gebhart/patrepeval huggingface dataset:
<title>ISO-IEC MPEG-2 software video codec</title> (1995)

Part 5 of the International Standard ISO/IEC 13818 `Generic Coding of Moving Pictures and Associated Audio' (MPEG-2) is a Technical Report, a sample software implementation of the procedures in parts 1, 2 and 3 of the standard (systems, video, and audio). This paper focuses on the video software, which gives an example of a fully compliant implementation of the standard and of a good video quality encoder, and serves as a tool for compliance testing. The implementation and some of the development aspects of the codec are described. The encoder is based on Test Model 5 (TM5), one of the best, published, non-proprietary coding models, which was used during MPEG-2 collaborative stage to evaluate proposed algorithms and to verify the syntax. The most important part of the Test Model is controlling the quantization parameter based on the image content and bit rate constraints under both signal-to-noise and psycho-optical aspects. The decoder has been successfully tested for compliance with the MPEG-2 standard, using the ISO/IEC MPEG verification and compliance bitstream test suites as stimuli.
Metabolism of Propane, n -Propylamine, and Propionate by Hydrocarbon-Utilizing Bacteria (1972)

Studies were conducted on the oxidation and assimilation of various three-carbon compounds by a gram-positive rod isolated from soil and designated strain R-22. This organism can utilize propane, propionate, or n-propylamine as sole source of carbon and energy. Respiration rates, enzyme assays, and (14)CO(2) incorporation experiments suggest that propane is metabolized via methyl ketone formation; propionate and n-propylamine are metabolized via the methylmalonyl-succinate pathway. Isocitrate lyase activity was found in cells grown on acetate and was not present in cells grown on propionate or n-propylamine. (14)CO(2) was incorporated into pyruvate when propionate and n-propylamine were oxidized in the presence of NaAsO(2), but insignificant radioactivity was found in pyruvate produced during the oxidation of propane and acetone. The n-propylamine dissimilatory mechanism was inducible in strain R-22, and amine dehydrogenase activity was detected in cells grown on n-propylamine. Radiorespirometer and (14)CO(2) incorporation studies with several propane-utilizing organisms indicate that the methylmalonyl-succinate pathway is the predominant one for the metabolism of propionate.
Evaluation and characterization of available bandwidth probing techniques (2003)

The packet pair mechanism has been shown to be a reliable method to measure the bottleneck link capacity on a network path, but its use for measuring available bandwidth is more challenging. In this paper, we use modeling, measurements, and simulations to better characterize the interaction between probing packets and the competing network traffic. We first construct a simple model to understand how competing traffic changes the probing packet gap for a single-hop network. The gap model shows that the initial probing gap is a critical parameter when using packet pairs to estimate available bandwidth. Based on this insight, we present two available bandwidth measurement techniques, the initial gap increasing (IGI) method and the packet transmission rate (PTR) method. We use extensive Internet measurements to show that these techniques estimate available bandwidth faster than existing techniques such as Pathload, with comparable accuracy. Finally, using both Internet measurements and ns simulations, we explore how the measurement accuracy of active probing is affected by factors such as the probing packet size, the length of probing packet train, and the competing traffic on links other than the tight link.
Superior Activity of the Type C Class of ISS In Vitro and In Vivo Across Multiple Species (2005)

CpG-C are a novel class of CpG motif-containing immunostimulatory sequences (ISS) that includes both a 5'-TCG element and a CpG-containing palindrome. CpG-C drive all known ISS activities and, in particular, are potent enhancers of IFN-alpha from plasmacytoid dendritic cells (PDCs). In our examination of CpG-C sequence requirements, we determined that optimal IFN-alpha-inducing activity could be achieved with longer palindromes. Longer palindromes also correlated with maintenance of the double-stranded (ds) form despite concentration and pH changes, indicating a preference for ds oligodeoxynucleotides (ODNs) by the ISS-induced signaling mechanism for IFN-alpha synthesis. This correlation did not hold for all arms of the ISS-induced immune response, since we did not observe increased B cell activity with the longer palindrome CpG-C ODNs. We further demonstrated that CpG-C retained activity in an in vitro primate system and induced the expression of several cytokines and IFN-alpha-inducible genes when CpG-C were administered in vivo to mice and primates. In conclusion, we have shown CpG-C to exert several types of immune functions across multiple species, and this novel class is thus an attractive candidate for ISS-based therapeutic strategies.
Purification and characterization of Cob(II)yrinic acid a,c-diamide reductase from Pseudomonas denitrificans (1992)

An NADH-dependent flavoenzyme exhibiting cob(II)yrinic acid a,c-diamide reductase activity was purified 6,300-fold to homogeneity from Pseudomonas denitrificans and sequenced at its N terminus. This enzyme of the cobalamin biosynthetic pathway reduced to the Co(I) state all of the Co(II)-corrinoids isolated from this microorganism.
The Presence of Platelet-Activating Factor-Acetylhydrolase in Human Middle Ear Effusions (1998)

Factors related to inflammation, including platelet-activating factor (PAF), apparently have a role in chronic otitis media with effusion. PAF is metabolized to the biologically inactive lyso-PAF by the enzyme PAF-acetylhydrolase (PAF-AH). We have obtained evidence that PAF-AH activity is present in human middle ear effusions in patients with chronic otitis media with effusion. The present study revealed the enzyme in human middle ear effusions to be the plasma type PAF-AH. We suggest that PAF-AH may be involved in regulating inflammation in the middle ear by inactivating PAF, the potent proinflammatory autacoid.
Genetic variants of ApoE and ApoER2 differentially modulate endothelial function (2014)

It is poorly understood why there is greater cardiovascular disease risk associated with the apolipoprotein E4 (apoE) allele vs. apoE3, and also greater risk with the LRP8/apolipoprotein E receptor 2 (ApoER2) variant ApoER2-R952Q. Little is known about the function of the apoE-ApoER2 tandem outside of the central nervous system. We now report that in endothelial cells apoE3 binding to ApoER2 stimulates endothelial NO synthase (eNOS) and endothelial cell migration, and it also attenuates monocyte-endothelial cell adhesion. However, apoE4 does not stimulate eNOS or endothelial cell migration or dampen cell adhesion, and alternatively it selectively antagonizes apoE3/ApoER2 actions. The contrasting endothelial actions of apoE4 vs. apoE3 require the N-terminal to C-terminal interaction in apoE4 that distinguishes it structurally from apoE3. Reconstitution experiments further reveal that ApoER2-R952Q is a loss-of-function variant of the receptor in endothelium. Carotid artery reendothelialization is decreased in ApoER2(-/-) mice, and whereas adenoviral-driven apoE3 expression in wild-type mice has no effect, apoE4 impairs reendothelialization. Moreover, in a model of neointima formation invoked by carotid artery endothelial denudation, ApoER2(-/-) mice display exaggerated neointima development. Thus, the apoE3/ApoER2 tandem promotes endothelial NO production, endothelial repair, and endothelial anti-inflammatory properties, and it prevents neointima formation. In contrast, apoE4 and ApoER2-R952Q display dominant-negative action and loss of function, respectively. Thus, genetic variants of apoE and ApoER2 impact cardiovascular health by differentially modulating endothelial function.
Requirement of Rac1 in the development of cardiac hypertrophy (2006)

The development of cardiac hypertrophy is mediated, in part, by increase in NADPH oxidase activity and myocardial oxidative stress. The Rho GTPase, Rac, regulates NADPH oxidase activity through interaction with gp91(phox) and p67(phox) (in which "phox" is phagocyte oxidase). However, it is not known which Rac isoform mediates this effect in the heart. Here we show that Rac1 is critical for generating oxidative stress and producing cardiac hypertrophy in the adult heart. The Rac1 gene was temporally and specifically deleted in adult mouse cardiomyocytes (c-Rac1(-/-)). Compared with wild-type or Rac1 heterozygous mice, the hearts of c-Rac1(-/-) mice showed decreased gp91(phox) and p67(phox) interaction, NADPH oxidase activity, and myocardial oxidative stress in response to angiotensin II (400 ng/kg per day for 2 weeks) stimulation. This result correlated with decreased myocardial hypertrophy. These results indicate that Rac1 is critical for the hypertrophic response in the heart and suggest that therapies which target myocardial Rac1 may be beneficial in the treatment of cardiac hypertrophy.
Relationship between ovarian steroids, gonadotrophins and relaxin during the menstrual cycle (1993)

The circulating levels of relaxin have been measured and their relationship with the plasma levels of oestradiol (E2), progesterone, luteinizing hormone (LH) and follicle-stimulating hormone (FSH) have been investigated during the normal menstrual cycle. In addition, the effect of human chorionic gonadotrophin (hCG) on plasma relaxin levels has been studied. In the first part of the study, blood samples were obtained on days 5, 10 and 15 of the follicular phase and on alternate days from the day of the LH surge (detected in early-morning urine and confirmed by circulating levels of LH) until day 6 of the following follicular phase in nine normally cycling female volunteers. In the second part of the study, a single intramuscular dose of hCG (10,000 IU) was given on day 11 of the menstrual cycle. Relaxin was detectable from the mid-luteal phase until the onset of menstruation. The plasma levels of relaxin on days 10 and 12 of the luteal phase were significantly greater than on day 6. Positive associations between the circulating levels of relaxin and E2 and negative associations between the plasma levels of FSH and those of both relaxin and E2 were found on days 8, 10 and 12 of the luteal phase. The relationship between E2 and FSH was stronger than that between relaxin and FSH. Exogenous hCG had no effect on plasma relaxin levels. The pattern of the relationship between E2 and relaxin suggests that a common mechanism may regulate their release or that plasma relaxin levels are determined by those of E2.(ABSTRACT TRUNCATED AT 250 WORDS)
Hypertension in postmenopausal women: pathophysiology and management (1995)

Hypertension, particularly systolic hypertension, afflicts over 50% of postmenopausal women and is an important risk factor for cardiovascular disease in this group. Hormone replacement therapy with estrogen or an estrogen/progestin combination does not alter blood pressure but has beneficial effects on other cardiovascular risk factors, so should be considered in all postmenopausal women unless contraindicated.
Addressing the Tertiary Structure of Human Parathyroid Hormone-(1–34) (1998)

Parathyroid hormone (PTH) regulates mineral metabolism and bone turnover by activating specific receptors located on osteoblastic and renal tubular cells and is fully functional as the N-terminal 1-34 fragment, PTH-(1-34). Previously, a "U-shaped" conformation with N- and C-terminal helices brought in close proximity by a turn has been postulated. The general acceptance of this hypothesis, despite limited experimental evidence, has altered the direction of the design of PTH-analogs. Examining the structure of human PTH-(1-34) under conditions that encompass the different environments the hormone may experience in the approach to and interaction with the G-protein-coupled receptor (including benign aqueous and saline solutions and in the presence of dodecylphosphocholine), we observe no evidence for a U-shape conformation or any tertiary structure. Instead, the N- and C-terminal helical domains, which vary in length and stability depending on the conditions, are separated by a highly flexible region of undefined conformation. These observations are in complete accord with recent conformational studies of PTH-related protein analogs containing lactams (Mierke, D. F., Maretto, S., Schievano, E. , DeLuca, D., Bisello, A., Mammi, S., Rosenblatt, M., Peggion, E., and Chorev, M. (1997) Biochemistry 36, 10372-10383) or a model amphiphilic alpha-helix (Pellegrini, M., Bisello, A., Rosenblatt, M., Chorev, M., and Mierke, D. F. (1997) J. Med. Chem. 40, 3025-3031). Reliable structural data from different environmental conditions are absolutely requisite for the next step in the design of non-peptide PTH analogs.
cis-Acting RNA packaging locus in the 115-nucleotide direct repeat of Rous sarcoma virus (1983)

The v-src gene of Schmidt-Ruppin strain A of Rous sarcoma virus is flanked by a 115-nucleotide direct repeat. Mutants that lack either the upstream or downstream copy replicate normally. However, mutants that lack both copies do not replicate. Cloned viral DNA lacking both copies of the 115-nucleotide sequence is capable of directing the transcription of viral RNA posttransfection. This viral RNA is polyadenylated, spliced, exported from the nucleus, and translated into protein normally. However, virions isolated from the culture medium 48 h posttransfection lack viral RNA. When mutant DNA is contransfected with wild-type DNA, the virions produced 48 h later contain wild-type RNA but not mutant RNA, even though both RNAs are present in the cytoplasm. We propose that the 115-nucleotide element of Rous sarcoma-avian leukosis virus encodes a cis-acting sequence that is necessary for the proper incorporation of viral RNA into virions.
Potential inhibitors of S-adenosylmethionine-dependent methyltransferases. 8. Molecular dissections of carbocyclic 3-deazaadenosine as inhibitors of S-adenosylhomocysteine hydrolase (1985)

A series of 9-(hydroxyalkyl)-3-deazaadenines, which are analogues of the carbocyclic derivative of 3-deazaadenosine (3-deaza-C-Ado), were synthesized. The analogues were tested as inhibitors of bovine liver S-adenosyl-L-homocysteine (AdoHcy) hydrolase (EC 3.3.1.1) and as inhibitors of vaccinia virus (WR) replication in clone 929 mouse L cells and the results were compared to those observed for the parent compound, 3-deaza-C-Ado. 4-Amino-1-(2,3-dihydroxy-1-propyl)imidazo[4,5-c]pyridine (14), the analogue which included the 1'-, 2'-, and 3'-carbons of 3-deaza-C-Ado, was the most active inhibitor toward purified AdoHcy hydrolase. The inhibitory effect of 14 (Ki = 768 nM) on AdoHcy hydrolase was significantly less than that observed for 3-deaza-C-Ado (Ki = 4 nM). Analogue 14 also exhibited inhibitory activity against vaccinia virus replication, but the activity was less than that observed with 3-deaza-C-Ado. 4-Amino-1-(4-hydroxy-1-butyl)imidazo[4,5-c]pyridine (15) showed little or no inhibitory activity toward AdoHcy hydrolase, but it did exhibit antiviral effects comparable to 14. These results suggest that 3-deaza-C-Ado and analogue 14 may be producing their antiviral effects by altering a critical viral methylation (e.g., methylation of the 5'-cap of viral mRNA), whereas analogue 15 may be acting through an alternative mechanism.
Changes in Fluid Compartments and Body Composition in Obese Women after Weight Loss Induced by Gastric Banding (2003)

LAP-BAND seems to achieve satisfactory weight losses while sparing FFM and causing only mild body fluid alterations.
Association of different tumor necrosis factor α promoter allele frequencies with ankylosing spondylitis in HLA-B27 positive individuals (1998)

These data indicate that allelic variations in the TNFalpha promoter influence disease susceptibility in HLA-B27 positive individuals. This protective effect of variant promoter alleles could be related to differences in TNFalpha production or could reflect the association of different B27 haplotypes with ankylosing spondylitis.
Polyethylene Glycol Conjugation at Cys 232 Prolongs the Half-Life of α 1 Proteinase Inhibitor (2002)

alpha1 Proteinase inhibitor (alpha1PI), a natural inhibitor of the serine proteinase leukocyte elastase, is also an intravenous therapeutic agent used to treat hereditary emphysema and may be useful in other respiratory disorders. However, to achieve sustained suppression of leukocyte elastase, alpha1PI must be given frequently and in large amounts, thus limiting its clinical use. We hypothesized that conjugating alpha1PI with polyethylene glycol (PEG) at Cys(232) could extend the in vivo half-life of alpha1PI in blood and lung. We present evidence that site-specific conjugation with either 20 or 40 kD PEG at Cys(232) of nonglycosylated recombinant human alpha1PI (rhalpha1PI) results in an active inhibitor with prolonged in vivo stability. In addition, 72 h after airway instillation PEG-rhalpha1PI was found to be significantly better than glycosylated alpha1PI in protecting the lung against leukocyte elastase-mediated lung hemorrhage. We conclude that thiol-specific PEGylation markedly improves the in vivo pharmacokinetic profile of rhalpha1PI and represents a simple, novel strategy to address the therapeutic goal of human leukocyte elastase inhibition.
Influence of genotype, dose and sex on pruritogen-induced scratching behavior in the mouse (2006)

Itch features considerable interindividual variability in humans, and initial studies using animal models have demonstrated a likely role of genetic factors in mediating such variability. In an attempt to systematically study genetic mediation of itch in the mouse such that gene identification by linkage mapping might be achieved, we examined scratching behavior induced by histamine and chloroquine in mice of 11 inbred mouse strains. Multiple chloroquine drug doses were used, revealing the existence of inverted-U dose-response relationships in every strain, allowing us to determine strain-dependent peak scratching behavior over the entire dose range. Peak chloroquine-induced scratching varied by 2.5-fold in this set of strains; scratching behavior shows moderate heritability in the mouse. The present data also reveal, for the first time, significant sex differences in pruritogen-induced scratching behavior, with female mice scratching an average of 23% more than males. Finally, a comparison of the strain means obtained here with previously collected data using nociceptive assays revealed a suggestive negative genetic correlation between chloroquine-induced itch and thermal pain, such that strains sensitive to pain are resistant to itch and vice versa. This finding may have implications both for our understanding of itch pathophysiology and for the identification of itch-related genes.
Soluble tumor necrosis factor α receptor type 1 in psoriasis patients treated with narrowband ultraviolet B (2005)

The results of the study confirm the role of sTNF-R1 as a marker of psoriasis severity and efficacy of treatment. They also suggest that NB-UVB influences the serum level of sTNF-R1.
Learning with Kernels (2001)

A comprehensive introduction to Support Vector Machines and related kernel methods. In the 1990s, a new type of learning algorithm was developed, based on results from statistical learning theory: the Support Vector Machine (SVM). This gave rise to a new class of theoretically elegant learning machines that use a central concept of SVMs—-kernels—for a number of learning tasks. Kernel machines provide a modular framework that can be adapted to different tasks and domains by the choice of the kernel function and the base algorithm. They are replacing neural networks in a variety of fields, including engineering, information retrieval, and bioinformatics. Learning with Kernels provides an introduction to SVMs and related kernel methods. Although the book begins with the basics, it also includes the latest research. It provides all of the concepts necessary to enable a reader equipped with some basic mathematical knowledge to enter the world of machine learning using theoretically well-founded yet easy-to-use kernel algorithms and to understand and apply the powerful algorithms that have been developed over the last few years.
Antibiotics as signalling molecules (2007)

We present the argument that the majority of low-molecular-weight organic compounds made and secreted by microbes play roles as cell-signalling molecules in the environment. Of the large number of compounds isolated to date, only a small fraction have been shown to possess useful therapeutic antibiotic activity. However, most microbial metabolites modulate gene transcription at low concentrations, and this is proposed to be the primary effect of the compounds in the maintenance of microbial communities in the environment. Thus, microbial metabolites constitute a large collection of cell-signalling molecules that regulate gene expression in microbial populations and possibly the interactions of these populations with the surrounding organisms.
Relationship between tissue selectivity and lipophilicity for inhibitors of HMG-CoA reductase (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRelationship between tissue selectivity and lipophilicity for inhibitors of HMG-CoA reductaseBruce D. Roth, Thomas M. A. Bocan, C. John Blankley, Alexander W. Chucholowski, Paul L. Creger, Mark W. Creswell, Erika Ferguson, Roger S. Newton, Patrick O'Brien, and Cite this: J. Med. Chem. 1991, 34, 1, 463–466Publication Date (Print):January 1, 1991Publication History Published online1 May 2002Published inissue 1 January 1991https://pubs.acs.org/doi/10.1021/jm00105a071https://doi.org/10.1021/jm00105a071research-articleACS PublicationsRequest reuse permissionsArticle Views454Altmetric-Citations51LEARN 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
NFATc2 and T-bet contribute to T-helper-cell-subset-specific regulation of IL-21 expression (2005)

T helper (Th) 2 cells selectively express IL-21 in addition to the classic Th2 cytokines IL-4, IL-5, and IL-13. In contrast to these clustered Th2 cell cytokine genes, the IL-21 gene resides on a different chromosome and is not coordinately regulated by the same locus control region that directs the expression of other Th2 cytokines. We demonstrate that the proximal promoter of IL-21 controls its Th-cell-subset-specific expression through the action of NFATc2 and T-bet. Whereas NFATc2 directly binds to and activates transcription of the IL-21 promoter in Th2 cells, T-bet represses IL-21 transcription by inhibiting the binding of NFATc2 to the promoter in Th1 cells. These data suggest that there are multiple mechanisms by which Th-cell-subset-specific cytokine genes are regulated.