gebhart/patrepeval huggingface dataset:
Simultaneous Nitrification, Denitrification, and Phosphorus Removal in Single‐Tank Low‐Dissolved‐Oxygen Systems Under Cyclic Aeration (2007)

Simultaneous nitrification and denitrification (SND or SNdN) may occur at low dissolved oxygen concentrations. In this study, bench-scale (approximately 6 L) bioreactors treating a continuous feed of synthetic wastewater were used to evaluate the effects of solids retention time and low dissolved oxygen concentration, under cyclic aeration, on the removal of organics, nitrogen, and phosphorus. The cyclic aeration was carried out with repeated cycles of 1 hour at a higher dissolved oxygen concentration (HDO) and 30 minutes at a lower (or zero) dissolved oxygen concentration (LDO). Compared with aeration at constant dissolved oxygen concentrations, the cyclic aeration, when operated with proper combinations of HDO and LDO, produced better-settling sludge and more complete nitrogen and phosphorus removal. For nitrogen removal, the advantage resulted from the more readily available nitrate and nitrite (generated by nitrification during the HDO period) for denitrification (during the LDO period). For phosphorus removal, the advantage of cyclic aeration came from the development of a higher population of polyphosphate-accumulating organisms, as indicated by the higher phosphorus contents in the sludge solids of the cyclically aerated systems. Nitrite shunt was also observed to occur in the LDO systems. Higher ratios of nitrite to nitrate were found in the systems of lower HDO (and, to less dependency, higher LDO), suggesting that the nitrite shunt took place mainly because of the disrupted nitrification at lower HDO. The study results indicated that the HDO used should be kept reasonably high (approximately 0.8 mg/L) or the HDO period prolonged, to promote adequate nitrification, and the LDO kept low (< or =0.2 mg/L), to achieve more complete denitrification and higher phosphorus removal. The above findings in the laboratory systems find strong support from the results obtained in full-scale plant implementation. Two plant case studies using the cyclic low-dissolved-oxygen aeration for creating and maintaining SND are also presented.
Identification ofLinotte, a New Gene Affecting Learning and Memory inDrosophila Melanogaster (1993)

AbstractWe describe the identification of linotte, a new autosomal gene in Drosophila involved with learning and memory. The linotte' mutant was derived from a PlacW transposon mutagenesis and was screened for three-hour memory deficits after classical conditioning of an olfactory avoidance response. Sensory and motor systems (olfactory acuity and shock reactivity) required for the classical conditioning experiments were normal in mutant linotte1 flies—indicating that the mutation disrupts learning/memory specifically. A chromosomal deficiency of the 37D region, where the linotte1 P insert was localized in situ, failed to complement linotte1's memory defect, and flies from two lines homozygous for independent PlacW excisions show normal memory—indicating that the P insertion is responsible for the mutant phenotype. Additional behavior-genetic data suggest that linotte gene is non-vital.Key Words: Classical conditioningolfactory avoidance responsetransposon-tagging mutagenesis
Osteogenic Evaluation of Glutaraldehyde Crosslinked Gelatin Composite with Fetal Rat Calvarial Culture Model (2001)

The cytotoxicity of the synthetic bone substitute composed of tricalcium phosphate and glutaraldehyde crosslinked gelatin (GTG) were evaluated by osteoblast cell culture. In a previous study, the GTG composites were soaked in distilled water for 1, 2, 4, 7, 14, 28, and 42 days, and then the solutions (or extracts) were cocultured with osteoblasts to evaluate the cytotoxicity of GTG composites by alive cell counting. In this study, the extracts were cocultured with the osteoblasts; thereafter, the concentration of transforming growth factor-beta (TGF-beta1) and prostaglandin E2 (PGE2) in the medium was analyzed to strictly reflect the biological effects of GTG composites on the growth of osteoblasts. In order to investigate the osteoconductive potential of the GTG composites on new bone formation in a relative short term, a model of neonatal rat calvarial organ culture was designed prior to animal experiments. Three experimental materials of 4, 8, and 12% GTG composites were evaluated by fetal rat calvarial organ culture for their ability for bone regeneration. Deproteinized bovine and porcine cancellous bone matrixes were used as the controlled materials. All the organ culture units were maintained in cultured medium for 5 weeks. Following the culture period, the morphology of tissue was observed under an optical microscope, and the quantitative evaluation of the new generation bone was determined by using a semiautomatic histomorphometeric method. Except in the initial 4 days, the concentration of TGF-beta1 of 4% and 8% GTG composites was higher than that of the blank group for all the other experimental time periods. The PGE2 concentration for 4% and 8% GTG composites was lower than that of the blank group. It revealed that the 4% and 8% GTG composites would not lead to inflammation and would promote osteoblast growth. The morphology and activity of the osteoblasts were not transformed or changed by the 2 GTG composites. For the 12% GTG composite, the performance of the in vitro condition was inferior to the blank group and the other 2 GTG composites. Although the concentration of TGF-beta1 and PGE2 was gradually back to normal after 14 days, the morphology of the osteoblasts was abnormal with features such as contracted cytoplast structures. The osteoblast was damaged perhaps in the initial stage. We suggested that the 4% and 8% GTG composites should be soaked in distilled water at least for 4 days before medical applications. The 12% GTG composite and the composites with a concentration of glutaraldehyde solution higher than 12% were not recommended as a medical prostheses in any condition. The fetal rat calvaria culture also showed the same results with the analysis of TGF-beta1 and PGE2. From the study, we could predict the results of animal experiments in the future.
Iterative and incremental development of component-based software architectures (2012)

While the notion of components has had a major positive impact on the way software architectures are conceptualized and represented, they have had relatively little impact on the processes and procedures used to develop software systems. In terms of software development processes, use case-driven iterative and incremental development has become the predominant paradigm, which at best ignores components and at worse is even antagonistic to them. However, use-case driven, I&I development (as popularized by agile methods) and component-based development have opposite strengths and weaknesses. The former's techniques for risk mitigation and prioritization greatly reduce the risks associated with software engineering, but often give rise to suboptimal architectures that emerge in a semi-ad hoc fashion over time. In contrast, the latter gives rise to robust, optimized architectures, but to date has poor process support. In principle, therefore, there is a lot to be gained by fundamentally aligning the core principles of component-based and I&I development into a single, unified development approach. In this position paper we discuss the key issues involved in attaining such a synergy and suggest some core ideas for merging the principles of component-based and I&I development.
In vitro assessment of the prebiotic potential of Aloe vera mucilage and its impact on the human microbiota (2014)

Aloe vera mucilage is reported to be rich in acemannan that is a polysaccharide with a backbone of β-(1→4)-D-mannose residues acetylated at the C-2 and C-3 positions and contains some side chains of galactose and arabinose attached to the C-6 carbon. The evaluation of the prebiotic potential of Aloe vera mucilage was carried out by in vitro fermentation using intestinal microbiota from six healthy donors as the inoculum. The prebiotic activity was assessed through the quantification of short chain fatty acids (SCFA) and the evaluation of dynamic bacterial population in mixed faecal cultures by fluorescence in situ hybridization (FISH). Our findings support the possible incorporation of the Aloe vera mucilage in the development of a variety of food products known as prebiotics aimed at improving gastrointestinal health.
Expression of monocyte chemoattractant protein 1 in macrophage-rich areas of human and rabbit atherosclerotic lesions. (1991)

The recruitment of monocyte-macrophages into the artery wall is one of the earliest events in the pathogenesis of atherosclerosis. Monocyte chemoattractant protein 1 (MCP-1) is a potent monocyte chemoattractant secreted by many cells in vitro, including vascular smooth muscle and endothelial cells. To test whether it is expressed in the artery in vivo, we used Northern blot analysis, in situ hybridization, and immunocytochemistry to study the expression of MCP-1 in normal and atherosclerotic human and rabbit arteries. Northern blot analysis showed that MCP-1 mRNA could be isolated from rabbit atherosclerotic lesions but not from the intima media of normal animals. Furthermore, MCP-1 mRNA was extracted from macrophage-derived foam cells isolated from arterial lesions of ballooned cholesterol-fed rabbits, whereas alveolar macrophages isolated simultaneously from the same rabbits did not express MCP-1 mRNA. MCP-1 mRNA was detected by in situ hybridization in macrophage-rich regions of both human and rabbit atherosclerotic lesions. No MCP-1 mRNA was found in sublesional medial smooth muscle cells or in normal arteries. By using immunocytochemistry, MCP-1 protein was demonstrated in human lesions, again only in macrophage-rich regions. Immunostaining of the serial sections with an antiserum against malondialdehyde-modified low density lipoprotein indicated the presence of oxidized low density lipoprotein indicated the presence of oxidized low density lipoprotein and/or other oxidation-specific lipid-protein adducts in the same areas that contained macrophages and MCP-1. We conclude that (i) MCP-1 is strongly expressed in a small subset of cells in macrophage-rich regions of human and rabbit atherosclerotic lesions and (ii) MCP-1 may, therefore, play an important role in the ongoing recruitment of monocyte-macrophages into developing lesions in vivo.
Structures and Transport Properties of Hydrated Water-Soluble Dendrimer-Grafted Polymer Membranes for Application to Polymer Electrolyte Membrane Fuel Cells:  Classical Molecular Dynamics Approach (2007)

We investigate a new molecular architecture in which water-soluble dendrimers are grafted onto a linear polymer for application to polymer electrolyte membrane fuel cells (PEMFC). Using full-atomistic molecular dynamics simulations, we examined the nanophase segregation and transport properties in hydrated membranes with this new architecture. In order to determine how the nature of the linear polymer backbone might affect membrane properties, we considered three different types of linear polymers, poly(epichlorohydrin) (PECH), polystyrene (PS), and poly(tetrafluoroethylene) (PTFE), each in combination with the second-generation sulfonic polyaryl ether dendrimer to form PECH-D2, PS-D2, and PTFE-D2. Our simulations show that the extent of nanophase segregation in the membrane increases in the order of PECH-D2 (∼20 Å) < PS-D2 (∼35 Å) < PTFE-D2 (∼40 Å) at the same water content, which can be compared to ∼30−50 Å for Nafion and ∼30 Å for Dendrion at the same water content. We find that the structure and dynamics of the water molecules and transport of protons are strongly affected by the extent of nanophase segregation and water content of the membrane. As the nanophase-segregation scale increases, the structure in water phase, the water dynamics, and the proton transport approach those in bulk water. On the basis of the predicted proton and water transport rates, we expect that the PTFE-D2 may have a performance comparable with Nafion and Dendrion.
Intraluminal stents in atherosclerotic iliac artery stenosis: preliminary report of a multicenter study. (1988)

Fifteen patients with symptomatic iliac artery stenosis were treated with intraluminal placement of balloon-expandable stents. Before treatment, 14 patients had intermittent claudication, and one had a limb at risk for amputation. One patient had diabetes mellitus, nine had hypertension, and all were long-term smokers. Two patients had surgical placement of the stent; in one patient this was part of a combined revascularization procedure. All other stents were placed percutaneously. The transstenotic gradient after injection of vasodilating drugs distal to the lesion decreased from a mean of 32.3 mm Hg +/- 16.7 to 3.1 mm Hg +/- 4.2 after stent placement. Ankle-arm Doppler systolic pressure index increased from a mean of 0.68 +/- 0.22 to 0.96 +/- 0.24 after the procedure. The treatment eliminated intermittent claudication in 14 patients and increased exercise tolerance to 500 m in the patient with a limb at risk for amputation before the procedure. The improved condition persisted in all patients during the follow-up of 6-12 months. Stent placement may be a valuable adjunct in the management of iliac artery disease.
Bayesian Poisson Tensor Factorization for Inferring Multilateral Relations from Sparse Dyadic Event Counts (2015)

We present a Bayesian tensor factorization model for inferring latent group structures from dynamic pairwise interaction patterns. For decades, political scientists have collected and analyzed records of the form "country i took action a toward country j at time t" - known as dyadic events - in order to form and test theories of international relations. We represent these event data as a tensor of counts and develop Bayesian Poisson tensor factorization to infer a low-dimensional, interpretable representation of their salient patterns. We demonstrate that our model's predictive performance is better than that of standard non-negative tensor factorization methods. We also provide a comparison of our variational updates to their maximum likelihood counterparts. In doing so, we identify a better way to form point estimates of the latent factors than that typically used in Bayesian Poisson matrix factorization. Finally, we showcase our model as an exploratory analysis tool for political scientists. We show that the inferred latent factor matrices capture interpretable multilateral relations that both conform to and inform our knowledge of international a airs.
Gene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human Microbiome Project's Most Wanted taxa (2014)

This paper describes a microfluidics-based workflow for genetically targeted isolation and cultivation of microorganisms from complex clinical samples. Data sets from high-throughput sequencing suggest the existence of previously unidentified bacterial taxa and functional genes with high biomedical importance. Obtaining isolates of these targets, preferably in pure cultures, is crucial for advancing understanding of microbial genetics and physiology and enabling physical access to microbes for further applications. However, the majority of microbes have not been cultured, due in part to the difficulties of both identifying proper growth conditions and characterizing and isolating each species. We describe a method that enables genetically targeted cultivation of microorganisms through a combination of microfluidics and on- and off-chip assays. This method involves (i) identification of cultivation conditions for microbes using growth substrates available only in small quantities as well as the correction of sampling bias using a "chip wash" technique; and (ii) performing on-chip genetic assays while also preserving live bacterial cells for subsequent scale-up cultivation of desired microbes, by applying recently developed technology to create arrays of individually addressable replica microbial cultures. We validated this targeted approach by cultivating a bacterium, here referred to as isolate microfluidicus 1, from a human cecal biopsy. Isolate microfluidicus 1 is, to our knowledge, the first successful example of targeted cultivation of a microorganism from the high-priority group of the Human Microbiome Project's "Most Wanted" list, and, to our knowledge, the first cultured representative of a previously unidentified genus of the Ruminococcaceae family.
Transport of molecules in the tumor interstitium: a review. (1987)

The transport of fluid and solute molecules in the interstitium is governed by the biological and physicochemical properties of the interstitial compartment as well as the physicochemical properties of the test molecule. The composition of the interstitial compartment of neoplastic tissues is significantly different from that of most normal tissues. In general the tumor interstitial compartment is characterized by large interstitial space, high collagen concentration, low proteoglycan and hyaluronate concentrations, high interstitial fluid pressure and flow, absence of anatomically well-defined functioning lymphatic network, high effective interstitial diffusion coefficient of macromolecules, as well as large hydraulic conductivity and interstitial convection compared to most normal tissues. While these factors favor movement of macromolecules in the tumor interstitium, high interstitial pressure and low microvascular pressure may retard extravasation of molecules and cells, especially in large tumors. These differences in transport parameters have major implications in tumor growth and metastases, as well as in tumor detection and treatment.
Clotting Factor Deficiency in Early Trauma-Associated Coagulopathy (2011)

Twenty percent of all severely injured patients had critical CF deficiency on admission, particularly of factor V. The observed factor V deficit aligns with current understanding of the mechanisms underlying early TAC. Critical deficiency of factor V impairs thrombin generation and profoundly affects hemostasis.
The Effects of Pore Structure On Displacement Efficiency in Reservoir Rocks and in Glass Micromodels (1980)

Abstract In strongly wetted reservoir rocks, the extent of non-wetting phase trapping is strongly dependent on the geometric and topologic properties of the pore system. It has been demonstrated that pore-throat size ratio and certain types of heterogeneity affect displacement efficiency adversely. Throat to pore coordination number or connectivity and the condition or roughness of pore surfaces are other important factors affecting displacement efficiency. Under conditions of intermediate wetting, pore geometry appears to be of reduced significance as a cause of trapping and, under these conditions, displacement efficiency is greater.
Peptide YY: a potential proabsorptive hormone for the treatment of malabsorptive disorders. (1996)

Peptide YY (PYY) is a 36 amino acid peptide that is released from the endocrine cells of the distal ileum, colon, and rectum following a meal. PYY is strongly proabsorptive in the small intestine. We studied the effects of intravenous PYY on colonic water and electrolyte transport in awake dogs. Dogs had 20 cm neurovascularly intact colon Thiry-Vella fistulas (TVS) surgically constructed. Colonic transport was studied in three experimental groups. Group 1 animals received a standard mixed meal. Group 2 animals were unfed and received intravenous PYY and 100 pmol/kg/hr for two hours. This dose of PYY has previously been shown to simulate the plasma levels of PYY normally seen after a meal. Group 3 received intravenous PYY at the same dose in addition to a mixed meal. Our study shows an increase in colonic water, Na+, and Cl- absorption after a meal (P < 0.05). Infusion of PYY at a 100 pmol/kg/hr was significantly proabsorptive beginning at 60 minutes (P < 0.01). Infusion of PYY in addition to a meal further increased absorption (P < 0.05). PYY is a potent proabsorptive agent in the colon of the conscious dog. PYY, or its analogs, may be useful clinical agents in intestinal malabsorptive disorders or after bowel resection.
Indole-2-carboxamide Inhibitors of Human Liver Glycogen Phosphorylase (1998)

ADVERTISEMENT RETURN TO ISSUEPREVLetterNEXTIndole-2-carboxamide Inhibitors of Human Liver Glycogen Phosphorylase†Dennis J. Hoover, Sheri Lefkowitz-Snow, Jana L. Burgess-Henry, William H. Martin, Sandra J. Armento, Ingrid A. Stock, R. Kirk McPherson, Paul E. Genereux, E. Michael Gibbs, and Judith L. TreadwayView Author Information Departments of Cardiovascular and Metabolic Diseases Medicinal Chemistry, Exploratory Medicinal Biology, and Cardiovascular and Metabolic Diseases Biology, Central Research Division, Pfizer Inc., Groton, Connecticut 06340 Cite this: J. Med. Chem. 1998, 41, 16, 2934–2938Publication Date (Web):July 30, 1998Publication History Received1 May 1998Published online30 July 1998Published inissue 1 July 1998https://pubs.acs.org/doi/10.1021/jm980264khttps://doi.org/10.1021/jm980264krapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views804Altmetric-Citations88LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Anatomy,Carbohydrates,Inhibition,Inhibitors,Peptides and proteins Get e-Alerts
Somatic alterations in the melanoma genome: A high‐resolution array‐based comparative genomic hybridization study (2010)

We performed DNA microarray-based comparative genomic hybridization to identify somatic alterations specific to melanoma genome in 60 human cell lines from metastasized melanoma and from 44 corresponding peripheral blood mononuclear cells. Our data showed gross but nonrandom somatic changes specific to the tumor genome. Although the CDKN2A (78%) and PTEN (70%) loci were the major targets of mono-allelic and bi-allelic deletions, amplifications affected loci with BRAF (53%) and NRAS (12%) as well as EGFR (52%), MITF (40%), NOTCH2 (35%), CCND1 (18%), MDM2 (18%), CCNE1 (10%), and CDK4 (8%). The amplified loci carried additional genes, many of which could potentially play a role in melanoma. Distinct patterns of copy number changes showed that alterations in CDKN2A tended to be more clustered in cell lines with mutations in the BRAF and NRAS genes; the PTEN locus was targeted mainly in conjunction with BRAF mutations. Amplification of CCND1, CDK4, and other loci was significantly increased in cell lines without BRAF-NRAS mutations and so was the loss of chromosome arms 13q and 16q. Our data suggest involvement of distinct genetic pathways that are driven either through oncogenic BRAF and NRAS mutations complemented by aberrations in the CDKN2A and PTEN genes or involve amplification of oncogenic genomic loci and loss of 13q and 16q. It also emerges that each tumor besides being affected by major and most common somatic genetic alterations also acquires additional genetic alterations that could be crucial in determining response to small molecular inhibitors that are being currently pursued.