gebhart/patrepeval huggingface dataset:
Discovery of SCH446211 (SCH6):  A New Ketoamide Inhibitor of the HCV NS3 Serine Protease and HCV Subgenomic RNA Replication (2006)

Introduction of various modified prolines at P(2) and optimization of the P(1) side chain led to the discovery of SCH6 (24, Table 2), a potent ketoamide inhibitor of the HCV NS3 serine protease. In addition to excellent enzyme potency (K(i)*= 3.8 nM), 24 was also found to be a potent inhibitor of HCV subgenomic RNA replication with IC(50) and IC(90) of 40 and 100 nM, respectively. Recently, antiviral activity of 24 was demonstrated with inhibition of the full-length genotype 2a HCV genome. In addition, 24 was found to restore the responsiveness of the interferon regulatory factor 3 (IRF-3) in cells containing HCV RNA replicons.
Magnetic resonance imaging and multi-detector computed tomography assessment of extracellular compartment in ischemic and non-ischemic myocardial pathologies (2014)

Myocardial pathologies are major causes of morbidity and mortality worldwide. Early detection of loss of cellular integrity and expansion in extracellular volume (ECV) in myocardium is critical to initiate effective treatment. The three compartments in healthy myocardium are: intravascular (approximately 10% of tissue volume), interstitium (approximately 15%) and intracellular (approximately 75%). Myocardial cells, fibroblasts and vascular endothelial/smooth muscle cells represent intracellular compartment and the main proteins in the interstitium are types I/III collagens. Microscopic studies have shown that expansion of ECV is an important feature of diffuse physiologic fibrosis (e.g., aging and obesity) and pathologic fibrosis [heart failure, aortic valve disease, hypertrophic cardiomyopathy, myocarditis, dilated cardiomyopathy, amyloidosis, congenital heart disease, aortic stenosis, restrictive cardiomyopathy (hypereosinophilic and idiopathic types), arrythmogenic right ventricular dysplasia and hypertension]. This review addresses recent advances in measuring of ECV in ischemic and non-ischemic myocardial pathologies. Magnetic resonance imaging (MRI) has the ability to characterize tissue proton relaxation times (T1, T2, and T2*). Proton relaxation times reflect the physical and chemical environments of water protons in myocardium. Delayed contrast enhanced-MRI (DE-MRI) and multi-detector computed tomography (DE-MDCT) demonstrated hyper-enhanced infarct, hypo-enhanced microvascular obstruction zone and moderately enhanced peri-infarct zone, but are limited for visualizing diffuse fibrosis and patchy microinfarct despite the increase in ECV. ECV can be measured on equilibrium contrast enhanced MRI/MDCT and MRI longitudinal relaxation time mapping. Equilibrium contrast enhanced MRI/MDCT and MRI T1 mapping is currently used, but at a lower scale, as an alternative to invasive sub-endomyocardial biopsies to eliminate the need for anesthesia, coronary catheterization and possibility of tissue sampling error. Similar to delayed contrast enhancement, equilibrium contrast enhanced MRI/MDCT and T1 mapping is completely noninvasive and may play a specialized role in diagnosis of subclinical and other myocardial pathologies. DE-MRI and when T1-mapping demonstrated sub-epicardium, sub-endocardial and patchy mid-myocardial enhancement in myocarditis, Behcet's disease and sarcoidosis, respectively. Furthermore, recent studies showed that the combined technique of cine, T2-weighted and DE-MRI technique has high diagnostic accuracy for detecting myocarditis. When the tomographic techniques are coupled with myocardial perfusion and left ventricular function they can provide valuable information on the progression of myocardial pathologies and effectiveness of new therapies.
The Arabidopsis leucine-rich repeat receptor kinase MIK2/LRR-KISS connects cell wall integrity sensing, root growth and response to abiotic and biotic stresses (2017)

Plants actively perceive and respond to perturbations in their cell walls which arise during growth, biotic and abiotic stresses. However, few components involved in plant cell wall integrity sensing have been described to date. Using a reverse-genetic approach, we identified the Arabidopsis thaliana leucine-rich repeat receptor kinase MIK2 as an important regulator of cell wall damage responses triggered upon cellulose biosynthesis inhibition. Indeed, loss-of-function mik2 alleles are strongly affected in immune marker gene expression, jasmonic acid production and lignin deposition. MIK2 has both overlapping and distinct functions with THE1, a malectin-like receptor kinase previously proposed as cell wall integrity sensor. In addition, mik2 mutant plants exhibit enhanced leftward root skewing when grown on vertical plates. Notably, natural variation in MIK2 (also named LRR-KISS) has been correlated recently to mild salt stress tolerance, which we could confirm using our insertional alleles. Strikingly, both the increased root skewing and salt stress sensitivity phenotypes observed in the mik2 mutant are dependent on THE1. Finally, we found that MIK2 is required for resistance to the fungal root pathogen Fusarium oxysporum. Together, our data identify MIK2 as a novel component in cell wall integrity sensing and suggest that MIK2 is a nexus linking cell wall integrity sensing to growth and environmental cues.
miRNAs in ancient tissue specimens of the Tyrolean Iceman (2016)

The analysis of nucleic acids in ancient samples is largely limited to DNA. Small noncoding RNAs (microRNAs) are known to be evolutionary conserved and stable. To gain knowledge on miRNAs measured from ancient samples, we profiled microRNAs in cryoconserved mummies. First, we established the approach on a World War One warrior, the "Kaiserjäger", which has been preserved for almost one century. Then, we profiled seven ancient tissue specimens including skeletal muscle, stomach mucosa, stomach content and two corpus organ tissues of the 5,300-year-old copper age mummy Iceman and compared these profiles to the presence of organ-specific miRNAs in modern tissues. Our analyses suggest the presence of specific miRNAs in the different Iceman's tissues. Of 1,066 analyzed human miRNAs, 31 were discovered across all biopsies and 87 miRNAs were detected only in a single sample. To check for potential microbiological contaminations, all miRNAs detected in Iceman samples and not present in ancient samples were mapped to 14,582 bacterial and viral genomes. We detected few hits (3.9% of miRNAs compared with 3.6% of miRNAs). Interestingly, the miRNAs with higher abundance across all ancient tissues were significantly enriched for Guanine (P value of 10-13) and Cytosine (P value of 10-7). The same pattern was observed for modern tissues. Comparing miRNAs measured from ancient organs to modern tissue patterns highlighted significant similarities, e.g., for miRNAs present in the muscle. Our first comprehensive analysis of microRNAs in ancient human tissues indicates that these stable molecules can be detected in tissue specimens after 5,300 years.
Adversarial Reprogramming of Neural Networks (2018)

Deep neural networks are susceptible to \emph{adversarial} attacks. In computer vision, well-crafted perturbations to images can cause neural networks to make mistakes such as confusing a cat with a computer. Previous adversarial attacks have been designed to degrade performance of models or cause machine learning models to produce specific outputs chosen ahead of time by the attacker. We introduce attacks that instead {\em reprogram} the target model to perform a task chosen by the attacker---without the attacker needing to specify or compute the desired output for each test-time input. This attack finds a single adversarial perturbation, that can be added to all test-time inputs to a machine learning model in order to cause the model to perform a task chosen by the adversary---even if the model was not trained to do this task. These perturbations can thus be considered a program for the new task. We demonstrate adversarial reprogramming on six ImageNet classification models, repurposing these models to perform a counting task, as well as classification tasks: classification of MNIST and CIFAR-10 examples presented as inputs to the ImageNet model.
Thermotropic Main-Chain Polyethers Based on Bis(4-hydroxyphenoxy)-p-xylene (1990)

Liquid crystalline main-chain polyethers based on bis(4-hydroxyphenoxy)-p-xylene, i.e. a non-rigid rodlike mesogen, and dibromoalkanes have been synthesized using a phase-transfer-catalyzed Williamson ether synthesis. The molecular weight of the polyethers follows a distinct odd-even dependence due to differences in solubility of the polymer during the polymerization. A difference in order between polymers having an odd or an even numbered spacer group was revealed by DSC and X-ray diffraction. The isotropic-smectic mesophase transition was studied at isothermal conditions, and it was shown that the transition which exhibits all the characteristics of a nucleation-controlled process, follows the Avrami equation with an exponent near 2.8. Dielectric relaxation measurements revealed a glass and a subglass process.
Incorporating Biology Into Breast Cancer Staging: American Joint Committee on Cancer, Eighth Edition, Revisions and Beyond (2018)

Higher-quality imaging, refined surgical procedures, enhanced pathologic evaluation, and improved understanding of the impact of tumor biology on treatment and prognosis have necessitated revisions of the AJCC breast cancer staging system. The eighth edition includes clinical and pathologic prognostic stages that incorporate biologic variables-grade, estrogen and progesterone receptor status, HER2 status, and multigene panels-with the anatomic extent of disease defined by tumor, node, and metastasis categories. The prognostic staging systems facilitate more refined stratification with respect to survival than anatomic stage alone. Because the prognostic staging systems are dependent on biologic factors, accuracy is dependent on rigorous pathologic evaluation of tumors and on administration of treatment dictated by tumor biology. It is anticipated that technological advances will facilitate even more refined determination of underlying biology within tumors and in the peripheral blood, which increasingly is being evaluated as a compartment that reflects the primary tumor and sites of distant metastases. Diseases should be staged according to the eighth edition staging system to accurately reflect prognosis and to allow standardized data collection. Such standardization will facilitate assessment of the impact of advances in diagnosis and treatment of patients with breast cancer.
Transient Calorimetric Measurement of Ferrite Core Losses (2020)

An accurate and fast transient calorimetric ferrite core-loss measurement method is proposed in this paper. In contrast to electrical measurements, the accuracy of the calorimetric approach is independent of the magnetic excitation and operating frequency. However, an accurate value of the thermal capacitance of the Core Under Test (CUT) is required, which can be achieved, e.g., by measuring the specific heat capacity of the measured core material using a Differential Scanning Calorimeter (DSC) or by using the CUT as a DC electric conductor and measuring its thermal response for known Joule heating. The proposed method is tested experimentally and compared successfully to a state-of-the-art electrical loss measurement method on MnZn ferrite cores.
New Communication Paradigms for Very Large-Scale Sensor Networks (2004)

In this poster, we will present work in progress on two novel approaches for efficient, scalable communication in truly large scale sensor networks. This work is a follow-up on our papers in IPSN 2004 [1], [2].
Modeling and Quantification of Acoustic Damping Induced by Vortex Shedding in Noncompact Thermoacoustic Systems (2019)

Abstract This paper presents a methodology to compute acoustic damping rates of transversal, high-frequency modes induced by vortex-shedding. The acoustic damping rate presents one key quantity for the assessment of the linear thermoacoustic stability of gas turbine combustors. State-of-the-art network models—as employed to calculate damping rates in low-frequency, longitudinal systems—cannot fulfill this task due to the acoustic noncompactness encountered in the high-frequency regime. Furthermore, it is yet unclear, whether direct eigensolutions of the linearized Euler equations (LEE), which capture the mechanism of vortex shedding, yield correct damping rate results constituted by the implicit presence of acoustic as well as hydrodynamic contributions in these solutions. The methodology's applicability to technically relevant systems is demonstrated by a validation test case using a lab-scale, swirl-stabilized combustion system.
Multicriteria decision-aid method and learning techniques to solve the surface treatment selection problem (2000)

info:eu-repo/semantics/published
On the synthesis and properties of ternary copper oxide sulfides (Cu2O1–xSx) (2013)

Abstract We report on the sputter deposition of copper oxide sulfides Cu 2 O 1– x S x up to a composition of Cu 2 O 0.61 S 0.39 . For higher sulfur contents the films first become amorphous and then change to Cu 2 S. Within the range 0 &lt; x &lt; 0.39 the cubic crystal structure is maintained and the lattice constant changes linearly with the sulfur content. The composition of the films is measured by energy dispersive X‐ray fluorescence and suggests the formation of a random alloy. The transmission spectra show a clear red shift of the order of 450 meV (from Cu 2 O to Cu 2 O 0.61 S 0.39 ) with an average transmission of 70%. (© 2013 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Quantum-error-correction benchmarks for continuous weak-parity measurements (2012)

We present an experimental procedure to determine the usefulness of a measurement scheme for quantum error correction (QEC). A QEC scheme typically requires the ability to prepare entangled states, carry out multiqubit measurements, and perform certain recovery operations conditioned on measurement outcomes. As a consequence, the experimental benchmark of a QEC scheme is a tall order because it requires the conjuncture of many elementary components. Our scheme opens the path to experimental benchmarks of individual components of QEC. Our numerical simulations show that certain parity measurements realized in circuit quantum electrodynamics are on the verge of being useful for QEC.
- Highly Filled Graphite–Polymer Composites: Synthesis, Processing, and Characterization (2012)

Tetravalent carbon has several ramications encompassing both good and bad effects on human life. As hydrocarbons, it is the primary source of fossil energy and thus constitutes the fabric of our daily life. It forms the backbone of various dietary nutritional elements such as carbohydrates, fat, and proteins. Lightweight plastic components used in automobiles, aircraft, and space craft and the bulk of rubber materials used in tires are derived from tetravalent carbon compounds primarily of hydrogen. Grocery bags and synthetic clothing materials are made of polymeric tetravalent carbon compounds to satiate the ever increasing demands of consumer industry. The oxides of carbon such as gaseous carbon monoxide and carbon dioxide are also tetravalent, but appear as the villain in almost all policy talks on sustainable environment. The environmental impacts of most chemical processes are now evaluated and measured in terms of carbon footprints.
A Brief History of Transparent Conducting Oxides for Photovolaics : Fluorine Doped SnO<sub>2</sub> Film Model Case (2007)

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Improving classifier fusion via Pool Adjacent Violators normalization (2016)

Classifier fusion is a well-studied problem in which decisions from multiple classifiers are combined at the score, rank, or decision level to obtain better results than a single classifier. Subsequently, various techniques for combining classifiers at each of these levels have been proposed in the literature. Many popular methods entail scaling and normalizing the scores obtained by each classifier to a common numerical range before combining the normalized scores using the sum rule or another classifier. In this research, we explore an alternative method to combine classifiers at the score level. The Pool Adjacent Violators (PAV) algorithm has traditionally been utilized to convert classifier match scores to confidence values that model posterior probabilities for test data. The PAV algorithm and other score normalization techniques have studied the same problem without being aware of each other. In this first ever study to combine the two, we propose the PAV algorithm for classifier fusion on publicly available NIST multi-modal biometrics score dataset. We observe that it provides several advantages over existing techniques and find that the interpretation learned by the PAV algorithm is more robust than the scaling learned by other popular normalization algorithms such as min-max. Moreover, the PAV algorithm enables the combined score to be interpreted as confidence and is able to further improve the results obtained by other approaches. We also observe that utilizing traditional normalization techniques first for individual classifiers and then normalizing the fused score using PAV offers a performance boost compared to only using the PAV algorithm.
Physical and microstructural effects of heat setting in polyester films (1999)

Abstract The effects of a controlled heat‐setting treatment on the properties and microstructure of biaxially stretched poly(ethylene terephthalate) (PET) and poly(ethylene‐2,6‐naphthalene dicarboxylate) (PEN) films are described. Substantial changes in crystalline fraction, crystallite size, glass transition temperature and significant enhancement in dimensional stability are observed for both film types upon increase in heat‐set temperature. A distinct melting peak in the vicinity of the heatset temperature, observed in differential scanning calorimetry thermograms for both materials, is shown to be an effective marker of the heat‐setting process underlying the dual nature of the morphology of the heat‐treated films. We also observe that the PET films undergo significant molecular realignment on heat setting, while the orientation of the PEN films is only weakly modified by the heat‐set conditions. A morphological transition is detected for both films at high heat‐set temperature (T HS *) near the onset of the primary melting range, marking a qualitative change in the physical response of the biaxially oriented films; Measurable drop in planar orientation and glass transition temperature, and a sharp rise in crystallite size are noted for films heat‐treated above T HS *. The morphological models of previous workers (Schultz et al. and Fischer and Fakirov), invoking the idea of fibrillar‐to‐lamellar transformation, are used to explain some of our observations.
The ice-nucleating ability of quartz immersed in water and its atmospheric importance compared to K-feldspar (2019)

Abstract. Mineral dust particles are thought to be an important type of ice-nucleating particle (INP) in the mixed-phase cloud regime around the globe. While K-rich feldspar (K-feldspar) has been identified as being a particularly important component of mineral dust for ice nucleation, it has been shown that quartz is also relatively ice-nucleation active. Given quartz typically makes up a substantial proportion of atmospheric desert dust, it could potentially be important for cloud glaciation. Here, we survey the ice-nucleating ability of 10 α-quartz samples (the most common quartz polymorph) when immersed in microlitre supercooled water droplets. Despite all samples being α-quartz, the temperature at which they induce freezing varies by around 12 ∘C for a constant active site density. We find that some quartz samples are very sensitive to ageing in both aqueous suspension and air, resulting in a loss of ice-nucleating activity, while other samples are insensitive to exposure to air and water over many months. For example, the ice-nucleation temperatures for one quartz sample shift down by ∼2 ∘C in 1 h and 12 ∘C after 16 months in water. The sensitivity to water and air is perhaps surprising, as quartz is thought of as a chemically resistant mineral, but this observation suggests that the active sites responsible for nucleation are less stable than the bulk of the mineral. We find that the quartz group of minerals is generally less active than K-feldspars by roughly 7 ∘C, although the most active quartz samples are of a similar activity to some K-feldspars with an active site density, ns(T), of 1 cm−2 at −9 ∘C. We also find that the freshly milled quartz samples are generally more active by roughly 5 ∘C than the plagioclase feldspar group of minerals and the albite end member has an intermediate activity. Using both the new and literature data, active site density parameterizations have been proposed for freshly milled quartz, K-feldspar, plagioclase and albite. Combining these parameterizations with the typical atmospheric abundance of each mineral supports previous work that suggests that K-feldspar is the most important ice-nucleating mineral in airborne mineral dust.
Functional analysis of the C-terminal boundary of the second nucleotide binding domain of the cystic fibrosis transmembrane conductance regulator and structural implications (2002)

The cystic fibrosis transmembrane conductance regulator (CFTR) contains two nucleotide-binding domains (NBDs) or ATP-binding cassettes (ABCs) that characterize a large family of membrane transporters. Although the three-dimensional structures of these domains from several ABC proteins have been determined, this is not the case for CFTR, and hence the domains are defined simply on the basis of sequence alignment. The functional C-terminal boundary of NBD1 of CFTR was located by analysis of chloride channel function [Chan, Csanady, Seto-Young, Nairn and Gadsby (2000) J. Gen. Physiol. 116, 163-180]. However, the boundary between the C-terminal end of NBD2 and sequences further downstream in the whole protein, that are important for its cellular localization and endocytotic turnover, has not been defined. We have now done this by assaying the influence of progressive C-terminal truncations on photolabelling of NBD2 by 8-azido-ATP, which reflects hydrolysis, as well as binding, at that domain, and on NBD2-dependent channel gating itself. The boundary defined in this way is between residues 1420 and 1424, which corresponds to the final beta-strand in aligned NBDs whose structures have been determined. Utilization of this information should facilitate the generation of monodisperse NBD2 polypeptides for structural analysis, which until now has not been possible. The established boundary includes within NBD2 a hydrophobic patch of four residues (1413-1416) previously shown to be essential for CFTR maturation and stability [Gentzsch and Riordan (2001) J. Biol. Chem. 276, 1291-1298]. This hydrophobic cluster is conserved in most ABC proteins, and on alignment with ones of known structure constitutes the penultimate beta-strand of the domain which is likely to participate in essential structure-stabilizing beta-sheet formation.