gebhart/patrepeval huggingface dataset:
Proteomic Analyses of aListeria monocytogenesMutant Lacking σBIdentify New Components of the σBRegulon and Highlight a Role for σBin the Utilization of Glycerol (2007)

In Listeria monocytogenes the alternative sigma factor sigmaB plays important roles in both virulence and stress tolerance. In this study a proteomic approach was used to define components of the sigmaB regulon in L. monocytogenes 10403S (serotype 1/2a). Using two-dimensional gel electrophoresis and the recently developed isobaric tags for relative and absolute quantitation technique, the protein expression profiles of the wild type and an isogenic delta sigB deletion strain were compared. Overall, this study identified 38 proteins whose expression was sigmaB dependent; 17 of these proteins were found to require the presence of sigmaB for full expression, while 21 were expressed at a higher level in the delta sigB mutant background. The data obtained with the two proteomic approaches showed limited overlap (four proteins were identified by both methods), a finding that highlights the complementarity of the two technologies. Overall, the proteomic data reaffirmed a role for sigmaB in the general stress response and highlighted a probable role for sigmaB in metabolism, especially in the utilization of alternative carbon sources. Proteomic and physiological data revealed the involvement of sigmaB in glycerol metabolism. Five newly identified members of the sigmaB regulon were shown to be under direct regulation of sigmaB using reverse transcription-PCR (RT-PCR), while random amplification of cDNA ends-PCR was used to map four sigmaB-dependent promoters upstream from lmo0796, lmo1830, lmo2391, and lmo2695. Using RT-PCR analysis of known and newly identified sigmaB-dependent genes, as well as proteomic analyses, sigmaB was shown to play a major role in the stationary phase of growth in complex media.
The Inflammatory Myelinopathy of Adreno-Leukodystrophy (1992)

Prominent inflammation in the demyelinative lesion of adreno-leukodystrophy (ALD) has suggested an immune-mediated pathogenetic component. Commercially available antibodies to T cells, B cells, macrophages, class I and II molecules, complement, IgG, IgM, IgA, interleukin-1 (IL-1), intercellular adhesion molecule-1 (ICAM-1) and tumor necrosis factor-alpha (TNF) were applied to paraffin sections of formaldehyde-fixed postmortem samples. Twenty-five primary demyelinative lesions from five juvenile ALD, three adult ALD, and three adrenomyeloneuropathic patients were evaluated with appropriate positive and negative controls. Macrophages and astrocytes were the predominant cells detected at the active edge; T lymphocytes, including T4 and CD45R subsets, were nearly as numerous but usually located around vessels within the lesion. B cells and plasma cells, usually containing IgG, were uncommon. The expression of class II molecules, restricted to one adult, was problematic; class I expression was increased in microvascular and other cells. Degraded myelin was labeled with antibodies to C3d and IL-1; IL-1 and ICAM-1 immunoreactivity was seen on microvessels and astrocytes. Tumor necrosis factor-alpha immunoreactivity was detected in macrophages, but more prominently in astrocytes. These data support a natural immune response in the demyelinative lesion of ALD, consisting predominantly of reactive astrocytes, macrophages, T cells and cytokines. A two-stage pathogenetic theory is discussed. The postulated roles of TNF and reactive astrocytes, in concert with a fundamental myelinolytic biochemical defect, suggest a different pathogenetic mechanism and raise novel therapeutic possibilities.
Analysis of Brain mRNAs by Translation in Vitro (2003)

In vitro translation systems are extremely important tools for studying protein biosynthesis. These systems have been most useful in revealing the intracellular sites of synthesis of numerous proteins, the nature of cotranslational proteolytic cleavage events, the process of core glycosylation, and the mechanisms underlying the interaction of nascent polypeptides with organelles (such as mitochondria) and with membrane vesicles (rough microsomes, RM) derived from the rough endoplasmic reticulum (RER) (see Blobel, 1980 1; Sabatini et al., 1982, 9 for reviews). When programmed with the total mRNA from an organ, translation systems will synthesize virtually all the encoded polypeptides, and so can also be useful in identifying antigenically-related proteins. Although precipitating antibodies to the proteins under study have in the past been required for these analyses, it is now possible to synthesize from cloned cDNAs large quantities of individual mRNAs, that, when used to program an in vitro translation system, yield a single polypeptide that can be directly studied.
CTLA-4 Blockade Enhances the Therapeutic Effect of an Attenuated Poxvirus Vaccine Targeting p53 in an Established Murine Tumor Model (2003)

p53 is overexpressed by half of all cancers, and is an attractive target for a vaccine approach to immunotherapy. p53 overexpression is frequently the result of point mutations, which leaves the majority of the protein in its wild-type form. Therefore, the majority of p53 sequence is wild type, making it a self-protein for which tolerance plays a role in limiting immune responses. To overcome tolerance to p53, we have expressed wild-type murine p53 in the nonpathogenic attenuated poxvirus, modified vaccinia virus Ankara (recombinant modified vaccinia virus Ankara expressing wild-type murine p53 (rMVAp53)). Mice immunized with rMVAp53 vaccine developed vigorous p53-specific CTL responses. rMVAp53 vaccine was evaluated for its ability to inhibit the outgrowth of the syngeneic murine sarcoma Meth A, which overexpresses mutant p53. Mice were inoculated with a lethal dose (5 x 10(5) cells injected s.c.) of Meth A tumor cells and vaccinated by i.p. injection 3 days later with 5 x 10(7) PFU of rMVAp53. The majority of mice remained tumor free and resistant to rechallenge with Meth A tumor cells. We wished to determine whether rMVAp53 immunization could effect the rejection of an established, palpable Meth A tumor. In subsequent experiments, mice were injected with 10(6) Meth A tumor cells, and treated 6 days later with anti-CTLA-4 Ab (9H10) and rMVAp53. The majority of treated mice had complete tumor regression along with lasting tumor immunity. In vivo Ab depletion confirmed that the antitumor effect was primarily CD8 and to a lesser extent CD4 dependent. These experiments demonstrate the potential of a novel cell-free vaccine targeting p53 in malignancy.
Germ cell defects and hematopoietic hypersensitivity to gamma- interferon in mice with a targeted disruption of the Fanconi anemia C gene (1996)

Abstract Fanconi anemia (FA) is an autosomal recessive chromosome instability syndrome characterized by progressive bone marrow (BM) failure, skeletal defects, and increased susceptibility to malignancy. FA cells are hypersensitive to DNA cross-linking agents, oxygen and have cell cycle abnormalities. To develop an animal model of the disease we generated mice homozygous for a targeted deletion of exon 9 of the murine FA complementation group C gene (fac). Mutant mice had normal neonatal viability and gross morphology, but their cells had the expected chromosome breakage and DNA cross-linker sensitivity. Surprisingly, male and female mutant mice had reduced numbers of germ cells and females had markedly impaired fertility. No anemia was detectable in the peripheral blood during the first year of life, but the colony forming capacity of marrow progenitor cells was abnormal in vitro in mutant mice. Progenitor cells from fac knock-out mice were hypersensitive to interferon gamma. This previously unrecognized phenotype may form the basis for BM failure in human FA.
IIeal dysfunction and bacterial overgrowth in patients with Crohn's disease (1981)

The intestinal bile acid metabolism was studied in sixty-one patients with non-operated Crohn's disease (twenty-seven ileitis and thirty-four ileocolitis patients) by means of the 14C-glycocholate breath test with marker-corrected faecal analysis before and after a short course of antibiotics. The results of the combined breath and faecal analysis were compared with the data of other tests detecting bacterial overgrowth and ileal dysfunction. Fifteen of the sixty-one patients (25%) presented with a 14C excretion pattern consistent with bacterial overgrowth of the small bowel. Repetition of the combined breath and faecal analysis after antibiotic treatment revealed that concurrent ileal dysfunction was present in at least six of these fifteen patients. In twenty other patients elevated marker-corrected 14C faecal excretion indicated ileal dysfunction. Thus, the overall incidence of ileal dysfunction amounted to 26/61 (44%). The sensitivity of the bile acid breath test with marker-corrected stool analysis was comparable to that of aerobic and anaerobic jejunal cultures in twenty non-selected patients for the detection of bacterial overgrowth, and to that of chemical bile acid measurement in stools for the detection of ileal dysfunction. The bile acid breath test with faecal analysis was more sensitive than measurement of glycine-taurine ratio in bile (twenty patients) and the Schilling test.
On dispersion of compound DMCs (2013)

Code for a compound discrete memoryless channel (DMC) is required to have small probability of error regardless of which channel in the collection perturbs the codewords. Capacity of the compound DMC has been derived classically: it equals the maximum (over input distributions) of the minimal (over channels in the collection) mutual information. In this paper the expression for the channel dispersion of the compound DMC is derived under certain regularity assumptions on the channel. Interestingly, dispersion is found to depend on a subtle interaction between the channels encoded in the geometric arrangement of the gradients of their mutual informations. It is also shown that the third-order term need not be logarithmic (unlike single-state DMCs). By a natural equivalence with compound DMC, all results (dispersion and bounds) carry over verbatim to a common message broadcast channel.
Endoproteolytic Processing of the Ebola Virus Envelope Glycoprotein: Cleavage Is Not Required for Function (1999)

Proteolytic processing is required for the activation of numerous viral glycoproteins. Here we show that the envelope glycoprotein from the Zaire strain of Ebola virus (Ebo-GP) is proteolytically processed into two subunits, GP1 and GP2, that are likely covalently associated through a disulfide linkage. Murine leukemia virions pseudotyped with Ebo-GP contain almost exclusively processed glycoprotein, indicating that this is the mature form of Ebo-GP. Mutational analysis identified a dibasic motif, reminiscent of furin-like protease processing sites, as the Ebo-GP cleavage site. However, analysis of Ebo-GP processing in LoVo cells that lack the proprotein convertase furin demonstrated that furin is not required for processing of Ebo-GP. In sharp contrast to other viral systems, we found that an uncleaved mutant of Ebo-GP was able to mediate infection of various cell lines as efficiently as the wild-type, proteolytically cleaved glycoprotein, indicating that cleavage is not required for the activation of Ebo-GP despite the conservation of a dibasic cleavage site in all filoviral envelope glycoproteins.
Recent Advances in the Synthesis and Application of Layered Double Hydroxide (LDH) Nanosheets (2012)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTRecent Advances in the Synthesis and Application of Layered Double Hydroxide (LDH) NanosheetsQiang Wang and Dermot O'Hare*View Author Information Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, U.K.*E-mail: [email protected]Cite this: Chem. Rev. 2012, 112, 7, 4124–4155Publication Date (Web):March 27, 2012Publication History Received18 November 2011Published online27 March 2012Published inissue 11 July 2012https://pubs.acs.org/doi/10.1021/cr200434vhttps://doi.org/10.1021/cr200434vreview-articleACS PublicationsCopyright © 2012 American Chemical SocietyRequest reuse permissionsArticle Views64498Altmetric-Citations2802LEARN 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:Anions,Inorganic compounds,Layers,Nanocomposites,Two dimensional materials Get e-Alerts
The distribution of oestrogenic isoflavones in the genus Trifolium (1967)

Of 100 Trifolium species tested prior to and during early flowering, 14 had isoflavone contents comparable with that of subterranean clover, and seven of these were closely related taxonomically. Intervarietal variation in isoflavone content was found in self-fertilized species containing isoflavones, but not in the cross-fertilized T. pratense L. In all species the isoflavones genistein, biochanin A, and formononetin were in glycosidic forms. The same isoflavone glycosides were represented in all species containing isoflavones in quantity. No species contained significant quantities of coumestrol, and many of the common naturalized species were virtually free of known oestrogens.
Synthesis, Characterization, and Polymerization of Glycidyl Methacrylate Derivatized Dextran (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis, Characterization, and Polymerization of Glycidyl Methacrylate Derivatized DextranW. N. E. van Dijk-Wolthuis, O. Franssen, H. Talsma, M. J. van Steenbergen, J. J. Kettenes-van den Bosch, and W. E. HenninkCite this: Macromolecules 1995, 28, 18, 6317–6322Publication Date (Print):August 1, 1995Publication History Published online1 May 2002Published inissue 1 August 1995https://pubs.acs.org/doi/10.1021/ma00122a044https://doi.org/10.1021/ma00122a044research-articleACS PublicationsRequest reuse permissionsArticle Views5963Altmetric-Citations328LEARN 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
The tyrosine kinase inhibitor tyrphostin blocks the cellular actions of nerve growth factor (1993)

A series of the synthetic protein kinase inhibitors known as tyrphostins were examined for their effects on the tyrosine autophosphorylation of the pp140c-trk, nerve growth factor (NGF) receptor. One of the tyrphostins, AG879, inhibited NGF-dependent pp140c-trk tyrosine phosphorylation, but did not affect tyrosine phosphorylation of epidermal growth factor or platelet-derived growth factor receptors. In addition, the tyrosine phosphorylation of the receptor-associated protein pp38 was also attenuated by the tyrphostin. This effect was time- and dose-dependent, although inhibition of pp38 phosphorylation occurred earlier and at lower concentrations of the compound. AG879 also inhibited NGF-induced PLC-gamma 1 phosphorylation, phosphatidylinositol-3 (PI3) kinase activation, the association of the tyrosine-phosphorylated proteins pp100 and pp110 with the p85 subunit of PI-3 kinase, mitogen activated protein and raf-1 kinases, and c-fos induction. In addition, AG879 inhibited NGF-induced neurite outgrowth in PC12 cells. These data indicate that tyrosine kinase activity of the pp140c-trk NGF receptor is essential for the cellular actions of this growth factor.
Use of intensity quotients and differences in absolute structure refinement (2013)

Several methods for absolute structure refinement were tested using single-crystal X-ray diffraction data collected using Cu Kα radiation for 23 crystals with no element heavier than oxygen: conventional refinement using an inversion twin model, estimation using intensity quotients in SHELXL2012, estimation using Bayesian methods in PLATON, estimation using restraints consisting of numerical intensity differences in CRYSTALS and estimation using differences and quotients in TOPAS-Academic where both quantities were coded in terms of other structural parameters and implemented as restraints. The conventional refinement approach yielded accurate values of the Flack parameter, but with standard uncertainties ranging from 0.15 to 0.77. The other methods also yielded accurate values of the Flack parameter, but with much higher precision. Absolute structure was established in all cases, even for a hydrocarbon. The procedures in which restraints are coded explicitly in terms of other structural parameters enable the Flack parameter to correlate with these other parameters, so that it is determined along with those parameters during refinement.
Execution Anomaly Detection in Distributed Systems through Unstructured Log Analysis (2009)

Detection of execution anomalies is very important for the maintenance, development, and performance refinement of large scale distributed systems. Execution anomalies include both work flow errors and low performance problems. People often use system logs produced by distributed systems for troubleshooting and problem diagnosis. However, manually inspecting system logs to detect anomalies is unfeasible due to the increasing scale and complexity of distributed systems. Therefore, there is a great demand for automatic anomalies detection techniques based on log analysis. In this paper, we propose an unstructured log analysis technique for anomalies detection. In the technique, we propose a novel algorithm to convert free form text messages in log files to log keys without heavily relying on application specific knowledge. The log keys correspond to the log-print statements in the source code which can provide cues of system execution behavior. After converting log messages to log keys, we learn a Finite State Automaton (FSA) from training log sequences to present the normal work flow for each system component. At the same time, a performance measurement model is learned to characterize the normal execution performance based on the log messages' timing information. With these learned models, we can automatically detect anomalies in newly input log files. Experiments on Hadoop and SILK show that the technique can effectively detect running anomalies.
Influence of TiO2 and Ag2O addition on tricalcium phosphate ceramics (2007)

Degradation of implanted ceramics allows for bone in-growth and eventual replacement with natural tissue. Calcium phosphate-based materials have gained the most significant attention because of their excellent biocompatibility and compositional similarities to natural bone. Adding various dopants to these ceramics significantly influences critical properties. In this study, tricalcium phosphate (TCP) compacts were fabricated via uniaxial compression with four compositions: (i) pure TCP, (ii) TCP with 1.0 wt % TiO(2), (iii) TCP with 0.5 wt % Ag(2)O, and (iv) ternary of TCP and 1.0 wt % TiO(2), and 0.5 wt % Ag(2)O. These compacts were sintered at 1250 degrees C for 4 h to obtain dense ceramic structures. Phase analyses were carried out using an X-ray diffractometer. The presence of TiO(2) in TCP improved densification and increased compression strength from 70 (+/-25) to 145 (+/-40) MPa. The ternary composition had the highest density and compression strength of 180 (+/-15) MPa. Human osteoblast cell growth behavior was studied using an osteoprecursor cell line (OPC 1) to assure that the biocompatibility of these ceramics was not altered due to the dopants. For long-term biodegradation studies, density, weight change, surface microstructure, and uniaxial compression strength were measured as a function of time in a simulated body fluid (SBF). Weight gain in SBF correlated strongly with precipitation viewed in the inter-connected pores of the samples. After 3 months in SBF, a 35% drop in compression strength was noticed for pure TCP, but for doped compositions, no strength loss was noticed.
A simplified method of CD34+ cell determination for peripheral blood progenitor cell transplantation and correlation with clinical engraftment. (1998)

Enumeration of CD34+ cells by flow cytometry is the recognized standard for quantitating progenitor cells for peripheral blood progenitor cell (PBPC) transplantation. Although many clinical studies have confirmed that the time to neutrophil and platelet engraftment is inversely proportional to the number of CD34+ cells infused, the minimum number of CD34+ cells necessary to acheive rapid engraftment has not been satisfactorily determined. The lack of a standardized method for quantitation of CD34+ cells by flow cytometry (FCM) is often cited as the reason for this ambiguity. This report describes an FCM method for CD34+ cell determination that is simple, highly reproducible, comparatively inexpensive, and validated by excellent correlation with clinical engraftment. Pheresis samples are stained and fixed within 4 hours of collection. Two hundred fifty thousand events are acquired as list mode data using a forward scatter threshold. The discrete CD34+ population is enumerated using a CD34-phycoerythrin FL2 vs. side scatter plot and Paint-A-Gate Pro software. The method was validated by excellent statistical correlation with clinical engraftment. Using this method, we determined the number of CD34+ progenitor cells necessary to achieve rapid engraftment to be 2 x 10(6)/kg.