gebhart/patrepeval huggingface dataset:
Identifying and engineering TCR specificity against solid tumor neoantigens (2019)

Abstract Neoantigens (NeoAg) offer attractive therapeutic targets for directing a patient’s immune response to the immunogenic subset of mutations expressed exclusively by their cancer cells. Despite the specificity with which NeoAg enable tumor recognition, the majority of approaches for their identification rely on purely predictive methods such as calculating the ability of mutated peptides to bind to a patient’s set of HLA molecules. These methods have met with limited success in revealing natural targets present on tumor cells. We have developed a novel HLA-agnostic functional approach to NeoAg identification which combines genomic sequencing with bioinformatic analysis to nominate mutations for subsequent functional analysis using patient’s own T cells in an effort to identify natural responses generated under physiologic conditions. Using this, we identified a missense mutation (V205I) in the ribosomal protein RPS2 that is recognized by CD8+ T cells from tumor-infiltrating lymphocytes (TIL) of a metastatic HPV16+ Head and Neck Squamous Cell Carcinoma lesion. We then performed adoptive cellular therapy (ACT) using either unseparated TIL or those enriched for RPS2 V205I-specific CD8+ T cells and found the latter to be superior in controlling outgrowth of tumor of a PDX cell line generated from this lesion in NSG mice. Finally, we used single-cell transcriptomics to isolate the genes encoding the RPS2-specific TCR and show that it recognizes the mutated peptide bound to HLA-B*07:02. These results demonstrate that high-affinity NeoAg-specific T cell responses can be identified in cancer patients, that ACT of these cells can control tumor growth, and that the relevant TCR can be isolated for use in TCR engineering-based immunotherapy.
Formation of C2+ hydrocarbons in methane/oxygen diffusion flames with chlorine, chloromethane, or hydrogen chloride additives (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFormation of C2+ hydrocarbons in methane/oxygen diffusion flames with chlorine, chloromethane, or hydrogen chloride additivesRemi Le Bec, Paul Marie Marquaire, and Guy Marie ComeCite this: Ind. Eng. Chem. Res. 1990, 29, 4, 539–544Publication Date (Print):April 1, 1990Publication History Published online1 May 2002Published inissue 1 April 1990https://pubs.acs.org/doi/10.1021/ie00100a007https://doi.org/10.1021/ie00100a007research-articleACS PublicationsRequest reuse permissionsArticle Views127Altmetric-Citations6LEARN 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
The Visibility of Symbolic Highway Signs Can Be Increased among Drivers of All Ages (1993)

Visibility and comprehension of standard text, standard symbolic, and improved symbolic highway signs were compared among young, middle-aged, and elderly observers. The average distance at which standard symbolic signs could be identified was about two times that of text signs for all three age groups. The visibility distances of the improved symbolic signs, which were designed using an optical blur (i.e., low-pass) approach in order to avoid higher spatial frequencies, exceeded those of both text and standard symbolic signs. Visibility distance was decreased significantly among older drivers on some signs but not others. There were no significant age differences in the comprehension of symbolic signs. Acuity, a good predictor of visibility distance of both text and standard symbolic signs, was only weakly related to the visibility distance of the improved symbolic signs. These findings demonstrate that low-pass symbolic signs have significant advantages in visibility over their test counterparts for all drivers.
Aluminium Chloride‐Catalyzed Intermolecular vs Intramolecular Friedel‐Crafts Reaction of Acrylanilides and 3‐Chloropropanamides (2000)

Abstract 3‐Phenylpropionanilide ( 4a ) is obtained in a yield of 89% from acrylanilide by the treatment with AlCl 3 /benzene, compared with a yield of 39% by the 1,4‐conjugate addition of phenyllithium. The formation of 4a indicated that an intermolecular Friedel‐Crafts reaction occurred, rather than the relatively more facile intramolecular ring cyclization, and provided a more efficient route than a conjugate addition of phenyllithium for the preparation of 3‐phenylpropionanilide and its derivatives. Although the methoxy group is an activator of the nucleophilic substitution, introduction of a methoxy substituent at N ‐phenyl did not increase the competitive capability of the intramolecular cyclization because of AlCl 3 ‐catalyzed demethylation to form the ArOAlCl 2 complex which decreased the availability of the π‐electron in the N ‐phenyl aromatic system.
Backward view synthesis prediction for 3D-HEVC (2013)

View synthesis prediction provides an effective way to reduce inter-view redundancy of multiview video in addition to conventional disparity compensated prediction. Traditional forward warping techniques incur high complexity since an entire picture is typically warped from one viewpoint to another. To reduce this complexity, block-based backward warping is considered as an alternative solution. One difficulty with this approach is that it requires depth information of the current block prior to its encoding. To solve this problem, a novel method is proposed to derive the depth information from neighboring blocks with high accuracy. With the proposed approach, backward warping is enabled using depth information derived from either neighboring spatial (inter-view) compensated blocks or temporal compensated blocks. As a generalization, the proposed backward warping scheme is not only applied at the pixel level, but at the sub-block level as well. Simulation results demonstrate that the proposed scheme achieves an average bitrate savings of 1.2% for coded video vs coded video bitrate, 1.1% for coded video vs total bitrate, and 1.0% for synthesized video vs total bitrate under common test conditions for 3D video coding using HEVC, with maximum gains of greater than 10% for dependent views.
Security Implications of Making Computing Resources Available via Computational Grids (2001)

This report inrvestigates the issues of securing access to computin,g resources in computation. al grids. Grid en,viron,men.ts are built orb top of platforms that corrtrol access to resources within a sin,gle adenin.istrative domairr, at the g.r-an,ular.ityo f a use,r. In wide-area multi-domain. grid en.viron,men.ts, the overhead of mainiainin,g user accounts is prohibitive, a.rad secu7.in,g access to resources via user accountability is impractical. Typically, these issues are han,dled by inlplenlert,ting checks that guaran,tee the safety of applic~ations, so [hat they can rurt. in shared use^ accour1.t~. This work shows that safety checks - lan,guage-based, compile-time, link-time, load-lime - curren.tly implemen.ted in most grid en.virorrmen.ts are either in,adequute or limit allowed grid users and applicatiorrs. Techn.ique.s without such li7nitations are presen.ted. Shadow accoun,ts allow reu.se of user accounts without administrative overheads, and run-time solution~s - run-time 7non.itorirt.y and virtu.tr1 machines - allow arbilrary code to execute while erilforciny a given resource access policy.
Formation, Characterization, and Hot Isostatic Pressing of Cr 2 O 3 ‐Doped ZrO 2 (0,3 mol% Y 2 O 3 ) Prepared by Hydrazine Method (1996)

In the ZrO 2 ‐Cr 2 O 3 system, metastable t ‐ZrO 2 solid solutions containing up to 11 mol% Cr 2 O 3 crystallize at low temperatures from amorphous materials prepared by the hydrazine method. The lattice parameter c decreases linearly from 0.5149 to 0.5077 nm with increased Cr 2 O 3 content, whereas the lattice parameter a is a constant value ( a = 0.5077 nm) regardless of the starting composition. At higher temperatures, transformation (decomposition) of the solid solutions proceeds in the following way: t (ss)→ t (ss) + m + Cr 2 O 3 → m + Cr 2 O 3 . Above 11 mol% Cr 2 O 3 addition, c‐ZrO 2 phases are formed in the presence of Cr 2 O 3 . The t ‐ZrO 2 solid solution powders have been characterized for particle size, shape, and surface area. They consist of very fine particles (15–30 nm) showing thin platelike morphology. Dense ZrO 2 (3Y)‐Cr 2 O 3 composite ceramics (∼99.7% of theoretical) with an average grain size of 0.3 μm have been fabricated by hot isostatic pressing for 2 h at 1400°C and 196 MPa. Their fracture toughness increases with increased Cr 2 O 3 content. The highest K Ic value of 9.5 MPa·;m 1/2 is achieved in the composite ceramics containing 10 mol% Cr 2 O 3 .
Supplementary Figure 2 from Protein Kinase Cι Is Required for Pancreatic Cancer Cell Transformed Growth and Tumorigenesis (2023)

Supplementary Figure 2 from Protein Kinase Cι Is Required for Pancreatic Cancer Cell Transformed Growth and Tumorigenesis
Emerging Nonlinear Optical Fibers: Revised Fundamentals, Fabrication and Access to Extreme Nonlinearity (2009)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> We review the properties of conventional and emerging nonlinear fibers. More specifically, we describe advances in soft glass microstructured fibers, including fabrication, the demonstration of extreme nonlinearity and a generalisation of the underpinning nonlinear theory. </para>
Frequency modulation of the superconducting parallel-plate microwave resonator by laser irradiation (1994)

We have studied the effect of chopped laser irradiation (λL=514 nm) on the resonant frequency (f0≊5.4 GHz) of a superconducting parallel-plate resonator (PPR) consisting of two thin epitaxial YBa2Cu3O7−x films. We demonstrate that laser irradiation shifts the resonant frequency of the PPR with negligible change of quality factor. Photoinduced deviation of f0 strongly depends on the chopping frequency and increases linearly with light intensity. The effect of illumination is attributed to the photoinduced change of the kinetic inductance due to laser heating. This effect may be used to produce phase modulation of the superconducting transmission lines.
Measurement of HbA1c from stored whole blood samples in the Atherosclerosis Risk in Communities study (2010)

Measurements of HbA1c from samples stored for up to 18 years are highly reliable when using state-of-the-art HPLC instruments, but with some bias introduced over time. The HbA1c data now available in the ARIC study should be invaluable for investigations into the clinical utility of HbA1c as a diagnostic test for diabetes.
Re-examining health IT policy: what will it take to derive value from our investment? (2014)

Despite substantial investments in health information technology (HIT), the nation's goals of reducing cost and improving outcomes through HIT remain elusive. This period of transition, with new Office of National Coordinator for HIT leadership, upcoming Meaningful Use Stage III definitions, and increasing congressional oversight, is opportune to consider needed course corrections in HIT strategy. This article describes current problems and recommended changes in HIT policy, including approaches to usability, interoperability, and quality measurement. Recommendations refrain from interim measures, such as electronic health record adoption rates, and instead focus on measurable national value to benefit the economy, to reduce healthcare costs, and to improve clinical efficiency and care quality.
2012 Infectious Diseases Society of America Clinical Practice Guideline for the Diagnosis and Treatment of Diabetic Foot Infectionsa (2013)

Foot infections are a common and serious problem in persons with diabetes. Diabetic foot infections (DFIs) typically begin in a wound, most often a neuropathic ulceration. While all wounds are colonized with microorganisms, the presence of infection is defined by ≥2 classic findings of inflammation or purulence. Infections are then classified into mild (superficial and limited in size and depth), moderate (deeper or more extensive), or severe (accompanied by systemic signs or metabolic perturbations). This classification system, along with a vascular assessment, helps determine which patients should be hospitalized, which may require special imaging procedures or surgical interventions, and which will require amputation. Most DFIs are polymicrobial, with aerobic gram-positive cocci (GPC), and especially staphylococci, the most common causative organisms. Aerobic gram-negative bacilli are frequently copathogens in infections that are chronic or follow antibiotic treatment, and obligate anaerobes may be copathogens in ischemic or necrotic wounds. Wounds without evidence of soft tissue or bone infection do not require antibiotic therapy. For infected wounds, obtain a post-debridement specimen (preferably of tissue) for aerobic and anaerobic culture. Empiric antibiotic therapy can be narrowly targeted at GPC in many acutely infected patients, but those at risk for infection with antibiotic-resistant organisms or with chronic, previously treated, or severe infections usually require broader spectrum regimens. Imaging is helpful in most DFIs; plain radiographs may be sufficient, but magnetic resonance imaging is far more sensitive and specific. Osteomyelitis occurs in many diabetic patients with a foot wound and can be difficult to diagnose (optimally defined by bone culture and histology) and treat (often requiring surgical debridement or resection, and/or prolonged antibiotic therapy). Most DFIs require some surgical intervention, ranging from minor (debridement) to major (resection, amputation). Wounds must also be properly dressed and off-loaded of pressure, and patients need regular follow-up. An ischemic foot may require revascularization, and some nonresponding patients may benefit from selected adjunctive measures. Employing multidisciplinary foot teams improves outcomes. Clinicians and healthcare organizations should attempt to monitor, and thereby improve, their outcomes and processes in caring for DFIs.
Effects of modulators of the renin???angiotensin???aldosterone system on cough (1994)

The incidence of cough related to the type 1 Ang II receptor antagonist losartan is significantly lower than that observed with lisinopril, and similar to that observed with hydrochlorothiazide in patients with a rechallenged ACE inhibitor cough. Type 1 Ang II receptor antagonists represent a potential new treatment for hypertensive patients in whom ACE inhibitors are indicated, but who develop a cough with these agents.
The semantic interpretation of definite noun phrases : uniqueness intuitions, telescope anaphora, and strong and weak readings in donkey sentences (1997)

L'auteur a accord6 une
Torsional barriers in NN′-diacylhydrazines (1967)

G. J. Bishop, B. J. Price and I. O. Sutherland, Chem. Commun. (London), 1967, 672 DOI: 10.1039/C19670000672
Clinical and Physiological Perspectives of β-Glucans: The Past, Present, and Future (2017)

β-Glucans are a group of biologically-active fibers or polysaccharides from natural sources with proven medical significance. β-Glucans are known to have antitumor, anti-inflammatory, anti-obesity, anti-allergic, anti-osteoporotic, and immunomodulating activities. β-Glucans are natural bioactive compounds and can be taken orally, as a food supplement, or as part of a daily diet, and are considered safe to use. The medical significance and efficiency of β-glucans are confirmed in vitro, as well as using animal- and human-based clinical studies. However, systematic study on the clinical and physiological significance of β-glucans is scarce. In this review, we not only discuss the clinical and physiological importance of β-glucans, we also compare their biological activities through the existing in vitro and animal-based in vivo studies. This review provides extensive data on the clinical study of β-glucans.
Use of a decoy peptide to purify p21 activated kinase-1 in cardiac muscle and identification of ceramide-related activation (2008)

The p(21) activated kinase-1 (Pak1) is a serine-threonine protein kinase directly activated by Cdc42 and Rac1. In cardiac myocytes, Pak1 activation leads to dephosphorylation of cTnI and C-protein through upregulation of phosphatase-2A (PP2A). Pak1 activity is directly correlated with its autophosphorylation, which occurs upon binding to the small GTPases and to some small organic molecules as well. In this report, we describe a novel method for rapid purification of endogenous Pak1 from bovine ventricle muscle. The method is simple and easy to carry out. The purified Pak1 demonstrated autophosphorylation in vitro that was enhanced by D-erythro-sphingosine-1, N-acetyl-D-erythro-sphingosine (C(2)-ceramide), and N-hexanoyl-D-erythro-sphingosine (C(6)-ceramide). Dihydro-L-threo-sphingosine (saphingol) also had some effect on Pak1 autophosphorylation. The method we developed provides a useful tool to study Pak1 activity and regulation in the heart. Moreover, our results indicate a potential role of the sphingolipids as unique signaling molecules inducing a direct activation of Pak1 that may modulate different cardiac functions.
Generating multilingual descriptions from linguistically annotated OWL ontologies: the NaturalOWL system (2007)

We introduce Naturalowl, an open-source multilingual natural language generator that produces descriptions of instances and classes, starting from a linguistically annotated ontology. The generator is heavily based on ideas from ilex and m-piro, but it is in many ways simpler and it provides full support for owl dl ontologies with rdf linguistic annotations. Naturalowl is written in Java, and it is supported by m-piro’s authoring tool, as well as an alternative plug-in for the Protégé ontology editor. 1
Stationary flow fields prediction of variable physical domain based on proper orthogonal decomposition and kriging surrogate model (2014)

In this paper a new flow field prediction method which is independent of the governing equations, is developed to predict stationary flow fields of variable physical domain. Predicted flow fields come from linear superposition of selected basis modes generated by proper orthogonal decomposition (POD). Instead of traditional projection methods, kriging surrogate model is used to calculate the superposition coefficients through building approximate function relationships between profile geometry parameters of physical domain and these coefficients. In this context, the problem which troubles the traditional POD-projection method due to viscosity and compressibility has been avoided in the whole process. Moreover, there are no constraints for the inner product form, so two forms of simple ones are applied to improving computational efficiency and cope with variable physical domain problem. An iterative algorithm is developed to determine how many basis modes ranking front should be used in the prediction. Testing results prove the feasibility of this new method for subsonic flow field, but also prove that it is not proper for transonic flow field because of the poor predicted shock waves.
Transposable elements potentiate radiotherapy-induced cellular immune reactions via RIG-I-mediated virus-sensing pathways (2023)

Radiotherapy (RT) plus immunotherapy is a promising modality; however, the therapeutic effects are insufficient, and the molecular mechanism requires clarification to further develop combination therapies. Here, we found that the RNA virus sensor pathway dominantly regulates the cellular immune response in NSCLC and ESCC cell lines. Notably, transposable elements (TEs), especially long terminal repeats (LTRs), functioned as key ligands for the RNA virus sensor RIG-I, and the mTOR-LTR-RIG-I axis induced the cellular immune response and dendritic cell and macrophage infiltration after irradiation. Moreover, RIG-I-dependent immune activation was observed in ESCC patient tissue. scRNA sequencing and spatial transcriptome analysis revealed that radiotherapy induced the expression of LTRs, and the RNA virus sensor pathway in immune and cancer cells; this pathway was also found to mediate tumour conversion to an immunological hot state. Here, we report the upstream and ligand of the RNA virus sensor pathway functions in irradiated cancer tissues.
Dysadipocytokinemia in Werner Syndrome and Its Recovery by Treatment With Pioglitazone (2004)

Werner syndrome (WS) (Mendelian Inheritance in Man no. 277700) is an autosomal recessive disorder known for progeroid phenotypes including graying and loss of hair, juvenile cataracts, insulin-resistant diabetes, skin atrophy, premature atherosclerosis, and cancer (1). Mutations in WRN , a RECQ family DNA/RNA helicase gene, have been identified to cause this disease. The mechanism for insulin resistance in WS remains to be elucidated.

Adipocytes secrete a number of hormones (or adipocytokines), such as tumor necrosis factor-α (TNF-α), leptin, adiponectin, and resistin, thereby regulating insulin sensitivity (2). WS patients typically show the lipoatrophic skinny extremities with an obese trunk (1). The accumulated intra-abdominal visceral fat (3) suggests an altered production of adipocytokines.

To investigate the role of adipocytokines in the pathophysiology of WS, we …
EVALUACION DEL EFECTO HIPOLIPEMIANTE DEL ACEITE DE SEMILLA DE NONI EN RATONES NORMOLIPIDICOS (2013)

EVALUACION DEL EFECTO HIPOLIPEMIANTE DEL ACEITE DE SEMILLA DE NONI EN RATONES NORMOLIPIDICOS
A DSM design flow (1998)

This paper presents an integrated design flowwhich combines floorplanning, technology mapping, andplacement using a dynamic programming algorithm. Theproposed design flow consists of five steps: maximum treesub-structure formation, levelized cluster tree construction,minimum area implementation using 2-D shape functions,critical path identification, and repeated application ofsimultaneous floorplanning, technology mapping and gateplacement along the timing critical paths. Experimentalresults obtained from an extensive set of benchmarksdemonstrate the effectiveness of the proposed flow.
Time‐Resolved Fluorometry Based Sandwich Hybridisation Assay for HLA‐DQA1 Typing (1998)

A microtitration plate based time-resolved fluorescence (TRF) hybridisation assay was developed for HLA typing utilising biotinylated sequence-specific catching probes and europium (Eu) labelled gene locus-specific detection probe to allow time-resolved fluorometer reading of the reaction. In an application for HLA-DQA typing a 228 base pair long region of the polymorphic exon 2 of DQA1 gene was amplified and the denatured PCR product distributed into streptavidin-coated microtitration wells together with the detection probe and one of the catching probes. After incubation and washes, the enhancement solution was added and specific hybridisation signal detected by measuring the emitted light. A series of 100 isolated genomic DNA samples were studied using biotinylated probes specific for DQA1*01, *0101/0104, *0103/0201/0601, *0201, *03, *0401/0601, *05 and *0502 alleles with results demonstrating the capacity of the test to detect aimed alleles. A series of whole blood spot samples were also studied and the results confirmed the applicability of this modification of the test.