gebhart/patrepeval huggingface dataset:
Functional Interaction of STAT3 Transcription Factor with the Cell Cycle Inhibitor p21 (2000)

Signal transducers and activators of transcription (STAT) factors are cytoplasmic proteins that induce gene activation in response to cytokine receptor stimulation. Following tyrosine phosphorylation, STAT proteins dimerize, translocate into the nucleus, and activate specific target genes. Activation is transient, and down-regulation of STAT signaling occurs within a few hours. In the present study, we show that the cyclin-dependent kinase inhibitor p21(WAF1/CIP1/SDI1) inhibits STAT3 transcriptional activation. Following leukemia inhibitory factor stimulation, p21(WAF1/CIP1/SDI1) was found to associate with STAT3 proteins in coimmunoprecipitation and pull down assays. In vivo, overexpression of p21(WAF1/CIP1/SDI1) reduced transcriptional activation by STAT3 proteins but did not modify DNA binding activity. Interestingly, pull down experiments showed that p21(WAF1/CIP1/SDI1) could interact with the CREB-binding coactivator protein, and inhibition of STAT3 activity by p21(WAF1/CIP1/SDI1) did not occur when CREB-binding protein was overexpressed. These results suggest a model by which p21(WAF1/CIP1/SDI1) functions as an inhibitor of STAT3 signaling and highlight a new activity for this cyclin-dependent kinase inhibitor.
Enhancing speech corpus resources with multiple lexical tag layers (2000)

We describe a general two-stage procedure for re-using a custom corpus for spoken language system development involving a transformation from character-based markup to XML, and DSSSL stylesheet-driven XML markup enhancement with multiple lexical tag trees.The procedure was used to generate a fully tagged corpus; alternatively with greater economy of computing resources, it can be employed as a parametrised 'tagging on demand' filter.The implementation will shortly be released as a public resource together with the corpus (German spoken dialogue, about 500k word form tokens) and lexicon (about 75k word form types).
ChemInform Abstract: Reaction of Azoles with Ethyl Bromopyruvate Oxime: Alkylation by Substitution and by Elimination‐Addition. (1988)

Abstract Imidazole (I) reacts with the oxime (II) to give the monoalkylation product (III) and the zwitterion (IV).
Variation-Aware Application Scheduling and Power Management for Chip Multiprocessors (2008)

Within-die process variation causes individual cores in a ChipMultiprocessor (CMP) to differ substantially in both static powerconsumed and maximum frequency supported. In this environment,ignoring variation effects whenscheduling applications or when managing power withDynamic Voltage and Frequency Scaling (DVFS) is suboptimal. This paper proposes variation-aware algorithms for applicationscheduling and power management. One such power managementalgorithm, called {\em LinOpt}, uses linear programmingto find the best voltage and frequency levels for each of thecores in the CMP --- maximizing throughput at a given power budget.In a 20-core CMP, the combination of variation-awareapplication scheduling and {\em LinOpt} increases the averagethroughput by 12--17\% and reduces the average $ED^2$ by 30--38\%--- all relative to using variation-awarescheduling together with a simple extension to Intel's Foxtonpower management algorithm.
ChemBank: a small-molecule screening and cheminformatics resource database (2007)

ChemBank (http://chembank.broad.harvard.edu/) is a public, web-based informatics environment developed through a collaboration between the Chemical Biology Program and Platform at the Broad Institute of Harvard and MIT. This knowledge environment includes freely available data derived from small molecules and small-molecule screens and resources for studying these data. ChemBank is unique among small-molecule databases in its dedication to the storage of raw screening data, its rigorous definition of screening experiments in terms of statistical hypothesis testing, and its metadata-based organization of screening experiments into projects involving collections of related assays. ChemBank stores an increasingly varied set of measurements derived from cells and other biological assay systems treated with small molecules. Analysis tools are available and are continuously being developed that allow the relationships between small molecules, cell measurements, and cell states to be studied. Currently, ChemBank stores information on hundreds of thousands of small molecules and hundreds of biomedically relevant assays that have been performed at the Broad Institute by collaborators from the worldwide research community. The goal of ChemBank is to provide life scientists unfettered access to biomedically relevant data and tools heretofore available primarily in the private sector.
The influence of CYP2D6 genotype on trough plasma perhexiline and cis‐OH‐perhexiline concentrations following a standard loading regimen in patients with myocardial ischaemia (2005)

Patients with only one functional allele and not CYP2D6*2 have diminished CYP2D6 metabolic capacity for perhexiline.
Synthesis of pseudocofactor analogs as potential inhibitors of the folate enzymes (1982)

Reaction of 5,6,7,8-tetrahydrofolic acid (THF,7) with phosgene, thiophosgene, and cyanogen bromide gave the bridged derivatives, 5,10-(CO)-THF (8), 5,10-(CS)-THF (9), and 5,10-(C = NH)-THF (11), respectively. Catalytic hydrogenation of 10-(chloroacetyl)folic acid (2) gave 5,10-(CH2CO)-THF (12). A similar reaction with 10-(3-chloropropionyl)folic acid (3) gave 10-(ClCH2CH2CO)-THF (14) rather than 5,10-(CH2CH2CO)-THF (13). In the catalytic hydrogenation of 10-ethoxalylfolic acid (5), the initial product 10-(EtO2CCO)-THF (22) rearranged readily to give 5-(EtO2CCO)-THF (21). Acylation of THF with chloroacetyl chloride gave a N5,N10-diacylated product (18 or 19), which could not be converted to 5,10-COCH2)-THF (17). Reductive alkylation of THF with glyoxylic acid and 5-hydroxypentanal, respectively, gave 5-(HO2CCH2)-THF (24) and 5-[HO(CH2)5]-THF (25). Reductive dialkylation of THF with formaldehyde gave 5,10-(CH3)2-THF (27), whereas glyoxal gave 5,10-CH2CH2)-THF (10). Also, both folic acid and 5-(CHO)-THF were reductively alkylated with formaldehyde to give 10-methylfolic acid (6) and 5-(CHO)-10-(CH3)-THF (28), respectively. These compounds were tested as inhibitors of the enzymes involved in folate metabolism and for activity against lymphocytic leukemia P388 in mice.
MicroRNA-214 Antagonism Protects against Renal Fibrosis (2013)

Renal tubulointerstitial fibrosis is the common end point of progressive renal disease. MicroRNA (miR)-214 and miR-21 are upregulated in models of renal injury, but the function of miR-214 in this setting and the effect of its manipulation remain unknown. We assessed the effect of inhibiting miR-214 in an animal model of renal fibrosis. In mice, genetic deletion of miR-214 significantly attenuated interstitial fibrosis induced by unilateral ureteral obstruction (UUO). Treatment of wild-type mice with an anti-miR directed against miR-214 (anti-miR-214) before UUO resulted in similar antifibrotic effects, and in vivo biodistribution studies demonstrated that anti-miR-214 accumulated at the highest levels in the kidney. Notably, in vivo inhibition of canonical TGF-β signaling did not alter the regulation of endogenous miR-214 or miR-21. Whereas miR-21 antagonism blocked Smad 2/3 activation, miR-214 antagonism did not, suggesting that miR-214 induces antifibrotic effects independent of Smad 2/3. Furthermore, TGF-β blockade combined with miR-214 deletion afforded additional renal protection. These phenotypic effects of miR-214 depletion were mediated through broad regulation of the transcriptional response to injury, as evidenced by microarray analysis. In human kidney tissue, miR-214 was detected in cells of the glomerulus and tubules as well as in infiltrating immune cells in diseased tissue. These studies demonstrate that miR-214 functions to promote fibrosis in renal injury independent of TGF-β signaling in vivo and that antagonism of miR-214 may represent a novel antifibrotic treatment in the kidney.
Detachment of Actinobacillus actinomycetemcomitans Biofilm Cells by an Endogenous β-Hexosaminidase Activity (2003)

When cultured in broth, fresh clinical isolates of the gram-negative periodontal pathogen Actinobacillus actinomycetemcomitans form tenaciously adherent biofilm colonies on surfaces such as plastic and glass. These biofilm colonies release adherent cells into the medium, and the released cells can attach to the surface of the culture vessel and form new colonies, enabling the biofilm to spread. We mutagenized A. actinomycetemcomitans clinical strain CU1000 with transposon IS903phikan and isolated a transposon insertion mutant that formed biofilm colonies which were tightly adherent to surfaces but which lacked the ability to release cells into the medium and disperse. The transposon insertion in the mutant strain mapped to a gene, designated dspB, that was predicted to encode a secreted protein homologous to the catalytic domain of the family 20 glycosyl hydrolases. A plasmid carrying a wild-type dspB gene restored the ability of biofilm colonies of the mutant strain to disperse. We expressed A. actinomycetemcomitans DspB protein engineered to contain a hexahistidine metal-binding site at its C terminus in Escherichia coli and purified the protein by using Ni affinity chromatography. Substrate specificity studies performed with monosaccharides labeled with 4-nitrophenyl groups showed that DspB hydrolyzed the 1-->4 glycosidic bond of beta-substituted N-acetylglucosamine, which is consistent with the known functions of other family 20 glycosyl hydrolases. When added to culture medium, purified DspB protein, but not heat-inactivated DspB, restored the ability of the mutant strain to release cells and disperse. DspB protein also caused the detachment of cells from preformed biofilm colonies of strain CU1000 grown attached to plastic and the disaggregation of highly autoaggregated clumps of CU1000 cells in solution. We concluded that dspB encodes a soluble beta-N-acetylglucosaminidase that causes detachment and dispersion of A. actinomycetemcomitans biofilm cells.
Control of the surface expression of uvomorulin after activation of mouse oocytes (1995)

Uvomorulin (E-cadherin) is the major cell adhesion molecule responsible for intercellular adhesion in early mouse embryos. In contrast to other cell adhesion molecules, it is not detectable on the cell surface until around 6 h after fertilisation or parthenogenetic activation, at the time when pronuclear formation occurs (Clayton, L., Stinchcombe, S.V. and Johnson, M.H., Zygote 1, 333-44, 1993). In order to investigate this developmental control of surface expression of uvomorulin, we examined the effects of inhibitors of various cellular processes on the appearance of uvomorulin at the oocyte surface, as assessed immunocytochemically. Inhibitors of cytoskeletal assembly (cytochalasin D and nocodazole), protein synthesis (puromycin and anisomycin), and DNA synthesis (aphidicolin) had no effect on surface expression. Brefeldin A, which inhibits intracellular transport and secretion, did prevent surface expression, but monensin did not. The effects of brefeldin were reversible; following 8 h of treatment, recovery of surface expression after removal of brefeldin began within 2 h. The time-course of surface expression post-activation suggested a link with pronuclear formation. However, when pronuclear formation was advanced experimentally using 6-dimethylaminopurine (DMAP), concomitant advancement of surface uvomorulin was not observed. Similarly, surface expression of uvomorulin did not accompany puromycin-induced pronuclear formation in maturing meiotic metaphase 1 (MI) oocytes in vitro. Thus, surface uvomorulin expression does not appear to be linked simply to pronuclear formation. Proteolytic processing of both newly synthesised and total uvomorulin to generate mature molecule from precursor increased within 30 min to 1 h after activation, and also occurred in the continued presence of brefeldin, suggesting that uvomorulin processing appears to be controlled independently of its surface expression.
Applying features of IEEE 754 to sign/logarithm arithmetic (1992)

Various features found in standard floating point arithmetic (IEEE 754) are examined in light of their appropriateness for sign/logarithm arithmetic. The emphasis is on a 32-b word size comparable to IEEE 754 single precision, although other word sizes are possible. A multilayer sign/logarithm format is considered. The lowest layer, similar to previous implementations, would provide only normalized representations but would not provide representations for zero, denormalized values, infinities, and NaNs. The highest layer would provide most of the features found in IEEE 754, including zeros, denormalized values, infinities, and NaNs. Novel algorithms for implementing logarithmic denormalized arithmetic are presented. Simulation results show that the error characteristics of the proposed logarithmic denormalized arithmetic algorithms are similar to those of the denormalized floating point arithmetic in IEEE 754.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Subband transitions in dual-band n-B-n InAs/GaSb superlattice infrared photodetector identified by photoresponse spectra (2009)

The subband transitions in dual-band n-B-n InAs/GaSb type-II superlattice infrared photodetector are identified by the photoresponse (PR) spectra. In the mid- and long-wavelength PR spectra measured by changing bias polarity, each spectrum individually shows a series of distinctive peaks related to the transitions from the hole subbands to the conduction one. The PR mechanism at each polarity is discussed in terms of diffusion and tunneling currents.
Vapor sensing using the optical properties of porous silicon Bragg mirrors (1999)

Large wavelength shifts have been measured in the reflectivity spectra of Bragg mirrors etched in porous silicon after exposure of the mirrors to vapor from organic solvents. The shift in the Bragg wavelength of the mirror arises from refractive index changes, induced by capillary condensation of the vapor in the mesoporous silicon, in the layers of the mirrors. Modeling of the reflectivity changes shows that the layer liquid volume fraction occurring in the measurements was 0.29 for acetone and 0.33 for chlorobenzene. Time-resolved measurements show that condensation occurs on the time scale of tens of seconds.
Charge Dependence of Ligand Release and Monolayer Stability of Gold Nanoparticles by Biogenic Thiols (2008)

The effect of surface charge on the stability of gold nanoparticles (AuNPs) to the biogenic thiols glutathione (GSH), dihydrolipoic acid (DHLA), and cysteine was quantified. It was observed that the rate of release of fluorescein-tagged ligand was determined by the surface charge of the AuNPs, with cationic particles much more labile than anionic analogues. This ability to tune stability is significant for the design of both delivery vehicles and intracellular probes.
Control of the Lateral Organization in Langmuir Monolayers via Molecular Aggregation of Dyes (2010)

This paper shows that it is possible to construct well-defined 2D structures at the air−water interface in which the lateral organization is controlled by means of the preparation of mixed films, and selecting the components so that there are attractive interactions between them. The goal here is to establish the lateral connection between components through self-aggregation of the dye. This can be achieved by selecting a suitable balance between the sizes of the hydrophobic and polar groups. In such a way, the domain structure depends on the ability of the tilt dye to fill the available area. Thus, the molecular organization and the domain morphology of mixed films containing dimyristoyl-phosphatidic acid (DMPA) and the hemicyanine dye, 4-[4-(dimethylamino)styryl]-1-docosylpyridinium bromide (SP), have been studied by using Grazing Incidence X-ray Diffraction (GIXD), Brewster angle microscopy (BAM), and reflection spectroscopy at the air−water interface. For this mixed system, the formation of circular domains with bright horizontal regions and dark vertical regions was observed. Furthermore, depending on the temperature, it is observed as branches grow from circular domains, whose brightness depends on the growth direction. Thus, BAM images allow us to observe some branches that, as their growth direction changes, their brightness also changes simultaneously. The GIXD experiment permits us to relate the circular domains with an orthorhombic phase and the branches grown from the circles with an Overbeck phase. In both cases, the formed structures are induced by the hemicyanine aggregation. Circular BAM domain textures have been simulated by using the Fresnel equations for biaxial anisotropic materials.
Off-line skilled forgery detection using stroke and sub-stroke properties (2002)

Research has been active in the field of forgery detection, but relatively little work has been done on the detection of skilled forgeries. We present an algorithm for detecting skilled forgeries based on a local correspondence between a questioned signature and a model obtained a priori. Writer-dependent properties are measured at the substroke level and a cost function is trained for each writer. When a candidate signature is presented, the same features are extracted and matched against the model. We present a description of the features and experimental results.
[Comparative analysis of premature labor markers]. (2000)

We compared the diagnostic value of foetal fibronectin (fFN), phosphorilated insulin-like growth factor protein binding-1 (Birth test) and insulin-like growth factor protein binding-1 (PROM test) as markers of premature rupture of membrane (PROM) and in prediction of preterm labor with intact membranes. The study population included 120 asymptomatic women (group 1), with gestation of 24-34 weeks; we also considered 21 patients with clinically confirmed PROM (group 2) and 26 patients with suspected PROM with gestation between 15 and 24 weeks (group 3) (as measured by sonography data). From our data, it seems that only the predictive value of each test is related to the characteristics of the population considered. The fFN test and the Birth test prove to be highly predictive in pregnant women without PROM, on the contrary the use of the PROM test is optimal in pregnant women with suspected PROM or with PROM, regardless of risk factor or with contractile activity.
Purification and properties of bovine liver aldehyde oxidase (1987)

Conference Article| October 01 1987 Purification and properties of bovine liver aldehyde oxidase FRANCESC CABRÉ; FRANCESC CABRÉ 1Department of Biochemistry and Physiology, University of Barcelona, Marti i Franquès, 1, 08028 Barcelona, Catalunya, Spain Search for other works by this author on: This Site PubMed Google Scholar ENRIC I. CANELA ENRIC I. CANELA 1Department of Biochemistry and Physiology, University of Barcelona, Marti i Franquès, 1, 08028 Barcelona, Catalunya, Spain Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1987) 15 (5): 882–883. https://doi.org/10.1042/bst0150882 Article history Received: March 24 1987 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share MailTo Twitter LinkedIn Cite Icon Cite Get Permissions Citation FRANCESC CABRÉ, ENRIC I. CANELA; Purification and properties of bovine liver aldehyde oxidase. Biochem Soc Trans 1 October 1987; 15 (5): 882–883. doi: https://doi.org/10.1042/bst0150882 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search Keywords: comparison with xanthine oxidase, AO, aldehyde oxidase, XO, xanthine oxidase This content is only available as a PDF. © 1987 Biochemical Society1987 Article PDF first page preview Close Modal You do not currently have access to this content.
Unusual Regioselectivity of the Dipolar Cycloaddition Reactions of Nitrile Oxides and Tertiary Cinnamides and Crotonamides1 (1998)

Benzonitrile oxides undergo 1,3-dipolar cycloaddition reactions with methyl cinnamate to produce the 5-phenyl and 4-phenyl regioisomers in approximately an 80:20 ratio. However, use of N,N-diethylcinnamide as the dipolarophile unexpectedly resulted in the formation of the 5-phenyl and 4-phenyl regioisomers in a 23:77 ratio. Studies have shown that this phenomena occurs only for tertiary cinnamides. In addition, it has been demonstrated that the phenyl group of tertiary cinnamides is not essential for the reversal of regioselectivity since crotonamides produce the same results and trends as the cinnamides. However, since acrylates and acrylamides both produce the 5-carbonyl regioisomers, it can be concluded that the beta-substituent is playing a key role for the unexpected results by possibly increasing steric interactions between the dipole and dipolarophile in the transition state. Transition state energies were calculated for the regioisomeric cycloadduct pairs derived from several crotonamides as well as methyl crotonate. These calculations indicate that steric factors are indeed responsible for the reversal of regioselectivity.
Initial stability of uncemented hip stems: an in-vitro protocol to measure torsional interface motion (1995)

The difficulty in quantitatively assessing the inherent variables of surgical stem insertion and interfemur differences continues to be a problem in experimental methodologies which assess hip stem stability. An in-vitro torsional stability protocol was developed which limited the mechanical testing variability and provided a reproducible micromotion measurement of an uncemented stem in synthetic composite femurs. Using a controlled mechanical stem insertion resulted in less interfemur variability within each group with the coefficient of variation being reduced from 35% overall to less than 20%. Femurs with shallow stem insertion depths had significantly larger micromotion than femurs having deep stem insertion depths. The sensitivity of the experimental protocol and the synthetic composite femurs to the varied functional behaviour of three different stem designs was demonstrated. The stem with a hollowed anterior-to-posterior proximal section experienced significantly more motion than the two stems with full proximal sections, reinforcing the need for proximal contact to ensure minimal micromotion in torsional loading.
Mining the web for answers to natural language questions (2001)

The web is now becoming one of the largest information and knowledge repositories. Many large scale search engines (Google, Fast, Northern Light, etc.) have emerged to help users find information. In this paper, we study how we can effectively use these existing search engines to mine the Web and discover the "correct" answers to factual natural language questions.We propose a probabilistic algorithm called QASM (Question Answering using Statistical Models) that learns the best query paraphrase of a natural language question. We validate our approach for both local and web search engines using questions from the TREC evaluation. We also show how this algorithm can be combined with another algorithm (AnSel) to produce precise answers to natural language questions.