gebhart/patrepeval huggingface dataset:
Design guidelines for optical resonator biochemical sensors (2009)

We propose a design tool for dielectric optical resonator-based biochemical refractometry sensors. Analogous to the widely accepted photodetector figure of merit, the detectivity D*, we introduce a new sensor system figure of merit, the time-normalized sensitivity S*, to permit quantitative, cross-technology-platform comparison between resonator sensors with distinctive device designs and interrogation configurations. The functional dependence of S* on device parameters, such as resonant cavity quality factor (Q), extinction ratio, system noise, and light source spectral bandwidth, is evaluated by using a Lorentzian peak fitting algorithm and Monte Carlo simulations to provide theoretical insights and useful design guidelines for optical resonator sensors. Importantly, we find that S* critically depends on the cavity Q factor, and we develop a method of optimizing sensor resolution and sensitivity to noise as a function of cavity Q factor. Finally, we compare the simulation predictions of sensor wavelength resolution with experimental results obtained in Ge17Sb12S71 resonators, and good agreement is confirmed.
Hepatitis B virus RNA element that facilitates accumulation of surface gene transcripts in the cytoplasm (1994)

Hepatitis B virus enhancers I and II are critical for high-level expression from the viral major surface gene promoter. These enhancers are in an unusual position, since both are entirely contained within the downstream transcribed region of the surface gene. In this report, we present data showing that a fragment of the viral genome encompassing enhancer II activates accumulation of surface gene transcripts at the posttranscriptional level. Specifically, the total steady-state amount of surface gene transcripts in the cell drops by more than fourfold when enhancer II is displaced to a position downstream of the transcription termination site. There is a similar decrease in the amount of cytoplasmic surface gene transcripts but not of nuclear transcripts. These changes in steady-state transcript levels do not result from a decrease in the rate of transcriptional initiation or from an increased rate of degradation in the cytoplasm. Reinsertion of enhancer II in the correct orientation into the surface gene transcribed region partially restores transcript levels. From these data, we conclude that a hepatitis B virus RNA element functions in cis to increase the steady-state levels of surface gene transcripts by facilitating cytoplasmic accumulation of these transcripts.
Plasma concentrations of artemether and its major plasma metabolite, dihydroartemisinin, following a 5-day regimen of oral artemether, in patients with uncomplicated falciparum malaria (1998)

Plasma concentrations of artemether and its active plasma metabolite (dihydroartemisinin) were measured in 49 male, Thai patients with acute, uncomplicated, multidrug-resistant, Plasmodium falciparum malaria, following their treatment with oral artemether (300 mg on the first day, then 100 mg daily for another 4 days). Four patients recrudesced (on days 19–22). After the first dose, artemether became undetectable in ≤ 18 h and this drug was also undetectable in samples collected immediately before each dose. Although dihydroartemisinin followed similar trends, three patients had detectable plasma concentrations of this metabolite 24 h after the first dose (i.e. immediately before the second dose). Median (range) values for plasma concentrations of dihydroartemisinin 6 h [354 (150–751) v. 196 (178–220) ng/ml] and 12 h [158 (25–420) v. 54 (25–115) ng/ml] after the initial dose, estimated antimalarial activities (calculated as dihydroartemisinin equivalents) 6 h [331 (78.2–644.1) v. 23 (183.3–270) nmol/litre] and 12 h [98.3 (10–192.2) v. 56.7 (9.8–59.4) nmol/litre] after the initial dose, and the corresponding ‘areas under the curves’ (AUC) [3684 (1562–8216) v. 834 (1401–2030) ng.h/ml] were all significantly higher in the patients with sensitive responses than in those who recrudesced.
Superactivation of integrin αvβ3 by low antagonist concentrations (2001)

Integrins are implicated in cell adhesion, migration and homeostasis. An important feature is their ability to adopt different affinity states that can be regulated by a variety of intra- and extracellular factors. To study affinity modulation of the integrin ectodomain by extracellular factors, we produced a soluble recombinant form of mouse integrin alphavbeta3 in a mammalian expression system and isolated it to purity. We show that the two transmembrane truncated integrin subunits stably associate to form a functional receptor, soluble recombinant alphavbeta3. The affinity of this receptor for its ligands vitronectin, fibronectin and fibrinogen can be modulated by the divalent cations magnesium, calcium and manganese. Most importantly, we found that a cyclic RGD-peptide has a biphasic effect on rsalphavbeta3and native purified alphavbeta3, with an antagonistic phase at high concentrations, and an agonistic phase at low concentrations. This integrin superactivation by low antagonist concentrations is shown in binding of sralphavbeta3 to immobilized ligands by ELISA, and in adhesion of cells that express the chimaeric integrin ligand KISS31 to immobilized rsalphavbeta3 and native purified alphavbeta3. Our results indicate that low concentrations of the ligand mimetic cyclo-RGD can result in superactivation of the extracellular domain of integrin alphavbeta3 to a comparable level as activation by manganese.
The Nature of Amyloid-like Glucagon Fibrils (2010)

Protein aggregation and formation of amyloid fibrils is a phenomenon usually associated with proteotoxicity and degenerative diseases, such as type 2 diabetes, Alzheimer's disease, and prion diseases. However, several protein and peptide hormones are known to have a high propensity to form amyloid-like fibrils in vitro raising concerns about safety and stability of pharmaceutical protein solutions. Comprehensive understanding of the aggregation mechanisms is an important prerequisite to the design of strategies to prevent fibril formation. Detailed kinetic, spectroscopic, and morphological studies have revealed that glucagon can form several types of fibrils that differ at the level of molecular packing of the peptide. Each type forms through distinct nucleation-dependent aggregation pathways influenced by solution conditions and can be self-propagated by seeding. An increasing number of functional amyloid-like structures have been discovered in nature, and it has recently been proposed that an amyloid-like state of glucagon may be utilized by the pancreatic α-cells as in vivo storage form. This article reviews the current state of our knowledge about the nature of the different types of amyloid-like glucagon fibrils, the mechanisms by which they form, and discusses implications for formulation strategies and the safety of glucagon pharmaceuticals.
Analysis of large-scale gene expression data (2001)

DNA microarray technology has resulted in the generation of large complex data sets, such that the bottleneck in biological investigation has shifted from data generation, to data analysis. This review discusses some of the algorithms and tools for the analysis and organisation of microarray expression data, including clustering methods, partitioning methods, and methods for correlating expression data to other biological data.
Learning Shape Templates With Structured Implicit Functions (2019)

Template 3D shapes are useful for many tasks in graphics and vision, including fitting observation data, analyzing shape collections, and transferring shape attributes. Because of the variety of geometry and topology of real-world shapes, previous methods generally use a library of hand-made templates. In this paper, we investigate learning a general shape template from data. To allow for widely varying geometry and topology, we choose an implicit surface representation based on composition of local shape elements. While long known to computer graphics, this representation has not yet been explored in the context of machine learning for vision. We show that structured implicit functions are suitable for learning and allow a network to smoothly and simultaneously fit multiple classes of shapes. The learned shape template supports applications such as shape exploration, correspondence, abstraction, interpolation, and semantic segmentation from an RGB image.
10-Ketomorphinan and 3-Substituted-3-desoxymorphinan Analogues as Mixed κ and μ Opioid Ligands:  Synthesis and Biological Evaluation of Their Binding Affinity at Opioid Receptors (2003)

A series of 10-ketomorphinan analogues were synthesized, and their binding affinity at all three opioid receptors was investigated. In most cases, high affinity at micro and kappa receptors, and lower affinity at delta receptor was observed, resulting in good selectivity for micro and kappa receptors. A wide range of substituents can be accommodated on the nitrogen position. The N-(S)-tetrahydrofurfuryl analogue 11 displayed the highest affinity at all three receptors. The N-cyclobutylmethyl analogue 13 gave both high affinity and selectivity at kappa receptor, and N-2-phenylethyl analogue 18 exhibited good affinity and selectivity at micro receptor. Further modifications of the 3-substituent indicated that one H-bond donor was an essential requirement for good affinity at micro and kappa receptors. Similar modifications were investigated at the 3-OH group of morphinans: levorphanol (2a), cyclorphan (2b), and MCL-101 (2c) lacking the 10-keto group. The 3-amino bioisosteric analogues (40 and 41) displayed reasonably good affinity at micro and kappa receptors. The 3-carboxamido replacement (compounds 46-48) in the morphinan subseries resulted in similar affinities comparable to their corresponding 3-OH congeners. The high affinity of these carboxamido analogues, along with their greater lipophilicity and metabolic stability, make them promising candidates for further pharmacological investigation.
A urine score for noninvasive accurate diagnosis and prediction of kidney transplant rejection (2020)

Accurate and noninvasive monitoring of renal allograft posttransplant is essential for early detection of acute rejection (AR) and to affect the long-term survival of the transplant. We present the development and validation of a noninvasive, spot urine-based diagnostic assay based on measurements of six urinary DNA, protein, and metabolic biomarkers. The performance of this assay for detecting kidney injury in both native kidneys and renal allografts is presented on a cohort of 601 distinct urine samples. The urinary composite score enables diagnosis of AR, with a receiver-operator characteristic curve area under the curve of 0.99 and an accuracy of 96%. In addition, we demonstrate the clinical utility of this assay for predicting AR before a rise in the serum creatinine, enabling earlier detection of rejection than currently possible by standard of care tests. This noninvasive, sensitive, and quantitative approach is a robust and informative method for the rapid and routine monitoring of renal allografts.
Conformation of protein secreted across bacterial outer membranes: a study of enterotoxin translocation from Vibrio cholerae. (1987)

The secretion of enterotoxin by Vibrio cholerae is punctuated by the transient entry of the toxin subunits into the periplasm. In this paper, we show that the subunits oligomerize into an assembled holotoxin within the periplasm prior to their secretion across the outer membrane. The rate of toxin assembly was studied by pulse-labeling cells with [35S]-methionine and then monitoring the turnover of radiolabeled subunits as they assembled within the periplasm. The subunits entered the periplasm as monomers and assembled into oligomers with a half-time of approximately 1 min. Since assembly was a rapid event compared to the rate of toxin efflux from the periplasm, which had a half-time of approximately 13 min, we conclude that all of the subunits that pass through the periplasm assemble before they traverse the outer membrane. The average concentration of subunit monomers and assembled holotoxin within the periplasm was calculated to be approximately 20 and approximately 260 micrograms/ml, respectively. This indicates that the periplasm is a suitably concentrated milieu where spontaneous toxin assembly can occur. Our findings suggest that protein movement across bacterial outer membranes, in apparent contrast to export across other biological membranes, involves translocation of polypeptides that have already folded into tertiary and even quaternary conformations.
The design and testing of moving-wave mechanical face seals under variable operating conditions in water (1986)

Conception et essai d'un joint mecanique axial dans lequel on impose une deformation elastique qui se deplace le long de la circonference. Etude du fonctionnement dans l'eau en regime variable
The HIV-1 Viral Protein R Induces Apoptosis via a Direct Effect on the Mitochondrial Permeability Transition Pore (2000)

Viral protein R (Vpr) encoded by HIV-1 is a facultative inducer of apoptosis. When added to intact cells or purified mitochondria, micromolar and submicromolar doses of synthetic Vpr cause a rapid dissipation of the mitochondrial transmembrane potential (DeltaPsi(m)), as well as the mitochondrial release of apoptogenic proteins such as cytochrome c or apoptosis inducing factor. The same structural motifs relevant for cell killing are responsible for the mitochondriotoxic effects of Vpr. Both mitochondrial and cytotoxic Vpr effects are prevented by Bcl-2, an inhibitor of the permeability transition pore complex (PTPC). Coincubation of purified organelles revealed that nuclear apoptosis is only induced by Vpr when mitochondria are present yet can be abolished by PTPC inhibitors. Vpr favors the permeabilization of artificial membranes containing the purified PTPC or defined PTPC components such as the adenine nucleotide translocator (ANT) combined with Bax. Again, this effect is prevented by addition of recombinant Bcl-2. The Vpr COOH terminus binds purified ANT, as well as a molecular complex containing ANT and the voltage-dependent anion channel (VDAC), another PTPC component. Yeast strains lacking ANT or VDAC are less susceptible to Vpr-induced killing than control cells yet recover Vpr sensitivity when retransfected with yeast ANT or human VDAC. Hence, Vpr induces apoptosis via a direct effect on the mitochondrial PTPC.
Ab-induced ectodomain shedding mediates hepatocyte growth factor receptor down-regulation and hampers biological activity (2006)

Targeting tyrosine kinase receptors (RTKs) with specific Abs is a promising therapeutic approach for cancer treatment, although the molecular mechanism(s) responsible for the Abs' biological activity are not completely known. We targeted the transmembrane RTK for hepatocyte growth factor (HGF) with a monoclonal Ab (DN30). In vitro, chronic treatment of carcinoma cell lines resulted in impairment of HGF-induced signal transduction, anchorage-independent growth, and invasiveness. In vivo, administration of DN30 inhibited growth and metastatic spread to the lung of neoplastic cells s.c. transplanted into immunodeficient nu/nu mice. This Ab efficiently down-regulates HGF receptor through a molecular mechanism involving a double proteolytic cleavage: (i) cleavage of the extracellular portion, resulting in "shedding" of the ectodomain, and (ii) cleavage of the intracellular domain, which is rapidly degraded by the proteasome. Interestingly, the "decoy effect" generated by the shed ectodomain, acting as a dominant negative molecule, enhanced the inhibitory effect of the Ab.
Integration of Satellite Imagery, Geology and Geophysical Data (2011)

Satellite imagery is a large scale surface geological mapping too, which offers the unique opportunity to investigate the geological characteristics of remote areas of the earth surface without the need to access the area on the ground. The resolution of the technique is limited by the resolution of the imagery. This chapter explains how geological information can be extracted from satellite imagery and how this information can be merged with geological and geophysical data to build consistent geological models for the surface and subsurface. On the one hand, the interpretation of satellite imagery can generate start models prior to the start of geophysical surveys. On the other hand, geological and geophysical data can calibrate models derived from satellite imagery.
In-Vitro Studies On Buccal Strips Of Glibenclamide Using Chitosan (1997)

As glibenclamide is metabolised completely in the liver, the principal metabolite being only very weakly active, buccal strip glibenclamide may be very useful for the treatment of diabetes more efficiently. The objective of this work is to investigate the possibility of obtaining a slow release, relatively constant effective levels of glibenclamide from buccal strips using chitosan. Here attempts were made to develop suitable chitosan-based buccal strips and to characterise it using different in vitro methods. Chitosan- based strips of glibenclamide showed suitability over Eudragit-based glibenclamide buccal strips for controlled release behaviour.
Optimal Pricing Solution for Cloud Offered Business (2013)

Cloud is a stylishness of computing where accessible and adaptable IT-related abilities are providing as a service to external customers using Internet technologies, The Cloud Model built upon the four mainstays of current computing system such as Infrastructure, Platform, database as a services and the Software or applications services and also Pay-per-use is another fundamental characteristic of cloud computing, Achieving this model necessitates, Elasticity scale resources according to actual usage, No over provisioning, No idle reserve machines, Sharing resources to share cost & Measuring precise usage, The cloud provisions caching of data in direction toward deliver eminence query services. Consumer expenditures cover query performance prices, preservation of cloud infrastructure and suffer cloud income. The contest exists in providing well organized with resource-economic query services while preserving a gainful cloud. In this paper propose an profitable price estimation model for user gratification & with cloud owner profit, Parallelization can be implemented with a load balancing appliance or a content switch that allocates incoming requests across a number of virtual machines and dynamic pricing method is using better correlation estimation on time efficient manner for posing a queries on cloud database with the help of cloud caches, The experimental study proves that the proposed solution is feasible for a variety of workloads and cost effective pricing.
Postexposure bake characteristics of a chemically amplified deep-ultraviolet resist (1992)

In the processing of chemically amplified resist systems, two `dose' parameters must be considered. The exposure dose dictates the amount of photoacid generated, and the thermal dose that is administered during the post-exposure bake (PEB) governs the extent to which the resin is chemically transformed by the acid. An Arrhenius relationship exists between these two dose variables, and the magnitude of the effective activation energy determines the degree of PEB temperature control required for a particular linewidth budget. PEB characteristics are presented for a chemically amplified positive-tone DUV resist used by IBM in the manufacture of 0.5 micrometers 16 Mb DRAMs. The effect of PEB temperature and time on resist sensitivity, contrast, resolution, and process latitude is presented. The influence of exposure and thermal dose on the chemical contamination effect is also discussed.
New combinations in Hoodia and Lavrania (Asclepiadaceae – Stapelieae) (1993)

Plowes (1992) transferred several species of Trichocaulon N.E. Brown to Hoodia Sweet ex Decne, in so doing anticipating some of the changes made in a revision of these genera (Bruyns, in press). So as not to have any more of the intended changes anticipated, the following new combinations are made. These will be discussed in detail in the revision mentioned above.
Bacterial succession within a biofilm in water supply lines of dental air–water syringes (1995)

Biofilms have been implicated as reservoirs for bacterial contamination of water delivered by dental air-water syringes. A 6-month study was done of bacterial colonization and biofilm formation in plastic water supply lines connected to dental air-water syringes. Changes in biofilm flora were observed by both scanning electron microscopy and bacteriologic culture. By day 7, many rod- and spiral-shaped bacteria had colonized the ridged surface of the luminal wall of the tubing, as revealed by scanning electron microscopy. By day 30, individual microcolonies were embedded in extracellular polymeric material. By day 120, these microcolonies had begun to coalesce, and by day 180 the biofilm had developed into a multilayered, heterogeneous mixture of microcolonies. The mean aerobic plate counts of colony-forming units of planktonic and biofilm populations were, in log10 values, 5.9 +/- 0.54/mL and 4.2 +/- 0.82/cm2, respectively. Early colonizers were predominantly Pseudomonas spp., but included Pasteurella, Moraxella, Ochrobactrum, and Aeromonas spp. Flavobacterium and Acinetobacter spp. were observed later. Many of these organisms are opportunistic pathogens. These results demonstrate the longitudinal dynamics of biofilm formation.
Syntheses of some new 4-amino-5-(N-methyl-arylsulfonamido)methyl-1,2,4-triazole-3-thiones and their derivatives (1996)

The cyclization of 4-amino-5-(N-methyl-arylsulfonamido)methyl-1,2,4-triazole-3-thiones II, synthesized by the Reid and Heindel approach, with α-chloroacetophenone yields 7II-6-aryl-3-(N-methyl-arylsulfon-amido)methyl-s-triazolo[3,4-b][1,3,4]-thiazines III. Novel compounds II also react with benzyl chloride to afford 4-amino-3-benzylthio-5-(N-methyl-arylsulfonamido)methyl-1,2,4-triazole IV. © 1996 John Wiley & Sons, Inc.
Biomechanical evaluation of implant placement in the reconstructed mandible. (2010)

Placement of an implant on the nonreconstructed side following partial resection and mandibular reconstruction presents no significant risk.
Two-Year Cognitive, Emotional, and Quality-of-Life Outcomes in Acute Respiratory Distress Syndrome (2004)

Acute respiratory distress syndrome (ARDS) has a high mortality and is associated with significant morbidity. Prior outcome studies have focused predominant on short-term outcomes (6-12 months). We assessed longitudinal neurocognitive, emotional, and quality of life in ARDS survivors at hospital discharge, and 1 and 2 years after hospital discharge using neuropsychologic tests and emotional and quality-of-life questionnaires. Neurocognitive sequelae occurred in 73% (54 of 74) of ARDS survivors at hospital discharge, 46% (30 of 66) at 1 year, and 47% (29 of 62) at 2 years. ARDS survivors report moderate to severe depression (16% and 23%) and anxiety (24% and 23%) at 1 and 2 years, respectively. The ARDS survivors had decreased quality of life, with the physical domains improving at 1 year, with no additional change at 2 years. Role emotional, pain, and general health did not change from hospital discharge to 2 years. Mental health improved during the first year and declined at 2 years. ARDS results in significant neurocognitive and emotional morbidity and decreased quality of life that persists at least 2 years after hospital discharge. ARDS can cause significant long-term, brain-related morbidity manifest by neurocognitive impairments and decreased quality of life.