gebhart/patrepeval huggingface dataset:
Frequency of levodopa‐related dyskinesias and motor fluctuations as estimated from the cumulative literature (2001)

There is no clear consensus regarding the frequency (and hence, the risk), of dyskinesias or motor fluctuations during chronic levodopa therapy for Parkinson's disease (PD). Multiple clinical series have tabulated these frequencies since the advent of levodopa over 30 years ago. We were interested in determining: (1) the aggregate frequency figures in the existing literature; and (2) how clinical series from the early levodopa era, which included patients with longer durations of parkinsonism, compare to more recent (modern era) series. We searched MEDLINE for all English language publications reporting the cumulative frequency of levodopa-induced dyskinesias or motor fluctuations during discrete intervals of treatment. This generated 2,478 publications spanning 1966 through September 2000. Papers with appropriate titles or abstracts were reviewed; reference lists from published clinical series were a source of additional papers for review. This ultimately yielded 74 publications with adequate data, relating to 112 intervals of levodopa treatment. Series that included patients with PD-onset well before levodopa availability (pre-levodopa era) were separately analyzed from all subsequent series. Series were grouped by duration of levodopa therapy and the median frequencies of dyskinesias and motor fluctuations were tabulated for each group. The data were analyzed both with and without adjustment for the number (N) in each series. Among series containing pre-levodopa era patients, the median dyskinesia frequency was already 50% by 5-6 months of treatment. This contrasts with the modern era series where dyskinesias were reported later in treatment. The median dyskinesia frequency was slightly less than 40% by 4-6 years of levodopa therapy among modern era patients. Motor fluctuations (wearing-off) were not tabulated in most of the early levodopa series. Among modern era reports, motor fluctuations were nil during the first year of levodopa therapy but were experienced by approximately 40% of patients by 4-6 years of treatment. Similar results were found when the analyses were restricted to only prospective studies where levodopa motor complications were targeted outcome measures. The conclusions reached were: (1) patients from the pre-levodopa era experienced dyskinesias much earlier during levodopa treatment than modern era patients, perhaps because of longer durations of pre-existing PD; (2) in the present era, patients treated with levodopa therapy for 4-6 years have approximately a 40% likelihood of experiencing motor fluctuations and a risk of dyskinesias just short of 40%; and (3) these findings represent incident data and the prevalence of clinically important morbidity may be substantially less.
4-Acetamidobutyrate Deacetylase in the Yeast Candida boidinii Grown on Putrescine or Spermidine as Sole Nitrogen Source and Its Probable Role in Polyamine Catabolism (1986)

SUMMARY: The yeast Candida boidinii (CBS 5777, ATCC 56897) when grown on spermidine, diaminopropane, putrescine, diaminopentane, diaminohexane, acetylputrescine or 4-acetamidobutyrate as sole nitrogen source contained a deacetylase (EC 3.5.1.–) catalysing the removal of the acetyl group from N-acetyl-β-alanine, 4-acetamidobutyrate and 5-acetamidopentanoate. The enzyme was synthesized early in the exponential growth phase when C. boidinii that had been grown in medium containing glucose and ammonium was transferred to medium in which putrescine replaced ammonium. The 4-acetamidobutyrate deacetylase was partially purified 250-fold. The stoicheiometry of the reaction was established using 4-acetamidobutyrate as substrate. The enzyme had a subunit relative molecular mass (M R) of 78 500 and a M R in the range 122000 to 143000. The pH optimum was 8∙0. The K m for 4-acetamidobutyrate was 0∙29 mm. The enzyme was found in a number of other yeast species and was usually associated with high levels of diamine acetyltransferase and acetylputrescine oxidase. The role of this enzyme in the catabolism of di- and polyamines (including those organisms able to use these amines as carbon source) is discussed.
Limited Efficacy of Antibacterial Vaccination Against Secondary Serotype 3 Pneumococcal Pneumonia Following Influenza Infection (2015)

The results show that induction of antibacterial humoral immunity is only partially effective in protection against secondary bacterial infections that occur following influenza, and suggest that additional therapeutic strategies to overcome defective antibacterial immunity should be explored.
Chemical and physical properties of aequorin and the green fluorescent protein isolated from Aequorea forskalea (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChemical and physical properties of aequorin and the green fluorescent protein isolated from Aequorea forskaleaFranklyn G. Prendergast and Kenneth G. MannCite this: Biochemistry 1978, 17, 17, 3448–3453Publication Date (Print):August 22, 1978Publication History Published online1 May 2002Published inissue 22 August 1978https://pubs.acs.org/doi/10.1021/bi00610a004https://doi.org/10.1021/bi00610a004research-articleACS PublicationsRequest reuse permissionsArticle Views4616Altmetric-Citations121LEARN 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
Scalable Multigigabit Pattern Matching for Packet Inspection (2008)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> In this paper, we consider hardware-based scanning and analyzing packets payload in order to detect hazardous contents. We present two pattern matching techniques to compare incoming packets against intrusion detection search patterns. The first approach, decoded partial CAM (DpCAM), predecodes incoming characters, aligns the decoded data, and performs logical <emphasis emphasistype="smcaps">and</emphasis> on them to produce the match signal for each pattern. The second approach, perfect hashing memory (PHmem), uses perfect hashing to determine a unique memory location that contains the search pattern and a comparison between incoming data and memory output to determine the match. Both techniques are well suited for reconfigurable logic and match about 2200 intrusion detection patterns using a single Virtex2 field-programmable gate-array device. We show that DpCAM achieves a throughput between 2 and 8 Gb/s requiring 0.58–2.57 logic cells per search character. On the other hand, PHmem designs can support 2–5.7 Gb/s using a few tens of block RAMs (630–1404 kb) and only 0.28–0.65 logic cells per character. We evaluate both approaches in terms of performance and area cost and analyze their efficiency, scalability, and tradeoffs. Finally, we show that our designs achieve at least 30% higher efficiency compared to previous work, measured in throughput per area required per search character. </para>
Nucleotide Sequence Analysis of the Class G Tetracycline Resistance Determinant from Vibrio anguillarum (1992)

The nucleotide sequence of the class G tetracycline resistance determinant previously isolated from Vibrio anguillarum has been determined. Two open reading frames of divergent polarity were identified. A resistance gene (tet A) encodes a protein of 393 amino acid residues (deduced molecular mass of 40.9 kDa), and a repressor gene (tet R) encodes a protein consisting of 210 amino acids with a calculated molecular mass of 23.6 kDa. Based on the deduced amino acid sequences, the proteins of tet A(G) and tet R(G) are about 60% homologous with those of RP1/Tn1721 (class A) and pSC101/pBR322 (class C), and about 50% homologous with Tn10 (class B). The relationship of the tet (G) sequence to five known tetracycline resistance determinants (class A to E) is discussed.
Design and Synthesis of Potent Retinoid X Receptor Selective Ligands That Induce Apoptosis in Leukemia Cells (1995)

Structural modifications of the retinoid X receptor (RXR) selective compound 4-[1-(3,5,5,8,8-pentamethyl-5,6,7,8-tetrahydro-2- naphthyl)ethenyl]benzoic acid (LGD1069), which is currently in phase I/IIA clinical trials for cancer and dermatological indications, have resulted in the identification of increasingly potent retinoids with > 1000-fold selectivity for the RXRs. This paper describes the design and preparation of a series of RXR selective retinoids as well as the biological data obtained from cotransfection and competitive binding assays which were used to evaluate their potency and selectivity. The most potent and selective of the analogs is 6-[1-(3,5,5,8,8-pentamethyl-5,6,7,8-tetrahydronaphthalen-2- yl)cyclopropyl]nicotinic acid (12d; LG100268). This compound has proven useful for investigating RXR dependent biological pathways including the induction of programmed cell death (PCD) and transglutaminase (TGase) activity. Our studies indicate that the induction of PCD and TGase in human leukemic myeloid cells is dependent upon activation of RXR-mediated pathways.
Arabidopsis NPH1: A Flavoprotein with the Properties of a Photoreceptor for Phototropism (1998)

The NPH1 gene of Arabidopsis thaliana encodes a 120-kilodalton serine-threonine protein kinase hypothesized to function as a photoreceptor for phototropism. When expressed in insect cells, the NPH1 protein is phosphorylated in response to blue light irradiation. The biochemical and photochemical properties of the photosensitive protein reflect those of the native protein in microsomal membranes. Recombinant NPH1 noncovalently binds flavin mononucleotide, a likely chromophore for light-dependent autophosphorylation. The fluorescence excitation spectrum of the recombinant protein is similar to the action spectrum for phototropism, consistent with the conclusion that NPH1 is an autophosphorylating flavoprotein photoreceptor mediating phototropic responses in higher plants.
Mapping of T cell epitopes of the 30-kDa alpha antigen of Mycobacterium bovis strain bacillus Calmette-Guérin in purified protein derivative (PPD)-positive individuals. (1995)

The fibronectin-binding 30-kDa alpha Ag is a major secretory protein of growing mycobacteria that stimulates in vitro lymphocyte blastogenesis in most healthy purified protein derivative-positive individuals, but only a minority of patients with active tuberculosis. T cell epitopes of the alpha Ag were assessed using blastogenic responses of PBMC from 12 healthy purified protein derivative-positive subjects to a set of synthetic peptides based on the 325-amino acid sequence of the alpha Ag of Mycobacterium bovis BCG. Because epitope-specific precursor cells are infrequent and randomly distributed, we used Poisson analysis to determine positive responses to 10 micrograms/ml of each peptide in 12 replicate culture wells. Seven immunodominant regions of the alpha Ag were identified. Each subjects responded to at least one of the two most dominant epitopes, which correspond to amino acids 131-155 and 233-257 (from N terminus). Peptides of these two epitopes induced production of IFN-gamma by sorted CD4+ T cells. The immunodominant peptides may have use a components of a vaccine and as tools to study the evolution of the immune response to M. tuberculosis. The two most dominant epitopes both occur in regions of the alpha Ag that differ from those of the atypical pathogens M. avium and M. kansasii. In addition, the M. bovis epitope of amino acids 133-155 differs from that of M. tuberculosis by a single amino acid. It may be possible to exploit the sequence differences for development of diagnostic tests with increased specificity.
Solid-State25Mg NMR Study of Inner-Sphere Mg2+Binding Complexes (1999)

A solid-state 25Mg NMR study is reported for four magnesium complexes with typical inner-sphere Mg2+ binding environments. The first 25Mg multiple quantum magic-angle spinning (MQMAS) experiment is demonstrated, which improves the resolution by approximately 20-fold.
Survey of Pulmonologistsʼ Perspectives on Thoracoscopy (2003)

Thoracoscopy is used increasingly as a diagnostic and therapeutic procedure in patients with pleural and pulmonary disease by thoracic surgeons and pulmonologists. The thoracic surgical community, through research and publications, has clearly delineated its scope in surgical practice. Data pertaining to pulmonologists' perceptions of thoracoscopy, however, are lacking. We surveyed a group of physicians attending a pleural disease course at the American Lung Association/American Thoracic Society 1999 International Conference to understand better the role of thoracoscopy in a pulmonologist's practice. A 14-item questionnaire was administered to all 142 attendees. Comparison of responses between groups was performed with the chi-square test, and p ≤ 0.05 was considered significant. One hundred forty-one fully completed questionnaires were analyzed. Ninety percent (n = 128) surveyed were pulmonologists, 9% (n = 12) were trainees, and 1% (n = 1) was not a pulmonologist. The majority worked in academic institutions and had been in practice for 5 years. Twenty-three percent reported having performed thoracoscopy, of which 10% practiced in the United States. Most preferred thoracoscopy to closed needle biopsy and chest tube pleurodesis, and were of the opinion that its role in pulmonary practice, although currently limited by the lack of training opportunities, was likely to increase in the future. Thoracoscopy was considered a valuable addition to a pulmonologist's armamentarium and could be performed by trained pulmonologists.
Common reflection point horizontal data stacking techniques (1962)

Abstract Techniques are described whereby multiple coverage of the subsurface is obtained. Detector spreads and shotpoints are arranged so that the channels representing common depth points are recorded with appreciably different horizontal distances between the shotpoints and detector stations. The channels which have a common reflection point are combined, or stacked, after appropriate corrections for angularity and travel time to datum have been applied. Reflections which follow the assumed travel paths are greatly enhanced, and other events are reduced. Methods for attenuating multiple reflections with respect to primaries are discussed in considerable detail. Typical field comparisons between conventional and stacked traverses are shown to illustrate the degree of improvement which can be obtained in the signal-to-noise ratio. General considerations applicable to field usage, and the geographic range of field experience are summarized.
A Homogeneous, Ligase-Mediated DNA Diagnostic Test (1998)

Single-nucleotide variations are the most widely distributed genetic markers in the human genome. A subset of these variations, the substitution mutations, are responsible for most genetic disorders. As single nucleotide polymorphism (SNP) markers are being developed for molecular diagnosis of genetic disorders and large-scale population studies for genetic analysis of complex traits, a simple, sensitive, and specific test for single nucleotide changes is highly desirable. In this report we describe the development of a homogeneous DNA detection method that requires no further manipulations after the initial reaction is set up. This assay, named dye-labeled oligonucleotide ligation (DOL), combines the PCR and the oligonucleotide ligation reaction in a two-stage thermal cycling sequence with fluorescence resonance energy transfer (FRET) detection monitored in real time. Because FRET occurs only when the donor and acceptor dyes are in close proximity, one can infer the genotype or mutational status of a DNA sample by monitoring the specific ligation of dye-labeled oligonucleotide probes. We have successfully applied the DOL assay to genotype 10 SNPs or mutations. By designing the PCR primers and ligation probes in a consistent manner, multiple assays can be done under the same thermal cycling conditions. The standardized design and execution of the DOL assay means that it can be automated for high-throughput genotyping in large-scale population studies.
Potent inhibition of microRNA in vivo without degradation (2008)

Chemically modified antisense oligonucleotides (ASOs) are widely used as a tool to functionalize microRNAs (miRNAs). Reduction of miRNA level after ASO inhibition is commonly reported to show efficacy. Whether this is the most relevant endpoint for measuring miRNA inhibition has not been adequately addressed in the field although it has important implications for evaluating miRNA targeting studies. Using a novel approach to quantitate miRNA levels in the presence of excess ASO, we have discovered that the outcome of miRNA inhibition can vary depending on the chemical modification of the ASO. Although some miRNA inhibitors cause a decrease in mature miRNA levels, we have identified a novel 2'-fluoro/2'-methoxyethyl modified ASO motif with dramatically improved in vivo potency which does not. These studies show there are multiple mechanisms of miRNA inhibition by ASOs and that evaluation of secondary endpoints is crucial for interpreting miRNA inhibition studies.
Platelets interact with fibrin only after activation (1985)

Interactions between platelets and fibrin have been visualized by phase contrast, epifluorescence, and scanning electron microscope examination of clots formed with dansylcadaverine-labeled fibrin and gel-filtered platelets. After thrombin activation, the platelets appeared as fluorescent aggregates with bridging strands of fibrin; formaldehyde-fixed platelets were not fluorescent under the same experimental conditions. Scanning electron micrographs demonstrated that thrombin-activated cells had numerous pseudopods to which the fibrin strands adhered; fixed platelets exhibited a smooth discoid appearance and did not interact with the clot. Platelets trapped in clots formed with Batroxobin (Pentapharm) (platelets are not activated by Batroxobin as confirmed by light-scattering aggregometry measurements) remained as nonfluorescent, discoid cells, whereas platelets first activated by adenosine diphosphate formed brightly fluorescent aggregates. Light-scattering data of thrombin activation (0.2 U/mL) indicated that preincubation of platelets with 0.1 mmol/L prostaglandin E1 (PGE1) prior to addition of thrombin decreased the extent and rate of platelet shape change and resulted in 100-fold slower aggregation. Clots formed in the presence of PGE1 revealed decreased fluorescence intensity and fewer platelet-fibrin contacts. Gly-Pro-Arg-Pro, which blocks fibrinogen binding and fibrin assembly, was also effective in blocking platelet-fibrin interactions. These results indicate that platelet activation is a prerequisite for attachment of platelets to fibrin.
Low-Cost Application-Aware DVFS for Multi-core Architecture (2008)

As technology scales down, energy/power consumption in the microprocessor has become a serious problem. Especially, as the industry moves on to multi-core processor systems, energy/power management in multi-core systems has become more and more important. In this paper, we propose new DVFS technique in multi-core systems. Our proposed technique finds the optimal DVFS level using Energy-Delay Product (EDP) and Energy-Delay2 Product (ED2P), which considers energy-efficiency of computation. According to determined DVFS level, the voltage and frequency of processor cores are changed. In our evaluations, our proposed technique shows 5.6% and 54.3% EDP reduction compared to the energy-biased and performance-biased scheme, respectively. In case of ED2P, our proposed technique reduces 36.4% and 14.7% of ED2P compared to the energy-biased and performance-biased scheme, respectively. The proposed technique can be a good alternative in future multi-core system where the both energy/power consumption and performance are critical.
Initiation and termination of DNA replication in human rRNA genes. (1993)

We have used the multicopy human rRNA genes as a model system to study replication initiation and termination in mammalian chromosomes. Enrichment for replicating molecules was achieved by isolating S-phase enriched populations of cells by centrifugal elutriation, purification of DNA associated with the nuclear matrix, and a chromatographic procedure that enriches for molecules containing single-stranded regions, a characteristic of replication forks. Two-dimensional agarose gel electrophoresis techniques were used to demonstrate that replication appears to initiate at multiple sites throughout most of the 31-kb nontranscribed spacer (NTS) of human ribosomal DNA but not within the 13-kb transcription unit or adjacent regulatory elements. Although initiation events were detected throughout the majority of the NTS, some regions may initiate more frequently than others. Termination of replication, the convergence of opposing replication forks, was found throughout the ribosomal DNA repeat units, and, in some repeats, specifically at the junction of the 3' end of the transcription unit and the NTS. This site-specific termination of replication is the result of pausing of replication forks near the sites of transcription termination. The naturally occurring multicopy rRNA gene family offers a unique system to study mammalian DNA replication without the use of chemical synchronization agents.
GLUT4 facilitates insulin stimulation and cAMP-mediated inhibition of glucose transport. (1992)

The glucose transporter isoform GLUT4 is found only in cells that exhibit insulin-sensitive glucose transport. To investigate the function of this transporter, L6 myoblasts were stably transfected with GLUT4 cDNA. GLUT4 underwent insulin-dependent movement to the cell surface in myoblasts overexpressing the transporter. One cell line (243-6) expressed sufficient levels of the GLUT4 protein to study insulin-dependent glucose transport. Unlike wild-type L6 cells, 243-6 myoblasts exhibited two features that are characteristic of differentiated muscle fibers and adipocytes in vivo: a large insulin-stimulated component of glucose transport and inhibition of this stimulated component by cAMP. Relative to normal L6 cells, 243-6 cells responded to insulin or insulin-like growth factor 1 with a 5-fold larger increase in 2-deoxy[3H]glucose uptake. N6,O2'-Dibutyryladenosine 3',5'-cyclic monophosphate (Bt2cAMP) did not inhibit transport in normal L6 myoblasts, which express only GLUT1, but inhibited IGF-1/insulin-stimulated transport by 50% in 243-6 cells. The effect of cAMP was investigated further by using Chinese hamster ovary cells transiently expressing GLUT1 and GLUT4. Bt2cAMP inhibited glucose transport only in Chinese hamster ovary cells expressing GLUT4. These results indicate that cAMP-mediated inhibition of glucose transport is dependent on expression of the GLUT4 isozyme.