gebhart/patrepeval huggingface dataset:
Spermine Metabolism and Anticancer Therapy (2009)

The natural polyamines (PA), putrescine (PUT), spermidine (SPD) and spermine (SPM) are ubiquitous constituents of eukaryotic cells. The increase of PA in malignant and proliferating cells attracted the interest of scientists during last decades, addressing PA depletion as a new strategy to inhibit cell growth. Selective enzyme inhibitors were developed for decreasing PA metabolism and to act as chemotherapeutic anticancer agents. Indeed, the complexity of the PA homoeostasis overcomes the PA perturbation by a single enzyme to take effect therapeutically. Recently, an increasing interest has been posed on spermine-oxidase (SMO), the only catabolic enzyme able to specifically oxidise SPM. Interestingly, the absence of SPM is compatible with life, but its accumulation and degradation is lethal. Augmented SMO activity provokes an oxidative stress rendering cells prone to die, and appears to be important in the cell differentiation pathway. Extra-cellular SPM is cytotoxic, but its analogues are capable of inhibiting cell growth at low concentrations, most likely by intracellular SPM depletion. These pivotal roles seem to evoke the biological processes of stress response, wherein balance is mandatory to live or to die. Thus, altering SPM metabolism could allow a multi-tasking therapeutic strategy, addressed not only to inhibit PA metabolism. Several tetramines are presently in early phases (I and II) of clinical trials, and it will be a matter of a few more years to understand whether SPM-related therapeutic approaches would be of benefit for composite treatment protocols of cancer.
Mullerian Inhibiting Substance Activity in Bovine Fetal, Newborn and Prepubertal Testes1 (1977)

A graded organ culture assay was used to detect Müllerian Inhibiting Substance activity in bovine testes. Müllerian Inhibiting Substance was present in all fetuses available for study from Day 110 to Day 210 of gestation. The assay detected similarly high activity during the first six weeks after birth. At eight weeks, activity was still present but diminished. Loss of activity, as in the rat, appeared to coincide with the time of weaning. Electron microscopic studies of the neonate calf testes demonstrate highly active Sertoli cells with a morphology suggestive of a protein secreting cell, and implicate the Sertoli cell as the source of Müllerian Inhibiting Substance. The neonate calf testes should be an excellent source of material for the isolation and biochemical characterization of Müllerian Inhibiting Substance.
An Aggregation Advisor for Ligand Discovery (2015)

Colloidal aggregation of organic molecules is the dominant mechanism for artifactual inhibition of proteins, and controls against it are widely deployed. Notwithstanding an increasingly detailed understanding of this phenomenon, a method to reliably predict aggregation has remained elusive. Correspondingly, active molecules that act via aggregation continue to be found in early discovery campaigns and remain common in the literature. Over the past decade, over 12 thousand aggregating organic molecules have been identified, potentially enabling a precedent-based approach to match known aggregators with new molecules that may be expected to aggregate and lead to artifacts. We investigate an approach that uses lipophilicity, affinity, and similarity to known aggregators to advise on the likelihood that a candidate compound is an aggregator. In prospective experimental testing, five of seven new molecules with Tanimoto coefficients (Tc's) between 0.95 and 0.99 to known aggregators aggregated at relevant concentrations. Ten of 19 with Tc's between 0.94 and 0.90 and three of seven with Tc's between 0.89 and 0.85 also aggregated. Another three of the predicted compounds aggregated at higher concentrations. This method finds that 61 827 or 5.1% of the ligands acting in the 0.1 to 10 μM range in the medicinal chemistry literature are at least 85% similar to a known aggregator with these physical properties and may aggregate at relevant concentrations. Intriguingly, only 0.73% of all drug-like commercially available compounds resemble the known aggregators, suggesting that colloidal aggregators are enriched in the literature. As a percentage of the literature, aggregator-like compounds have increased 9-fold since 1995, partly reflecting the advent of high-throughput and virtual screens against molecular targets. Emerging from this study is an aggregator advisor database and tool ( http://advisor.bkslab.org ), free to the community, that may help distinguish between fruitful and artifactual screening hits acting by this mechanism.
Mesostructure-Induced Selectivity in CO2 Reduction Catalysis (2015)

Gold inverse opal (Au-IO) thin films are active for CO2 reduction to CO with high efficiency at modest overpotentials and high selectivity relative to hydrogen evolution. The specific activity for hydrogen evolution diminishes by 10-fold with increasing porous film thickness, while CO evolution activity is largely unchanged. We demonstrate that the origin of hydrogen suppression in Au-IO films stems from the generation of diffusional gradients within the pores of the mesostructured electrode rather than changes in surface faceting or Au grain size. For electrodes with optimal mesoporosity, 99% selectivity for CO evolution can be obtained at overpotentials as low as 0.4 V. These results establish electrode mesostructuring as a complementary method for tuning selectivity in CO2-to-fuels catalysis.
Latency-aware elastic scaling for distributed data stream processing systems (2014)

Elastic scaling allows a data stream processing system to react to a dynamically changing query or event workload by automatically scaling in or out. Thereby, both unpredictable load peaks as well as underload situations can be handled. However, each scaling decision comes with a latency penalty due to the required operator movements. Therefore, in practice an elastic system might be able to improve the system utilization, however it is not able to provide latency guarantees defined by a service level agreement (SLA).
Isolation and characterization of type VIII collagen synthesized by cultured rabbit corneal endothelial cells. A conventional structure replaces the interrupted-helix model. (1986)

Radioactive proline-labeled type VIII collagen was biosynthesized in the presence of beta-aminoproprionitrile by rabbit corneal endothelial cells and isolated from the culture medium. Type VIII was purified in the presence of protease inhibitors and at neutral pH by ultrafiltration, precipitation with 3.9 M NaCl, sedimentation in sucrose gradients, and DEAE-Sephacel chromatography. The major components of this collagen, VIII-1, -2, and -3, exhibited apparent molecular weights of greater than 194,000, 124,000, and 61,000, respectively, and were shown to contain identical CNBr peptides. Following separation of VIII-1, -2, and -3 from each other and any residual proteases by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, exposure to acetic acid led to the conversion of VIII-1 to VIII-2 and VIII-3. Thus, VIII-1 is not a continuous single peptide chain, and the preliminary interrupted-helix model of the type VIII structure (Benya, P. D. (1980) Renal Physiol. 3, 30-35) was revised. VIII-3 appears to be the parent alpha 1 (VIII)-chain, with VIII-2 and VIII-1 representing beta- and gamma-chain configurations stabilized by strong noncovalent acid-labile interactions and beta-aminoproprionitrile-insensitive covalent cross-links. Based on two-dimensional CNBr peptide mapping, the alpha-chain is composed of six peptides. Mr 5,300-19,600. The terminal peptides are pepsin sensitive and correlate with two noncollagenous domains, NC1 (Mr 14,700) and NC2 (Mr 4-5,000). NC1 contains the site of acid-labile chain association.
Aspiration Cytology of 147 Adnexal Cysts with Histologic Correlation (2001)

Examination of the cyst fluids obtained by aspiration demonstrated low sensitivity, with 43% of inadequate samples obtained from all types of cysts. Malignant cystic neoplasms may be overlooked in inadequate samples. Our study also revealed that specificity in this type of analysis is high in inadequate samples, provided that the technique is carried out correctly.
Guided Face Cartoon Synthesis (2011)

In this paper, we propose a new method, called guided synthesis, to synthesize a face cartoon from a face photo. The guided synthesis is defined as a local linear model, which generates a cartoon image by incorporating the content of guidance images taken from the training set. Our synthesis operation is achieved based on four weight functions. The first is a photo-photo weight that aims to measure the similarity between an input photo patch and a training photo patch. The second is defined as a photo-cartoon weight, which is used to compute the likelihood by computing the similarity between a cartoon patch and an input photo patch. The third weight is defined in the synthesized photos, which is to set a smoothness constraint between neighboring synthesized patches. The final weight is designed to evaluate the similarity of a synthesized patch to an input patch based on the spatial distance. Experimental evaluation on a number of face photos demonstrates the good performance of the proposed method on the face cartoon synthesis.
Metabolism of 4- N -Hydroxy-Cytidine in Escherichia coli (1971)

4-N-hydroxy-cytidine was found to substitute for uridine as a pyrimidine supplement for the growth of Escherichia coli Bu(-). Measurement of the incorporation of 4-N-hydroxy-cytidine-2-(14)C into ribonucleic acid and deoxyribonucleic acid revealed that this compound was converted to cytidine or uridine before utilization. Two pathways for metabolism were considered: (i) the reduction of 4-N-hydroxy-cytidine to cytidine followed by deamination, (ii) the direct hydrolysis of hydroxylamine from 4-N-hydroxy-cytidine to yield uridine. A threefold increase in cytidine (deoxycytidine) deaminase (EC 3.5.4.5) activity, when the cells were grown on 4-N-hydroxy-cytidine, suggested the involvement of this enzyme. More direct proof was obtained by purifying the deaminase 185-fold and finding that it released hydroxylamine from 4-N-hydroxy-cytidine at one-fiftieth the rate at which ammonia was removed from cytidine. This result is consistent with the slower rate of growth of the Bu(-) cells on 4-N-hydroxy-cytidine than cytidine and suggests that the second pathway is the major route for utilization of this compound.
SNX9 – a prelude to vesicle release (2008)

The sorting nexin SNX9 has, in the past few years, been singled out as an important protein that participates in fundamental cellular activities. SNX9 binds strongly to dynamin and is partly responsible for the recruitment of this GTPase to sites of endocytosis. SNX9 also has a high capacity for modulation of the membrane and might therefore participate in the formation of the narrow neck of endocytic vesicles before scission occurs. Once assembled on the membrane, SNX9 stimulates the GTPase activity of dynamin to facilitate the scission reaction. It has also become clear that SNX9 has the ability to activate the actin regulator N-WASP in a membrane-dependent manner to coordinate actin polymerization with vesicle release. In this Commentary, we summarize several aspects of SNX9 structure and function in the context of membrane remodeling, discuss its interplay with various interaction partners and present a model of how SNX9 might work in endocytosis.
Dual Excitation Ratiometric Fluorescent pH Sensor for Noninvasive Bioprocess Monitoring: Development and Application (2002)

The development and application of a fluorescent excitation-ratiometric, noninvasive pH sensor for continuous on-line fermentation monitoring is presented. The ratiometric approach is robust and insensitive to factors such as source intensity, photobleaching, or orientation of the patch, and since measurements can be made with external instrumentation and without direct contact with the patch, detection is completely noninvasive. The fluorescent dye 8-hydroxy-1,3,6-pyrene trisulfonic acid was immobilized onto Dowex strongly basic anion-exchange resin, which was subsequently entrapped into a proton-permeable hydrogel layer. The sensor layer was polymerized directly onto a white microfiltration membrane backing that provided an optical barrier to the fluorescence and scatter of the fermentation medium. The ratio of emission intensity at 515 nm excited at 468 nm to that excited at 408 nm correlated well with the pH of clear buffers, over the pH range of 6-9. The sensor responded rapidly (<9 min) and reversibly to changes in the solution pH with high precision. The sterilizable HPTS sensor was used for on-line pH monitoring of an E. coli fermentation. The output from the indwelling sensor patch was always in good agreement with the pH recorded off-line with an ISFET probe, with a maximum discrepancy of 0.05 pH units. The sensor is easily adaptable to closed-loop feedback control systems.
Applying the Semantic Web: The VICODI Experience in Creating Visual Contextualization for History (2005)

Semantic Web applications in the humanities that visualize knowledge are still few and far between. The Visual Contextualization of Digital Content (VICODI) project brought together Semantic Web technologies with the concepts of contextualization and visualization of knowledge, an approach which we term visual contextualization. The goal was to enhance users' understanding of digital content in the domain of history. It succeeded in doing this by creating an ontology-based web portal of European history where extra historical knowledge or ‘context’ is added to resources and visualized through textual hyperlinks and interactive Scalable Vector Graphics historical maps. VICODI also created a history-specific ontology. In this article the novel approach of visual contextualization is introduced in conjunction with a detailed explanation of the core elements of the VICODI portal. The article also addresses several of the problems encountered in developing a Semantic Web application for a humanities domain.
Determination of Serum Antibody toBordetella pertussisAdenylate Cyclase Toxin in Vaccinated and Unvaccinated Children and in Children and Adults with Pertussis (2004)

Presence of antibody to adenylate cyclase toxin (ACT) has been noted following Bordetella pertussis infection. Because ACT is not presently in any acellular pertussis vaccines, it has been considered as a possible antigen to use in B. pertussis diagnostic enzyme-linked immunosorbent assay (ELISA) studies. We determined antibody to B. pertussis ACT by ELISA and Western blot tests in serum samples obtained from unvaccinated children, from children vaccinated with several diphtheria and tetanus toxoid vaccines (DTP vaccines), from children vaccinated with vaccines containing acellular pertussis components in combination with diphtheria and tetanus toxoids (DTaP vaccines), and from children and adults with pertussis. Primary infections with either B. pertussis or Bordetella parapertussis stimulated a vigorous antibody response to ACT. In contrast, patients in whom DTP and DTaP vaccines failed had minimal ACT antibody responses. The lack of a significant ACT antibody response in children in whom the vaccine failed is of interest but would seem to preclude the use of ACT in diagnostic tests.
Omega-3 long-chain PUFA and triglyceride lowering: minimum effective intakes (2001)

Early studies on the cardioprotective effects of high doses (up to 20 g of eicosapentaenoic and docosahexaenoic acids, EPA and DHA, per day) of omega-3 fatty acids (FAs) suggested that these FAs primarily lowered triglyceride levels. These supraphysiological intake studies soon gave way to trials using lower and lower intakes of omega-3 FAs such that it is now clear that up to 45% lowering of serum triglyceride levels can be achieved with 3–4 g of EPA + DHA. This is an intake that can hardly be achieved by dietary means; direct supplementation is required. This is a public health challenge since implementing wide-scale supplementation programmes would be difficult. Relatively few investigators have examined the effects of low (<2 g) EPA+DHA on serum lipid profiles, presumably because until recently there was little expectation that any benefit would be detectable. With the publication of the DART study and more recently the GISSI-Prevenzione Study, it is becoming clear that small intakes of omega-3 FAs can significantly impact CHD risk. A review of the studies on the effects of small doses (<2 g · day−1) of omega-3 FAs on serum triglyceride levels suggests that serum triglyceride levels decreased in every study (compared with control or placebo treatment). The decreases were often not statistically significant, but this is to be expected with small doses given for short time-periods. Four of the five studies that examined postprandial lipids (PPL) reported significant reductions in this parameter even when fasting levels were not altered. This suggests that chronic intake of small amounts of omega-3 FAs may reduce overall (day-long) triglyceride-rich lipoprotein levels which could have long-term implications for the reduction of CHD risk. Whilst the cardioprotective effects of omega-3 FAs are becoming well documented, the question of whether such beneficial effects of omega-3 FAs are at least partially mediated by changes in serum levels of triglyceride-rich lipoproteins or their remnants remains open. Further studies to examine the effects of this low level of intake are clearly needed to determine the relative contribution of hypolipidaemic mechanisms versus those involving diminished platelet function, altered adhesion molecule expression, improvements in endothelial function and antiarrhythmic or hypotensive effects.
Rapid chemical ligation of oligonucleotides by the Diels–Alder reaction (2010)

Extremely fast and efficient Diels-Alder chemical ligation of furan and maleimide oligonucleotides has been carried out in aqueous buffer. It was possible to ligate three oligonucleotides simultaneously in a controlled manner with the aid of a complementary splint. The templated reactions proceeded within 1 min at room temperature whereas non-templated reactions were slow and incomplete. Rapid and clean methods of DNA ligation such as the one demonstrated here have potential uses in biology and nanotechnology.
Piezoelectric chemical sensors (IUPAC Technical Report) (2004)

Abstract Piezoelectric chemical and electrochemical sensors are classified. Basic terms and definitions related to piezoelectric materials and sensing devices, electric transducers, and analytical measurements with piezoelectric chemical sensors are provided. In addition, the more essential response equations are presented.
Targeting Tumor Vasculature Using VEGF-Toxin Conjugates (2003)

Tumor growth beyond a size of 1-2 mm3 requires new blood supply to sustain the nutritional and oxygen demands of the proliferating cancer cells (1). Tumor neovascularization is a complex process involving endothelial cell proliferation, matrix degradation, endothelial cell migration and tube formation. Vascular endothelial growth factor (VEGF), also known as vascular permeability factor (VPF), is an important angiogenic mediator secreted by tumor cells (2). VEGF binds to receptor tyrosine kinases flt-1 and KDR/flk-1, which are expressed primarily on endothelial cells. Receptor expression is increased under hypoxia, and recent studies suggest that VEGF itself can upregulate their levels on endothelial cells. In situ hybridization and immunocytochemical analyses have identified that VEGF receptors are overexpressed on the endothelial cells of intratumoral and peritumoral blood vessels. In contrast, blood vessels in the adjoining normal tissues showed almost undetectable levels of VEGF receptors (2). These results suggest that VEGF can be used to target toxin polypeptides to tumor vascular endothelium to inhibit angiogenesis. In this chapter, we will focus on VEGF-DT385 toxin conjugates prepared by chemical means, and we will describe methods to evaluate their biologic activity. Furthermore, a protocol is described to prepare VEGF-toxin fusion proteins.
Quantitation of microRNAs using a modified Invader assay (2004)

The short lengths of microRNAs (miRNAs) present a significant challenge for detection and quantitation using conventional methods for RNA analysis. To address this problem, we developed a quantitative, sensitive, and rapid miRNA assay based on our previously described messenger RNA Invader assay. This assay was used successfully in the analysis of several miRNAs, using as little as 50-100 ng of total cellular RNA or as few as 1,000 lysed cells. Its specificity allowed for discrimination between miRNAs differing by a single nucleotide, and between precursor and mature miRNAs. The Invader miRNA assay, which can be performed in unfractionated detergent lysates, uses fluorescence detection in microtiter plates and requires only 2-3 h incubation time, allowing for parallel analysis of multiple samples in high-throughput screening analyses.
Are Chinese Walls the Best Solution to the Problems of Insider Trading and Conflicts of Interest in Broker-Dealers? (2004)

The once-thriving "new" American economy is a thing of the past with the bursting of the dot-com bubble.After the huge losses in the financial markets, investors and the Securities and Exchange Commission ("SEC") have focused on cases of fraud in the financial markets.The SEC has continued its long-standing focus on insider trading in broker-dealers, but it has now begun to concentrate on conflicts of interest, particularly conflicts of securities analysts.'"Chinese Walls" are an important element of broker-dealer regulation because they attempt to resolve both of these problems.Traditionally, a Chinese Wall has been an information barrier that prevents insider trading. 2 Recently, the SEC and Congress have advocated the use of a Chinese Wall as a structural technique to help reduce analysts' conflicts of interest.' .
Additive/synergistic antitumoral effects on prostate cancer cells in vitro following treatment with a combination of docetaxel and zoledronic acid (2005)

Once bone metastasized and androgen independent, prostate cancer is often associated with skeletal morbidity and disability. New treatment modalities that can palliate symptoms from the skeleton and inhibit further progression are warranted. In this study, the antitumoral effects following treatment with a combination of docetaxel and the new generation bisphosphonate, zoledronic acid, were investigated on two hormone-refractory prostate cancer cell lines: PC3 and DU145. The prostate cancer cells were treated with increasing concentrations of zoledronic acid in the absence or presence of docetaxel. Toxicity was measured using fluorometric microculture cytotoxic assay technique. A concentration of 25 µM, zoledronic acid reduced the viable cell number to 68% and 98% for PC3 and DU145 cells respectively. Docetaxel, on the other hand, at a concentration of 0.1 ng/ml, had no effect on the viability. However, a combination of zoledronic acid and docetaxel reduced the cell number to 60% and 81% respectively. Furthermore, zoledronic acid in the concentration range 12.5 µM–50 µM enhanced the antitumoral effects of docetaxel (0.01–1 ng/ml) in an additive and/or synergistic manner for both cell lines. These data support the hypothesis that zoledronic acid, in addition to having bone resorption inhibiting properties, also exhibits anti-tumoral effects. It also appears that combined treatment with docetaxel causes additive and/or synergistic cytostatic effects on prostate cancer cells.