gebhart/patrepeval huggingface dataset:
PowerBLAST: A New Network BLAST Application for Interactive or Automated Sequence Analysis and Annotation (1997)

As the rate of DNA sequencing increases, analysis by sequence similarity search will need to become much more efficient in terms of sensitivity, specificity, automation potential, and consistency in annotation. PowerBLAST was developed, in part, to address these problems. PowerBLAST includes a number of options for masking repetitive elements and low complexity subsequences. It also has the capacity to restrict the search to any level of NCBI's taxonomy index, thus supporting "comparative genomics" applications. Postprocessing of the BLAST output using the SIM series of algorithms produces optimal, gapped alignments, and multiple alignments when a region of the query sequence matches multiple database sequences. PowerBLAST is capable of processing sequences of any length because it divides long query sequences into overlapping fragments and then merges the results after searching. The results may be viewed graphically, as a textual representation, or as an HTML page with links to GenBank and Entrez. For matching database sequences, annotated features are superimposed on the aligned query sequence in the output, thus greatly increasing the ease of interpretation. Such features may be used for automated annotation of new sequence because PowerBLAST output in ASN.1 form may be "dragged and dropped" into NCBI's Sequin program for sequence annotation and submission. PowerBLAST is capable of analyzing and annotating a 100-kb query in 60 min on NCBI's BLAST server.
Bexarotene as Add-On to Antipsychotic Treatment in Schizophrenia Patients (2008)

This short-term pilot study supports bexarotene as a potential valuable adjunct in management of schizophrenia. Low doses of bexarotene were well tolerated. A double-blind controlled study should be performed to replicate these preliminary positive results.
Safety profiles of anti-VEGF drugs: bevacizumab, ranibizumab, aflibercept and ziv-aflibercept on human retinal pigment epithelium cells in culture (2014)

At clinical doses, neither ranibizumab nor aflibercept produced evidence of mitochondrial toxicity or cell death. However, bevacizumab and ziv-aflibercept showed mild mitochondrial toxicity at clinically relevant doses.
Radio-over-fiber transport for the support of wireless broadband services [Invited] (2009)

Some of the work carried out within the EU Network of Excellence ISIS on radio-over-fiber systems for the support of current and emerging wireless networks is reviewed. Direct laser modulation and externally modulated links have been investigated, and demonstrations of single-mode fiber and multimode fiber systems are presented. The wireless networks studied range from personal area networks (such as ZigBee and ultrawideband) through wireless local area networks to wireless metropolitan area networks (WiMAX) and third-generation mobile communications systems. The performance of the radio-over-fiber transmission is referenced to the specifications of the relevant standard, protocol operation is verified, and complete network demonstrations are implemented.
The Significance of Digital Gene Expression Profiles (1997)

Genes differentially expressed in different tissues, during development, or during specific pathologies are of foremost interest to both basic and pharmaceutical research. "Transcript profiles" or "digital Northerns" are generated routinely by partially sequencing thousands of randomly selected clones from relevant cDNA libraries. Differentially expressed genes can then be detected from variations in the counts of their cognate sequence tags. Here we present the first systematic study on the influence of random fluctuations and sampling size on the reliability of this kind of data. We establish a rigorous significance test and demonstrate its use on publicly available transcript profiles. The theory links the threshold of selection of putatively regulated genes (e.g., the number of pharmaceutical leads) to the fraction of false positive clones one is willing to risk. Our results delineate more precisely and extend the limits within which digital Northern data can be used.
Leaky tumor vessels: consequences for tumor stroma generation and for solid tumor therapy. (1990)

Our results may be summarized as follows: 1) The tumor microvasculature is hyperpermeable to macromolecular tracers, as compared with the vessels supplying many normal tissues. 2) In the case of the several solid transplantable animal tumors studied, leaky vessels are well-differentiated venules and small veins, lined by a continuous endothelium with mostly closed interendothelial junctions. Leaky vessels are concentrated at the tumor-host interface and in bands of stroma interspersed between tumor nodules; in contrast, tumor-penetrating vessels exhibit little or no leakage of macromolecules. 3) The mechanisms of vascular leakage have yet to be established but apparently cannot be attributed to vessel immaturity, structural defects, interendothelial cell gaps, vessel injury or development of a specialized (e.g., fenestrated or sinusoidal) endothelium. 4) Macromolecules that extravasate from leaky vessels also accumulate in tumors at higher concentrations than in the blood or control tissues. Increased tracer accumulation in tumors is attributable to increased tracer influx and possibly also to reduced tracer clearance (perhaps resulting from the absence or obstruction of lymphatics). However, the high molecular weight FITC-D tracers that extravasate into solid tumors remain largely confined to tumor stroma, do not extend far from the vessels from which they leaked, and make little contact with malignant cells. 5) In contrast, smaller tracers (e.g., 3 kD FITC-D) extravasate from tumor-penetrating vessels, from the capillaries of normal tissues, as well as from hyperpermeable vessels, and, unlike larger FITC-D, diffuse readily throughout solid tumors.
Map location of the gene for a 130,000-dalton glycoprotein of bovine herpesvirus 1 (1986)

A bovine herpesvirus 1 variant (mar6) containing a mutation in a viral glycoprotein with a molecular weight of 130,000 (g130) was isolated by selecting for resistance to a neutralizing monoclonal antibody (130-6) directed against g130. Mar6 was completely resistant to neutralization by monoclonal antibody 130-6 in the presence and absence of complement, but was neutralized by polyvalent immune sera. The mar6 mutant synthesized and processed g130, but produced plaques which failed to react with monoclonal antibody 130-6 in an in situ immunoassay (black plaque). However, monoclonal antibody 130-6 was capable of binding and immunoprecipitating g130 from infected-cell extracts produced by lysis of mar6-infected cells with nonionic detergents. The mutation in mar6 was mapped by marker rescue with cloned bovine herpesvirus 1 restriction enzyme fragments to a 3.8-kilobase fragment at approximate map units 0.405 to 0.432. In addition, it was found that a DNA probe containing the glycoprotein B gene of herpes simplex type 1 hybridized uniquely to the same 3.8-kilobase fragment which was shown by marker rescue to contain the mutation site in the gene for bovine herpesvirus 1 g130.
The Cypher stent: no longer efficacious at three months in the porcine model? (2004)

See article by Carter et al. [2] (pages 617–624) in this issue .

Drug-eluting stents have represented one of the most exciting, innovative technologies, and the 0% restenosis rate has led to overwhelming enthusiasm in the medical world, even if a careful examination of the results did not show any effect on the occurrence of death and acute myocardial infarction [1]. The study of Carter et al. [2] in this issue of Cardiovascular Research brings a key message that tempers our enthusiasm, since they surprisingly discovered that, in the pig model, the Cypher stent failed to reduce restenosis at 3 and 6 months. Moreover, although the drug is still present, there is more smooth muscle cell proliferation and inflammation with the Cypher stent than with the bare stent. Since the study was conducted by Robert Falotico, the “father” of the Cypher stent [3], there is no doubt regarding the validity of these data. This initiates a huge controversy: now the question is, how is this possible? The primary suspect is the anti-restenosis strategy, i.e., inhibition of smooth muscle cell proliferation via the cell cycle [4]. Impairing the healing may not automatically mean that the reaction to the injury process is definitely abolished … 

*Fax: +33 1 5609 2664. Email address: antoine.lafont{at}egp.ap-hop-paris.fr
The influence of focal brain cooling on neurophysiopathology: validation for clinical application (2009)

The present study confirmed that the focal cooling of the cortex for 1 hour above the temperature of 0 degrees C did not induce any irreversible histological change or motor dysfunction. These results suggest that focal brain cooling above 0 degrees C has the potential to be a minimally invasive and valuable modality for the treatment of severe brain injury or to assist in the examination of brain function.
Loss analysis and interference effect in semiconductor integrated waveguide turning mirrors (1996)

Semiconductor integrated waveguide turning mirrors (IWTM) are investigated using the beam propagation method. A mirror is fabricated and modeled along with realistic geometries in the presence of offset and roughness of the mirror surface. An interference effect between waves reflected at different surfaces in the device is evidenced, that has strong impact on the device performance in the case of weakly-confining structures. A widely-accepted fabrication approach is criticized in view of this effect. A solution is outlined that minimizes the losses due to either technological limitations or interference.
Can physiological variables and early warning scoring systems allow early recognition of the deteriorating surgical patient?* (2007)

Some commonly used physiologic variables have reasonable power in determining the difference between patients requiring intensive care unit admission, but others are poor. Existing early warning scores have comparatively good discriminatory power. We have derived functions with excellent predictive power in this derivation cohort.
Properties of n-type tetrahedral amorphous carbon (ta-C)/p-type crystalline silicon heterojunction diodes (1995)

Heterojunction diodes fabricated by filtered cathodic vacuum arc (FCVA) deposition of n-type (nitrogen-doped) tetrahedral amorphous carbon (ta-C) on p-type crystalline silicon are analyzed in terms of their electronic and photoresponse properties. The thin ta-C films are deposited at room temperature allowing the ready formation of ideal step junctions. The abrupt nature of the heterojunctions is confirmed from SIMS measurements. Capacitance-voltage (C-V) characteristics also show that with an abrupt heterojunction between ta-C and Si, an interface state density of the order of 10/sup 11/ cm/sup -2/ is obtained. Dark forward current density-voltage-temperature (J-V-T) characteristics are consistent with a current transport mechanism predominantly controlled by a tunnelling-recombination process through states at the ta-C/Si interface. The photospectral response and photovoltaic behavior of the junction are also presented as a function of doping in the ta-C. The response time of these unoptimized diodes is found to be in the range of 0.1-1.5 /spl mu/s.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Prevention of experimental allergic encephalomyelitis by targeting nitric oxide and peroxynitrite: Implications for the treatment of multiple sclerosis (1997)

In this study we provide further evidence associating activated cells of the monocyte lineage with the lesions of multiple sclerosis (MS). Using a combination of immunohistochemistry and reverse transcriptase-dependent in situ polymerase chain reaction analysis, we have identified monocytes expressing inducible nitric oxide synthase (iNOS) to be prevalent in the plaque areas of post mortem brain tissue from patients with MS. In addition, we have obtained evidence of the nitration of tyrosine residues in brain areas local to accumulations of iNOS-positive cells. In parallel studies we have assessed the effects of inhibitors of iNOS induction, as well as scavengers of nitric oxide and peroxynitrite in the experimental allergic encephalomyelitis model. Significant therapeutic effects were seen with the inhibitor of iNOS induction, tricyclodecan-9-xyl-xanthogenate, a nitric oxide scavenger, 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide, and a peroxynitrite scavenger, uric acid. In particular, treatment with high doses of uric acid virtually prevented clinical symptoms of the disease. Together with our demonstration of the presence of activated macrophages expressing high levels of iNOS and evidence of peroxynitrite formation in brain tissue from patients with MS, these findings are of importance in the development of approaches to treat this disease.
Schedule dependency of the antitumor activity and toxicity of polyethylene glycol-modified interleukin 2 in murine tumor models. (1989)

Modification of recombinant human interleukin 2 (rhIL-2) with monomethoxy polyethylene glycol has been shown to alter its pharmacokinetic properties. Therefore, we investigated the pharmacological parameters of schedule and dose in order to assess the impact on the in vivo antitumor activity of this modification. The antitumor efficacy, as well as the toxicity, of polyethylene glycol-interleukin 2 (PEG-IL-2) was compared to that of rhIL-2 in three transplantable syngeneic murine tumor models, Meth A fibrosarcoma, B16 melanoma, and Pan-02 pancreatic carcinoma. At equitoxic dose levels, the antitumor activity of PEG-IL-2 was far superior to that of rhIL-2 in all three tumor models. This efficacy of PEG-IL-2 was dose dependent and was greatest on a Q7D x 2 schedule in Meth A and B16. When the same total doses were further divided and delivered on any of several alternative schedules, either the efficacy was reduced or the toxicity of the treatments was increased. In Pan-02, a rhIL-2-resistant tumor, PEG-IL-2 treatment on either the Q7D x 2, Q4D x 3, or Q3D x 4 schedule resulted in approximately a 200% increase in lifespan; however, the toxicity of the treatment increased as the interval between doses was shortened. Simulations of the pharmacokinetic profiles of these various regimens suggested that the toxicity of PEG-IL-2 and rhIL-2 was related to the minimum plasma concentration that was obtained and the time interval between peak levels. The efficacy of the treatment was associated with the interleukin 2 plasma peak height, since a dose response was observed; however, peak plasma concentration did not appear to be the only parameter which determined efficacy. We hypothesize that this observed schedule dependence is also affected by the kinetics of the host's biological response to rhIL-2.
PPARγ accelerates cellular senescence by inducing p16INK4α expression in human diploid fibroblasts (2008)

Peroxisome proliferator-activated receptor gamma (PPARgamma) plays an important role in the inhibition of cell growth by promoting cell-cycle arrest, and PPARgamma activation induces the expression of p16(INK4alpha) (CDKN2A), an important cell-cycle inhibitor that can induce senescence. However, the role of PPARgamma in cellular senescence is unknown. Here, we show that PPARgamma promotes cellular senescence by inducing p16(INK4alpha) expression. We found several indications that PPARgamma accelerates cellular senescence, including enhanced senescence-associated (SA)-beta-galactosidase staining, increased G1 arrest and delayed cell growth in human fibroblasts. Western blotting studies demonstrated that PPARgamma activation can upregulate the expression of p16(INK4alpha). PPARgamma can bind to the p16 promoter and induce its transcription, and, after treatment with a selective PPARgamma agonist, we observed more-robust expression of p16(INK4alpha) in senescent cells than in young cells. In addition, our data indicate that phosphorylation of PPARgamma decreased with increased cell passage. Our results provide a possible molecular mechanism underlying the regulation of cellular senescence.
Measurement of packet processing time of an Internet host using asynchronous packet capture at the data-link layer (2013)

As transmission speeds increase faster than processing speeds, the packet processing time (PPT) of a host (i.e., workstation) is becoming more significant in the measurement of different network parameters, in which packet processing by the host is involved. The PPT of a host is the time elapsed between the arrival of a packet at the data-link layer and the time the packet is processed at the application layer of the TCP/IP protocol stack (RFCs 2679 and 2681). In this paper, we propose a methodology to measure the PPT of a host using Internet Control Message Protocol (ICMP) packet and a specialized packet-capture card that does not require synchronization between the host under test and the packet-capture card. We tested the proposed methodology on two hosts with different specifications. The experimental results show that the proposed methodology consistently measures PPT.
Bioorthogonal Tetrazine-Mediated Transfer Reactions Facilitate Reaction Turnover in Nucleic Acid-Templated Detection of MicroRNA (2014)

Tetrazine ligations have proven to be a powerful bioorthogonal technique for the detection of many labeled biomolecules, but the ligating nature of these reactions can limit reaction turnover in templated chemistry. We have developed a transfer reaction between 7-azabenzonorbornadiene derivatives and fluorogenic tetrazines that facilitates turnover amplification of the fluorogenic response in nucleic acid-templated reactions. Fluorogenic tetrazine-mediated transfer (TMT) reaction probes can be used to detect DNA and microRNA (miRNA) templates to 0.5 and 5 pM concentrations, respectively. The endogenous oncogenic miRNA target mir-21 could be detected in crude cell lysates and detected by imaging in live cells. Remarkably, the technique is also able to differentiate between miRNA templates bearing a single mismatch with high signal to background. We imagine that TMT reactions could find wide application for amplified fluorescent detection of clinically relevant nucleic acid templates.
Fas and Perforin Pathways as Major Mechanisms of T Cell-Mediated Cytotoxicity (1994)

Two molecular mechanisms of T cell-mediated cytotoxicity, one perforin-based, the other Fas-based, have been demonstrated. To determine the extent of their contribution to T cell-mediated cytotoxicity, a range of effector cells from normal control or perforin-deficient mice were tested against a panel of target cells with various levels of Fas expression. All cytotoxicity observed was due to either of these mechanisms, and no third mechanism was detected. Thus, the perforin- and Fas-based mechanisms may account for all T cell-mediated cytotoxicity in short-term in vitro assays.
Studies of the immunosuppressive agent FK-506: synthesis of an advanced intermediate (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStudies of the immunosuppressive agent FK-506: synthesis of an advanced intermediateJohn A. Ragan, Masashi Nakatsuka, David B. Smith, David E. Uehling, and Stuart L. SchreiberCite this: J. Org. Chem. 1989, 54, 18, 4267–4268Publication Date (Print):September 1, 1989Publication History Published online1 May 2002Published inissue 1 September 1989https://pubs.acs.org/doi/10.1021/jo00279a004https://doi.org/10.1021/jo00279a004research-articleACS PublicationsRequest reuse permissionsArticle Views421Altmetric-Citations24LEARN 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 Get e-Alerts
Interferon- γ Inhibits Transgene Expression Driven by SV40 or CMV Promoters but Augments Expression Driven by the Mammalian MHC I Promoter (1995)

The use of mammalian gene expression vectors has become increasingly important for transgenics and gene therapy as well as basic research. Essential for the success of these vectors in medical research applications is the proper choice of promoter linked to the gene of interest. Many mammalian expression vectors use promoter elements from pathogenic viruses, including simian virus 40 (SV40) and cytomegalovirus (CMV). Lymphokines produced by the immune response to proteins expressed by these vectors could inhibit further transcription initiation by viral promoters. Our objective was to determine the effect of interferon-gamma (IFN-gamma) on transgene expression driven by a viral SV40 or CMV promoter/enhancer and the mammalian promoter/enhancer for the major histocompatibility complex class I (MHC I) gene. We transfected the luciferase gene driven by these three promoters into 14 cell lines of many tissues and several species. Luciferase assays of transfected cells untreated or treated with IFN-gamma indicated that, although the viral promoters could drive luciferase production in all cell lines tested to greater or lesser levels than the MHC I promoter, treatment with IFN-gamma caused inhibition of transgene expression in most of the cell lines and amplification of the MHC I promoter-driven transgene expression in all cell lines. These data indicate that the SV40 and CMV promoter/enhancers may not be a suitable choice for gene delivery especially for immune response applications or in patients where IFN levels may be elevated. The MHC I promoter/enhancer, on the other hand, may be an ideal transgene promoter for applications involving the immune system.
OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds (2013)

A crucial step in analyzing mRNA-Seq data is to accurately and efficiently map hundreds of millions of reads to the reference genome and exon junctions. Here we present OLego, an algorithm specifically designed for de novo mapping of spliced mRNA-Seq reads. OLego adopts a multiple-seed-and-extend scheme, and does not rely on a separate external aligner. It achieves high sensitivity of junction detection by strategic searches with small seeds (~14 nt for mammalian genomes). To improve accuracy and resolve ambiguous mapping at junctions, OLego uses a built-in statistical model to score exon junctions by splice-site strength and intron size. Burrows-Wheeler transform is used in multiple steps of the algorithm to efficiently map seeds, locate junctions and identify small exons. OLego is implemented in C++ with fully multithreaded execution, and allows fast processing of large-scale data. We systematically evaluated the performance of OLego in comparison with published tools using both simulated and real data. OLego demonstrated better sensitivity, higher or comparable accuracy and substantially improved speed. OLego also identified hundreds of novel micro-exons (<30 nt) in the mouse transcriptome, many of which are phylogenetically conserved and can be validated experimentally in vivo. OLego is freely available at http://zhanglab.c2b2.columbia.edu/index.php/OLego.