gebhart/patrepeval huggingface dataset:
Abstract B02: Distinct CD8+ T-cell recognition profiles driven by conformational plasticity of recurrent neuroblastoma neoepitopes (2018)

Abstract The identification of tumor neoantigens driving T-cell responses for immunotherapy poses a significant bottleneck in the development of approaches for precision cancer therapeutics. Here, we employ a bioinformatics method, Prediction Of T Cell Epitopes for Cancer Therapy (ProTECT), using sequencing data from neuroblastoma patients to identify a recurrent Anaplastic Lymphoma Kinase mutation (ALK R1275Q) that leads to two high-affinity neoepitopes when expressed in complex with common HLA alleles. Analysis of the x-ray structures of nonamer and decamer peptides bound to HLA-B*15:01 reveals that the neoepitopes adopt distinct conformations that confer measurable differences in stability in vitro, while the self-antigen is excluded from binding due to steric hindrance. MHC tetramer staining of peripheral blood mononuclear cells from HLA-matched donors shows that the two neoepitopes elicit distinct CD8+ T-cell recognition profiles. To expand the range of patients who could mount a T-cell response to our ALK neoepitopes, we additionally characterize HLA binding repertoire using Rosetta comparative modeling simulations. Subsequent determination of the x-ray structure of decamer-bound HLA-A*01:01 further validates the Rosetta predictions. This work provides a novel approach towards robust, high-throughput identification and detailed characterization of highly stable neoantigen/HLA targets with desired T-cell recognition features for cancer immunotherapy. Citation Format: Sofie R. Salama, Jugmohit S. Toor, Arjun A. Rao, Andrew C. McShan, Mark Yarmarkovich, Sarvind Tripathi, Santrupti Nerli, Ada A. Madejska, Son Nguyen, Karissa Yamaguchi, John M. Maris, David Haussler, Nikolaos G. Sgourakis. Distinct CD8+ T-cell recognition profiles driven by conformational plasticity of recurrent neuroblastoma neoepitopes [abstract]. In: Proceedings of the AACR Special Conference: Pediatric Cancer Research: From Basic Science to the Clinic; 2017 Dec 3-6; Atlanta, Georgia. Philadelphia (PA): AACR; Cancer Res 2018;78(19 Suppl):Abstract nr B02.
Supplementary Table S1 from Targeting CREB Pathway Suppresses Small Cell Lung Cancer (2023)

&lt;p&gt;Supplementary Table S1. Status of CREB and NF-κB pathway activation in human lung cancers.&lt;/p&gt;
Tandem [4+2]/[3+2] Cycloadditions of Nitroalkenes (1996)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTandem [4+2]/[3+2] Cycloadditions of NitroalkenesScott E. Denmark and Atli ThorarensenView Author Information Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801 Cite this: Chem. Rev. 1996, 96, 1, 137–166Publication Date (Web):February 1, 1996Publication History Received5 October 1995Revised8 November 1995Published online1 February 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/cr940277fhttps://doi.org/10.1021/cr940277fresearch-articleACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views5822Altmetric-Citations625LEARN 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 SUBJECTS:Addition reactions,Cyclization,Ethers,Molecular structure,Vinyl Get e-Alerts
Supplementary Figure 2 from Sef Downregulation by Ras Causes MEK1/2 to Become Aberrantly Nuclear Localized Leading to Polyploidy and Neoplastic Transformation (2023)

&lt;p&gt;PDF file - 3.3MB&lt;/p&gt;
Large-scale simulation of the human cranial arterial tree: utility in hydrocephalus (2009)

Background Recent work in hydrocephalus modelling has drawn attention to the potential role of disruption of a pulsation absorber mechanism in the intracranial compartment. Therefore, characterization of cerebral hemodynamics is essential for understanding complex intracranial dynamics under normal and diseased conditions, diagnosing and treating patients suffering from hydrocephalus, and designing medical devices. To this end, we have developed a procedure for generating physiologically accurate models of the cerebral hemodynamics by coupling clinical data and the multiscale modelling approach.
A phase I dose escalation study of oxaliplatin plus oral S-1 and pelvic radiation in patients with locally advanced rectal cancer (SHOGUN trial) (2015)

This trial was registered with Clinicaltrials.gov (identifier: NCT01227239 ).
De Novo Synthesis of Sugar‐Aza‐Crown Ethers via a Domino Staudinger Aza‐Wittig Reaction. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Monique Dondin-Payre, Exercice du pouvoir et continuité gentilice. Les Acilii Glabriones (1995)

Le Bohec Yann. Monique Dondin-Payre, Exercice du pouvoir et continuite gentilice. Les Acilii Glabriones. In: L'antiquite classique, Tome 64, 1995. pp. 479-480.
Protein-Bacteriophage Conjugates: Application in Detection of Antibodies and Antigens (1969)

Covalent attachment of proteins to bacteriophage yielded modified phage preparations with which it is possible to detect antibodies to proteins at concentrations as low as 0.5 to 2.0 nanograms per milliliter. Similarly, antibodies may be linked covalently to phage, and the resulting antibody-phage conjugate is useful in detecting proteins. An alternative method for quantitative determination of proteins is suggested, in which the inactivation of protein-phage by antibodies to protein is inhibited by the protein tested. With rabbit immunoglobulin G as the protein, as little as 0.3 nanogram per milliliter could he determind.
Demo: AIML-as-a-Service for SLA management of a Digital Twin Virtual Network Service (2021)

This demonstration presents an AI/ML platform that is offered as a service (AIMLaaS) and integrated in the management and orchestration (MANO) workflow defined in the project 5Growth following the recommendations of various standardization organizations. In such a system, SLA management decisions (scaling, in this demo) are taken at runtime by AI/ML models that are requested and downloaded by the MANO stack from the AI/ML platform at instantiation time, according to the service definition. Relevant metrics to be injected into the model are also automatically configured so that they are collected, ingested, and consumed along the deployed data engineering pipeline. The use case to which it is applied is a digital twin service, whose control and motion planning function has stringent latency constraints (directly linked to its CPU consumption), eventually determining the need for scaling out/in to fulfill the SLA.
A new marking scheme to defend against distributed denial of service attacks (2005)

In this paper, we propose a new mechanism to defend against distributed denial of service (DDoS) attacks with path information rather than IP address information. Instead of the complete binary tree model, our proposal is based on the four color theorem. The salient feature of the theorem is that it allows color reuse so that even if some portions of the map have more than 4 neighbors, 4 colors are still sufficient to mark all their borders. This idea of reuse is very important because some routers have many interfaces and the length of the ID field in the header of an IP packet, where the marking information is embedded, is very limited. Furthermore, our marking scheme takes the Internet hierarchy into account, and greatly relaxes the limitation on the number of interfaces of routers, thus making the scheme more practical. Simulation results have validated our design.
Heat Exchanger Design for Ocean Thermal Difference Power Plants (1975)

This paper discusses variations in heat exchanger design and configuration for a class of ocean thermal power plants. Details of the heat exchanger models are summarized and analytical results for component and cycle variations are presented. A heat exchanger optimization program is discussed in detail and preliminary results for this study are given.
Analysis of sprayed Carbon nanotube films on rigid and flexible substrates (2014)

We report on the morphological, electrical and optical characteristics of Carbon nanotube (CNT) films on different transparent substrates, obtained using spray deposition. The effect of different substrate materials on the characteristics of spayed CNT films with varying thickness is investigated. While film morphology is shown to depend on the underlying surface characteristics, no significant changes in work function are observed. These results are compared to films deposited onto flexile substrates. Further, time-resolved THz spectroscopy reveals picosecond transient photoconductivity dynamics in sprayed CNT films on flexible PET substrates.
[Preliminary comparison research of thoracoscopy and thoracotomy lobectomy for clinical N0 and post-operatively pathological N2 non-small cell lung cancer]. (2011)

With respect to the safety,thoroughness and recent effect, VATS is not inferior to open thoracotomy in the treatment of cN0-pN2 non-small cell lung cancer.
ChemInform Abstract: Novel Aerobic Oxidation of Primary Sulfones to Carboxylic Acids. (2011)

Abstract With commercially available 13 C‐labeled methyl phenyl sulfone, the preparation of useful labeled carboxylic acids is possible.
Selection of the fall armyworm Spodoptera frugiperda (Smith) (Lepidoptera: Noctuidae) for survival on Cry 1A (b) Bt toxin. (2010)

Plantas transgênicas que expressam toxinas da bactéria Bacillus thuringiensis (Bt) representam um importante avanço para o controle de lepidópteros-pragas de milho. Híbridos de milho Bt expressando a toxina Cry1A(b) têm mostrado significativo nível de resistência à lagarta-do-cartucho (LCM), Spodoptera frugiperda (Smith) (Lepidoptera: Noctuidae), embora larvas dessa espécie tenham sido observadas em campo e em laboratório sobrevivendo nesses híbridos. Resistência de S. frugiperda também tem sido registrada para diferentes inseticidas. Em bioensaios, seleção de insetos sobreviventes mostrou um aumento do nível de tolerância à toxina do Bt Cry1A(b) em populações da lagarta-do-cartucho, após quatro gerações, indicando que essa tolerância é herdada. Palavras-chave: Insecta, resistência, plantas transgênicas.
Antibody‐Secreting Cell Precursor Frequencies among the Sheep‐Erythrocyte‐Binding Cells after Immunization (1983)

Controversy concerning the immunologic role of antigen-binding cells (ABC) has prompted us to attempt to quantitate the proportion of stimulable ABC, in immunized animals, which are precursors for cells producing antibody specific for the antigen bound. Using a lipopolysaccharide (LPS)-driven limiting dilution analysis system, the precursor frequency (PF) of cells secreting IgM and IgG and sheep erythrocyte (SRBC)-specific IgM and IgG was established for highly purified SRBC antigen-binding cell (SRBC-ABC) and unfractionated populations taken from CBA/J mouse spleens on days 5, 12 and 180 of the in vivo primary immune response to SRBC. At all these times, almost all SRBC-ABC spontaneously secreting immunoglobulin (Ig) secreted SRBC-specific Ig, and almost all precursors of Ig-secreting cells in the ABC populations were precursors of cells secreting specific anti-SRBC antibody. In SRBC-ABC populations, the PF for total and SRBC-specific Ig secretion was seen to decrease on days 5 and 12 after immunization and to increase to 3.5 to 7 times nonimmune levels 180 days after immunization. The absolute number of precursors, within the SRBC-ABC population, for the secretion of SRBC-specific Ig decreased on day 12 after immunization. In the unfractionated population, the PF for SRBC-specific Ig secretion temporarily increased after immunization, reaching peak levels 5 days (IgM) and 12 days (IgG) after immunization. These two changes may be related, representing the progress of stimulated cells out of the ABC pool as they lose receptors en route to full maturation. The small clone sizes on days 5 and 12 indicate that ABC divide less in response to LPS when already engaged in a response to antigen. In contrast, the PF for total IgM and IgG secretion in the unfractionated population was not greatly affected by immunization.
Assessing Biomarkers of Breast Cancer Risk in Underserved Women in a Midwestern County (2021)

On the basis of this small pilot study, vitamin D insufficiency is common in this study population. Owing to the small sample size, an association between vitamin D insufficiency and breast density was not clear. Additional unexpected findings included substantial barriers in initial access to care and longitudinal follow-up in this population. Further study of these issues is needed.
High density lipoproteins improve insulin sensitivity in high-fat diet-fed mice by suppressing hepatic inflammation (2013)

Obesity-induced liver inflammation can drive insulin resistance. HDL has anti-inflammatory properties, so we hypothesized that low levels of HDL would perpetuate inflammatory responses in the liver and that HDL treatment would suppress liver inflammation and insulin resistance. The aim of this study was to investigate the effects of lipid-free apoAI on hepatic inflammation and insulin resistance in mice. We also investigated apoAI as a component of reconstituted HDLs (rHDLs) in hepatocytes to confirm results we observed in vivo. To test our hypothesis, C57BL/6 mice were fed a high-fat diet (HFD) for 16 weeks and administered either saline or lipid-free apoAI. Injections of lipid-free apoAI twice a week for 2 or 4 weeks with lipid-free apoAI resulted in: i) improved insulin sensitivity associated with decreased systemic and hepatic inflammation; ii) suppression of hepatic mRNA expression for key transcriptional regulators of lipogenic gene expression; and iii) suppression of nuclear factor κB (NF-κB) activation. Human hepatoma HuH-7 cells exposed to rHDLs showed suppressed TNFα-induced NF-κB activation, correlating with decreased NF-κB target gene expression. We conclude that apoAI suppresses liver inflammation in HFD mice and improves insulin resistance via a mechanism that involves a downregulation of NF-κB activation.
The emerging role of epigenetics in human autoimmune disorders (2019)

Epigenetic pathways play a pivotal role in the development and function of the immune system. Over the last decade, a growing body of studies has been published out seeking to explain a correlation between epigenetic modifications and the development of autoimmune disorders. Epigenetic changes, such as DNA methylation, histone modifications, and noncoding RNAs, are involved in the pathogenesis of autoimmune diseases mainly by regulating gene expression. This paper reviews the importance of epigenetic alterations during the development of the most prevalent human autoimmune diseases, such as systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), systemic sclerosis (SSc), Sjogren's syndrome (SS), autoimmune thyroid diseases (AITD), and type 1 diabetes (T1D), aiming to provide new insights in the pathogenesis of autoimmune diseases and the possibility to develop novel therapeutic approaches targeting the epigenome.
Demographic, socioeconomic, and behavioral factors affecting patterns of tooth decay in the permanent dentition: principal components and factor analyses (2012)

Taken together, these results support the notion that caries experience is separable into patterns attributable to distinct risk factors. This study demonstrates the utility of such novel caries patterns as new outcomes for exploring the complex, multifactorial nature of dental caries.
T-cell lymphoblastic lymphoma in children and adolescents: The experience of the Israel Society of Pediatric Hematology Oncology. (2010)

9574 Background: Survival in T-cell lymphoblastic lymphoma (T-LBL) has improved over the past 30 years, largely through treatment protocols derived from regimens designed for children with acute lymphoblastic leukemia. We report the results of a retrospective multi-institutional, non randomized study performed in Israel and based on the NHL-BFM-95 in 1999-2006. Methods: From January 1999 through December 2006, 37 eligible patients were enrolled from six centers in Israel. The main goal of our work was to conduct a retrospective study regarding T-cell lymphoma and its prevalence, clinical characteristics, pathological characteristics, prognostic factors, overall survival (OS) and event-free survival (EFS). Our study included children and adolescents up to age 21 from all the centers in Israel where the patients were treated in pediatric departments. All patients had a minimal follow up of 2 years after diagnosis. Results: At a median follow-up of 4 years (range, 2-9 years), OS and EFS for all patients was 86.5% and 83.8%, respectively. OS was 86.6% and 83.3% for patients with stage III and stage IV, respectively, and EFS was 83.3% and 83.3%, respectively. EFS for Arabic patients was 62.5% and 89.7% for Jewish patients (p=0.014). Patients who did not express CD45 antigen showed superior survival (p=0.028). Five (13.5%) patients relapsed, four of whom died of their disease. Death as a consequence of therapy toxicity was documented in one patient while on the re-induction protocol (protocol IIA). Conclusions: Our retrospective study of children and adolescents with T-LBL showed similar results to other international studies. However, there is a need for comparing the epidemiological results between Israel and other countries in the Middle East, Europe, and the United States. Randomized trials are warranted to define the characteristics of microscopic disease, to detect minimal residual disease, and to monitor response to therapy. No significant financial relationships to disclose.
Implementation of stochastic computing in activation functions using stochastic arithmetic components (2023)

A new computing method using stochastic-based numbers is gaining importance as an approximate computing method to save area, energy, and computation time based on the accuracy required. This works uses stochastic computing, which is suitable for enhancing the efficiency of neural network. Herein we focus on developing activation functions that are essential parameters in the design of neural networks. The activation function in stochastic computing is typically a threshold function that maps the input bits to a binary output based on a probability distribution. This paper presents the development of modified activation functions tanh and COS using SC-based arithmetic components. Two different types of stochastic number generators (SNGs) have been used. Error analysis has been done based on the computation using two SNGs. Also, accuracy measurement is performed using error analysis for these complex functions mentioned above.
A Single Adaptive Mutation in Sodium Taurocholate Cotransporting Polypeptide Induced by Hepadnaviruses Determines Virus Species-specificity (2018)

Abstract Hepatitis B virus (HBV) and its hepadnavirus relatives infect a wide range of vertebrates from fish to human. Hepadnaviruses and their hosts have a long history of acquiring adaptive mutations. However, there are no reports providing direct molecular evidence for such a coevolutionary “arms race” between hepadnaviruses and their hosts. Here, we present evidence suggesting the adaptive evolution of the sodium taurocholate cotransporting polypeptide (NTCP), an HBV receptor, has been influenced by virus infection. Evolutionary analysis of the NTCP-encoding genes from 20 mammals showed that most NTCP residues are highly conserved among species, exhibiting evolution under negative selection (dN/dS &lt; 1); this observation implies that the evolution of NTCP is restricted by maintaining its original protein function. However, 0.7 % of NTCP amino acid (aa) residues exhibit rapid evolution under positive selection (dN/dS &gt; 1). Notably, a substitution at aa 158, a positively selected residue, converting the human NTCP to a monkey-type sequence abrogated the capacity to support HBV infection; conversely, a substitution at this residue converting the monkey Ntcp to the human sequence was sufficient to confer HBV susceptibility. Together, these observations suggested that positive selection at aa 158 was induced by virus infection. Moreover, the aa 158 sequence determined attachment of the HBV envelope protein to host cell, demonstrating the mechanism whereby HBV infection would create positive selection at this residue in NTCP. In summary, we provide the first evidence in agreement with the function of hepadnavirus as a driver for inducing an adaptive mutation in host receptor. Importance Hepatitis B virus (HBV) and its hepadnavirus relatives infect a wide range of vertebrates, with a long infectious history (hundreds of millions of years). Such a long history generally allows adaptive mutations in hosts to escape from infection, while simultaneously allowing adaptive mutations in viruses to overcome host barriers. However, there is no published molecular evidence for such a coevolutionary “arms race” between hepadnaviruses and hosts. In the present study, we performed coevolutionary phylogenetic analysis between hepadnaviruses and the sodium taurocholate cotransporting polypeptide (NTCP), an HBV receptor, combined with virological experimental assays for investigating the biological significance of NTCP sequence variation. Our data provide the first molecular evidences supporting that HBV-related hepadnaviruses drive adaptive evolution in the NTCP sequence, including a mechanistic explanation of how NTCP mutations determine host viral susceptibility. Our novel insights enhance our understanding of how hepadnaviruses evolved with their hosts, permitting the acquisition of strong species-specificity.
Nanoscale multipolar chromophores for optical limiting in the visible-NIR range based on multiphoton absorption (2004)

A series of structurally-related multipolar chromophores of different symmetry (dipolar, quadrupolar, octupolar, dendritic...), and shape (rod-like, Y-shaped...) propeller-shaped, were investigated for optical power limiting based on multiphoton absorption processes. Their design is based on the functionalization of nanoscale linear or branched conjugated backbones with electro-active (i.e. electron-releasing or electron-withdrawing) peripheral and core/node groups. Their two-photon absorption (TPA) spectra were determined by investigating their two-photon-excited fluorescence properties in the NIR region using pulsed excitation in the femtosecond regime. These studies provide evidence that the charge symmetry plays an important role, the quadrupolar chromophores leading to giant TPA cross-sections in the visible red. Furthermore, modulation of the nonlinear absorptivity/transparency/photostability trade-off can be achieved by playing on the nature of the electroactive groups and of the spacers. Interestingly, higher-order charge symmetries and branched structures provide an innovative route for TPA amplification and/or spectral broadening in the NIR region.