gebhart/patrepeval huggingface dataset:
MetricScalpel: Analyzing Diagnostic Outcomes with Exploratory Data Visualization (2016)

Healthcare data is the emerging force to push ahead smarter clinical solutions. However, unforeseen challenges like unmanaged massive data and costly access to it make it difficult for domain experts to easily derive actionable insights. In collaboration with a local diagnostic service provider, we designed MetricScalpel, a web-based visualization tool to help people quickly look into the real-life diagnostic data in the local community. The tool enables swift exploration into the multivariate diagnostic data sets from different sources and facilitates data selection/subsetting for deeper analysis. It can be used to reveal overlooked health conditions on almost any level without the requirement of heavy technical knowledge. Such design makes it easier to be accepted by a wider user group in the healthcare related organizations. It was proven to well serve the domain experts in validating pre-exist hypotheses in cohort analysis as well as revealing undiscovered patterns of health conditions in the local community. External evaluation shows operation cost was remarkably confined as domain experts were assisted with direct and intuitive access to the relevant data in need.
Mechanistic Study of the Conversion of Superoxide to Oxygen and Hydrogen Peroxide in Carbon Nanoparticles (2016)

Hydrophilic carbon clusters (HCCs) are oxidized carbon nanoparticles with a high affinity for electrons. The electron accepting strength of HCCs, employing the efficient conversion of superoxide (O2(•-)) to molecular oxygen (O2) via single-electron oxidation, was monitored using cyclic voltammetry and electron paramagnetic resonance spectroscopy. We found that HCCs possess O2 reduction reaction (ORR) capabilities through a two-electron process with the formation of H2O2. By comparing results from aprotic solvents to those obtained from ORR activity in aqueous media, we propose a mechanism for the origin of the antioxidant and superoxide dismutase mimetic properties of poly(ethylene glycolated) hydrophilic carbon clusters (PEG-HCCs).
A New NMR-Based Height Saturation Model of a Low Permeability Carbonate Reservoir (2018)

Abstract Formation evaluation studies suggest that high in the hydrocarbon column, the resistivity logs can precisely quantify fluid saturation due to the large contrast in the resistivities of hydrocarbon-bearing and water-bearing formations. However, in the transition zone where water and oil reside in more or less equal volumes, the determination of hydrocarbon saturation by resistivity value becomes challenging. Some of these intervals exhibit low resistivity pay (LRP) characteristics where resistivity-based log analysis predicts high water saturation, yet they can produce little or no water-cut. Conventional log-based saturation and rock quality evaluation in a low permeability carbonate reservoir is difficult due to the lack of the input measurement's sensitivity to pore size and the amount of pore-filling fluids. Pore size information provided by Nuclear Magnetic Resonance (NMR) logs from this LRP provides good sensitivity, but it needs to be calibrated for quantitative use. The objective of this study is to determine a height-based NMR Bulk Volume Irreducible (HBVI) cutoff to distinguish and quantify the amounts of reservoir fluids across a wellbore using NMR logs. The procedure consists of two-part workflow. The first part describes the acquisition of a data base that includes high-quality laboratory NMR and capillary pressure measurements to determine the pore aspect ratio and the effect of temperature on the formation's NMR properties using core samples from the target reservoir. These measurements are then used to underpin the mathematical description of the HBVI cutoff as a function of displacement pressure that is translated to height above the free water level (HAFWL). The second part of the workflow is a well-log processing scheme where the new formula is implemented to calculate a continuous fluid saturation profile across the well using NMR logs. The laboratory measurements suggest a good agreement between the capillary pressure and NMR T2 measurements. Both data sets indicate a well sorted pore size distribution. The T2 relaxation time increases with temperature, which is then considered in the downhole implementation of the HBVI model. The NMR-based saturation log is consistent with wireline formation testing (WFT) observations and mercury injection capillary pressure (MICP)-based saturation height modeling results in a low resistivity pay reservoir. The results of this study suggest that the laboratory calibration and NMR log processing workflows described herein provide a viable alternative for the calculation of fluid saturations in complex reservoirs where the conventional log-based saturation evaluation faces uncertainties.
Molecular Phylogenetic Diversity, Multilocus Haplotype Nomenclature, and In Vitro Antifungal Resistance within theFusarium solaniSpecies Complex (2008)

Members of the species-rich Fusarium solani species complex (FSSC) are responsible for approximately two-thirds all fusarioses of humans and other animals. In addition, many economically important phytopathogenic species are nested within this complex. Due to their increasing clinical relevance and because most of the human pathogenic and plant pathogenic FSSC lack Latin binomials, we have extended the multilocus haplotype nomenclatural system introduced in a previous study (D. C. Chang, G. B. Grant, K. O'Donnell, K. A. Wannemuehler, J. Noble-Wang, C. Y. Rao, L. M. Jacobson, C. S. Crowell, R. S. Sneed, F. M. T. Lewis, J. K. Schaffzin, M. A. Kainer, C. A. Genese, E. C. Alfonso, D. B. Jones, A. Srinivasan, S. K. Fridkin, and B. J. Park, JAMA 296:953-963, 2006) to all 34 species within the medically important FSSC clade 3 to facilitate global epidemiological studies. The typing scheme is based on polymorphisms in portions of the following three genes: the internal transcribed spacer region and domains D1 plus D2 of the nuclear large-subunit rRNA, the translation elongation factor 1 alpha gene (EF-1alpha), and the second largest subunit of RNA polymerase II gene (RPB2). Of the 251 isolates subjected to multilocus DNA sequence typing, 191 sequence types were differentiated, and these were distributed among three strongly supported clades designated 1, 2, and 3. All of the mycosis-associated isolates were restricted to FSSC clade 3, as previously reported (N. Zhang, K. O'Donnell, D. A. Sutton, F. A Nalim, R. C. Summerbell, A. A. Padhye, and D. M. Geiser, J. Clin. Microbiol. 44:2186-2190, 2006), and these represent at least 20 phylogenetically distinct species. Analyses of the combined DNA sequence data by use of two separate phylogenetic methods yielded the most robust hypothesis of evolutionary relationships and genetic diversity within the FSSC to date. The in vitro activities of 10 antifungals tested against 19 isolates representing 18 species that span the breadth of the FSSC phylogeny show that members of this complex are broadly resistant to these drugs.
Adaptive Immunity in Atherosclerosis (2012)

Arterial inflammation is a key factor in the growth and destabilization of atherosclerotic lesions. Accumulating evidence has shown that this inflammation is fuelled by autoimmune responses against modified self-antigens such as oxidized low density lipoprotein. However, it has also become clear that the role of adaptive immunity in atherosclerosis is complex and that both pathogenic and protective immunity exist. Activation of Th1 cells promotes plaque growth and inflammation while regulatory T cells inhibit these processes. The observations suggest that it may be possible to develop novel immunomodulatory therapies targeting the Th1/Treg balance in atherosclerotic lesions.
Immunization with glycosylated Kb‐binding peptides generates carbohydrate‐specific, unrestricted cytotoxic T cells (1996)

Cytotoxic T cells (CTL) recognize target proteins as short peptides presented by major histocompatibility complex (MHC) class I restriction elements. However, there is also evidence for peptide-independent T cell receptor (TCR) recognition of target proteins and non-protein structures. How such T cell responses are generated is presently unclear. We generated carbohydrate (CHO)-specific, MHC-unrestricted CTL responses by coupling di- and trisaccharides to Kb- or Db-binding peptides for direct immunization in mice. Four peptides and three CHO have been analyzed with the CHO either in terminal or central position on the carrier peptide. With two of these glycopeptides, with galabiose (Gal alpha 1-4Gal; Gal2) bound to a homocysteine (via an ethylene spacer arm) in position 4 or 6 in a vesicular stomatitis virus nucleoprotein-derived peptide (RGYVYQGL binding to Kb), CTL were generated which preferentially killed target cells treated with glycopeptide compared to those treated with the core peptide. Polyclonal CTL were also found to kill target cells expressing the same Gal2 epitope in a glycolipid. By fractionation of CTL, preliminary data indicate that glycopeptide-specific Kb-restricted CTL and unrestricted CHO-specific CTL belong to different T cell populations with regard to TCR expression. The results demonstrate that hapten-specific unrestricted CTL responses can be generated with MHC class I-binding carrier peptides. Different models that might explain the generation of such responses are discussed.
Filterbank-based fingerprint matching (2000)

With identity fraud in our society reaching unprecedented proportions and with an increasing emphasis on the emerging automatic personal identification applications, biometrics-based verification, especially fingerprint-based identification, is receiving a lot of attention. There are two major shortcomings of the traditional approaches to fingerprint representation. For a considerable fraction of population, the representations based on explicit detection of complete ridge structures in the fingerprint are difficult to extract automatically. The widely used minutiae-based representation does not utilize a significant component of the rich discriminatory information available in the fingerprints. Local ridge structures cannot be completely characterized by minutiae. Further, minutiae-based matching has difficulty in quickly matching two fingerprint images containing a different number of unregistered minutiae points. The proposed filter-based algorithm uses a bank of Gabor filters to capture both local and global details in a fingerprint as a compact fixed length FingerCode. The fingerprint matching is based on the Euclidean distance between the two corresponding FingerCodes and hence is extremely fast. We are able to achieve a verification accuracy which is only marginally inferior to the best results of minutiae-based algorithms published in the open literature. Our system performs better than a state-of-the-art minutiae-based system when the performance requirement of the application system does not demand a very low false acceptance rate. Finally, we show that the matching performance can be improved by combining the decisions of the matchers based on complementary (minutiae-based and filter-based) fingerprint information.
On Dynamic Ray Tracing and Anticipative Channel Prediction for Dynamic Environments (2023)

Ray tracing (RT) algorithms, which can simulate multipath radio propagation in the presence of geometric obstacles such as buildings, objects, or vehicles, are becoming quite popular, due to the increasing availability of digital environment databases and high-performance computation platforms, such as multicore computers and cloud computing services. When objects or vehicles are moving, which is the case of industrial or vehicular environments, multiple successive representations of the environment (“snapshots”) and multiple RT runs are often necessary, which require a great human effort and a great deal of computation resources. Recently, the dynamic RT (DRT) approach has been proposed to predict the multipath evolution within a given time lapse on the base of the current multipath geometry, assuming constant speeds and/or accelerations for moving objects, using analytical extrapolation formulas. This is done without rerunning a full RT for every “snapshot” of the environment, therefore with a great reduction in both human labor and computation time. When DRT is embedded in a mobile radio system and used in real time, ahead-of-time (or anticipative) field prediction is possible, which opens the way to interesting applications. In the present work, a full-3-D DRT algorithm is presented, which allows to account for multiple reflections, edge diffraction, and diffuse scattering for the general case where moving objects can translate and rotate. For the purpose of validation, the model is first applied to some ideal cases and then to realistic cases where results are compared with conventional RT simulation and measurements available in the literature.
ChemInform Abstract: Novel Methods for the Construction of the β‐Lactam Ring (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Metastatic castration-resistant prostate cancer: targeting the mechanisms of resistance to abiraterone acetate and enzalutamide (2015)

Persistent androgen receptor (AR) axis is a functionally important pathway for prostate cancer cells and it is currently regarded as a critical therapeutic target. Although the impressive clinical activity of new hormonal agents, such as the second-generation AR antagonist enzalutamide (formerly MDV3100) and the selective inhibitor of cytochrome P450 17A1 (CYP17A1) abiraterone acetate (AA), in patients with metastatic castration-resistant prostate cancer (mCRPC), innate or acquired resistance invariably arises. To date, emerging hypotheses are different, but the mechanisms of resistance to these drugs have not yet been clarified. The aim of this review is to summarize the main data available on the evaluation of the multiple levels of development of resistance to next-generation AR-directed therapies. Understanding how the AR is activated may have clinical implications in defining which patients will respond to existing therapeutic agents and provide a proof for making novel strategies.
(R)- and (S)-2,2′-Bis(diphenylphosphino)-6,6′-dimethoxy-1,1′-biphenyl (2016)

(R-)[133545-16-1] InChI = 1S/C38H32O2P2/c1-39-33-25-15-27-35(41(29-17-7-3-8-18-29)30-19-9-4-10-20-30)37(33)38-34(40-2)26-16-28-36(38)42(31-21-11-5-12-22-31)32-23-13-6-14-24-32/h3-28H,1-2H3 InChIKey = KRJVQCZJJSUHHO-UHFFFAOYSA-N (S-) [133545-17-2] C38H32O2P2 (MW 582.62) InChI = 1S/C38H32O2P2/c1-39-33-25-15-27-35(41(29-17-7-3-8-18-29)30-19-9-4-10-20-30)37(33)38-34(40-2)26-16-28-36(38)42(31-21-11-5-12-22-31)32-23-13-6-14-24-32/h3-28H,1-2H3 InChIKey = KRJVQCZJJSUHHO-UHFFFAOYSA-N (chiral bisphosphine ligand for transition metals; the complexes show high enantioselectivity and reactivity in a variety of organic synthetic transformations)1, 2 Alternate Name: MeOBIPHEP. Physical Data: mp 212–213 °C; [ α ] D 20 − 42.5 ( c = 1.0 , CHCl 3 ) for (S)-MeOBIPHEP. Preparative Methods: enantiomerically pure MeOBIPHEP ligand is industrially obtained by the resolution of its racemic oxide. Its congeners, in contrast, are prepared by the resolution of the common racemic precursor 6,6′-dimethoxy-1,1′-biphenyl-2,2′-diyl-bis(phosphonic acid diethyl ester), followed by the conversion to the corresponding bis(phosphonic dichloride), reaction with aryl or alkyl Grignard, and reduction of phosphine oxide.1 An alternative preparation has been described recently based on a Pd-catalyzed PC coupling of chiral bisphosphane with phenyl iodide, leading to MeOBIPHEP ligands in 50% yield (two steps), starting from chiral biphenyl bisphosphonate.3 Solubility: dichloromethane 36 w%, THF 24 w%, toluene 10 w%, AcOEt 2 w%, TBME 0.5 w%, EtOH <0.1 w%, MeOH <0.1 w%; insoluble in water. Form Supplied in: colorless solid. Purification: crystallization from toluene/EtOH. Handling, Storage, and Precautions: air-stable in solid form in closed bottles over years; slowly air oxidized to the monoxide in solution.
Chemistry and physico-chemistry of phycocolloids (2001)

A review on the chemistry, physico-chemistry and some gel characteristics of major phycocolloids is presented. These concern mainly agar, gelling carrageenans from red seaweeds, alginate from brown seaweeds and ulvans from green seaweeds. Based on the available data, future research areas are proposed to better define the relationships between the different structural levels of these polysaccharides and their use as texturing agents.
Magnetic Assembly of Nonmagnetic Particles into Photonic Crystal Structures (2010)

We report the rapid formation of photonic crystal structures by assembly of uniform nonmagnetic colloidal particles in ferrofluids using external magnetic fields. Magnetic manipulation of nonmagnetic particles with size down to a few hundred nanometers, suitable building blocks for producing photonic crystals with band gaps located in the visible regime, has been difficult due to their weak magnetic dipole moment. Increasing the dipole moment of magnetic holes has been limited by the instability of ferrofluids toward aggregation at high concentration or under strong magnetic field. By taking advantage of the superior stability of highly surface-charged magnetite nanocrystal-based ferrofluids, in this paper we have been able to successfully assemble 185 nm nonmagnetic polymer beads into photonic crystal structures, from 1D chains to 3D assemblies as determined by the interplay of magnetic dipole force and packing force. In a strong magnetic field with large field gradient, 3D photonic crystals with high reflectance (83%) in the visible range can be rapidly produced within several minutes, making this general strategy promising for fast creation of large-area photonic crystals using nonmagnetic particles as building blocks.
Data from Biochemical, Molecular, and Clinical Characterization of Succinate Dehydrogenase Subunit A Variants of Unknown Significance (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Patients who inherit a pathogenic loss-of-function genetic variant involving one of the four succinate dehydrogenase (SDH) subunit genes have up to an 86% chance of developing one or more cancers by the age of 50. If tumors are identified and removed early in these high-risk patients, they have a higher potential for cure. Unfortunately, many alterations identified in these genes are variants of unknown significance (VUS), confounding the identification of high-risk patients. If we could identify misclassified SDH VUS as benign or pathogenic SDH mutations, we could better select patients for cancer screening procedures and remove tumors at earlier stages.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; In this study, we combine data from clinical observations, a functional yeast model, and a computational model to determine the pathogenicity of 22 &lt;i&gt;SDHA&lt;/i&gt; VUS. We gathered &lt;i&gt;SDHA&lt;/i&gt; VUS from two primary sources: The OHSU Knight Diagnostics Laboratory and the literature. We used a yeast model to identify the functional effect of a VUS on mitochondrial function with a variety of biochemical assays. The computational model was used to visualize variants' effect on protein structure.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; We were able to draw conclusions on functional effects of variants using our three-prong approach to understanding VUS. We determined that 16 (73%) of the alterations are actually pathogenic, causing loss of SDH function, and six (27%) have no effect upon SDH function.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; We thus report the reclassification of the majority of the VUS tested as pathogenic, and highlight the need for more thorough functional assessment of inherited SDH variants. &lt;i&gt;Clin Cancer Res; 23(21); 6733–43. ©2017 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Adherence of Salmonellae and Native Gut Microflora to the Gastrointestinal Mucosa of Chicks (1982)

A. S. Soerjadi, Robyn Rufner, G. H. Snoeyenbos, Olga M. Weinack, Adherence of Salmonellae and Native Gut Microflora to the Gastrointestinal Mucosa of Chicks, Avian Diseases, Vol. 26, No. 3 (Jul. - Sep., 1982), pp. 576-584
Double-Blind, Multicenter, Active-Controlled, Randomized Clinical Trial to Assess the Safety and Efficacy of Orally Administered Nicorandil in Patients With Stable Angina Pectoris in China (2007)

Nicorandil is beneficial as treatment for AP.
BER analysis of Joint Network/Channel decoding in block Rayleigh fading channels (2013)

This paper studies the four-node Multiple Access Relay Channel (MARC) under quasi-static block Rayleigh fading channels and Gaussian noise environment. A relay employs Demodulate-and-Forward (DMF) protocol in order to help two channel-encoded sources to communicate with a destination. The contributions of the paper are threefold: i) we propose a Near Optimal Joint Network/Channel decoding (NO-JNCD) algorithm at the destination. The NO-JNCD employs Cooperative Maximum Ratio Combining (C-MRC) detector and the BCJR algorithm applied to a compound code which trellis consists of all possible states of two single trellises at sources; ii) we compute extended distance spectrum of the compound code containing input weights for each source and output weights on each fading channel; and iii) from the extended distance spectrum, we derive the Bit Error Rate (BER) upper bound for the compound code as well as for each source. It is shown by simulation that the proposed decoder provides performance very close to that of the optimal JNCD with both DMF and Decode-and-Forward (DF) relaying protocols. Finally, the analysis is checked by simulation.
Molecular Signaling in Tumorigenesis of Gastric Cancer (2018)

Gastric cancer (GC) is regarded as the fifth most common cancer and the third cause of cancer-related deaths worldwide. Mechanism of GC pathogenesis is still unclear and relies on multiple factors, including environmental and genetic characteristics. One of the most important environmental factors of GC occurrence is infection with Helicobacter pylori that is classified as class one carcinogens. Dysregulation of several genes and pathways play an essential role during gastric carcinogenesis. Dysregulation of developmental pathways such as Wnt/-catenin signaling, Hedgehog signaling, Hippo pathway, Notch signaling, nuclear factor-kB, and epidermal growth factor receptor have been found in GC. Epithelial-mesenchymal transition, as an important process during embryogenesis and tumorigenesis, is supposed to play a role in initiation, invasion, metastasis, and progression of GC. Although surgery is the main therapeutic modality of the disease, the understanding of biological processes of cell signaling pathways may help to develop new therapeutic targets for GC.