gebhart/patrepeval huggingface dataset:
Biosynthetic thiolase from Zoogloea ramigera. III. Isolation and characterization of the structural gene. (1987)

The gene coding for the biosynthetic thiolase from Zoogloea ramigera has been isolated by using antibody screening methods to detect its expression in Escherichia coli under the transcriptional control of the lac promoter. We have located and determined the nucleotide sequence of the gene. The structural gene is 1173 nucleotides long and codes for a polypeptide of 391 amino acids; 282 nucleotides 5' and 58 nucleotides 3' to the coding sequence are also reported. By comparing the amino acid sequence data predicted from the gene with data determined experimentally, we have derived the complete primary structure of thiolase. A catalytically essential cysteine is located at residue 89. The DNA sequence presented has a very high G/C content, 66.2%, typical of the Z. ramigera genome. In the coding region, this increases to 68.2% and is strongly reflected in the codon usage which demonstrates a strong preference for G or C in the third position. Examination of the 5'-flanking sequence establishes that the NH2-terminal methionine is specified by an ATG codon, 7 nucleotides downstream from a Shine-Dalgarno sequence.
Enzyme system of Clostridium stercorarium for hydrolysis of arabinoxylan: reconstitution of the in vivo system from recombinant enzymes (2004)

Four extracellular enzymes of the thermophilic bacterium Clostridium stercorarium are involved in the depolymerization of de-esterified arabinoxylan: Xyn11A, Xyn10C, Bxl3B, and Arf51B. They were identified in a collection of eight clones producing enzymes hydrolysing xylan (xynA, xynB, xynC), beta-xyloside (bxlA, bxlB, bglZ) and alpha-arabinofuranoside (arfA, arfB). The modular enzymes Xyn11A and Xyn10C represent the major xylanases in the culture supernatant of C. stercorarium. Both hydrolyse arabinoxylan in an endo-type mode, but differ in the pattern of the oligosaccharides produced. Of the glycosidases, Bxl3B degrades xylobiose and xylooligosaccharides to xylose, and Arf51B is able to release arabinose residues from de-esterified arabinoxylan and from the oligosaccharides generated. The other glycosidases either did not attack or only marginally attacked these oligosaccharides. Significantly more xylanase and xylosidase activity was produced during growth on xylose and xylan. This is believed to be the first time that, in a single thermophilic micro-organism, the complete set of enzymes (as well as the respective genes) to completely hydrolyse de-esterified arabinoxylan to its monomeric sugar constituents, xylose and arabinose, has been identified and the enzymes produced in vivo. The active enzyme system was reconstituted in vitro from recombinant enzymes.
IGF-IR Signaling in Breast Cancer (2000)

Abstract : The insulin-like growth factor I receptor (IGF-IR) is a multifunctional tyrosine kinase that has been implicated in breast cancer. The IGF-IR is often overexpressed in ER-positive breast tumors and this feature predicts tumor drug and radioresistance and cancer recurrence at the primary site. Over the period 1996-2000, we studied IGF-IR signaling pathways that may contribute to breast cancer development and progression. We developed different cell lines with either overexpression or downregulation of the IGF-IR or its major signaling substrates. Using these model systems, we characterized cross-talk between estrogen receptor and IGF-IR signaling, and we provided the first evidence that the IGF-IR, especially the IGF-IR/IRS- l/PI-3K pathway, plays a major role in 2 processes involved in cancer progression: antiestrogen-resistance and estrogen%independence. We also described, for the first time, interactions between the IGF-IR and cell-cell (cadherins and catenins) and cell-substrate (integrins) systems. Our data indicated that the IGF-I signal can increase cell adhesion and motility, the functions that are critical for metastatic cell spread. Recently, we demonstrated that in ER-negative metastatic cells, IGF-1-induced motility is mediated through PI-3 and p38 kinases, and is inhibited by the activation of ERKl/ERK2 kinases.
Optimization techniques for queries with expensive methods (1998)

Object-relational database management systems allow knowledgeable users to define new data types as well as new methods (operators) for the types. This flexibility produces an attendant complexity, which must be handled in new ways for an object-relational database management system to be efficient. In this article we study techniques for optimizing queries that contain time-consuming methods. The focus of traditional query optimizers has been on the choice of join methods and orders; selections have been handled by “pushdown” rules. These rules apply selections in an arbitrary order before as many joins as possible, using th e assumption that selection takes no time. However, users of object-relational systems can embed complex methods in selections. Thus selections may take significant amounts of time, and the query optimization model must be enhanced. In this article we carefully define a query cost framework that incorporates both selectivity and cost estimates for selections. We develop an algorithm called Predicate Migration, and prove that it produces optimal plans for queries with expensive methods. We then describe our implementation of Predicate Migration in the commercial object-relational database management system Illustra, and discuss practical issues that affect our earlier assumptions. We compare Predicate Migration to a variety of simplier optimization techniques, and demonstrate that Predicate Migration is the best general solution to date. The alternative techniques we present may be useful for constrained workloads.
Nucleotide sequence of human adenovirus type 12 DNA: comparative functional analysis (1994)

A fresh inoculum of human adenovirus type 12 (Ad12) was obtained from the American Type Culture Collection and passaged once on human embryonic kidney cells, and Ad12 DNA was prepared from the first-passage yield to avoid higher passages which might have generated host-virus DNA recombinants. The 18 PstI fragments of Ad12 DNA were cloned into the pBluescript KS vector, and the entire nucleotide sequence of both strands from all 18 fragments was determined by using successive oligodeoxyribonucleotide primers. Ad12 DNA extends over 34,125 nucleotide pairs, and its molecular weight is calculated to be about 22 x 10(6). The nucleotide sequence of Ad12 DNA was subjected to computer analyses that determined possible open reading of frames on the two strands, the leader sequences, the position of the virus-associated RNA coding region, possible TATA, and polyadenylation signals. The distribution of the Ad12 open reading frames was similar to that in the previously sequenced Ad2 DNA, but there were also distinct differences. Ad12 DNA has an inverted terminal redundancy of 161 nucleotides, compared with 102 nucleotides in Ad2 DNA. There were stretches of sequence identity between Ad2 and Ad12 DNAs at both termini; the overall sequence similarity between the two viral genomes ranged between 59% (polypeptide IX) and 77% (in the E2 region), with high homology also in the sequences for the adenovirus DNA polymerase.
Conditional Models on the Ranking Poset (2002)

A distance-based conditional model on the ranking poset is presented for use in classification and ranking. The model is an extension of the Mallows model, and generalizes the classifier combination methods used by several ensemble learning algorithms, including error correcting output codes, discrete AdaBoost, logistic regression and cranking. The algebraic structure of the ranking poset leads to a simple Bayesian interpretation of the conditional model and its special cases. In addition to a unifying view, the framework suggests a probabilistic interpretation for error correcting output codes and an extension beyond the binary coding scheme.
Retracted:Advanced glycation endproduct (AGE) accumulation and AGE receptor (RAGE) up‐regulation contribute to the onset of diabetic cardiomyopathy (2008)

Diabetic cardiomyopathy is manifested by compromised systolic and diastolic function. This study was designed to examine the role of advanced glycation endproduct (AGE) and AGE receptor (RAGE) in diabetic cardiomyopathy. Heart function was assessed in isolated control and streptozotocin-induced diabetic hearts following in vivo RAGE gene knockdown using RNA interference. Cardiomyocyte mechanical properties were evaluated including peak shortening (PS), time-to-PS (TPS) and time-to-90% relengthening (TR(90)). RAGE was assayed by RT-PCR and immunoblot. Diabetes significantly enhanced cardiac MG, AGE and RAGE levels accompanied with colocalization of AGE and RAGE in cardiomyocytes. Diabetes-elicited increase in RAGE was inhibited by in vivo siRNA interference. The AGE formation inhibitor benfotiamine significantly attenuated diabetes-induced elevation in MG, AGE, RAGE and collagen cross-linking without affecting hypertriglyceridaemia and hypercholesterolaemia in diabetes. Diabetes markedly decreased LV contractility, as evidenced by reduced +/-dP/dt and LV developed pressure (LVDP), which were protected by RAGE gene knockdown. In addition, MG-derived AGE (MG-AGE) up-regulated cardiac RAGE mRNA and triggered cardiomyocyte contractile dysfunction reminiscent of diabetic cardiomyopathy. The MG-AGE-elicited prolongation of TPS and TR(90) was ablated by an anti-RAGE antibody in cardiomyocytes. Interestingly, MG-AGE-induced cardiomyocyte dysfunction was associated with mitochondrial membrane potential (MMP) depolarization and reduced GSK-3beta inactivation in control cardiomyocytes, similar to those from in vivo diabetes. Treatment with siRNA-RAGE ablated diabetes-induced MMP depolarization and GSK-3beta inactivation. Collectively, our result implicated a role of AGE-RAGE in the pathogenesis of diabetic cardiomyopathy.
Scientists Mobilize To Increase Supply of Anticancer Drug Taxol (1991)

RETURN TO ISSUEPREVNewsNEXTScientists Mobilize To Increase Supply of Anticancer Drug TaxolTotal and partial synthesis, leaf extraction, tissue culture, and cultivation eyed as potential sources of natural product now obtained only from baric of Pacific yew treeSTU BORMANView Author Information C&EN WashingtonCite this: Chem. Eng. News 1991, 69, 35, 11–18Publication Date (Print):September 2, 1991Publication History Published online10 November 2010Published inissue 2 September 1991https://pubs.acs.org/doi/10.1021/cen-v069n035.p011https://doi.org/10.1021/cen-v069n035.p011newsACS PublicationsCopyright © 1991 American Chemical SocietyArticle Views48Altmetric-Citations35LEARN 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 SUBJECTS:Cancer Get e-Alerts
Reactive Oxygen Species and Age‐Related Genes p66Shc, Sirtuin, FoxO3 and Klotho in Senescence (2009)

Reactive oxygen species (ROS) superoxide and hydrogen peroxide perform important signaling functions in many physiological and pathophysiological processes. Cell senescence and organismal age are not exemptions.Aging-regulating genes p66shc, Sirtuin, FOXO3a and Klotho are new important factors which are stimulated by ROS signaling. It has been shown that ROS participate in initiation and prolongation of gene-dependent aging development.ROS also participate in the activation of protein kinases Akt/PKB and extracellular signal-regulated kinase ERK, which by themselves or through gene activation stimulates or retards cell senescence.Different retarding/stimulating effects of ROS might depend on the nature of signaling species-superoxide or hydrogen peroxide. Importance of radical anion superoxide as a signaling molecule with"super-nucleophilic" properties points to the possibility of the use of superoxide scavengers (SOD mimetics, ubiquinones and flavonoids) for retarding the development of aging.
Studies relating to the synthesis of the immunosuppressive agent FK-506: coupling of fragments via a stereoselective trisubstituted olefin forming reaction sequence (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStudies relating to the synthesis of the immunosuppressive agent FK-506: coupling of fragments via a stereoselective trisubstituted olefin forming reaction sequenceA. Brian Jones, Masahiko Yamaguchi, Arthur Patten, Samuel J. Danishefsky, John A. Ragan, David B. Smith, and Stuart L. SchreiberCite this: J. Org. Chem. 1989, 54, 1, 17–19Publication Date (Print):January 1, 1989Publication History Published online1 May 2002Published inissue 1 January 1989https://pubs.acs.org/doi/10.1021/jo00262a008https://doi.org/10.1021/jo00262a008research-articleACS PublicationsRequest reuse permissionsArticle Views544Altmetric-Citations52LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Mechanisms of lymphocyte killing by HIV (1997)

One of the remaining mysteries of HIV infection is what causes the destruction of the CD4+ T cells. Several reports in the past year have linked viral load to disease progression, strengthening the conclusion that the virus is responsible for CD4+ T-cell depletion. We discuss several possible mechanisms of T-cell death, including the killing of uninfected CD4+ T cells. We also discuss the possibility that the virus protects the cell it infects at least until viral replication can be completed.
Distinct effects of <i>Lactobacillus plantarum</i> KL30B and <i>Escherichia coli</i> 3A1 on the induction and development of acute and chronic inflammation (2016)

Our results show that distinct effects of bacterial administration on the development of ongoing inflammation is strain specific and depends on the final effect of cross-talk between bacteria and cells of the innate immune system.
Ultrasmall Rigid Particles as Multimodal Probes for Medical Applications (2011)

Ultraklein, aber multifunktionell: Starre Bildgebungspartikel mit Größen unter 5 nm wurden durch einen Top-down-Prozess ausgehend von einer Kern-Schale-Struktur erhalten (Kern: Gadoliniumoxid; Schale: Polysiloxan). Es sind die ersten multifunktionellen Siliciumdioxid-Partikel, die hinreichend klein sind, um sich der hepatischen Clearance zu entziehen, und die eine In-vivo-Bildgebung mit vier komplementären Techniken ermöglichen. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Detection of mRNA Transcripts and Active Transcription in Persistent Mycobacterium tuberculosis Induced by Exposure to Rifampin or Pyrazinamide (2000)

Mycobacterium tuberculosis can persist in an altered physiological state for many years after initial infection, and it may reactivate to cause active disease. An analogous persistent state, possibly consisting of several different subpopulations of bacteria, may arise during chemotherapy; this state is thought to be responsible for the prolonged period required for effective chemotherapy. Using two models of drug-induced persistence, we show that both microaerophilic stationary-phase M. tuberculosis treated with a high dose of rifampin in vitro and pyrazinamide-induced persistent bacteria in mice are nonculturable yet still contain 16S rRNA and mRNA transcripts. Also, the in vitro persistent, plate culture-negative bacteria incorporate radioactive uridine into their RNA in the presence of rifampin and can rapidly up-regulate gene transcription after the replacement of the drug with fresh medium and in response to heat shock. Our results show that persistent M. tuberculosis has transcriptional activity. This finding provides a molecular basis for the rational design of drugs targeted at persistent bacteria.
Treatment of Orthostatic Hypotension with Octreotide* (1989)

The purpose of this study was to evaluate the therapeutic potential of the somatostatin analog octreotide in patients with orthostatic hypotension. Octreotide was administered sc, and its pressor effect was assessed while the patients were semirecumbent and on the tilt table. We also studied the effect of octreotide on blood pressure while patients walked. The efficacy of therapy was assessed by measuring the duration of walking (walking time) before the onset of hypotension. Low doses of octreotide (0.2-0.4 micrograms/kg) had a pressor effect in all patients with progressive autonomic failure (n = 7), multiple system atrophy (n = 7), and diabetic autonomic neuropathy (n = 8), but not in patients with sympathotonic orthostatic hypotension (n = 6). Larger doses (0.4-1.6 micrograms/kg) resulted in a sustained (greater than or equal to 50 min) increase in blood pressure during walking in four of six patients with progressive autonomic failure and in one of six patients with multiple system atrophy. Some patients in whom octreotide failed to stabilize upright blood pressure had a satisfactory response to the drug after pretreatment with dihydroergotamine (10 micrograms/kg, sc). Patients with diabetic autonomic neuropathy, although sensitive to the pressor effect of octreotide, often developed nausea or abdominal cramps after moderate doses (greater than 1.0 micrograms/kg). These results indicate that the pressor effect of octreotide is sufficiently potent to prevent orthostatic hypotension in some patients with autonomic neuropathy. Others require treatment with both dihydroergotamine and octreotide to achieve a stable upright blood pressure.
Design of an exact data deduplication cluster (2012)

Data deduplication is an important component of enterprise storage environments. The throughput and capacity limitations of single node solutions have led to the development of clustered deduplication systems. Most implemented clustered inline solutions are trading deduplication ratio versus performance and are willing to miss opportunities to detect redundant data, which a single node system would detect. We present an inline deduplication cluster with a joint distributed chunk index, which is able to detect as much redundancy as a single node solution. The use of locality and load balancing paradigms enables the nodes to minimize information exchange. Therefore, we are able to show that, despite different claims in previous papers, it is possible to combine exact deduplication, small chunk sizes, and scalability within one environment using only a commodity GBit Ethernet interconnect. Additionally, we investigate the throughput and scalability limitations with a special focus on the intra-node communication.
A Model-Based Detection of Vulnerable and Malicious Browser Extensions (2013)

Attacks such as XSS and SQL injections are still common in browser extensions due to the presence of potential vulnerabilities in extensions and some extensions are also malicious by design. As a consequence, much effort in the past has been spent on detecting vulnerable and malicious browser extensions. These techniques are limited to only detect either new forms of vulnerable or malicious extensions but not both. In this paper, we present a model-based approach to detect vulnerable and malicious browser extensions by widening and complementing existing techniques. We observe and utilize various common and distinguishing characteristics of benign, vulnerable, and malicious extensions to build our detection models. The models are well trained using a set of features extracted from a number of widely used browser extensions together with user supplied specifications. We implemented the approach for Mozilla Firefox extensions and evaluated it in a number of browser extensions. Our evaluation indicates that the approach not only detects known vulnerable and malicious extensions, but also identifies previously undetected extensions with a negligible performance overhead.
Identification ofa myeloperoxidase inhibitor fromnormalhumanserum (1991)

SUMMARY An inhibitor of myeloperoxidase (MPO) has been identified in normal human serum. Initialexperiments confirmed that high levels of MPOinhibitory activity are present in sera andthat the inhibitor did not act by interfering with the assay. Purification of the inhibitor activity by salt precipitation followed by ion exchange and affinity chromatography revealed the presence of a proteinof150kD.Thepurified inhibitoryactivity displayed doseandtime dependency and was not associatedwith IgG or IgA. It is consideredthathuman serum contains an inhibitorofextracellularMPOcapableofprotectingagainst hypohalous acidreleaseinhosttissuesandthatifinhibitorlevels are reduced such protection may fail.Keywords myeloperoxidase inhibitor human serum INTRODUCTIONNeutrophils play a key role in defence of the host againstmicrobialattack. They execute this functionthrough two majorpathways of killing: dependent and independent on oxygen.After phagocytosis of an invading microbe into an enclosedphagolysosome within the cell, activation of
The feasibility of inertial-confinement fusion (1982)

So concluded the chairman of a Department of Energy ad hoc committee of experts in 1979, after a comprehensive review of the US inertial-confinement fusion program. In spite of this positive evaluation, the role of inertial-confinement fusion in the total US energy program continues to be a subject of disagreement. Before I mention the issues of contention, let me describe inertial-confinement fusion briefly. In a typical scheme, a pea-sized target pellet containing hydrogen isotopes is projected into a reactor chamber, where it is suddenly irradiated with an intense beam of light or ions from a “driver” (see figure 1). As the surface of the target blasts away, the rocket-like reaction forces implode the target's interior to densities and temperatures sufficient to cause the hydrogen nuclei to fuse, releasing an amount of energy equivalent to that of a barrel of oil (see PHYSICS TODAY, August 1973, page 46).