gebhart/patrepeval huggingface dataset:
Infections à Morbillivirus chez les ruminants : la peste bovine en voie d'éradication et la peste des petits ruminants en extension vers le nord (2009)

La peste bovine et la peste des petits ruminants sont des maladies contagieuses affectant les ruminants domestiques et sauvages et entraînant des taux de mortalités souvent élevés. Elles sont provoquées par deux virus différents mais très apparentés antigéniquement et appartenant au genre Morbillivirus, famille des Paramyxoviridae. Les outils de contrôle effectif de ces deux maladies (vaccins et tests de diagnostic spécifiques) sont disponibles. Ils ont été mis à profit lors du programme mondial d'éradication de la peste bovine, (GREP pour Global Rinderpest Eradication Programme). Grâce à ce programme, il sera certainement possible de déclarer l'éradication de la peste bovine à l'échelle du globe en 2010. Malheureusement une telle campagne mondiale n'existe pas pour la peste des petits ruminants qui est en pleine expansion. Avec l'infection de la Turquie et du Maroc, elle se trouve maintenant aux portes de l'Europe. Pour une lutte plus efficace contre cette maladie, supportable sur le plan économique, la mise au point d'un vaccin marqueur ou DIVA (differentiation of infected and vaccinated animals) et d'un test sérologique discriminant serait un atout supplémentaire. Les outils de génétique inverse permettent désormais d'envisager cette possibilité.
Multiple source multiple destination topology inference using network coding (2009)

In this paper, we combine network coding and tomographic techniques for topology inference. Our goal is to infer the topology of a network by sending probes between a given set of multiple sources and multiple receivers and by having intermediate nodes perform network coding operations. We combine and extend two ideas that have been developed independently. On one hand, network coding introduces topology-dependent correlation, which can then be exploited at the receivers to infer the topology. On the other hand, it has been shown that a traditional (i.e., without network coding) multiple source, multiple receiver tomography problem can be decomposed into multiple two source, two receiver subproblems. Our first contribution is to show that, when intermediate nodes perform network coding, topological information contained in network coded packets allows to accurately distinguish among all different 2-by-2 subnetwork components, which was not possible with traditional tomographic techniques. Our second contribution is to use this knowledge to merge the subnetworks and accurately reconstruct the general topology. Our approach is applicable to any general Internet-like topology, and is robust to the presence of delay variability and packet loss.
Defective muscle ketone body oxidation disrupts BCAA catabolism by altering mitochondrial branched-chain aminotransferase (2023)

Ketone bodies are an endogenous fuel source generated primarily by the liver to provide alternative energy for extrahepatic tissues during prolonged fasting and exercise. Skeletal muscle is an important site of ketone body oxidation that occurs through a series of reactions requiring the enzyme succinyl-CoA:3-ketoacid-CoA transferase (SCOT/<i>Oxct1</i>). We have previously shown that deleting SCOT in the skeletal muscle protects against obesity-induced insulin resistance by increasing pyruvate dehydrogenase (PDH) activity, the rate-limiting enzyme of glucose oxidation. However, it remains unclear whether inhibiting muscle ketone body oxidation causes hypoglycemia and affects fuel metabolism in the absence of obesity. Here, we show that lean mice lacking skeletal muscle SCOT (SCOT<sup>SkM-/-</sup>) exhibited no overt phenotypic differences in glucose and fat metabolism from their human α-skeletal actin-Cre (HSA<i><sup>Cre</sup></i>) littermates. Of interest, we found that plasma and muscle branched-chain amino acid (BCAA) levels are elevated in SCOT<sup>SkM-/-</sup> lean mice compared with their HSA<i><sup>Cre</sup></i> littermates. Interestingly, this alteration in BCAA catabolism was only seen in SCOT<sup>SkM-/-</sup> mice under low-fat feeding and associated with decreased expression of mitochondrial branched-chain aminotransferases (BCATm/<i>Bcat2</i>), the first enzyme in BCAA catabolic pathway. Loss- and gain-of-function studies in C2C12 myotubes demonstrated that suppressing SCOT markedly diminished BCATm expression, whereas overexpressing SCOT resulted in an opposite effect without influencing BCAA oxidation enzymes. Furthermore, SCOT overexpression in C2C12 myotubes significantly increased luciferase activity driven by a <i>Bcat2</i> promoter construct. Together, our findings indicate that SCOT regulates the expression of the <i>Bcat2</i> gene, which, through the abundance of its product BCATm, may influence circulating BCAA concentrations.<b>NEW & NOTEWORTHY</b> Most studies investigated ketone body metabolism under pathological conditions, whereas the role of ketone body metabolism in regulating normal physiology has been relatively understudied. To address this gap, we used lean mice lacking muscle ketone body oxidation enzyme SCOT. Our work demonstrates that deleting muscle SCOT has no impact on glucose and fat metabolism in lean mice, but it disrupts muscle BCAA catabolism and causes an accumulation of BCAAs by altering BCATm.
Direct Observations of Rapid Diffusion of Cu in Au Thin Films using In-Situ X-ray Diffraction (2005)

In-situ x-ray diffraction was performed while annealing thin-film Au/Cu binary diffusion couples to directly observe diffusion at elevated temperatures. The temperature dependence of the interdiffusion coefficient was determined from isothermal measurements at 700 C, 800 C, and 900 C, where Cu and Au form a disordered continuous face centered cubic solid solution. Large differences in the lattice parameters of Au and Cu allowed the initial diffraction peaks to be easily identified, and later tracked as they merged into one diffraction peak with increased diffusion time. Initial diffusion kinetics were studied by measuring the time required for the Cu to diffuse through the Au thin film of known thickness. The activation energy for interdiffusion was measured to be 65.4 kJ/mole during this initial stage, which is approximately 0.4x that for bulk diffusion and 0.8x that for grain boundary diffusion. The low activation energy is attributed to the high density of columnar grain boundaries combined with other defects in the sputter deposited thin film coatings. As interdiffusion continues, the two layers homogenize with an activation energy of 111 kJ/mole during the latter stages of diffusion. This higher activation energy falls between the reported values for grain boundary and bulk diffusion, and may be related to grain growth occurring at these temperatures which accounts for the decreasing importance of grain boundaries on diffusion.
BLOOD GLUCOSE AND PLASMA GLYCEROL RESPONSE TO EPINEPHRINE INFUSION IN NORMAL AND PREDIABETIC SUBJECTS (1971)

Abstract. The effect of epinephrine infusion (at a rate of 0.08 to 0.11 μg/kg/min) on blood glucose and plasma glycerol has been investigated in six normal subjects and nine individuals with normal glucose tolerance but decreased and delayed insulin response to glucose (prediabetic subjects). Responsiveness to epinephrine, as measured by the magnitude of elevation in blood glucose and plasma glycerol, was of similar degree in both groups of subjects. It is concluded that the ability to mobilize glycogen and lipid is not altered in prediabetes. The mechanisms responsible for maintaining a normal glucose tolerance in the presence of decreased insulin secretion in prediabetic subjects thus do not seem to involve a diminished ability to generate cyclic AMP in the liver and fat cells.
Preparation of Triethylammonium Tetra-Arylborates (TEATABs): Coupling Partners for the Suzuki Reaction (2011)

Abstract Six triethylammonium tetra-arylborates (TEATABs) were synthesized via a convenient reproducible procedure and characterized by spectroscopic methods (1H, 13C, 11B NMR and electrospray ionization–high-resolution mass spectrometry). The compounds could be stored at ambient temperature and were useful as reactants in the Suzuki reaction in aqueous conditions when using commercially available catalysts.
PTK787/ZK 222584 enhances efficacy of cytostatics in human xenografts and does not interfere with their uptake in tumor tissue. (2004)

Proc Amer Assoc Cancer Res, Volume 45, 2004

2373 

The inhibition of neo-angiogenesis is a new treatment paradigm in cancer therapy intended to stop the disease progress and to shift the disease from an acute to a chronic state. Favourable in vitro and animal experiments with PTK787/ZK222584 (PTK/ZK), an angiogenesis inhibitor blocking the known VEGF receptor kinases, were translated in phase I and I/II studies and revealed encouraging efficacy associated with a favourable side effect profile in patients after once daily oral treatment. Two double blind, controlled phase III studies in first and second line colon cancer therapy have started recently (CONFIRM 1 and CONFIRM 2). The efficacy and low side effect profile of the compound is explained by its high selectivity for VEGFR 1, 2 and 3, c-fms, c-kit, and PDGFR. VEGF receptors were inhibited in cellular assays with IC50s between 20-50 nM; c-fms, c-kit and PDGFR kinases are inhibited 10 fold weaker. Other kinases were not inhibited up to 100-fold concentrations. VEGF receptor kinase inhibition blocks endothelial cell proliferation and migration without affecting tumor cells directly. PDGFR inhibition destabilizes the interaction of endothelium with the pericytes and the smooth muscle cells. The anti angiogenic effects of PTK/ZK resulted in efficacious inhibition of tumor growth in various models, without impairing animal weights. Since combination therapy is predominant for the majority of cancer indications, we performed a number of experiments combining a cytostatic agent and PTK/ZK for therapy. In the hormone-dependent prostate tumor model CWR22 we used a combination with an anti androgen (CPA) and measured the prostate specific antigen (PSA) as a biomarker. The drug combination inhibited tumor growth similarly well as orchiectomy and led to a simultaneous decrease of the PSA levels. PTK/ZK combined with taxol in the lung tumor model A 549 neither influenced toxicity nor weight gain compared to taxol treatment alone, whereas the efficacy in tumor growth inhibition was additive. Similar results were obtained with models for mammary and colon carcinomas as well as melanoma (MATU, HT29 and B16F10). To analyze the role of permeability reduction (VEGF= V ascular P ermeability F actor) by PTK/ZK in more detail, we investigated the consequences of a pretreatment with PTK/ZK followed by an application of cytostatic agents: We found no change of the uptake of the cytostatics in tumors after pretreatment with PTK/ZK using two independent analytical methods.In conclusion, combinations of PTK/ZK with cytostatics and antihormones were superior to a single agent treatment. There was no change in tolerability. Thus, PTK/ZK is well tolerated and may represent an additional treatment option for solid tumors either as single agent or in combination therapy. * PTK787/ZK 222584 is being co-developed by Schering AG, Germany and Novartis, Switzerland
Molecular Dynamics Simulations of Platinum Plasma Sputtering: A Comparative Case Study (2016)

Molecular Dynamics simulations are carried out for investigating atomic processes of platinum sputtering. Sputtered Pt atom energy distribution functions (EDF) are determined at different sputtering argon ionenergies: 100, 500, and 1000 eV. Calculated EDF show a cross-over from Thompson theory to binary collision model when increasing argon ion energy and Pt atom sputtered energy. Implanted argon ion number is depending on its kinetic energy, while it is not the case in binary collision approximation. Finally sputtering yields are greater for Thompson theory than for binary collision model at low energy, but converge to the close values at high energy.
Figure S6 from Inhibiting ERK5 Overcomes Breast Cancer Resistance to Anti-HER2 Therapy By Targeting the G<sub>1</sub>–S Cell-Cycle Transition (2023)

&lt;p&gt;The effect of lapatinib and JWG-045 as single treatments was compared to that achieved in combination therapy on the cell cycle profile of sensitive and resistant breast cancer cell lines.&lt;/p&gt;
Portable Pesticide Electrochem-sensor: A Label-Free Detection of Glyphosate in Human Urine (2022)

The toxicity levels of and exposure to glyphosate, a widely used herbicide and desiccant, are significant public health issues. In this study, we aim to design a highly sensitive, label-free, portable sensor for the direct detection of glyphosate in human urine. The sensor platform consists of a portable, printed circuit board circular platform with gold working and reference electrodes to enable nonfaradic electrochemical impedance spectroscopy. The sensing platform was an immunoassay-based, gold electrode surface immobilized with a monolayer of dithiobis(succinimidyl propionate) (DSP), a thiol-based cross-linker, which was then modified with a glyphosate antibody (Glyp-Ab) through the bonding of the ester group of DSP with the amide of the antibody (Glyp-Ab). The sensor was tested electrochemically, first using the laboratory-based benchtop method for the glyphosate-spiked urine samples, resulting in a dynamic response in the concentration range of 0.1-72 ng/mL with a limit of detection of 0.1 ng/mL. The platform showed high selectivity in the presence of major interfering analytes in urine [malathion (Mal), 3-phenoxybenzoic acid (PBA), and chlorpyrifos (Chlp)] and high reproducibility. The sensing platform was then translated into a portable device that showed a performance correlation (<i>r</i> = 0.994) with the benchtop (laboratory method). This developed portable sensing approach can be a highly reliable alternate sensor platform for the direct detection of pesticides in human bodily fluids.
Stabilization of Metastable W2C Nanoparticles by Carbon and Formation of WC Core-W Shell Nanoparticles by Thermal Treatment of a W/C Monolith (2016)

Investigations of low-temperature-transformation pathways that exist during tungsten carbide formation revealed the novel formation of ‘inverted’ core-shell nanoparticles comprising a tungsten carbide (WC) core and a tungsten shell assisted by an ‘asymmetric heating’ of a compacted tungsten/carbon monolith. X-ray Diffraction (XRD) characterization of the product revealed that tungsten was present in both elemental and carbide forms. The core-shell morphology of the tungsten carbide particles was deciphered from High Resolution Transmission Electron Microscopy (HRTEM) measurements and results from the thermal decomposition of the initially formed metastable W2C nanoparticles. Simultaneously, a portion of the initially formed metastable W2C nanoparticles in the vicinity of excess carbon became stabilized producing carbonensheathed W2C nanoparticles. These findings open new avenues to access unique core-shell morphologies of refractory carbides and for the ambient stabilization of metastable nanoparticles by means of asymmetric heating of monoliths of selected binary or higher compositions. Furthermore, the obtained core-shell nanoparticles provide a platform to produce other experimentally challenging structures. Keywords: Asymmetric, benzene, carbon, core, core-shell, decomposition, disproportionation, heating, HRTEM, shell, solid-state, thermal, tungsten carbide, tungsten, W2C, WC, XRD.
Absence of BBSome function leads to astrocyte reactivity in the brain (2019)

In humans, dysfunctional primary cilia result in Bardet-Biedl syndrome (BBS), which presents with clinical features including intellectual disabilities, obesity, and retinal degeneration, and, in mouse models, the added feature of hydrocephalus. We observed increased Glial Fibrillary Acidic Protein (GFAP) immunoreactivity in BBS mouse brains. Increased GFAP expression is a hallmark of astrocyte reactivity that is associated with microglia activation and neuro-inflammation. To gain a better understanding of reactive astrocytes observed in BBS mice, we used two mouse models of BBS8, a BBSome protein, to characterize the reactive astrocyte phenotype. The finding of reactive astrocytes in young BBS mouse brains led us to hypothesize that loss of BBSome function leads to reactive astrocytes prior to hydrocephalus and obesity. By using two mouse models of BBS8, a congenital BBS8 knockout with hydrocephalus, and a tamoxifen-inducible BBS8 knockout without hydrocephalus, we were able to molecularly phenotype the reactive astrocytes. Molecular phenotype of reactive astrocytes shows differential regulation of inducers of Pan, A1 neurotoxic, and A2 neuroprotective astrocytes that are significantly altered in brains of both congenital and induced knockouts of BBS8, but without microglia activation. We find evidence for neuroinflammation in the brains of congenital knockout mice, but not in induced knockout mice. Protein levels of GFAP, SERPINA3N and post-synaptic density 95 (PSD95) are significantly increased in congenital knockout mice, but remain unchanged in induced knockout mice. Thus, despite the reactive astrocyte phenotype being present in both models, the molecular signature of reactive astrocytes in BBS8 mice models are distinct. Together, these findings suggest that BBS8, and by extension the BBSome, plays a role in neuro-astrocyte functions independent of hydrocephalus, and its dysregulation is associated with astrocyte reactivity without microglia activation. (Total word count 278).
Targeted mutagenesis in wheat microspores using CRISPR/Cas9 (2018)

CRISPR/Cas9 genome editing is a transformative technology that will facilitate the development of crops to meet future demands. However, application of gene editing is hindered by the long life cycle of many crop species and because desired genotypes generally require multiple generations to achieve. Single-celled microspores are haploid cells that can develop into double haploid plants and have been widely used as a breeding tool to generate homozygous plants within a generation. In this study, we combined the CRISPR/Cas9 system with microspore technology and developed an optimized haploid mutagenesis system to induce genetic modifications in the wheat genome. We investigated a number of factors that may affect the delivery of CRISPR/Cas9 reagents into microspores and found that electroporation of a minimum of 75,000 cells using 10-20 µg DNA and a pulsing voltage of 500 V is optimal for microspore transfection using the Neon transfection system. Using multiple Cas9 and sgRNA constructs, we present evidence for the seamless introduction of targeted modifications in an exogenous DsRed gene and two endogenous wheat genes, including TaLox2 and TaUbiL1. This study demonstrates the value and feasibility of combining microspore technology and CRISPR/Cas9-based gene editing for trait discovery and improvement in plants.
A platform for eXtreme Analytics (2013)

With the rapid increase in the volume of data that enterprises are producing, enterprises are adopting large-scale data processing platforms such as Hadoop® to store, manage, and run deep analytics to gain actionable insights from their “big data.” At IBM Research - Almaden, we have been helping enterprise customers build solutions exploiting data-intensive analytics. Our deep experience with actual users has led to an extensive understanding of the platform requirements needed to support these solutions, and our goal is to provide a powerful analytics platform, which we call eXtreme Analytics Platform (XAP), that can be used to create solutions for customer problems that have not been economically feasible to solve until now. XAP provides Jaql [i.e., JavaScript® Object Notation (JSON) query language, a scripting language to specify data flows, tools, and techniques to optimize the runtime execution of these flows], an improved task scheduler, connectors to data warehouses, and libraries for advanced analytics. Many of these technologies have been transferred to the IBM InfoSphere BigInsights™ product. In this paper, we describe the overall design principles and technology of XAP.
A bottom-up energy simulation framework to accurately compare PV module topologies under non-uniform and dynamic operating conditions (2017)

Non-uniform operating conditions of photovoltaic modules have a huge impact on the energy generation of PV installations. To increase the energy yield of PV modules under non-uniform conditions, innovative module topologies have been proposed. However, a complete exploration of these topologies cannot be performed on the field, given the huge cost/time investment required for the realization of all potential topologies, as well as the large time required for comprehensively testing them in a real installation. Thus, it is more efficient and effective to compare them through simulations. An accurate and versatile simulation approach is proposed here which allows exploration of different PV module topologies under realistic timeand spatiallyvarying shading scenarios. The latter are created by matching measured weather data with simulated non-uniform and dynamic operating scenarios created by using the software SketchUp. The use of a physics-based bottom-up modeling approach for the different PV module topologies allows for accurate evaluation of the energy generated by each topology in the given operating conditions. Simulation results are presented that substantiate the feasibility of the methodology. Four relevant PV module topologies are compared, showing the better performance of reconfigurable topologies when uniform operating conditions are not dominant.
RH5.1-CyRPA-Ripr antigen combination vaccine shows little improvement over RH5.1 in a preclinical setting (2022)

An RCR combination vaccine may not induce substantially improved protective immunity as compared with RH5 as a single immunogen in a clinical setting and leaves the development pathway open for other antigens to be combined with RH5 as a next generation malaria vaccine.
Recurrent major depression and right hippocampal volume: A bivariate linkage and association study (2015)

Previous work has shown that the hippocampus is smaller in the brains of individuals suffering from major depressive disorder (MDD) than those of healthy controls. Moreover, right hippocampal volume specifically has been found to predict the probability of subsequent depressive episodes. This study explored the utility of right hippocampal volume as an endophenotype of recurrent MDD (rMDD). We observed a significant genetic correlation between the two traits in a large sample of Mexican American individuals from extended pedigrees (ρg = -0.34, p = 0.013). A bivariate linkage scan revealed a significant pleiotropic quantitative trait locus on chromosome 18p11.31-32 (LOD = 3.61). Bivariate association analysis conducted under the linkage peak revealed a variant (rs574972) within an intron of the gene SMCHD1 meeting the corrected significance level (χ(2) = 19.0, p = 7.4 × 10(-5)). Univariate association analyses of each phenotype separately revealed that the same variant was significant for right hippocampal volume alone, and also revealed a suggestively significant variant (rs12455524) within the gene DLGAP1 for rMDD alone. The results implicate right-hemisphere hippocampal volume as a possible endophenotype of rMDD, and in so doing highlight a potential gene of interest for rMDD risk.
Mashup service conflict detection and visualization method for Internet of Things (2017)

Many Internet of Things applications provide methods to create mashup services with if-then-else approaches due to its simplicity. When a number of mashup services are increased, it may be suffered by service conflict, that is, mashup services may perform opposite actions or abnormal behavior at the same time. To overcome this issue, this paper proposes the concept of context descriptor to detect service conflict and visualize their situations.