gebhart/patrepeval huggingface dataset:
Regular Grape Intake Reduces Cardiac and Renal Dysfunction and Metabolic Syndrome in Obesity‐Prone Rats (2010)

Metabolic Syndrome is characterized by increased systemic inflammation, abdominal fat, high triglycerides, low HDL, hypertension, and insulin resistance. The presence of some or all of these risk factors predisposes one to Type II diabetes and cardiovascular disease. Epidemiologic studies suggest that higher intake of fruits/vegetables could modify risk factors for metabolic syndrome. Phytochemicals may be vital to the observed health effects. Grapes are a rich, whole‐food source of phytochemicals. In the obesity‐prone Zucker Fatty rat, we tested the effect of a higher fat diet(45% kcal) with added whole table grape powder(3% w:w). Rats were fed for 90 days. Compared to a macronutrient and calorie‐matched control group, the grape diet had no significant effect on body weight or DEXA‐determined body composition. Grape intake reduced blood pressure and proteinuria while improving cardiac output. The grape‐fed group had reduced heart weight, kidney weight, and liver weight. The grape‐fed animals had reduced fasting serum triglycerides and hyperinsulinemia but not total cholesterol(p=0.12). Finally, grape intake reduced plasma inflammatory markers C‐reactive protein, TNF‐α and IL‐6, and reduced plasma oxidative stress marker 8‐isoprostane. The results suggest that regular intake of grapes reduced several risk factors for cardiovascular disease and metabolic syndrome.
The Lon protease of Pseudomonas aeruginosa is induced by aminoglycosides and is involved in biofilm formation and motility (2007)

Pseudomonas aeruginosa is an important nosocomial opportunistic human pathogen and a major cause of chronic lung infections in individuals with cystic fibrosis. Serious infections by this organism are often treated with a combination of aminoglycosides and semi-synthetic penicillins. Subinhibitory concentrations of antibiotics are now being recognized for their role in microbial persistence and the development of antimicrobial resistance, two very important clinical phenomena. An extensive screen of a P. aeruginosa PAO1 luciferase gene fusion library was performed to identify genes that were differentially regulated during exposure to subinhibitory gentamicin. It was demonstrated that subinhibitory concentrations of gentamicin and tobramycin induced a set of genes that are likely to affect the interaction of P. aeruginosa with host cells, including the gene encoding Lon protease, which is known to play a major role in protein quality control. Studies with a lon mutant compared to its parent and a complemented strain indicated that this protein was essential for biofilm formation and motility in P. aeruginosa.
Mechanism of Actin Polymerization in Cellular ATP Depletion (2004)

Cellular ATP depletion in diverse cell types results in the net conversion of monomeric G-actin to polymeric F-actin and is an important aspect of cellular injury in tissue ischemia. We propose that this conversion results from altering the ratio of ATP-G-actin and ADP-G-actin, causing a net decrease in the concentration of thymosinactin complexes as a consequence of the differential affinity of thymosin beta4 for ATP- and ADP-G-actin. To test this hypothesis we examined the effect of ATP depletion induced by antimycin A and substrate depletion on actin polymerization, the nucleotide state of the monomer pool, and the association of actin monomers with thymosin and profilin in the kidney epithelial cell line LLC-PK1. ATP depletion for 30 min increased F-actin content to 145% of the levels under physiological conditions, accompanied by a corresponding decrease in G-actin content. Cytochalasin D treatment did not reduce F-actin formation during ATP depletion, indicating that it was predominantly not because of barbed end monomer addition. ATP-G-actin levels decreased rapidly during depletion, but there was no change in the concentration of ADP-G-actin monomers. The decrease in ATP-G-actin levels could be accounted for by dissociation of the thymosin-G-actin binary complex, resulting in a rise in the concentration of free thymosin beta4 from 4 to 11 microm. Increased detection of profilin-actin complexes during depletion indicated that profilin may participate in catalyzing nucleotide exchange during depletion. This mechanism provides a biochemical basis for the accumulation of F-actin aggregates in ischemic cells.
Structural Biology of Mutant IDH2 Inhibition (2014)

A number of human cancers harbor somatic point mutations in the genes encoding isocitrate dehydrogenases- 1 and -2 (IDH1, IDH2)[1]. These mutations alter residues in the enzyme active sites and confer a gain-of-function in cancer cells, resulting in the accumulation and secretion of the oncometabolite R (-)-2-hydroxyglutarate (2HG). 2HG is a potent inhibitor of DNA methylating enzymes such as TET2[2]. This suggests a connection between cancer related IDH mutations and aberrant epigenetics. As such, IDH represents an important new druggable target in the pursuit of novel cancer therapies. We have developed a small molecule, AGI-6780, that potently and selectively inhibits the tumor-associated mutant IDH2/R140Q. A crystal structure of AGI-6780 complexed with IDH2/R140Q revealed that the inhibitor binds in an allosteric manner at the dimer interface[3]. While structures of IDH1 and IDH2 were known, this is the first ever structure of an inhibited IDH protein and shows a novel conformation of IDH2. The results of steady-state enzymology analysis were consistent with allostery and slow-tight binding by AGI-6780. Treatment with AGI-6780 induced differentiation of TF-1 erythroleukemia and primary human acute myelogenous leukemia (AML) cells in vitro. These data provide proof-of- concept that inhibitors targeting mutant IDH2/R140Q could have potential applications as a differentiation therapy for cancer.
Thickness dependent self limiting 1-D tin oxidenanowire arrays by nanosecond pulsed laser irradiation (2010)

Fast, sensitive and discriminating detection of hydrogen at room temperature is crucial for storage, transportation, and distribution of hydrogen as an energy source. One dimensional nanowires of SnO2 are potential candidates for improved H2 sensor performance. The single directional conducting continuous nanowires can decrease electrical noise, and their large active surface area could improve the response and recovery time of the sensor. In this work we discuss synthesis and characterization of nanowire arrays made using nanosecond ultraviolet wavelength (266 nm) laser interference processing of ultrathin SnO2 films on SiO2 substrates. The laser energy was chosen to be above the melting point of the films. The results show that the final nanowire formation is dominated by preferential evaporation as compared to thermocapillary flow. The nanowire height (and hence wire aspect ratio) increased with increasing initial film thickness h0 and with increasing laser energy density Eo. Furthermore, a self-limiting effect was observed where-in the wire formation ceased at a specific final remaining thickness of SnO2 that was almost independent of h0 for a given Eo. To understand these effects, finite element modeling of the nanoscale laser heating was performed. This showed that the temperature rise under laser heating was a strong non-monotonic function of film thickness. As a result, the preferential evaporation rate varies as wire formation occurs, eventually leading to a shut-off of evaporation at a characteristic thickness. This results in the stoppage of wire formation. This combination of nanosecond pulsed laser experiments and thermal modeling shows that several unique synthesis approaches can be utilized to control the nanowire characteristics.
DURABILITY ISSUES IN PRECIOUS-GROUP-METAL FREE PEMFC CATHODES (2017)

Replacement of noble metal catalysts used in oxygen reduction reaction (ORR) is a research goal in the proton membrane fuel cells. In this work, mass transport limiting phenomena in Fe-N-C catalyst layers are studied. A specific methodology, that combines in-situ characterization of performance and modelling activity, is adopted to elucidate the contribution of electronic/ionic transport losses in catalyst layer with controlled properties. CCL impedance spectra, which take into account ORR activation and electron, proton, and oxygen transport losses are simulated. Analysis shows that a regime of mixed ion and electron transport limitations describes correctly the main features of impedance spectra. Degradation is negligible under nitrogen at 0.6V, supporting catalysts materials oxidation or water formation as main reasons for performance loss.
Reaction-diffusion equations. (2015)

&lt;p&gt;Description: [&lt;i&gt;c&lt;/i&gt;]&lt;sub&gt;&lt;i&gt;in&lt;/i&gt;&lt;/sub&gt;: compound concentration inside the cell, [&lt;i&gt;c&lt;/i&gt;]&lt;sub&gt;&lt;i&gt;out&lt;/i&gt;&lt;/sub&gt;: compound concentration outside the cell, &lt;i&gt;D&lt;/i&gt;&lt;sub&gt;&lt;i&gt;d&lt;/i&gt;&lt;/sub&gt;: diffusion constant of the compound, &lt;i&gt;D&lt;/i&gt;&lt;sub&gt;&lt;i&gt;m&lt;/i&gt;&lt;/sub&gt;: permeability of the membrane to compound, &lt;/p&gt;&lt;p&gt;&lt;/p&gt;&lt;p&gt;&lt;/p&gt;&lt;p&gt;&lt;mi&gt;D&lt;/mi&gt;&lt;mo&gt;˜&lt;/mo&gt;&lt;/p&gt;&lt;p&gt;&lt;/p&gt;&lt;p&gt;&lt;/p&gt;: is the vector of diffusion constants.&lt;p&gt;&lt;/p&gt;&lt;p&gt;Reaction-diffusion equations.&lt;/p&gt;
Smartphone-based real-time classification of noise signals using subband features and random forest classifier (2016)

This paper presents the real-time implementation and field testing of an app running on smartphones for classifying noise signals involving subband features and a random forest classifier. This app is compared to a previously developed app utilizing mel-frequency cepstral coefficients features and a Gaussian mixture model classifier. The real-time implementation has been carried out on both the Android and iOS smartphones. The field testing results indicate the superiority of this newly developed app over the previously developed app in terms of classification rates.
Plasma Membrane Rafts Complete Cholesterol Synthesis by Participating in Retrograde Movement of Precursor Sterols (2007)

Mammalian cells synthesize significant amounts of precursor sterols, in addition to cholesterol, at the endoplasmic reticulum (ER). The newly synthesized sterols rapidly move to the plasma membrane (PM). The mechanism by which precursor sterols move back to the ER for their enzymatic processing to cholesterol is essentially unknown. Here we performed pulse-chase experiments and showed that the C29/C30 sterols rapidly move from the PM to the ER and are converted to cholesterol. The retrograde precursor sterol transport is largely independent of the Niemann-Pick type C proteins, which play important roles in late endosomal cholesterol transport. In contrast, disrupting lipid rafts significantly retards the conversion of C29/C30 and C28 sterols to cholesterol, causing the accumulation of precursor sterols at the PM. Our results reveal a previously undisclosed function of the PM lipid rafts: they bring cholesterol biosynthesis to completion by participating in the retrograde movement of precursor sterols back to the ER.
Machine Learning Methods for Barret’s and Dysplasia classification from In Vivo Optical Coherence Tomography Images of Human Esophagus (2020)

Comparison of machine learning methods for classification of esophageal tissues from in vivo OCT images. A neural network approach provided the best discrimination between normal tissue, Barrett’s and dysplasia, using various features, with 87% accuracy.
Supplemental Figure S4 from Guidance Molecule SEMA3A Restricts Tumor Growth by Differentially Regulating the Proliferation of Tumor-Associated Macrophages (2023)

&lt;p&gt;MACROPHAGE DEPLETION BY ANTI-CSF1.&lt;/p&gt;
Statins in the Reduction of Cardiovascular Events (2011)

Abstract The major advances in coronary heart disease (CHD) diagnosis and treatment in the past half‐century include the detection of thrombosis or a mechanism of acute coronary syndromes that leads to heart attacks and discovery of major risk factors that leads to progression of atherosclerosis. Next was the role of aspirin in prevention. The most eradicable risk factor is smoking cessation in the prevention of CHD. Most modifiable risk factor is lipoprotein (LDL)‐cholesterol reduction that has been shown to cause regression of atherosclerosis and reduction in cardiac events. Statins play a major role in reducing LDL‐cholesterol, hence reducing cardiac events in every study. Statins not only have their effects through LDL‐cholesterol reduction, but have LDL‐cholesterol‐independent effects. The significance of the pleitropic effects is not well defined. Statins are, nonetheless, the only class of drugs that has been shown to consistently reduce CHD risk.
Associations between common fibrinogen gene polymorphisms and cardiovascular disease in older adults (2008)

Elevated plasma fibrinogen is a risk factor for cardiovascular disease (CVD), but associations between fibrinogen single nucleotide polymorphisms (SNPs) and disease risk are inconsistent. We investigated whether common (> or = 5% minor allele frequency) variation in the fibrinogen genes (FGA, FGB, FGG) is associated with fibrinogen concentration, carotid artery intima-medial thickness (IMT) and risk of incident myocardial infarction (MI), ischemic stroke and CVD mortality in European- (EA) and African-descent (AA) adults (> or = 65 years) from the Cardiovascular Health Study. TagSNPs were genotyped in 3,969 EA and 719 AA free of MI or stroke at baseline. Race-specific models included multiple testing correction and adjustment for sex, age and site. Among EA, minor alleles of FGA3807, FGB1437 and FGG902 were associated with higher fibrinogen levels; whereas FGA251, FGA2224, FGA6534 and FGG10034 were associated with lower levels, p<0.004 for each. Strongest associations were seen for FGB1437; each additional copy of the minor allele was associated with 13 mg/dl (95%CI: 9-16) higher fibrinogen level. Similar trends in AA were not significant. Fibrinogen haplotypes were not significantly associated with internal or common carotid IMT. No associations with MI or CVD mortality were seen in EA, though FGB1038 and FGG902 were significantly associated with increased and decreased risk of stroke in men, respectively, as were related haplotypes. FGB1038 was also associated with CVD mortality in AA, HR = 1.9 (95%CI: 1.3-2.7). In conclusion, while fibrinogen genetic variation was strongly associated with fibrinogen levels, there was less evidence of association with the more complex outcomes of IMT and CVD events.
City or hinterland – site potentials for upscaled aquaponics in a Berlin case study (2022)

Abstract Sustainably feeding the rapidly growing urban populations requires resource-efficient food production solutions, such as aquaponics. To assess its upscaled fruition in city regions, we applied system analysis to depict determinants of aquaponics at a mesoscale. Using Berlin as a case study, site potentials regarding the production of freshwater fish, tomatoes, and lettuce to achieve self-sufficiency were investigated. We analysed planning documents by text mining and applied geographic information system procedures to evaluate this technology’s spatial efficacy in intra- and peri-urban spaces, considering aspects of economy, sustainability and spatial distribution. In a facility-based approach, we contrasted specific intra- and peri-urban site potentials with their different boundary conditions. A thereupon-based scenario allocates approximately 20% of the production volume in Berlin, 80% in its hinterland, and emphasises the crucial use of circular economy resources in both spaces. Policy recommendations and the transferability of this realistic approach will support the implementation of aquaponics.
Static Analysis: The Workhorse of a End-to-End Securitye Testing Strategy (2016)

Security testing is an important part of any security lifecycle (SDL) and, thus, should be a part of any software (development) lifecycle. Still, security testing is often understood as an activity done by security testers in the time between end of development and offering the product to customers.Learning from traditional testing that the fixing of bugs is the more costly the later it is done in development, security testing should be integrated, as early as possible, into the daily activities. The fact that static analysis can be deployed as soon as the first line of code is written, makes static analysis the right workhorse to start security testing activities.In this lecture, I will present a risk-based security testing strategy that is used at a large European software vendor. While this security testing strategy combines static and dynamic security testing techniques, I will focus on static analysis. This lecture provides a introduction to the foundations of static analysis as well as insights into the challenges and solutions of rolling out static analysis to more than 20000 developers, distributed across the whole world.
ChemInform Abstract: COMPLEXATION OF ENT‐8,13β‐EPOXYLABDANE‐12,14‐DIOLS WITH BORIC ACID. A METHOD FOR ESTABLISHING THE C(14) CONFIGURATION (1985)

Abstract Das natürlich vorkommende Diterpenoid Varodiol (Ia) wird als Ausgangsmaterial für die Herstellung aller anderen im Formelschema gezeigten Verbindungen (Ib)‐(IId) eingesetzt.
ChemInform Abstract: Stereoselective Synthesis of 3‐Amino 1,2‐Diols via Intermolecular Pinacol Cross‐Coupling of α‐((Alkoxycarbonyl)amino) Aldehydes with Aliphatic Aldehydes. Short Asymmetric Syntheses of Two 2,3,6‐ Trideoxy 3‐Amino Sugars. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
On the Simulation of Mitral Valve Function in Health, Disease, and Treatment (2019)

The mitral valve (MV) is the heart valve that regulates blood ?ow between the left atrium and left ventricle (LV). In situations where the MV fails to fully cover the left atrioventricular ori?ce during systole, the resulting regurgitation causes pulmonary congestion, leading to heart failure and/or stroke. The causes of MV insuf?ciency can be either primary (e.g. myxomatous degeneration) where the valvular tissue is organically diseased, or secondary (typically inducded by ischemic cardiomyopathy) termed ischemic mitral regurgitation (IMR), is brought on by adverse LV remodeling. IMR is present in up to 40% of patients and more than doubles the probability of cardiovascular morbidity after 3.5 years. There is now agreement that adjunctive procedures are required to treat IMR caused by lea?et tethering. However, there is no consensus regarding the best procedure. Multicenter registries and randomized trials would be necessary to prove which procedure is superior. Given the number of proposed procedures and the complexity and duration of such studies, it is highly unlikely that IMR procedure optimization will be achieved by prospective clinical trials. There is thus an urgent need for cell and tissue physiologically based quantitative assessments of MV function to better design surgical solutions and associated therapies. Novel computational approaches directed towards optimized surgical repair procedures can substantially reduce the need for such trial-and-error approaches. We present the details of our MV modeling techniques, with an emphasis on what is known and investigated at various length scales.
Intraspecies Genomic Groups in Enterococcus faecium and Their Correlation with Origin and Pathogenicity (2002)

Seventy-eight Enterococcus faecium strains from various sources were characterized by random amplified polymorphic DNA (RAPD)-PCR, amplified fragment length polymorphism (AFLP), and pulsed-field gel electrophoresis (PFGE) analysis of SmaI restriction patterns. Two main genomic groups (I and II) were obtained in both RAPD-PCR and AFLP analyses. DNA-DNA hybridization values between representative strains of both groups demonstrated a mean DNA-DNA reassociation level of 71%. PFGE analysis revealed high genetic strain diversity within the two genomic groups. Only group I contained strains originating from human clinical samples or strains that were vancomycin-resistant or beta-hemolytic. No differentiating phenotypic features between groups I and II were found using the rapid ID 32 STREP system. The two groups could be further subdivided into, respectively, four and three subclusters in both RAPD-PCR and AFLP analyses, and a high correlation was seen between the subclusters generated by these two methods. Subclusters of group I were to some extent correlated with origin, pathogenicity, and bacteriocinogeny of the strains. Host specificity of E. faecium strains was not confirmed.
Tailoring Exchange‐Dominated Synthetic Layered Antiferromagnets: From Collective Magnetic Reversal to Exchange Bias (2022)

Not only since the progressive reduction of structure sizes in modern micro- and nanotechnology, surface and interface effects have played an ever-increasing role and nowadays often dominate the behavior of entire systems. Therefore, understanding the nature of surface and interface effects and being able to fully control them is of fundamental importance, in particular in modern thin-film technology. In this study, it is revealed how Co/Pt multilayer-based synthetic antiferromagnets (SAFs) with perpendicular magnetic anisotropy in the regime of dominating antiferromagnetic interlayer exchange can be employed to control the collective magnetic reversal via systematically altering surface and interface effects. The specifically designed samples and experiments highlight the superior tunability of synthetic systems as compared to their intrinsic stoichiometric counterparts, where the antiferromagnetism is directly tied to the indivisible discrete atomic nature and crystal structure of the materials. Thus, it is demonstrated that in SAFs, it becomes possible to energetically heal the broken magnetic symmetry at the surface, thereby enabling either on demand suppression or controlled enhancement of respective surface and interface effects, as demonstrated here in this study for the surface spin-flop and the exchange bias effect.
Toward a terawatt-scale sub-10-fs laser technology (1998)

Powerful techniques for spectral broadening and ultrabroad-band dispersion control, which allow compression of high-energy femtosecond pulses to a duration of a few optical cycles, are analyzed. Spectral broadening in a gas-filled hollow fiber and compression by chirped mirrors with high-energy 20-fs input pulses are presented. Using 1-mJ seed pulses we have demonstrated the generation of 0.5-mJ 5-fs pulses at 0.8-/spl mu/m and 1-kHz repetition rate. General design criteria to scale the compression technique toward the terawatt level are presented.
Spectrum and Power Allocation for Vehicular Communications With Delayed CSI Feedback (2017)

Channel state information (CSI) at the base station (BS) is critical to resource allocation design for wireless networks, but it is hard to obtain accurate CSI in a high mobility vehicular environment. In this letter, we study the spectrum and power allocation problem in device-to-device-enabled vehicular networks, where CSI of vehicular links is only reported to the BS periodically. We maximize the sum throughput of all vehicle-to-infrastructure (V2I) links while guaranteeing the reliability of each vehicle-to-vehicle (V2V) link with the delayed CSI feedback. We propose a low-complexity algorithm to find the optimal spectrum sharing strategy among V2I and V2V links and properly adjust their transmit powers. Its desirable performance is confirmed by computer simulation.