gebhart/patrepeval huggingface dataset:
Characterization of V3 Sequence Heterogeneity in Subtype C Human Immunodeficiency Virus Type 1 Isolates from Malawi: Underrepresentation of X4 Variants (1999)

We have examined the nature of V3 sequence variability among subtype C human immunodeficiency virus type 1 (HIV-1) sequences from plasma-derived viral RNA present in infected men from Malawi. Sequence variability was assessed by direct sequence analysis of the V3 reverse transcription-PCR products, examination of virus populations by a subtype C V3-specific heteroduplex tracking assay (V3-HTA), and selected sequence analysis of molecular clones derived from the PCR products. Sequence variability in V3 among the subtype C viruses was not associated with the presence of basic amino acid substitutions. This observation is in contrast to that for subtype B HIV-1, where sequence variability is associated with such substitutions, and these substitutions are determinants of altered coreceptor usage. Evolutionary variants in subtype C V3 sequences, as defined by the V3-HTA, were not correlated with the CD4 level in the infected person, while such a correlation was found with subtype B V3 sequences. Viruses were isolated from a subset of the subjects; all isolates used CCR5 and not CXCR4 as a coreceptor, and none was able to grow in MT-2 cells, a hallmark of the syncytium-inducing phenotype that is correlated with CXCR4 usage. The overall sequence variability of the subtype C V3 region was no greater than that of the conserved regions of gp120. This limited sequence variability was also a feature of subtype B V3 sequences that do not carry the basic amino acid substitutions associated with altered coreceptor usage. Our results indicate that altered coreceptor usage is rare in subtype C HIV-1 isolates in sub-Saharan Africa and that sequence variability is not a feature of the V3 region of env in the absence of altered coreceptor usage.
Antibacterial Agents. Some New Guanyhydrazone Derivatives (1961)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAntibacterial Agents. Some New Guanyhydrazone DerivativesG. Cavallini, E. Massarani, D. Nardi, L. Mauri, and P. MantegazzaCite this: J. Med. Chem. 1961, 4, 1, 177–182Publication Date (Print):July 1, 1961Publication History Published online1 May 2002Published inissue 1 July 1961https://doi.org/10.1021/jm50017a013RIGHTS & PERMISSIONSArticle Views137Altmetric-Citations11LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (256 KB) Get e-Alerts
Rapid and automatic detection of brain tumors in MR images (2004)

An algorithm to automatically detect brain tumors in MR images is presented. The key concern is speed in order to process efficiently large brain image databases and provide quick outcomes in clinical setting. The method is based on study of asymmetry of the brain. Tumors cause asymmetry of the brain, so we detect brain tumors in 3D MR images using symmetry analysis of image grey levels with respect to the midsagittal plane (MSP). The MSP, separating the brain into two hemispheres, is extracted using our previously developed algorithm. By removing the background pixels, the normalized grey level histograms are calculated for both hemispheres. The similarity between these two histograms manifests the symmetry of the brain, and it is quantified by using four symmetry measures: correlation coefficient, root mean square error, integral of absolute difference (IAD), and integral of normalized absolute difference (INAD). A quantitative analysis of brain normality based on 42 patients with tumors and 55 normals is presented. The sensitivity and specificity of IAD and INAD were 83.3% and 89.1%, and 85.7% and 83.6%, respectively. The running time for each symmetry measure for a 3D 8bit MR data was between 0.1 - 0.3 seconds on a 2.4GHz CPU PC.
Chromatin accessibility maps of chronic lymphocytic leukaemia identify subtype-specific epigenome signatures and transcription regulatory networks (2016)

Chronic lymphocytic leukaemia (CLL) is characterized by substantial clinical heterogeneity, despite relatively few genetic alterations. To provide a basis for studying epigenome deregulation in CLL, here we present genome-wide chromatin accessibility maps for 88 CLL samples from 55 patients measured by the ATAC-seq assay. We also performed ChIPmentation and RNA-seq profiling for ten representative samples. Based on the resulting data set, we devised and applied a bioinformatic method that links chromatin profiles to clinical annotations. Our analysis identified sample-specific variation on top of a shared core of CLL regulatory regions. IGHV mutation status-which distinguishes the two major subtypes of CLL-was accurately predicted by the chromatin profiles and gene regulatory networks inferred for IGHV-mutated versus IGHV-unmutated samples identified characteristic differences between these two disease subtypes. In summary, we discovered widespread heterogeneity in the chromatin landscape of CLL, established a community resource for studying epigenome deregulation in leukaemia and demonstrated the feasibility of large-scale chromatin accessibility mapping in cancer cohorts and clinical research.
RIE-Texturing of Industrial Multicrystalline Silicon Solar Cells (2003)

We developed a maskless plasma texturing technique for multicrystalline Si (mc-Si) cells using Reactive Ion Etching (RIE) that results in higher cell performance than that of standard untextured cells. Elimination of plasma damage has been achieved while keeping front reflectance to low levels. Internal quantum efficiencies higher than those on planar and wet-textured cells have been obtained, boosting cell currents and efficiencies by up to 6% on tricrystalline Si cells.
Reactions of Horseradish Peroxidase with Azide. Evidence for a Methionine Residue at the Active Site<sup>*</sup> (1967)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReactions of Horseradish Peroxidase with Azide. Evidence for a Methionine Residue at the Active Site*Arthur S. Brill and Ira WeinrybCite this: Biochemistry 1967, 6, 11, 3528–3535Publication Date (Print):November 1, 1967Publication History Published online1 May 2002Published inissue 1 November 1967https://pubs.acs.org/doi/10.1021/bi00863a026https://doi.org/10.1021/bi00863a026research-articleACS PublicationsRequest reuse permissionsArticle Views1902Altmetric-Citations37LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Architecture of Configurable K-Way C-Access Interleaved Memory (2011)

A new efficient memory system approach towards realizing configurable C-access interleaved memory architecture has been described in this paper. Massively decreasing size, power consumption and cost of digital circuits mainly lead the development of memory architectures for pipelined processors, multiprocessors and VLIW processors. This evolves the development of high-throughput memory system by using interleaved memory architecture and provides flexibility by configuring interleaved factor for K-way interleaved memory architecture. It employs N = 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sup> identical memory modules of W-words, each word of B-byte size, which can be configured as K-way (K=1, 2, 4, ..., N i.e.; K ∈ 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">k</sup> , where 0≤k≤n) interleaved memory system and its data bus and address bus can be internally programmed/controlled by Data Routing Scheme (DRS) and Address Decoding Scheme (ADS) respectively. In the proposed system, processor configures the interleaving factor of the memory organization through the system data bus by a set of control bits of n+1.
Role of Crystal Symmetry in the Reversibility of Stacking-Sequence Changes in Layered Intercalation Electrodes (2017)

The performance of many technologies, such as Li- and Na-ion batteries as well as some two-dimensional (2D) electronics, is dependent upon the reversibility of stacking-sequence-change phase transformations. However, the mechanisms by which such transformations lead to degradation are not well understood. This study explores lattice-invariant shear as a source of irreversibility in stacking-sequence changes, and through an analysis of crystal symmetry shows that common electrode materials (graphitic carbon, layered oxides, and layered sulfides) are generally susceptible to lattice-invariant shear. The resulting irreversible changes to microstructure upon cycling ("electrochemical creep") could contribute to the degradation of the electrode and capacity fade.
The Development and Testing of an Active Particulate Regeneration System Using Model Based Control (2006)

<div class="htmlview paragraph">With ever tightening vehicle emissions standards the fitment of Diesel Particulate Filter (DPF) systems will become common in the US, Europe and Japan. While in most circumstances filters may be regenerated passively there is a risk that this will not always be possible due to the low exhaust gas temperatures in certain stop-start duty cycles (such as urban buses, garbage trucks, etc.). In order to operate in such cycles active regeneration will be required.</div> <div class="htmlview paragraph">A potential active regeneration method is to inject diesel fuel upstream of a catalyst and use the resulting exotherm from the combustion of the fuel to regenerate the particulate trap. In order for this to occur, the catalyst must be above the light off temperature, so it is necessary to understand the condition of the catalyst prior to initiating regeneration. Using diesel fuel for regeneration obviously has an impact on the fuel consumption of the vehicle so it is important to understand the soot loading of a particulate trap during operation to maximize the time between active regenerations.</div> <div class="htmlview paragraph">This paper describes the development and testing of an active regeneration system including a catalyst, a particulate trap and a model based control system. The control system will model the soot loading and passive regeneration of the filter to allow the maximum time between active regeneration events, thus minimizing fuel penalty. The system also models the condition of the catalyst and uses this for both active and passive regeneration calculations for the particulate trap subroutine of the control algorithm.</div>
Supporting document and data views of source code (2002)

The paper describes the use of an XML format to store and represent program source code. A new XML application, srcML (SouRCe Markup Language), is presented. srcML presumes a document view of source code where information about the syntactic structure is layered over the original source code document. The resultant multi-layered document has a base layer of all the original text (and formatting). The second layer is the syntactic information, derived from the grammar of the programming language, and is encoded in XML. This multi-layered view supports both the creation and viewing of the source code in its original form and the use of XML technologies (for tasks such as analysis and transformation of the source). Although directed at source code documents, (particularly C++) srcML is also applicable to other programming languages and to languages with a strict syntax. srcML represents a departure from the compiler centric manner in which source code is commonly stored, instead a document point of view is taken thus better supporting the manipulation and management of the large numbers of source documents typical in modern software systems.
Oxidized Low-Density Lipoprotein Inhibits Nitric Oxide-Mediated Coronary Arteriolar Dilation by Up-regulating Endothelial Arginase I (2010)

Oxidized low-density lipoprotein (OxLDL) causes impairment of endothelium-dependent, nitric oxide (NO)-mediated vasodilation involving l-arginine deficiency. However, the underlying mechanism remains elusive. Since arginase and endothelial NO synthase (eNOS) share the substrate l-arginine, we hypothesized that OxLDL may reduce l-arginine availability to eNOS for NO production, and thus vasodilation, by up-regulating arginase. To test this hypothesis, porcine subepicardial arterioles (70-130 μm) were isolated for vasomotor study and for immunohistochemical detection of arginase and eNOS expressions. The coronary arterioles dilated dose-dependently to the endothelium-dependent NO-mediated vasodilator serotonin. This vasodilation was inhibited in the same manner by NOS inhibitor N(G)-nitro-l-arginine methyl ester and by lumenal OxLDL (0.5 mg protein/mL). The inhibitory effect of OxLDL was reversed after treating the vessels with either l-arginine (3 mM) or arginase inhibitor difluoromethylornithine (DFMO; 0.4 mM). Consistent with vasomotor alterations, OxLDL inhibited serotonin-induced NO release from coronary arterioles and this inhibition was reversed by DFMO. Vascular arginase activity was significantly elevated by OxLDL. Immunohistochemical analysis indicated that OxLDL increased arginase I expression in the vascular wall without altering eNOS expression. Taken together, these results suggest that OxLDL up-regulates arginase I, which contributes to endothelial dysfunction by reducing l-arginine availability to eNOS for NO production and thus vasodilation.
Mobile Intelligent Agents for Document Classification and Retrieval: A Machine Learning Approach (1998)

This paper describes an implementation of intelligent, customizable mobile software agents for document classification and retrieval. The mobile agents are implemented using the Voyager platform. The agents learn user&apos;s interests by interacting with the user. Results of experiments using three different approaches -- TFIDF, Bayesian and DistAl (neural network classifier) -- for the design of trainable document classifiers are presented. The performance of each classifier with and without feature subset selection (using genetic algorithms) was explored. Experiments with retrieval of journal paper abstracts and news articles demonstrate the feasibility of using machine learning to design mobile intelligent agents for customized information retrieval. 1 Introduction Agents are software or hardware entities that performs a set of tasks on behalf of a user with some degree of autonomy [ Russell and Norvig, 1995; Honavar, 1998 ] . In order to do this, an agent has to embody a certain amoun...
Learning from the Best: Rationalizing Prediction by Adversarial Information Calibration (2020)

Explaining the predictions of AI models is paramount in safety-critical applications, such as in legal or medical domains. One form of explanation for a prediction is an extractive rationale, i.e., a subset of features of an instance that lead the model to give its prediction on the instance. Previous works on generating extractive rationales usually employ a two-phase model: a selector that selects the most important features (i.e., the rationale) followed by a predictor that makes the prediction based exclusively on the selected features. One disadvantage of these works is that the main signal for learning to select features comes from the comparison of the answers given by the predictor and the ground-truth answers. In this work, we propose to squeeze more information from the predictor via an information calibration method. More precisely, we train two models jointly: one is a typical neural model that solves the task at hand in an accurate but black-box manner, and the other is a selector-predictor model that additionally produces a rationale for its prediction. The first model is used as a guide to the second model. We use an adversarial-based technique to calibrate the information extracted by the two models such that the difference between them is an indicator of the missed or over-selected features. In addition, for natural language tasks, we propose to use a language-model-based regularizer to encourage the extraction of fluent rationales. Experimental results on a sentiment analysis task as well as on three tasks from the legal domain show the effectiveness of our approach to rationale extraction.
A Cognitive Radio Receiver Supporting Wide-Band Sensing (2008)

IEEE 802.22 defines the world-wide first cognitive radio (CR) standard. In the range between 41 MHz and 910 MHz CR overlay-systems can be installed besides licensed radio services such as radio and TV broadcasting. In order to fulfill the regulative guidelines for interference limitations, adequate spectral sensing and user detection has to be supported by the CR terminals. The wide frequency range specified in IEEE 802.22 and the high dynamic range of signals in this band lead to high demands on the CR receiver's front-end. Especially the performance requirements on analog-to-digital converters (ADCs) increase significantly compared to current wireless systems. Based on measurements taken in the frequency range between 41 MHz and 910 MHz requirements to CR's ADCs are figured out. Furthermore, the measurement results are analyzed regarding expectable allocation scenarios and their impacts on spectral sensing. Derived from these results and a comparison of general spectral sensing mechanisms, an approach for a CR receiver enabling wide-band sensing is presented. By combining a-priori information resulting from scenario analysis with adapted information processing in the CR terminal, the ADC's performance requirements can be reduced.
Cations and the secretion of insulin from rabbit pancreas <i>in vitro</i> (1968)

1. Insulin secretion from pieces of rabbit pancreas incubated in vitro was studied in media of different ionic compositions.2. Insulin secretion stimulated by glucose was abolished by removal of calcium from the incubation medium and inhibited by a twofold rise in the calcium concentration to 10.2 m-equiv/l. Removal of magnesium from the medium did not affect glucose-stimulated secretion but a tenfold rise in the extracellular magnesium concentration to 24 m-equiv/l. abolished secretion.3. The replacement of calcium by an equivalent amount of barium (5.1 m-equiv/l.) stimulated insulin secretion. Barium stimulation declined with time and was inhibited by the presence of calcium, 5.1 m-equiv/l., or abolished by the presence of magnesium, 24 m-equiv/l., in the incubation medium.4. The interactions of mono- and divalent cations on insulin secretion were studied by using ouabain or potassium as tools to raise intracellular sodium concentration and barium as a calcium analogue. Ouabain and potassium were effective stimuli only in the presence of calcium, and barium only stimulated insulin secretion in the presence of sodium.5. The results of these experiments suggest that both calcium and sodium must act at the beta cell membrane or enter the cell before insulin release can occur in response to a variety of stimuli.
Record Charge Carrier Diffusion Length in Colloidal Quantum Dot Solids via Mutual Dot‐To‐Dot Surface Passivation (2015)

Through a combination of chemical and mutual dot-to-dot surface passivation, high-quality colloidal quantum dot solids are fabricated. The joint passivation techniques lead to a record diffusion length for colloidal quantum dots of 230 ± 20 nm. The technique is applied to create thick photovoltaic devices that exhibit high current density without losing fill factor.
Mobile application usage prediction through context-based learning (2013)

The purchase and download of new applications on all types of smartphones and tablet computers has become increasingly popular. On each mobile device, many applications are installed, often resulting in crowded icon-based interfaces. In this paper, w
Spontaneous proliferation of peripheral blood lymphocytes increased in patients with HTLV‐I‐associated myelopathy (1988)

We found unstimulated (spontaneous) peripheral blood lymphocyte (PBL) proliferation significantly increased in 14 patients with human T-lymphotropic virus (HTLV)-I-associated myelopathy (HAM) compared with findings in HTLV-I seropositive non-HAM carriers (N = 8) or HTLV-I seronegative controls (N = 16). The proliferative response to phytohemagglutinin, concanavalin A, or pokeweed mitogen was decreased in the HAM patients. Cell clusters were frequent in cultures of unstimulated PBL from the HAM patients, but much less common in the controls or carriers. This spontaneous PBL proliferation was depressed when adherent-cell populations were depleted from the cultures. IL-2 activity increased in the supernatant of 3-day cultured cells from HAM patients, but not in cultured cells from the controls. Since IL-2 receptor positive cells increased in HAM, this spontaneous PBL proliferation is probably a response to IL-2 through the expression of IL-2 receptors.
Naturally occurring prostate cancer antigen‐specific T cell responses of a Th1 Phenotype can be detected in patients with prostate cancer (2001)

Patients with prostate cancer can have detectable Th-cell responses specific for the prostate cancer-associated proteins PSA and PAP. The presence of antigen-specific Th1 immune responses in prostate cancer patients suggests that an immune environment capable of supporting antigen-specific CTL may exist in vivo. Prostate 47:222-229, 2001.
Alcoholic Fermentation of <scp>d</scp> -Xylose by Yeasts (1984)

Type strains of 200 species of yeasts able to ferment glucose and grow on xylose were screened for fermentation of d-xylose. In most of the strains tested, ethanol production was negligible. Nineteen were found to produce between 0.1 and 1.0 g of ethanol per liter. Strains of the following species produce more than 1 g of ethanol per liter in the fermentation test with 2% xylose: Brettanomyces naardenensis, Candida shehatae, Candida tenuis, Pachysolen tannophilus, Pichia segobiensis, and Pichia stipitis. Subsequent screening of these yeasts for their capacity to ferment d-cellobiose revealed that only Candida tenuis CBS 4435 was a good fermenter of both xylose and cellobiose under the test conditions used.