gebhart/patrepeval huggingface dataset:
HtrA in Porphyromonas gingivalis can regulate growth and gingipain activity under stressful environmental conditions (2006)

In several micro-organisms, HtrA, a serine periplasmic protease, is considered an important virulence factor that plays a regulatory role in oxidative and temperature stress. The authors have previously shown that the vimA gene product is an important virulence regulator in Porphyromonas gingivalis. Further, purified recombinant VimA physically interacted with the major gingipains and the HtrA from P. gingivalis. To further evaluate a role for HtrA in the pathogenicity of this organism, a 1.5 kb fragment containing the htrA gene was PCR-amplified from the chromosomal DNA of P. gingivalis W83. This gene was insertionally inactivated using the ermF-ermAM antibiotic-resistance cassette and used to create an htrA-deficient mutant by allelic exchange. In one randomly chosen isogenic mutant designated P. gingivalis FLL203, there was increased sensitivity to hydrogen peroxide. Growth of this mutant at an elevated temperature was more inhibited compared to the wild-type. Further, in contrast to the wild-type, there was a significant decrease in Arg-gingipain activity after heat shock in FLL203. However, the gingipain activity in the mutant returned to normal levels after a further 30 min incubation at room temperature. Collectively, these data suggest that HtrA may play a similar role in oxidative and temperature stress in P. gingivalis as observed in other organisms.
BioPhony: an open system to measure the airway area by acoustic reflection (2002)

Describes an open system called BioPhony for non-invasive measurement of the airway area. BioPhony, in use at Henri Mondor Hospital (Creteil, France), is based on a recent acoustic reflection method (B. Louis et al., "Airway area by acoustic reflection: the two-microphone method," J. Biomech. Eng., vol. 115, p. 278-85, 1993). BioPhony relies on object-oriented paradigm and specific programming techniques have been used to take into account time constraints. BioPhony offers a friendly user interface, facilities to communicate with other applications, and support for future extensions.
Comparison of Ablation Zone Between 915- and 2,450-MHz Cooled-Shaft Microwave Antenna: Results in In Vivo Porcine Livers (2009)

The 915-MHz cooled-shaft microwave antenna can lead to deeper penetration of liver tissue and can yield a significantly larger ablation zone than the 2,450-MHz cooled-shaft antenna in in vivo porcine livers. In light of the result, 915-MHz cooled-shaft microwaves may be more effective for tumor ablation, especially for large tumors.
Convolutional neural networks for mammography mass lesion classification (2015)

Feature extraction is a fundamental step when mammography image analysis is addressed using learning based approaches. Traditionally, problem dependent handcrafted features are used to represent the content of images. An alternative approach successfully applied in other domains is the use of neural networks to automatically discover good features. This work presents an evaluation of convolutional neural networks to learn features for mammography mass lesions before feeding them to a classification stage. Experimental results showed that this approach is a suitable strategy outperforming the state-of-the-art representation from 79.9% to 86% in terms of area under the ROC curve.
Designing Biostable Polyurethane Elastomers for Biomedical Implants (2003)

The chemical structure, synthesis, morphology, and properties of polyurethane elastomers are briefly discussed. The current understanding of the effect of chemical structure and the associated morphology on the stability of polyurethanes in the biological environments is reviewed. The degradation of conventional polyurethanes appears as surface or deep cracking, stiffening, and deterioration of mechanical properties, such as flex-fatigue resistance. Polyester and poly(tetramethylene oxide) based polyurethanes degrade by hydrolytic and oxidative degradation of ester and ether functional groups, respectively. The recent approaches to develop polyurethanes with improved long-term biostability are based on developing novel polyether, hydrocarbon, polycarbonate, and siloxane macrodiols to replace degradation-prone polyester and polyether macrodiols in polyurethane formulations. The new approaches are discussed with respect to synthesis, properties and biostability based on reported in vivo studies. Among the newly developed materials, siloxane-based polyurethanes have exhibited excellent biostability and are expected to find many applications in biomedical implants.
Development And test of a solar decomposer of sulphuric acid for thermochemical hydrogen production (2011)

Decomposition of sulphuric acid is a key step of sulphur based thermochemical cycles for hydrogen production by thermal splitting of water. The Hybrid Sulphur Cycle (HyS) consisting of two reaction steps [1] is considered as one of the most promising cycles: Firstly, sulphuric acid is decomposed by high temperature heat of 800-1200°C forming sulphur dioxide (SO2), which in a second step is used to electrochemically split water. Compared to conventional water electrolysis only about a tenth of the theoretical voltage is required making the HyS one of the most efficient processes to produce hydrogen by concentrated solar radiation [2]. As a result, this thermochemical cycle has the potential to significantly reduce the amount of energy required for water splitting and to efficiently generate hydrogen free of carbon dioxide emissions. The European research project HycycleS (Materials and components for Hydrogen production by sulphur based thermochemical cycles) [4] aims at a technical realisation of the Hybrid Sulphur Cycle. One objective of the project is to develop and qualify a solar interface, meaning a device to couple concentrated solar radiation into the endothermal steps of the chemical process. Therefore a test reactor for decomposition of sulphuric acid by concentrated solar radiation was developed and tested in the solar furnace of DLR in Cologne. Based on the preceding project HYTHEC (HYdrogen THErmochemical Cycles) [3] an optimised reactor concept with two chambers was constructed [5]: In the
Supplementary Methods from A Phase I Study of APX005M and Cabiralizumab with or without Nivolumab in Patients with Melanoma, Kidney Cancer, or Non–Small Cell Lung Cancer Resistant to Anti-PD-1/PD-L1 (2023)

&lt;p&gt;Supplementary Methods&lt;/p&gt;
P4‐210: G protein coupling of galanin, muscarinic and cannabinoid receptors in areas related to the control of memory and cognitive functions of Alzheimer patients (2009)

The cholinergic basal forebrain shows an hyperinnervation by the neuropeptide galanin in AD patients and the galanin receptors are modulated throughout the progression of the disease in the frontal cortex, amygdala, basal nucleus of Meynert and hippocampus. Thus, the aim of this study was to evaluate the coupling of the cholinergic muscarinic receptor M2/M4, the galanin receptor GalR1 and cannabinoid receptor CB1 to Gi/o proteins in the previously mentioned areas and in the striatum, which is a cholinergic area not affected by AD. AD patients were classified in three groups depending on the stage of dementia and histopathological markers (I-II/A, III-IV/B, V-VI/C). [35S]GTPgammaS autoradiography was used in postmortem brain samples. The greater the progression of the disease, the more reduced was the basal activity of the whole population of G protein coupled receptors (GPCR) in all the layers of the frontal cortex of AD. Nevertheless, the Gi/o protein activity induced by galanin was increased in layer VI, independently of the AD stage. No significant changes were observed in the activity of muscarinic receptors when the different cortical layers were independently analyzed. Also, the basal activity of the GPCR was found to be decreased in several hippocampal areas of AD patients, such as pyramidal CA1, radiatum CA3, and hilus and molecular layers of dentate gyrus. No significant changes were observed in the activity of galanin and muscarinic receptors in the hippocampus, but the function of the cannabinoid receptors was reduced depending on the AD stage. On the other hand, the basal activity of GPCR in the striatum was not altered in AD patients, but the activity of the cannabinoid receptors was reduced in the most advanced stages. The observed decrease of GPCR basal activity might be the result of the synaptic impairment observed in the frontal cortex and hippocampus of AD patients that could be compensated by the enhancement of the galanin receptor signalling, the neuroprotective actions of this neuropeptide being known.
Catalytic and Stereoselective Glycosylation with Disarmed Glycosyl Fluoride Having Phthaloyl or Dichlorophthaloyl Protected Amino Function Using a 1 : 2 Combination of Stannic Chloride and Silver Tetrakis(pentafluorophenyl)borate (2001)

Abstract A catalytic and stereoselective glycosylation of various glycosyl acceptors with disarmed glycosyl fluorides having phthaloyl or dichlorophthaloyl protected amino function is successfully carried out by using a combination of stannic chloride (SnCl4) and silver tetrakis(pentafluorophenyl)borate [AgB(C6F5)4] in the coexistence of MS 5A, and the corresponding 1,2-trans disaccharides are obtained in high yields.
Ferritic Stainless Steel SOFC Interconnects with Thermally Grown (Mn, Co)3O4 Spinel Protection Layers (2008)

To protect solid oxide fuel cells (SOFC5) from chromium poisoning and improve metallic interconnect stability, manganese cobaltite spinel protection layers with a nominal composition of Mn1.5Co1.5O4 were thermally grown on ferritic stainless steels. Thermal, electrical and electrochemical investigations indicated that the spinel protection layers not only significantly decreased the contact resistance, but also effectively acted as a mass barrier to both the oxygen inward and the chromium outward diffusion. A long-term thermal cycling test demonstrated excellent structural and thermomechanical stability of these spinel protection layers.
Flexible, compressible, hydrophobic, floatable, and conductive carbon nanotube-polymer sponge (2013)

A flexible, compressible, hydrophobic, ice-repelling, floatable, and conductive carbon nanotube (CNT)-polydimethylsiloxane (PDMS) sponge is presented. The microporous sponge-like PDMS scaffold fabricated with a sugar cube template is capable of CNT uptake. The CNT-PDMS sponge (CPS) is deformable and compressible up to 90%. The Young's modulus varies from 22 KPa to 200 KPa depending on the applied strain. The conductive pathways via the CNT network increase with compressive strain similar to a variable resistor or pressure sensor. The softness of the CPS can be utilized for artificial skin to grip sensitive objects. In addition, the contact angle of water droplets on CPS shows 141°, and thus the hydrophobic nature of the CPS can be exploited as a floating electrode. Furthermore, the hydrophobicity is maintained below freezing temperature, allowing an ice-repelling electrode.
Reflected and Transmitted Irradiance from Area Sources using Vertex Tracing (2001)

Computing irradiance analytically from polygonal luminaires in polygonal environments has proven effective for direct lighting applications in diffuse radiosity environments. Methods for analytic integration have traditionally used edge-based solutions to the irradiance integral; our previous work presented a vertex-based analytic solution, allowing irradiance to be computed incrementally by ray tracing the apparent vertices of the luminaire. In this work we extend the vertex tracing technique to the analytic computation of irradiance from a polygonal luminaire in other indirect lighting applications: transmission through non-refractive transparent polygons, and reflection off perfectly specular polygons. Furthermore we propose an approximate method for computing transmitted irradiance through refractive polyhedra. The method remains effective in the presence of blockers.
Influence of β-glucanase-producing Lactobacillus strains on intestinal characteristics and feed passage rate of broiler chickens (2005)

Two experiments were conducted to study the effects of beta-glucanase produced by transformed Lactobacillus strains on the intestinal characteristics and feed passage rate of broiler chickens fed barley-based diets. Supplementation of transformed Lactobacillus strains to the diet of chickens significantly (P < 0.05) reduced the intestinal fluid viscosity by 21 to 46% compared with chickens fed an unsupplemented diet or a diet supplemented with parental Lactobacillus strains. The relative weights of pancreas, liver, duodenum, jejunum, ileum, ceca, and colon were reduced (P < 0.05) by 6 to 27%, and the relative length of duodenum, jejunum, ileum, and ceca was reduced (P < 0.05) by 8 to 15%. Histological examination of the intestinal tissues showed that the jejunal villus height of chickens fed a diet supplemented with transformed Lactobacillus strains was significantly (P < 0.05) higher than that of chickens fed other dietary treatments. The transformed Lactobacillus strains were found to reduce (P < 0.05) the time of feed passage rate by 2.2 h. Supplementation of transformed Lactobacillus strains to the diet improved the intestinal characteristics and feed, passage rate of the chickens.
Iterative test suites refinement for elastic computing systems (2013)

Elastic computing systems can dynamically scale to continuously and cost-effectively provide their required Quality of Service in face of time-varying workloads, and they are usually implemented in the cloud. Despite their wide-spread adoption by industry, a formal definition of elasticity and suitable procedures for its assessment and verification are still missing. Both academia and industry are trying to adapt established testing procedures for functional and non-functional properties, with limited effectiveness with respect to elasticity. In this paper we propose a new methodology to automatically generate test-suites for testing the elastic properties of systems. Elasticity, plasticity, and oscillations are first formalized through a convenient behavioral abstraction of the elastic system and then used to drive an iterative test suite refinement process. The outcomes of our approach are a test suite tailored to the violation of elasticity properties and a human-readable abstraction of the system behavior to further support diagnosis and fix.
[Effect of dapsone on survival in HIV infected patients: a meta- analysis of finished trials]. (2000)

Dapsone may be used safely as a primary prophylactic regimen for PCP or toxoplasmosis. However, no definitive recommendation can be made for the use of dapsone as secondary PCP prophylaxis.
Elucidating the Mechanism of the Asymmetric Aza‐Michael Reaction (2007)

The mechanism of the palladium-catalysed asymmetric aza-Michael addition of aniline to alpha,beta-unsaturated N-imide was examined from several aspects using a combination of techniques, including X-ray crystallography, mass spectrometry, NMR, UV/Vis spectroscopy, and kinetic studies. The binding of aniline to the dicationic palladium(II) metal centre was found to occur in two consecutive steps: The binding of the first aniline is fast and reversible, whereas the binding of the second aniline is slower and irreversible. This occurs in competition with the binding of the N-imide, which forms a planar six-membered chelate ring with the metal centre; coordinating through the 1,3-dicarbonyl moiety. Isotopic labelling revealed that the addition of N-H occurs in a highly stereoselective manner, allowing the synthesis of optically active beta(2)- and beta(2,3)-amino acid derivatives. The stereochemistry of the addition is postulated to be syn. In situ kinetic studies provided evidence for product inhibition. The binding of the N-imide to the catalyst was found to be the rate-limiting step. Aniline was found to be an inhibitor of the pre-catalyst. The study culminated in the design of a new reaction protocol. By maintaining a low concentration of the aniline substrate during the course of the reaction, significant enhancement of yield and enantioselectivity can be achieved.
Clinicopathologic features and outcomes of lymphoplasmacytic lymphoma patients with monoclonal IgG or IgA paraprotein expression (2015)

Lymphoplasmacytic lymphoma secreting IgG or IgA (non-IgM LPL) is rarely seen. Systematic studies of the clinical features and treatment outcomes are lacking in these patients. This study evaluated 17 patients with non-IgM LPL. The paraprotein secreted by these tumors was IgA (n=8; 47%) and IgG (n=9; 53%). The median serum level of paraprotein was 2,475 mg/dl (range=747-5260) for IgA and 2580 mg/dl (range=1900-7100) for IgG. The IgA-LPL group was more likely to present with B symptoms, a high beta2-microglobulin level and extramedullary involvement. Compared with patients with Waldenström macroglobulinemia (WM), patients with non-IgM LPL showed similar clinical and pathologic features, but a higher mortality within the first year after diagnosis (p<0.001) and worse overall survival (p=0.024), with no difference in progression-free survival and disease-specific survival. Rituximab alone or rituximab-based therapy was used frequently and was effective as either first-line or salvage therapy.
HIGH EFFICIENCY SYNGAS GENERATION (2005)

This project investigated an efficient and low cost method of auto-thermally reforming natural gas to hydrogen and carbon monoxide. Reforming is the highest cost step in producing products such as methanol and Fisher Tropsch liquids (i.e., gas to liquids); and reducing the cost of reforming is the key to reducing the cost of these products. Steam reforming is expensive because of the high cost of the high nickel alloy reforming tubes (i.e., indirectly fired reforming tubes). Conventional auto-thermal or Partial Oxidation (POX) reforming minimizes the size and cost of the reformers and provides a near optimum mixture of CO and hydrogen. However POX requires pure oxygen, which consumes power and significantly increases the cost to reforming. Our high efficiency process extracts oxygen from low-pressure air with novel oxygen sorbent and transfers the oxygen to a nickel-catalyzed reformer. The syngas is generated at process pressure (typically 20 to 40 bar) without nitrogen dilution and has a 1CO to 2H{sub 2} ratio that is near optimum for the subsequent production of Fisher-Tropsch liquid to liquids and other chemicals (i.e., Gas to Liquids, GTL). Our high process efficiency comes from the way we transfer the oxygen into the reformer. All of the components of the process, except for the oxygen sorbent, are commonly used in commercial practice. A process based on a longlived, regenerable, oxygen transfer sorbent could substantially reduce the cost of natural gas reforming to syngas. Lower cost syngas (CO + 2H{sub 2}) that is the feedstock for GTL would reduce the cost of GTL and for other commercial applications (e.g., methanol, other organic chemicals). The vast gas resources of Alaska's North Slope (ANS) offer more than 22 Tcf of gas and GTL production in this application alone, and could account for as much as 300,000 to 700,000 bpd for 20 to 30+ years. We developed a new sorbent, which is an essential part of the High Efficiency Oxygen Process (HOP). We tested the sorbent and observed that it has both a good oxygen capacity and operates as a highly effective reforming catalyst. We conducted a long duration tests of the sorbent (1,500 hours of continuous operation in the HOP cycle). Although the sorbent lost some oxygen capacity with cycling, the sorbent oxygen capacity stabilized after 1,000 hours and remained constant to the end of the test, 1,500 hour. The activity of the catalyst to reform methane to a hydrogen and carbon monoxide mixture was unchanged through the oxidation/reduction cycling. Our cost and performance analyses indicated a significant reduction in the cost of GTL production when using the HOP process integrated into a GTL plant.
ErgoSAM: A preproduction risk identification tool (2005)

Simulating work in a workstation with computer manikins is for many companies too expensive to acquire and master. An alternative method to detect high musculoskeletal loads early in the planning process is ErgoSAM. This article describes the users' and potential users' view of ErgoSAM and the suggestions of possible and desired improvements. Some improvements were introduced in a new version of ErgoSAM and validated at Volvo Car Corporation, Sweden. The new version demonstrates improved capacity to predict the occurrence of high loads on the operator when performing an assembly task, described in the MTM method SAM and in an assembly environment. © 2005 Wiley Periodicals, Inc. Hum Factors Man 15: 309–325, 2005.
225. CONTROLLED GAIT ANALYSIS IN PATIENTS WITH TKA VERSUS NORMAL CONTROLS (2011)

Purpose of the study: How does a total knee arthroplasty (TKA) function? Do all prostheses provide the excellent results reported in the literature? This gait analysis compared patients with a TKA versus normal subjects in order to obtain a 3D quantification of the kinematic and dynamic differences between patients with a very good functional result and controls. Material and methods: Twenty patients who had a TKA for less than one year and whose functional outcome was scored very good (KSS knee >85/100, VAS ≤1/10) were compared in a double blind study with 20 normal controls. The knees were masked so that the investigators were unaware of the type of subject (operated or not), the side operated, or the type of implant. The analysis as performed on an AMTI platform with six infrared cameras which followed the displacements of 36 reflectors. Motion Analysis software was applied. The gait parameters recorded were: speed, step length, flexion angle, duration of weight bearing/oscillation phases, and dynamic variables: flexion-extension moment, varus-valgus moment, internal/external rotation moment. Results: Adjusted for age and height, step length, walking speed, and duration of the weight bearing phase were identical in the operated and control populations. Kinematic and dynamic variables demonstrated significant differences. At lift-off, all of the TKA subjects were in functional permanent flexion (m=10); the flexion moment of the quadriceps was less than in the non-operated subjects. In the frontal plane, the weight-bearing phase was identical between the operated subjects and controls, but with a varus dynamic (m=4) during the oscillating phase. In the horizontal plane, there was an external rotation of the tibia (m=+5) during weight bearing. Discussion: Gait analysis provides quantitative information which is not perceptible at physical examination nor with videoscopic explorations. Even patients with an excellent KSS score exhibit important anomalies despite the fact that the physical exam finds a normal range of motion and normal muscle force. The degree by degree 3D gait analysis reveals the difference. Conclusion: Despite a clinical score considered to be very good, patients with a TKA have a functional deficit of the extensor system during take-off, even when the knee has complete active extension; the weight-bearing phase of the step is in external rotation and the oscillating phase exhibits varus laxity.