gebhart/patrepeval huggingface dataset:
Evolution of the cytoskeleton (2007)

The eukaryotic cytoskeleton appears to have evolved from ancestral precursors related to prokaryotic FtsZ and MreB. FtsZ and MreB show 40-50% sequence identity across different bacterial and archaeal species. Here I suggest that this represents the limit of divergence that is consistent with maintaining their functions for cytokinesis and cell shape. Previous analyses have noted that tubulin and actin are highly conserved across eukaryotic species, but so divergent from their prokaryotic relatives as to be hardly recognizable from sequence comparisons. One suggestion for this extreme divergence of tubulin and actin is that it occurred as they evolved very different functions from FtsZ and MreB. I will present new arguments favoring this suggestion, and speculate on pathways. Moreover, the extreme conservation of tubulin and actin across eukaryotic species is not due to an intrinsic lack of variability, but is attributed to their acquisition of elaborate mechanisms for assembly dynamics and their interactions with multiple motor and binding proteins. A new structure-based sequence alignment identifies amino acids that are conserved from FtsZ to tubulins. The highly conserved amino acids are not those forming the subunit core or protofilament interface, but those involved in binding and hydrolysis of GTP.
Pulsed Laser-Induced Shattering of Water Drops (1980)

Water droplets with radii ranging from 0.1 to 1.5 mm were irradiated by 10 jts pulses from a pulsed CO2 laser (A = 10.6 j*m) operating at intensities between 10 and 6xl0 W/cm. The absorption length (-10 jun) was much smaller than the droplet radii so that the laser-drop interaction was a surface phenomenon leading to overpressures on the irradiated front surface which exceeded surface tension forces by at least an order of magnitude. However, these high overpressures did not cause all droplets to shatter. There appeared to be a critical laser fluence of 0.8-2.5 J/cm required for shattering, essentially independent of radius. Above the critical fluence the drops were deformed into thin liquid films with subsequent breakup into smaller satellite droplets. For fixed pulse duration the shattering time decreases with increasing intensity and with decreasing initial drop size. Simple scaling and energy conservation relations are used to predict the radii of the satellite droplets and to estimate a critical impulse parameter.
Isolation and characterization of a cytochrome P-450 from rat kidney mitochondria that catalyzes the 24-hydroxylation of 25-hydroxyvitamin D3 (1991)

A cytochrome P-450 that catalyzes the 24-hydroxylation of 25-hydroxyvitamin D3 (P-450cc24: P-450cholecalciferol24) was purified to electrophoretic homogeneity from the kidney mitochondria of female rats treated with vitamin D3 (Ohyama, Y., Hayashi, S., and Okuda, K. (1989) FEBS Lett. 255, 405-408). The molecular weight was 53,000, and its absorption spectrum showed peaks characteristic of cytochrome P-450. The turnover number was 22 min-1 and the specific content was 2.8 nmol/mg protein. The N-terminal amino acid sequence, Arg-Ala-Pro-Lys-Glu-Val-Pro-Leu-, is different from the N-terminal sequence of any other cytochrome P-450s so far reported. Upon reconstitution with the electron-transferring system of the adrenal mitochondria, the enzyme showed a high activity in hydroxylating 25-hydroxyvitamin D3 as well as 1 alpha,25-dihydroxyvitamin D3 at position 24. However, the purified enzyme hydroxylated neither vitamin D3 nor 1 alpha-hydroxyvitamin D3. The enzyme was also inactive toward xenobiotics. The enzyme hydroxylated 25-hydroxyvitamin D3 at position 24 but not at 1 alpha, indicating that the enzyme is distinct from that catalyzing 1 alpha-hydroxylation. The reaction followed Michaelis-Menten kinetics, and the Km value for 25-hydroxyvitamin D3 was 2.8 microM. Both vitamin D3 and 1 alpha-hydroxyvitamin D3 inhibited the 24-hydroxylation of 25-hydroxyvitamin D3 in a competitive, concentration-dependent manner. 25-Hydroxyvitamin D3 24-hydroxylase activity was significantly inhibited by 7,8-benzoflavone, ketoconazole, and CO, whereas it was only slightly inhibited by aminoglutethimide, metyrapone, and SKF-525A. Mouse antibodies raised against the cytochrome P-450 inhibited the reaction about 70% and reacted with the P-450cc24 in immunoblotting but did not react with other kinds of cytochrome P-450 in rat liver microsomes and mitochondria.
A sample-and-clean framework for fast and accurate query processing on dirty data (2014)

In emerging Big Data scenarios, obtaining timely, high-quality answers to aggregate queries is difficult due to the challenges of processing and cleaning large, dirty data sets. To increase the speed of query processing, there has been a resurgence of interest in sampling-based approximate query processing (SAQP). In its usual formulation, however, SAQP does not address data cleaning at all, and in fact, exacerbates answer quality problems by introducing sampling error. In this paper, we explore an intriguing opportunity. That is, we explore the use of sampling to actually improve answer quality. We introduce the Sample-and-Clean framework, which applies data cleaning to a relatively small subset of the data and uses the results of the cleaning process to lessen the impact of dirty data on aggregate query answers. We derive confidence intervals as a function of sample size and show how our approach addresses error bias. We evaluate the Sample-and-Clean framework using data from three sources: the TPC-H benchmark with synthetic noise, a subset of the Microsoft academic citation index and a sensor data set. Our results are consistent with the theoretical confidence intervals and suggest that the Sample-and-Clean framework can produce significant improvements in accuracy compared to query processing without data cleaning and speed compared to data cleaning without sampling.
Schistosome N‐glycans containing core α3‐fucose and core β2‐xylose epitopes are strong inducers of Th2 responses in mice (2003)

During murine schistosomiasis, egg-derived glycoconjugates play a key role in skewing the immune response towards a Th2 phenotype. Among the candidates responsible for this effect, complex-type N-glycans containing the core alpha 3-fucose and core beta 2-xylose determinants, two glycan epitopes found in some invertebrate- and plant-derived allergens, may be important. Here, we show that core alpha 3-fucose and core beta 2-xylose determinants are expressed in the different developmental stages of Schistosoma mansoni, particularly in the excretory-secretory systems of schistosomula and adult worms and in eggs deposited in the liver. Glycosyltransferase assays confirmed the presence of core alpha 3-fucosyltransferase and core beta 2-xylosyltransferase activities in egg extracts. Using a model of immunization with pulsed dendritic cells, we show that egg-derived glycoproteins containing the core alpha 3-fucose and core beta 2-xylose determinants generate a strong Th2-biased cellular response in mice and that the glycan moieties of this extract are important in this effect. During murine infection, these complex-type N-glycans induce a glycan-specific Th2 cellular response and elicit T-dependent anti-core alpha 3-fucose and anti-core beta 2-xylose IgG1 (a Th2-associated isotype), but not IgG2b (a Th1-associated isotype) Ab. Taken together, our results point out the importance of core fucosylated/xylosylated N-glycans in the Th2 immune response during murine schistosomiasis.
Antibodies against Dengue Viral Proteins in Primary and Secondary Dengue Hemorrhagic Fever (1991)

Antibodies against dengue viral proteins were demonstrated in sera from dengue-infected patients by polyacrylamide gel electrophoresis, Western blotting, and enzyme immunoassay. Primary dengue cases showed low titers of IgG class antibodies to envelope (E) proteins and two non-structural proteins, NS3 and NS5, in sera collected during the convalescent phase. Secondary dengue- infected patients always demonstrated IgG antibodies to E proteins in sera collected during the acute phase, and high titers of IgG antibodies to many other proteins, including NS1, NS3, NS5, and C proteins in sera collected during the convalescent phase. Appearance of antibodies to E, NS3, and NS5 could be detected within five days after the onset of fever. These three dengue viral proteins and their corresponding antibodies may be involved in the immunopathologic mechanism underlying this disease. For diagnostic purposes, identifying the non-structural proteins such as NS3 and NS5 may be the best means for early confirmation of the disease.
Notch signaling is required for arterial-venous differentiation during embryonic vascular development (2001)

Recent evidence indicates that acquisition of artery or vein identity during vascular development is governed, in part, by genetic mechanisms. The artery-specific expression of a number of Notch signaling genes in mouse and zebrafish suggests that this pathway may play a role in arterial-venous cell fate determination during vascular development. We show that loss of Notch signaling in zebrafish embryos leads to molecular defects in arterial-venous differentiation, including loss of artery-specific markers and ectopic expression of venous markers within the dorsal aorta. Conversely, we find that ectopic activation of Notch signaling leads to repression of venous cell fate. Finally, embryos lacking Notch function exhibit defects in blood vessel formation similar to those associated with improper arterial-venous specification. Our results suggest that Notch signaling is required for the proper development of arterial and venous blood vessels, and that a major role of Notch signaling in blood vessels is to repress venous differentiation within developing arteries. Movies available on-line
Automated blood pressure measurement: Reasons for measurement variability uncovered (2009)

The most common automated blood pressure devices determine systolic, diastolic and mean arterial blood pressure (SBP, DBP and MAP) by analysing the oscillometric pulse waveform. The aim of this study was to assess the variability of the amplitude of oscillometric pulse waveform characteristics at SBP, DBP and MAP.
Sunitinib: a novel tyrosine kinase inhibitor. A brief review of its therapeutic potential in the treatment of renal carcinoma and gastrointestinal stromal tumors (GIST) (2007)

Sunitinib malate is a novel oral multitargeted tyrosine kinase inhibitor with antitumor and antiangiogenic activities. Sunitinib was recently approved in first-line treatment for patients with advanced renal cell carcinoma (RCC) and for the treatment of patients with gastrointestinal stromal tumors (GIST) after disease progression or intolerance to imatinib mesylate therapy. We report the very interesting results of the phase II trials after cytokin failure and of the randomized recent trial of sunitinib versus cytokin-based therapy in first-line treatment for patients with metastatic RCC, as well as the promising results of the recent trials on patients with GIST after disease progression or intolerance to imatinib mesylate therapy. Oral sunitinib demonstrates a high level of efficacy with acceptable tolerability with the 50 mg daily for 4 weeks followed by 2 weeks off schedule; a continuous schedule could be of interest. Hypertension and asthenia are the most common side effects with sunitinib. Regardless of these encouraging results, studies investigating sunitinib in first-line treatment (for patients with GIST), adjuvant and neoadjuvant settings are awaited, as well as trials using sunitinb in combination with chemotherapy or other targeted therapies. Clinical trials investigating sunitinib in other tumor types are ongoing.
Novel Heterolayer Organic Light-Emitting Diodes Based on a Conjugated Dendrimer (2002)

We demonstrate a novel organic light-emitting diode (LED) heterolayer structure that contains a conjugated dendrimer as the light-emitting molecule. The LED was prepared by spin-coating two dendrimer layers from the same solvent. The device consists of a graded bilayer structure formed from a neat dendrimer film covered with a film consisting of the same dendrimer but doped with the electron-transporting material 2-(4-biphenylyl)-5-phenyl-1,3,4-oxadiazole (PBD). In this device, the heterojunction interface present in conventional bilayer organic light-emitting diodes is eliminated, and is replaced by a graded interlayer. By optimizing the concentration of PBD in the dendrimer, a peak electroluminescence (EL) external quantum efficiency of 0.16 % at 600 cd m–2 was obtained. The EL quantum efficiency is significantly enhanced in comparison with devices based on a single layer, a conventional bilayer, and a single-layer doped with PBD. The EL quantum efficiency is a factor of eight larger than that of a conventional bilayer LED made with the conjugated dendrimer as the emissive layer and poly(methylmethacrylate) (PMMA) doped with PBD as the electron-transporting layer. The best blended device exhibited only one third of the efficiency of the graded device. The improvement in the operating characteristics of the graded device is attributed to the efficient device structure, in which exciton formation is improved by a graded doping profile of electron- and hole-transporting components.
Assignment of the L30-mRNA complex using selective isotopic labeling and RNA mutants (1999)

The helix-loop-helix structure formed in the pre-mRNA and the mRNA of L30, a ribosomal protein from the yeast Saccharomyces cerevisiae, serves as an auto-regulatory binding site for the protein to suppress the L30 synthesis upon overproduction. Using a 33-nucleotide model RNA, the structures of the L30 binding site RNA in the presence and absence of the protein were investigated using nuclear magnetic resonance (NMR) spectroscopy. Homonuclear and(13)C/(15)N-based resonance assignments and spectral comparisons indicated that the purine-rich internal loop is dynamic in the free RNA but becomes ordered in the presence of L30 protein. Although the resonances in the loop region are sharper and more disperse in the bound RNA, their assignment was extremely challenging, due to spectral complexity and broadened resonances caused by local dynamics. Two strategies, namely selective(13)C/(15)N-labeling and NMR analyses of five complexes with RNA mutants, were used to overcome these difficulties. Only using these approaches could assignment of the internal loop resonances and identification of the unusual NOEs and nucleotide conformations within the internal loop be made. In the case of structural determination of the L30-mRNA complex, it was critical to be able to take advantage of the available biochemical information in order to complete the structure determination.
Development and Implementation of a Miniaturized High-Throughput Time-Resolved Fluorescence Energy Transfer Assay to Identify Small Molecule Inhibitors of Polo-Like Kinase 1 (2007)

Polo-like kinase (Plk) 1 is a key enzyme involved in regulating the mammalian cell cycle that is also a validated anticancer drug target. Nonetheless, there are relatively few readily available potent and selective small molecule inhibitors of Plk1. To increase the availability of pharmacologically valuable Plk1 inhibitors, we describe herein the development, variability assessment, validation, and implementation of a 384-well automated, miniaturized high-throughput time-resolved fluorescence energy transfer screening assay designed to identify Plk1 kinase inhibitors. Using a small molecule library of pharmaceutically active compounds to gauge high-throughput assay robustness and reproducibility, we found nine general kinase inhibitors, including H-89, which was selected as the minimum control. We then interrogated a 97,101 compound library from the National Institutes of Health repository for small molecule inhibitors of Plk1 kinase activity. The initial primary hit rate in a single 10 microM concentration format was 0.21%. Hit compounds were subjected to concentration-response confirmation and interference assays. Identified in the screen were seven compounds with 50% inhibitory concentration (IC50) values below 1 microM, 20 compounds with IC50 values between 1 microM and 5 microM, and eight compounds with IC50 values between 5 and 10 microM, which could be assigned to seven distinct chemotype classes. Hit compounds were also examined for their ability to inhibit other kinases such as protein kinase D, focal adhesion kinase, rho-associated coiled coil protein kinase 2, c-jun NH2-terminal kinase 3, and protein kinase A via experimentation or data-mining. These compounds should be useful as probes for the biological activity of Plk1 and as leads for the development of new selective inhibitors of Plk1.
Effects of acute renal denervation on kidney function in deoxycorticosterone acetate-hypertensive swine. (1986)

Deoxycorticosterone acetate-induced hypertension in Yucatan miniature swine appears to involve elevated peripheral sympathetic activity. Abnormalities in renal function in these hypertensive animals are also apparent. To determine the extent to which renal nerve activity controls kidney function in animals with established deoxycorticosterone acetate hypertension, the effects of acute renal surgical denervation were assessed in five normal and 10 deoxycorticosterone acetate-treated swine. After 12 to 16 weeks of treatment, mean arterial pressure rose from the normal level of 110 to 120 to 164 +/- 4 mm Hg but was decreased to 131 +/- 4 mm Hg by anesthesia. In the normal animals, blood pressure under anesthesia was 114 +/- 9 mm Hg. Acute left kidney surgical denervation significantly decreased renal vascular resistance and increased renal blood flow, glomerular filtration rate, urine flow, and sodium excretion only in the treated animals. In an additional group of six normal and eight deoxycorticosterone acetate-treated swine, the responses to renal pharmacological denervation with intrarenal guanethidine were evaluated. Guanethidine had no significant effect on renal blood flow, vascular resistance, glomerular filtration rate, urine flow, or sodium excretion in the normal animals. In contrast, in the mineralocorticoid-hypertensive animals, guanethidine significantly decreased renal vascular resistance and caused a diuresis and natriuresis with no change in glomerular filtration rate. We conclude that, in deoxycorticosterone acetate-treated miniature swine with established hypertension, renal nerve activity appears to be elevated and important in determining renal hemodynamics and sodium and water excretion.
Involvement of Protein Kinase Cε (PKCε) in Thyroid Cell Death (1999)

The protein kinase C (PKC) family has been implicated in the regulation of apoptosis. However, the contribution of individual PKC isozymes to this process is not well understood. We reported amplification of the chromosome 2p21 locus in 28% of thyroid neoplasms, and in the WRO thyroid carcinoma cell line. By positional cloning we identified a rearrangement and amplification of the PKCepsilon gene, that maps to 2p21, in WRO cells. This resulted in the overexpression of a chimeric/truncated PKCepsilon (Tr-PKCepsilon) mRNA, coding for N-terminal amino acids 1-116 of the isozyme fused to an unrelated sequence. Expression of the Tr-PKCepsilon protein in PCCL3 cells inhibited activation-induced translocation of endogenous PKCepsilon, but its kinase activity was unaffected, consistent with a dominant negative effect of the mutant protein on activation-induced translocation of wild-type PKCepsilon and/or displacement of the isozyme to an aberrant subcellular location. Cell lines expressing Tr-PKCepsilon grew to a higher saturation density than controls. Moreover, cells expressing Tr-PKCepsilon were resistant to apoptosis, which was associated with higher Bcl-2 levels, a marked impairment in p53 stabilization, and dampened expression of Bax. These findings point to a role for PKCepsilon in apoptosis-signaling pathways in thyroid cells, and indicate that a naturally occurring PKCepsilon mutant that functions as a dominant negative can block cell death triggered by a variety of stimuli.
Amplification of MET may identify a subset of cancers with extreme sensitivity to the selective tyrosine kinase inhibitor PHA-665752 (2006)

The success of molecular targeted therapy in cancer may depend on the selection of appropriate tumor types whose survival depends on the drug target, so-called "oncogene addiction." Preclinical approaches to defining drug-responsive subsets are needed if initial clinical trials are to be directed at the most susceptible patient population. Here, we show that gastric cancer cells with high-level stable chromosomal amplification of the growth factor receptor MET are extraordinarily susceptible to the selective inhibitor PHA-665752. Although MET activation has primarily been linked with tumor cell migration and invasiveness, the amplified wild-type MET in these cells is constitutively activated, and its continued signaling is required for cell survival. Treatment with PHA-665752 triggers massive apoptosis in 5 of 5 gastric cancer cell lines with MET amplification but in 0 of 12 without increased gene copy numbers (P = 0.00016). MET amplification may thus identify a subset of epithelial cancers that are uniquely sensitive to disruption of this pathway and define a patient group that is appropriate for clinical trials of targeted therapy using MET inhibitors.
Human tenascin: primary structure, pre-mRNA splicing patterns and localization of the epitopes recognized by two monoclonal antibodies (1991)

By sequencing cDNA clones which cover the complete coding region of human tenascin (TN), we have established its primary structure. This confirms that, as in the case of chicken, TN is mainly made up of three groups of sequences with a high homology to Epidermal Growth Factor (EGF) fibronectin (FN) type III repeat and fibrinogen. Furthermore, we have determined the amino-terminal sequence of the mature peptide directly on purified TN. The main differences with respect to the chicken TN molecule are that in the human there are 14 and half EGF-like repeats compared to 13 and half in the chicken and that, as previously reported, there are 15 FN-like repeats compared to 11 in the chicken. By Polymerase Chain Reaction (PCR) amplification we have also studied the different splicing patterns of the TN pre-mRNA in cultured cells. The results show the presence of at least four different isoforms containing different numbers of FN-like type III repeats. Using purified human TN as immunogen, we have obtained numerous monoclonal antibodies (Mabs) to TN. By screening a human melanoma cDNA library in the expression vector lambda gt11 with these Mabs and subsequently sequencing the insert of the positive clones, we have been able to localize, within the TN molecule, the epitopes recognized by two of these Mabs: BC-4, which recognizes an epitope within the EGF-like sequence and BC-2 which recognizes an epitope within the FN like type III repeats whose expression is regulated by alternative splicing of the TN pre-mRNA. Thus, while the Mab BC-4 may be useful in studies on TN distribution (since it recognizes all different TN isoforms) BC-2 may be useful in the study of the expression of particular TN isoforms generated by the alternative splicing of the TN primary transcript.
Inhaled Nitric Oxide for the Early Treatment of Persistent Pulmonary Hypertension of the Term Newborn: A Randomized, Double-Masked, Placebo-Controlled, Dose-Response, Multicenter Study (1998)

For term infants with PPHN, early I-NO as the sole adjunct to conventional management produced an acute and sustained improvement in oxygenation for 24 hours without short-term side effects (5 and 20 ppm doses), and the suggestion that ECMO use may be reduced.