gebhart/patrepeval huggingface dataset:
Molecular cloning and analysis of functional envelope genes from human immunodeficiency virus type 1 sequence subtypes A through G. The WHO and NIAID Networks for HIV Isolation and Characterization (1996)

Present knowledge of human immunodeficiency virus type 1 (HIV-1) envelope immunobiology has been derived almost exclusively from analyses of subtype B viruses, yet such viruses represent only a minority of strains currently spreading worldwide. To generate a more representative panel of genetically diverse envelope genes, we PCR amplified, cloned, and sequenced complete gp160 coding regions of 35 primary (peripheral blood mononuclear cell-propagated) HIV-1 isolates collected at major epicenters of the current AIDS pandemic. Analysis of their deduced amino acid sequences revealed several important differences from prototypic subtype B strains, including changes in the number and distribution of cysteine residues, substantial length differences in hypervariable regions, and premature truncations in the gp41 domain. Moreover, transiently expressed glycoprotein precursor molecules varied considerably in both size and carbohydrate content. Phylogenetic analyses of full-length env sequences indicated that the panel included members of all major sequence subtypes of HIV-1 group M (clades A to G), as well as an intersubtype recombinant (F/B) from an infected individual in Brazil. In addition, all subtype E and three subtype G viruses initially classified on the basis of partial env sequences were found to cluster in subtype A in the 3' half of their gp41 coding region, suggesting that they are also recombinant. The biological activity of PCR-derived env genes was examined in a single-round virus infectivity assay. This analysis identified 20 clones, including 1 from each subtype (or recombinant), which expressed fully functional envelope glycoproteins. One of these, derived from a patient with rapid CD4 cell decline, contained an amino acid substitution in a highly conserved endocytosis signal (Y721C), as mediated virus entry with very poor efficiency, although they did not contain sequence changes predicted to alter protein function. These results indicate that the env genes of primary HIV-1 isolates collected worldwide can vary considerably in their genetic, phylogenetic, and biological properties. The panel of env constructs described here should prove valuable for future structure-function studies of naturally occurring envelope glycoproteins as well as AIDS vaccine development efforts targeted against a broader spectrum of viruses.
LIQUID DIET TECHNIQUE OF ETHANOL ADMINISTRATION: 1989 UPDATE (1989)

A technique of feeding alcohol as part of a liquid diet is reviewed that achieves an alcohol consumption of clinical relevance, while maintaining dietary control and providing adequate nutrition. With this procedure, blood alcohol levels are obtained which mimic clinical conditions and allow experimental duplications of many pathological complications caused by alcohol. In the rat, the liquid diet technique provides a model for the alcoholic fatty liver, various alcohol-induced metabolic, endocrine and central nervous system abnormalities (including tolerance and dependence) and the interaction of ethanol with industrial solvents, many commonly used drugs, analgesics, carcinogens and nutrients. This technique also resulted in the discovery of a new pathway of ethanol metabolism in the microsomes involving an ethanol-specific cytochrome P-450 (P450IIE1), which has now been confirmed in man. P450IIE1 contributes not only to the metabolic tolerance to ethanol, but also explains the enhanced susceptibility of the alcoholic to many ubiquitous xenobiotic agents. The liquid diet technique provides the flexibility to adjust to special experimental or physiological needs by allowing for various substitutions including changes in lipids, proteins or other dietary constituents. This procedure is thereby ideally suited for the study of the interactions of alcohol with deficiency or excess of various nutrients. The technique also facilitates the comparison with controls by simplifying pair feeding procedures. Although the flexibility of the liquid diet technique is one of its key advantages, a standard 'all purpose' liquid diet is described which is appropriate for most experimental applications. In addition, two other general formulae are given, namely a low fat diet (that allows the study of the effects of ethanol in the presence of minimal hepatic lipid accumulation) and a high protein diet (to meet increased needs, e.g. during pregnancy and lactation). The optimal amount of ethanol for the rat liquid diet was found to be 5 g/dl or 36% of total energy. With lesser amounts of alcohol, intake falls below a critical threshold; blood levels of alcohol then become negligible and the model becomes irrelevant to clinical conditions. In the rat, amounts of ethanol above 5 g/dl were not found to be associated with any further gain in alcohol ingestion. By contrast, in the baboon, the ethanol content could be raised profitably to 7 g/dl or 50% of total energy and resulted in the development of cirrhosis. This higher alcohol intake, together with species difference, may explain the greater severity of liver lesions produced by alcohol in the baboon.(ABSTRACT TRUNCATED AT 400 WORDS)
Synthesis of Photochromic 1,2-Dihetarylethene Using Regioselective Acylation of Thienopyrroles (2002)

[formula: see text] The influence of catalysts, acid chlorides, and solvents in the acylation of methyl 2-methyl-4H-thieno[3,2-b]pyrrole-5-carboxylate was studied. Conditions for the regioselective acylation processes were found. Thienopyrrole-based photochrome was synthesized for the first time.
Dissolved Alkali Metals in Zeolites (1996)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDissolved Alkali Metals in ZeolitesPeter P. Edwards*Peter P. EdwardsSchool of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K. In papers with more than one author, the asterisk indicates the name of the author to whom inquiries about the paper should be addressed.More by Peter P. Edwards, Paul A. AndersonPaul A. AndersonSchool of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.More by Paul A. Anderson, and John Meurig Thomas*John Meurig ThomasThe Royal Institution of Great Britain, Davy Faraday Research Laboratory, London W1X 4BS, U.K. In papers with more than one author, the asterisk indicates the name of the author to whom inquiries about the paper should be addressed.More by John Meurig ThomasCite this: Acc. Chem. Res. 1996, 29, 1, 23–29Publication Date (Web):January 10, 1996Publication History Received27 July 1995Published online10 January 1996Published inissue 10 January 1996https://pubs.acs.org/doi/10.1021/ar950152chttps://doi.org/10.1021/ar950152cresearch-articleACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views872Altmetric-Citations112LEARN 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:Alkali metals,Cluster chemistry,Electron paramagnetic resonance spectroscopy,Metal clusters,Zeolites Get e-Alerts
Site of binding of IgG2b and IgG2a by mouse macrophage Fc receptors by using cyanogen bromide fragments. (1985)

Cyanogen bromide fragments of murine IgG2b and IgG2a immunoglobulins were used to localize the sequences that are bound by specific IgG2b and IgG2a Fc receptors on murine macrophages. One fragment from the CH2 domain of IgG2b bound to the gamma 2b Fc receptor. Two fragments from IgG2a--one one from the CH2 domain, differing by only four amino acids from the homologous IgG2b fragment, and the other from the CH3 domain--specifically bound to the gamma 2a Fc receptor. In both a rosetting assay and a radioactive binding assay, these two fragments from IgG2a competed with intact IgG2a: however, they did not compete with each other. Rather, binding of the fragment from the CH3 domain of IgG2a augmented the binding of the fragment from the CH2 domain of IgG2a but not that of the homologous fragment from IgG2b. The binding of both IgG2a fragments was abolished by trypsin treatment of macrophages. These data suggest that 1) a sequence in the CH2 domain of IgG2b is sufficient for binding to the gamma 2b Fc receptor, 2) sequences from both the CH2 and CH3 domains of IgG2a bind to the gamma 2a Fc receptor, and 3) the binding of sequences from the CH3 domain of IgG2a may induce a conformational change in the gamma 2a Fc receptor that leads to enhanced binding of sequences from the CH2 domain.
Modeling, Detection, and Localization of High-Impedance Faults In Low-Voltage Distribution Feeders (2003)

High-impedance faults (HIFs) on distribution feeders are abnormal electrical conditions that cannot be detected by conventional protection schemes. These faults pose a threat on human lives when neighboring objects become in contact with the line’s bare and energized conductors. An accurate electrical model for a HIF is implemented to investigate typical patterns in the line’s current that allow for the detection of these faults. The occurrence of HIFs is detected with harmonic-current phase analysis and localized with recloser-sectionalizer technology as presented in this work. A sectionalizer algorithm is then presented showing the decision criteria for HIF declaration and shown to discriminate against nominal behavior in distribution feeders of similar harmonic content. Finally, it is shown that the algorithm will not produce a misreading when a current transformer enters saturation. iii
Nitric Oxide Inhibits the Positive Inotropic Response to β-Adrenergic Stimulation in Humans With Left Ventricular Dysfunction (1995)

Nitric oxide produced in the heart attenuates the positive inotropic response to beta-adrenergic stimulation in humans with LV dysfunction. NO may contribute to beta-adrenergic hyporesponsiveness in patients with LV dysfunction.
Axon Loss in the Spinal Cord Determines Permanent Neurological Disability in an Animal Model of Multiple Sclerosis (2002)

Multiple sclerosis (MS) is an inflammatory demyelinating disease of the central nervous system (CNS). Most patients undergo an initial relapsing-remitting (RR-MS) course that transforms into a relentless neurodegenerative disorder, termed secondary progressive (SP)-MS. Reversible inflammation and demyelination account readily for the pattern of RR-MS but provide an unsatisfactory explanation for irrevocable decline in SP-MS. Axon loss is thought to be responsible for progressive, non-remitting neurological disability during SP-MS. There is considerable potential for neuroprotective therapies in MS, but their application awaits animal models in which axonal loss correlates with permanent neurological disability. In this report, we describe quantitative immunohistochemical methods that correlate inflammation and axonal loss with neurological disability in chronic-relapsing experimental autoimmune encephalomyelitis (EAE). At first attack, CNS inflammation, but not axon loss, correlated with the degree of neurological disability. In contrast, fixed neurological impairment in chronic EAE correlated with axon loss that, in turn, correlated with the number of symptomatic attacks. As proposed for MS, these observations imply a causal relationship between inflammation, axon loss, and irreversible neurological disability. This chronic-relapsing EAE model provides an excellent platform for 2 critical objectives: investigating mechanisms of axon loss and evaluating efficacy of neuroprotective therapies.
[Impact of hydrogen sulfide donor on experimental pulmonary hypertension induced by high pulmonary flow and endogenous carbon monoxide/heme oxygenase pathway]. (2006)

NaHS might prevent pulmonary hypertension and pulmonary artery structural remodeling induced by high pulmonary flow, and its mechanism might be associated with the changes in endogenous CO/HO pathway.
Expression of surface lymphotoxin and tumor necrosis factor on activated T, B, and natural killer cells (1992)

The expression of membrane-associated forms of lymphotoxin (LT) and TNF were examined on cell lines of T, B, and myeloid origin, IL-2 dependent T cell clones, and peripheral blood lymphocytes. Inducible and constitutive patterns of surface LT expression were found on T cells as exemplified by the II-23.D7, a CD4+T cell hybridoma, and HUT-78, a T cell lymphoma. Phorbol ester induced surface LT expression on Ramos, an EBV transformed B cell line, but at a slower rate of appearance when compared to the II-23.D7. Secretion of LT was rapidly inducible by phorbol ester in II-23.D7 and also in HUT-78 but with slower kinetics; surface LT expression continued in both lines after secretion had ceased. Low levels of membrane TNF were transiently induced on II-23.D7 and HUT-78, but none was observed on Ramos. Peripheral blood monocytes and some myeloid tumor lines did not express surface LT. Several T cell clones expressed surface LT after Ag-specific stimulation, and expression persisted several days. Stimulation through the TCR or by IL-2 rapidly induced surface LT on resting peripheral T cells and CD56+ NK cells; pokeweed mitogen activation induced expression on CD20+ B cells. Consistent with previous results, immunoprecipitation with anti-LT mAb showed that LT was complexed with a distinct 33 kDa glycoprotein (p33) on cells that expressed surface LT, whereas secreted LT was not associated with p33. Surface and secreted modes of LT expression by activated T, B, and NK cells suggests that LT can be utilized as either a localized or diffusible mediator in immune responses.
Anti-Platelet Aggregation and Chemical Constituents from the Rhizome ofGynura japonica (2003)

A novel quinonoid terpenoid, (-)- alpha-tocospirone, a new chromanone, (-)-gynuraone, as well as three new steroids, (22 E,24 S)-7 alpha-hydroperoxystigmasta-5,22-dien-3 beta-ol, (22 E,24 S)-stigmasta-1,4,22-trien-3-one, and (24 R)-stigmasta-1,4-dien-3-one, together with 15 known components, were isolated from the rhizome of Formosan Gynura japonica. Structures of the new compounds were determined through spectral analyses and chemical evidence. Several of the isolated compounds, caryophyllene oxide, 6-acetyl-2,2-dimethylchroman-4-one, vanillin, 2,6-dimethoxy-1,4-benzoquinone, and benzoic acid exhibited significant anti-platelet aggregation activity in vitro.
Control of lymphocyte recirculation in man. I. Differential regulation of the peripheral lymph node homing receptor L-selectin on T cells during the virgin to memory cell transition (1993)

Conventional virgin lymphocytes of a given class show relatively homogeneous recirculation through secondary lymphoid tissues, whereas memory/effector populations are composed of distinct subsets with differential, often tissue-selective migratory capability. In keeping with these observations, CD45RAhigh/ROlow "virgin" T cells in human peripheral blood uniformly express the peripheral lymph node homing receptor (HR) L-selectin, whereas among the CD45RAlow/ROhigh "memory/effector" subset, the expression of this HR is bimodal. To investigate the mechanisms responsible for the generation of memory/effector T cell subsets with differential homing potential, we developed a multiparameter flow cytometric technique that defines a common pathway of post-thymic T cell differentiation in secondary lymphoid tissues. Our analyses indicate that the virgin to memory T cell transition is characterized by a stepwise, unidirectional progression through distinct CD45RA+/RO+ intermediates that allow the in vivo discrimination of early, middle, and late transitional T cells. In normal peripheral blood, few T cells with a transitional phenotype are identified, but in secondary lymphoid tissues, 2 to 10% of T cells have this phenotype, including those CD45RA+ T cells that 1) are morphologically blasts, 2) are in S or G2/M phase of the cell cycle, or 3) express activation Ag. General adhesion molecules (LFA-1, LFA-3, ICAM-1) are uniformly up-regulated concordant with changes in T cell expression of CD45RA/RO in all tissues examined. Early in the transition, L-selectin is also uniformly up-regulated, but in subsequent stages, T cell expression of this HR is preferentially down-regulated in mucosal lymphoid tissues, and retained in peripheral lymph node. Differential regulation of L-selectin can also be demonstrated in vitro by the activation of virgin T cells in the presence of specific cytokines--IL-2 induces L-selectin down-regulation, whereas IL-6 and particularly TGF-beta 1 promote L-selectin up-regulation. Taken together, these findings support the hypothesis that local microenvironments within particular secondary lymphoid tissues influence HR expression at the time of CD45RA/RO conversion, and thereby contribute to the formation of CD45RAlow/ROhigh memory/effector T cell populations with tissue-selective homing behavior.
Automated Correction for Syntax Errors in Programming Assignments using Recurrent Neural Networks (2016)

We present a method for automatically generating repair feedback for syntax errors for introductory programming problems. Syntax errors constitute one of the largest classes of errors (34%) in our dataset of student submissions obtained from a MOOC course on edX. The previous techniques for generating automated feed- back on programming assignments have focused on functional correctness and style considerations of student programs. These techniques analyze the program AST of the program and then perform some dynamic and symbolic analyses to compute repair feedback. Unfortunately, it is not possible to generate ASTs for student pro- grams with syntax errors and therefore the previous feedback techniques are not applicable in repairing syntax errors. We present a technique for providing feedback on syntax errors that uses Recurrent neural networks (RNNs) to model syntactically valid token sequences. Our approach is inspired from the recent work on learning language models from Big Code (large code corpus). For a given programming assignment, we first learn an RNN to model all valid token sequences using the set of syntactically correct student submissions. Then, for a student submission with syntax errors, we query the learnt RNN model with the prefix to- ken sequence to predict token sequences that can fix the error by either replacing or inserting the predicted token sequence at the error location. We evaluate our technique on over 14, 000 student submissions with syntax errors. Our technique can completely re- pair 31.69% (4501/14203) of submissions with syntax errors and in addition partially correct 6.39% (908/14203) of the submissions.
Role of the Cytoplasmic Tails of CXCR1 and CXCR2 in Mediating Leukocyte Migration, Activation, and Regulation (2003)

IL-8 (or CXCL8) activates the receptors CXCR1 (IL-8RA) and CXCR2 (IL-8RB) to induce chemotaxis in leukocytes, but only CXCR1 mediates cytotoxic and cross-regulatory signals. This may be due to the rapid internalization of CXCR2. To investigate the roles of the intracellular domains in receptor regulation, wild-type, chimeric, phosphorylation-deficient, and cytoplasmic tail (C-tail) deletion mutants of both receptors were expressed in RBL-2H3 cells and studied for cellular activation, receptor phosphorylation, desensitization, and internalization. All but one chimeric receptor bound IL-8 and mediated signal transduction, chemotaxis, and exocytosis. Upon IL-8 activation, the chimeric receptors underwent receptor phosphorylation and desensitization. One was resistant to internalization, yet it mediated normal levels of beta-arrestin 2 (beta arr-2) translocation. The lack of internalization by this receptor may be due to its reduced association with beta arr-2 and the adaptor protein-2 beta. The C-tail-deleted and phosphorylation-deficient receptors were resistant to receptor phosphorylation, desensitization, arrestin translocation, and internalization. They also mediated greater phosphoinositide hydrolysis and exocytosis and sustained Ca(2+) mobilization, but diminished chemotaxis. These data indicate that phosphorylation of the C-tails of CXCR1 and CXCR2 are required for arrestin translocation and internalization, but are not sufficient to explain the rapid internalization of CXCR2 relative to CXCR1. The data also show that receptor internalization is not required for chemotaxis. The lack of receptor phosphorylation was correlated with greater signal transduction but diminished chemotaxis, indicating that second messenger production, not receptor internalization, negatively regulates chemotaxis.
Coherent Error Suppression in Multiqubit Entangling Gates (2012)

We demonstrate a simple pulse shaping technique designed to improve the fidelity of spin-dependent force operations commonly used to implement entangling gates in trapped ion systems. This extension of the Mølmer-Sørensen gate can theoretically suppress the effects of certain frequency and timing errors to any desired order and is demonstrated through Walsh modulation of a two qubit entangling gate on trapped atomic ions. The technique is applicable to any system of qubits coupled through collective harmonic oscillator modes.
Methods for Constructing and Producing Retroviral Vectors (2003)

Vectors derived from murine retroviruses have been used extensively for gene transfer in both preclinical and clinical studies. Retroviruses are small RNA viruses that replicate through a double-stranded DNA intermediate. The ability of retroviral vectors to integrate efficiently into the host DNA of infected cells, resulting in stable gene expression, makes them well suited for certain gene therapy applications. The majority of the applications using retroviral vectors have involved ex vivo methods in which cells are genetically modified in culture prior to introduction into the animal (,). However, the recent improvement in methods for production and concentration of retroviruses now allows for direct, in vivo applications (see Notes 1 and 2). This chapter will give a brief background on Moloney Murine Leukemia Virus- (MLV) based retroviruses and describe how to construct, produce, and titer replication-defective retroviral vectors.
Gene Therapy for Severe Combined Immunodeficiency (2005)

Studies of severe combined immunodeficiency (SCID), a group of rare monogenic disorders, have provided key findings about the physiology of immune system development. The common characteristic of these diseases is the occurrence of a block in T cell differentiation, always associated with a direct or indirect impairment of B cell immunity. The resulting combined immunodeficiency is responsible for the clinical severity of SCID, which, without treatment, leads to death within the first year of life. Eleven distinct SCID phenotypes have been identified to date. Mutations of ten genes have been found to cause SCID. Identifying the pathophysiological basis of most SCID conditions has led to the possibility of molecular therapy as an alternative to allogeneic hematopoietic stem cell transplantation. This review discusses recent developments in SCID identification and treatment.