gebhart/patrepeval huggingface dataset:
Synergistic and additive killing by antimicrobial factors found in human airway surface liquid (2000)

Airway surface liquid contains multiple factors thought to provide a first line of defense against bacteria deposited in the airways. Although the antimicrobial action of individual factors has been studied, less is known about how they work in combination. We examined the combined action of six antimicrobial peptides found in airway surface liquid. The paired combinations of lysozyme-lactoferrin, lysozyme-secretory leukocyte protease inhibitor (SLPI), and lactoferrin-SLPI were synergistic. The triple combination of lysozyme, lactoferrin, and SLPI showed even greater synergy. Other combinations involving the human beta-defensins, LL-37, and tobramycin (often administered to cystic fibrosis patients by inhalation) were additive. Because the airway surface liquid salt concentration may be elevated in cystic fibrosis patients, we examined the effect of salt on the synergistic combinations. As the ionic strength increased, synergistic interactions were lost. Our data suggest that the antibacterial potency of airway surface liquid may be significantly increased by synergistic and additive interactions between antimicrobial factors. These results also suggest that increased salt concentrations that may exist in cystic fibrosis could inhibit airway defenses by diminishing these synergistic interactions.
Factors influencing the binding of calpain I to human erythrocyte inside-out vesicles. (1990)

The mechanism for binding of human erythrocyte calpain I to human erythrocyte inside-out vesicles was studied by immunoelectrophoretic blot analysis. Binding of calpain I to inside-out vesicles was observed both in the absence and presence of Ca2+. Moreover, in the absence of Ca2+, acidic proteins like casein, ovalbumin and calpastatin suppressed while basic proteins like arginase and lysozyme did not affect the binding of calpain I to inside-out vesicles. Here, we propose a model for the binding of calpain to the membrane.
In situ mechanical characterization of mouse oocytes using a cell holding device (2010)

This paper presents a cellular force measurement technique that allows for mechanical characterization of mouse oocytes during microinjection (i.e., in situ) without requiring a separate characterization process. The technique employs an elastic cell holding device and a sub-pixel computer vision tracking algorithm to resolve cellular forces in real time with a nanonewton force measurement resolution (2 nN at 30 Hz). Mechanical properties (i.e., stiffness) of both healthy and defective mouse oocytes are characterized. The experimental results suggest that the in situ obtained force-deformation data are useful for distinguishing healthy mouse oocytes from those with aging-induced cellular defects, promising an approach for oocyte quality assessment during microinjection. Biomembrane and cytoskeleton structures of the healthy and defective oocytes are also investigated in an attempt to correlate the measured subtle mechanical difference to cellular structure changes.
Long-Term Plasma Glucose Normalization in Experimental Diabetic Rats With Macroencapsulated Implants of Benign Human Insulinomas (1986)

Permselective tubular membranes (1 mm i.d.) were filled with fragments of nine freshly resected human insulinomas, closed at both ends, and implanted in the peritoneal cavity of 30 streptozocin-induced diabetic rats. In 14 animals, nonfasting plasma glucose (PG) and insulin levels were normalized by these immunoprotected transplants for up to 1 yr (PG from 520 +/- 12 to 142 +/- 3 mg/100 ml; insulin from 6 +/- 0.5 to 44 +/- 3 microU/ml). These animals showed the same weight gain after 12 mo of observation as 20 controls. The remaining 16 animals showed an incomplete or transient correction of their diabetes and survived 4-6 mo, versus less than 8 wk in untreated animals. Removal of the membrane-encapsulated insulin-secreting tissue from 8 successfully treated rats led to hyperglycemia and death within 10 days. Histology and electron microscopy of insulinoma tissue retrieved after long-term implantation showed functionally active endocrine cells and no evidence of graft rejection. In vitro perifusion gave similar results for encapsulated and nonencapsulated insulinoma tissue. The amount of insulin secreted was quite variable, and responsiveness of the insulinoma to changes in glucose concentration of the surrounding medium was observed in three out of the five tumors studied. These observations establish the effectiveness of immunoseparation by a synthetic membrane in a pancreatic xenograft model.
A Role for Endogenous Transforming Growth Factor β1 in Langerhans Cell Biology:  The Skin of   Transforming Growth Factor β1 Null Mice Is Devoid of  Epidermal Langerhans Cells (1996)

Transforming growth factor beta 1 (TGF-beta 1) regulates leukocytes and epithelial cells. To determine whether the pleiotropic effects of TGF-beta 1, a cytokine that is produced by both keratinocytes and Langerhans cells (LC), extend to epidermal leukocytes, we characterized LC (the epidermal contingent of the dendritic cell [DC] lineage) and dendritic epidermal T cells (DETC) in TGF-beta 1 null (TGF-beta 1 -/-) mice. I-A+ LC were not detected in epidermal cell suspensions or epidermal sheets prepared from TGF-beta 1 -/- mice, and epidermal cell suspensions were devoid of allostimulatory activity. In contrast, TCR-gamma delta + DETC were normal in number and appearance in TGF-beta 1 -/- mice and, importantly, DETC represented the only leukocytes in the epidermis. Immunolocalization studies revealed CD11c+ DC in lymph nodes from TGF-beta 1 -/- mice, although gp40+ DC were absent. Treatment of TGF-beta 1 -/- mice with rapamycin abrogated the characteristic inflammatory wasting syndrome and prolonged survival indefinitely, but did not result in population of the epidermis with LC. Thus, the LC abnormality in TGF-beta 1 -/- mice is not a consequence of inflammation in skin or other organs, and LC development is not simply delayed in these animals. We conclude that endogenous TGF-beta 1 is essential for normal murine LC development or epidermal localization.
Mitogenic, Chemotactic, and Synthetic Responses of Rat Periodontal Ligament Fibroblastic Cells to Polypeptide Growth Factors In Vitro (1992)

The mitogenic, chemotactic, and synthetic responses of rat periodontal ligament (PDL) fibroblastic cells to epidermal growth factor (EGF), transforming growth factor-beta (TGF-beta), recombinant human platelet-derived growth factor (rhPDGF)-AB, rhPDGF-BB, natural (n) PDGF-AB, and insulin-like growth factor-I (IGF-I) were examined in vitro using PDL cells obtained from the coagulum of healing tooth sockets. PDGFs and IGF-I have potent and comparable mitogenic effects on PDL fibroblastic cells. The maximum mitogenic effect of PDGFs was observed at the concentration of 10 ng/ml, whereas that of IGF-I was seen at concentrations higher than 100 ng/ml. In contrast, EGF induced moderate, and TGF-beta inhibitory mitogenic responses. The combination of rhPDGF-AB with either EGF or TGF-beta demonstrated comparable mitogenic potency, equivalent to the level of PDGF alone regardless of the mitogenic effect of other growth factors. The combination of rhPDGF-AB and IGF-I, however, showed a synergistic effect revealing the highest mitogenic effect among all individual growth factors as well as any combinations of the growth factors tested. Similarly, PDL fibroblastic cells demonstrated strong chemotactic responses to both IGF-I and PDGFs. The maximum effect was observed by IGF-I at concentrations higher than 10 ng/ml, followed by rhPDGF-BB at 0.1 ng/ml, rhPDGF-AB and nPDGF at concentrations ranging from 0.1 to 1 ng/ml. TGF-beta revealed no, and EGF slightly increased, chemotactic effects. IGF-I slightly enhanced the synthesis of total protein, whereas other factors had no significant effect. However, both rhPDGF-AB and TGF-beta stimulated collagen synthesis. On the other hand, IGF-I showed no effect on collagen synthesis, while EGF suppressed collagen synthesis. These findings suggest that rhPDGF-BB and IGF-I stimulate proliferation and chemotaxis of PDL fibroblastic cells. In addition, the combination of these growth factors further increases the mitogenic effect. rhPDGF-AB also stimulates collagen synthesis by PDL fibroblastic cells. Thus, rhPDGF-BB and IGF-I may have important roles in promotion of PDL healing, and consequently, may be useful for clinical application in periodontal regenerative procedures.
Digital Circuit Realization of Piecewise-Affine Functions With Nonuniform Resolution: Theory and FPGA Implementation (2010)

This brief proposes a digital circuit architecture implementing a class of continuous piecewise-affine (PWA) functions. The work rests on a previous architecture realizing PWA functions with uniform resolution. By using PWA mapping that can be implemented through a few simple functional blocks, it is possible to extend the representation capabilities of the architecture to PWA functions with nonuniform resolution. After defining the mapping and the corresponding functional blocks, the proposed architecture is implemented in a field-programmable gate array, and a simple example is shown.
The Radiation Induced cis-trans Isomerization of Polybutadiene. II<sup>1</sup> (1959)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Radiation Induced cis-trans Isomerization of Polybutadiene. II1Morton A. GolubCite this: J. Am. Chem. Soc. 1959, 81, 1, 54–58Publication Date (Print):January 1, 1959Publication History Published online1 May 2002Published inissue 1 January 1959https://pubs.acs.org/doi/10.1021/ja01510a012https://doi.org/10.1021/ja01510a012research-articleACS PublicationsRequest reuse permissionsArticle Views224Altmetric-Citations31LEARN 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
Colonization of Arabidopsis roots by Pseudomonas fluorescens primes the plant to produce higher levels of ethylene upon pathogen infection (2003)

Plants develop an enhanced defensive capacity against a broad spectrum of plant pathogens after colonization of the roots by selected strains of non-pathogenic, fluorescent Pseudomonas spp. In Arabidopsis thaliana, this rhizobacteria-induced systemic resistance (ISR) functions independently of salicylic acid but requires responsiveness to the plant hormones jasmonic acid and ethylene. Leaves of plants of which the roots are colonized by ISR-inducing Pseudomonas fluorescens WCS417r bacteria show an enhanced capacity to convert the ethylene precursor 1-aminocyclopropane-1-carboxylate (ACC) to ethylene. Here we show that this enhanced ACC-converting capacity leads to a potentiated expression of the ethylene-responsive genes PDF1·2 and HEL after treatment of the leaves with 1 mM ACC, and a significantly higher level of ethylene emission after challenge inoculation with the bacterial pathogen Pseudomonas syringae pv. tomato DC3000/avrRpt2. P. fluorescens WCS374r bacteria that are unable to induce ISR against P. syringae pv. tomato DC3000 in Arabidopsis likewise enhanced the in vivo ACC oxidase acitivity in Col-0 plants. Moreover, the ISR-compromised mutants jar1-1 and npr1-1 also showed a significant increase in their ability to convert ACC to ethylene after treatment of the roots with P. fluorescens WCS417r. These results suggest that the induction of an enhanced ACC-converting capacity is a general response of plants to P. fluorescens bacteria and that this response does not contribute to ISR against P. syringae pv. tomato DC3000 in Arabidopsis. Nevertheless, P. fluorescens strains clearly prime the plant to produce more ethylene upon pathogen infection. The increased capacity for ethylene production might contribute to an enhanced defensive capacity against pathogens that are sensitive to ethylene-dependent defense responses.
Synthesis of β-<i>C</i>-Glycosides of <i>N</i>-Acetylglucosamine via Keck Allylation Directed by Neighboring Phthalimide Groups (1996)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTSynthesis of β-C-Glycosides of N-Acetylglucosamine via Keck Allylation Directed by Neighboring Phthalimide GroupsBarbara A. Roe, Constantine G. Boojamra, Jennifer L. Griggs, and Carolyn R. BertozziView Author Information Department of Chemistry, University of California, Berkeley, California 94720 Cite this: J. Org. Chem. 1996, 61, 18, 6442–6445Publication Date (Web):September 6, 1996Publication History Received6 May 1996Published online6 September 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/jo960819ohttps://doi.org/10.1021/jo960819obrief-reportACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views2138Altmetric-Citations74LEARN 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:Anions,Carbohydrates,Oligosaccharides,Reaction products,Stereoselectivity Get e-Alerts
Supply Chain Risk Management (2007)

The lifeblood of any business is the timely delivery of products and services. In the best possible world, if one plans accordingly, disruptions never occur. However, in the real world, disruptions do and will occur and the best business plans are those that anticipate and prepare for this inevitability, especially when dealing with international s
Semi-formal test generation with genevieve (2001)

This paper describes the first application of the Genevieve test generation methodology. The Genevieve approach uses semi-for-mal techniques derived from “model-checking” to generate test suites for specific behaviours of the design under test. An “interest-ing” behaviour is claimed to be unreachable. If a path from an ini-tial state to the state of interest does exist, a counter-example is generated. The sequence of states specifies a test for the desired behaviour.
n‐Butyl (<i>E</i>)‐7,9‐decadienoate: sex pheromone component of the nettle caterpillar, <i>Darna pallivitta</i> (2007)

Abstract The nettle caterpillar, Darna pallivitta (Moore) (Lepidoptera: Limacodidae), is an invasive pest on the island of Hawai’i, causing defoliation of ornamental nursery stock and posing a human health hazard due to their urticating hairs that can cause painful stings. Wind tunnel and field tests with 2–3‐day‐old moths revealed behavioral responses of males to caged females, which is indicative of a female‐released sex pheromone. Coupled gas chromatography‐electroantennogram detection (GC‐EAD) analysis of female abdominal tip extracts revealed two male electroantennographically active compounds produced by female D. pallivitta . Mass spectral analysis and subsequent synthesis identified the active compounds as n‐butyl ( E )‐7,9‐decadienoate (major component) and ethyl ( E )‐7,9‐decadienoate (minor component), both structurally similar to sex pheromone components previously reported from related Darna spp. Additionally, methyl ( E )‐7,9‐decadienoate was identified from female abdominal tip extracts and a strong EAD response was elicited by the synthetic compound. n‐Butyl ( E )‐7,9‐decadienoate was the only component detected by solid phase microextraction (SPME) collections from single calling female moths, however, the apparent absence of minor components may be a result of their lower abundance. Field trials showed significant attraction of male moths to all lures containing the n‐butyl ester, while the methyl and ethyl esters did not increase trap captures at the levels and ratios tested. Synthetic pheromone lures (2.5 mg) outperformed virgin moths as attractant baits and could be used for monitoring D. pallivitta populations of the island of Hawai’i and detection on other Hawai’ian islands and at ports and nurseries that receive plants from Hawai’i (e.g., California and Florida).
Computing SI and CCPP using spreadsheet programs (1998)

Spreadsheets can automate any chemical equilibrium calculation that can be performed by hand. Lotus 1‐2‐3 ® worksheets for calculating the calcite saturation index (SI) and calcium carbonate precipitation potential of a water sample are described. A simplified worksheet illustrates the principles of the method, and a more complex worksheet suitable for modeling most potable water sources is briefly described. Both worksheets include ion pairing and adjustments of equilibrium constants for temperature and ionic strength. For several test cases with a wide range of temperature, alkalinity, pH, and calcium concentration, the worksheet SI values differed <1 percent from those computed by WATEQX. For water quality modeling, spreadsheets have several advantages compared with large equilibrium codes: flexible input and output, ease of maintaining the thermodynamic database, and relatively small memory and mass‐storage requirements. Modeling of archived chemical data is possible through the combination of database management and computational capabilities of many commercially available programs. The worksheets can be obtained from the authors.
An Improved Multiobjective Particle Swarm Optimization Based on Culture Algorithms (2017)

In this paper, we propose a new approach to raise the performance of multiobjective particle swam optimization. The personal guide and global guide are updated using three kinds of knowledge extracted from the population based on cultural algorithms. An epsilon domination criterion has been employed to enhance the convergence and diversity of the approximate Pareto front. Moreover, a simple polynomial mutation operator has been applied to both the population and the non-dominated archive. Experiments on two series of bench test suites have shown the effectiveness of the proposed approach. A comparison with several other algorithms that are considered good representatives of particle swarm optimization solutions has also been conducted, in order to verify the competitive performance of the proposed algorithm in solve multiobjective optimization problems.
Efficient ssODN-Mediated Targeting by Avoiding Cellular Inhibitory RNAs through Precomplexed CRISPR-Cas9/sgRNA Ribonucleoprotein (2021)

Combined with CRISPR-Cas9 technology and single-stranded oligodeoxynucleotides (ssODNs), specific single-nucleotide alterations can be introduced into a targeted genomic locus in induced pluripotent stem cells (iPSCs); however, ssODN knockin frequency is low compared with deletion induction. Although several Cas9 transduction methods have been reported, the biochemical behavior of CRISPR-Cas9 nuclease in mammalian cells is yet to be explored. Here, we investigated intrinsic cellular factors that affect Cas9 cleavage activity in vitro. We found that intracellular RNA, but not DNA or protein fractions, inhibits Cas9 from binding to single guide RNA (sgRNA) and reduces the enzymatic activity. To prevent this, precomplexing Cas9 and sgRNA before delivery into cells can lead to higher genome editing activity compared with Cas9 overexpression approaches. By optimizing electroporation parameters of precomplexed ribonucleoprotein and ssODN, we achieved efficiencies of single-nucleotide correction as high as 70% and loxP insertion up to 40%. Finally, we could replace the HLA-C1 allele with the C2 allele to generate histocompatibility leukocyte antigen custom-edited iPSCs.
Visualizing Dataflow Graphs of Deep Learning Models in TensorFlow (2017)

We present a design study of the TensorFlow Graph Visualizer, part of the TensorFlow machine intelligence platform. This tool helps users understand complex machine learning architectures by visualizing their underlying dataflow graphs. The tool works by applying a series of graph transformations that enable standard layout techniques to produce a legible interactive diagram. To declutter the graph, we decouple non-critical nodes from the layout. To provide an overview, we build a clustered graph using the hierarchical structure annotated in the source code. To support exploration of nested structure on demand, we perform edge bundling to enable stable and responsive cluster expansion. Finally, we detect and highlight repeated structures to emphasize a model's modular composition. To demonstrate the utility of the visualizer, we describe example usage scenarios and report user feedback. Overall, users find the visualizer useful for understanding, debugging, and sharing the structures of their models.
Free-radical mechanisms involved in the formation of sequence-dependent bistranded DNA lesions by the antitumor antibiotics bleomycin, neocarzinostatin, and calicheamicin (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFree-radical mechanisms involved in the formation of sequence-dependent bistranded DNA lesions by the antitumor antibiotics bleomycin, neocarzinostatin, and calicheamicinPeter C. Dedon and Irving H. GoldbergCite this: Chem. Res. Toxicol. 1992, 5, 3, 311–332Publication Date (Print):May 1, 1992Publication History Published online1 May 2002Published inissue 1 May 1992https://pubs.acs.org/doi/10.1021/tx00027a001https://doi.org/10.1021/tx00027a001research-articleACS PublicationsRequest reuse permissionsArticle Views603Altmetric-Citations182LEARN 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