gebhart/patrepeval huggingface dataset:
Comparative effects of vasopressin, norepinephrine, and l-canavanine, a selective inhibitor of inducible nitric oxide synthase, in endotoxic shock (2004)

Norepinephrine (NE), a standard of care, AVP, an alternative candidate, and L-canavanine (LC), a selective inhibitor of inducible nitric oxide synthase, were compared for efficacy and innocuousness on global and regional hemodynamics, plasmatic and tissue lactate-to-pyruvate ratio (L/P), tissue high-energy phosphates, renal function, and tissue capillary permeability in a rat model of endotoxic normokinetic shock. Mean arterial pressure (MAP) decreased ( approximately 35%) but aortic blood flow increased during endotoxin infusion (P < 0.05 vs. control). Additionally, there was a decrease in mesenteric (MBF) and renal (RBF) blood flows along with regional-to-systemic ratio (P < 0.05 vs. control). All tested drugs restored MAP to basal levels but slightly decreased abdominal aortic flow; however, RBF and MBF remained unchanged. Endotoxin significantly decreased diuresis and inulin clearance ( approximately 3- to 4-fold), whereas AVP or LC attenuated this drop (P < 0.05 vs. control). In contrast, NE did not improve endotoxin-induced renal dysfunction. Endotoxin induced gut and lung hyperpermeability (P < 0.05 vs. control). Endotoxin-induced gut hyperpermeability was inhibited by AVP, LC, and NE. Endotoxin-induced lung hyperpermeability was further worsened by NE ( approximately 2-fold increase) but not AVP infusion (P < 0.05 vs. endotoxin). LC significantly improved endotoxin-induced pulmonary hyperpermeability. Endotoxin increased renal lactate and decreased renal ATP. NE did not change renal lactate or renal ATP. AVP and LC decreased renal lactate and normalized renal ATP. Finally, endotoxin was associated with increased lactate levels and L/P ( approximately 2- and 1.5-fold increases vs. control, respectively), whereas AVP and LC, but not NE, normalized both parameters after endotoxin challenge. These results suggest that, in a short-term endotoxic shock model, AVP improves systemic hemodynamics without side effects and has particular beneficial effects on renal function.
Inhibition of fibrinogen binding to stimulated human platelets by a monoclonal antibody. (1983)

Fibrinogen binding to receptors on stimulated platelets is a prerequisite for platelet aggregation. To gain further insight into the role of fibrinogen in platelet aggregation and to identify the platelet fibrinogen receptor, we developed a monoclonal anti-platelet antibody that inhibited platelet aggregation. The purified antibody, designated A2A9, inhibited platelet aggregation stimulated by 10 microM ADP, 10 microM epinephrine, and thrombin at 1 unit/ml without inhibiting platelet shape change or platelet secretion. A2A9 was also a competitive inhibitor of fibrinogen binding to ADP-stimulated platelets. Fifty percent inhibition of fibrinogen binding occurred at 65 nM A2A9. Direct binding studies using radiolabeled A2A9 demonstrated 47,000 A2A9 binding sites on unstimulated platelets, with a dissociation constant of 60 nM. Platelets from two individuals with Glanzmann thrombasthenia bound essentially no A2A9. Therefore, these data support the hypothesis that receptor-bound fibrinogen mediates platelet aggregation. In order to identify the platelet fibrinogen receptor, A2A9 immobilized on agarose was used for affinity chromatography. Two platelet polypeptides with Mr = 140,000 and 93,000 were recovered from the immobilized A2A9. After disulfide reduction, these Mr values were altered to 125,000 and 116,000. The smaller polypeptide was also found to contain the PlA1 antigen. These data localize the epitope recognized by A2A9 to the platelet membrane glycoprotein IIb-IIIa complex and suggest that this complex forms the physiologic platelet fibrinogen receptor.
Remodelling: therapeutic opportunities. (1997)

Restenosis after angioplasty has been recently attributed to a lack of compensatory enlargement and/or chronic constrictive remodelling, rather than neointimal growth. Also, restenosis occurring after stent has been clearly related to neointimal growth. This clarification has dramatically helped in designing strategies targeted against the appropriate mechanisms. The mechanism of stent-related restenosis has been the most studied and several antiproliferative agents including gene therapy and radioactive stents have been successfully tested. Constrictive remodelling has been identified more recently and its pathophysiological mechanism remains poorly understood. Control of extracellular matrix metabolism might be an important pathway. Moreover, detection of the arteries that will 'enlarge' should avoid any preventive strategy including systematic stenting.
Effect of RenaGel(R), a non-absorbable, cross-linked, polymeric phosphate binder, on urinary phosphorus excretion in rats (1997)

In vitro binding studies demonstrate that RenaGel has an extremely high phosphate binding capacity. At an estimated physiological concentration of 5 mM phosphate, RenaGel binds 2.6 mmole phosphate/g of phosphate binder. The in vivo binding study shows that RenaGel mixed into the diet decreased urinary phosphorus excretion in a dose dependent manner. RenaGel particles with a 23 microns mean diameter are more efficacious than the larger ones. In conclusion, the above studies indicate that RenaGel is a potent phosphate binder. RenaGel contains no calcium or aluminum and offers an alternative to existing phosphate binder treatments.
Color Fingerprinting of Proteins by Calixarenes Embedded in Lipid/Polydiacetylene Vesicles (2006)

"Naked eye" color detection of proteins was achieved by embedding calixarene receptors within vesicles comprising phospholipids and the chromatic polymer polydiacetylene. Dramatic visible absorbance changes were induced through electrostatic interactions between the protein surface and the vesicle-incorporated hosts. The colorimetric responses could be induced by micromolar protein concentrations, and furthermore, specific protein fingerprints could be obtained by incorporating different receptors within the vesicles. Fluorescence and circular dichroism experiments confirmed the relationship between the colorimetric phenomena and protein docking on the surface of the chromatic vesicles. The colorimetric assay constitutes a generic platform for high-sensitivity detection of soluble proteins and for evaluation of protein surface charge distribution.
Synopses for Massive Data: Samples, Histograms, Wavelets, Sketches (2011)

Methods for Approximate Query Processing (AQP) are essential for dealing with massive data. They are often the only means of providing interactive response times when exploring massive datasets, and are also needed to handle high speed data streams. These methods proceed by computing a lossy, compact synopsis of the data, and then executing the query of interest against the synopsis rather than the entire dataset. We describe basic principles and recent developments in AQP. We focus on four key synopses: random samples, histograms, wavelets, and sketches. We consider issues such as accuracy, space and time efficiency, optimality, practicality, range of applicability, error bounds on query answers, and incremental maintenance. We also discuss the tradeoffs between the different synopsis types.
Sacral Neuromodulation for Genitourinary Problems (2015)

Sacral neuromodulation (SNM) is a minimally invasive therapeutic option for many voiding dysfunction conditions. It is approved by the US FDA for refractory overactive bladder with and without incontinence and nonobstructive retention. Since SNM has shown a favorable response for these approved indications, other therapeutic applications have been proposed for various conditions such as painful bladder syndrome, chronic pelvic pain and neurological voiding dysfunction in both adult and pediatric age groups. SNM therapy with the most commonly used dedicated SNM device (InterStim) involves insertion of electrode(s) in the third and/or fourth sacral foramen next to the nerve root. The electrode is then connected to a battery-operated pulse generator. All patients need to have a test trial period before definitive device insertion. Here we discuss SNM therapy in functional urinary disorders and the technique of device insertion with the potential pitfalls.
Ultrastructural Localization of a Cuticle-degrading Protease Produced by the Entomopathogenic Fungus Metarhizium anisopliae during Penetration of Host (Manduca sexto) Cuticle (1989)

Gold-labelled rabbit antiserum was used to demonstrate that a cuticle-degrading protease (Pr1) is produced by Metarhizium anisopliae during penetration of host (Manduca sexta) procuticle. The protease was secreted by infection structures (appressoria) on the cuticle surface and by the penetrant hyphae within the cuticle. Penetration of the procuticle was by a combination of enzymic degradation and mechanical pressure. Initially Pr1 was confined to the immediate vicinity of the fungal structures; however the enzyme diffused throughout the cuticle during later stages of pathogenesis. When hyphae were labelled during growth in culture under conditions conducive to rapid synthesis of Pr1, gold particles distributed over the fungal cell wall, indicating binding of Pr1 to hyphae.
Preparation, Characterization, and Electroluminescence Characteristics of α-Diimine-type Platinum(II) Complexes with Perfluorinated Phenyl Groups as Ligands (2005)

Abstract The α-diimine-type platinum(II) complexes having bulky perfluorinated phenyl groups were prepared and the molecular and crystal structures were revealed by X-ray analysis. They showed phosphorescence and electron-accepting properties. The organic light-emitting diode (OLED) devices showing green luminescence were fabricated.
Ammonia recovery from anaerobically digested cattle manure by steam stripping (2006)

Ammonia recovery from anaerobically digested cattle manure effluents through steam stripping was studied at a stripping tower temperature of 98-99 degrees C and a steam-water ratio approximately 56-72 g/L. The digested manure effluents were first treated by microfiltration and then the permeate was used as feed in steam stripping. The stripping performance was evaluated under different feed pH values, ammonia concentrations and temperatures. The increase of the initial feed pH does not significantly improve ammonia stripping efficiency due to the fact that the stripped effluent pH is increased during steam stripping. This suggests that steam stripping of anaerobically digested manure effluents for ammonia recovery may not need pre-raised pH. In contrast, the pH value of the synthetic ammonia wastewater containing NH4Cl dramatically decreases after steam stripping. Increasing the feed temperature slightly improves ammonia stripping efficiency, but reduces the concentration of the recovered ammonia in the condensate due to an increased condensate volume at a higher feed temperature. Therefore, the feed temperature should be controlled at an optimum point that can compromise the condensate ammonia concentration and the ammonia stripping efficiency. Experimental results indicate that recovery of ammonia from anaerobically digested cattle manure effluents as NH4OH is technically feasible.
Association of overexpression of TIF1γ with colorectal carcinogenesis and advanced colorectal adenocarcinoma (2011)

The findings suggest that over-expression of TIF1γ occurs in early stages of colorectal carcinogenesis, is inversely related with Smad4 loss, and may be a prognostic indicator for poor outcome.
Regulation of Cyclin D1 by Calpain Protease (1997)

Cyclin D1, a critical positive regulator of G1 progression, has been implicated in the pathogenesis of certain cancers. Regulation of cyclin D1 occurs at the transcriptional and posttranscriptional level. Here we present evidence that cyclin D1 levels are regulated at the posttranscriptional level by the Ca2+-activated protease calpain. Serum starvation of NIH 3T3 cells resulted in rapid loss of cyclin D1 protein that was completely reversible by calpain inhibitors. Actinomycin D and lovastatin induced rapid loss of cyclin D1 in prostate and breast cancer cells that was reversible by calpain inhibitors and not by phenylmethylsulfonyl fluoride, caspase inhibitors, or lactacystin, a specific inhibitor of the 26 S proteasome. Treatment of intact NIH 3T3, prostate, and breast cancer cells with a calpain inhibitor dramatically increased the half-life of cyclin D1 protein. Addition of purified calpain to PC-3-M lysates resulted in Ca2+-dependent cyclin D1 degradation. Transient expression of the calpain inhibitor calpastatin increased cyclin D1 protein in serum-starved NIH 3T3 cells. Cyclins A, E, and B1 have been reported to be regulated by proteasome-associated proteolysis. The data presented here implicate calpain in cyclin D1 posttranslational regulation.
The polymeric hemoglobin molecule of Artemia. Interpretation of translated cDNA sequence of nine domains (1991)

Translated cDNA for Artemia hemoglobin provided sequence data for almost nine domains, from the fourth residue of the A helix of one domain through 1405 residues to a stop codon after the ninth domain. The domain sequences were all different (homology between pairs 17-38%) but aligned well with each other and with conventional globins, satisfying the requirements for Phe at CD1, His at F8 and most other highly conserved features of globins including His at E7. Features found to be characteristic of Artemia globin and present in all nine domains were Phe at B10, Tyr at C4, Gly at F5, Phe at G5 and Gly at H22. Approximately 14 residues including a consensus -Val-Asp-Pro-Val-Thr-Gly-Leu- were available to form the linker between each pair of domains. The Artemia sequence data were compared with the crystal structures of Chironomus thummi thummi erythrocruorin III and sperm whale myoglobin in order to identify features of structural similarity and to examine the consequences of the differences. The Artemia sequences were compatible with the main helices and critical features of the globin fold. Possible modifications to the C helix, FG turn, and GH turn were studied in terms of molecular coordinates.
Modelling groundwater flow and transport in the Chalk (1993)

Abstract At this stage it is convenient to review the transport mechanisms in the Chalk and the factors that have to be considered when creating models of the Chalk’s flow systems. Modelling is a discipline that requires a clear understanding of the processes occurring in the Chalk. The increasing ability to construct sophisticated models has focused attention on these processes and led to more rigorous and realistic conceptual models of the aquifer for examining both flow and pollution problems.
Comparison of Preproject Planning for Green and Conventional Buildings (2013)

The importance of green buildings has been frequently highlighted. However, barriers such as greater complexity, lack of understanding of sustainability, and the perception of a greater possibility of cost overrun have hindered the dissemination of green buildings. More planning efforts for green buildings can presumably help mitigate these barriers. This paper investigates preproject planning efforts for green and conventional building projects. Project-level data were collected (124 in total, 71 from conventional building projects and 53 from green building projects), with project data consisting of general information about the project, a Project Definition Rate Index (PDRI) survey, and cost performance. The project data were categorized into four groups based on their project type (green and conventional) and cost performance (actual cost on/under budget and over budget). For the four groups, a two-way analysis of variance test was used to compare the degree of preproject planning efforts measured by PDRI. The analysis indicated that green projects tend to have more investment in preproject planning efforts than conventional projects, and the difference was marginally statistically significant at the level of α=0.05. In addition, a comparison of the mean PDRI values of the four groups revealed that green projects with a superior cost performance invest more in preproject planning efforts than other groups, and the difference was statistically meaningful. From the interaction effect, we also found that the impact of preproject planning on cost performance is more critical for green projects than for conventional projects. Regarding the preproject planning category, we found that green projects with superior cost performance tend to involve more planning with regard to business strategy, project requirements, site information, building programming, and building/project design parameters. These findings make two contributions. First, the findings help practitioners justify additional preproject planning efforts for green projects. Second, some of the results of this study will be useful to practitioners initiating sustainable projects by helping with the determination of which aspects of green buildings should involve more extensive planning. These findings will help reduce the possibility of cost overruns and allow more green projects to be deployed in order to address the need for sustainability.
trans-Cycloalkenes. Part II. Application of the dioxolan olefin synthesis to the stereospecific formation of trans-cyclo-octene derivatives. (1SR,2RS)-trans-Cyclo-oct-2-en-1-ol (1971)

The reaction of benzylidene derivatives of 3-substituted trans-cyclo-octane-1,2-diols with n-butyl-lithium leads to 3-substituted trans-cyclo-octenes. By appropriate choice of precursors the stereochemistry of the products can be controlled, and diastereoisomeric derivatives of trans-cyclo-octene where the 3-substituent is MeO, OH, or Bun have been prepared.
Expedited Approach toward the Rational Design of Noncovalent SARS-CoV-2 Main Protease Inhibitors (2021)

The main protease (M<sup>pro</sup>) of SARS-CoV-2 is a validated antiviral drug target. Several M<sup>pro</sup> inhibitors have been reported with potent enzymatic inhibition and cellular antiviral activity, including <b>GC376</b>, <b>boceprevir</b>, <b>calpain inhibitors II</b>, and <b>XII</b>, with each containing a reactive warhead that covalently modifies the catalytic Cys145. Coupling structure-based drug design with the one-pot Ugi four-component reaction, we discovered one of the most potent noncovalent inhibitors, <b>23R</b> (<b>Jun8-76-3A</b>) that is structurally distinct from the canonical M<sup>pro</sup> inhibitor <b>GC376</b>. Significantly, <b>23R</b> is highly selective compared with covalent inhibitors such as <b>GC376</b>, especially toward host proteases. The cocrystal structure of SARS-CoV-2 M<sup>pro</sup> with <b>23R</b> revealed a previously unexplored binding site located in between the S2 and S4 pockets. Overall, this study discovered <b>23R</b>, one of the most potent and selective noncovalent SARS-CoV-2 M<sup>pro</sup> inhibitors reported to date, and a novel binding pocket in M<sup>pro</sup> that can be explored for inhibitor design.
Immittance Electroanalysis in Diagnostics (2014)

Impedance derived electroanalytical assays are inherently spectroscopic (frequency resolved) and potentially exceedingly sensitive indicators of interfacial change (such as target binding at an appropriate receptor). We introduce here the use of a portfolio of mathematically derived immittance functions and related components, capable, from the same raw data sets, of enabling increased assay sensitivity and markedly shorter assay times in comparison to traditional impedance analyses. The methodology, applied herein to faradaic (redox probe amplified) and non-faradaic assays, requires no equivalent circuit analysis or prior assumption of response. Its focus is to optimize analytical potency and to enable the user to select and apply the most frequency-optimized reporter of interfacial change and to, thereafter, run rapid (optimized) analyses at single frequencies.
Rigorous optical modeling of multilayer organic light-emitting diode devices (2001)

We present an exact classical solution to the problem of dipole emission in a planar multilayer light-emitting device. The inputs to the model are the photoluminescence and quantum yield of the emitter material, and the device layer thicknesses and indices of refraction. The results of the model are applied to predicting the radiant intensity of organic light-emitting diodes as a function of varying device layer thickness. It is shown that the predicted radiances are in excellent agreement with the data. We also present results for the Poynting power distribution from a randomly aligned dipole for positions both internal and external to the diodes.
Design and Implementation of a High-efficiency Three-level Inverter Using GaN HEMTs (2015)

In this paper, a three-level Neutral Point Clamped (NPC) single phase inverter using GaN HEMT devices is discussed. A simple low cost three-level boot-strap driver circuit is applied. Using non-isolated power for the driver avoids interference between the drive and control circuits due to the very high dv/dt switching speed of GaN. Finally, a 2 kVA 100 kHz threelevel inverter using 600 V GaN HEMTs is designed and tested for validation.
Chirality of Amyloid Suprastructures (2008)

Amyloids are pathological fibrillar aggregates of proteins related to more than 20 different diseases. Amyloid fibers have a characteristic cross-beta structure consisting of a series of beta-strands extended perpendicular to the fiber axis and joined by hydrogen bonds parallel to the fiber direction. Fibril aggregation results in helical suprastructures. Here we used high-resolution SEM and cryo-SEM for the study of chirality in the amyloid suprastructure. We found that amyloids of Abeta1-40 and hen lysozyme form at all hierarchical levels always and only left-handed helices. In contrast, amyloid fibers formed by the N-terminal sequence of serum amyloid A (SAA1-12) consist of right-handed helices exclusively. Consistently, the peptide enantiomer, formed of (R)-aminoacids, aggregates exclusively in left-handed helices. We conclude that the opposite handedness of the SAA1-12 amyloids is an intrinsic feature of the peptide structure. The left-handed chirality observed for the Abeta1-40 and hen lysozyme amyloid suprastructures is consistent with the conventional beta-sheet structural model. In contrast, the right-handedness observed in (all-S) SAA1-12 fibers indicates that the cross-beta structure of SAA1-12 fibers is probably not formed of beta-sheets. Whatever the answer to the dilemma of the right-handed helicity of SAA1-12 amyloid fibers is, its existence shows that the supramolecular chirality of amyloid fibers is not only dictated by the molecular chirality of the component molecules but also by their structural organization.