technologies. The optical path layer concept proposed exploits and consolidates the layered transport network architecture and optical technologies, and will open up new opportunities for creating a B-ISDN that is bandwidth abundant and has a high degree of integrity.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Development and Validation of Oxygen Radical Absorbance Capacity Assay for Lipophilic Antioxidants Using Randomly Methylated β-Cyclodextrin as the Solubility Enhancer (2002)

We recently reported the improved oxygen radical absorbance capacity (ORAC) assay using fluorescein (FL) as the fluorescent probe. The current ORAC(FL) assay is limited in hydrophilic antioxidant due to the aqueous environment of the assay. Lipophilic antioxidants mainly include the vitamin E family and carotenoids, which play a critical role in biological defense systems. In this paper, we expanded the current ORAC(FL) assay to lipophilic antioxidants. Randomly methylated beta-cyclodextrin (RMCD) was introduced as the water solubility enhancer for lipophilic antioxidants. Seven percent RMCD (w/v) in a 50% acetone-H(2)O mixture was found to sufficiently solubilize vitamin E compounds and other lipophilic phenolic antioxidants in 75 mM phosphate buffer (pH 7.4). This newly developed ORAC assay (abbbreviated ORAC(FL-LIPO)) was validated through linearity, precision, accuracy, and ruggedness. The validation results demonstrate that the ORAC(FL-LIPO) assay is reliable and robust. For the first time, by using 6-hydroxy-2,5,7,8-tetramethyl-2-carboxylic acid as a standard (1.0), the ORAC values of alpha-tocopherol, (+)-gamma-tocopherol, (+)-delta-tocopherol, alpha-tocopherol acetate, tocotrienols, 2,6-di-tert-butyl-4-methylphenol, and gamma-oryzanol were determined to be 0.5 +/- 0.02, 0.74 +/- 0.03, 1.36 +/- 0.14, 0.00, 0.91 +/- 0.04, 0.16 +/- 0.01, and 3.00 +/- 0.26, respectively. The structural information of oxidized alpha-tocopherol obtained by liquid chromatography/mass spectrometry reveals that the mechanism for the reaction between the vitamin E and the peroxyl radical follows the hydrogen atom transfer mechanism, which is in agreement with the notion that vitamin E is the chain-breaking antioxidant.
Differential Effects of the Integrins α9β1, αvβ3, and αvβ6 on Cell Proliferative Responses to Tenascin (1996)

Members of the integrin family manifest considerable overlap in ligand specificity, and many cells have the capacity to express multiple integrin receptors for the same ligand. For example, at least 5 different integrins recognize tenascin as a ligand, and 4 of these bind to the same region of the protein, the third fibronectin type III repeat (TNfn3). We utilized colon carcinoma cells (SW480) that do not normally attach to TNfn3 to examine the possibility that ligation of different integrin receptors for this ligand would induce different effects on cell behavior and intracellular signaling. Heterologous expression of the tenascin receptors alphavbeta3 and alpha9beta1 produced comparable effects on cell adhesion and spreading on TNfn3, but alphavbeta3-transfectants proliferated considerably better on each concentration examined. alphavbeta6-transfectants attached (although less avidly), but completely failed to spread or proliferate. Expression of a chimeric beta subunit composed of the beta3 extracellular domain fused to the beta6 transmembrane and cytoplasmic domains resulted in adhesion and spreading similar to that seen with beta3-transfectants, but considerably less proliferation. When the same cell lines were plated on fibronectin, alphavbeta6-transfectants spread and proliferated as well as cells transfected with the chimeric beta3/beta6 subunit, but, again, neither cell line proliferated as well as cells expressing alphavbeta3. Cell proliferation was always associated with spreading and with phosphorylation of the focal adhesion kinase, paxillin, and the mitogen-activated kinase, Erk2, but cell attachment in the absence of spreading or proliferation was not associated with phosphorylation of any of these proteins. These data suggest that different integrin receptors for a single ligand can produce markedly different effects on cell proliferation, and that both the extracellular and cytoplasmic domains of integrin beta subunits contribute to these differences.
Feline Interleukin-31 Shares Overlapping Epitopes with the Oncostatin M Receptor and IL-31RA (2020)

Interleukin-31 (IL-31) is a major protein involved in severe inflammatory skin disorders. Its signaling pathway is mediated through two type I cytokine receptors, IL-31RA (also known as the gp130-like receptor) and the oncostatin M receptor (OSMR). Understanding molecular details in these interactions would be helpful for developing antagonist anti-IL-31 monoclonal antibodies (mAbs) as potential therapies. Previous studies suggest that human IL-31 binds to IL-31RA and then recruits OSMR to form a ternary complex. In this model, OSMR cannot interact with IL-31 in the absence of IL-31RA. In this work, we show that feline IL-31 (fIL-31) binds independently with feline OSMR using surface plasmon resonance, an enzyme-linked immunosorbent assay, and yeast surface display. Moreover, competition experiments suggest that OSMR shares a partially overlapping epitope with IL-31RA. We then used deep mutational scanning to map the binding sites of both receptors on fIL-31. In agreement with previous studies of the human homologue, the binding site for IL31-RA contains fIL-31 positions E20 and K82, while the binding site for OSMR comprises the "PADNFERK" motif (P103-K110) and position G38. However, our results also revealed a new overlapping site, composed of positions R69, R72, P73, D76, D81, and E97, between both receptors that we called the "shared site". The conformational epitope of an anti-feline IL-31 mAb that inhibits both OSMR and IL-31RA also mapped to this shared site. Combined, our results show that fIL-31 binds IL-31RA and OSMR independently through a partially shared epitope. These results suggest reexamination of the putative canonical mechanisms for IL-31 signaling in higher animals.
Inhibition of Rous sarcoma virus replication by antisense RNA (1987)

Previous results have indicated that Rous sarcoma virus env gene expression is specifically inhibited by antisense RNA (L.-J. Chang and C. M. Stoltzfus, Mol. Cell. Biol. 5:2341-2348, 1985). In this study, we compare the extents of inhibition by antisense RNA derived from different parts of the Rous sarcoma virus genome, and we show that antisense constructs containing the 3'-end noncoding region inhibit env expression to a similar extent as those containing the 5'-end noncoding region or coding region. Furthermore, we show that antisense RNA inhibits virus replication at other levels in addition to translation.
Design of standard cells used in low-power ASIC's exploiting the multiple-supply-voltage scheme (2002)

ASIC design utilizing the multiple-supply-voltage (MSV) scheme has been shown to be efficient in reducing the power consumption. A new layout style of standard cells to be used in ASIC designs is proposed to effectively exploit the advantages afforded by the MSV scheme. Each standard cell is designed to use two power rails that are fed with different supply voltages. Then, the cells can be butted together arbitrarily no matter whether the cells are supplied from a high or low voltage, and the existing P&R tool can place and route the circuit as usual. As compared to the design with only one supply voltage, the average saving of power consumption of the new design (using the new cells and adopting the MSV scheme) is over 30%, but the average area overhead is only about 8%. Meanwhile, the average interconnection length is only increased by about 7.5%.
Insulin Resistance: A Multifaceted Syndrome Responsible for NIDDM, Obesity, Hypertension, Dyslipidemia, and Atherosclerotic Cardiovascular Disease (1991)

Diabetes mellitus is commonly associated with systolic/diastolic hypertension, and a wealth of epidemiological data suggest that this association is independent of age and obesity. Much evidence indicates that the link between diabetes and essential hypertension is hyperinsulinemia. Thus, when hypertensive patients, whether obese or of normal body weight, are compared with age- and weight-matched normotensive control subjects, a heightened plasma insulin response to a glucose challenge is consistently found. A state of cellular resistance to insulin action subtends the observed hyperinsulinism. With the insulin/glucose-clamp technique, in combination with tracer glucose infusion and indirect calorimetry, it has been demonstrated that the insulin resistance of essential hypertension is located in peripheral tissues (muscle), is limited to nonoxidative pathways of glucose disposal (glycogen synthesis), and correlates directly with the severity of hypertension. The reasons for the association of insulin resistance and essential hypertension can be sought in at least four general types of mechanisms: Na+ retention, sympathetic nervous system overactivity, disturbed membrane ion transport, and proliferation of vascular smooth muscle cells. Physiological maneuvers, such as calorie restriction (in the overweight patient) and regular physical exercise, can improve tissue sensitivity to insulin; evidence indicates that these maneuvers can also lower blood pressure in both normotensive and hypertensive individuals. Insulin resistance and hyperinsulinemia are also associated with an atherogenic plasma lipid profile. Elevated plasma insulin concentrations enhance very-low-density lipoprotein (VLDL) synthesis, leading to hypertriglyceridemia. Progressive elimination of lipid and apolipoproteins from the VLDL particle leads to an increased formation of intermediate-density and low-density lipoproteins, both of which are atherogenic. Last, insulin, independent of its effects on blood pressure and plasma lipids, is known to be atherogenic. The hormone enhances cholesterol transport into arteriolar smooth muscle cells and increases endogenous lipid synthesis by these cells. Insulin also stimulates the proliferation of arteriolar smooth muscle cells, augments collagen synthesis in the vascular wall, increases the formation of and decreases the regression of lipid plaques, and stimulates the production of various growth factors. In summary, insulin resistance appears to be a syndrome that is associated with a clustering of metabolic disorders, including non-insulin-dependent diabetes mellitus, obesity, hypertension, lipid abnormalities, and atherosclerotic cardiovascular disease.
Real-time stroke volume measurements for the optimization of cardiac resynchronization therapy parameters (2010)

Real-time SV measurements can be used to optimize CRT at the time of implant. Improvement in SV correlates with improvement in LVEF, LVEDD, and 6 min walk, and improvement in echocardiographic dyssynchrony.
Enterobactin Biosynthesis in Escherichia coli:  Isochorismate Lyase (EntB) Is a Bifunctional Enzyme That Is Phosphopantetheinylated by EntD and Then Acylated by EntE Using ATP and 2,3-Dihydroxybenzoate (1997)

In Escherichia coli, the siderophore molecule enterobactin is synthesized in response to iron deprivation by formation of an amide bond between 2,3-dihydroxybenzoate (2,3-DHB) and l-serine and formation of ester linkages between three such N-acylated serine residues. We show that EntB, previously described as the isochorismate lyase required for production of 2,3-DHB, is a bifunctional protein that also serves as an aryl carrier protein (ArCP) with a role in enterobactin assembly. EntB is phosphopantetheinylated near the C terminus in a reaction catalyzed by EntD with a kcat of 5 min-1 and a Km for apo-EntB of 6.5 microM. This holo-EntB is then acylated with 2,3-DHB in a reaction catalyzed by EntE, previously described as the 2,3-DHB-AMP ligase, with a kcat of 100 min-1 and a Km of <<1 microM for holo-EntB. The N-terminal 187 amino acids of EntB (isochorismate lyase domain) are not needed for reaction of EntB with either EntD or EntE as demonstrated by the equivalent catalytic efficiencies of the full-length EntB (residues 1-285) and the C-terminal EntB ArCP domain (residues 188-285) as substrates for both EntD and EntE.