gebhart/patrepeval huggingface dataset:
Data from Shifts in the Fecal Microbiota Associated with Adenomatous Polyps (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Background:&lt;/b&gt; Adenomatous polyps are the most common precursor to colorectal cancer, the second leading cause of cancer-related death in the United States. We sought to learn more about early events of carcinogenesis by investigating shifts in the gut microbiota of patients with adenomas.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Methods:&lt;/b&gt; We analyzed 16S rRNA gene sequences from the fecal microbiota of patients with adenomas (&lt;i&gt;n&lt;/i&gt; = 233) and without (&lt;i&gt;n&lt;/i&gt; = 547).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Multiple taxa were significantly more abundant in patients with adenomas, including &lt;i&gt;Bilophila, Desulfovibrio&lt;/i&gt;, proinflammatory bacteria in the genus &lt;i&gt;Mogibacterium&lt;/i&gt;, and multiple Bacteroidetes species. Patients without adenomas had greater abundances of &lt;i&gt;Veillonella, Firmicutes&lt;/i&gt; (Order Clostridia), and &lt;i&gt;Actinobacteria&lt;/i&gt; (family &lt;i&gt;Bifidobacteriales&lt;/i&gt;). Our findings were consistent with previously reported shifts in the gut microbiota of colorectal cancer patients. Importantly, the altered adenoma profile is predicted to increase primary and secondary bile acid production, as well as starch, sucrose, lipid, and phenylpropanoid metabolism.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; These data hint that increased sugar, protein, and lipid metabolism along with increased bile acid production could promote a colonic environment that supports the growth of bile-tolerant microbes such as &lt;i&gt;Bilophilia&lt;/i&gt; and &lt;i&gt;Desulfovibrio&lt;/i&gt;. In turn, these microbes may produce genotoxic or inflammatory metabolites such as H&lt;sub&gt;2&lt;/sub&gt;S and secondary bile acids, which could play a role in catalyzing adenoma development and eventually colorectal cancer.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Impact:&lt;/b&gt; This study suggests a plausible biological mechanism to explain the links between shifts in the microbiota and colorectal cancer. This represents a first step toward resolving the complex interactions that shape the adenoma–carcinoma sequence of colorectal cancer and may facilitate personalized therapeutics focused on the microbiota. &lt;i&gt;Cancer Epidemiol Biomarkers Prev; 26(1); 85–94. ©2016 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Substituted 1-Phenyl-3-(pyridin-2-yl)urea Negative Allosteric Modulators of mGlu5: Discovery of a New Tool Compound VU0463841 with Activity in Rat Models of Cocaine Addiction (2013)

Cocaine is a powerful and highly addictive stimulant that disrupts the normal reward circuitry in the central nervous system (CNS), producing euphoric effects. Cocaine use can lead to acute and life threatening emergencies, and abuse is associated with increased risk for contracting infectious diseases. Though certain types of behavioral therapy have proven effective for treatment of cocaine addiction, relapse remains high, and there are currently no approved medications for the treatment of cocaine abuse. Evidence has continued to accumulate that indicates a critical role for the metabotropic glutamate receptor subtype 5 (mGlu5) in the modulation of neural circuitry associated with the addictive properties of cocaine. While the small molecule mGlu5 negative allosteric modulator (NAM) field is relatively advanced, investigation into the potential of small molecule mGlu5 NAMs for the treatment of cocaine addiction remains an area of high interest. Herein we describe the discovery and characterization of a potent and selective compound 29 (VU0463841) with good CNS exposure in rats. The utility of 29 (VU0463841) was demonstrated by its ability to attenuate drug seeking behaviors in relevant rat models of cocaine addiction.
Enzymatic Removal of Sialic Acid from Human Factor IX and Factor X Has No Effect on Their Coagulant Activity (1995)

Factor IX and factor X have sialic acid in O-linked and N-linked oligosaccharides on their activation peptides, and a terminal sialic acid is found on a recently described O-linked tetrasaccharide at Ser-61 in the light chain of human factor IXa. In studies presented here, the potential role of sialic acid residues in mediating activity of human coagulation factors IX and X was tested after enzymatic removal of sialic acid residues. In contrast to previous reports, treatment of factor IX or factor IXa with recombinant sialidase did not decrease the rate of factor IX activation or proteolytic properties of human factor IXa. The activation rates of factor IX and desialated factor IX were indistinguishable when treated with factor XIa, with factor VIIa/tissue factor complex, and with the factor X activating enzyme from Russell's viper venom. Desialated human factor IXa showed full activity in the non-activated partial thromboplastin time assay and retained full "tenase" activity in a coupled amidolytic assay. Similar experiments with human factor X showed no detectable loss of clotting activity in the prothrombin time assay after desialation. Additionally, desialated human factor X was cleaved by the factor X activating enzyme from Russell's viper venom and intrinsic tenase at the same rate as untreated factor X when analyzed by SDS-polyacrylamide gel electrophoresis. These studies have shown that factor IX and factor X clotting activity are not dependent on sialic acid content. Further studies are needed to determine whether desialated factor IX binds to endothelial cells, and whether factors IX and X are more rapidly cleared from circulation or have altered susceptibility to proteolysis after enzymatic removal of sialic acid.
Xanthates and Related Derivatives as Radical Precursors Synthetic Strategies and Applications (2012)

This chapter deals with the various radical reactions involving dithiocarbonates (xanthates) and related structures. It will revolve around two main topics: (i) cleavage of the CO bond and (ii) cleavage of the CS bond. The first mode corresponds to the Barton-McCombie reaction and variants thereof. The mechanism of this important reaction is discussed in detail and then illustrated with a few varied examples taken from the recent literature (in order not to overlap too much with existing reviews). Modifications not using organotin hydrides are also described, with emphasis on the practical aspects. The incorporation of the Barton-McCombie process in various CC bond-forming radical sequences is also be presented. Included in this part is an O → S radical chain rearrangement that is sometimes observed. The second mode encompasses the degenerative fragmentation of xanthates. Radicals generated this way have a relatively long lifetime in the medium, allowing various transformations otherwise difficult to perform. Intermolecular additions to unactivated olefins are one such case. The possibility of using the adduct, itself a xanthate, for another radical sequence can also be exploited. Intra- and intermolecular additions to aromatic and heteroaromatic rings, as well as radical-based modifications of the xanthate group, are other possibilities that are described and illustrated with examples
Variability: For headache and profit (2010)

The paper discusses hardware security. The author mention that there were best times and worst times for hardware security. Numerous factors facilitate, both qualitatively and quantitatively an essentially unlimited potential for attacks. Factors include an increasingly popular and profitable horizontal semiconductor business model, sharply reduced controllability and observability ultracheap silicon, expensive testing, ultra-large-scale integration, manufacturing variability aging, thermal and operational sensitivity, crosstalk, and many other physical properties of deep submicron technologies. Hardware Trojan horses, physical unclonable functions, cryptography were some of the issues mentioned and discussed in this paper.
α-Substituted N-(Sulfonamido)alkyl-β-aminotetralins:  Potent and Selective Neuropeptide Y Y5 Receptor Antagonists (2000)

ADVERTISEMENT RETURN TO ISSUEPREVLetterNEXTα-Substituted N-(Sulfonamido)alkyl-β-aminotetralins: Potent and Selective Neuropeptide Y Y5 Receptor AntagonistsMark A. Youngman, James J. McNally, Timothy W. Lovenberg, Allen B. Reitz, Nicole M. Willard, Diane H. Nepomuceno, Sandy J. Wilson, Jeffrey J. Crooke, Daniel Rosenthal, Anil H. Vaidya, and Scott L. DaxView Author Information Drug Discovery, The R. W. Johnson Pharmaceutical Research Institute, Welsh and McKean Roads, Spring House, Pennsylvania 19477, and 3210 Merryfield Row, San Diego, California 92121 Cite this: J. Med. Chem. 2000, 43, 3, 346–350Publication Date (Web):January 19, 2000Publication History Received16 September 1999Published online19 January 2000Published inissue 1 February 2000https://pubs.acs.org/doi/10.1021/jm990468ghttps://doi.org/10.1021/jm990468grapid-communicationACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views367Altmetric-Citations40LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Antagonists,Food,Molecular structure,Receptors,Screening assays Get e-Alerts
A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0 (2018)

This version 10.0 of RegulonDB is a first step toward what should become the unifying access point for current and future knowledge on gene regulation in E. coli K-12. Furthermore, this model platform and associated methodologies and criteria can be emulated for gathering knowledge on other microbial organisms.
Triangulation With Large Dynamical Range (1986)

We describe how to expand the dynamical range of active triangulation systems. The method is based on the expansion of depth of focus, in order to achieve a larger measuring range - and on the reduction of coherent noise, in order to achieve better resolution of depth. With a 1024 element linear photodiode array we could achieve about 15000 resolvable depth positions, in preliminary experiments.
Low temperature hot-wire polysilicon waveguides (2013)

We fabricated and measured low loss polysilicon waveguides deposited using Hot-Wire Chemical Vapor Deposition (HWCVD) at 240°C. The optical propagation loss was measured to be 11.9 dB/cm at λ = 1550 nm.
Transformation of Nanodiamonds to Onion-like Carbons by Ambient Electrospray Deposition (2021)

Onion-like carbons (OLCs) are a class of fullerene-like circular nanoallotropes of carbon, typically synthesized from nanodiamond (ND) via thermal annealing, plasma spraying, and laser ablation. These methods require high temperature, high vacuum, or inert gas. Here, we report an ambient electrospray deposition (AESD) process to transform NDs (11 ± 1 nm in size) into OLCs (50 ± 13 nm in size) in water. Transmission electron microscopy (TEM), field emission scanning electron microscopy (FESEM), Raman spectroscopy, and X-ray photoelectron spectroscopy (XPS) were used for the characterization of NDs and OLCs. High-resolution TEM images showed an increased interplanar spacing from ND (0.23 nm) to OLC (0.39 nm). Raman spectra showed a shift in the ND peak from 1336 cm–1 to D-band at 1349 cm–1, and XPS quantitatively estimated an increase in the graphitization ratio (sp2/sp3) from 0.95 to 3.16 after AESD. Comparison of electrospray with sonic spray confirmed that such a transformation required an external voltage as well. AESD was also performed for NDs dispersed in ethanol and acetonitrile, which showed a solvent-dependent transformation.
In situ liquid transmission electron microscopy reveals self-assembly-driven nucleation in radiolytic synthesis of iron oxide nanoparticles in organic media (2022)

We have investigated the early stages of the formation of iron oxide nanoparticles from iron stearate precursors in the presence of sodium stearate in an organic solvent by <i>in situ</i> liquid phase transmission electron microscopy (IL-TEM). Before nucleation, we have evidenced the spontaneous formation of vesicular assemblies made of iron polycation-based precursors sandwiched between stearate layers. Nucleation of iron oxide nanoparticles occurs within the walls of the vesicles, which subsequently collapse upon the consumption of the iron precursors and the growth of the nanoparticles. We then evidenced that fine control of the electron dose, and therefore of the local concentration of reactive iron species in the vicinity of the nuclei, enables controlling crystal growth and selecting the morphology of the resulting iron oxide nanoparticles. Such a direct observation of the nucleation process templated by vesicular assemblies in a hydrophobic organic solvent sheds new light on the formation process of metal oxide nanoparticles and therefore opens ways for the synthesis of inorganic colloidal systems with tunable shape and size.
In vivo detection of γ-glutamyl-transferase up-regulation in glioma using hyperpolarized γ-glutamyl-[1-13C]glycine (2020)

Glutathione (GSH) is often upregulated in cancer, where it serves to mitigate oxidative stress. γ-glutamyl-transferase (GGT) is a key enzyme in GSH homeostasis, and compared to normal brain its expression is elevated in tumors, including in primary glioblastoma. GGT is therefore an attractive imaging target for detection of glioblastoma. The goal of our study was to assess the value of hyperpolarized (HP) γ-glutamyl-[1-<sup>13</sup>C]glycine for non-invasive imaging of glioblastoma. Nude rats bearing orthotopic U87 glioblastoma and healthy controls were investigated. Imaging was performed by injecting HP γ-glutamyl-[1-<sup>13</sup>C]glycine and acquiring dynamic <sup>13</sup>C data on a preclinical 3T MR scanner. The signal-to-noise (SNR) ratios of γ-glutamyl-[1-<sup>13</sup>C]glycine and its product [1-<sup>13</sup>C]glycine were evaluated. Comparison of control and tumor-bearing rats showed no difference in γ-glutamyl-[1-<sup>13</sup>C]glycine SNR, pointing to similar delivery to tumor and normal brain. In contrast, [1-<sup>13</sup>C]glycine SNR was significantly higher in tumor-bearing rats compared to controls, and in tumor regions compared to normal-appearing brain. Importantly, higher [1-<sup>13</sup>C]glycine was associated with higher GGT expression and higher GSH levels in tumor tissue compared to normal brain. Collectively, this study demonstrates, to our knowledge for the first time, the feasibility of using HP γ-glutamyl-[1-<sup>13</sup>C]glycine to monitor GGT expression in the brain and thus to detect glioblastoma.
Bile acid aspiration in people with cystic fibrosis before and after lung transplantation (2015)

Cystic fibrosis (CF) is a genetic condition that is caused by abnormalities in the CF transmembrane conductance regulator ( CFTR ) gene. People with CF experience life-long morbidity and premature mortality, the vast majority of which is associated with lung disease. Bile acids are detectable in the lower airway in advanced CF lung disease and persist after lung transplantation <http://ow.ly/RTvNW> We gratefully acknowledge the help of the patients involved in this study along with all members of the wider cardiothoracic transplantation team at the Freeman Hospital.
Variable geometry turbine (VGT) strategies for improving diesel engine in-vehicle response: a simulation study (2004)

An artificial neural network methodology was applied to variable geometry turbine (VGT) modelling in order to enable representation of the VGT characteristics for any blade (nozzle) position. The VGT model was integrated with the diesel engine system, which was in turn linked to the driveline and the vehicle dynamics module to form a complete, high-fidelity vehicle simulation. Two VGT strategies were developed and analysed. A performance-oriented control strategy was aimed at increasing low speed boost and improving transient response. An EGR-enabling control strategy was aimed at providing the necessary pressure difference between the exhaust and intake manifold for exhaust gas recirculation (EGR) and emission control during normal driving. The effectiveness of the proposed strategies was evaluated for different driving scenarios for a Class VI truck, e.g. hard acceleration from stand-still and Federal Highway and Urban Driving Schedules. It was shown that VGT can virtually eliminate turbocharger lag. Furthermore, VGT is able to provide very accurate control of EGR level during highway driving, and a satisfactory level of EGR control during urban driving.
Climatology of Arctic polar stratospheric clouds as measured by lidar in Ny‐Ålesund, Spitsbergen (79°N, 12°E) (2006)

Polar stratospheric clouds (PSCs) are observed by lidar at the Koldewey Station in Ny‐Ålesund, Spitsbergen (79°N, 12°E). Here we present a PSC climatology for the period 1995/1996–2003/2004, when the Arctic stratosphere was not disturbed by the presence of volcanic aerosols. The study is restricted to only five of these winters, i.e., when the stratospheric temperatures over Spitsbergen were cold enough for PSC formation. The typical altitude range where PSCs are found is 20–24 km, with a downward shifting of the cloud altitude level occurring during the season. Liquid PSCs, the majority of the observations, are usually detected from mid‐January onward; nitric acid trihydrate (NAT) is more frequent in early winter. Furthermore, NAT is generally located at lower altitudes than the liquid clouds. In this data set we rarely observe NAT enhanced PSCs, and ice clouds are entirely absent. In addition to the traditional PSC classification scheme (types Ia/Ib and II) the detected clouds are distinguished according to their vertical thickness, and they are grouped in two categories (thick and thin PSCs), as in a previous study performed on the Antarctic McMurdo PSC data set. The analysis reveals that in Ny‐Ålesund the spatial‐temporal distribution of thick and thin PSCs corresponds to NAT and liquid cloud signatures, respectively. Comparison between the Ny‐Ålesund and the McMurdo PSC climatologies is also reported. In both records, thick and thin PSCs show similar altitude distribution, while discrepancies between the Arctic and Antarctic cases exist for the appearance of NAT and liquid PSCs during the polar winter.
Regulation of T-cell life and death in the periphery (2002)

1. Summary Peripheral T-lymphocytes exert crucial helper and effector functions in adaptive immune defence against infectious pathogens, and contribute to innate responses by the release of inflammatory and/or anti-inflammatory cytokines. These diverse T-cell functions are prone to tight regulation, exerted at the level of the T-cell interaction with the antigen-presenting cell, and its modulation by autocrine and paracrine cytokines present in the T-cell environment. As a consequence, TCR activation of naive T-cells may result in inactivation by either anergy or apoptosis, or alternatively in proliferation and differentiation into helper or cytotoxic effectors. Also T-cell effectors are confronted with life and death decisions. bearing on immune principles such as self-tolerance, restoration of lymphocyte homeostasis and generation of immune memory. The current perception that longevity of naive and memory T-cells is not a cell-intrinsic feature adds up to the listing of life and death decisions that are regulated by extrinsic factors. In this chapter, we discuss recent insights into the regulation of T-cell life and death in the different functional stages a T-cell may go through during its lifespan.
High Dynamic Range Agile Radio over Fiber Transmitter’s Architectures for 5G/NR Applications (2022)

<title>Abstract</title> In this paper, we proposed a novel radio over fiber (RoF) transmitter architecture to achieve high dynamic range (DR) suitable for millimeter wave (mm-wave) applications, supported by simulation and experimental validations. The designed test benches achieved more than-41 dBc adjacent carrier leakage ratio (ACLR) for a fifth generation/new radio (5G/NR) signal of 100 MHz bandwidth, transmitted in the upper frequency range (FR2) at 28 GHz. The key for this achievement is the utilization of the electrical mixing with proper phase shift before optical modulation. The mixing of the local oscillator (LO) and the intermediate frequency (IF) signals in the electrical domain, reduces the unwanted beating between optical bands prior to the photo-detection stage, hence preventing photodetector saturation, which leads to higher optical-to-electrical conversion.
Roughness of the SiC/SiO2 vicinal interface and atomic structure of the transition layers (2014)

The SiC/SiO2 interface is generally considered to be the cause for the reduced electron mobility of SiC power devices. Previous studies have shown a correlation between the mobility and the transition layer width at the SiC/SiO2 interface. The authors investigated this interface with atomic resolution Z-contrast imaging and electron energy-loss spectroscopy, and discovered that this transition region was due to the roughness of the vicinal interface. The roughness of a vicinal interface consisted of atomic steps and facets deviating from the ideal off-axis cut plane. The authors conclude that this roughness is limiting the mobility in the channels of SiC MOSFETs.
Enhancing target detection using a hybrid human-computer system (2009)

Our goal is to develop an assistive technology for image analysts, which helps them to extract information (e.g., detect targets) efficiently. The images are displayed using the rapid serial visual presentation (RSVP) paradigm, in which a large image is broken into numerous smaller chips which are then displayed serially in the center of the monitor at a high rate. Detection performance is affected by several factors, one of which is the target eccentricity. We show how computer vision (CV) can be used to reduce the mean eccentricity in a manner that is expected to improve detection performance, while maintaining overall throughput.