gebhart/patrepeval huggingface dataset:
Prolonged Replication of a Type 1 Vaccine-Derived Poliovirus in an Immunodeficient Patient (1998)

VP1 sequences were determined for poliovirus type 1 isolates obtained over a 189-day period from a poliomyelitis patient with common variable immunodeficiency syndrome (a defect in antibody formation). The isolate from the first sample, taken 11 days after onset of paralysis, contained two poliovirus populations, differing from the Sabin 1 vaccine strain by approximately 10%, differing from diverse type 1 wild polioviruses by 19 to 24%, and differing from each other by 5.5% of nucleotides. Specimens taken after day 11 appeared to contain only one major poliovirus population. Evolution of VP1 sequences at synonymous third-codon positions occurred at an overall rate of approximately 3.4% per year over the 189-day period. Assuming this rate to be constant throughout the period of infection, the infection was calculated to have started approximately 9.3 years earlier. This estimate is about the time (6. 9 years earlier) the patient received his last oral poliovirus vaccine dose, approximately 2 years before the diagnosis of immunodeficiency. These findings may have important implications for the strategy to eliminate poliovirus immunization after global polio eradication.
Exercise Is Associated with Reduced Risk for Incident Dementia among Persons 65 Years of Age and Older (2006)

These results suggest that regular exercise is associated with a delay in onset of dementia and Alzheimer disease, further supporting its value for elderly persons.
A Chemiluminescence Fiber-Optic Biosensor for Detection of DNA Hybridization (1999)

ABSTRACT A novel fiber-optic DNA biosensor based on chemiluminescence is proposed. DNA probes were covalently immobilized onto the distal end of the optical fiber bundle. Hybridization of HRP (horseradish peroxidase)-labeled complementary nucleotides to the immobilized probes was detected by enhanced chemiluminescence. The detection limit (S/N=3) is 0.1 ppm. The approach is shown to be specific, sensitive and capable of diagnostic applications. Keywords:: DNA hybridizationfiber opticschemiluminescence
A Systematic Review of Molecular and Biological Tumor Markers in Neuroblastoma (2004)

This systematic review forms a knowledge base of the tumor markers studied thus far in neuroblastoma, and has identified some of the most important prognostic markers, which should be considered in future research and treatment strategies. Importantly, the review has also highlighted some general problems across primary tumor marker studies, in particular poor and heterogeneous reporting. These need to be addressed to allow better clinical interpretation and enable more appropriate evidence-based reviews in the future. In particular, collaboration of cancer research groups is needed to enable bigger sample sizes, standardize methods of analysis and reporting, and facilitate the pooling of individual patient data.
Parallelizing nonnumerical code with selective scheduling and software pipelining (1997)

Instruction-level parallelism (ILP) in nonnumerical code is regarded as scarce and hard to exploit due to its irregularity. In this article, we introduce a new code-scheduling technique for irregular ILP called “selective scheduling” which can be used as a component for superscalar and VLIW compilers. Selective scheduling can compute a wide set of independent operations across all execution paths based on renaming and forward-substitution and can compute available operations across loop iterations if combined with software pipelining. This scheduling approach has better heuristics for determining the usefulness of moving one operation versus moving another and can successfully find useful code motions without resorting to branch profiling. The compile-time overhead of selective scheduling is low due to its incremental computation technique and its controlled code duplication. We parallelized the SPEC integer benchmarks and five AIX utilities without using branch probabilities. The experiments indicate that a fivefold speedup is achievable on realistic resources with a reasonable overhead in compilation time and code expansion and that a solid speedup increase is also obtainable on machines with fewer resources. These results improve previously known characteristics of irregular ILP.
Rectifying interfaces using two-layer films of electrochemically polymerized vinylpyridine and vinylbipyridine complexes of ruthenium and iron on electrodes (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRectifying interfaces using two-layer films of electrochemically polymerized vinylpyridine and vinylbipyridine complexes of ruthenium and iron on electrodesH. D. Abruna, P. Denisevich, M. Umana, Thomas J. Meyer, and Royce W. MurrayCite this: J. Am. Chem. Soc. 1981, 103, 1, 1–5Publication Date (Print):January 1, 1981Publication History Published online1 May 2002Published inissue 1 January 1981https://pubs.acs.org/doi/10.1021/ja00391a001https://doi.org/10.1021/ja00391a001research-articleACS PublicationsRequest reuse permissionsArticle Views1610Altmetric-Citations344LEARN 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
A New Transcription Factor Family Associated with Human Leukemias (1995)

The proteins known as the polyoma enhancer binding protein 2 or core-binding factor (PEBP2/CBF) are heterodimeric transcription factors that contain a DNA-binding subunit (CBF alpha), and a subunit that does not bind DNA independently (CBF beta). PEBP2 and CBF were identified independently as proteins that regulate transcription of viral and cellular enhancers, and also as proteins whose genes are disrupted by chromosomal abnormalities in human leukemias. This review traces the history of the discovery of the PEBP2 and CBF protein family and describes the biochemical properties of the normal and oncogenic forms of these proteins.
Deciphering the transcriptional network of the dendritic cell lineage (2012)

Although much progress has been made in the understanding of the ontogeny and function of dendritic cells (DCs), the transcriptional regulation of the lineage commitment and functional specialization of DCs in vivo remains poorly understood. We made a comprehensive comparative analysis of CD8(+), CD103(+), CD11b(+) and plasmacytoid DC subsets, as well as macrophage DC precursors and common DC precursors, across the entire immune system. Here we characterized candidate transcriptional activators involved in the commitment of myeloid progenitor cells to the DC lineage and predicted regulators of DC functional diversity in tissues. We identified a molecular signature that distinguished tissue DCs from macrophages. We also identified a transcriptional program expressed specifically during the steady-state migration of tissue DCs to the draining lymph nodes that may control tolerance to self tissue antigens.
Src-dependent Phosphorylation of Membrane Type I Matrix Metalloproteinase on Cytoplasmic Tyrosine 573 (2007)

Membrane type 1 matrix metalloproteinase (MT1-MMP) is a transmembrane MMP that plays important roles in migratory processes underlying tumor invasion and angiogenesis. In addition to its matrix degrading activity, MT1-MMP also contains a short cytoplasmic domain whose involvement in cell locomotion seems important but remains poorly understood. In this study, we show that MT1-MMP is phosphorylated on the unique tyrosine residue located within this cytoplasmic sequence (Tyr(573)) and that this phosphorylation requires the kinase Src. Using phosphospecific antibodies recognizing MT1-MMP phosphorylated on Tyr(573), we observed that tyrosine phosphorylation of the enzyme is rapidly induced upon stimulation of tumor and endothelial cells with the platelet-derived chemoattractant sphingosine-1-phosphate, suggesting a role in migration triggered by this lysophospholipid. Accordingly, overexpression of a nonphosphorylable MT1-MMP mutant (Y573F) blocked sphingosine-1-phosphate-induced migration of Human umbilical vein endothelial cells and HT-1080 (human fibrosarcoma) cells and failed to stimulate migration of cells lacking the enzyme (bovine aortic endothelial cells). Altogether, these findings strongly suggest that the Src-dependent tyrosine phosphorylation of MT1-MMP plays a key role in cell migration and further emphasize the importance of the cytoplasmic domain of the enzyme in this process.
Microevolution of Canine Influenza Virus in Shelters and Its Molecular Epidemiology in the United States (2010)

Canine influenza virus (CIV) emerged around 2000 when an equine influenza virus (EIV) was transmitted to dogs in Florida. After 2003, the canine virus was carried by infected greyhounds to various parts of the United States and then became established in several large animal shelters, where it has continued to circulate. To better understand the evolution of CIV since its emergence, and particularly its microevolution in spatially restricted populations, we examined multiple gene segments of CIV from dogs resident in two large animal shelters in New York City during the period 2006 to 2009. In particular, we focused on viruses circulating in the two shelters in 2008 and 2009, which we found shared a common ancestor. While viruses in each shelter were generally monophyletic, we observed some gene flow between them. These shelter sequences were compared to earlier CIV isolates. The shelter viruses differed in 1 to 6 amino acids in each gene segment compared to viruses isolated in Florida between 2003 and 2005 and in Colorado in 2006 and 2008. A comparison of the sequences of equine and canine viruses revealed amino acid replacements that distinguished the viruses from the two hosts, but no clear evidence of positive selection indicative of host adaptation was detected, suggesting that any host range adaptation in CIV occurred early in the emergence of this virus or even before it transferred to dogs.
The Effect of an Opiate Receptor Antagonist on the Heal Brake Mechanism in the Rat (1993)

Studies investigated the effect of the opiate antagonist naloxone (10 mg/kg) on stomach to caecum transit (SCTT) during ileal infusion of saline or Intralipid. SCTT of the head of the meal was measured by hydrogen analysis and meal distribution by the radiolabelled meal technique. Intralipid delayed SCTT by delaying both gastric emptying (p < 0.01) and small bowel transit. Naloxone did not affect SCTT during ileal saline infusion, but produced a distal shift (p < 0.05) in the geometric centre of the meal and increased radioactivity in the caecum (p < 0.001) 100 min after gavage. Naloxone abolished the delayed SCTT of the meal induced by ileal lipid infusion, with an associated increase in radioactivity in the caecum at 200 min (p < 0.01), although the geometric centre was shifted proximally within the intestine (p < 0.01). The results suggest that the ileal brake is mediated in part by endogenous opiate pathways.
Epidemiology of inhibitor formation with recombinant factor VIII replacement therapy (2006)

This article reviews the epidemiology of inhibitor formation in patients receiving recombinant factor VIII (rFVIII) replacement therapy for haemophilia A. Data from pivotal trial programmes, post-marketing surveillance studies, and pharmacovigilance studies for all available rFVIII products were reviewed. To date, no comparative studies have been performed, and in the non-comparative studies, there were differences in the patient population enrolled and study design (including the number of patient exposure days). In the absence of comparative clinical trials, it is not possible to make comparisons between inhibitor data for the various rFVIII products. This review of the epidemiological data shows that across the pivotal trial programmes for rFVIII products, the observed incidence of inhibitors was in the range of 15-32% in previously untreated patients (PUPs) and 0.9-2.9% in previously treated patients (PTPs). High-titre inhibitors (peak >5 BU) were detected in 10-16% of PUPs and 0-2.3% of PTPs. Several initiatives proposed to help standardize collection and interpretation of inhibitor data for patients receiving rFVIII treatment are described. Such standardization would help to clarify the epidemiology of inhibitor formation across FVIII treatments.
Improvement of the anti-C3 activity of compstatin using rational and combinatorial approaches (2004)

Compstatin is a 13-residue cyclic peptide that has the ability to inhibit the cleavage of C3 to C3a and C3b. The effects of targeting C3 cleavage are threefold, and result in hindrance of: (i) the generation of the pro-inflammatory peptide C3a, (ii) the generation of opsonin C3b (or its fragment C3d), and (iii) further complement activation of the common pathway (beyond C3) with the end result of the generation of the membrane attack complex. We will report on our progress on: (i) rational design of more active compstatin analogues based on the three-dimensional structure of compstatin, (ii) experimental combinatorial design based on the generation of a phage-displayed peptide library partially randomized with the implementation of structure-induced restraints, and (iii) theoretical combinatorial design based on a novel computational optimization method, structure-induced restraints and flexible structural templates. All three approaches have resulted in analogues with improved activities. Currently, the lead analogue has the sequence acetyl-I[CVYQDWGAHRC]T-NH(2) (where the brackets denote cyclization), and is 16-fold more active than the parent peptide. We will also report on our progress towards understanding the dynamic character of compstatin using molecular dynamics simulations. The identification of an ensemble of interconverting conformers of compstatin with variable populations is a first step towards the incorporation of dynamic elements in the design of new analogues using dynamics-activity relationships in addition to structure-activity relationships.
Synthesis, Antitubulin and Antimitotic Activity, and Cytotoxicity of Analogs of 2-Methoxyestradiol, an Endogenous Mammalian Metabolite of Estradiol That Inhibits Tubulin Polymerization by Binding to the Colchicine Binding Site (1995)

In order to define the structural parameters associated with the antitubulin activity and cytotoxicity of 2-methoxyestradiol, a mammalian metabolite of estradiol, an array of analogs was synthesized and evaluated. The potencies of the new congeners as inhibitors of tubulin polymerization and colchicine binding were determined using tubulin purified from bovine brain, and the cytotoxicities of the new compounds were studied in a variety of cancer cell cultures. Maximum antitubulin activity was observed in estradiols having unbranched chain substituents at the 2-position with three non-hydrogen atoms. 2-Ethoxyestradiol and 2-((E)-1-propenyl)-estradiol were substantially more potent than 2-methoxyestradiol itself. The tubulin polymerization inhibitors in this series displayed significantly higher cytotoxicities in the MDA-MB-435 breast cancer cell line than in the other cell lines studied. The potencies of the analogs as cytotoxic and antimitotic agents in cancer cell cultures correlated with their potencies as inhibitors of tubulin polymerization, supporting the hypothesis that inhibition of tubulin polymerization is the mechanism of the cytotoxic action of 2-methoxyestradiol and its congeners. Several of the more potent analogs were tested in an estrogen receptor binding assay, and their affinities relative to estradiol were found to be very low.
Pharmacokinetic and Pharmacodynamic Properties of Oral Anticoagulants, Especially Phenprocoumon (1999)

Anticoagulants of the cumarin-type (warfarin, phenprocoumon, and acenocoumarol) are drugs for the long-term treatment and prevention of thromboembolic disorders. Because of their narrow therapeutic range, many patients have bleedings of variable severity or have recurrent thrombotic events. For this reason, the study of the pharmacokinetic parameters of phenprocoumon (PPC), considering its influence on blood clotting factors, is of high interest. The elimination kinetics of PPC, its interaction with phytomenadion (vitamin K), and the pharmacokinetic behavior of the anticoagulant under steady-state conditions have been investigated in studies with healthy volunteers and patients taking anticoagulants. The maintenance dose and the plasma levels of PPC were correlated with prothrombin time (PT) in 89 patients treated with PPC. Varying parameters in each patient (e.g., elimination kinetics of PPC, activity of the cumarin-dependent blood-clotting factors, endogenous phytomenadion stores), render it impossible to use a different means of monitoring than that of PT determination.
Probing the structure of bacteriophage phi 29 prohead RNA with specific mutations (1994)

Bacteriophage phi 29 of Bacillus subtilis packages its double-stranded DNA genome into a preformed prohead in an ATP-dependent reaction. A 174-residue phi 29-encoded RNA molecule (pRNA) is a structural component of the prohead and is essential for DNA packaging. The secondary and tertiary structures of the prohead binding site on pRNA have been probed using a series of specific mutant pRNAs and by measuring binding to RNA-free proheads and in vitro packaging of the DNA-gene product 3 (DNA.gp3) complex. A pseudoknot in pRNA inferred from phylogenetic studies was confirmed with specific mutations, and this pseudoknot was necessary for DNA.gp3 packaging activity. pRNA was truncated progressively from the 5' and 3' ends to isolate the prohead binding site, and three truncated pRNAs of 79, 71, and 62 residues retained prohead binding activity but could not reconstitute proheads for DNA.gp3 packaging. Mutation resulting in changes of the D hairpin loop and its connecting residues within the prohead binding site of pRNA and DNA packaging studies demonstrated that some alteration of secondary structure in this helix was permissible. The analyses provided further confirmation of a discrete prohead binding domain in pRNA and further delineated specific structural requirements for DNA.gp3 packaging activity which may not be required for prohead binding.
An integrative approach to CTL epitope prediction: A combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions (2005)

Reverse immunogenetic approaches attempt to optimize the selection of candidate epitopes, and thus minimize the experimental effort needed to identify new epitopes. When predicting cytotoxic T cell epitopes, the main focus has been on the highly specific MHC class I binding event. Methods have also been developed for predicting the antigen-processing steps preceding MHC class I binding, including proteasomal cleavage and transporter associated with antigen processing (TAP) transport efficiency. Here, we use a dataset obtained from the SYFPEITHI database to show that a method integrating predictions of MHC class I binding affinity, TAP transport efficiency, and C-terminal proteasomal cleavage outperforms any of the individual methods. Using an independent evaluation dataset of HIV epitopes from the Los Alamos database, the validity of the integrated method is confirmed. The performance of the integrated method is found to be significantly higher than that of the two publicly available prediction methods BIMAS and SYFPEITHI. To identify 85% of the epitopes in the HIV dataset, 9% and 10% of all possible nonamers in the HIV proteins must be tested when using the BIMAS and SYFPEITHI methods, respectively, for the selection of candidate epitopes. This number is reduced to 7% when using the integrated method. In practical terms, this means that the experimental effort needed to identify an epitope in a hypothetical protein with 85% probability is reduced by 20-30% when using the integrated method. The method is available at http://www.cbs.dtu.dk/services/NetCTL. Supplementary material is available at http://www.cbs.dtu.dk/suppl/immunology/CTL.php.
Natively Inhibited Trypanosoma brucei Cathepsin B Structure Determined by Using an X-ray Laser (2012)

The Trypanosoma brucei cysteine protease cathepsin B (TbCatB), which is involved in host protein degradation, is a promising target to develop new treatments against sleeping sickness, a fatal disease caused by this protozoan parasite. The structure of the mature, active form of TbCatB has so far not provided sufficient information for the design of a safe and specific drug against T. brucei. By combining two recent innovations, in vivo crystallization and serial femtosecond crystallography, we obtained the room-temperature 2.1 angstrom resolution structure of the fully glycosylated precursor complex of TbCatB. The structure reveals the mechanism of native TbCatB inhibition and demonstrates that new biomolecular information can be obtained by the "diffraction-before-destruction" approach of x-ray free-electron lasers from hundreds of thousands of individual microcrystals.
Recycling of Plastic Waste into Fuels, a Review (2014)

Plastics have become common materials of our everyday lives, and many of their properties, such as durability, versatility and lightweight, can be a significant factor in achieving sustainable development. A common problem with recycling plastics is that plastics are often made up of more than one kind of polymer or there may be some sort of fiber added to the plastic (a composite) to give added strength. This can make recovery difficult. Rejected or waste material usually has good characteristics for recycling and will be clean. Although the quantity of material available is sometimes small, the quantities tend to be growing as consumption, and therefore production, increases. Recycling is a method preventing accumulation the excessive waste quantity through their second processing and utilization in the production process of new materials. The aim of this review was focused on the introducing of the technologies (methods) used to convert waste plastic to fuels and to call researchers on production of fuels from waste plastic and other related materials.
Long‐term expression of gene introduction into normal human T‐lymphocytes by retroviral‐mediated gene transfer (1991)

Human T-lymphocytes are long lived, easily accessible, mature, and capable of proliferation. They are theoretically a suitable target for retroviral mediated gene transfer. To test this hypothesis, normal human T-cells obtained from bone marrow and peripheral blood were stimulated with phytohemagglutinin (PHA) and infected 24 h later with the retroviral vector N2 which carries the bacterial neo gene. T-lymphocytes were propagated in culture for up to 14 weeks with interleukin-2 (IL-2). Analysis by whole cell RNA dot/blot using a single stranded RNA probe demonstrated persistent expression of the neo gene. Preliminary functional studies revealed that both helper and suppressor functions were preserved in the infected cells in culture. These results demonstrate that normal T-cells are capable of long-term expression of genes introduced by retroviral mediated gene transfer and are potential target cells for somatic gene therapy.