gebhart/patrepeval huggingface dataset:
A statistical multiprocessor cache model (2006)

The introduction of general-purpose microprocessors running multiple threads will put a focus on methods and tools helping a programmer to write efficient parallel applications. Such a tool should be fast enough to meet a software developer's need for short turn-around time, but also be accurate and flexible enough to provide trend-correct and intuitive feedback. This paper presents a novel sample-based method for analyzing the data locality of a multithreaded application. Very sparse data is collected during a single execution of the studied application. The architectural-independent information collected during the execution is fed to a mathematical memory-system model for predicting the cache miss ratio. The sparse data can be used to characterize the application's data locality with respect to almost any possible memory system, such as complicated multiprocessor multilevel cache hierarchies. Any combination of cache size, cache-line size and degree of sharing can be modeled. Each modeled design point takes only a fraction of a second to evaluate, even though the application from which the sampled data was collected may have executed for hours. This makes the tool not just usable for software developers, but also for hardware developers who need to evaluate a huge memory-system design space. The accuracy of the method is evaluated using a large number of commercial and technical multi-threaded applications. The result produced by the algorithm is shown to be consistent with results from a traditional (and much slower) architecture simulation.
Inhibition of prolyl 4-hydroxylase in vitro and in vivo by members of a novel series of phenanthrolinones (2001)

Examples of a novel series of phenanthrolinones are shown to be potent competitive inhibitors of avian prolyl 4-hydroxylase, and of collagen hydroxylation, in embryonic chick tendon cells and human foreskin fibroblasts in vitro and in the oestradiol-stimulated rat uterus in vivo. Two compounds, Compound 1 (1,4-dihydrophenanthrolin-4-one-3-carboxylic acid) and Compound 5 [8-(N-butyl-N-ethylcarbamoyl)-1,4-dihydrophenathrolin-4-one-3-carboxylic acid], with comparable potencies in vivo, were chosen to investigate the effect of the inhibition of the hydroxylation of newly synthesized uterine collagen on the turnover of this protein in vivo. Inhibition of hydroxylation by more than 50% for approx. 8h following single oral doses of the compounds was associated with significant losses of radiolabelled proline and 4-hydroxyproline from collagen during this period. Progressive hydroxylation of collagen over 48h, as the inhibitory action of the compounds declined, was accompanied by a decreased loss of radiolabel from the uterine collagen. Earlier reports indicated that underhydroxylated collagen, accumulating within the endoplasmic reticulum in cells where prolyl 4-hydroxylase is inactivated, is slowly degraded, but is then rapidly hydroxylated and secreted when the activity of prolyl 4-hydroxylase is restored. Taken with the present results, this suggests that the potential use of inhibitors of prolyl 4-hydroxylase to control excessive collagen deposition in pathological fibrosis may be limited by the need to maintain continuous inhibition of collagen hydroxylation so as to facilitate intracellular degradation of the accumulated protein.
Liver Receptor Homologue-1 Mediates Species- and Cell Line-specific Bile Acid-dependent Negative Feedback Regulation of the Apical Sodium-dependent Bile Acid Transporter (2003)

Intestinal reclamation of bile salts is mediated in large part by the apical sodium-dependent bile acid transporter (ASBT). The bile acid responsiveness of ASBT is controversial. Bile acid feeding in mice results in decreased expression of ASBT protein and mRNA. Mouse but not rat ASBT promoter activity was repressed in Caco-2, but not IEC-6, cells by chenodeoxycholic acid. A potential liver receptor homologue-1 (LRH-1) cis-acting element was identified in the bile acid-responsive region of the mouse but not rat promoter. The mouse, but not rat, promoter was activated by LRH-1, and this correlated with nuclear protein binding to the mouse but not rat LRH-1 element. The short heterodimer partner diminished the activity of the mouse promoter and could partially offset its activation by LRH-1. Interconversion of the potential LRH-1 cis-elements between the mouse and rat ASBT promoters was associated with an interconversion of LRH-1 and bile acid responsiveness. LRH-1 protein was found in Caco-2 cells and mouse ileum, but not IEC-6 cells or rat ileum. Bile acid response was mediated by the farnesoid X receptor, as shown by the fact that overexpression of a dominant-negative farnesoid X-receptor eliminated the bile acid mediated down-regulation of ASBT. In addition, ASBT expression in farnesoid X receptor null mice was unresponsive to bile acid feeding. In summary cell line- and species-specific negative feedback regulation of ASBT by bile acids is mediated by farnesoid X receptor via small heterodimer partner-dependent repression of LRH-1 activation of the ASBT promoter.
Ligation-mediated PCR of restriction fragments from large DNA molecules. (1992)

A general method is described for PCR amplification of single restriction fragments from large DNA molecules. The method involves sequence-specific ligation of synthetic oligonucleotides to ambiguous 4-base 5' overhangs produced by type IIS restriction endonucleases. Such "adapter-tags" provide one target for primer annealing in subsequent PCR reactions. The second target for primer annealing is provided by a universal "bubble-tag" ligated to blunt ends produced with another endonuclease. The key advantage of this approach is that specific fragments can be isolated without any prior knowledge of the nucleotide sequence of the target. Using bacteriophage lambda DNA as a test system, unique PCR products could be generated consistently. Conditions of temperature, ionic strength, and substrate concentration in the adapter-tag ligations--which affect sequence specificity--were found to have a major influence on the purity of PCR-generated fragments. In principle, the method permits the amplification of virtually any sequence from purified cosmid or YAC DNA using a library of only 240 adapter-tags.
In vitro assay for drug‐induced hepatosteatosis using rat primary hepatocytes, a fluorescent lipid analog and gene expression analysis (2009)

To evaluate new drugs' potential for hepatosteatosis, we developed a cell-based assay using a fluorescent fatty acid analog: BODIPY558/568 C12. Rat primary hepatocytes were exposed to positive reference compounds [cyclosporine A (CsA), clofibrate (CFR), tetracycline (TC), valproic acid (VPA), carbon tetrachloride (CCl4), tamoxifen (TMX)] in the presence of BODIPY558/568 C12. The formation of fluorscecent particles or lipid droplets in the cytoplasm was confirmed by confocal laser scanning microscopy and electron microscopy respectively. The accumulation of BODIPY558/568 C12 was measured by fluorometry and high content imaging method. All positive reference compounds increased fluorescent particles in number and fluorescence intensity. High content imaging was more sensitive and selective method than fluorometry to detect fluorescent particles. Gene expression analysis of the hepatocytes showed two patterns: genes related to lipid metabolism/synthesis were down-regulated by oxidative stress inducing compounds: CsA, TC and TMX, and up-regulated by peroxisome proliferator-activated receptor-alpha agonists: CFR and VPA. From these findings, we concluded that the cell-based assay developed in this study is an appropriate method to predict drugs' potential for hepatosteatosis, and gene expression analysis is useful to profile the mechanism of the hepatosteatosis.
Expression of Granulosa Cell-Specific Genes and Induction of Apoptosis in Conditionally Immortalized Granulosa Cell Lines Established from H-2Kb-tsA58 Transgenic Mice (1999)

Granulosa cell lines have been established from H-2Kb-tsA58 transgenic mice. Using immunocytochemistry, significant amounts of insulin-like growth factor-I (IGF-I) were found in all cell lines investigated, whereas estrogen and progesterone receptor expression could be detected in only some of the lines. All cell lines showed low basal production of the gonadal steroids estradiol and progesterone. The genes for the ovarian paracrine regulators IGF-I and basic fibroblast growth factor were expressed, as well as the genes for anti-Müllerian hormone and for the P450 side-chain cleavage enzyme (P450scc). Expression of P450scc could be shown to be up-regulated in the cell lines under conditions mimicking the hormonal environment of the luteinizing granulosa cells in vivo. Inactivation of the temperature-sensitive SV40 T antigen by a shift of the cell lines to the nonpermissive temperature of 39.5 degrees C led to massive induction of apoptosis in several cell lines. These cell lines will allow a detailed study of the mechanisms regulating the expression of granulosa cell-specific functions, as well as the induction of granulosa cell apoptosis.
Substrate Specificity of Protein Tyrosine Phosphatases 1B, RPTPα, SHP-1, and SHP-2 (2011)

We determined the substrate specificities of the protein tyrosine phosphatases (PTPs) PTP1B, RPTPα, SHP-1, and SHP-2 by on-bead screening of combinatorial peptide libraries and solution-phase kinetic analysis of individually synthesized phosphotyrosyl (pY) peptides. These PTPs exhibit different levels of sequence specificity and catalytic efficiency. The catalytic domain of RPTPα has very weak sequence specificity and is approximately 2 orders of magnitude less active than the other three PTPs. The PTP1B catalytic domain has modest preference for acidic residues on both sides of pY, is highly active toward multiply phosphorylated peptides, but disfavors basic residues at any position, a Gly at the pY-1 position, or a Pro at the pY+1 position. By contrast, SHP-1 and SHP-2 share similar but much narrower substrate specificities, with a strong preference for acidic and aromatic hydrophobic amino acids on both sides of the pY residue. An efficient SHP-1/2 substrate generally contains two or more acidic residues on the N-terminal side and one or more acidic residues on the C-terminal side of pY but no basic residues. Subtle differences exist between SHP-1 and SHP-2 in that SHP-1 has a stronger preference for acidic residues at the pY-1 and pY+1 positions and the two SHPs prefer acidic residues at different positions N-terminal to pY. A survey of the known protein substrates of PTP1B, SHP-1, and SHP-2 shows an excellent agreement between the in vivo dephosphorylation pattern and the in vitro specificity profiles derived from library screening. These results suggest that different PTPs have distinct sequence specificity profiles and the intrinsic activity/specificity of the PTP domain is an important determinant of the enzyme's in vivo substrate specificity.
Personalising docetaxel and G-CSF schedules in cancer patients by a clinically validated computational model (2012)

The new computational method can serve for tailoring efficacious cytotoxic and supportive treatments, minimising side effects to individual patients. Prospective clinical validation is warranted.
Noncanonical agonist PPARγ ligands modulate the response to DNA damage and sensitize cancer cells to cytotoxic chemotherapy (2018)

The peroxisome-proliferator receptor-γ (PPARγ) is expressed in multiple cancer types. Recently, our group has shown that PPARγ is phosphorylated on serine 273 (S273), which selectively modulates the transcriptional program controlled by this protein. PPARγ ligands, including thiazolidinediones (TZDs), block S273 phosphorylation. This activity is chemically separable from the canonical activation of the receptor by agonist ligands and, importantly, these noncanonical agonist ligands do not cause some of the known side effects of TZDs. Here, we show that phosphorylation of S273 of PPARγ occurs in cancer cells on exposure to DNA damaging agents. Blocking this phosphorylation genetically or pharmacologically increases accumulation of DNA damage, resulting in apoptotic cell death. A genetic signature of PPARγ phosphorylation is associated with worse outcomes in response to chemotherapy in human patients. Noncanonical agonist ligands sensitize lung cancer xenografts and genetically induced lung tumors to carboplatin therapy. Moreover, inhibition of this phosphorylation results in deregulation of p53 signaling, and biochemical studies show that PPARγ physically interacts with p53 in a manner dependent on S273 phosphorylation. These data implicate a role for PPARγ in modifying the p53 response to cytotoxic therapy, which can be modulated for therapeutic gain using these compounds.
A planning approach for message-oriented semantic web service composition (2007)

In this paper, we consider the problem of composing a set of web services, where the requirements are spec-ified in terms of the input and output messages of the composite workflow. We propose a semantic model of messages using RDF graphs that encode OWL ABox assertions. We also propose a model of web service operations where the input message requirements and output message characteristics are modeled using RDF graph patterns. We formulate the message-oriented se-mantic web service composition problem and show how it can be translated into a planning problem. There are, however, significant challenges in scalably doing plan-ning in this domain, especially since DL reasoning may be performed to check if an operation can be given a cer-
Decongestive lymphatic therapy for patients with breast carcinoma‐associated lymphedema (2002)

When IPC is used adjunctively with other, established elements of DLT, it provides an enhancement of the therapeutic response. IPC is well tolerated and remarkably free of complications.
THE EFFECT OF ANTITHYROID DRUGS ON B AND T CELL ACTIVITY IN VITRO (1988)

This study examined the abilities of methimazole, propylthiouracil (PTU) and propranolol to exert an immunosuppressive effect in vitro. Incubation of peripheral blood lymphocytes (PBL) with propranolol showed the drug to have no effect on either B- or T-cell activity. Methimazole or PTU at concentrations of greater than or equal to 10(-5)M resulted in significantly lower amounts of IgG and IgM being released into the culture medium. Both drugs were also found to have a direct effect on T-cell function as they caused the percentage of total and suppressor cells to increase towards normal levels. The three drugs were all found to have some free radical scavenging ability. These ranked PTU greater than methimazole greater than propranolol. These in-vitro findings would suggest that both methimazole and PTU have some direct effect on the immune system. It would seem more likely however that these effects are mediated via interleukin 2 rather than by their ability to act as free radical scavengers.
Magnetoresistive Effect in Ferromagnetic Thin Films( II) (1994)

In order to fabricate magnetoresistive sensor, Fe-Ni and Co-Ni alleys were evaporated on the slide glass and the silicon wafers. Saturation magnetic induction(), coercive field strength() and magnetoresistance were measured for fabricated samples. The evaporated Fe-Ni thin films show that the saturation magnetic induction was 0.65 T, and coercive field strength was 0.379 A/cm, and this value was changed to 0.370 A/cm(//), 0.390 A/cm(), respectively after magnetic annealing. For the measurement of coercive field strength, magnetizing frequency of 1 kHz was used. For the fabricated sensor element, the change of magnetoresistance () was excessively unstable due to oxidation in the process of fabrication. The evaporated Co-Ni alloy thin films show that saturation magnetic induction was 0.66 T, and coercive field strengthes were 5.895 A/cm(//), 5.898 A/cm(), respectively, after magnetic annelaing. The change of magnetoresistance() was of which value was excessively stable to room temperature. Fe-Ni thin film could have many problems due to large affinity in the process of fabrication of magnetoresistance sensor, but Co-Ni thin film could be a suitable material for fabrication of magnetoresistance sensor, because of its small affinity and definite magnetoresistance effects.
Steroidal Sapogenins1a (1947)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSteroidal Sapogenins1aRussell E. Marker, R. B. Wagner, Paul R. Ulshafer, Emerson L. Wittbecker, Dale P. J. Goldsmith, and Clarence H. RuofCite this: J. Am. Chem. Soc. 1947, 69, 9, 2167–2230Publication Date (Print):September 1, 1947Publication History Published online1 May 2002Published inissue 1 September 1947https://pubs.acs.org/doi/10.1021/ja01201a032https://doi.org/10.1021/ja01201a032research-articleACS PublicationsRequest reuse permissionsArticle Views1002Altmetric-Citations145LEARN 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
31 P NMR Spectroscopy in Oligonucleotide Research and Development (1997)

31P NMR is an extremely valuable tool for oligonucleotide research and development. This brief commentary, which is directed to scientists who do not regularly use 31P NMR in their work, attempts to outline some of the principles, considerations, and representative applications of 31P NMR spectroscopy in oligonucleotide research and development.
Confidence-based data management for personal area sensor networks (2004)

The military is working on embedding sensors in a "smart uniform" that will monitor key biological parameters to determine the physiological status of a soldier. The soldier's status can only be determined accurately by combining the readings from several sensors using sophisticated physiological models. Unfortunately, the physical environment and the low-bandwidth, push-based personal-area network (PAN) introduce uncertainty in the inputs to the models. Thus the model must produce a confidence level as well as a physiological status value. This paper explores how confidence levels can be used to influence data management decisions. In particular, we look at power-efficient ways to keep the confidence above a given threshold. We also contrast push-based broadcast schedules with other schedules that are made possible by two-way communication.
Automotive diagnostics using trainable classifiers: statistical testing and paradigm selection (1990)

An analysis is presented of the requirements for developing a practical trainable classifier to detect and identify faults in vehicle powertrain systems. An examination is made of requirements on the data sets used for training and testing and the criteria needed to select the most appropriate classifier for a particular family of problems. Empirical results supporting the authors' hypothesis are presented based on an analysis of two data sets drawn under rather different circumstances from test vehicles with faults introduced. Several different classifier forms are applied to these data sets, and their performance is evaluated. Despite similar performance on simple statistical tests, the classifies exhibit significant performance variations on more rigorous tests, and therefore viable criteria for selecting the most appropriate classifiers can be established
The Essential Component in DNA-Based Information Storage System: Robust Error-Tolerating Module (2014)

The size of digital data is ever increasing and is expected to grow to 40,000 EB by 2020, yet the estimated global information storage capacity in 2011 is <300 EB, indicating that most of the data are transient. DNA, as a very stable nano-molecule, is an ideal massive storage device for long-term data archive. The two most notable illustrations are from Church et al. and Goldman et al., whose approaches are well-optimized for most sequencing platforms - short synthesized DNA fragments without homopolymer. Here, we suggested improvements on error handling methodology that could enable the integration of DNA-based computational process, e.g., algorithms based on self-assembly of DNA. As a proof of concept, a picture of size 438 bytes was encoded to DNA with low-density parity-check error-correction code. We salvaged a significant portion of sequencing reads with mutations generated during DNA synthesis and sequencing and successfully reconstructed the entire picture. A modular-based programing framework - DNAcodec with an eXtensible Markup Language-based data format was also introduced. Our experiments demonstrated the practicability of long DNA message recovery with high error tolerance, which opens the field to biocomputing and synthetic biology.
The Saccharomyces cerevisiae cyclin Clb2p is targeted to multiple subcellular locations by cis- and trans-acting determinants (2001)

The cyclin-dependent kinase Cdc28p associates with the cyclin Clb2p to induce mitosis in the yeast Saccharomyces cerevisiae. Several cell cycle regulatory proteins have been shown to require specific nuclear transport events to exert their regulatory functions. Therefore, we investigated the subcellular localization of wild-type Clb2p and several mutant versions of the protein using green fluorescent protein (GFP) fusion constructs. Wild-type Clb2p is primarily nuclear at all points of the cell. A point mutation in a potential leucine-rich nuclear export signal (NES) enhances the nuclear localization of the protein, and delta-yrb2 cells exhibit an apparent Clb2p nuclear export defect. Clb2p contains a bipartite nuclear localization signal (NLS), and its nuclear localization requires the alpha and beta importins (Srp1p and Kap95p), as well as the yeast Ran GTPase and its regulators. Deletion of the Clb2p NLS causes increased cytoplasmic localization of the protein, as well as accumulation at the bud neck. These data indicate that Clb2p exists in multiple places in the yeast cell, possibly allowing Cdc28p to locally phosphorylate substrates at distinct subcellular sites.
Two-Dimensional birefringence imaging in biological tissue using phase and polarization sensitive optical coherence tomography. (1998)

Polarization sensitive optical coherence tomography (PS-OCT) was used to obtain images of optical birefringence in biological tissues. Through simultaneous detection of two orthogonal polarization states of the signal formed by interference of light backscattered from the biological sample and a mirror in the reference arm of a Michelson interferometer, the optical phase delay between light propagating along the fast and slow axes of birefringence was measured. Simultaneous detection of both polarizations also permits reconstruction of the electro-magnetic wave backscattered from the sample. Inasmuch as any fibrous structure will influence the polarization of light, PS-OCT is a potentially powerful technique in the field of biomedical imaging. It allows rapid non-contact investigation of tissue structural properties through spatially resolved imaging of birefringence.