gebhart/patrepeval huggingface dataset:
Dynamic frequency hopping in cellular systems with network assisted resource allocation (2002)

We propose an implementation of dynamic frequency hopping (DFH) for cellular systems with synchronized bases. The implementation uses network assisted resource allocation (NARA), which is based upon "real-time" inter-base signaling. We review the concept of DFH and propose a supporting network and signaling structure for DFH with NARA. We find that the resulting system complexity, in terms of the mobile measurements, over the air signaling, and inter-base signaling, is not high. Using voice traffic as an example, we find that for the system considered, DFH has twice the user capacity compared to traditional random frequency hopping schemes.
Electrochemical fountain pen nanofabrication of vertically grown platinum nanowires (2007)

Local electrochemical deposition of freestanding platinum nanowires was demonstrated with a new approach—electrochemical fountain pen nanofabrication (ec-FPN). The ec-FPN exploits the meniscus formed between an electrolyte-filled nanopipette ('the fountain pen') and a conductive substrate to serve as a confined electrochemical cell for reducing and depositing metal ions. Freestanding Pt nanowires were continuously grown off the substrate by moving the nanopipette away from the substrate while maintaining a stable meniscus between the nanopipette and the nanowire growth front. High quality and high aspect-ratio polycrystalline Pt nanowires with diameter of ∼150 nm and length over 30 µm were locally grown with ec-FPN. The ec-FPN technique is shown to be an efficient and clean technique for localized fabrication of a variety of vertically grown metal nanowires and can potentially be used for fabricating freeform 3D nanostructures.
Electroporation and DNA‐dependent cell death in murine macrophages (1993)

The difficulty of transfecting primary macrophages and macrophage cell lines has meant that relatively few studies on regulation of gene expression have been performed in these cells. This study has optimized an electroporation procedure for the macrophage cell line RAW 264, but shows that introduction of DNA into the cytoplasm of primary macrophages by electroporation is toxic to the cells. It is proposed that this cell death may have a physiological role in defence against certain viral infections which result in accumulation of cytoplasmic DNA. RAW 264 cells were efficiently transfected by electroporation, but electroporated bone marrow derived macrophages (BMM) showed large scale cell death over a period of 12 h. Electroporation without DNA was not toxic and DNase treatment of samples before transfection prevented cell death. The toxicity of DNA was concentration-dependent and sequence-independent. Synthetic, genomic and plasmid DNA all caused cell death. This sensitivity to DNA seems to be distinct from the antiviral state induced by double-stranded RNA and may be part of an uncharacterized viral defence system.
Evaluation of Methods for Sampling, Recovery, and Enumeration of Bacteria Applied to the Phylloplane (1991)

Determining the fate and survival of genetically engineered microorganisms released into the environment requires the development and application of accurate and practical methods of detection and enumeration. Several experiments were performed to examine quantitative recovery methods that are commonly used or that have potential applications. In these experiments, Erwinia herbicola and Enterobacter cloacae were applied in greenhouses to Blue Lake bush beans (Phaseolus vulgaris) and Cayuse oats (Avena sativa). Sampling indicated that the variance in bacterial counts among leaves increased over time and that this increase caused an overestimation of the mean population size by bulk leaf samples relative to single leaf samples. An increase in the number of leaves in a bulk sample, above a minimum number, did not significantly reduce the variance between samples. Experiments evaluating recovery methods demonstrated that recovery of bacteria from leaves was significantly better with stomacher blending, than with blending, sonication, or washing and that the recovery efficiency was constant over a range of sample inoculum densities. Delayed processing of leaf samples, by storage in a freezer, did not significantly lower survival and recovery of microorganisms when storage was short term and leaves were not stored in buffer. The drop plate technique for enumeration of bacteria did not significantly differ from the spread plate method. Results of these sampling, recovery, and enumeration experiments indicate a need for increased development and standardization of methods used by researchers as there are significant differences among, and also important limitations to, some of the methods used.
Peptide architecture. Design of stable .alpha.-helical metallopeptides via a novel exchange-inert ruthenium(III) complex (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPeptide architecture. Design of stable .alpha.-helical metallopeptides via a novel exchange-inert ruthenium(III) complexM. Reza Ghadiri and A. Katharina FernholzCite this: J. Am. Chem. Soc. 1990, 112, 26, 9633–9635Publication Date (Print):December 1, 1990Publication History Published online1 May 2002Published inissue 1 December 1990https://pubs.acs.org/doi/10.1021/ja00182a030https://doi.org/10.1021/ja00182a030research-articleACS PublicationsRequest reuse permissionsArticle Views728Altmetric-Citations118LEARN 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
Identification of group A rotavirus gene 4 types by polymerase chain reaction (1992)

Five genetically distinct human rotavirus (HRV) gene 4 groups have been described on the basis of comparative nucleotide sequencing and the predicted amino acid sequences, and at least four of them represent distinct VP4 antigenic types. To identify each gene 4 type and investigate its distribution in HRV isolates from patients with diarrhea, we developed a polymerase chain reaction (PCR) typing method using sequence information available for four genetically distinct gene 4 types. Rotavirus double-stranded RNAs (dsRNAs) isolated from stool samples were first reverse transcribed and amplified by PCR by using two oligonucleotide primers that correspond to regions that are highly conserved among all known HRV gene 4 types. The 876-bp dsDNA products were then reamplified by PCR in the presence of a cocktail containing one conserved plus-sense primer and four type-specific minus-sense primers (selected from the hypervariable region of gene 4), resulting in products of 345, 483, 267, and 391 bp corresponding to gene 4 types 1, 2, 3, and 4, respectively. This method reliably identified the gene 4 types of 16 well-characterized HRV isolates. Our results were independently confirmed for all 16 strains by reverse transcription and PCR amplification of HRV dsRNA in the presence of alternate type-specific primer pairs. For direct gene 4 typing of HRV in stool samples, we developed a method to extract rotavirus dsRNA from stool specimens by using glass powder. Our results suggest that gene 4 typing will be useful in providing more a complete characterization of HRV strains of epidemiologic or vaccine-related interest.
The NLRP1 Inflammasome Attenuates Colitis and Colitis-Associated Tumorigenesis (2015)

Nucleotide-binding domain and leucine-rich repeat (NLR) proteins are a diverse family of pattern recognition receptors that are essential mediators of inflammation and host defense in the gastrointestinal system. Recent studies have identified a subgroup of inflammasome forming NLRs that modulate the mucosal immune response during inflammatory bowel disease (IBD) and colitis associated tumorigenesis. To better elucidate the contribution of NLR family members in IBD and cancer, we conducted a retrospective analysis of gene expression metadata from human patients. These data revealed that NLRP1, an inflammasome forming NLR, was significantly dysregulated in IBD and colon cancer. To better characterize the function of NLRP1 in disease pathogenesis, we used Nlrp1b(-/-) mice in colitis and colitis-associated cancer models. In this paper, we report that NLRP1 attenuates gastrointestinal inflammation and tumorigenesis. Nlrp1b(-/-) mice demonstrated significant increases in morbidity, inflammation, and tumorigenesis compared with wild-type animals. Similar to data previously reported for related inflammasome forming NLRs, the increased inflammation and tumor burden was correlated with attenuated levels of IL-1β and IL-18. Further mechanistic studies using bone marrow reconstitution experiments revealed that the increased disease pathogenesis in the Nlrp1b(-/-) mice was associated with nonhematopoietic-derived cells and suggests that NLRP1 functions in the colon epithelial cell compartment to attenuate tumorigenesis. Taken together, these data identify NLRP1 as an essential mediator of the host immune response during IBD and cancer. These findings are consistent with a model whereby multiple NLR inflammasomes attenuate disease pathobiology through modulating IL-1β and IL-18 levels in the colon.
Atp8b1 and Abcb11 Analysis in 62 Children With Normal Gamma-Glutamyl Transferase Progressive Familial Intrahepatic Cholestasis (Pfic): Phenotypic Differences Between Pfic1 and Pfic2 and Natural History (2010)

PFIC1 and PFIC2 differ clinically, biochemically, and histologically at presentation and/or during the disease course. A small proportion of normal-GGT PFIC is likely not due to ATP8B1 or ABCB11 mutations.
Effects of Metrifonate on Cognitive Decline in Alzheimer Disease (1998)

Forty-seven patients with probable Alzheimer disease (AD) completed a 6-month double-blind study to compare metrifonate with placebo. The Alzheimer Disease Assessment Scale cognitive subscale score of the metrifonate group treated to a 50-70% inhibition of red blood cell acetylcholinesterase activity differed significantly from the placebo group score by 1.8 points (p < 0.03) due to a deterioration in cognitive performance in the placebo group (p < 0.01). Statistically significant deterioration also occurred in the Mini-Mental State Examination scores (p < 0.01) in the placebo-treated group. Adverse effects were uncommon and did not require adjustment of the dose of metrifonate or discontinuation of treatment. These findings extend our previous report of a favorable effect of metrifonate on cognitive symptoms in AD by showing clinical, not only statistical, significance.
Support-limited extrapolation of offset Fourier data (2005)

We investigate the usefulness of support-limited extrapolation as a tool for improving the estimate of the magnitude of a finite extent complex-valued signal from samples of its Fourier transform that are offset from the origin. The motivating application is spotlight mode synthetic aperture radar where the complex-valued signal to be recovered is microwave reflectivity and the measured Fourier samples of this reflectivity constitute the signal to be extrapolated. Both analytical and simulation results are presented supporting an earlier conjecture that extrapolation will be of little benefit unless the width of the known Fourier data is less than or equal to the bandwidth of just the magnitude of the reflectivity.
A novel Fcγ receptor ligand augments humoral responses by targeting antigen to Fcγ receptors (2007)

Generating efficient antibody (Ab) responses against weak antigens remains challenging. Ab responses require antigen (Ag) uptake by antigen-presenting cells (APC), followed by presentation of processed Ag to T cells. Limited uptake of antigenic peptides by APC constrains Ab responses. Here we improve vaccine efficacy by targeting Ag to Fcgamma receptors (FcgammaR) using R4, a recombinant FcgammaR ligand. R4 has four repeats per chain of the hinge region and CH2 domain (HCH2) of human IgG1. HCH2 encompasses the FcgammaR binding site. The repeats are linked to the human IgG1 framework. To test R4 in augmenting Ag uptake, we expressed human serum albumin domain 1 (HSA1) at the N terminus of R4 to produce HSA1R4. HSA1R4 (50 microg) administered to mice in Ribi adjuvant induces up to 1100-fold higher HSA1-specific IgG titers than HSA1 (p<0.001). HSA1R4 (250 ng) induces up to 130 times more anti-HSA1 Ab than HSA1Fc, a protein with HSA1 linked to the IgG1 framework (p<0.001). HSA-reactive T cells proliferate more briskly to HSA1R4 than to HSA1Fc (p<0.008). Immunization with HSA1R4 yields greater T cell reactivity to HSA1 ex vivo than immunization with HSA1Fc (p<0.004). Linking antigenic peptides to linear HCH2 polymers may facilitate vaccine development.
Rapid optimization and prototyping for therapeutic antibody-like molecules (2013)

Multispecific antibody-like molecules have the potential to advance the standard-of-care in many human diseases. The design of therapeutic molecules in this class, however, has proven to be difficult and, despite significant successes in preclinical research, only one trivalent antibody, catumaxomab, has demonstrated clinical utility. The challenge originates from the complexity of the design space where multiple parameters such as affinity, avidity, effector functions, and pharmaceutical properties need to be engineered in concurrent fashion to achieve the desired therapeutic efficacy. Here, we present a rapid prototyping approach that allows us to successfully optimize these parameters within one campaign cycle that includes modular design, yeast display of structure focused antibody libraries and high throughput biophysical profiling. We delineate this approach by presenting a design case study of MM-141, a tetravalent bispecific antibody targeting two compensatory signaling growth factor receptors: insulin-like growth factor 1 receptor (IGF-1R) and v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (ErbB3). A MM-141 proof-of-concept (POC) parent molecule did not meet initial design criteria due to modest bioactivity and poor stability properties. Using a combination of yeast display, structured-guided antibody design and library-scale thermal challenge assay, we discovered a diverse set of stable and active anti-IGF-1R and anti-ErbB3 single-chain variable fragments (scFvs). These optimized modules were reformatted to create a diverse set of full-length tetravalent bispecific antibodies. These re-engineered molecules achieved complete blockade of growth factor induced pro-survival signaling, were stable in serum, and had adequate activity and pharmaceutical properties for clinical development. We believe this approach can be readily applied to the optimization of other classes of bispecific or even multispecific antibody-like molecules.
Salmonella typhimurium activates virulence gene transcription within acidified macrophage phagosomes. (1992)

Survival of Salmonella typhimurium within macrophage phagosomes requires the coordinate expression of bacterial gene products. This report examines the contribution of phagosomal pH as a signal for expression of genes positively regulated by the S. typhimurium virulence regulators PhoP and PhoQ. Several hours after bacterial phagocytosis by murine bone marrow-derived macrophages, PhoP-activated gene transcription increased 50- to 77-fold. In contrast, no difference in PhoP-activated gene expression was observed after infection of cultured epithelial cells, suggesting that the membrane sensor PhoQ recognized signals unique to macrophage phagosomes. The increase in PhoP-regulated gene expression was abolished when macrophage culture medium contained NH4Cl or chloroquine, weak bases that raise the pH of acidic compartments. Measurements of pH documented that S. typhimurium delayed and attenuated acidification of its intracellular compartment. Phagosomes containing S. typhimurium required 4-5 hr to reach pH < 5.0. In contrast, within 1 hr vacuoles containing heat-killed bacteria were measured at pH < 4.5. The eventual acidification of phagosomes to pH < 5.0 correlated with the period of maximal PhoP-dependent gene expression. These observations implicate phagosome acidification as an intracellular inducer of PhoP-regulated gene expression and suggest that Salmonella survival is dependent on its ability to attenuate phagosome acidification.
Dehydrative Glycosylation with Activated Diphenyl Sulfonium Reagents. Scope, Mode of C(1)-Hemiacetal Activation, and Detection of Reactive Glycosyl Intermediates (2000)

The development of a method for direct dehydrative glycosylations with 1-hydroxyglycosyl donors employing the reagent combination of triflic anhydride and diphenyl sulfoxide is described. The one-pot coupling method is a facile process which is applicable to a variety of carbohydrate coupling partners. Oxygen-18-labeling studies are consistent with the first step in carbohydrate activation being the formation of an anomeric oxosulfonium intermediate. This reactive glycosyl species (35) is observable in low-temperature NMR experiments when 2,3,4,6-tetra-O-methyl-d-mannopyranose is activated as the glycosyl donor. When the dehydrative glycosylation reaction is performed in the presence of the triflic acid scavenger 2-chloropyridine, NMR analysis reveals that the glycosyl oxosulfonium intermediate 35 is converted to the corresponding anomeric 2-chloropyridinium species 36.
A new reflective FPD technology using interferometric modulation (1997)

Abstract— The Interferometric Modulator™ (IMod™) is a micromachined, deformable optical cavity whose reflected color changes with the application of a voltage. Exhibiting switching speeds &lt;50 kHz and prominent hysteresis, these devices show much promise as the basis for video‐rate full‐color reflective FPDs. Their development status will be presented.
Lateral flow microarrays: a novel platform for rapid nucleic acid detection based on miniaturized lateral flow chromatography (2007)

Widely used nucleic acid assays are poorly suited for field deployment where access to laboratory instrumentation is limited or unavailable. The need for field deployable nucleic acid detection demands inexpensive, facile systems without sacrificing information capacity or sensitivity. Here we describe a novel microarray platform capable of rapid, sensitive nucleic acid detection without specialized instrumentation. The approach is based on a miniaturized lateral flow device that makes use of hybridization-mediated target capture. The miniaturization of lateral flow nucleic acid detection provides multiple advantages over traditional lateral flow devices. Ten-microliter sample volumes reduce reagent consumption and yield analyte detection times, excluding sample preparation and amplification, of <120 s while providing sub-femtomole sensitivity. Moreover, the use of microarray technology increases the potential information capacity of lateral flow. Coupled with a hybridization-based detection scheme, the lateral flow microarray (LFM) enables sequence-specific detection, opening the door to highly multiplexed implementations for broad-range assays well suited for point-of-care and other field applications. The LFM system is demonstrated using an isothermal amplification strategy for detection of Bacillus anthracis, the etiologic agent of anthrax. RNA from as few as two B. anthracis cells was detected without thermocycling hardware or fluorescence detection systems.
Towards Workflow Pattern Support of Event-Driven Process Chains ( EPC ) (2005)

Abstract: The 20 workflow patterns proposed by van der Aalst et al. provide a comprehensive benchmark for comparing process modelling languages. In this paper, we present a workflow pattern analysis of Event-Driven Process Chains (EPCs) which is novel in its degree of detailing. Building on this analysis, we propose three extensions to EPCs in order to provide for workflow pattern support. These are the introduction of the so-called empty connector; inclusion of multiple instantiation concepts; and a cancellation construct. The latter two are inspired by YAWL. Furthermore, describe how these extensions can be represented in EPC Markup Language (EPML). 1
Clearance and tissue distribution of recombinant human interleukin 1 beta in rats. (1990)

Clearance and tissue distribution of recombinant human interleukin 1 beta (IL-1 beta) were investigated by determining the growth-inhibitory activity on tumor cells in rats after i.v. or s.c. administration. A single 100 micrograms/kg i.v. bolus was biphasically eliminated with a terminal half-life of 19.0 min in normal rats. Serum IL-1 beta activity reached a maximum level 1 h after s.c. administration and then declined with a half-life of 1.59 h. The absolute bioavailability was 40.5%. IL-1 beta activity was mainly located in the kidney and was particularly accumulated in the lysosomal fraction. A 14-fold increase in the elimination half-life of IL-1 beta activity was found in nephrectomized rats, in comparison with sham-treated control rats. Pretreatment with E-64 and leupeptin, both of which are thiol protease inhibitors, had no effect on the plasma levels of IL-1 beta activity, but a 2-fold increase in plasma level was found in rats pretreated with pepstatin A, a carboxyl protease inhibitor. Since excreted IL-1 beta activity was not detected in urine, these results suggest that the kidney is the main site of its metabolic degradation and that carboxyl protease is involved in its metabolic inactivation.
Data fusion (2009)

The development of the Internet in recent years has made it possible and useful to access many different information systems anywhere in the world to obtain information. While there is much research on the integration of heterogeneous information systems, most commercial systems stop short of the actual integration of available data. Data fusion is the process of fusing multiple records representing the same real-world object into a single, consistent, and clean representation. This article places data fusion into the greater context of data integration, precisely defines the goals of data fusion, namely, complete, concise, and consistent data, and highlights the challenges of data fusion, namely, uncertain and conflicting data values. We give an overview and classification of different ways of fusing data and present several techniques based on standard and advanced operators of the relational algebra and SQL. Finally, the article features a comprehensive survey of data integration systems from academia and industry, showing if and how data fusion is performed in each.