gebhart/patrepeval huggingface dataset:
Supplemental Figure 1 from Detection of an Immunogenic HERV-E Envelope with Selective Expression in Clear Cell Kidney Cancer (2023)

&lt;p&gt;Example of gating strategy to identify peptide and tumor reactive T cells stimulated from healthy donors: analysis of TM1 peptide stimulated CTLs from donor 4 is shown.&lt;/p&gt;
Identification and Characterization of Novel Rat Polyomavirus 2 in a Colony of X-SCID Rats by P-PIT assay (2016)

Polyomaviruses (PyVs) are known to infect a wide range of vertebrates and invertebrates and are associated with a broad spectrum of diseases, including cancers, particularly in immune-suppressed hosts. A novel polyomavirus, designated rat polyomavirus 2 (RatPyV2), was identified from a breeding colony of rats having X-linked severe combined immunodeficiency. Using a human panpolyomavirus immunohistochemistry test (P-PIT), RatPyV2 was initially detected in the parotid salivary gland of a colony member. Rolling circle amplification using DNA from harderian and parotid glands identified a novel 5.1-kb polyomavirus genome closely related to human Washington University (WU) and Karolinska Institute (KI) and vole polyomaviruses but notably divergent from <i>Rattus norvegicus</i> PyV1 (RnorPyV1; also designated RatPyV1). Further screening showed RatPyV2 inclusion body infection in the lung epithelium and variably in other respiratory, reproductive, and glandular tissues of 12/12 (100%) rats. <b>IMPORTANCE</b> Although P-PIT was developed to detect diseases associated with known human polyomaviruses, the identification of a new polyomavirus in rats suggests that it may have utility as a broad-based screen for new, as well as known polyomaviruses. Our findings suggest that RatPyV2 may be a commensal infection of laboratory rats that can lead to disseminated disease in T cell immune-deficient rats. Infection of the X-SCID rats with RatPyV2 and <i>Pneumocystis carinii</i> is a potential model for coinfection pathogenesis and treatment options during transplant preclinical studies.
Partialsynthese von Tetrahydroverrucarin J (1978)

Partial Synthesis of Tetrahydroverrucarin J Tetrahydroverrucarin J (18) , a macrocyclic triester, has been synthesized from the sesquiterpene alcohol verrucarol (3) .
Investigations on pre-oxidation nitrogen implantation for the improvement of channel mobility in 4H-SiC MOSFETs (2009)

In this context, a new process in which preoxidation N implants have been used in conjunction with NO post-oxidation annealing has been directly compared to the 'NO only' case. The additional pre-oxidation N implants leads to an impressive improvement of the mobility but also decreases the threshold voltage. Interestingly, the NO+N process is significantly superior with respect to reduced border trapping, consistent with previous work on NO nitride oxides.
Preparation of Cyan Dyes from 6-Diethylaminobenzo[b]furan-2-carboxaldehyde (2010)

Abstract 6-Diethylaminobenzo[b]furan-2-carboxaldehyde was synthesized in four steps and 48% overall yield starting from 4-diethylaminosalicylaldehyde. Five cyan dyes were made from this aldehyde using malononitrile dimer and 2-dicyanomethylene-3-cyano-4,5,5-trimethyl-2,5-dihydrofuran. The crystal structures of two dyes are included. Keywords: Benzofurandyesmalononitrile dimerpolyene ACKNOWLEDGMENTS The authors thank several colleagues from Naval Air Warfare Center: Dr. Andrew P. Chafin for molecular modeling of structures related to dyes 3 and 6; Brad Douglas for preparing the piperidinium acetate; Dr. Richard A. Hollins for preparing the TCF acceptor; Dr. Geoffrey A. Lindsay for advice and encouragement throughout the course of this work; Ann M. Moorehead and Linda L. Robinett of the Technical Library for obtaining Refs. 1 and 25; and Dr. Zachary A. Sechrist for assistance with UV/vis spectroscopy. Notes This article is not subject to U.S. copyright laws.
Elucidating the mechanism of photochemical CO2 reduction to CO using a cyanide-bridged di-manganese complex (2022)

The complex, [{[Mn(bpy)(CO)<sub>3</sub>]<sub>2</sub>}(μ-CN)]<sup>+</sup> (Mn2CN+), has previously been shown to photochemically reduce CO<sub>2</sub> to CO. The detailed mechanism behind its reactivity was not elucidated. Herein, the photoevolution of this reaction is studied in acetonitrile (MeCN) using IR and UV-vis spectroscopy. Samples were excited into the Mn<sup>I</sup> → π* bpy metal-to-ligand charge transfer (MLCT) absorption band triggering CO loss, and rapid MeCN solvent ligation at the open coordination site. It is concluded that this process occurs selectively at the Mn axial ligation site that is <i>trans</i> to the C-end of the bridging cyanide. Upon further photolysis, the metal-metal bonded dimeric species, [(CO)<sub>3</sub>(bpy)Mn-Mn(bpy)(CO)<sub>3</sub>] (Mn-Mn) is observed to form under anaerobic conditions. The presence of this dimeric species coincides with the observation of CO production. When oxygen is present, CO<sub>2</sub> photoreduction does not occur, which is attributed to the inability of Mn2CN+ to convert to the metal-metal bonded dimer. Photolysis experiments, where the Mn-Mn dimer is formed photochemically under argon first and then exposed to CO<sub>2</sub>, reveal that it is the radical species, [Mn(bpy)(CO)<sub>3</sub><sup>˙</sup>] (<b>Mn˙</b>), that interacts with the CO<sub>2</sub>. Since the presence of Mn-Mn and light is required for CO production, [Mn(bpy)(CO)<sub>3</sub>˙] is proposed to be a photochemical reagent for the transformation of CO<sub>2</sub> to CO.
Carboxamides as Modulators of Sodium Channels (2020)

ADVERTISEMENT RETURN TO ISSUEPREVPatent HighlightNEXTCarboxamides as Modulators of Sodium ChannelsBenjamin E. Blass*Benjamin E. BlassTemple University School of Pharmacy, Moulder Center for Drug Discovery Research, Department of Pharmaceutical Sciences, Philadelphia, Pennsylvania 19140, United States*Email: [email protected]More by Benjamin E. Blasshttp://orcid.org/0000-0003-2449-4503Cite this: ACS Med. Chem. Lett. 2020, 11, 12, 2364–2365Publication Date (Web):December 1, 2020Publication History Received9 November 2020Published online1 December 2020Published inissue 10 December 2020https://pubs.acs.org/doi/10.1021/acsmedchemlett.0c00590https://doi.org/10.1021/acsmedchemlett.0c00590editorialACS PublicationsCopyright © 2020 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views999Altmetric-Citations-LEARN 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 PDF (872 KB) Get e-AlertscloseSUBJECTS:Alkyls,Diseases and disorders,Neurophysiology,Phenyls,Substituents Get e-Alerts
Terahertz time-domain derivative spectrometer using a large-aperture piezoelectric micromachined device (2021)

The engineering of optomechanical systems has exploded over the past decades, with many geometries and applications arising from the coupling of light with mechanical motion. The modulation of electromagnetic radiation in the terahertz (THz) frequency range through optomechanical systems is no exception to this research effort. However, some fundamental modulation capabilities for THz communications and/or high-speed data processing applications are yet to be established. Here, we demonstrate a THz time-domain derivative spectrometer based on a piezoelectric micromachined (PM) device. Insertion of the PM device into the THz beam path provides reference modulation for the lock-in detection unit, which in turn provides access to the nth-order derivative information of the incoming THz signal. Strikingly, the integration of the recorded derived signal leads to a recovered reference signal with an equivalent or even better signal-to-noise ratio, opening the door to a new type of highly sensitive THz measurements in the time domain.
Protection against tetanus toxin using a plant‐based vaccine (2005)

Plant-expressed vaccines may provide a unique opportunity for generating anti-pathogen immunity, especially in countries where cold storage is lacking. In the following study, we show that soluble protein from tobacco leaves expressing fragment C of tetanus toxin protected mice against a lethal tetanus toxin challenge. More importantly, we show that a single intranasal (i.n.) vaccination was as efficient as oral delivery, inducing high levels of activated CD4(+) T cells and anti-toxin antibody. Unlike the oral route, i.n. delivery did not require the presence of adjuvant (cholera toxin). Indeed, addition of cholera toxin induced bystander immune responses to plant proteins as well. This is the first study documenting protective immunity by a single i.n. dose of plant vaccine. Plant-based vaccines are promising because they are more heat stable, are easy to produce, cheap and do not require needles.
Composite Structure of Silicon Carbide Fiber Reinforced Metals by Squeeze Casting (1985)

The present paper deals with microstructures and segregations of silicon carbide fiber reinforced copper-added aluminum and aluminum -added magnesium alloy composites, fabricated by squeeze casting, and refers to the effect of the microstructure on the tensile strength of composites. The results obtained are as follows: The results obtained are as follows: 1) Microscopic examination showed a solute element rich layer with semicircle surrounding was locally formed on fibers in the composites, whichever matrix alloy was used. The layer was identified as a eutectic constitution by EPMA decreased in thickness and area fraction, and for the case of 1% copper-aluminum matrix, no copper-rich layer was detected. 2) The appearance of the layer decreases the tensile strength of composites because of its brittleness.
The Nonmevalonate Pathway of Isoprenoid Biosynthesis in Mycobacterium tuberculosis Is Essential and Transcriptionally Regulated by Dxs (2010)

Mycobacterium tuberculosis synthesizes isoprenoids via the nonmevalonate or DOXP pathway. Previous work demonstrated that three enzymes in the pathway (Dxr, IspD, and IspF) are all required for growth in vitro. We demonstrate the essentiality of the key genes dxs1 and gcpE, confirming that the pathway is of central importance and that the second homolog of the synthase (dxs2) cannot compensate for the loss of dxs1. We looked at the effect of overexpression of Dxr, Dxs1, Dxs2, and GcpE on viability and on growth in M. tuberculosis. Overexpression of dxs1 or dxs2 was inhibitory to growth, whereas overexpression of dxr or gcpE was not. Toxicity is likely to be, at least partially, due to depletion of pyruvate from the cells. Overexpression of dxs1 or gcpE resulted in increased flux through the pathway, as measured by accumulation of the metabolite 4-hydroxy-3-methyl-but-2-enyl pyrophosphate. We identified the functional translational start site and promoter region for dxr and demonstrated that it is expressed as part of a polycistronic mRNA with gcpE and two other genes. Increased expression of this operon was seen in cells overexpressing Dxs1, indicating that transcriptional control is effected by the first enzyme of the pathway via an unknown regulator.
Unnecessary contraindications for mobile-bearing unicompartmental knee replacement (2011)

The contraindications for unicompartmental knee replacement (UKR) remain controversial. The views of many surgeons are based on Kozinn and Scott's 1989 publication which stated that patients who weighed more than 82 kg, were younger than 60 years, undertook heavy labour, had exposed bone in the patellofemoral joint or chondrocalcinosis, were not ideal candidates for UKR. Our aim was to determine whether these potential contraindications should apply to patients with a mobile-bearing UKR. In order to do this the outcome of patients with these potential contraindications was compared with that of patients without the contraindications in a prospective series of 1000 UKRs. The outcome was assessed using the Oxford knee score, the American Knee Society score, the Tegner activity score, revision rate and survival. The clinical outcome of patients with each of the potential contraindications was similar to or better than those without each contraindication. Overall, 678 UKRs (68%) were performed in patients who had at least one potential contraindication and only 322 (32%) in patients deemed to be ideal. The survival at ten years was 97.0% (95% confidence interval 93.4 to 100.0) for those with potential contraindications and 93.6% (95% confidence interval 87.2 to 100.0) in the ideal patients. We conclude that the thresholds proposed by Kozinn and Scott using weight, age, activity, the state of the patellofemoral joint and chondrocalcinosis should not be considered to be contraindications for the use of the Oxford UKR.
ChemInform Abstract: Diastereoselective Epoxidation of Monofluorinated Allyl Alcohols. (1990)

Abstract Independent of the epoxidation method the title reaction of monofluorinated allyl alcohols yields isomers of type (II) as major products.
Facile Synthesis of Imidazo[1,5-a]pyrazin-8(7H)-ones from Mesoionic 1,3-Oxazolium-5-olates via a Multistep One-Pot Transformation (2016)

by the reaction with TosMIC is described.The structure of the product was determined by single-crystal X-ray analysis.The imidazo[1,5-a]pyrazine A has a five-membered imidazole and a six-membered pyrazine ring with a
Femtosecond laser-induced refractive index modification in multicomponent glasses (2005)

We present a comprehensive study on femtosecond laser-induced refractive index modification in a wide variety of multicomponent glasses grouped as borosilicate, aluminum–silicate, and heavy-metal oxide glasses along with lanthanum–borate and sodium–phosphate glasses. By using high-spatial resolution refractive index profiling techniques, we demonstrate that under a wide range of writing conditions the refractive index modification in multicomponent glasses can be positive, negative, or nonuniform, and exhibits a strong dependence on the glass composition. With the exception of some aluminum–silicate glasses all other glasses exhibited a negative/nonuniform index change. We also demonstrate direct writing of waveguides in photosensitive Foturan® glass with a femtosecond laser without initiating crystallization by thermal treatment. Upon ceramization of lithium–aluminum–silicate glasses such as Foturan®, Zerodur®, and Robax® we observe switching of laser-induced refractive index change from being positive to negative. The measured transmission losses in the waveguides at 1550nm agree with the index profile measurements in alkali-free aluminum–silicate glasses.
Three-, Two-, One-, and Six-Dimensional Color Constancy (2018)

CONTENTS 3.1 Introduction..........................................................................................................................55 3.2 Three-Dimensional Color Constancy ...............................................................................59 3.3 Two-Dimensional Chromaticity Constancy.....................................................................63 3.4 One-Dimensional Scalar Constancy..................................................................................65 3.5 Six-Dimensional Constancy ...............................................................................................67
Ringer: web automation by demonstration (2016)

With increasing amounts of data available on the web and a diverse range of users interested in programmatically accessing that data, web automation must become easier. Automation helps users complete many tedious interactions, such as scraping data, completing forms, or transferring data between websites. However, writing web automation scripts typically requires an expert programmer because the writer must be able to reverse engineer the target webpage. We have built a record and replay tool, Ringer, that makes web automation accessible to non-coders. Ringer takes a user demonstration as input and creates a script that interacts with the page as a user would. This approach makes Ringer scripts more robust to webpage changes because user-facing interfaces remain relatively stable compared to the underlying webpage implementations. We evaluated our approach on benchmarks recorded on real webpages and found that it replayed 4x more benchmarks than a state-of-the-art replay tool.
Auroral plasma transport processes in the presence of kV potential structures (1994)

We have simulated plasma transport processes in the presence of a quasi‐ two‐dimensional current filament, that generated kV potential structure in the auroral region. The simulation consists of a set of one‐dimensional flux tube simulations with different imposed time‐dependent, field‐aligned currents. The model uses the 16 moment system of equations and simultaneously solves coupled continuity and momentum equations and equations describing the transport along the magnetic field lines of parallel and perpendicular thermal energy and heat flows for each species. The lower end of the simulation is at an altitude of 800 km, in the collisional topside ionosphere, while the upper end is at 10 R E in the magnetosphere. The plasma consists of hot electrons and protons of magnetospheric origin and low‐energy electrons, protons, and oxygen ions of ionospheric origin. The dynamical interaction of the individual current filaments with ionospheric and magnetospheric plasma generates a potential structure in the horizontal direction and kilovolt field‐aligned potential drops along the field lines. The side‐by‐side display exhibits the evolution of the implied potential structure in the horizontal direction. In the presence of this potential structure and parallel electric field the ionospheric plasma density is depleted and velocity is reduced, while density enhancement and increased velocity is observed in magnetospheric plasma. The ionospheric and magnetospheric electron temperatures increase below 2 R E due to magnetic mirror force on converging geomagnetic field lines. The primary cross‐field motion produced by the horizontal E field ( E × B drift) is perpendicular to both of the significant spatial directions and is thus ignorable in this geometry. The effects of other cross‐field drift processes are discussed. The simulation thus provides insight into the dynamical evolution of two‐dimensional potential structures driven by an imposed finite width, field‐aligned current profile.
Ampicillin-Resistant Listeria monocytogenes Meningitis in a Previously Healthy 14-Year-Old Athlete (1984)

We report a case of ampicillinresistantListeria monocytogenesmeningitis in a previously healthy 14-year-old athlete.Listeria monocytogenesusually occurs as a purulent disease of the CNS. Seldom is any obvious source of infection discovered, but susceptibility to the organism is noted in the very young or old, the immunocompromised, and those afflicted with chronic disease.1Varying antibiotic susceptibility ofL monocytogenesis commonly reported, but in some cases may be due to different laboratory techniques.2Ampicillin has been suggested as the drug of choice for treatment ofL monocytogenesinfection.1 REPORT OF A CASE A 14-year-old boy who was a high school wrestler with no health problems was admitted to another hospital on March 1, 1983, after a four-day history of progressively increasing headache, fever, nausea, and vomiting. Nuchal rigidity was present. Results of a lumbar puncture disclosed the following values: RBCs, 959/cu mm polymorphonuclear cells, 961/cu
La famille des protéine phosphatases PP2A (2011)

Protein phosphatase 2A (PP2A) is a large family of holoenzymes that comprises 1% of total cellular proteins and accounts for the majority of Ser/Thr phosphatase activity in eukaryotic cells. PP2A proteins are made of a core dimer, composed of a catalytic (C) subunit and a structural (A) subunit, in association with a third variable -regulatory (B) subunit. Although initially considered as a constitutive housekeeping enzyme, PP2A is indeed highly regulated by post-translational modifications of its catalytic subunit or by the identity of a regulatory type B subunit, which determines substrate specificity, subcellular localization and enzymatic activity of a defined holoenzyme. During the two last decades, multiple studies of structural and functional regulation of PP2A holoenzymes by viral proteins led to the identification of critical pathways for both viral biology and tumorigenesis. To date a dozen of different viruses (ADN/ARN or retrovirus) have been identified that encode viral proteins associated to PP2A. In this review, we analyze a biological strategy, used by various viruses based on the targeting of PP2A enzymes by viral proteins, in order to specifically deregulate cellular pathways of their hosts. The impact of such PP2A targeting for biomedical search, and in further therapeutic developments against cancer, will also be discussed.
Combined Proteomic and Transcriptomic Interrogation of the Venom Gland of Conus geographus Uncovers Novel Components and Functional Compartmentalization (2014)

Cone snails are highly successful marine predators that use complex venoms to capture prey. At any given time, hundreds of toxins (conotoxins) are synthesized in the secretory epithelial cells of the venom gland, a long and convoluted organ that can measure 4 times the length of the snail's body. In recent years a number of studies have begun to unveil the transcriptomic, proteomic and peptidomic complexity of the venom and venom glands of a number of cone snail species. By using a combination of DIGE, bottom-up proteomics and next-generation transcriptome sequencing the present study identifies proteins involved in envenomation and conotoxin maturation, significantly extending the repertoire of known (poly)peptides expressed in the venom gland of these remarkable animals. We interrogate the molecular and proteomic composition of different sections of the venom glands of 3 specimens of the fish hunter Conus geographus and demonstrate regional variations in gene expression and protein abundance. DIGE analysis identified 1204 gel spots of which 157 showed significant regional differences in abundance as determined by biological variation analysis. Proteomic interrogation identified 342 unique proteins including those that exhibited greatest fold change. The majority of these proteins also exhibited significant changes in their mRNA expression levels validating the reliability of the experimental approach. Transcriptome sequencing further revealed a yet unknown genetic diversity of several venom gland components. Interestingly, abundant proteins that potentially form part of the injected venom mixture, such as echotoxins, phospholipase A2 and con-ikots-ikots, classified into distinct expression clusters with expression peaking in different parts of the gland. Our findings significantly enhance the known repertoire of venom gland polypeptides and provide molecular and biochemical evidence for the compartmentalization of this organ into distinct functional entities.