gebhart/patrepeval huggingface dataset:
Calcium-sensitive Transcriptional Activation of the Proximal CCAAT Regulatory Element of the grp78/BiP Promoter by the Human Nuclear Factor CBF/NF-Y (1996)

Transcription of the gene encoding GRP78/BiP, a calcium-binding molecular chaperone localized in the endoplasmic reticulum, is induced in mammalian cells through gradual depletion of the intracellular calcium stores. The multimeric CCAAT binding factor, CBF/NF-Y, binds to the most proximal CCAAT regulatory element (C1) of the grp78 promoter required for both basal level expression and stress response. Using an in vitro transcription system, we show through factor competition and immunodepletion that the grp78 C1-mediated enhancement of transcription requires primarily CBF. Correlating with the previous observation that CBF binding to the 78C1 site is enhanced by EGTA and EDTA, these divalent cation chelators specifically stimulate 78C1-directed transcription. In contrast, increasing amounts of calcium ions are inhibitory. These results provide evidence that CBF is functionally important in transactivating the grp78 C1 transcriptional activity, and suggest a possible mechanism by which grp78 transcription is stimulated by calcium depletion. We further discovered that in addition to binding CBF, both the 78C1 element and the CBF binding site of the alpha2(I) collagen promoter interact weakly with the multifunctional transcription factor YY1. Our studies show that the binding sites for CBF and YY1 are distinct for the two promoter sites, suggesting that YY1 and other interacting factors could exert differential effects on individual promoters bearing the same CBF site.
Markers of Myocardial Damage and Inflammation in Relation to Long-Term Mortality in Unstable Coronary Artery Disease (2000)

In unstable coronary artery disease, elevated levels of troponin T and C-reactive protein are strongly related to the long-term risk of death from cardiac causes. These markers are independent risk factors, and their effects are additive with respect to each other and other clinical indicators of risk.
Inter-organization networks: implications of access control: requirements for interconnection protocol (1986)

When two or more distinct organizations interconnect their internal computer networks they form an Inter-Organization Network(ION) . IONs support the exchange of cad/cam data between manufacturers and subcontractors, software distribution from vendors to users, customer input to suppliers' order-entry systems, and the shared use of expensive computational resources by research laboratories, as examples. This paper analyzes the technical implications of interconnecting networks across organization boundaries. After analyzing the organization context in which IONs are used, we demonstrate that such interconnections are not satisfied by traditional network design criteria of connectivity and transparency. To the contrary, a primary high-level requirement is access control, and participating organizations must be able to limit connectivity and make network boundaries visible. We describe a scheme based on non-discretionary control which allows interconnecting organizations to combine gateway, network, and system-level mechanisms to enforce cross-boundary control over invocation and information flow, while minimizing interference with internal operations. Access control requirements such as these impose new requirements on the underlying interconnection protocols. We demonstrate such alternative interconnection protocols that support loose coupling across administrative boundaries and that accommodate the necessary control mechanisms. Message-based gateways that support non-real-time invocation of services (e.g., file and print servers, financial transactions, VLSI design tools, etc.) are a promising basis for such loose couplings.
Developing subunit immunogens using B and T cell epitopes and their constructs derived from the F1 antigen of<i>Yersinia pestis</i>using novel delivery vehicles (2003)

Yersinia pestis is the etiological agent of pneumonic and bubonic plague. As the currently licensed vaccines for plague have their own limitations, there is a need for a rational and more effective form of a subunit vaccine to combat both forms of the disease. Newer methods of antigen delivery coupled with adjuvant offer an alternative approach toward a plague vaccine. In order to develop a new generation vaccine against plague, we chose an immunodominant, outer membrane capsular protein, F1 of Y. pestis. The immunogenicity of the peptide sequences, predicted to possess B (three sequences, B1, B2 and B3) and T (two sequences, T1 and T2) cell determinants, was studied in a murine model with different genetic backgrounds, using alhydrogel and liposomes as delivery vehicles. All the peptide sequences are immunogenic in all mouse strains and showed primary and secondary immune response. B2 peptide was found to be most immunogenic, followed by B1 and B3 peptides. Chimeras made between B and T structures proved highly immunogenic and the antibody levels are comparable with native F1 antigen, thereby proving that T1 and T2 are helper sequences. Interestingly, the liposome mode of immunization was found to be more immunogenic and generated higher affinity antibodies than the alum-based preparation. Immunization using a mixture of all the peptides further proved B2 to be immunodominant. The IgG isotype profile showed predominance of IgG1, IgG2b followed by IgG2a for all the formulations irrespective of mode of antigen delivery. Lymphocyte proliferation of spleen cells primed in vivo with peptides, B-T conjugates and F1 antigen followed by in vitro stimulation with these antigens in soluble (medium) and particulate (liposome) form, showed dose-dependent stimulation of T cells, while B-T constructs showed a higher stimulation index, comparable to F1 antigen. The liposome mode of antigen presentation showed higher lymphoproliferation of spleen cells. Of all the peptides tested, T1 and T2 sequences showed the highest stimulation indices. The pattern of cytokine levels was in the following order: interferon-gamma>interleukin-2>interleukin-4. In vivo protective studies of the B-T conjugates revealed that B1T1 and a mixture of conjugates showed a survival rate of 10 days. Thus, the study highlights the importance of B and T cell epitopes as peptide-based immunogens, being a serious alternative for plague vaccine.
Biotinylated GHK peptide incorporated collagenous matrix: A novel biomaterial for dermal wound healing in rats (2005)

Matrikines are small peptide fragments of extracellular matrix proteins that display potent tissue repair activities. Difficulties in achieving sustained delivery of bioactive concentration of matrikines in the affected area limits their therapeutic use. The present study evaluates the effects biotinylated matrikine peptide (bio-glycyl-histidyl-lysine) incorporated collagen membrane for dermal wound healing processes in rats. Biotinylated peptide incorporated collagen matrix (PIC) showed better healing when compared to wounds treated with collagen matrix [CF (collagen film)] and without collagen [CR (control)]. Binding studies indicate that biotinylated GHK (Bio-GHK) binds effectively to the collagen matrix and red blood cell (RBC) membrane when compared with t-butyloxycarbonyl substituted GHK (Boc-GHK). Wound contraction, increased cell proliferation, and high expression of antioxidant enzymes in PIC treated group indicate enhanced wound healing activity when compared to CF and CR groups. Interestingly Bio-GHK incorporated collagen increases the copper concentration by ninefold at the wound site indicating the wound healing property of Bio-GHK can also be linked with both copper localization and matrikine activities. These results demonstrate the possibility of using Bio-GHK incorporated collagen film as a therapeutic agent in the wound healing process.
Helicobacter pylori: Its Role in Disease (1992)

Journal Article Helicobacter pylori: Its Role in Disease Get access Martin J. Blaser Martin J. Blaser From the Division of Infectious Diseases, Department of Medicine and Department of Microbiology and Immunology, Vanderbilt University School of Medicine; and Department of Veterans Affairs Medical Center, Nashville, Tennessee Reprints or correspondence: Dr. Martin J. Blaser, Vanderbilt University School of Medicine, Division of Infectious Diseases, A-3310 Medical Center North, Nashville, Tennessee 37232-2605. Search for other works by this author on: Oxford Academic PubMed Google Scholar Clinical Infectious Diseases, Volume 15, Issue 3, September 1992, Pages 386–393, https://doi.org/10.1093/clind/15.3.386 Published: 01 September 1992 Article history Received: 06 May 1992 Revision received: 28 May 1992 Published: 01 September 1992
Temperature Dependence of Diffusion in Aqueous Solutions (1954)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTemperature Dependence of Diffusion in Aqueous SolutionsL. G. LongsworthCite this: J. Phys. Chem. 1954, 58, 9, 770–773Publication Date (Print):September 1, 1954Publication History Published online1 May 2002Published inissue 1 September 1954https://pubs.acs.org/doi/10.1021/j150519a017https://doi.org/10.1021/j150519a017research-articleACS PublicationsRequest reuse permissionsArticle Views2581Altmetric-Citations188LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Using static single assignment form in a code optimizer (1992)

Static single assignment form represents data dependences elegantly and provides a basis for powerful optimizations. Table-driven techniques for peephole optimization and code generation are straightforward and effective. it is natural to want to use both together in a code optimizer. However, doing so reveals that static single assignment form does not remove all antidependences, and that it conflicts with table-driven code generation for 2-address machines. This paper describes these problems and how to solve them.
The PAAD/PYRIN-Family Protein ASC Is a Dual Regulator of a Conserved Step in Nuclear Factor κB Activation Pathways (2002)

Apoptosis-associated speck-like protein containing a Caspase recruitment domain (ASC) belongs to a large family of proteins that contain a Pyrin, AIM, ASC, and death domain-like (PAAD) domain (also known as PYRIN, DAPIN, Pyk). Recent data have suggested that ASC functions as an adaptor protein linking various PAAD-family proteins to pathways involved in nuclear factor (NF)-kappaB and pro-Caspase-1 activation. We present evidence here that the role of ASC in modulating NF-kappaB activation pathways is much broader than previously suspected, as it can either inhibit or activate NF-kappaB, depending on cellular context. While coexpression of ASC with certain PAAD-family proteins such as Pyrin and Cryopyrin increases NF-kappaB activity, ASC has an inhibitory influence on NF-kappaB activation by various proinflammatory stimuli, including tumor necrosis factor (TNF)alpha, interleukin 1beta, and lipopolysaccharide (LPS). Elevations in ASC protein levels or of the PAAD domain of ASC suppressed activation of IkappaB kinases in cells exposed to pro-inflammatory stimuli. Conversely, reducing endogenous levels of ASC using siRNA enhanced TNF- and LPS-induced degradation of the IKK substrate, IkappaBalpha. Our findings suggest that ASC modulates diverse NF-kappaB induction pathways by acting upon the IKK complex, implying a broad role for this and similar proteins containing PAAD domains in regulation of inflammatory responses.
Towards Provenance-Based Anomaly Detection in MapReduce (2015)

MapReduce enables parallel and distributed processing of vast amount of data on a cluster of machines. However, such computing paradigm is subject to threats posed by malicious and cheating nodes or compromised user submitted code that could tamper data and computation since users maintain little control as the computation is carried out in a distributed fashion. In this paper, we focus on the analysis and detection of anomalies during the process of MapReduce computation. Accordingly, we develop a computational provenance system that captures provenance data related to MapReduce computation within the MapReduce framework in Hadoop. In particular, we identify a set of invariants against aggregated provenance information, which are later analyzed to uncover anomalies indicating possible tampering of data and computation. We conduct a series of experiments to show the efficiency and effectiveness of our proposed provenance system.
Polysialic acid is required for optimal growth of axons on a neuronal substrate (1992)

Formation of axonal pathways involves a variety of molecules that influence cell-cell interactions. The polysialic acid (PSA) moiety of the neural cell adhesion molecule (NCAM) is present on neuronal surfaces during process outgrowth. Our studies reveal that the removal of PSA causes a decrease in the rate of elongation of retinal cell processes on a substrate of neuronal membranes derived from chick tectum. This effect was partially reversed by antibodies against the L1 adhesion molecule, but not by antibodies against NCAM, N-cadherin, or beta 1-integrins. This predominant effect of PSA on L1 was also observed in short-term, cell-cell adhesion assays, suggesting that PSA promotes optimal outgrowth on neuronal substrates by limiting the consequences of L1-mediated adhesion.
Flat-panel detector, CCD cameras, and electron-beam-tube-based video for use in portal imaging (1998)

This paper provides a comparison of some imaging parameters of four portal imaging systems at 6 MV: a flat panel detector, two CCD cameras and an electron beam tube based video camera. Measurements were made of signal and noise and consequently of signal-to-noise per pixel as a function of the exposure. All systems have a linear response with respect to exposure, and with the exception of the electron beam tube based video camera, the noise is proportional to the square-root of the exposure, indicating photon-noise limitation. The flat-panel detector has a signal-to-noise ratio, which is higher than that observed with both CCD-Cameras or with the electron beam tube based video camera. This is expected because most portal imaging systems using optical coupling with a lens exhibit severe quantum-sinks. The measurements of signal-and noise were complemented by images of a Las Vegas-type aluminum contrast detail phantom, located at the ISO-Center. These images were generated at an exposure of 1 MU. The flat-panel detector permits detection of Aluminum holes of 1.2 mm diameter and 1.6 mm depth, indicating the best signal-to-noise ratio. The CCD-cameras rank second and third in signal-to- noise ratio, permitting detection of Aluminum-holes of 1.2 mm diameter and 2.2 mm depth (CCD_1) and of 1.2 mm diameter and 3.2 mm depth (CCD_2) respectively, while the electron beam tube based video camera permits detection of only a hole of 1.2 mm diameter and 4.6 mm depth. Rank Order Filtering was applied to the raw images from the CCD-based systems in order to remove the direct hits. These are camera responses to scattered x-ray photons which interact directly with the CCD of the CCD-Camera and generate 'Salt and Pepper type noise,' which interferes severely with attempts to determine accurate estimates of the image noise. The paper also presents data on the metal-phosphor's photon gain (the number of light-photons per interacting x-ray photon).
A two-dimensional transducer array for real-time 3D medical ultrasound imaging (2002)

A high density 2D transducer array designed for 3 MHz echocardiography imaging has been developed in the frame of a real-time 3D ultrasound system project. This 2D array is using advanced interconnect and microstructuring technologies. The interconnect structure is fabricated through the backing material by placing microflex circuits perpendicular to the array plane. The structuring of small transducer elements with 308 micrometer pitch is done by a combination of controlled saw dicing of the piezoelectric material and laser ablation of the matching layers. Design, fabrication and characterization of the first prototypes are presented.
Using defined finger–finger interfaces as units of assembly for constructing zinc-finger nucleases (2013)

Zinc-finger nucleases (ZFNs) have been used for genome engineering in a wide variety of organisms; however, it remains challenging to design effective ZFNs for many genomic sequences using publicly available zinc-finger modules. This limitation is in part because of potential finger–finger incompatibility generated on assembly of modules into zinc-finger arrays (ZFAs). Herein, we describe the validation of a new set of two-finger modules that can be used for building ZFAs via conventional assembly methods or a new strategy—finger stitching—that increases the diversity of genomic sequences targetable by ZFNs. Instead of assembling ZFAs based on units of the zinc-finger structural domain, our finger stitching method uses units that span the finger–finger interface to ensure compatibility of neighbouring recognition helices. We tested this approach by generating and characterizing eight ZFAs, and we found their DNA-binding specificities reflected the specificities of the component modules used in their construction. Four pairs of ZFNs incorporating these ZFAs generated targeted lesions in vivo, demonstrating that stitching yields ZFAs with robust recognition properties.
Photolysis of regioisomeric diazides of 1,2-diphenylacetylenes studied by matrix-isolation spectroscopy and DFT calculations (2003)

A series of diazides of 1,2-diphenylacetylenes was photolyzed in matrices at low temperature and transient photoproducts were characterized by using IR, UV/vis methods combined with ESR studies. Theoretical calculations were also used to understand the experimental findings. The introduction of phenylethynyl groups on phenyl azides has little effect on the photochemical pathway. Thus, upon photoexcitation, (phenylethynyl)phenyl azides afforded the corresponding triplet nitrene, which is in photoequilibrium with the corresponding azacycloheptatetraene. In marked contrast, azidophenylethynyl groups exhibited a dramatic effect not only on the photochemical pathway of phenyl azides but also on the electronic and molecular structure of the photoproducts. The patterns of the effect depended upon the relative position of azide groups in the diphenylacetylene unit. Whenever two azide groups were situated in a conjugating position with respect to each other, as in p,p'-, o,o'-, and p,o'-bis(azides), the azides always resulted in the formation of a quinoidal diimine diradical in which unpaired electrons were extensively delocalizedin the pi-conjugation. The situation changed rather dramatically when azide groups were introduced in the meta position. Thus, the formation of azacycloheptatetraene was noted in the photolysis of the m.m'-isomer. ESR studies indicated the generation of a quintet state that was shown to be a thermally populated state with a very small energy gap of ca. 100 cal mol(-1). The m,p'-isomer was shown to be an excellent precursor for the high-spin quintet dinitrene. The IR spectra of the photoproduct showed no bands ascribable to azacycloheptatetraene. The observed spectra were in good agreement with that calculated for the quintet state. Strong EPR signals assignable to the quintet state were observed, along with rather weak signals due to mononitrenes. Moreover, the quintet bis(nitrene) was rather photostable under these conditions.
Genetic Polymorphism of Paraoxonase and the Risk of Coronary Heart Disease (1997)

Recent studies have implicated paraoxonase, an HDL-associated enzyme, in providing protection against LDL oxidation, thus affecting the risk of coronary heart disease (CHD) in the general population. In this study, we evaluated the distribution of a biallelic PON polymorphism at codon 192 (A and B alleles) and its relationship with plasma lipids and CHD in two racial groups comprising Asian Indians and Chinese from Singapore. The frequency of the B allele was significantly higher in Chinese control subjects than in Indian control subjects (0.58 versus 0.33; P < .0001). With the exception of a marginal effect on apolipoprotein A-I levels in Indians, no other significant association was observed between the PON polymorphism and quantitative lipid traits in either racial group. However, there was a race-specific association of the B allele with CHD in Indians but not in Chinese. The Indian CHD patients had a significantly higher frequency of the B allele than control subjects (.43 versus .33; P = .014). The age- and sex-adjusted odds ratio for developing CHD with the B allele (BB+AB genotypes) was 2.01 (95% CI, 1.17 to 3.45; P = .011) compared with the A allele (AA genotype). When the Indian patients were stratified into subgroups, the association remained significant in nondiabetic patients (odds ratio, 2.29; P = .008), and it became stronger in patients with myocardial infarction (odds ratio, 2.94; P = .004) than in patients without myocardial infarction (odds ratio, 1.11; P = .76). These data indicate that a common polymorphism in the PON gene is an independent risk factor for CHD in populations with white ancestry.
Widespread Distribution of a Group I Intron and Its Three Deletion Derivatives in the Lysin Gene of <i>Streptococcus thermophilus</i> Bacteriophages (2000)

Of 62 Streptococcus thermophilus bacteriophages isolated from various ecological settings, half contain a lysin gene interrupted by a group IA2 intron. Phage mRNA splicing was demonstrated. Five phages possess a variant form of the intron resulting from three distinct deletion events located in the intron-harbored open reading frame (orf 253). The predicted orf 253 gene sequence showed a significantly lower GC content than the surrounding intron and lysin gene sequences, and the predicted protein shared a motif with endonucleases found in phages from both gram-positive and gram-negative bacteria. A comparison of the phage lysin genes revealed a clear division between intron-containing and intron-free alleles, leading to the establishment of a 14-bp consensus sequence associated with intron possession. The conserved intron was not found elsewhere in the phage or S. thermophilus bacterial genomes. Folding of the intron RNA revealed secondary structure elements shared with other phage introns: first, a 38-bp insertion between regions P3 and P4 that can be folded into two stem-loop structures (shared with introns from Bacillus phage SPO1 and relatives); second, a conserved P7.2 region (shared with all phage introns); third, the location of the stop codon from orf 253 in the P8 stem (shared with coliphage T4 and Bacillus phage SPO1 introns); fourth, orf 253, which has sequence similarity with the H-N-H motif of putative endonuclease genes found in introns from Lactococcus, Lactobacillus, and Bacillus phages.