gebhart/patrepeval huggingface dataset:
Benign and Intermediate-grade Melanocytic Tumors With BRAF Mutations and Spitzoid Morphology (2021)

The current classification of Spitz neoplasms in the World Health Organization (WHO), Fourth Edition defines Spitz neoplasms as melanocytic proliferations with characteristic Spitz morphology and a Spitz-associated genomic fusion or HRAS mutation. In contrast, melanocytic neoplasms with BRAF mutations are considered typical of common acquired nevi, dysplastic nevi, and melanomas from intermittent sun-damaged skin. However, increased utilization of ancillary testing methods such as BRAF V600E immunohistochemistry and sequencing studies have made apparent a subgroup of benign-grade and intermediate-grade melanocytic neoplasms with Spitzoid morphology that harbor BRAF V600E mutations. We refer to these cases as BRAF mutated and morphologically Spitzoid (BAMS) nevi and tumors. Two experienced dermatopathologists reviewed a series of 36 BAMS nevi/tumors. Cases in which a diagnosis of melanoma was favored were excluded. The histomorphologic, clinical, and molecular findings were assessed by immunohistochemistry, fluorescence in situ hybridization, and next-generation sequencing using validated gene panels. Characteristics of BAMS nevi/tumors were compared with a control set of Spitz tumors with previously reported fusion proteins. BAMS nevi/tumors had a decreased proportion of Kamino bodies ( P =0.03) and a higher proportion of cytoplasmic pigmentation ( P &lt;0.00001). There were no differences in other morphologic features such as the silhouette, epidermal hyperplasia, pagetosis, and cytologic atypia compared with fusion-induced Spitz tumors. In 6/17 cases where next-generation sequencing studies were available, recurrent mutations in the KMT gene family were seen. This was higher than the proportion of such mutations seen in fusion Spitz tumors and lower than the frequency in cutaneous melanoma.
OpinioNetIt (2011)

The wikileaks documents or the economic crises in Ireland and Portugal are some of the controversial topics being played on the news everyday. Each of these topics has many different aspects, and there is no absolute, simple truth in answering questions such as: should the EU guarantee the financial stability of each member country, or should the countries themselves be solely responsible? To understand the landscape of opinions, it would be helpful to know which politician or other stakeholder takes which position - support or opposition - on these aspects of controversial topics. In this paper, we describe our system, named OpinioNetIt (pronounced similar to "opinionated"), which aims to automatically derive a map of the opinions-people network from news and other Web documents.
<title>Dual-detector polarimetry for compensation of motion artifact in a glucose sensing system</title> (2002)

Much work has been done to make the optical measurement of glucose concentrations in the aqueous humor a feasible, non- invasive, alternative for the blood finger stick, method currently used by people with diabetes mellitus. Recent work has demonstrated that the time lag between blood and aqueous humor glucose levels is within five minutes but there is still work to be done in overcoming the confounding effects of changing birefringence, due to motion artifact, on the detected glucose signal during in-vivo measurements. To address this issue, we designed and implemented a dual orthogonal polarization detection system. We present promising preliminary results that indicate that this method, with some slight modifications and optimization of our system, has the potential to extract glucose concentration information from a birefringent sample in the presence of motion artifact.
Identification and Functional Characterization of Sphingomonas macrogolitabida Strain TFA Genes Involved in the First Two Steps of the Tetralin Catabolic Pathway (2003)

Five genes involved in the two initial steps of the tetralin biodegradation pathway of Sphingomonas macrogolitabida strain TFA have been characterized. ThnA1A2 and ThnA3A4, components of the ring-hydroxylating dioxygenase, were encoded in divergently transcribed operons. ThnA1, ThnA2, and ThnA3 were essential for tetralin ring-hydroxylating dioxygenase activity. ThnB was identified as a dehydrogenase required for tetralin biodegradation.
Few‐Volt Operation of Printed Organic Ferroelectric Capacitor (2015)

The fabrication of single-crystalline thin-film arrays for an organic ferroelectric small molecule is achieved by a simple solution process without additional thermal annealing. Based on a cooperative proton tautomerism through a hydrogen-bonding network, films show the polarity switching with an operating voltage of less than 5 V at room temperature. This approach provides a low-cost and eco-friendly fabrication of ferroelectric devices.
Caractérisation moléculaire des mécanismes de résistance aux macrolides chez Campylobacter (2006)

Diplôme : Dr. d'Université
Surface swarming motility by Pectobacterium atrosepticum is a latent phenotype that requires O antigen and is regulated by quorum sensing (2013)

We describe a previously cryptic phenotype associated with the opportunistic phytopathogen Pectobacterium atrosepticum (Pca): surface swarming. We found that when Pca was spotted onto plates containing <0.5% (w/v) agar, the culture produced copious amounts of extracellular matrix material containing highly motile cells. Once produced, this 'slime layer' spread rapidly across the plate either as an advancing front or as tendrils. Transposon mutagenesis was used to identify mutants that were affected in swarming. Hypo-swarmer mutants mostly carried insertions in a horizontally acquired island (HAI5), which encodes a cluster of genes involved in O antigen biosynthesis. Hyper-swarmer mutants mostly carried insertions in hexY, a known antagonist of the class I flagellar master regulator, FlhD4C2. In addition, we found that the nucleoid protein, histone-like nuclear structuring protein 2 (H-NS2), also regulated swarming behaviour. A mutant in which hns2 was overexpressed displayed a hyper-swarming phenotype, whereas a mutant in which the hns2 ORF was inactivated had a hypo-swarming phenotype. Swarming was also regulated by quorum sensing (QS) and by the carbon source being utilized. We show, using a range of epistasis experiments, that optimal swarming requires both motility and O antigen biosynthesis, and that H-NS2 and QS both promote swarming through their effects on motility.
Tetrathiafulvalene-containing polymers for simultaneous non-covalent modification and electronic modulation of MoS2 nanomaterials (2016)

Transition metal dichalcogenides (TMDCs) such as MoS<sub>2</sub> comprise an important class of 2D semiconductors with numerous interesting electronic and mechanical features. Full utilization of TMDCs in materials and devices, however, necessitates robust functionalization methods. We report well-defined tetrathiafulvalene (TTF)-based polymers, exploiting synthetic routes that overcome challenges previously associated with these systems. These platforms enable basal plane coordinative interactions with MoS<sub>2</sub>, conceptually in parallel with pyrene-containing platforms for graphene and carbon nanotube modification. Not yet reported for TMDCs, these non-covalent interactions are universal and effective for MoS<sub>2</sub> irrespective of the lattice structure, affording significantly enhanced solution stabilization of the nanosheets. Additionally, the TTF-functionalized polymers offer electronic structure modulation of MoS<sub>2</sub> by ground state charge transfer and work function reduction, demonstrated using Kelvin probe force microscopy (KPFM). Notably, coordination and electronic effects are amplified for the TTF-polymers over TTF itself. Experiments are supported by first-principles density functional theory (DFT) calculations that probe polymer-TTF surface interactions with MoS<sub>2</sub> and the resultant impact on electronic properties.
Pelea sucia tras la quiebra: el Derrumbre de Solyndra propaga sus efectos (2011)

La empresa estadounidense de energia solar fotovoltaica Solyndra, receptora de importantes subvenciones concedidas desde Washington, ha quebrado. Pero todo el sector se vera afectado, pues de momento ya se ha suspendido uno de los programas de fomento. Ademas, las subvenciones a la energia solar se estan convirtiendo en un tema controvertido para las proximas elecciones presidenciales en EEUU.
Scintillator light yield nonproportionality: calculating photon response using measured electron response (1997)

To study the effects of scintillator light yield nonproportionality, a technique has been developed to calculate photon response. A discrete convolution of measured electron response and the electron energy distribution for a particular scintillator yields the photon response. By establishing the ability to accurately calculate photon response, the experimental implications of scintillator light yield nonproportionality and geometry effects can be studied without the requirement for experimental measurements. This technique also provides a more detailed characterization of photon response than experimental techniques that rely on the use of multiple gamma-ray and X-ray sources. To demonstrate this technique, NaI(Tl), CaF/sub 2/(Eu), and LSO(Ce) photon responses have been calculated. By comparing calculated results to both measured photon responses and previously published photon responses for these scintillators, this technique has been validated.
Interactome of the Autoimmune Risk Protein ANKRD55 (2019)

The ankyrin repeat domain-55 (<i>ANKRD55</i>) gene contains intronic single nucleotide polymorphisms (SNPs) associated with risk to contract multiple sclerosis, rheumatoid arthritis or other autoimmune disorders. Risk alleles of these SNPs are associated with higher levels of ANKRD55 in CD4<sup>+</sup> T cells. The biological function of ANKRD55 is unknown, but given that ankyrin repeat domains constitute one of the most common protein-protein interaction platforms in nature, it is likely to function in complex with other proteins. Thus, identification of its protein interactomes may provide clues. We identified ANKRD55 interactomes via recombinant overexpression in HEK293 or HeLa cells and mass spectrometry. One hundred forty-eight specifically interacting proteins were found in total protein extracts and 22 in extracts of sucrose gradient-purified nuclei. Bioinformatic analysis suggested that the ANKRD55-protein partners from total protein extracts were related to nucleotide and ATP binding, enriched in nuclear transport terms and associated with cell cycle and RNA, lipid and amino acid metabolism. The enrichment analysis of the ANKRD55-protein partners from nuclear extracts is related to sumoylation, RNA binding, processes associated with cell cycle, RNA transport, nucleotide and ATP binding. The interaction between overexpressed ANKRD55 isoform 001 and endogenous RPS3, the cohesins SMC1A and SMC3, CLTC, PRKDC, VIM, β-tubulin isoforms, and 14-3-3 isoforms were validated by western blot, reverse immunoprecipitaton and/or confocal microscopy. We also identified three phosphorylation sites in ANKRD55, with S436 exhibiting the highest score as likely 14-3-3 binding phosphosite. Our study suggests that ANKRD55 may exert function(s) in the formation or architecture of multiple protein complexes, and is regulated by (de)phosphorylation reactions. Based on interactome and subcellular localization analysis, ANKRD55 is likely transported into the nucleus by the classical nuclear import pathway and is involved in mitosis, probably via effects associated with mitotic spindle dynamics.
Bioinspired THz applications for chemical analysis and microorganism fingerprinting (2014)

This report presents THz spectroscopy as a valuable tool to discover unique signatures in a variety of analytes. Biomolecules and bacterial spores have been demonstrated to have characteristic signatures in the absorption patterns. Examples presented are the absorption band of thymine and the double bands of Bacillus sp. spores. In the case of thymine, the absorption band exactly matched the results of molecular modeling at 1.27 THz. The signatures are associated with collective polar vibrations within the structures of the materials, and can be used for fingerprint type sensing.
Type‐I and Type‐II Nanoscale Heterostructures Based on CdTe Nanocrystals: A Comparative Study (2008)

The synthesis and optical properties of core/shell and core/shell/shell nanocrystals based on CdTe nanocrystals are described. The influence of the different charge-carrier separation in the CdTe/CdS nanocrystals (type-I heterostructure) and the CdTe/CdSe nanocrystals (type-II heterostructure) is examined. The behavior of CdTe/CdS/CdSe nanocrystals (see image) in comparison to two core/shell systems is also studied. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2296/2008/smll200800287_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Structural and spectroscopic studies of transition metal nitrite complexes. VII. Crystal structures and spectra of two dinuclear and trinuclear species with stoichiometry [Ni(methylpyridine)2(NO2)2] containing bridging nitrite groups (1981)

The crystal structures of the dimer [Ni(?mpy)2(NO2)2]2,2C6H6 and the trimer [Ni( ß mpy)2(NO2)2]3,- C6Hs (?mpy = 4-methylpyridine, ßmpy = 3-methylpyridine) are reported, the latter being the redetermination of a structure described previously. The ligand coordination geometry in each oligomer is essentially octahedral, with neighbouring nickel(II) ions being bridged by two nitrite groups, one through a single oxygen atom and the second through an oxygen and the nitrogen atom. The amine ligands occupy trans coordination sites with the terminal bond positions in both species being taken up by chelating nitrite ions. In both compounds the oligomers pack so that the amine rings form sheets with potential voids in the lattice being filled by clathrated benzene molecules. The electronic spectra of the complexes in the visible region are unusual, showing peaks centred at c. 17500 and c. 20500 cm-1, and the assignment of these is discussed. The infrared stretching frequencies of the nitrite groups in these and other compounds are found to correlate well with the observed nitrogen-oxygen bond lengths.
Perspective from the heart: The potential of human pluripotent stem cell‐derived cardiomyocytes (2012)

Human pluripotent stem cells (hPSC) are self-renewing cells with the potential to differentiate into a variety of human cells. They hold great promise for regenerative medicine and serve as useful in vitro models for studying human biology. For the past few years, there is vast interest in applying these cells to advance cardiovascular medicine. Human cardiomyocytes can be readily generated from hPSC and they have been characterized extensively with regards to molecular and functional properties. They have been transplanted into animal models of cardiovascular diseases and also shown to be potentially useful reagents for drug discovery. Yet, despite great progress in this field, significant technical hurdles remain before these cells could be used clinically or for pharmaceutical research and development. Further research using novel approaches will be required to overcome these bottlenecks.
Pulmonary vasoconstriction produced by protamine and protamine-heparin complex in the isolated cat lung perfused with blood or dextran (1975)

Injections of protamine sulphate, protamine-heparin complex, and the supernatant from this mixture produced a rise in pulmonary artery pressure during constant flow perfusion in the isolated cat lung. The rise in pressure occurred with both blood and dextran perfusates. This suggests that the pulmonary vasoconstriction produced by protamine may be partly due to a direct action on the pulmonary vasculature or to the release of vasoactive substances from the lungs.
The Biobrane * Stent (1998)

For a successful take, skin grafts must be immobilized when applying dressings. Surgical beds requiring a stent to maintain contact between the graft and wound bed can be treated with Biobrane (Dow B. Hickam, Inc., Sugarland, Texas), which is held in place with skin staples at the periphery. Moistened gauze is placed over the grafted area, the redundant Biobrane stretched over the gauze, and this top layer again stapled at the periphery. When the stent is no longer needed, the top layer of Biobrane and gauze are removed, leaving a graft adherent to the bed and covered with Biobrane. This allows the surgeon to quickly construct an effective stent.
ChemInform Abstract: Enantioselective Synthesis of 2‐Benzyloxy Alcohols and 1,2‐Diols via Alkylation of Chiral Glycolate Imides. A Convenient Approach to Optically Active Glycerol Derivatives. (1989)

Abstract Alkylation of the chiral enolates of the glycolate imides (Ia) and (Ib) proceeds in a highly diastereoselective manner to give substituted products such as (III).
SU‐E‐QI‐14: Quantitative Variogram Detection of Mild, Unilateral Disease in Elastase‐Treated Rats (2014)

Purpose: Determining the presence of mild or early disease in the lungs can be challenging and subjective. We present a rapid and objective method for evaluating lung damage in a rat model of unilateral mild emphysema based on a new approach to heterogeneity assessment. We combined octree decomposition (used in three‐dimensional (3D) computer graphics) with variograms (used in geostatistics to assess spatial relationships) to evaluate 3D computed tomography (CT) lung images for disease. Methods: Male, Sprague‐Dawley rats (232 ± 7 g) were intratracheally dosed with 50 U/kg of elastase dissolved in 200 μL of saline to a single lobe (n=6) or with saline only (n=5). After four weeks, 3D micro‐CT images were acquired at end expiration on mechanically ventilated rats using prospective gating. Images were masked, and lungs were decomposed to homogeneous blocks of 2×2×2, 4×4×4, and 8×8×8 voxels using octree decomposition. The spatial variance – the square of the difference of signal intensity – between all pairs of the 8×8×8 blocks was calculated. Variograms – graphs of distance vs. variance – were made, and data were fit to a power law and the exponent determined. The mean HU values, coefficient of variation (CoV), and the emphysema index (EI) were calculated and compared to the variograms. Results: The variogram analysis showed that significant differences between groups existed (p&lt;0.01), whereas the mean HU (p=0.07), CoV (p=0.24), and EI (p=0.08) did not. Calculation time for the variogram for a typical 1000 block decomposition was ∼6 seconds, and octree decomposition took ∼2 minutes. Decomposing the images prior to variogram calculation resulted in a ∼700x decrease in time as compared to other published approaches. Conclusions: Our results suggest that the approach combining octree decomposition and variogram analysis may be a rapid, non‐subjective, and sensitive imaging‐based biomarker for quantitative characterization of lung disease.
Cannabidiol in Mental Health Disorders (2019)

Cannabidiol (CBD) was initially isolated from the cannabis sativa plant in the 1940s by R. Adams and A. R. Todd. Raphael Mechoulam’s laboratory characterized its chemical structure. In the following year, his group identified delta-9-tetrahydrocannabinol (THC) as the primary psychoactive compound present in the plant, starting a new era of cannabinoid research. The initial clinical observation that CBD, in healthy volunteers, prevented the anxiogenic effects of high doses of THC, prompted Brazilian researchers to investigate if it could induce anxiolytic effects by itself in rodents. In addition to acute effects in animal models of general anxiety, CBD was similarly effective in rodents tested in animal models associated with specific anxiety and stressful disorders. Similar to its other effects, CBD anxiolytic action seems to involve several targets depending on drug concentrations, species, and animal models being tested. The molecular and neurochemical mechanisms involved in CBD antidepressant effects are still poorly understood.
Design and Development of An Artificial Neural Network for Estimation of Formation Permeability (1995)

Summary Permeability is one of the most important characteristics of hydrocarbon-bearing formations and one of the most important pieces of information in the design and management of enhanced recovery operations. With accurate knowledge of permeability, petroleum engineers can manage the production process of a field efficiently. Although formation permeability is often measured in the laboratory from cores or evaluated from well-test data, core analysis and well-test data are only available from a few wells in a field, while the majority of wells are logged. In this study, we have designed an artificial neural network that can accurately predict the permeability of the formations by use of the data provided by geophysical well logs. Artificial neural network, a biologically inspired computing method which has an ability to learn, self-adjust, and be trained, provides a powerful tool in solving pattern recognition problems. In the past, others have attempted to use well logs to predict permeability.1 The problems with previous approaches, however, were two-fold: the limited number of variables (only one variable— porosity) and the use of regression analysis as the main tool for correlations. The approach introduced in this paper attempts to overcome these shortcomings. We do this by first, using many variables from well logs that may provide information about the permeability, and second, recognizing the existence of possible patterns between these variables and formation permeability by use of artificial neural networks. Neural nets are analog, inherently parallel, distributive systems. These characteristics enable artificial neural networks to be successful in predicting the formation permeability in rocks from well-log data.
Mobile ATM: architecture, protocols and implementation (2002)

Mobile ATM offers a common wired network infrastructure to support mobility of wireless terminals, independent of the wireless access protocol. In addition, it allows seamless migration to future wireless broadband services, such as wireless ATM, by enabling mobility of end-to-end ATM connections. In spite of the diversity in mobile networking technologies (e.g. cellular telephony, mobile-IP, packet data services, PCS), all of them require two fundamental mechanisms: location management and handoff. This paper introduces a network architecture that integrates location management and handoff within the ATM signalling and control framework.
Preparation and Modification of Polyacrylonitrile Microcellular Foam Films for Use as Electrodes in Supercapacitors (2001)

Results obtained for polyacrylonitrile microcellular foam thin films deposited on carbon fibers are presented. It appears that surface modifications by CO2 flow or water steam ar high temperature lead to an increase of the film surface area, as well as a proportional increase of capacitance. The films were characterized by Fourier transform infrared spectroscopy, scanning electron microscopy. and the Brunauer-Emmett-Teller technique. Extensive electrochemical studies (cyclic voltnmmetry, ae impedance, galvanic cycles, and cycle life tests) were performed both in aqueous and organic media in order to evaluate their use ax electrodes in a supercapacitor. The importance of the nature of the electrolyte was demonstrated using lithium perchlorate and tetraalkyl-based salts. The high performances of these activated materials were correlated both to their high surface area and their microporous distribution. (C) 2000 The Electrochemical Society. S0013-4651(00)04-096-9. All rights reserved.