gebhart/patrepeval huggingface dataset:
Overcoming Resistance to Interferon-Induced Apoptosis of Renal Carcinoma and Melanoma Cells by DNA Demethylation (2006)

Epigenetic editing of gene expression by aberrant methylation of DNA may help tumor cells escape attack from the innate and acquired immune systems. Resistance to antiproliferative effects and apoptosis induction by interferons (IFNs) was postulated to result from silencing of IFN response genes by promoter hypermethylation. Treatment of human ACHN renal cell carcinoma (RCC) and A375 melanoma cells with the DNA demethylating nucleoside analog 5-AZA-2'-deoxycytidine (5-AZA-dC) synergistically augmented antiproliferative effects of IFN- alpha (alpha) 2 and IFN-beta (beta). Either 5-AZA-dC or an antisense to DNA methyltransferase 1 (DNMT1) overcame resistance to apoptosis induction by IFNs with up to 85% apoptotic cells resulting from the combinations. No similar potentiation occurred in normal kidney epithelial cells. IFN response genes were augmented more than 10 times in expression by 5-AZA-dC. Demethylation by 5-AZA-dC of the promoter of the prototypic, apoptosis-associated IFN response gene XAF1 was confirmed by methylation-specific polymerase chain reaction. siRNA to XAF1 inhibited IFN-induced apoptosis; conversely, overexpression of XAF1 overcame resistance to apoptosis induction by IFN-beta. As occurred with apoptosis-resistant melanoma cells in vitro, tumor growth inhibition in the nude mouse of human A375 melanoma xenografts resulted from treatment with 5-AZA-dC in combination with IFN-beta, an effect not resulting from either single agent. The importance of epigenetic remodeling of expression of immune-modifying genes in tumor cells was further suggested by identifying reactivation of the cancer-testis antigens MAGE and RAGE in ACHN cells after DNMT1 depletion. Thus, inhibitors of DNMT1 may have clinical relevance for immune modulation by augmentation of cytokine effects and/or expression of tumor-associated antigens.
Deep Space Terminal Demonstration (1999)

The Deep Space Terminal (DS-T) was a task that validated the concept of a fully automated, autonomous deep-space ground station. The DS-T successfully demonstrated “lights out”-mode ground-station operations using a Deep Space Network 34-meter beam-waveguide antenna that tracked a NASA deep-space probe orbiting Mars. The DS-T receives, processes, records, and distributes telemetry data to the project, without operator intervention. The DS-T task was a cooperative effort between JPL and industry, leveraging JPL’s specialized knowledge with industry’s fast implementation cycle.
Purification and substrate specificity of heparitinase I and heparitinase II from Flavobacterium heparinum. Analyses of the heparin and heparan sulfate degradation products by 13C NMR spectroscopy. (1990)

The purification of two heparitinases and a heparinase, in high yields from Flavobacterium heparinum was achieved by a combination of molecular sieving and cation-exchange chromatography. Heparinase acts upon N-sulfated glucosaminido-L-iduronic acid linkages of heparin. Substitution of N-sulfate by N-acetyl groups renders the heparin molecule resistant to degradation by the enzyme. Heparitinase I acts on N-acetylated or N-sulfated glucosaminido-glucuronic acid linkages of the heparan sulfate. Sulfate groups at the 6-position of the glucosamine moiety of the heparan sulfate chains seem to be impeditive for heparitinase I action. Heparitinase II acts upon heparan sulfate producing disulfated, N-sulfated and N-acetylated-6-sulfated disaccharides, and small amounts of N-acetylated disaccharide. These and other results suggest that heparitinase II acts preferentially upon N,6-sulfated glucosaminido-glucuronic acid linkages. The total degradation of heparan sulfate is only achieved by the combined action of both heparitinases. The 13C NMR spectra of the disaccharides formed from heparan sulfate and a heparin oligosaccharide formed by the action of the heparitinases are in accordance to the proposed mode of action of the enzymes. Comparative studies of the enzymes with the commercially available heparinase and heparitinase are described.
PATHOGENESIS OF WEST NILE VIRUS ENCEPHALITIS IN MICE AND RATS: I. INFLUENCE OF AGE AND SPECIES ON MORTALITY AND INFECTION (1967)

Journal Article PATHOGENESIS OF WEST NILE VIRUS ENCEPHALITIS IN MICE AND RATS: I. INFLUENCE OF AGE AND SPECIES ON MORTALITY AND INFECTION Get access ADNAN H. ELDADAH, ADNAN H. ELDADAH Department of Epidemiology, School of Hygiene, The Johns Hopkins University615 North Wolfe Street, Baltimore, Maryland 21205. Search for other works by this author on: Oxford Academic PubMed Google Scholar NEAL NATHANSON, NEAL NATHANSON Department of Epidemiology, School of Hygiene, The Johns Hopkins University615 North Wolfe Street, Baltimore, Maryland 21205. Search for other works by this author on: Oxford Academic PubMed Google Scholar Roger Sarsitis Roger Sarsitis Department of Epidemiology, School of Hygiene, The Johns Hopkins University615 North Wolfe Street, Baltimore, Maryland 21205. Search for other works by this author on: Oxford Academic PubMed Google Scholar American Journal of Epidemiology, Volume 86, Issue 3, November 1967, Pages 765–775, https://doi.org/10.1093/oxfordjournals.aje.a120785 Published: 01 November 1967
Open questions about the function and evolution of bacterial Min systems (2013)

OPINION article Front. Microbiol., 09 December 2013Sec. Microbial Physiology and Metabolism Volume 4 - 2013 | https://doi.org/10.3389/fmicb.2013.00378
Inventory of High-Abundance mRNAs in Skeletal Muscle of Normal Men (1999)

G42875rial analysis of gene expression (SAGE) method was used to generate a catalog of 53,875 short (14 base) expressed sequence tags from polyadenylated RNA obtained from vastus lateralis muscle of healthy young men. Over 12,000 unique tags were detected. The frequency of occurrence of each tag reflects the relative abundance of the corresponding mRNA. The mRNA species that were detected 10 or more times, each comprising >/=0.02% of the mRNA population, accounted for 64% of the mRNA mass but <10% of the total number of mRNA species detected. Almost all of the abundant tags matched mRNA or EST sequences cataloged in GenBank. Mitochondrial transcripts accounted for approximately 20% of the polyadenylated RNA. Transcripts encoding proteins of the myofibrils were the most abundant nuclear-encoded mRNAs. Transcripts encoding ribosomal proteins, and those encoding proteins involved in energy metabolism, also were very abundant. The database can be used as a reference for investigations of alterations in gene expression associated with conditions that influence muscle function, such as muscular dystrophies, aging, and exercise.
Isolation of an intracellular bacterium from hamsters (Mesocricetus auratus) with proliferative ileitis and reproduction of the disease with a pure culture (1991)

An intracellular bacterium was isolated from hamsters (Mesocricetus auratus) with proliferative ileitis. The organism was isolated in Intestine 407 and GPC-16 cell cultures (incubated in a microaerophilic atmosphere) from isolated and lysed epithelial cells from hamsters with proliferative ileitis. The bacterium measured 1.4 to 1.7 microns in length by 0.26 to 0.34 microns in width, was slightly curved, and had an irregular trilaminar cell wall. Inoculation of hamsters with a cell culture lysate containing the organism or a 0.65-microns-pore-size filtrate of an infected-cell lysate resulted in the typical lesions of proliferative ileitis in approximately 50% of the animals in 28 days. Hamsters inoculated with uninfected cells or a 0.2-microns-pore-size filtrate of an infected-cell lysate remained uninfected. Attempts to propagate the organism on cell-free media have been unsuccessful.
Mannose-Binding Lectin as a Predictor of Microalbuminuria in Type 1 Diabetes (2005)

Inflammation and complement activation via the mannose-binding lectin (MBL) pathway have been suggested to play a role in the pathogenesis of diabetic microvascular complications. The association between the complement-activating protein MBL and the development of persistent microalbuminuria was evaluated in an inception cohort of 286 newly diagnosed type 1 diabetic patients consecutively admitted to the Steno Diabetes Center between 1 September 1979 and 31 August 1984. Serum MBL was measured with an immunofluorometric assay in 270 of the patients (159 men) after 3 years of diabetes duration. During the median (range) follow-up period of 18.0 (1.0-21.8) years, 75 patients subsequently progressed to persistent micro- or macroalbuminuria (urinary albumin excretion rate >30 mg/24 h). In patients with MBL levels above the median (1,597 microg/l), the cumulative incidence of persistent micro- or macroalbuminuria was 41% (CI 31-50) as compared with 26% (CI 17-34) in patients with MBL levels below the median (log-rank test, P = 0.003). In a Cox proportional hazard model with sex and age as fixed covariates, MBL was independently associated with later development of persistent micro- or macroalbuminuria (hazard ratio 1.21 [CI 1.02-1.42] per 1,000 microg/l increase in MBL; P = 0.03) after adjusting for possible confounders. In our study, high levels of MBL early in the course of type 1 diabetes was significantly associated with later development of persistent micro- or macroalbuminuria, suggesting that complement activation initiated by MBL may be involved in the pathogenesis of diabetic microvascular complications.
RNase L Mediates the Antiviral Effect of Interferon through a Selective Reduction in Viral RNA during Encephalomyocarditis Virus Infection (1998)

The 2',5'-oligoadenylate (2-5A) system is an RNA degradation pathway which plays an important role in the antipicornavirus effects of interferon (IFN). RNase L, the terminal component of the 2-5A system, is thought to mediate this antiviral activity through the degradation of viral RNA; however, the capacity of RNase L to selectively target viral RNA has not been carefully examined in intact cells. Therefore, the mechanism of RNase L-mediated antiviral activity was investigated following encephalomyocarditis virus (EMCV) infection of cell lines in which expression of transfected RNase L was induced or endogenous RNase L activity was inhibited. RNase L induction markedly enhanced the anti-EMCV activity of IFN via a reduction in EMCV RNA. Inhibition of endogenous RNase L activity inhibited this reduction in viral RNA. RNase L had no effect on IFN-mediated protection from vesicular stomatitis virus. RNase L induction reduced the rate of EMCV RNA synthesis, suggesting that RNase L may target viral RNAs involved in replication early in the virus life cycle. The RNase L-mediated reduction in viral RNA occurred in the absence of detectable effects on specific cellular mRNAs and without any global alteration in the cellular RNA profile. Extensive rRNA cleavage, indicative of high levels of 2-5A, was not observed in RNase L-induced, EMCV-infected cells; however, transfection of 2-5A into cells resulted in widespread degradation of cellular RNAs. These findings provide the first demonstration of the selective capacity of RNase L in intact cells and link this selective activity to cellular levels of 2-5A.
Chlorophyll fluorescence—a practical guide (2000)

Chlorophyll fluorescence analysis has become one of the most powerful and widely used techniques available to plant physiologists and ecophysiologists. This review aims to provide an introduction for the novice into the methodology and applications of chlorophyll fluorescence. After a brief introduction into the theoretical background of the technique, the methodology and some of the technical pitfalls that can be encountered are explained. A selection of examples is then used to illustrate the types of information that fluorescence can provide.
Intravenous liposomal delivery of the snake venom disintegrin contortrostatin limits breast cancer progression (2004)

Despite significant research in this area, metastatic breast cancer remains a disease with a poor prognosis. Until an effective therapy is developed, it is imperative that new treatment modalities be investigated. In this report, we describe an effective method for delivery of a novel snake venom disintegrin, contortrostatin (CN), in an orthotopic, xenograft model of human mammary cancer in immunodeficient mice. CN (Mr 13,500) is a homodimeric disintegrin isolated from venom of the Southern Copperhead snake. The homodimer possesses two Arg-Gly-Asp sites, which modulate its interaction with integrins on tumor cells and angiogenic vascular endothelial cells. Although our laboratory has previously described the antitumor activity of CN in a mouse model of human mammary cancer, the method of delivery, daily intratumor injection, was not translatable to clinical application. We now describe a clinically relevant method of administering CN, liposomal delivery (LCN). A unique liposomal system has been designed for i.v. administration of a biologically active protein with full retention of biological activity. Pharmacokinetics, biodistribution, platelet reactivity, and immunogenicity of LCN were determined and compared with similar characteristics of native, unencapsulated CN. There are several advantages to liposomal delivery of CN: (1) LCN has a significantly prolonged circulatory half-life compared with native CN; (2) LCN is passively accumulated in the tumor; (3) LCN has no platelet reactivity; and (4) LCN is not recognized by the immune system. Finally, antiangiogenic activity is an important component of CN's mechanism of antitumor action. We have demonstrated that i.v. delivery of LCN leads to potent antiangiogenic activity in the orthotopic, xenograft human mammary tumor model.
Statistical Timing Analysis Considering Spatial Correlations using a Single Pert-Like Traversal (2003)

We present an efficient statistical timing analysis algorithm that predicts the probability distribution of the circuit delay while incorporating the effects of spatial correlations of intra-die parameter variations, using a method based on principal component analysis. The method uses a PERT-like circuit graph traversal, and has a run-time that is linear in the number of gates and interconnects, as well as the number of grid partitions used to model spatial correlations. On average, the mean and standard deviation values computed by our method have errors of 0.2% and 0.9%, respectively, in comparison with a Monte Carlo simulation.
Artificial bacterial flagella: Fabrication and magnetic control (2009)

Inspired by the natural design of bacterial flagella, we report artificial bacterial flagella (ABF) that have a comparable shape and size to their organic counterparts and can swim in a controllable fashion using weak applied magnetic fields. The helical swimmer consists of a helical tail resembling the dimensions of a natural flagellum and a thin soft-magnetic “head” on one end. The swimming locomotion of ABF is precisely controlled by three orthogonal electromagnetic coil pairs. Microsphere manipulation is performed, and the thrust force generated by an ABF is analyzed. ABF swimmers represent the first demonstration of microscopic artificial swimmers that use helical propulsion. Self-propelled devices such as these are of interest in fundamental research and for biomedical applications.
Application of multi-omics in single cells (2018)

In recent years, single cell assays have made exciting progresses, overcoming the issue of heterogeneity associated with bulk populations. The fast-developing sequencing methods now enable unbiased, high-throughput and highresolution view of the heterogeneity from individual cell within a population, in terms of its fate decisions, identity and function. The cell's state is regulated at different levels, such as DNA, RNA and protein, by complex interplay of intrinsic molecules existing in the organism and extrinsic stimuli such as local environment. Comprehensive profiling of single cell requires a simultaneously dissection from different levels (multi-omics) to avoid incomplete information generated from single cell. In this short review, we first examine the whole genome amplification methods, and then survey the features of the single cell approaches for genome, epigenome, transcriptome, proteome and metabolome profiling. Finally, we briefly analyze advantages of multi-omics measurement from single cells as compared to separate measurement of each molecular type, and discuss opportunities and challenges of combining single cell multiomics information on resolving phenotype variants.
Internucleobase-Interaction-Directed Self-Assembly of Nanofibers from Homo- and Heteroditopic 1,ω-Nucleobase Bolaamphiphiles (2001)

The complementary 1,omega-thymine, 1,omega-adenine, and 1,omega-(thymine, adenine) bolaamphiphiles, [N,N'-bis[3-(2,4-dihydroxy-5-methylpyrimidine-1-yl)propionyl]1,n-diaminoalkane [T-n-T (n = 10, 11, 12)], N, N'-bis[3-(6-aminopurine-9-yl)propionyl]1,n-diaminoalkane [A-n-A (n = 10, 11, 12)], and N-[3-(2,4-dihydroxy-5-methylpyrimidine-1-yl)propionyl], N'-[3-(6-aminopurine-9-yl)propionyl]1,n-diaminoalkane [T-n-A (n = 10, 11, 12)], respectively] have been synthesized. The spontaneous homo- and heteroassembly of these nucleobase-based bolaamphiphiles has been studied by light microscopy, energy-filtering transmission electron microscopy, FT-IR, and powder X-ray diffraction analyses. The achiral T-10-T bolaamphiphile produced in 10% ethanolic/aqueous solutions unprecedented double-helical ropes of 1-2 microm in widths and several hundred micrometers in length, whereas the complementary homologue A-10-A gave only microcrystalline solids of 1-10 microm in size. In contrast, an equimolar mixture of T-10-T and A-10-A yielded supramolecular fibers of 15-30 nm in width. (1)H NMR, CD, and UV studies of solution photoreactions of T-10-T suggested that under natural light the chiral rope formation is triggered by photodimerization of trace amounts of the thymine moieties in the T-10-T assemblies. Complementary hydrogen bond formation between the thymine-adenine heterobase pairs was found to prevent such a photoreaction and resulted in no chiral rope formation. The heteroditopic T-12-A bolaamphiphile self-assembled to form supramolecular fibers. Multilamellar organization was proposed for the homo- and heteroassemblies made of T-n-T and A-n-A.
Chemical Warfare Agent Detectors Probe The Fogs Of War (1994)

RETURN TO ISSUEPREVNewsNEXTChemical Warfare Agent Detectors Probe The Fogs Of War■ Equipment generally worked well during the Gulf War, but some warning alarms still can't be explainedLOIS R. EMBERView Author Information C&EN WashingtonCite this: Chem. Eng. News 1994, 72, 31, 26–32Publication Date (Print):August 1, 1994Publication History Published online11 November 2010Published inissue 1 August 1994https://pubs.acs.org/doi/10.1021/cen-v072n031.p026https://doi.org/10.1021/cen-v072n031.p026newsACS PublicationsCopyright © 1994 American Chemical SocietyArticle Views8Altmetric-Citations1LEARN 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 options SUBJECTS:Chemical warfare,Probes,Stress Get e-Alerts
Recent Progress in Protein Drug Design and Discovery with a Focus on Novel Approaches to the Development of Anticocaine Medications (2009)

Cocaine is highly addictive and no anti-cocaine medication is currently available. Accelerating cocaine metabolism, producing biologically inactive metabolites, is recognized as an ideal anti-cocaine medication strategy, especially for the treatment of acute cocaine toxicity. However, currently known wild-type enzymes have either too low a catalytic efficiency against the abused cocaine, in other words (-)-cocaine, or the in vivo half-life is too short. Novel computational strategies and design approaches have been developed recently to design and discover thermostable or high-activity mutants of enzymes based on detailed structures and catalytic/inactivation mechanisms. The structure- and mechanism-based computational design efforts have led to the discovery of high-activity mutants of butyrylcholinesterase and thermostable mutants of cocaine esterase as promising anti-cocaine therapeutics. The structure- and mechanism-based computational strategies and design approaches may be used to design high-activity and/or thermostable mutants of many other proteins that have clear therapeutic potentials and to design completely new therapeutic enzymes.
Recent Advances in the Measurement of Enantiomeric Excesses (2002)

The elaboration of an ever increasing number of chiral catalysts or reagents demands fast and sensitive methods to measure enantiomeric excesses of the products. This review discusses the various ways to solve these problems. Mass spectrometry, chromatographic or chiroptical methodologies, fluorescence, liquid crystals, enzymatic methods, and immunoassays, are some of the technologies which may be used. Kinetic resolution is often a convenient and complementary tool for analysing a mixture of enantiomers.
Via hole formation in semi-insulating InP using wet photoelectrochemical etching (2002)

Laser-assisted wet photoelectrochemical etching has been used in conjunction with a metal mask to make via holes in semi-insulating InP. It was found that the incident laser intensity and applied bias can control the degree of sidewall taper in the via holes as well as the vertical and lateral etch rates. It was found that the etch rate is faster for smaller via hole dimensions due to the smaller anode-to-cathode path length. There are however geometric limitations to the overall etched depth for small vias etched at low intensities due to the taper of the sidewalls. This method has demonstrated high etch rates and minimal undercut. Custom tailoring of the etch profile is achievable through adjustment of the etch parameters.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A general standard of WebGIS integration (2009)

Nowadays, existing WebGIS applications are isolated from each other. It is meaningful and challenging to integrate these existing applications to reduce resource loss. In this paper, the concept of WebGIS integration service is presented and its classification including width integration and depth integration is brought out. According to width integration and depth integration, a general standard of WebGIS integration is proposed. The merits of WebGIS integration service are analyzed with the representative examples from both of the two classes mentioned above.