gebhart/patrepeval huggingface dataset:
Downregulation of cell-surface CD4 expression by simian immunodeficiency virus Nef prevents viral super infection. (1993)

The nef gene product encoded by the mac239 proviral clone of simian immunodeficiency virus (SIV) markedly enhances viral replication and pathogenesis in vivo. We have used this biologically active nef isolate to examine the phenotype of Nef in retrovirally transduced human T cells in culture. SIV Nef is shown to dramatically inhibit cell-surface expression of the CD4 glycoprotein without significantly affecting the total steady-state level of cellular CD4. This downregulation of the cell-surface CD4 receptor for human immunodeficiency virus type 1 (HIV-1) infection correlated with the acquisition of resistance to superinfection by HIV-1. However, SIV Nef did not affect the level of gene expression directed by the HIV-1 long terminal repeat. It is hypothesized that downregulation of cell-surface CD4 by Nef facilitates the efficient release of infectious progeny virions and, hence, viral spread in vivo.
Scale Continuous Microwave Dry-Media Reactor - Part II: Application to Waxy Esters Production (2000)

The solvent free esterification reaction between stearic acid and stearyl alcohol has been examined with a montmorillonite clay as catalyst. To aim for industrial application the system has been studied on reaction rate, product purity, catalyst behavior and water removal as function of the process conditions. To avoid an etherification side reaction and to aim for the highest reaction rate, the temperature should be strictly maintained at 170 °C. This is provided on larger scale by the application of microwave heating. Although the examined Brønsted acid clay was found to lose its catalytic activity at very low water activities, a yield of 95 % pure stearyl stearate can be obtained by simply filtering of the clay without solvent extraction or distillation. The “waxy” esterification reaction was investigated with the pilot plant continuous microwave dry-media reactor (CMDR). The reaction time needed for 95 % yield was reduced by a factor 20–30 in comparison with industrial conventional reactors. This was due to the more homogeneous heat transfer of microwaves, which allows to reach a higher bulk temperature.
Utility of Amsel Criteria, Nugent Score, and Quantitative PCR for Gardnerella vaginalis , Mycoplasma hominis , and Lactobacillus spp. for Diagnosis of Bacterial Vaginosis in Human Immunodeficiency Virus-Infected Women (2005)

Bacterial vaginosis (BV) is a clinical syndrome presenting with a malodorous vaginal discharge and increased vaginal pH. Diagnosis has been based on clinical Amsel criteria and direct Gram stain of vaginal secretions. Human immunodeficiency virus (HIV)-infected participants in the Women's Interagency HIV Study contributed cervicovaginal lavage (CVL) samples. Lactobacilli, Gardnerella vaginalis, and Mycoplasma hominis in cervicovaginal lavage samples were quantified by PCR. Gynecologic evaluation included Nugent score and Amsel criterion assessment. We compared the gold standard Nugent score to Amsel criteria and quantitative bacterial PCR for diagnosing BV in 203 CVL samples from women with Nugent scores of 7 to 10 (BV group) and 203 samples from women with BV Nugent scores of 0 to 3 ("No-BV" group). Only 75 of the 203 CVL samples from women with Nugent scores of 7 to 10 met positive Amsel criteria. Increasing levels of G. vaginalis and M. hominis and decreasing levels of lactobacilli were significantly associated with BV by Nugent score. Of the group with Nugent scores of 7 to 10, 83% and 81% had log(10) G. vaginalis counts and log(10) M. hominis counts greater than 6.81 and 4.82, respectively, while only 30% and 31% of the group with Nugent scores of 0 to 3 were above these thresholds, respectively. There was significant overlap in the log(10) lactobacillus counts between the two groups. Utilizing all three log(10) bacterial counts (G. vaginalis, M. hominis, and lactobacilli) in our model improved the sensitivity and specificity to 83% and 78%, respectively, in comparison with Nugent score. In this cohort, Amsel criteria were poorly predictive of BV. PCR quantification of G. vaginalis and M. hominis from CVL is significantly more sensitive than Amsel criteria for diagnosing BV.
Chiral allenylboronic esters as practical reagents for enantioselective carbon-carbon bond formation. Facile synthesis of (-)-ipsenol (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChiral allenylboronic esters as practical reagents for enantioselective carbon-carbon bond formation. Facile synthesis of (-)-ipsenolNobuo. Ikeda, Isao. Arai, and Hisashi. YamamotoCite this: J. Am. Chem. Soc. 1986, 108, 3, 483–486Publication Date (Print):February 1, 1986Publication History Published online1 May 2002Published inissue 1 February 1986https://pubs.acs.org/doi/10.1021/ja00263a020https://doi.org/10.1021/ja00263a020research-articleACS PublicationsRequest reuse permissionsArticle Views1647Altmetric-Citations143LEARN 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
Evaluation of lysis filtration as an adjunct to conventional blood culture. (1986)

A lysis filtration system was used in conjunction with conventional broth culture for 1112 blood cultures. The system, which entailed collection of 5 ml of blood into bottles containing 50 ml isotonic phosphate buffer, Tween 20, and Rhozyme with subsequent filtration using a 0.45 micron Millipore field monitor, was simple and economical to use. Positive results were obtained earlier than those obtained with conventional broth cultures, and almost twice as many fungi and yeasts were isolated. Some fastidious organisms such as Haemophilus influenzae and Streptococcus pneumoniae however, were not recovered from the lysis system, and contaminants in lysis cultures were three times as common as in conventional culture. The number of positive cultures was also adversely influenced by incubation of the blood lysis mixture overnight before filtration. We conclude that this lysis filtration system is useful as an adjunct to conventional broth culture in selected patients in cases in which filtration can be carried out soon after collection.
Sindbis virus attachment: isolation and characterization of mutants with impaired binding to vertebrate cells (1993)

Sindbis virus can infect a broad range of insect and vertebrate cell types. The ability to restrict tissue tropism and target virus infection to specific cell types would expand the usefulness of engineered alphaviruses as gene expression vectors. In this study, virus pools derived from libraries of full-length Sindbis virus cDNA clones containing random insertion mutations in the PE2 or E1 virion glycoprotein gene were screened for mutants defective for binding to vertebrate cells. Binding-competent mutants were depleted by serial adsorption to chicken embryo fibroblast (CEF) monolayers at 4 degrees C, and the remaining population was amplified by immune-enhanced infection of P388D1 cells. From the PE2 libraries, 12 candidate mutants showing reduced cytopathic effects on CEF monolayers were isolated and three representative mutants, NB1, NB2, and NB12, were characterized in detail. Insertion mutations for NB1 and NB12 were found near the PE2 cleavage site, whereas the insertion in NB2 occurred between residues 69 and 74 of E2. Although virion assembly and release occurred normally for all three mutants, PE2 cleavage was completely (NB1) or partially (NB12) blocked for the mutants with insertions near the PE2 cleavage site. Both NB1 and NB2 were defective for binding to CEF and BHK-21 cells. Mild trypsin digestion of isolated NB1 virions resulted in PE2 cleavage and partially restored binding to CEF. Besides defective binding, NB1 also exhibited slower CEF penetration kinetics. Consistent with previous work, these results implicate PE2 cleavage and domains in the N-terminal portion of E2 as important determinants of alphavirus binding and penetration. Binding-defective mutants such as NB2, which exhibit normal particle assembly, release, and penetration, may be useful for future efforts to target Sindbis virus infection.
Elevated levels of mannan-binding leptin (MBL) and eosinophilia in patients of bronchial asthma with allergic rhinitis and allergic bronchopulmonary aspergillosis associate with a novel intronic polymorphism in MBL (2006)

Mannan-binding lectin (MBL), an important component of innate immunity, binds to a range of foreign antigens and initiates the lectin complement pathway. Earlier studies have reported high plasma MBL levels in allergic patients in comparison to healthy controls. In view of varied plasma MBL levels being determined by genetic polymorphisms in its collagen region, we investigated the association of single nucleotide polymorphisms (SNPs) in the collagen region of human MBL with respiratory allergic diseases. The study groups comprised patients of bronchial asthma with allergic rhinitis (n = 49) and allergic bronchopulmonary aspergillosis (APBA) (n = 11) and unrelated age-matched healthy controls of Indian origin (n = 84). A novel intronic SNP, G1011A of MBL, showed a significant association with both the patient groups in comparison to the controls (P < 0.01). Patients homozygous for the 1011A allele showed significantly higher plasma MBL levels and activity than those homozygous for the 1011G allele (P < 0.05). The 1011A allele also showed a significant correlation with high peripheral blood eosinophilia (P < 0.05) and low forced expiratory volume in 1 s (FEV(1)) (P < 0.05) of the patients. We conclude that the 1011A allele of MBL may contribute to elevated plasma MBL levels and activity and to increased severity of the disease markers in patients of bronchial asthma with allergic rhinitis and ABPA.
Detection of SNPs in the Plasma of Pregnant Women and in the Urine of Kidney Transplant Recipients by Mass Spectrometry (2006)

Recently, it has been discovered that cell-free fetal DNA is smaller than corresponding maternal DNA. Therefore, circulating fetal DNA can be enriched by size-fractionation. Such a selection improves the non-invasive prenatal diagnosis of paternally inherited single gene mutations. Recent studies showed that MALDI-TOF mass spectrometry (MS) can be used to reliably detect fetal-specific single-nucleotide polymorphisms (SNPs) in maternal plasma. In this study, we looked at whether the size-fractionation approach could improve the detection of paternally inherited SNPs by MS assay. Our results indicated that the size-fractionation approach improved the analysis of paternally inherited SNP alleles. Our previous studies showed that donor-derived STR sequences could be detected in the urine of kidney transplant recipients. Here, we also examined whether donor-specific SNPs could be detected in recipient's urine by MS.
Enhanced wear performance of highly crosslinked UHMWPE for artificial joints (2000)

It is well known that osteolysis induced by polyethylene wear debris is the main cause of long-term failure of hip and knee prostheses. We developed a treatment of medical-grade ultra-high molecular-weight polyethylene (UHMWPE) in order to improve its tribologic properties and reduce its wear. Medical-grade UHMWPE was irradiated with a 200 kGy dose of radiation, thermally stabilized at a temperature close to the melting point, and then sterilized with ethylene oxide. The irradiation treatment was performed to crosslink the UHMWPE. The thermal stabilization treatment, contributing to the reaction between the free radicals generated by the irradiation process, was chosen to enhance crosslinking and to prevent oxidation and the shortening of chains. The non-invasive sterilization process with ethylene oxide was chosen to prevent the re-formation of free radicals. The wear performance of this material was compared to UHMWPE, untreated or treated with different sterilization techniques, using gamma and beta irradiation. Insoluble crosslinked constituents were measured with an extraction method. Wear was evaluated using a flat-on-ring wear test machine. While small differences were found among the different sterilization processes, 200 kGy-irradiated UHMWPE followed by thermal treatment and sterilization with ethylene oxide had the least wear and the greatest amount of crosslinking.
Synthesis and characterization of disulfide cross-linked oligonucleotides (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and characterization of disulfide cross-linked oligonucleotidesAnn E. Ferentz, Thomas A. Keating, and Gregory L. VerdineCite this: J. Am. Chem. Soc. 1993, 115, 20, 9006–9014Publication Date (Print):October 1, 1993Publication History Published online1 May 2002Published inissue 1 October 1993https://pubs.acs.org/doi/10.1021/ja00073a016https://doi.org/10.1021/ja00073a016research-articleACS PublicationsRequest reuse permissionsArticle Views769Altmetric-Citations75LEARN 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-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
Block recycling schemes and their cost-based optimization in nand flash memory based storage system (2007)

Flash memory has many merits such as light weight, shock resistance, and low power consumption, but also has limitations like the erase-before-write property. To overcome such limitations and to use it efficiently as storage media in mobile systems, Flash memory based storage systems require special address mapping software called the FTL (Flash-memory Translation Layer). Like cleaning in Log-structured file system (LFS), the FTL often performs a merge operation for block recycling and its efficiency affects the performance of the storage system. To reduce the block recycling costs in NAND Flash memory based storage, we introduce another block recycling scheme that we call migration. Our cost-models and experimental results show that cost-based selection of merge or migration for each block recycling can decrease block recycling costs and, therefore, improve performance of Flash memory based storage systems. Also, we derive the macroscopic optimal migration/merge sequence minimizing block recycling costs for each migration/merge combination period. Experimental results show that the performance of Flash memory based storage can be further improved by the macroscopic optimization than the simple cost-based selection.
Dendritic Cells Infected with PoxvIn Vitro iruses Encoding MART-1/ Melan A Sensitize T Lymphocytes In Vitro (1997)

Dendritic cells (DC) are potent professional antigen-presenting cells that can activate naive T lymphocytes and initiate cellular immune responses. As adjuvants, DC may be useful in enhancing the immunogenicity of tumor antigens and mediating tumor regression. Endogenous expression of antigen by DC offers the potential advantage of allowing prolonged constitutive presentation of endogenously processed epitopes and exploitation of multiple restriction elements for the presentation of the same antigen. In this report, we show that human DC are (a) capable of infection by recombinant poxviruses encoding melanoma-associated antigen (MAA) genes and (b) capable of efficiently processing and presenting these MAA to cytotoxic T cells. In 6/6 HLA A*0201-expressing melanoma patients tested, the virally driven expression of MART-1/Melan A MAA by DC was sufficient to generate CD8+ T lymphocytes that could recognize naturally processed epitopes on tumor cells. In most cases, specific anti-MART-1 reactivity could be detected after a single stimulation. Analysis of epitope dominance revealed that the amino acid sequence recognized by these cytotoxic T lymphocytes (CTL) corresponded to the MART-1(27-35) residues previously shown to be most commonly recognized by cytotoxic T lymphocytes expanded from metastatic melanoma lesions. These data show that the virally driven expression of MAA by DC can be exploited for the efficient induction of clinically relevant cytotoxic T-cell responses. This has clinical implications for active immunization therapy, and currently vaccine trials have been proposed for patients with metastatic melanoma.
Granivory in Desert Ecosystems (1979)

Species distribution models (SDMs) are numerical tools that combine observations of species occurrence or abundance with environmental estimates. They are used to gain ecological and evolutionary insights and to predict distributions across landscapes, ...Read More
Spiral K‐space MR imaging of cortical activation (1995)

Brain function can be mapped with magnetic resonance (MR) imaging sensitized to regional changes in blood oxygenation due to cortical activation. Several MR imaging methods, including conventional imaging and echo-planar imaging, have been successfully used for this purpose. The authors investigated spiral k-space MR imaging, implemented with an unmodified 1.5-T clinical imager, for imaging of cortical activation. A gradient-echo, spiral k-space imaging method was used to measure activation in the primary visual cortex (number sequence task), primary motor cortex (fist-clenching task), and prefrontal cortex (verbal fluency task). Comparison of conventional and spiral k-space imaging in the visual and motor cortex, in which signal-to-noise ratio, voxel size, and imaging time were matched, showed that artifacts were reduced with the spiral k-space method, while the area and degree of activation were similar. The number of sections that could be imaged in a fixed time interval was increased by a factor of four with this implementation of spiral k-space imaging compared with conventional imaging.
Susceptibility to Diabetic Nephropathy Is Related to Dicarbonyl and Oxidative Stress (2005)

Dicarbonyl and oxidative stress may play important roles in the development of diabetes complications, and their response to hyperglycemia could determine individual susceptibility to diabetic nephropathy. This study examines the relationship of methylglyoxal, 3-deoxyglucosone (3DG), and oxidative stress levels to diabetic nephropathy risk in three populations with diabetes. All subjects in the Overt Nephropathy Progressor/Nonprogressor (ONPN) cohort (n = 14), the Natural History of Diabetic Nephropathy study (NHS) cohort (n = 110), and the Pima Indian cohort (n = 45) were evaluated for clinical nephropathy, while renal structural measures of fractional mesangial volume [Vv(Mes/glom)] and glomerular basement membrane (GBM) width were determined by electron microscopy morphometry in the NHS and Pima Indian cohorts. Methylglyoxal and 3DG levels reflected dicarbonyl stress, while reduced glutathione (GSH) and urine 8-isoprostane (8-IP) measured oxidative stress. Cross-sectional measures of methylglyoxal production by red blood cells incubated in 30 mmol/l glucose were increased in nephropathy progressors relative to nonprogressors in the ONPN (P = 0.027) and also reflected 5-year GBM thickening in the NHS cohort (P = 0.04). As nephropathy progressed in the NHS cohort, in vivo levels of methylglyoxal (P = 0.036), 3DG (P = 0.004), and oxidative stress (8-IP, P = 0.007 and GSH, P = 0.005) were seen, while increased methylglyoxal levels occurred as nephropathy progressed (P = 0.0016) in the type 2 Pima Indian cohort. Decreased glyceraldehyde-3-phosphate dehydrogenase activity also correlated with increased methylglyoxal levels (P = 0.003) in the NHS cohort. In conclusion, progression of diabetic nephropathy is significantly related to elevated dicarbonyl stress and possibly related to oxidative stress in three separate populations, suggesting that these factors play a role in determining individual susceptibility.
Does Isoform Diversity Explain Functional Differences in the 14-3-3Protein Family? (2006)

The 14-3-3 family of proteins was originally identified in 1967 as simply an abundant brain protein. However it took almost 25 years before the ubiquitous role of 14-3-3 in cell biology was recognized when it was found to interact with several signalling and proto-oncogene proteins. Subsequently 14-3-3 proteins were the first protein recognized to bind a discrete phosphoserine/threonine-binding motifs. In mammals the 14-3-3 protein family is comprised of seven homologous isoforms. The 14-3-3 family members are expressed in all eukaryotes and although no single conserved function of the 14-3-3s is apparent, their ability to bind other proteins seems a crucial characteristic. To date more than 300 binding partners have been identified, of which most are phosphoproteins. Consequently, it has become clear that 14-3-3 proteins are involved in the regulation of most cellular processes, including several metabolic pathways, redox-regulation, transcription, RNA processing, protein synthesis, protein folding and degradation, cell cycle, cytoskeletal organization and cellular trafficking. In this review we include recent reports on the regulation of 14-3-3 by phosphorylation, and discuss the possible functional significance of the existence of distinct 14-3-3 isoforms in light of recent proteomics studies. In addition we discuss 14-3-3 interaction as a possible drug target.
Innate and Adaptive Immune Responses Determine Protection against Disseminated Infection by West Nile Encephalitis Virus (2003)

WNV continues to spread throughout the Western Hemisphere as virus activity in insects and animals has been reported in the United States, Canada, Mexico, and the Caribbean islands. West Nile virus (WNV) infects the central nervous system and causes severe disease primarily in humans who are immunocompromised or elderly. In this review, we discuss the mechanisms by which the immune system limits dissemination of WNV infection. Recent experimental studies in animals suggest important roles for both the innate and the adaptive immune responses in controlling WNV infection. Interferons, antibody, complement components and CD8+ T cells coordinate protection against severe infection and disease. These findings are analyzed in the context of recent approaches to vaccine development and immunotherapy against WNV.