gebhart/patrepeval huggingface dataset:
Purification and properties of benzoate-coenzyme A ligase, a Rhodopseudomonas palustris enzyme involved in the anaerobic degradation of benzoate (1988)

A soluble benzoate-coenzyme A (CoA) ligase was purified from the phototrophic bacterium Rhodopseudomonas palustris. Synthesis of the enzyme was induced when cells were grown anaerobically in light with benzoate as the sole carbon source. Purification by chromatography successively on hydroxylapatite, phenyl-Sepharose, and hydroxylapatite yielded an electrophoretically homogeneous enzyme preparation with a specific activity of 25 mumol/min per mg of protein and a molecular weight of 60,000. The purified enzyme was insensitive to oxygen and catalyzed the Mg2+ ATP-dependent formation of acyl-CoA from carboxylate and free reduced CoA, with high specificity for benzoate and 2-fluorobenzoate. Apparent Km values of 0.6 to 2 microM for benzoate, 2 to 3 microM for ATP, and 90 to 120 microM for reduced CoA were determined. The reaction product, benzoyl-CoA, was an effective inhibitor of the ligase reaction. The kinetic properties of the enzyme match the kinetics of substrate uptake by whole cells and confirm a role for benzoate-CoA ligase in maintaining entry of benzoate into cells as well as in catalyzing the first step in the anaerobic degradation of benzoate by R. palustris.
Some practical considerations and applications of the national cancer institute in vitro anticancer drug discovery screen (1995)

Abstract During 1985–1990 the U.S. National Cancer Institute (NCI) phased out its murine leukemia P388 anticancer drug screening program and developed as the replacement a new in vitro primary screen based upon a diverse panel of human tumor cell lines. For each substance tested, the screen generates a remarkably reproducible and characteristic profile of differential in vitro cellular sensitivity, or lack thereof, across the 60 different cell lines comprising the panel. Several investigational approaches to display, analysis, and interpretation of such profiles and databases, derived from the testing of tens of thousands of substances during the past 4–5 years since the NCI screen became fully operational, have been explored. A variety of useful, practical applications of the in vitro screen have become apparent. As these applications continue to evolve, they are proving to be complementary to diverse other anticancer screening and drug discovery strategies being developed or pursued elsewhere. Reviewed herein are some practical considerations and selected specific examples, particularly illustrating research applications of the NCI screen that may be more broadly applicable to the search for new anticancer drug development leads with novel profiles of antitumor activity and/or mechanisms of action. © 1995 Wiley‐Liss, Inc. This article is a US Government work and, as such, is in the public domain in the United States of America.
Enhanced fetal hemoglobin production by phenylacetate and 4- phenylbutyrate in erythroid precursors derived from normal donors and patients with sickle cell anemia and beta-thalassemia (1993)

In both sickle cell (SS) anemia and beta-thalassemia (beta-thal), an increase in fetal hemoglobin (HbF) ameliorates the clinical symptoms of the underlying disease. Several pharmacologic agents have been used to elevate HbF levels in adults; however, concerns regarding adverse effects of the prevailing drugs raise an urgent need for other agents capable of stimulating HbF production. We show here that sodium phenylacetate (NaPA) and its precursor, sodium 4-phenylbutyrate (NaPB), can enhance HbF production in cultured erythroid progenitor derived from normal donors and patients with SS anemia or beta-thal, when used at pharmacologic concentrations. Treatment resulted in (1) reduced cell proliferation, (2) elevated hemoglobin (Hb) content per cell (mean cellular Hb [MCH]), and (3) an increased proportion of HbF produced, associated with elevated levels of gamma-globin mRNA. Moreover, the active phenyl-fatty acids, with NaPA as a prototype, potentiated HbF induction by other drugs of clinical interest, including hydroxyurea (HU), sodium butyrate, and 5-azacytidine (5AzaC). Efficacy could be further enhanced by introducing chlorine substituents at the phenyl ring to increase drug lipophilicity. Our findings indicate that NaPA and NaPB, both already proven safe and effective in treatment of children with urea cycle disorders, might benefit also patients with severe hemoglobinopathies. The two-phase liquid culture procedure used in this study should prove valuable in further studies exploring the mechanisms of HbF induction by these agents, and might provide an assay to predict patient response in the clinical setting.
Middle East respiratory syndrome coronavirus: quantification of the extent of the epidemic, surveillance biases, and transmissibility (2013)

Medical Research Council, Bill & Melinda Gates Foundation, EU FP7, and National Institute of General Medical Sciences.
Alarmins: awaiting a clinical response (2012)

Alarmins are endogenous molecules that are constitutively available and released upon tissue damage and activate the immune system. Current evidence indicates that uncontrolled and excessive release of alarmins contributes to the dysregulated processes seen in many inflammatory and autoimmune conditions, as well as tumorigenesis and cancer spread. Conversely, alarmins have also been found to play a major role in the orchestration of tissue homeostasis, including repair and remodeling in the heart, skin, and nervous system. Here, we provide an update and overview on alarmins, highlighting the areas that may benefit from this clinical translation.
Forced Brillouin Spectroscopy Using Frequency-Tunable Continuous Wave Lasers (1995)

We have developed a new method of phonon spectroscopy using forced Brillouin scattering: A scanning interference pattern produced by intersecting two cw lasers generates the density variation (acoustic phonons) through the thermal expansion for a light-absorbing liquid. When the dispersion relation of phonons is satisfied, phonons are generated resonantly in the liquid. Continuous tuning of the frequency difference between the two lasers enables us to measure a resonance spectrum of light-excited phonons using light scattering phenomena. We demonstrate that this resonance spectrum is equivalent to the Brillouin spectrum of thermal phonons both experimentally and theoretically.
ABSCESS-FORMING FACTOR(S) PRODUCED BY STAPHYLOCOCCUS AUREUS II (1963)

Lam, Gow T. (Jefferson Medical College, Philadelphia, Pa.), Francis J. Sweeney, Jr., Charlotte M. Witmer, and Robert I. Wise. Abscess-forming factor(s) produced by Staphylococcus aureus. II. Abscess formation and immunity by a Staphylococcus and its mutants. J. Bacteriol. 86:87-91. 1963.-Three mutants were derived from a virulent parent strain of Staphylococcus aureus by ultraviolet irradiation. One mutant retained coagulase but lost its hemolytic activity; a second had no coagulase but retained its hemolysin; and a third contained hemolysin and bound coagulase but no free coagulase. The parent strain was coagulase-positive, hemolysin-positive, and possessed all the known extracellular products. All four strains were compared by bacteriophage typing, mannitol utilization, and antibiotic sensitivity tests. The four isolates were studied for their pathogenicity in Swiss albino mice and four strains of inbred mice. Their immunological characteristics as studied by repeated subcutaneous injections are reported. The importance of hemolysin and the coagulase in abscess formation is discussed. Local immunity was produced only by the parent strain, but abscesses were produced by all the strains containing coagulase.
Six degree-of-freedom haptic rendering of complex polygonal models (2003)

This paper describes a haptic rendering algorithm for arbitrary polygonal models using a six degree-of-freedom haptic interface. The algorithm supports activities such as virtual prototyping of complex polygonal models and adding haptic interaction to virtual environments. The underlying collision system computes local minimum distances between the model controlled by the haptic device and the rest of the scene. The haptic rendering computes forces and torques on the moving model based on these local minimum distances.
Type 1 fimbriation and fimE mutants of Escherichia coli K-12 (1991)

We reexamined the influence of fimE, also referred to as hyp, on type 1 fimbriation in Escherichia coli K-12. We found that one strain used previously and extensively in the analysis of type 1 fimbriation, strain CSH50, is in fact a fimE mutant; the fimE gene of CSH50 contains a copy of the insertion sequence IS1. Using a recently described allelic exchange procedure, we transferred the fimE::IS1 allele from CSH50 to our present wild-type strain, MG1655. Characterization of this IS1-containing strain (AAEC137), together with another fimE mutant of MG1655 (AAEC143), led to two conclusions about the role of fimE. First, the formation of phase variant colony types, reported widely in strains of E. coli, depends on mutation of fimE, at least in K-12 strain MG1655. Here we showed that this phenomenon reflects the ability of fimE to stimulate the rapid inversion of the fim invertible element from on to off when the bacteria are grown on agar. Second, our analysis of fimE mutants, which is limited to chromosomal constructs, provided no evidence that they are hyperfimbriate. We believe that these results, which are at odds with a previous study using fim-containing multicopy plasmids, reflect differences in gene copy number.
Thermodynamic and Kinetic Characterization of the Binding of the TATA Binding Protein to the Adenovirus E4 Promoter (1995)

A thermodynamic analysis of the binding of the TATA binding protein (TBP) from Saccharomyces cerevisiae to the adenovirus E4 promoter was conducted using quantitative DNase I "footprint" titration techniques. These studies were conducted to provide a foundation for studies of TBP structure-function relations and its assembly into transcription preinitiation complexes. The binding of TBP to the E4 promoter is well described by the Langmuir binding polynomial, suggesting that no linked equilibria contribute to the binding reaction under the conditions examined. Van't Hoff analysis yielded a nonlinear dependence on temperature with the TBP-E4 promoter interaction displaying maximal affinity at 30 degrees C. An unusually negative value of the apparent standard heat capacity change, delta Cp degrees = -3.5 +/- 0.5 kcal/mol.K, was determined from these data. The dependence of the TBP-E4 promoter interaction on [KCl] indicates that 3.6 +/- 0.3 K+ ions are displaced upon complex formation. Within experimental error, no linkage of proton binding with the TBP-E4 promoter interaction is detectable between pH 5.9 and 8.7. Rates of association of TBP for the E4 promoter were obtained using a novel implementation of a quench-flow device and DNase I "footprinting" techniques. The value determined for the second-order rate constant at pH 7.4, 100 mM KCl, 5 mM MgCl2, 1 mM CaCl2, 30 degrees C (ka = 5.2 +/- 0.5) x 10(5) M-1 s-1) confirms the results obtained by Hawley and co-workers [Hoopes, B.C., LeBlanc, J.F., & Hawley, D.K. (1992) J. Biol. Chem. 267, 11539-11547] and extends them through TBP concentrations of 636 nM.(ABSTRACT TRUNCATED AT 250 WORDS)
Metal Complex Conjugates of Antisense DNA Which Display Ribozyme-Like Activity (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTMetal Complex Conjugates of Antisense DNA Which Display Ribozyme-Like ActivityDarren Magda, Meredith Wright, Shaun Crofts, Alice Lin, and Jonathan L. SesslerView Author Information Pharmacyclics, Inc., 995 East Arques Avenue Sunnyvale, California 94086 Department of Chemistry and Biochemistry University of Texas at Austin, Austin, Texas 78712 Cite this: J. Am. Chem. Soc. 1997, 119, 29, 6947–6948Publication Date (Web):July 23, 1997Publication History Received9 April 1997Published online23 July 1997Published inissue 1 July 1997https://pubs.acs.org/doi/10.1021/ja9711223https://doi.org/10.1021/ja9711223rapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views394Altmetric-Citations68LEARN 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 (1)»Supporting Information Supporting Information SUBJECTS:Assays,Chemical structure,Conjugate acid-base pairs,Crystal cleavage,Genetics Get e-Alerts
Statistical Models: Theory and Practice (2006)

1. Observational studies and experiments 2. The regression line 3. Matrix algebra 4. Multiple regression 5. Multiple regression: special topics 6. Path models 7. Maximum likelihood 8. The bootstrap 9. Simultaneous equations 10. Issues in statistical modeling.
The 2012 Hormone Therapy Position Statement of The North American Menopause Society (2012)

Recent data support the initiation of HT around the time of menopause to treat menopause-related symptoms and to prevent osteoporosis in women at high risk of fracture. The more favorable benefit-risk ratio for ET allows more flexibility in extending the duration of use compared with EPT, where the earlier appearance of increased breast cancer risk precludes a recommendation for use beyond 3 to 5 years.
Evaluation of total hip arthroplasty devices using a total joint replacement registry (2012)

Clinically rich data from a registry with linkages to electronic health records and other administrative databases improve identification of exposures, outcomes, and patient subgroups in medical device evaluation. These various data sources facilitate refined adjustment for potential confounders such as hospital, surgeon, and patient factors and ensure comprehensive device performance evaluation within registries.
Subcellular distribution of epothilones in human tumor cells (2001)

Epothilones are a new class of natural and potent antineoplastic agents that stabilize microtubules. Although 12,13-epoxide derivatives are potent antiproliferative agents, the activities of the corresponding 12,13-olefin analogs are significantly decreased. These data were confirmed for two new analogs, 6-propyl-EpoB (pEB) and 6-propyl-EpoD (pED), in comparison with the natural compounds EpoB/EpoD, by using human A431, MCF7, and MDR1-overexpressing NCI/Adr cells. By using tritiated pEB/pED, compound uptake, release, and nuclear accumulation were investigated in A431 and NCI/Adr cells. In these cells, epothilones can principally be recognized and exported by Verapamil-sensitive efflux pumps, which are not identical to MDR1. The degree of export depends on the structure, olefin vs. epoxide-analog, and also on the intracellular drug concentration. The accumulation of pED used at 3.5 or 70 nM, respectively, was increased in the presence of 10 microM Verapamil in both cell lines 2- to 8-fold. In contrast, the intracellular levels of pEB were affected by Verapamil only at 3.5 nM pEB in NCI/Adr (2-fold) and not in A431 cells. In addition, strong nuclear accumulation was observed for pEB (40-50%) but not paclitaxel or pED (5-15%) in both cell lines. Our study suggests that differences in growth inhibitory efficacy between epoxide and olefin analogs may be based on different mechanisms of drug accumulation and subcellular distribution.
Tumour antigen targeted monoclonal antibodies incorporating a novel multimerisation domain significantly enhance antibody dependent cellular cytotoxicity against colon cancer (2013)

Tumour antigen targeted antibodies (mAbs) can induce natural killer (NK) cells to kill tumours through antibody dependent cellular cytotoxicity (ADCC) upon engagement of NK cell expressed FcγRIIIa. FcγRIIIa polymorphisms partially dictate the potency of the ADCC response. The high affinity FcγRIIIa-158-valine (V) polymorphism is associated with more potent ADCC response than the low affinity FcγRIIIa-158-phenylalanine (F) polymorphism. Because approximately 45% of patients are homozygous for the FcγRIIIa-158-F polymorphism (FF genotype), their ability to mount ADCC is impaired. We investigated whether a novel mAb capable of binding multiple antigen specific targets and engaging multiple low affinity FcγRIIIa receptors could further enhance ADCC against colon cancer in vitro. Specifically, we generated a novel anti-epidermal growth factor receptor (EGFR) antibody (termed a stradobody) consisting of an unmodified Fab sequence and two Immunoglobulin G, subclass 1 (IgG1) Fc domains separated by an isoleucine zipper domain and the 12 amino-acid IgG2 hinge. The stradobody framework induced multimerisation and was associated with increased binding to the EGFR and FcγRIIIa. From a functional perspective, when compared to an unmodified anti-EGFR mAb with a sequence identical to cetuximab (a commercially available anti-EGFR mAb), stradobodies significantly enhanced ADCC. These effects were observed using both KRAS wild type HT29 and KRAS mutant SW480 colon cancer cells as targets, and by NK cells obtained from healthy donors and a cohort of patients with colon cancer. These data suggest that high avidity cross-linking of multiple tumour surface antigens and multiple NK cell associated FcγRIIIa molecules can enhance ADCC and partially overcome impaired ADCC by FF genotype individuals in vitro.
Co-occurrence of anxiety and depression amongst older adults in low- and middle-income countries: findings from the 10/66 study (2011)

Given the close association of co-morbid anxiety and depression with disability, new policies to improve prevention, recognition and treatment will be needed to adapt to ageing populations and their mental health needs.
Association between fish consumption, long chain omega 3 fatty acids, and risk of cerebrovascular disease: systematic review and meta-analysis (2012)

Available observational data indicate moderate, inverse associations of fish consumption and long chain omega 3 fatty acids with cerebrovascular risk. Long chain omega 3 fatty acids measured as circulating biomarkers in observational studies or supplements in primary and secondary prevention trials were not associated with cerebrovascular disease. The beneficial effect of fish intake on cerebrovascular risk is likely to be mediated through the interplay of a wide range of nutrients abundant in fish.
Genes Responsible for Quantitative Regulation of Antibody Production (1996)

Evidence is first presented demonstrating that the individual capacity for antibody responsiveness has an inheritable component. The main evidence consists of spontaneous mutations causing either immunodeficiency or predisposition to autoimmunity in human and animals, and the involvement of some obvious candidate genes (in particular those belonging to the highly polymorphic histocompatibility and Igh loci), extensively analyzed in many mouse strain combinations. One finding constantly emerging from these studies is that single gene expression depends on environmental effects, lowering the genotype/phenotype correlation, but also on multigenic interactions appearing as background effects. The models available for the analysis of this multigenic regulation are discussed with special emphasis on the high and low antibody responder mice produced for this purpose by bidirectional selective breeding. The major advantage of this model is that the interline difference is huge and multispecifically expressed. The second part of the review presents the recent results on positional mapping of genes with immunomodulatory effects in this model and in one appropriate recombinant congenic strain series. This in vivo genetic dissection of antibody responsiveness discriminated the involvement of candidate genes and suggested that unsuspected genes might be identified by means of this wide open search.
Localization of nascent RNA and CREB binding protein with the PML-containing nuclear body (1998)

The cellular role of the PML-containing nuclear bodies also known as ND10 or PODs remains elusive despite links to oncogenesis and viral replication. Although a potential role in transcription has been considered, direct evidence has been lacking. By developing a novel in vivo nucleic acid labeling approach, we demonstrate the existence of nascent RNA polymerase II transcripts within this nuclear body. In addition, PML and the transactivation cofactor, CREB binding protein (CBP), colocalize within the nucleus. Furthermore, we show that CBP in contrast to PML is distributed throughout the internal core of the structure. Collectively, these findings support a role for this nuclear body in transcriptional regulation.
The Anion of 4-Dimethoxymethylpyridine. A Convenient Synthesis of Some 4-Pyridyl Ketones A convienient synthesis of some 4-pyridyl ketones (1993)

Abstract n-Butyllithium at −78°C abstracts the methine proton from 4-dimethoxymethylpyridine. The anion reacts efficiently with electrophiles. Simple ketal products can be readily hydrolysed to 4-pyridyl ketones.
Generation of Antigen-Specific, Foxp3-Expressing CD4+ Regulatory T Cells by Inhibition of APC Proteosome Function (2005)

We tested the hypothesis that immature APC, whose NF-kappaB-signaling pathway and thus maturation was blocked by the proteosome inhibitor benzyloxycarbonyl-isoleucyl-glutamyl(O-tert-butyl)-alanyl-leucinal (PSI), could be a source of Ag-specific regulatory T (Treg) cells. DO11.10 CD4(+) T cells that were incubated with Ag- and PSI-pulsed APC proliferated poorly, produced less IL-2, IFN-gamma, and IL-10 in secondary cultures, and inhibited the response of both naive and memory CD4(+) T cells stimulated by Ag-pulsed APC. The generation of PSI-APC Treg cells required IL-10 production by APC. PSI-APC Treg cell inhibition required cell-cell contact but not IL-10 or TGF-beta. Addition of IL-2 did not reverse, but Ab to CTLA-4 did reverse partially the inhibitory effect. Depletion of CD25(+) T cells before initial culture with PSI-APC did not affect Treg generation. PSI-APC Treg cells expressed high levels of Foxp3, inhibited proliferation of naive DO11.10 T cells in vivo, and abrogated colitis driven by a memory Th1 response to bacterial-associated Ag. We conclude that NF-kappaB-blocked, immature APC are able to induce the differentiation of Treg cells that can function in vitro and in vivo in an Ag-specific manner.