gebhart/patrepeval huggingface dataset:
Phenotypic and Functional Analysis of Immune CD8+ T Cell Responses Induced by a Single Injection of a HIV DNA Vaccine in Mice (2007)

HIV DNA vaccines are potent inducers of cell-mediated immune (CMI) response in mice but elicit poor HIV-specific IFN-gamma-producing T cells in monkeys and humans. In this study, we performed kinetic analyses on splenocytes of BALB/c mice that were immunized by a single injection with a unique DNA vaccine. Using IFN-gamma-ELISPOT and multiparametric FACS analysis, we characterized the induced CMI response. We found that the response was detectable for at least 63 wk. ELISPOT detection of IFN-gamma-producing T cells showed a profile with two waves separated by a long period of minimal response. Multiparametric FACS analysis showed two populations of CD3(+)CD8(+) T cells that were specific for all HIV Ags. These cells had similar robust proliferation abilities and contained granzyme B. However, only a few produced IFN-gamma. Both IFN-gamma-producing and non-IFN-gamma-producing HIV-specific CD8(+) T cells were detected in the early stage (week (W)1 and W2 postimmunization (PI)), in the prolonged intermediate period of minimal response (W4-W26 PI), and in the final late phase of increased response (W30-W63 PI). Our longitudinal characterization showed that both subsets of cells underwent expansion, contraction, and memory generation/maintenance phases throughout the lifespan of the animal. Altogether, these findings bring insight to the heterogeneity of the immune T cell response induced by a single immunization with this DNA and strengthen the concept that used of the IFN-gamma-ELISPOT assay alone may be insufficient to detect critical T cell responses to candidate HIV vaccines.
A Simple "Back of the Envelope" Method for Estimating the Densities and Molecular Volumes of Liquids and Solids (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA Simple "Back of the Envelope" Method for Estimating the Densities and Molecular Volumes of Liquids and SolidsGregory S. Girolami Cite this: J. Chem. Educ. 1994, 71, 11, 962Publication Date (Print):November 1, 1994Publication History Received3 August 2009Published online1 November 1994Published inissue 1 November 1994https://doi.org/10.1021/ed071p962RIGHTS & PERMISSIONSArticle Views741Altmetric-Citations63LEARN 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 InReddit PDF (2 MB) Get e-Alerts Get e-Alerts
An Early Hierarchic Role of U1 Small Nuclear Ribonucleoprotein in Spliceosome Assembly (1988)

Splicing of nuclear precursor messenger RNA (pre-mRNA) occurs on a large ribonucleoprotein complex, the spliceosome. Several small nuclear ribonucleoproteins (snRNP's) are subunits of this complex that assembles on the pre-mRNA. Although the U1 snRNP is known to recognize the 5' splice site, its roles in spliceosome formation and splice site alignment have been unclear. A new affinity purification method for the spliceosome is described which has provided insight into the very early stages of spliceosome formation in a yeast in vitro splicing system. Surprisingly, the U1 snRNP initially recognizes sequences at or near both splice junctions in the intron. This interaction must occur before the other snRNP's (U2, U4, U5, and U6) can join the complex. The results suggest that interaction of the two splice site regions occurs at an early stage of spliceosome formation and is probably mediated by U1 snRNP and perhaps other factors.
Sequence and structure alignment of paramyxovirus hemagglutinin-neuraminidase with influenza virus neuraminidase (1993)

A model is proposed for the three-dimensional structure of the paramyxovirus hemagglutinin-neuraminidase (HN) protein. The model is broadly similar to the structure of the influenza virus neuraminidase and is based on the identification of invariant amino acids among HN sequences which have counterparts in the enzyme-active center of influenza virus neuraminidase. The influenza virus enzyme-active site is constructed from strain-invariant functional and framework residues, but in this model of HN, it is primarily the functional residues, i.e., those that make direct contact with the substrate sialic acid, which have identical counterparts in neuraminidase. The framework residues of the active site are different in HN and in neuraminidase and appear to be less strictly conserved within HN sequences than within neuraminidase sequences.
Palladium-Catalyzed Reppe Carbonylation (2001)

PdX2L2/L/HA (A = weakly coordinating anion, L = phosphine) complexes are active catalysts in the hydroesterification of alkenes, alkynes, and conjugated dienes. Shell, the only major corporate player in the field, recently developed two very active catalyst systems tailored to the hydroesterification of either alkenes or alkynes. The hydroesterification of propyne with their Pd(OAc)2/PN/HA (PN = (2-pyridyl)diphenylphosphine, HA = strong acid with weakly coordinating anion, like methanesulfonic acid) catalyst has been declared commercially ready. However, despite the significant progress in the activity of Pd-hydroesterification catalysts, further improvements are warranted. Thus, for example, activity maintenance still seems to be an issue. Homogeneous Pd catalysts are prone to a number of deactivation reactions. Activity and stability promoters are often corrosive and add to the complexity of the system, making it less attractive. Nonetheless, the versatility of the process and its tolerance toward the functional groups of substrates should appeal especially to the makers of specialty products. Although hydroesterification yields esters from alkenes, alkynes, and dienes in fewer steps than hydroformylation does, the latter has some advantages at the current state of the art. (1) Hydroformylation catalysts, particularly some recently published phosphine-modified Rh systems, can achieve very high regioselectivity for the linear product that hydroesterification catalysts cannot match yet. By analogy with hydroformylation, bulkier ligands ought to be tested in hydroesterification to increase normal-ester selectivity. (2) Hydroformylation is proven, commercial. Hydroesterification can only replace it if it can provide significant economic incentives. Similar or just marginally better performance could not justify the cost of development of a new technology. (3) Hydroesterification requires pure CO while hydroformylation uses syngas, a mixture of CO and H2. The latter is typically more available and less expensive (for industrial applications CO is most often separated from syngas). (4) The acid component of the hydroesterification catalyst makes the process corrosive. It would be desirable to develop new hydroesterification catalysts that do not require acid stabilizer/activity booster. Clearly, any new hydroesterification technology will directly compete with the hydroformylation route. This is especially true for olefin feeds, since both processes add one CO to the olefin, yielding oxygenates that can be converted into identical products. For some niche applications, like the production of MMA from propyne, hydroesterification seems to have an advantage as compared to hydroformylation due to the high activity and selectivity of the Pd(OAc)2/(2-pyridyl)diphenylphosphine catalyst. Since hydroesterification is an emerging technology, it is reasonable to assume that the potential for improvement is greater than in the mature hydroformylation. It is therefore possible that hydroesterification will become competitive in the future; thus, continued effort in the field is warranted.
Predictive Theory for Viscous Fingering in Compositional Displacement (1994)

Summary A theory of compositional viscous fingering with no adjustable parameters that reduces to the Todd and Longstaff model for miscible floods is presented. The theory gives excellent predictive agreement with simulation results for a wide range of recovery processes. The high-resolution compositional simulations used to validate the theory are the first to resolve viscous fingering adequately in flow other than miscible flow.
Transactivation of Vascular Endothelial Growth Factor (VEGF) Receptor Flk-1/KDR Is Involved in Sphingosine 1-Phosphate-stimulated Phosphorylation of Akt and Endothelial Nitric-oxide Synthase (eNOS) (2002)

Sphingosine 1-phosphate (S1P) and vascular endothelial growth factor (VEGF) elicit numerous biological responses including cell survival, growth, migration, and differentiation in endothelial cells mediated by the endothelial differentiation gene, a family of G-protein-coupled receptors, and fetal liver kinase-1/kinase-insert domain-containing receptor (Flk-1/KDR), one of VEGF receptors, respectively. Recently, it was reported that S1P or VEGF treatment of endothelial cells leads to phosphorylation at Ser-1179 in bovine endothelial nitric oxide synthase (eNOS), and this phosphorylation is critical for eNOS activation. S1P stimulation of eNOS phosphorylation was shown to involve G(i) protein, phosphoinositide 3-kinase, and Akt. VEGF also activates eNOS through Flk-1/KDR, phosphoinositide 3-kinase, and Akt, which suggested that S1P and VEGF may share upstream signaling mediators. We now report that S1P treatment of bovine aortic endothelial cells acutely increases the tyrosine phosphorylation of Flk-1/KDR, similar to VEGF treatment. S1P-mediated phosphorylation of Flk-1/KDR, Akt, and eNOS were all inhibited by VEGF receptor tyrosine kinase inhibitors and by antisense Flk-1/KDR oligonucleotides. Our study suggests that S1P activation of eNOS involves G(i), calcium, and Src family kinase-dependent transactivation of Flk-1/KDR. These data are the first to establish a critical role of Flk-1/KDR in S1P-stimulated eNOS phosphorylation and activation.
Transient Hypoxia Stimulates Mitochondrial Biogenesis in Brain Subcortex by a Neuronal Nitric Oxide Synthase-Dependent Mechanism (2008)

The adaptive mechanisms that protect brain metabolism during and after hypoxia, for instance, during hypoxic preconditioning, are coordinated in part by nitric oxide (NO). We tested the hypothesis that acute transient hypoxia stimulates NO synthase (NOS)-activated mechanisms of mitochondrial biogenesis in the hypoxia-sensitive subcortex of wild-type (Wt) and neuronal NOS (nNOS) and endothelial NOS (eNOS)-deficient mice. Mice were exposed to hypobaric hypoxia for 6 h, and changes in immediate hypoxic transcriptional regulation of mitochondrial biogenesis was assessed in relation to mitochondrial DNA (mtDNA) content and mitochondrial density. There were no differences in cerebral blood flow or hippocampal PO2 responses to acute hypoxia among these strains of mice. In Wt mice, hypoxia increased mRNA levels for peroxisome proliferator-activated receptor-gamma coactivator-1alpha (PGC-1 alpha), nuclear respiratory factor-1, and mitochondrial transcription factor A. After 24 h, new mitochondria, localized in reporter mice expressing mitochondrial green fluorescence protein, were seen primarily in hippocampal neurons. eNOS-/- mice displayed lower basal levels but maintained hypoxic induction of these transcripts. In contrast, nuclear transcriptional regulation of mitochondrial biogenesis in nNOS-/- mice was normal at baseline but did not respond to hypoxia. After hypoxia, subcortical mtDNA content increased in Wt and eNOS-/- mice but not in nNOS-/- mice. Hypoxia stimulated PGC-1alpha protein expression and phosphorylation of protein kinase A and cAMP response element binding (CREB) protein in Wt mice, but CREB only was activated in eNOS-/- mice and not in nNOS-/- mice. These findings demonstrate that hypoxic preconditioning elicits subcortical mitochondrial biogenesis by a novel mechanism that requires nNOS regulation of PGC-1alpha and CREB.
Current Status of Ketamine and Related Compounds for Depression (2013)

Article Abstract Because this piece does not have an abstract, we have provided for your benefit the first 3 sentences of the full text. Several clinical trials have demonstrated the rapid antidepressant effects of the N-methyl-d-aspartate (NMDA) antagonist ketamine for the treatment of both major depressive disorder (MDD) and the depressed state of bipolar disorder.1 While these results from academic settings are promising, generalizability to "real-world" clinical populations is a looming question. This brief review will address pragmatic clinical issues and highlight recent developments regarding ketamine and related compounds for depression.
Clinical review: Severe malaria. (2003)

Malaria represents a medical emergency because it may rapidly progress to complications and death without prompt and appropriate treatment. Severe malaria is almost exclusively caused by Plasmodium falciparum. The incidence of imported malaria is increasing and the case fatality rate remains high despite progress in intensive care and antimalarial treatment. Clinical deterioration usually appears 3-7 days after onset of fever. Complications involve the nervous, respiratory, renal, and/or hematopoietic systems. Metabolic acidosis and hypoglycemia are common systemic complications. Intravenous quinine and quinidine are the most widely used drugs in the initial treatment of severe falciparum malaria, whereas artemisinin derivatives are currently recommended for quinine-resistant cases. As soon as the patient is clinically stable and able to swallow, oral treatment should be given. The intravascular volume should be maintained at the lowest level sufficient for adequate systemic perfusion to prevent development of acute respiratory distress syndrome. Renal replacement therapy should be initiated early. Exchange blood transfusion has been suggested for the treatment of patients with severe malaria and high parasitemia. For early diagnosis, it is paramount to consider malaria in every febrile patient with a history of travel in an area endemic for malaria.
The SARS-CoV-2 outbreak from a one health perspective (2020)

The severe acute respiratory syndrome cornavirus (SARS-CoV-2) is a new human coronavirus candidate recently detected in China that is now reported in people on inhabited continents. The virus shares a high level of identity with some bat coronaviruses and is recognised as a potentially zoonotic virus. We are utilizing the One Health concept to understand the emergence of the virus, as well as to point to some possible control strategies that might reduce the spread of the virus across the globe; thus, containment of such virus would be possible.
International Trial of the Edmonton Protocol for Islet Transplantation (2006)

Islet transplantation with the use of the Edmonton protocol can successfully restore long-term endogenous insulin production and glycemic stability in subjects with type 1 diabetes mellitus and unstable control, but insulin independence is usually not sustainable. Persistent islet function even without insulin independence provides both protection from severe hypoglycemia and improved levels of glycated hemoglobin. (ClinicalTrials.gov number, NCT00014911 [ClinicalTrials.gov].).
Rat Insulin Genes: Construction of Plasmids Containing the Coding Sequences (1977)

Recombinant bacterial plasmids have been constructed that contain complementary DNA prepared from rat islets of Langerhans messenger RNA. Three plasmids contain cloned sequences representing the complete coding region of rat proinsulin I, part of the preproinsulin I prepeptide, and the untranslated 3' terminal region of the mRNA. A fourth plasmid contains sequences derived from the A chain region of rat preproinsulin II.
DGAT1 promoter polymorphism associated with alterations in body mass index, high density lipoprotein levels and blood pressure in Turkish women (2002)

Triglyceride synthesis is catalyzed by acyl CoA:diacylglycerol acyltransferases (DGAT), microsomal enzymes that use diacylglycerol and fatty acyl CoAs as substrates. Because DGAT1 expression is up-regulated during adipocyte differentiation and DGAT1 deficiency is associated with leanness in mice, we hypothesized that alterations in DGAT1 expression may affect human body weight. We identified five polymorphisms in the human DGAT1 promoter and 5' non-coding sequence in a random Turkish population. Functional analysis of one common variant, C79T, revealed reduced promoter activity for the 79T allele in cultured cell lines. In 476 Turkish women, the 79T allele was associated with lower body mass index (BMI) (p = 0.004), conferring an odds ratio of 2.0 (95% CI = 1.30-3.07, p = 0.0001) for BMI </= 20. Interestingly, after controlling for the influence of BMI, the 79T allele was also associated with higher plasma HDL cholesterol levels (p = 0.0006) and lower diastolic blood pressure (p = 0.019) in these women. No association was found in Turkish men (n = 846). Our findings suggest that genetic variation at the DGAT1 locus may influence BMI and other metabolic parameters associated with cardiovascular risk in selected human populations.
Cisplatin Sensitizes Cancer Cells to Ionizing Radiation via Inhibition of Nonhomologous End Joining (2005)

The combination of cisplatin and ionizing radiation (IR) treatment represents a common modality for treating a variety of cancers. These two agents provide considerable synergy during treatment, although the mechanism of this synergy remains largely undefined. We have investigated the mechanism of cisplatin sensitization to IR using a combination of in vitro and in vivo experiments. A clear synergistic interaction between cisplatin and IR is observed in cells proficient in nonhomologous end joining (NHEJ) catalyzed repair of DNA double-strand breaks (DSB). In contrast, no interaction between cisplatin and IR is observed in NHEJ-deficient cells. Reconstituted in vitro NHEJ assays revealed that a site-specific cisplatin-DNA lesion near the terminus results in complete abrogation of NHEJ catalyzed repair of the DSB. These data show that the cisplatin-IR synergistic interaction requires the DNA-dependent protein kinase-dependent NHEJ pathway for joining of DNA DSBs, and the presence of a cisplatin lesion on the DNA blocks this pathway. In the absence of a functional NHEJ pathway, although the cells are hypersensitive to IR, there is no synergistic interaction with cisplatin.
IL-4 and IL-5 mRNA and Protein in Bronchial Biopsies From Patients With Atopic and Nonatopic Asthma: Evidence Against "Intrinsic" Asthma Being a Distinct Immunopathologic Entity (1996)

Intrinsic (nonatopic) asthma is considered to be a distinct pathogenetic variant of asthma since, unlike extrinsic (atopic) asthma, patients with the disease are skin test-negative to common aeroallergens, and have total serum IgE concentrations within the normal range. Nevertheless, the recent demonstration of increased numbers of cells expressing the high-affinity IgE receptor in bronchial biopsies from atopic and nonatopic asthmatic subjects, together with epidemiologic evidence indicating that serum IgE concentrations relate closely to asthma prevalence regardless of atopic status, suggests that IgE-mediated mechanisms may participate in the pathogenesis of both atopic and nonatopic asthma. Furthermore both variants of the disease are associated with bronchial mucosal eosinophilic inflammation. Interleukin-4 (IL-4) is an essential cofactor for IgE synthesis, and there is strong evidence that IL-5 plays a major role in eosinophil accumulation in asthmatic inflammation. For these reasons we compared the expression of IL-4 and IL-5 mRNA and protein product using a semiquantitative reverse transcriptase-polymerase chain reaction (RT-PCR) amplification, in situ hybridization, and immunohistochemistry in bronchial biopsies from symptomatic atopic and nonatopic asthmatic subjects and atopic and nonatopic controls. The results showed that as compared with controls, biopsies from both groups of asthmatic subjects had increased numbers of IL-4 and IL-5 mRNA copies relative to beta-actin mRNA as detected by RT-PCR. Similarly, in situ hybridization and immunohistochemistry demonstrated increased numbers of cells expressing IL-4 and IL-5 mRNA and protein in asthmatic subjects, irrespective of their atopic status. We conclude that individuals with either atopic or nonatopic asthma show infiltration of the bronchial mucosa with cells expressing Th2-type cytokines, providing further evidence for similarities in the immunopathogenesis of these clinically distinct forms of asthma.
A Facile and Selective Procedure for Oxidation of Sulfides to Sulfoxides on Silica Gel Supported Magnesium Monoperoxyphthalate (MMPP) in Dichloromethane (1997)

The scope of the magnesium monoperoxyphthalate (MMPP) oxidation of sulfides to sulfoxides has been extended by using hydrated silica gel as a solid support in dichloromethane media. This procedure works in the presence of a number of functional groups on the sulfides, including carbonyl and alkene groups that have been known to undergo Baeyer-Villiger oxidation and epoxidation with MMPP when using more conventional procedures. To our knowledge, this is the first example of oxidation of sulfides containing a carbonyl group with MMPP in non-aqueous media without any Baeyer-Villiger reaction. The reported procedure is easy to perform, product separation is trivial and it produces excellent yields.
Real Time Automated Tone Mapping System for HDR Video (2012)

Tone Mapping of HDR Images has been studied extensively since the introduction of digital HDR capture methods. However, until recently HDR video has not been realized in a viable form as that given by Tocci et al.[1], which will lead to readily available HDR video cameras. Because they capture video with much broader dynamic range than can currently be displayed, these cameras present a unique challenge. In order to maintain backward-compatibility with legacy broadcast, recording, and display equipment, HDR video cameras need to provide a real-time tonemapped LDR video stream without the benefit of post-processing steps. The purpose of this research is to present a complete TMO solution that can be implemented in real time hardware to yield a high-quality automated LDR video stream suitable for direct use by today’s recording, broadcast, and display equipment. Index Terms — HDR, TMO, video 1.