gebhart/patrepeval huggingface dataset:
The Expanding Role of TNF-Receptor Super Family Member CD40 (tnfrsf5) in Autoimmune Disease: Focus on Th40 Cells (2010)

CD40 is a member of the TNF receptor super family (tnfrsf) thats role in autoimmunity has been long established. Predominantly studies focus on CD40 as an antigen presenting cell receptor. We and others determined that CD40 acts as a functional receptor on T cells. In fact CD40 is a co-stimulus for T cells potentially precluding the CD28 – B7 costimulation axis. CD40+ T cells (Th40) are highly pathogenic - transferring type 1 diabetes (T1D) to SCID mice. The number and percentage of Th40 cells increases concurrently with insulitits through diabetes onset. An important finding was that blocking CD40 – CD154 interactions prevents T1D onset, and reestablishes homeostatic balance between Th40 cells and traditional, naturally occurring regulatory T cells (Tregs). We discovered a distinct dysregulation between Th40 cells and Tregs during autoimmunity. The actual number and function of Tregs in NOD mice, the model of T1D, is in fact normal. The percentage of Tregs is skewed to appear abnormally low. We determined that Th40 cells over time in NOD mice radically outpace Tregs in number and percentage. Mechanistically Th40 cells have lower levels of the death inducing Fas molecule and are highly resistant to cell death. Th40 cells are capable of producing Th1 cytokines including IFNγ and TNFα but also can produce IL-17A, demonstrating a pro-inflammatory phenotype.
HLA typing from RNA-Seq sequence reads (2012)

We present a method, seq2HLA, for obtaining an individual's human leukocyte antigen (HLA) class I and II type and expression using standard next generation sequencing RNA-Seq data. RNA-Seq reads are mapped against a reference database of HLA alleles, and HLA type, confidence score and locus-specific expression level are determined. We successfully applied seq2HLA to 50 individuals included in the HapMap project, yielding 100% specificity and 94% sensitivity at a P-value of 0.1 for two-digit HLA types. We determined HLA type and expression for previously un-typed Illumina Body Map tissues and a cohort of Korean patients with lung cancer. Because the algorithm uses standard RNA-Seq reads and requires no change to laboratory protocols, it can be used for both existing datasets and future studies, thus adding a new dimension for HLA typing and biomarker studies.
Intermodulation characteristics of the television broadcast satellite receivers (1983)

A 25-year-old paraplegic woman suffered cardiopulmonary arrest due to a major pulmonary embolism during intravenous mannitol therapy. Although it is possible that the mannitol caused an acute episode of hemagglutination, we postulate that rapid administration of mannitol caused dilation of her venous system, causing a preexisting clot to break loose.
Characterization of the epidermal growth factor receptor in human glioma cell lines and xenografts. (1990)

Both permanent cultured cell lines and athymic mouse xenografts were established from two human glioblastomas. Biopsies from D-245 MG and D-270 MG contained amplified and rearranged epidermal growth factor receptor (EGFR) genes. Although the gene amplification and rearrangement seen originally was maintained in the xenografts, cultured cell lines established from these biopsies lost the amplified rearranged genes in vitro. Analysis of these cell lines and 11 additional permanent human glioma cell lines with normal EGFR gene copy number showed from 2.7 x 10(3) to 4.1 x 10(5) high affinity EGFRs/cell by radioreceptor assay. The RNase A protection assay showed minimal differences in the quantity of EGFR mRNA among the 13 glioma lines, while the D-245 MG and D-270 MG xenografts expressed approximately 10-20 times as much EGFR mRNA as the corresponding cell lines. Immunoprecipitation of EGFR from these lines, including D-245 MG and D-270 MG, demonstrated only the intact Mr 170,000 Da form, while truncated Mr 145,000 Da and 100,000 Da EGFR proteins were immunoprecipitated from the D-270 MG and D-245 MG xenografts, respectively. These studies demonstrate that gliomas with amplification of the EGFR gene are capable of establishing in culture but that the amplified rearranged genes are not maintained. Possible explanations are that the abnormal genes are lost during serial passage or that the cells with amplified rearranged genes only represent a minor subpopulation of cells, which are unable to grow in culture. In either case, these observations suggest that high expression and structural abnormalities of EGFR proteins generated by amplification and rearrangement of the EGFR gene provide a growth advantage for gliomas in vivo but not in vitro.
CXCR3 ligands: redundant, collaborative and antagonistic functions (2011)

CXCR3 is a chemokine receptor that is rapidly induced on naïve T cells following activation, and preferentially remains highly expressed on type-1 helper (Th1)-type CD4(+) T cells, effector CD8(+) T cells and innate-type lymphocytes, such as natural killer (NK) and NKT cells. CXCR3 is activated by three interferon (IFN)-γ-inducible ligands CXCL9 (monokine induced by gamma-interferon), CXCL10 (interferon-induced protein-10) and CXCL11 (interferon-inducible T-cell alpha chemoattractant). Although some studies have revealed that these ligands have redundant functions in vivo, other studies have demonstrated that the three CXCR3 ligands can also collaborate and even compete with each other. Differential regulation of the three ligands at specific times in defined anatomically restricted locations in vivo likely participates in the fine control of T-cell trafficking over the course of an immune response. Among the differences in regulation, CXCL10 is induced by a variety of innate stimuli that induce IFN-α/β as well as the adaptive immune cell cytokine IFN-γ, whereas CXCL9 induction is restricted to IFN-γ. In this review, we will discuss how the balance, timing and pattern of CXCR3 ligand expression appears to regulate the generation of effector T cells in the lymphoid compartment and subsequent migration into peripheral sites of Th1-type inflammation in which the CXCR3 ligands also then regulate the interactions and migratory behavior of effector T cells in an inflamed peripheral tissue.
Concurrent Chronic Lymphocytic Leukemia Cutis and Acute Myelogenous Leukemia Cutis in a Patient with Untreated CLL (2001)

Patients who have chronic lymphocytic leukemia (CLL) are known to have a high frequency of second malignant neoplasms. However, acute myelogenous leukemia (AML) occurring concurrent with or after a diagnosis of CLL is extremely rare. In this article we report a case of AML developing in a 55-year-old male with a 6-year history of untreated CLL. The diagnosis was facilitated by touch preparation of a skin punch biopsy specimen. The patient presented with a two-week history of fever, weakness, anasarca, and a skin rash. Physical examination revealed pink to skin-colored firm papules, which coalesced into indurated plaques on his trunk, upper extremities, and face. The lesions, in combination with generalized edema, produced a leonine facies. Touch prep of the biopsy showed medium to large blasts, large monocytoid cells, and numerous small mature lymphocytes, providing the preliminary diagnosis of a second, previously undiagnosed myelomonocytic malignancy in this patient. The initial diagnosis was subsequently confirmed by histologic, cytochemical, immunohistochemical and flow cytometry studies. This is the first reported case of CLL with concurrent AML in which rapid touch prep of a skin punch biopsy facilitated diagnosis.
Maintaining HIV therapies: adherence conference excerpts--part 2 of 3. (1998)

A seminar hosted by Body Positive and the Clinical Education Initiative at Mount Sinai Medical Center discussed the problems with adhering to HIV therapies. Such problems include difficulties in tolerating treatments and unpleasant side effects. Two case studies are presented. One describes the problems in adhering to a child's treatment schedule, and the other discusses problems associated with long-term treatment. Medical panelists discuss both cases and emphasize the need to educate patients on the importance of maintaining a dosing schedule, especially when taking protease inhibitors.
Four Years of ACS Sustainable Chemistry & Engineering: Reflections and New Developments (2017)

ADVERTISEMENT RETURN TO ISSUEEditorialNEXTFour Years of ACS Sustainable Chemistry & Engineering: Reflections and New DevelopmentsDavid T. Allen, Danielle Julie Carrier, Bing-Joe Hwang, Peter Licence, Audrey Moores, Thalappil Pradeep, Bert Sels, Bala Subramaniam, Michael K.C. Tam, and Rhea M. WilliamsCite this: ACS Sustainable Chem. Eng. 2017, 5, 1, 1–2Publication Date (Web):January 3, 2017Publication History Received16 December 2016Published online3 January 2017Published inissue 3 January 2017https://pubs.acs.org/doi/10.1021/acssuschemeng.6b03062https://doi.org/10.1021/acssuschemeng.6b03062editorialACS PublicationsCopyright © 2017 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 Views5344Altmetric-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 PDF (287 KB) Get e-AlertscloseSUBJECTS:Chemical engineering and industrial chemistry,Green chemistry,Physical and chemical processes,Sustainability Get e-Alerts
Formal verification in a commercial setting (1997)

This tutorial addresses the following questions: why do formal verification? who is doing it today? what are they doing? how are they doing it? what about the future?
The English get-passive in spoken discourse: description and implications for an interpersonal grammar (1999)

Using a 1.5-million-word sample from the CANCODE spoken English corpus, we present a description of the get -passive in informal spoken British English. Previous studies of the get -passive are reviewed, and their focus on contextual and interpersonal meanings is noted. A number of related structures are then considered and the possibility of a passive gradient is discussed. The corpus sample contains 139 get -passives of the type X get + past participle (by Y) ( e.g. He got killed ), of which 124 occur in contexts interpreted as adversative or problematic from the speaker's viewpoint. Very few examples contain an explicit agent or adverbials. Main verb frequency is also considered. Where contexts are positive rather than adversative, newsworthiness or focus of some kind on the subject and/or events is still apparent. The corpus evidence is used to evaluate the terms upon which an interpersonal grammar of English might be developed, and a contrast is drawn between deterministic grammars and probabilistic ones, with probabilistic grammars offering the best potential for the understanding of interpersonal features.
Metabolic pathway for the utilization of L-arginine, L-ornithine, agmatine, and putrescine as nitrogen sources in Escherichia coli K-12 (1985)

The pathway for the utilization of L-arginine, agmatine, L-ornithine, and putrescine as the sole nitrogen source by Escherichia coli K-12 has been elucidated. Mutants impaired in the utilization of one or more of the above compounds were isolated, and their growth on the different compounds as a sole source of nitrogen and the activities of enzymes of the putative pathway were examined. Our results show that L-arginine is first decarboxylated to agmatine, which is hydrolyzed to urea and putrescine. L-Ornithine is decarboxylated to putrescine. Putrescine is transaminated to gamma-aminobutyraldehyde, which is oxidized to gamma-aminobutyric acid. gamma-Aminobutyric acid is degraded to succinate. The gene for putrescine aminotransferase was located at 89 min on the E. coli K-12 chromosome, and the gene for gamma-aminobutyraldehyde (pyrroline) dehydrogenase was mapped at approximately 30 min.
EFFECTS OF IN VIVO ADMINISTRATION OF MONOCLONAL ANTIBODIES SPECIFIC FOR HUMAN T CELL SUBPOPULATIONS ON THE IMMUNE SYSTEM IN A RHESUS MONKEY MODEL (1983)

Monoclonal antibodies specific for human T cell subsets have been tested for their immunosuppressive effect in a rhesus monkey skin graft model. Rhesus monkeys were injected i.v. daily with antibodies specific for helper T cells (OKT4 and 4A), for cytotoxic/suppressor T cells (OKT8A), or all peripheral T cells (OKT11A), and they received an allogeneic skin graft one or two days after the initial antibody treatment. The OKT4, 4A, and 11A antibodies prolonged skin graft survival, but OKT8A did not. All animals were carefully monitored regarding levels of T cell subsets and antibody formation to the injected monoclonal antibody. The relevant T cell subset was not eliminated from the circulation when OKT4 and OKT4A antibodies were given separately. The OKT4+ cells remained in the circulation coated with antibody. OKT4+ cells could no longer be demonstrated when both OKT4 and 4A were given simultaneously. However, this difference in effect on the OKT4+ cells did not influence skin graft survival time. All animals receiving monoclonal antibody treatment developed antimouse-Ig antibodies after 10 to 13 days of treatment, which presumably counteracted the effect of the antibodies. From these data it appears that the rhesus monkey is a useful animal model in which to investigate the potential of monoclonal antibodies against human lymphocyte subpopulations to modify and regulate the immune response in an orderly fashion.
Crystalline Pancreatic Amylase. II. Improved Method for its Preparation from Hog Pancreas Glands and Additional Studies of its Properties1 (1952)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCrystalline Pancreatic Amylase. II. Improved Method for its Preparation from Hog Pancreas Glands and Additional Studies of its Properties1M. L. Caldwell, Mildred Adams, Jo-fen Tung Kung, and Gloria C. ToralballaCite this: J. Am. Chem. Soc. 1952, 74, 16, 4033–4035Publication Date (Print):August 1, 1952Publication History Published online1 May 2002Published inissue 1 August 1952https://pubs.acs.org/doi/10.1021/ja01136a018https://doi.org/10.1021/ja01136a018research-articleACS PublicationsRequest reuse permissionsArticle Views80Altmetric-Citations38LEARN 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
ANNINE-6plus, a voltage-sensitive dye with good solubility, strong membrane binding and high sensitivity (2007)

We present a novel voltage-sensitive hemicyanine dye ANNINE-6plus and describe its synthesis, its properties and its voltage-sensitivity in neurons. The dye ANNINE-6plus is a salt with a double positively charged chromophore and two bromide counterions. It is derived from the zwitterionic dye ANNINE-6. While ANNINE-6 is insoluble in water, ANNINE-6plus exhibits a high solubility of around 1 mM. Nonetheless, it displays a strong binding to lipid membranes. In contrast to ANNINE-6, the novel dye can be used to stain cells from aqueous solution without surfactants or organic solvents. In neuronal membranes, ANNINE-6plus exhibits the same molecular Stark effect as ANNINE-6. As a consequence, a high voltage-sensitivity is achieved with illumination and detection in the red end of the excitation and emission spectra, respectively. ANNINE-6plus will be particularly useful for sensitive optical recording of neuronal excitation when organic solvents and surfactants must be avoided as with intracellular or extracellular staining of brain tissue.
Structural basis for high‐affinity volatile anesthetic binding in a natural 4‐helix bundle protein (2005)

Physiologic sites for inhaled anesthetics are presumed to be cavities within transmembrane 4-alpha-helix bundles of neurotransmitter receptors, but confirmation of binding and structural detail of such sites remains elusive. To provide such detail, we screened soluble proteins containing this structural motif, and found only one that exhibited evidence of strong anesthetic binding. Ferritin is a 24-mer of 4-alpha-helix bundles; both halothane and isoflurane bind with K(A) values of approximately 10(5) M(-1), higher than any previously reported inhaled anesthetic-protein interaction. The crystal structures of the halothane/apoferritin and isoflurane/apoferritin complexes were determined at 1.75 A resolution, revealing a common anesthetic binding pocket within an interhelical dimerization interface. The high affinity is explained by several weak polar contacts and an optimal host/guest packing relationship. Neither the acidic protons nor ether oxygen of the anesthetics contribute to the binding interaction. Compared with unliganded apoferritin, the anesthetic produced no detectable alteration of structure or B factors. The remarkably high affinity of the anesthetic/apoferritin complex implies greater selectivity of protein sites than previously thought, and suggests that direct protein actions may underlie effects at lower than surgical levels of anesthetic, including loss of awareness.
Myrosinase: gene family evolution and herbivore defense in Brassicaceae. (2000)

Glucosinolates are a category of secondary products present primarily in species of the order Capparales. When tissue is damaged, for example by herbivory, glucosinolates are degraded in a reaction catalyzed by thioglucosidases, denoted myrosinases, also present in these species. Thereby, toxic compounds such as nitriles, isothiocyanates, epithionitriles and thiocyanates are released. The glucosinolate-myrosinase system is generally believed to be part of the plant's defense against insects, and possibly also against pathogens. In this review, the evolution of the system and its impact on the interaction between plants and insects are discussed. Further, data suggesting additional functions in the defense against pathogens and in sulfur metabolism are reviewed.
Mapping the protein surface of human immunodeficiency virus type 1 gp120 using human monoclonal antibodies from phage display libraries (1997)

Panels of hybridoma-derived monoclonal antibodies against diverse epitopes are widely used in defining protein surface topography, particularly in the absence of crystal or NMR structural information. Here we show that recombinant monoclonal antibodies from phage display libraries provide a rapid alternative for surface epitope mapping. Diverse epitopes are accessed by presenting antigen to the library in different forms, such as sequential masking of epitopes with existing antibodies or ligands prior to selection and selection on peptides. The approach is illustrated for a recombinant form of the human immunodeficiency virus type 1 (HIV-1) surface glycoprotein gp120 which has been extensively mapped by rodent and human monoclonal antibodies derived by cellular methods. Human recombinant Fab fragments to most of the principal epitopes on gp120 are selected including Fabs to the C1 region, a C1/C5 epitope, a C1/C2 epitope, the V2 loop, the V3 loop and the CD4 binding domain. In addition an epitope linked to residues in the V2 loop and CD4 binding domain is identified. Most of these specificities are associated with epitopes presented poorly on native multimeric envelope, consistent with the notion that these antibodies are associated with immunization by forms of gp120 differing in conformation from that found on whole virus or infected cells.
Arrhythmia Classification Based on Multi-Domain Feature Extraction for an ECG Recognition System (2016)

Automatic recognition of arrhythmias is particularly important in the diagnosis of heart diseases. This study presents an electrocardiogram (ECG) recognition system based on multi-domain feature extraction to classify ECG beats. An improved wavelet threshold method for ECG signal pre-processing is applied to remove noise interference. A novel multi-domain feature extraction method is proposed; this method employs kernel-independent component analysis in nonlinear feature extraction and uses discrete wavelet transform to extract frequency domain features. The proposed system utilises a support vector machine classifier optimized with a genetic algorithm to recognize different types of heartbeats. An ECG acquisition experimental platform, in which ECG beats are collected as ECG data for classification, is constructed to demonstrate the effectiveness of the system in ECG beat classification. The presented system, when applied to the MIT-BIH arrhythmia database, achieves a high classification accuracy of 98.8%. Experimental results based on the ECG acquisition experimental platform show that the system obtains a satisfactory classification accuracy of 97.3% and is able to classify ECG beats efficiently for the automatic identification of cardiac arrhythmias.
Complementary filter design on the special orthogonal group SO(3) (2006)

This paper considers the problem of obtaining high quality attitude extraction and gyros bias estimation from typical low cost intertial measurement units for applications in control of unmanned aerial vehiccles. Two different non-linear complementary filters are proposed: Direct complementary filter and Passive non-linear complementary filter. Both filters evolve explicity on the special orthogonal group SO(3) and can be expressed in quaternion form for easy implementation. An extension to the passive ocmplementary filter is proposed to provide adaptive gyro bias estimation.
Beyond microsatellite testing: assessment of tumor mutational burden identifies subsets of colorectal cancer who may respond to immune checkpoint inhibition (2018)

Concurrent TMB assessment accurately classifies MSI tumors as TMB-high and simultaneously identifies nearly 3% or CRC as MSS/TMB-high. This subgroup may expand the population of CRC who may benefit from immune checkpoint inhibitor based therapeutic approaches.