gebhart/patrepeval huggingface dataset:
Clearance ofCitrobacter rodentiumRequires B Cells but Not Secretory Immunoglobulin A (IgA) or IgM Antibodies (2004)

Citrobacter rodentium, a murine model pathogen for human enteropathogenic Escherichia coli, predominantly colonizes the lumen and mucosal surface of the colon and cecum and causes crypt hyperplasia and mucosal inflammation. Mice infected with C. rodentium develop a secretory immunoglobulin A (IgA) response, but the role of B cells or secretory antibodies in host defense is unknown. To address this question, we conducted oral C. rodentium infections in mice lacking B cells, IgA, secreted IgM, polymeric Ig receptor (pIgR), or J chain. Normal mice showed peak bacterial numbers in colon and feces at 1 week and bacterial eradication after 3 to 4 weeks. B-cell-deficient mice were equally susceptible initially but could not control infection subsequently. Tissue responses showed marked differences, as infection of normal mice was accompanied by transient crypt hyperplasia and mucosal inflammation in the colon and cecum at 2 but not 6 weeks, whereas B-cell-deficient mice had few mucosal changes at 2 weeks but severe epithelial hyperplasia with ulcerations and mucosal inflammation at 6 weeks. The functions of B cells were not mediated by secretory antibodies, since mice lacking IgA or secreted IgM or proteins required for their transport into the lumen, pIgR or J chain, cleared C. rodentium normally. Nonetheless, systemic administration of immune sera reduced bacterial numbers significantly in normal and pIgR-deficient mice, and depletion of IgG abrogated this effect. These results indicate that host defense against C. rodentium depends on B cells and IgG antibodies but does not require production or transepithelial transport of IgA or secreted IgM.
Chitinases of fungi and plants: their involvement in morphogenesis and host-parasite interaction (1993)

There has been a considerable amount of recent research aimed at elucidating the roles of chitinase in fungi and plants. In filamentous fungi and yeasts, chitinase is involved integrally in cell wall morphogenesis. Chitinase is also involved in the early events of host—parasite interactions of biotrophic and necrotrophic mycoparasites, entomopathogenic fungi and vesicular arbuscular mycorrhizal fungi. In plants, induction of chitinase and other hydrolytic enzymes is one of a coordinated, often complex and multifaceted defense mechanism triggered in response to phytopathogen attack. Chitinase induction in plants is not considered solely as an antifungal resistance mechanism. Plant chitinases can be induced by various abiotic factors as well and there is some circumstantial evidence to suggest a morphogenetic role despite the apparent absence of the substrate in plant cells. Finally, some chitinases and other chitin-binding proteins including some plant lectins share chitin-binding domains as part of their molecular structure and provide fuel for the so-called 'lectin-chitinase' debate and speculation for the origin of chitinase in plants.
What to use to express the variability of data: Standard deviation or standard error of mean? (2012)

Statistics plays a vital role in biomedical research. It helps present data precisely and draws the meaningful conclusions. While presenting data, one should be aware of using adequate statistical measures. In biomedical journals, Standard Error of Mean (SEM) and Standard Deviation (SD) are used interchangeably to express the variability; though they measure different parameters. SEM quantifies uncertainty in estimate of the mean whereas SD indicates dispersion of the data from mean. As readers are generally interested in knowing the variability within sample, descriptive data should be precisely summarized with SD. Use of SEM should be limited to compute CI which measures the precision of population estimate. Journals can avoid such errors by requiring authors to adhere to their guidelines.
5-HT1A- versus D2-Receptor Selectivity of Flesinoxan and AnalogousN 4-SubstitutedN 1-Arylpiperazines (1997)

We investigated the structural requirements for high 5-HT1A affinity of the agonist flesinoxan and its selectivity versus D2 receptors. For this purpose a series of arylpiperazine congeners of flesinoxan were synthesized and evaluated for their ability to displace [3H]-8-OH-DPAT and [3H]spiperone from their specific binding sites in rat frontal cortex homogenates and rat striatum, respectively. Variations were made in the N4-substituent and the arylpiperazine region. Effects of N4-substitution in the investigated compounds appeared to be quite similar for 5-HT1A- and D2-receptor affinity. Lipophilicity at a distance of four carbon atoms from the piperazine N4 atom seems to be the main contributing factor to affinity for both receptors. Our data show that the amide group in the flesinoxan N4-substituent is unlikely to interact with the 5-HT1A receptor but, instead, acts as a spacer. In contrast to the structure-affinity relationships (SARs) of the N4-substituents, selectivity for 5-HT1A versus D2 receptors was gained by the arylpiperazine substitution pattern of flesinoxan. Restriction of flexibility of the N4-(benzoylamino)ethyl substituent and its effect on 5-HT1A-receptor affinity and activity were also studied. Our data show that in the bioactive conformation, the N4-[(p-fluorobenzoyl)amino]ethyl substituent is probably directed anti-periplanar relative to the HN4 atom. These results were used to dock flesinoxan (1) and two of its congeners (27 and 33) into a model of the 5-HT1A receptor that we previously reported. Amino acid residues surrounding the N4-[(p-fluorobenzoyl)amino]ethyl substituent of flesinoxan and its congeners are also present in D2 receptors. In contrast, several residues that contact the benzodioxane moiety differ from those in D2 receptors. These observations from the 3D model agree with the 5-HT1A SAR data and probably account for the selectivity of flesinoxan versus D2 receptors.
Use of Statistical Information in X-ray Crystallography with Application to the Holographic Method (1998)

The holographic method solves the crystallographic inverse problem in real space. In addition to the measured structure-factor amplitudes, it uses other available information such as the positivity of the electron density, knowledge of part of the structure as well as MIR and/or MAD data. In the present paper, the range of useful information is extended to include knowledge that is statistical in nature. For example, it is known that the distribution of the structure-factor amplitudes of large molecules is described by Wilson statistics. Bayesian methods are used to optimize the signal-to-noise ratio of experimental measurements, to estimate missing reflections and to extrapolate measured data to higher resolution. In a similar vein, the cost function in the holographic algorithm is modified to account for the uncertainties of the measured structure factors. It is also shown how statistical knowledge about the unsolved part of the molecule may be utilized.
Nanoimprinted Semitransparent Metal Electrodes and Their Application in Organic Light‐Emitting Diodes (2007)

Semitransparent metal electrodes fabricated by nanoimprint lithography (NIL) in the form of nanoscale periodically perforated metal films are reported. They show high transmittance in the visible wavelength range as well as excellent electrical conductivities (see figure), and both characteristics can be tuned separately by changing the aperture ratio and the metal thickness. The fabrication of organic light-emitting diodes (OLEDs) incorporating these transparent conducting electrodes demonstrates their potential use.
Infective Factors in Exacerbations of Bronchitis and Asthma (1972)

Infections of the respiratory tract were studied in a group of families each containing a patient with chronic bronchitis or with asthma. A wide variety of infective agents may be associated with exacerbations in susceptible subjects, but the types of organism to which patients are most at risk differ according to the family structure. Exacerbations in the susceptible subject are more likely to be related to viral infections when the family contains children than when it does not.Two patients with asthma experienced frequent respiratory infections, many of which provoked attacks of asthma.
Comparison of bacteria growth in single and pooled platelet concentrates after deliberate inoculation and storage (1995)

The potential during storage for greater total bacteria levels in pools than in single PCs is a consequence of the greater volume of the pool.
The Gulf of Mexico Decommissioning Market (2006)

The Gulf of Mexico offshore decommissioning market is the most diverse and competitive service contract environment in the world. The purpose of this paper is to describe the business, engineering, and market environment of decommissioning services in the Gulf of Mexico, and to provide a first-order approximation of the number of structures expected to be removed over a 25 year time horizon. Decommissioning activities associated with offshore production are an important and specialized segment of marine construction that has received limited attention in the academic literature, yet is compelling because few industrial sectors have such well-understood and widely adopted abandonment requirements. This paper should appeal to practitioners and researchers interested in learning the processes involved in deconstruction and the basic structure of the industry. The regulatory requirements and primary stages of decommissioning are reviewed, and the management, bid/tender process, and negotiation strategies are described. A life expectancy model of the number of structures expected to be removed from the Gulf of Mexico is presented, along with a discussion of the model uncertainty and the limitations of the analysis.
Heterologous combinations of heavy and light chains from botulinum neurotoxin A and tetanus toxin inhibit neurotransmitter release in Aplysia (1991)

The neuroparalytic activities of botulinum neurotoxin type A (BoNT A), tetanus toxin (TeTx), or homologous and heterologous combinations of their constituent polypeptides were examined at cholinergic and non-cholinergic synapses of Aplysia californica. When applied extracellularly, BoNT A or a mixture of its heavy (HC) and light (LC) chains were far more potent in blocking transmitter release at cholinergic than non-cholinergic synapses. The reverse was true for TeTx or a mixture its constituent chains. Such selectivity was assigned to differences in neuronal targetting and uptake of the neurotoxins since both exhibited similar potencies when injected directly into the cell body of either cell type. When bath-applied, heterologous combinations of the toxins' HC and LC appeared as effective as the parent neurotoxins from whence each HC was derived. Moreover, targetting/internalization was attributable to the analogous N-terminal moieties, H2 and beta 2, of the HC from BoNT A and TeTx. Thus, it may be postulated that the latter regions possess two functional domains, one being distinct and responsible for the divergent neuronal specificity, whereas the other serves a common role in translocating the LC of either toxin. Also, it was shown that the C-terminal portion of the HC of TeTx is unable to play the intracellular role of its counterpart in BoNT A.
A Terahertz Microscopy Technique for Sweat Duct Detection (2018)

We propose a THz imaging technique that uses high reflective index optics to improve spatial resolution and enable a novel biometrics imaging tool. Specifically, with the use of THz waves we can penetrate the drier outer skin layers and provide anatomical information on the skin's layered morphology and the underlying structures (e.g. sweat ducts). Sweat ducts are subcutaneous helical structures that exhibit absorption in the sub-THz frequency range. The proposed THz microscopy configuration can acquire high spatial resolution images of the human skin and classify sweat ducts based on the backscattered THz spectrum. In this paper, the theoretical background of the microscopy technique and the experimental design are discussed. Finally, THz images of human fingerprints are presented, verifying the imaging capabilities of the proposed configuration.
Spam, Spam, Spam, Spam, Spam, the FTC, and Spam (2003)

The Federal Trade Commission held a forum on spam in Washington, D.C., April 30 to May 2. Rather to my surprise, it was a really good, content-full event. The FTC folks had done their homework and had assembled panelists that ran the gamut from ardent anti-spammers all the way to hard-core spammers and everyone in between: lawyers, legitimate marketers, and representatives from vendor groups.
Identification of T Cell Determinants on Human Type II Collagen Recognized by HLA-DQ8 and HLA-DQ6 Transgenic Mice (1999)

HLA-DQA1*0301 and HLA-DQB1*0302 genes encoding the HLA-DQ8 molecule and HLA-DQA1*0103 and HLA-DQB1*0601 genes encoding the HLA-DQ6 molecule were introduced into H-2Abetao knockout mice. Three lines of transgenic mice were established: HLA-DQ8, HLA-DQ6, and HLA-DQ8beta6alpha. HLA-DQ8 mice are susceptible to collagen-induced arthritis, while HLA-DQ6 mice are resistant. HLA-DQ8beta6alpha mice develop polychrondritis in addition to arthritis. Transgenic mice were primed and challenged with individual synthetic peptides representing human type II collagen. A total of 101 synthetic peptides were tested in each transgenic line of mice. HLA-DQ8 mice responded to 15 synthetic peptides representing all cyanogen bromide fragments. In contrast, HLA-DQ6 mice responded to a subset of the peptides recognized by HLA-DQ8 T cells. HLA-DQ8beta6alpha mice, although exhibiting diminished responses to the majority of HLA-DQ8-restricted determinants, elicited enhanced responses to two peptides. In addition, HLA-DQ8beta6alpha mice respond to two unique peptide determinants contained within cyanogen bromide fragments CB10 and CB11 showing the significance of mixed isotype dimers in the immune response. The determinants recognized by the HLA-DQ transgenic mice are distinct from those previously identified using conventional laboratory mice. These results suggest that human class II transgenic mice offer a means of identifying human class II-restricted epitopes associated with potential human autoantigens.
The crystal structures of two cuticle–degrading proteases from nematophagous fungi and their contribution to infection against nematodes (2009)

Cuticle-degrading proteases are involved in the breakdown of cuticle/eggshells of nematodes or insects, a hard physical barrier against fungal infections. Understanding the 3-dimensional structures of these proteins can provide crucial information for improving the effectiveness of these fungi in biocontrol applications, e.g., by targeted protein engineering. However, the structures of these proteases remain unknown. Here, we report the structures of two cuticle-degrading proteases from two species of nematophagous fungi. The two structures were solved with X-ray crystallography to resolutions of 1.65 A (Ver112) and 2.1 A (PL646), respectively. Crystal structures of PL646 and Ver112 were found to be very similar to each other, and similar to that of proteinase K from another fungus Tritirachium album. Differences between the structures were found among residues of the substrate binding sites (S1 and S4). Experimental studies showed that the enzymes differed in hydrolytic activity to synthetic peptide substrates. Our analyses of the hydrophobic/hydrophilic and electrostatic features of these two proteins suggest that their surfaces likely play important roles during fungal infection against nematodes. The two crystal structures provide a solid basis for investigating the relationship between structure and function of cuticle-degrading proteases.
Identification of a Small Molecule Inhibitor of the IL-2/IL-2Rα Receptor Interaction Which Binds to IL-2 (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTIdentification of a Small Molecule Inhibitor of the IL-2/IL-2Rα Receptor Interaction Which Binds to IL-2Jefferson W. Tilley, Li Chen, David C. Fry, S. Donald Emerson, Gordon D. Powers, Denise Biondi, Tracey Varnell, Richard Trilles, Robert Guthrie, Francis Mennona, Gerry Kaplan, Ronald A. LeMahieu, Mathew Carson, Ru-Jen Han, C.-M. Liu, Robert Palermo, and Grace JuView Author Information Roche Research Center, Hoffmann-La Roche Inc. Nutley, New Jersey 07110 Cite this: J. Am. Chem. Soc. 1997, 119, 32, 7589–7590Publication Date (Web):August 13, 1997Publication History Received4 March 1997Revised27 May 1997Published online13 August 1997Published inissue 1 August 1997https://pubs.acs.org/doi/10.1021/ja970702xhttps://doi.org/10.1021/ja970702xrapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views1362Altmetric-Citations107LEARN 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,Inhibition,Inhibitors,Molecular interactions,Receptors Get e-Alerts
Cutting Edge: Activation of the Aryl Hydrocarbon Receptor by 2,3,7,8-Tetrachlorodibenzo- p -dioxin Generates a Population of CD4+CD25+ Cells with Characteristics of Regulatory T Cells (2005)

Activation of the aryl hydrocarbon receptor (AhR) by its most potent ligand, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), leads to immune suppression in mice. Although the underlying mechanisms responsible for AhR-mediated immune suppression are not known, previous studies have shown that activation of the AhR must occur within the first 3 days of an immune response and that CD4+ T cells are primary targets. Using the B6-into-B6D2F1 model of an acute graft-vs-host response, we show that activation of AhR in donor T cells leads to the generation of a subpopulation of CD4+ T cells that expresses high levels of CD25, along with CD62L(low), CTLA-4, and glucocorticoid-induced TNFR. These donor-derived CD4+ CD25+ cells also display functional characteristics of regulatory T cells in vitro. These findings suggest a novel role for AhR in the induction of regulatory T cells and provide a new perspective on the mechanisms that underlie the profound immune suppression induced by exposure to TCDD.
Predictive motion field segmentation for image sequence coding (2002)

A method is described for improving block-based motion-compensation techniques by segmenting blocks into regions corresponding to objects moving with distinct velocities. The method uses standard block motion-estimation techniques and assumes that each distinct velocity within a block is approximated by one of the motion estimates in a neighborhood of that block. A multiresolution approach to segmenting each block is taken. It is based on a Markov random-field model of the segmentation field and incorporates additional constraints which reflect an assumption that the blocks are small relative to objects in the scene. In order to avoid transmitting the segmentation, the method computes the segmentation of previous frames at the receiver and transmitter and predicts the current segmentation from past ones. Experimental results show that the method eliminates most artifacts due to block motion compensation at edges of moving objects and achieves 30-50% reductions in displaced frame-difference energy in frames where reliable motion estimates are available.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
An investigation of rhizobacteria as biofertilizer on Mentha L. compounds change (2012)

The aim of current research was application of rhizobacteria as native biofertilizers and study of its effect on mint compounds change. Soil samples were collected from rhizosphere zone of Mentha L. and rhizobacteria were isolated on BHI agar, Nutrient agar and Soil extract agar media. The ability of isolated species to utilize nitrate, nitrite and phosphate solubility was assessed by spectrophotometer and Pikovskayas assay respectively and the best bacterial species were selected as biofertilizer. Pots of Mentha L. roots were inoculated by biofertilizer during 20 days at 75% humidity, 25°C temperature and 12 hours lighting and plant morphological was determined. Leaf and stem compounds change was evaluated by ethanolic extraction and GC/MS analysis. The best candidate bacterial species for use as biofertilizers were evaluated by 16S rRNA. 17 species with Bacillus genus as the most bacterial diversity were isolated and three strains were collected for further research. 11.7, 52.9 and 47% of strains had ability to use nitrite, nitrate and phosphorus solubility, respectively. The most size of leaf and internode distance was determined after treating the pots by strains 6 and 3 with average size 1.7 and 3.2cm, respectively. The results of synergetic effect of 3 strains were increased in leaf size and internodes distance, with average 1.8 and 4.4cm, respectively. Propene, Benzofuro benzopyran, Pentanoic acid, Decaborane, chloro A˜ÂŒHeptan1-nitr Methoxycarbonyl and Hepten-1-ol were determined as the significant compounds in leaf plant sample which were inoculated with strains 3, 6, 10 and combination of three strains. Molecular analysis determined Bacillus subtilis, Bacillus endophyticus and Bacillus thuringiensis as strains 3, 6 and 10 respectively.
Manufacturing Processes for Technology (1994)

I. FUNDAMENTALS OF MANUFACTURING. 1. An Approach to Manufacturing Processes. 2. Properties of Materials. 3. Measurements in Manufacturing. II. MATERIAL REMOVAL. 4. Mechanical Methods of Material Removal. 5. Electrical Methods of Material Removal. 6. Chemical Methods of Material Removal. 7. Thermal and Other Methods of Material Removal. III. MATERIAL ADDITION. 8. Material Addition. IV. CHANGE OF FORM. 9. Thermal Methods of Change of Form. 10. Powder Methods of Change of Form. 11. Mechanical and Other Methods of Change of Form. V. CHANGE OF CONDITION. 12. Change of Condition. VI. MATERIAL JOINING. 13. Adhesives. 14. Welding. 15. Mechanical Methods of Joining. VII. FINISHING. 16. Mechanical Surface Finishing Processes. 17. Surface Treatment Processes and Coatings. VIII. MANUFACTURING WITH PLASTICS AND COMPOSITES. 18. Manufacturing with Plastics. 19. Manufacturing with Composites. IX. INDUSTRIAL SAFETY AND HEALTH. 20. Industrial Safety and Health. X. PRODUCTION CONTROL. 21. Production Control. APPENDICES. A. Glossary. B. Derivation of Equations. C. Formulas and Equations. D. Answers to Odd-Numbered Problems. E. Conversion Factors. Index.
The Incorporation of a Photoisomerizable Amino Acid into Proteins in E. c oli (2005)

An orthogonal aminoacyl tRNA synthetase/tRNA pair has been evolved that allows the incorporation of the photoisomerizable amino acid phenylalanine-4'-azobenzene (AzoPhe) into proteins in E. coli in response to the amber nonsense codon. Further, we show that AzoPhe can be used to photoregulate the binding affinity of catabolite activator protein to its promoter. The ability to selectively incorporate AzoPhe into proteins at defined sites should make it possible to regulate a variety of biological processes with light, including enzyme, receptor, and ion channel activity.