gebhart/patrepeval huggingface dataset:
A New Strategy for the Site-Specific Modification of Proteins in Vivo (2003)

We recently developed a method for genetically incorporating unnatural amino acids site-specifically into proteins expressed in Escherichia coli in response to the amber nonsense codon. Here we describe the selection of an orthogonal tRNA-TyrRS pair that selectively and efficiently incorporates m-acetyl-l-phenylalanine into proteins in E. coli. We demonstrate that proteins containing m-acetyl-l-phenylalanine or p-acetyl-l-phenylalanine can be selectively labeled with hydrazide derivatives not only in vitro but also in living cells. The labeling reactions are selective and in general proceed with yields of >75%. In specific examples, m-acetyl-l-phenylalanine was substituted for Lys7 of the cytoplasmic protein Z domain, and for Arg200 of the outer membrane protein LamB, and the mutant proteins were selectively labeled with a series of fluorescent dyes. The genetic incorporation of a nonproteinogenic "ketone handle" into proteins provides a powerful tool for the introduction of biophysical probes for the structural and functional analysis of proteins in vitro or in vivo.
Implementation of the Axially Symmetrical and Three Dimensional Finite Element Models to the Determination of the Heat Transfer Coefficient Distribution on the Hot Plate Surface Cooled by the Water Spray Nozzle (2012)

Plate and strip hot rolling lines are equipped with water cooling systems used to control the deformed material temperature. This system has a great importance in the case of thermal - mechanical deformation of steel which is focused on formation a proper microstructure and mechanical properties. The desired rate of cooling is achieved by water spray or laminar cooling applied to the hot surface of a strip. The water flow rate and pressure can be changed in a wide range and it will result in a very different heat transfer from the cooled material to the cooling water. The suitable cooling rate and the deformed material temperature can be determined based on numerical simulations. In this case thermal boundary conditions have to be specified on the cooled surface. The determination of the heat transfer coefficient distribution in the area of the water spray nozzle would improve numerical simulations significantly. In the paper an attempt is made to determine the heat transfer coefficient distribution on the hot plate surface cooled by the water spray nozzle. In the inverse method direct axially symmetrical and three dimensional solutions to the plate temperature field have been implemented. The computation time and the achieved accuracy have been compared for five cases. The studied cases differed in the maximum value of the heat transfer coefficient in nozzle spray axis and its distribution in the cooling time.
Human Cytomegalovirus Glycoproteins gB and gH/gL Mediate Epithelial Cell-Cell Fusion When Expressed either in cis or in trans (2008)

Herpesviruses use a cascade of interactions with different cell surface molecules to gain entry into cells. In many cases, this involves binding to abundant glycosaminoglycans or integrins followed by interactions with more limited cell surface proteins, leading to fusion with cellular membranes. Human cytomegalovirus (HCMV) has the ability to infect a wide variety of human cell types in vivo. However, very little is known about which HCMV glycoproteins mediate entry into various cell types, including relevant epithelial and endothelial cells. For other herpesviruses, studies of cell-cell fusion induced by viral proteins have provided substantial information about late stages of entry. In this report, we describe the fusion of epithelial, endothelial, microglial, and fibroblast cells in which HCMV gB and gH/gL were expressed from nonreplicating adenovirus vectors. Fusion frequently involved the majority of cells, and gB and gH/gL were both necessary and sufficient for fusion, whereas no fusion occurred when either glycoprotein was omitted. Coexpression of UL128, UL130, and UL131 did not enhance fusion. We concluded that the HCMV core fusion machinery consists of gB and gH/gL. Coimmunoprecipitation indicated that HCMV gB and gH/gL can interact. Importantly, expression of gB and gH/gL in trans (gB-expressing cells mixed with other gH/gL-expressing cells) resulted in substantial fusion. We believe that this is the first description of a multicomponent viral fusion machine that can be split between cells. If gB and gH/gL must interact for fusion, then these molecules must reach across the space between apposing cells. Expression of gB and gH/gL in trans with different cell types revealed surface molecules that are required for fusion on HCMV-permissive cells but not on nonpermissive cells.
Characterization of cDNAs encoding two isoforms of granule‐bound starch synthase which show differential expression in developing storage organs of pea and potato (1992)

We have isolated cDNA clones to two isoforms of granule-bound starch synthase (GBSS) from pea embryos and potato tubers. The sequences of both isoforms are related to that of glycogen synthase from E. coli and one, GBSSI, is very similar to the waxy protein of maize and other species. In pea, GBSSII carries a novel 203-amino-acid domain at its N-terminus. Genes encoding both proteins are expressed during pea embryo development, but GBSSII is most highly expressed earlier in development than GBSSI. Similarly, GBSSI and GBSSII are differentially expressed in developing potato tubers. Expression of both isoforms is much lower in other organs of pea than in embryos. GBSSII is expressed in every organ tested while GBSSI is not expressed in roots, stipules or flowers. The possible consequences of this differential use of GBSS isoforms are discussed.
Controlled incremental filtration: a simplified approach to design and fabrication of high-throughput microfluidic devices for selective enrichment of particles (2014)

The number of microfluidic strategies aimed at separating particles or cells of a specific size within a continuous flow system continues to grow. The wide array of biomedical and other applications that would benefit from successful development of such technology has motivated the extensive research in this area over the past 15 years. However, despite promising advancements in microfabrication capabilities, a versatile approach that is suitable for a large range of particle sizes and high levels of enrichment, with a volumetric throughput sufficient for large-scale applications, has yet to emerge. Here we describe a straightforward method that enables the rapid design of microfluidic devices that are capable of enriching/removing particles within a complex aqueous mixture, with an unprecedented range of potential cutoff diameter (below 1 μm to above 100 μm) and an easily scalable degree of enrichment/filtration (up to 10-fold and well beyond). A simplified model of a new approach to crossflow filtration - controlled incremental filtration - was developed and validated for its ability to generate microfluidic devices that efficiently separate particles on the order of 1-10 μm, with throughputs of tens of μL min(-1), without the use of a pump. Precise control of the amount of fluid incrementally diverted at each filtration "gap" of the device allows for the gap size (~20 μm) to be much larger than the particles of interest, while the simplicity of the model allows for many thousands of these filtration points to be readily incorporated into a desired device design. This new approach should enable truly high-throughput microfluidic particle-separation devices to be generated, even by users only minimally experienced in fluid mechanics and microfabrication techniques.
Hybridization Analysis of DNA Blots (1993)

Restriction endonucleases recognize short DNA sequences and cleave double-stranded DNA at specific sites within or adjacent to the recognition sequences. Restriction endonuclease cleavage of DNA into discrete fragments is one of the most basic procedures in molecular biology. This appendix describes restriction endonucleases and their properties.
Biomolecular Feedback Systems (2015)

This book provides an accessible introduction to the principles and tools for modeling, analyzing, and synthesizing biomolecular systems. It begins with modeling tools such as reaction-rate equations, reduced-order models, stochastic models, and specific models of important core processes. It then describes in detail the control and dynamical systems tools used to analyze these models. These include tools for analyzing stability of equilibria, limit cycles, robustness, and parameter uncertainty. Modeling and analysis techniques are then applied to design examples from both natural systems and synthetic biomolecular circuits. In addition, this comprehensive book addresses the problem of modular composition of synthetic circuits, the tools for analyzing the extent of modularity, and the design techniques for ensuring modular behavior. It also looks at design trade-offs, focusing on perturbations due to noise and competition for shared cellular resources. Featuring numerous exercises and illustrations throughout, Biomolecular Feedback Systems is the ideal textbook for advanced undergraduates and graduate students. For researchers, it can also serve as a self-contained reference on the feedback control techniques that can be applied to biomolecular systems. Provides a user-friendly introduction to essential concepts, tools, and applications Covers the most commonly used modeling methods Addresses the modular design problem for biomolecular systems Uses design examples from both natural systems and synthetic circuits Solutions manual (available only to professors at press.princeton.edu) An online illustration package is available to professors at press.princeton.edu
Evaluation of Current Activities of Fluoroquinolones against Gram-Negative Bacilli Using Centralized In Vitro Testing and Electronic Surveillance (2001)

Given the propensity for Enterobacteriaceae and clinically significant nonfermentative gram-negative bacilli to acquire antimicrobial resistance, consistent surveillance of the activities of agents commonly prescribed to treat infections arising from these organisms is imperative. This study determined the activities of two fluoroquinolones, levofloxacin and ciprofloxacin, and seven comparative agents against recent clinical isolates of Enterobacteriaceae, Pseudomonas aeruginosa, Acinetobacter baumannii, and Stenotrophomonas maltophilia using two surveillance strategies: 1) centralized in vitro susceptibility testing of isolates collected from 27 hospital laboratories across the United States and 2) analysis of data from The Surveillance Network Database-USA, an electronic surveillance network comprising more than 200 laboratories nationwide. Regardless of the surveillance method, Enterobacteriaceae, P. aeruginosa, and A. baumannii demonstrated similar rates of susceptibility to levofloxacin and ciprofloxacin. Susceptibilities to the fluoroquinolones approached or exceeded 90% for all Enterobacteriaceae except Providencia spp. (</=65%). Approximately 70% of P. aeruginosa and 50% of A. baumanii isolates were susceptible to both fluoroquinolones. Among S. maltophilia isolates, 50% more isolates were susceptible to levofloxacin than to ciprofloxacin. Overall, the rate of ceftazidime nonsusceptibility among Enterobacteriaceae was 8.7%, with fluoroquinolone resistance rates notably higher among ceftazidime-nonsusceptible isolates than ceftazidime-susceptible ones. Multidrug-resistant isolates were present among all species tested but were most prevalent for Klebsiella pneumoniae and Enterobacter cloacae. No gram-negative isolates resistant only to a fluoroquinolone were encountered, regardless of species. Thus, while levofloxacin and ciprofloxacin have maintained potent activity against Enterobacteriaceae, the potential for fluoroquinolone resistance, the apparent association between fluoroquinolone and cephalosporin resistance, and the presence of multidrug resistance in every species examined emphasize the need to maintain active surveillance of resistance patterns among gram-negative bacilli.
Front Matter (2013)

No AccessMar 2013Front MatterAuthors/Editors: William R. Sutton, Jitendra P. Srivastava, James E. NeumannWilliam R. Sutton, Jitendra P. Srivastava, James E. Neumannhttps://doi.org/10.1596/9780821397688_FMAboutView ChaptersPDF (1.1 MB) ToolsAdd to favoritesDownload CitationsTrack Citations ShareFacebookTwitterLinked In Next chapter FiguresreferencesRecommendeddetails View Published: March 2013ISBN: 978-0-8213-9768-8e-ISBN: 978-0-8213-9769-5 Copyright & Permissions PDF DownloadLoading ...
Onset and duration of effect of incobotulinumtoxinA, onabotulinumtoxinA, and abobotulinumtoxinA in the treatment of glabellar frown lines: a randomized, double-blind study (2013)

IncobotulinumtoxinA demonstrated a more rapid onset and a longer duration of treatment effect than onabotulinumtoxinA (1:1 dose ratio) and abobotulinumtoxinA (1:3 dose ratio). Onset of effect was faster and duration of effect was longer in female subjects compared to male subjects.
Cytoplasmic Domain Heterogeneity and Functions of IgG Fc Receptors in B Lymphocytes (1992)

B lymphocytes and macrophages express closely related immunoglobulin G (IgG) Fc receptors (Fc gamma RII) that differ only in the structures of their cytoplasmic domains. Because of cell type-specific alternative messenger RNA splicing, B-cell Fc gamma RII contains an insertion of 47 amino acids that participates in determining receptor function in these cells. Transfection of an Fc gamma RII-negative B-cell line with complementary DNA's encoding the two splice products and various receptor mutants indicated that the insertion was responsible for preventing both Fc gamma RII-mediated endocytosis and Fc gamma RII-mediated antigen presentation. The insertion was not required for Fc gamma RII to modulate surface immunoglobulin-triggered B-cell activation. Instead, regulation of activation involved a region of the cytoplasmic domain common to both the lymphocyte and macrophage receptor isoforms. In contrast, the insertion did contribute to the formation of caps in response to receptor cross-linking, consistent with suggestions that the lymphocyte but not macrophage form of the receptor can associate with the detergent-insoluble cytoskeleton.
Community-acquired pneumonia (2003)

Community-acquired pneumonia (CAP) remains an important cause of morbidity and mortality. Streptococcus pneumoniae is the most common pathogen and respiratory syncitial virus the most important viral pathogen in children. The role of urinary antigen testing and PCR for the diagnosis for S. pneumoniae infection has been an important adjunct to clinical examination, showing good sensitivity and specificity. Host-related immune responses play an important role in defining the severity of illness. Other than the use of Activated Protein C and immunization, the clinical use of therapies designed to modulate these abnormal responses remains largely experimental. The 7-valent vaccine represents a major advance in the prevention of invasive pneumococcal disease. The importance of effective triage and the deleterious effects of deviation from protocols are underscored. Continuous positive pressure ventilation and noninvasive mechanical ventilation are available as options for respiratory support in cases of severe CAP and require further evaluation.
Early adverse experience as a developmental risk factor for later psychopathology: Evidencefrom rodent and primate models (2001)

Increasing evidence supports the view that the interaction of perinatal exposure to adversity with individual genetic liabilities may increase an individual's vulnerability to the expression of psycho- and physiopathology throughout life. The early environment appears to program some aspects of neurobiological development and, in turn, behavioral, emotional, cognitive, and physiological development. Several rodent and primate models of early adverse experience have been analyzed in this review, including those that "model" maternal separation or loss, abuse or neglect, and social deprivation. Accumulating evidence shows that these early traumatic experiences are associated with long-term alterations in coping style, emotional and behavioral regulation. neuroendocrine responsiveness to stress, social "fitness,' cognitive function, brain morphology, neurochemistry, and expression levels of central nervous system genes that have been related to anxiety and mood disorders. Studies are underway to identify important aspects of adverse early experience, such as (a) the existence of "sensitive periods" during development associated with alterations in particular output systems. (b) the presence of "windows of opportunity" during which targeted interventions (e.g., nurturant parenting or supportive-enriching environment) may prevent or reverse dysfunction, (c) the identity of gene polymorphisms contributing to the individual's variability in vulnerability, and (d) a means to translate the timing of these developmental "sensitive periods" across species.
Prostasin is a novel human serine proteinase from seminal fluid. Purification, tissue distribution, and localization in prostate gland. (1994)

A novel serine proteinase, designated as prostasin, has been purified from human seminal fluid to apparent homogeneity by DEAE-Sepharose CL-6B and aprotinin-affinity chromatography. The purified protein migrates as two close bands with an apparent molecular mass of 40 kDa on SDS-polyacrylamide gel electrophoresis under reducing conditions. It can be labeled with [14C]diisopropyl fluorophosphate and has a pI ranging from 4.5 to 4.8. Sequence analysis reveals that the two protein bands have an identical NH2-terminal amino acid sequence which is different from any known protein sequence in the SwissPro or GenBank data base. The NH2-terminal 20-amino acid sequence shares 50-55% identity with human alpha-tryptase, elastase 2A and 2B, chymotrypsin, acrosin, and the catalytic chains of hepsin, plasma kallikrein, and coagulation factor XI. Prostasin has trypsin-like activity with a pH optimum of 9.0, hydrolyzing peptidyl fluorogenic substrates: D-Pro-Phe-Arg-MCA, D-Phe-Phe-Arg-MCA, D-Val-Leu-Arg-MCA, and Z-Gly-Pro-Arg-AFC. It is inhibited by aprotinin, antipain, leupeptin, and benzamidine. The tissue distribution of prostasin was determined by a newly developed radioimmunoassay. Linear displacement curves for immunoreactive prostasin in body fluids and tissues were parallel with the standard curve of purified prostasin, indicating their immunological identity. Immunoreactive prostatin levels were 8.61 +/- 0.42 microgram/ml in the seminal fluid and 0.201 +/- 0.029 microgram/ml in urine. Prostasin is present at high levels in the prostate gland (143.7 +/- 15.9 ng/mg protein), moderate levels (2-6 ng/mg protein) in colon, lung, kidney, pancreas, salivary gland, liver, and bronchi, but it is not detected in the brain, muscle, testis, ventricle, atrium, and aorta. Immunohistochemical localization reveals that prostasin is present in epithelial cells and ducts of the prostate gland. These studies indicate that prostasin purified from seminal fluid is a novel serine proteinase and originates from the prostate gland.
[Application of an automatic blood cell counter, MICROX, to experimental animals. II. Leukocyte differential count in rabbits, rats, and mice]. (1983)

Automatic blood cell analyzer "MICROX" was examined for possible applicability to the differential count of white blood cell in the rabbit, rat and mouse. Spun blood smear slides prepared from 37 rabbits were treated with Wright-Giemsa stain, and those from 49 rats and 46 mice were stained with Wright's dye. Totals of 4272 white blood cells of rabbit, 5484 cells of rat and 5329 cells of mouse were counted, respectively. The identification rate of MICROX was checked by the cell-by-cell counting method. Analysis of the data was made to examine correlation between the results with a MICROX and those of visual counting by optical microscopy on the same slides. 1) Corrected identification rates were 98.0%, 98.2% and 97.8% respectively in rabbits, rats and mice. 2) A high degree of correlation was observed between the results by MICROX and by optical microscopy in respect of segmented neutrophils and lymphocytes. 3) There were an average of 13.2 cells counted as unknown cells in rabbit blood, 10.5 in rat blood and 13.6 in mouse blood per 100 cells, respectively. Of the unknown cells about 30 to 40% were closely disposed leukocytes within the same counting squares. Almost all of atypical lymphocytes and erythroblasts were also counted as unknown cells on the analyzer. The data support the feasibility of the use of MICROX for the differential count of white blood cells of normal rabbits, rats and mice as well as monkeys and dogs.
Identification of Commensal Bacterial Strains That Modulate Yersinia enterocolitica and Dextran Sodium Sulfate-Induced Inflammatory Responses: Implications for the Development of Probiotics (2007)

An increasing body of evidence suggests that probiotic bacteria are effective in the treatment of enteric infections, although the molecular basis of this activity remains elusive. To identify putative probiotics, we tested commensal bacteria in terms of their toxicity, invasiveness, inhibition of Yersinia-induced inflammation in vitro and in vivo, and modulation of dextran sodium sulfate (DSS)-induced colitis in mice. The commensal bacteria Escherichia coli, Bifidobacterium adolescentis, Bacteroides vulgatus, Bacteroides distasonis, and Streptococcus salivarius were screened for adhesion to, invasion of, and toxicity for host epithelial cells (EC), and the strains were tested for their ability to inhibit Y. enterocolitica-induced NF-kappaB activation. Additionally, B. adolescentis was administered to mice orally infected with Y. enterocolitica and to mice with mucosae impaired by DSS treatment. None of the commensal bacteria tested was toxic for or invaded the EC. B. adolescentis, B. distasonis, B. vulgatus, and S. salivarius inhibited the Y. enterocolitica-induced NF-kappaB activation and interleukin-8 production in EC. In line with these findings, B. adolescentis-fed mice had significantly lower results for mean pathogen burden in the visceral organs, intestinal tumor necrosis factor alpha mRNA expression, and loss of body weight upon oral infection with Y. enterocolitica. In addition, the administration of B. adolescentis decelerated inflammation upon DSS treatment in mice. We suggest that our approach might help to identify new probiotics to be used for the treatment of inflammatory and infectious gastrointestinal disorders.