gebhart/patrepeval huggingface dataset:
Catalytic test reactions for the evaluation of hierarchical zeolites (2016)

Hierarchical zeolites have received increasing attention in the last decade due to their outstanding catalytic performance. Several types of hierarchical zeolites can be prepared by a large number of different techniques. Hierarchical zeolites combine the intrinsic catalytic properties of conventional zeolites and the facilitated access and transport in the additional meso- or macropore system. In this tutorial review, we discuss several test reactions that have been explored to show the benefit of the hierarchical pore system with respect to their suitability to prove the positive effects of hierarchical porous zeolites. It is important to note that positive effects on activity, stability and less frequently selectivity observed for hierarchically structured catalysts not necessarily are only a consequence of the additional meso- or macropores but also the number, strength and location of active sites as well as defects and impurities. With regard to these aspects, the test reaction has to be chosen carefully and potential changes in the chemistry of the catalyst have to be considered as well. In addition to the determination of conversion, yield and selectivity, we will show that the calculation of the activation energy and the determination of the Thiele modulus and the effectiveness factor are good indicators of the presence or absence of diffusion limitations in hierarchical zeolites compared to their parent materials.
Retro-Binding Tripeptide Thrombin Active-Site Inhibitors: Discovery, Synthesis, and Molecular Modeling (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRetro-Binding Tripeptide Thrombin Active-Site Inhibitors: Discovery, Synthesis, and Molecular ModelingEdwin J. Iwanowicz, Wan F. Lau, James Lin, Daniel G. M. Roberts, and Steven M. SeilerCite this: J. Med. Chem. 1994, 37, 14, 2122–2124Publication Date (Print):July 1, 1994Publication History Published online1 May 2002Published inissue 1 July 1994https://pubs.acs.org/doi/10.1021/jm00040a001https://doi.org/10.1021/jm00040a001research-articleACS PublicationsRequest reuse permissionsArticle Views80Altmetric-Citations20LEARN 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 Get e-Alerts
Epigenetic imprinting by commensal probiotics inhibits the IL-23/IL-17 axis in an in vitro model of the intestinal mucosal immune system (2012)

The pathophysiology of IBD is characterized by a complex interaction between genes and the environment. Genetic and environmental differences are attributed to the heterogeneity of the disease pathway and to the epigenetic modifications that lead to altered gene expression in the diseased tissues. The epigenetic machinery consists of short interfering RNA, histone modifications, and DNA methylation. We evaluated the effects of Bifidobacterium breve (DSMZ 20213) and LGG (ATCC 53103), as representatives of commensal probiotics on the expression of IL-17 and IL-23, which play an important role in IBD, and on the epigenetic machinery in a 3D coculture model composed of human intestinal HT-29/B6 or T84 cells and PBMCs. The cells were treated with LPS in the presence or absence of bacteria for 48 h, and the expression of IL-17, IL-23, and CD40 at the mRNA and protein levels was assessed using TaqMan qRT-PCR and ELISA, respectively. Western blotting was used to assess the expression of the MyD88, the degradation of IRAK-1 and IκBα, the expression of the NF-κB p50/p65 subunits, the p-p38 MAPK and p-MEK1, as well as histone modifications. NF-κB activity was assessed by NF-κB-dependent luciferase reporter gene assays. The accumulation of Ac-H4 and DNA methylation was quantitatively assessed using colorimetric assays. B. breve and LGG diminished the LPS-induced expression of IL-17, IL-23, CD40, and histone acetylation, while slightly enhancing DNA methylation. These effects were paralleled by a decrease in the nuclear translocation of NF-κB, as demonstrated by a decrease in the expression of MyD88, degradation of IRAK-1 and IκBα expression of the nuclear NF-κB p50/p65 subunits, p-p38 MAPK and p-MEK1, and NF-κB-dependent luciferase reporter gene activity in LPS-stimulated cells. B. breve and LGG may exert their anti-inflammatory effects in the gut by down-regulating the expression of the IBD-causing factors (IL-23/IL-17/CD40) associated with epigenetic processes involving the inhibition of histone acetylation and the optimal enhancement of DNA methylation, reflected in the limited access of NF-κB to gene promoters and reduced NF-κB-mediated transcriptional activation. We describe a new regulatory mechanism in which commensal probiotics inhibit the NF-κB-mediated transcriptional activation of IBD-causing factors (IL-23/IL-17/CD40), thereby simultaneously reducing histone acetylation and enhancing DNA methylation.
Femtosecond pulse laser ablation of metallic, semiconducting, ceramic, and biological materials (1994)

Production of holes and grooves of &lt; 30 micrometers diameter with high aspect ratio value is a delicate task either for mechanical tools, or for conventional nanosecond pulse lasers like e.g. pulsed Nd:YAG or excimer lasers. They later tend to cause microcracks extending from an annular melting zone, or substantial disruption, respectively. Experimental results are presented which demonstrate that the development of intense ultrashort pulse laser systems (&gt;&gt; 10<SUP>12</SUP> W cm<SUP>-2</SUP>, (tau) &lt; 1 ps) opens up possibilities for materials processing by cold plasma generation and ablation of metals, semiconductors, ceramics, composites, and biological materials. A femtosecond and a nanosecond dye laser with pulse durations of 300 fs (&lt; 200 (mu) J) and 7 ns (&lt; 10 mJ), and center wavelengths at 612 and 600 nm, respectively, both focused on an area of the order of 10<SUP>-5</SUP> cm<SUP>2</SUP>, have been applied either to absorbing substrates, like polycrystalline gold, silicon (111), aluminum nitride ceramics, or transparent materials, like synthetic and human dental hydroxyapatite composites, bone material, and human cornea transplants. The fs-laser generates its own absorption in transparent materials by a multiphoton absorption process, and thus forces the absorption of visible radiation. Because the time is too short (&lt; ps) for significant transport of mass and energy, the beam interaction generally results in the formation of a thin plasma layer of approximately solid state density. Only after the end of the subpicosecond laser pulse, it expands rapidly away from the surface without any light absorption and further plasma heating. Therefore, energy transfer (heat and impulse) to the target material, and thermal and mechanical disruption are minimized. In contrast to heat- affected zones (HAZ's) generated by conventional nanosecond pulse lasers of the order of 1 - 10 micrometers , HAZ's of less than 0.02 micrometers were observed.
Uses of Silicon-Containing Compounds in the Synthesis of Natural Products (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTUses of Silicon-Containing Compounds in the Synthesis of Natural ProductsElke Langkopf and Dieter SchinzerCite this: Chem. Rev. 1995, 95, 5, 1375–1408Publication Date (Print):July 1, 1995Publication History Published online1 May 2002Published inissue 1 July 1995https://pubs.acs.org/doi/10.1021/cr00037a011https://doi.org/10.1021/cr00037a011research-articleACS PublicationsRequest reuse permissionsArticle Views3407Altmetric-Citations472LEARN 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
Antigen-Specific CD4+T Cells Recognize Epitopes of Protective Antigen following Vaccination with an Anthrax Vaccine (2007)

Detection of antigen-specific CD4+ T cells is facilitated by the use of fluorescently labeled soluble peptide-major histocompatibility complex (MHC) multimers which mirror the antigen specificity of T-cell receptor recognition. We have used soluble peptide-MHC class II tetramers containing peptides from the protective antigen (PA) of Bacillus anthracis to detect circulating T cells in peripheral blood of subjects vaccinated with an anthrax vaccine. PA-specific HLA class II-restricted T lymphocytes were isolated which displayed both TH1- and TH2-like characteristics, indicating heterogeneity of the lymphocyte lineage within the CD4+ response. Presentation of antigen to these T-cell clones by HLA-matched antigen-presenting cells exposed to the intact PA protein confirmed that the identified epitopes are indeed naturally processed by the human immune system. Specific tetramer-derived T-cell profiling may be useful for monitoring helper CD4+ T-cell responses to anthrax vaccination.
Rechanneling the cardiac proarrhythmia safety paradigm: A meeting report from the Cardiac Safety Research Consortium (2013)

This white paper provides a summary of a scientific proposal presented at a Cardiac Safety Research Consortium/Health and Environmental Sciences Institute/Food and Drug Administration-sponsored Think Tank, held at Food and Drug Administration's White Oak facilities, Silver Spring, MD, on July 23, 2013, with the intention of moving toward consensus on defining a new paradigm in the field of cardiac safety in which proarrhythmic risk would be primarily assessed using nonclinical in vitro human models based on solid mechanistic considerations of torsades de pointes proarrhythmia. This new paradigm would shift the emphasis from the present approach that strongly relies on QTc prolongation (a surrogate marker of proarrhythmia) and could obviate the clinical Thorough QT study during later drug development. These discussions represent current thinking and suggestions for furthering our knowledge and understanding of the public health case for adopting a new, integrated nonclinical in vitro/in silico paradigm, the Comprehensive In Vitro Proarrhythmia Assay, for the assessment of a candidate drug's proarrhythmic liability, and for developing a public-private collaborative program to characterize the data content, quality, and approaches required to assess proarrhythmic risk in the absence of a Thorough QT study. This paper seeks to encourage multistakeholder input regarding this initiative and does not represent regulatory guidance.
Digital Breast Tomosynthesis: Initial Experience in 98 Women with Abnormal Digital Screening Mammography (2007)

Subjectively, tomosynthesis has comparable or superior image quality to that of film-screen mammography in the diagnostic setting, and it has the potential to decrease the recall rate when used adjunctively with digital screening mammography.
Towards peakless, reproducible and long‐acting insulins. An assessment of the basal analogues based on isoglycaemic clamp studies (2007)

While the advantages of the two basal insulin analogues, glargine and detemir, over neutral protamine Hagedorn are well established, the relative merit of the two compared with each other has been a matter of some controversy. The two analogues are popularly perceived to differ from each other in their pharmacodynamic (PD) profiles, in particular with regard to 'flatness' and duration of action. The aim of this review, therefore, is to give a complete overview on the available PD data of both analogues as derived with the glucose clamp technique. In order to improve parity across studies, a common definition for duration of action (time from injection to plasma glucose >8.3 mmol/l) was applied and study data were recalculated when necessary. Despite differences in methodological details, the results of most clamp studies were very consistent. Glargine and detemir both typically show a gentle rise and fall in glucose-lowering action over time. Duration of action with both analogues is dose dependent, but in the clinically relevant range of 0.35-0.8 U/kg it is close to 24 h in people with type 1 diabetes and in excess of this in people with type 2 diabetes. While both analogues seem to be very similar with regard to the mean shape of their PD profile and duration of action, detemir shows less within-subject variability in its metabolic effect. These findings in experimental glucose clamp studies are consistent with observations in clinical trials and support routine once daily use with either analogue, in particular in people with type 2 diabetes.
Reactions of Hydrosilanes with Transition-Metal Complexes:  Formation of Stable Transition-Metal Silyl Compounds (1998)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReactions of Hydrosilanes with Transition-Metal Complexes: Formation of Stable Transition-Metal Silyl CompoundsJoyce Y. Corey and Janet Braddock-WilkingView Author Information Department of Chemistry, University of MissouriSt. Louis, 8001 Natural Bridge Road, St. Louis, Missouri 63121 Cite this: Chem. Rev. 1999, 99, 1, 175–292Publication Date (Web):December 29, 1998Publication History Received1 April 1998Revised9 October 1998Published online29 December 1998Published inissue 13 January 1999https://pubs.acs.org/doi/10.1021/cr9701086https://doi.org/10.1021/cr9701086research-articleACS PublicationsCopyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views5209Altmetric-Citations660LEARN 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:Group 14 compounds,Inorganic compounds,Metals,Reaction products,Silicon Get e-Alerts
OUT-OF-BAG ESTIMATION (1996)

In bagging, predictors are constructed using bootstrap samples from the training set and then aggregated to form a bagged predictor. Each bootstrap sample leaves out about 37 % of the examples. These left-out examples can be used to form accurate estimates of important quantities. For instance, they can be used to give much improved estimates of node probabilities and node error rates in decision trees. Using estimated outputs instead of the observed outputs improves accuracy in regression trees. They can also be used to give nearly optimal estimates of generalization errors for bagged predictors. * Partially supported by NSF Grant 1-444063-21445 Introduction: We assume that there is a training set T = {(yn,xn), n=1,...,N} and a method for constructing a predictor Q(x,T) using the given training set. The output variable y can either be
k‐t BLAST and k‐t SENSE: Dynamic MRI with high frame rate exploiting spatiotemporal correlations (2003)

Dynamic images of natural objects exhibit significant correlations in k-space and time. Thus, it is feasible to acquire only a reduced amount of data and recover the missing portion afterwards. This leads to an improved temporal resolution, or an improved spatial resolution for a given amount of acquisition. Based on this approach, two methods were developed to significantly improve the performance of dynamic imaging, named k-t BLAST (Broad-use Linear Acquisition Speed-up Technique) and k-t SENSE (SENSitivity Encoding) for use with a single or multiple receiver coils, respectively. Signal correlations were learned from a small set of training data and the missing data were recovered using all available information in a consistent and integral manner. The general theory of k-t BLAST and k-t SENSE is applicable to arbitrary k-space trajectories, time-varying coil sensitivities, and under- and overdetermined reconstruction problems. Examples from ungated cardiac imaging demonstrate a 4-fold acceleration (voxel size 2.42 x 2.52 mm(2), 38.4 fps) with either one or six receiver coils. k-t BLAST and k-t SENSE are applicable to many areas, especially those exhibiting quasiperiodic motion, such as imaging of the heart, the lungs, the abdomen, and the brain under periodic stimulation.
Therapeutic Effect of Erythromycin on Influenza Virus-induced Lung Injury in Mice (1998)

Erythromycin (EM) is an antibiotic with potent antiinflammatory effects that is used for treating chronic lower respiratory tract infections. It has been shown that free radicals, such as the superoxide anion and nitric oxide (NO), are pathogenic molecules in viral disease. Much attention has been given to a critical role of NO in the pathologic events of various inflammatory diseases. In the present study, we evaluated the effects of EM on influenza-virus-induced pneumonia in mice infected with a lethal dose of influenza virus A/Kumamoto/Y5/67 (H2N2). The administration of EM at a dose of 3.3 mg/kg/d (intraperitoneally, from Days 1 to 6 after infection), significantly improved the survival rate of mice infected with influenza virus, and the survival rate of the virus-infected mice at Day 20 after infection increased in a dose-dependent fashion with EM administered to the animals, from 14% among controls to 42% among animals given EM at 1.0 mg/kg/d and 57% among those given EM at 3.3 mg/kg/d. The induction of interferon-gamma (IFN-gamma) in the mouse lung was inhibited by EM treatment on Day 6 after infection. Simultaneously, the number of inflammatory cells recovered in lung lavage fluid 6 d after virus infection was significantly reduced by the treatment with EM. The EM treatment resulted in a dose-dependent decrease in the level of nitrite/nitrate (metabolites of NO) in the serum and the NO synthase (NOS)-inducting potential in the lungs of the virus-infected mice. These results indicate that EM may have substantial therapeutic value for various acute inflammatory disorders such as influenza-virus-induced pneumonia, by inhibiting inflammatory-cell responses and suppressing NO overproduction in the lung.
Agents that increase the permeability of the outer membrane (1992)

The outer membrane of gram-negative bacteria provides the cell with an effective permeability barrier against external noxious agents, including antibiotics, but is itself a target for antibacterial agents such as polycations and chelators. Both groups of agents weaken the molecular interactions of the lipopolysaccharide constituent of the outer membrane. Various polycations are able, at least under certain conditions, to bind to the anionic sites of lipopolysaccharide. Many of these disorganize and cross the outer membrane and render it permeable to drugs which permeate the intact membrane very poorly. These polycations include polymyxins and their derivatives, protamine, polymers of basic amino acids, compound 48/80, insect cecropins, reptilian magainins, various cationic leukocyte peptides (defensins, bactenecins, bactericidal/permeability-increasing protein, and others), aminoglycosides, and many more. However, the cationic character is not the sole determinant required for the permeabilizing activity, and therefore some of the agents are much more effective permeabilizers than others. They are useful tools in studies in which the poor permeability of the outer membrane poses problems. Some of them undoubtedly have a role as natural antibiotic substances, and they or their derivatives might have some potential as pharmaceutical agents in antibacterial therapy as well. Also, chelators (such as EDTA, nitrilotriacetic acid, and sodium hexametaphosphate), which disintegrate the outer membrane by removing Mg2+ and Ca2+, are effective and valuable permeabilizers.
Influence of serum on in vitro susceptibility testing of echinocandins for Candida parapsilosis and Candida guilliermondii (2011)

Echinocandins are antifungal drugs used for the treatment of invasive candidiasis and aspergillosis. They bind to serum proteins within a rate of 96 to >99%. The effect of serum on in vitro echinocandin susceptibility tests of certain Candida and Aspergillus species was reported. This study was performed to determine the effect of human serum on in vitro susceptibility testing of echinocandins for clinical isolates of Candida parapsilosis and Candida guilliermondii, the species which generally have higher minimum inhibitor concentrations compared with other Candida species. One hundred C. parapsilosis and 20 C. guilliermondii isolates were included in the study. The susceptibility tests of caspofungin, micafungin and anidulafungin were performed using microdilution method, either in the presence or absence of 50% human serum, according to the Clinical and Laboratory Standards Institute (CLSI) M27-A3 guidelines. It was demonstrated that human serum significantly affects the in vitro susceptibility results of echinocandins for C. parapsilosis and C. guilliermondii isolates, mostly yielding an increase in MICs. The most prominent fold changes were for micafungin and anidulafungin in C. parapsilosis, and for anidulafungin in C. guilliermondii isolates. Serum influences the in vitro echinocandin susceptibility in C. parapsilosis and C. guilliermondii. The mechanism and clinical significance of this in vitro change need to be clarified.