gebhart/patrepeval huggingface dataset:
Negative Regulation of MAVS-Mediated Innate Immune Response by PSMA7 (2009)

Innate immunity to viruses involves receptors such as Retinoic Acid Induced Gene-1 (RIG-I), which senses viral RNA and triggers a signaling pathway involving the outer mitochondrial membrane protein mitochondrial antiviral signaling (MAVS). Recent work has identified that NLRX1, a member of another class of innate immune receptors, sequesters MAVS away from RIG-I and thereby prevents mitochondrial antiviral immunity. In this study, we demonstrate that the proteasome PSMA7 (alpha4) subunit associates with MAVS in vivo and in vitro. Expression of PSMA7 results in a potent inhibition of RIG-1 and MAVS-mediated IFN-beta promoter activity; conversely, depletion of PSMA7 with small interference RNA enhances virus-induced type I IFN production, with consequent reduction of virus replication. Furthermore, a striking reduction in the abundance of endogenous MAVS with overexpressed PSMA7 was found and virus infection leads to transient increase in the endogenous PSMA7 protein level. Cumulatively, these results suggest that PSMA7 is a negative regulator of the MAVS-mediated innate immunity that probably serves to attenuate the establishment of an antiviral state during viral infection, highlighting the biological significance of PSMA7-MAVS association as an important cellular regulatory control.
ChemInform Abstract: Ambigol A and B: New Biologically Active Polychlorinated Aromatic Compounds from the Terrestrial Blue‐Green Alga Fischerella ambigua. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Supplementary Figure 2 from A Naturally Derived Small Molecule Disrupts Ligand-Dependent and Ligand-Independent Androgen Receptor Signaling in Human Prostate Cancer Cells (2023)

&lt;p&gt;PDF file - 26K, Effect of mahanine on hTERT and c-myc promoter activity.&lt;/p&gt;
A-site size effect in a family of unfilled ferroelectric tetragonal tungsten bronzes: Ba4R0.67Nb10O30 (R = La, Nd, Sm, Gd, Dy and Y) (2014)

The effect of A-cation size on the structural and electrical properties in a family of ferroelectric tetragonal tungsten bronzes (TTBs) Ba4R(0.67)□(1.33)Nb10O30 (R = La, Nd, Sm, Gd, Dy and Y; □ = vacancy) was investigated. In each case, the crystal structure, as determined from lab-based ambient powder X-ray diffraction (PXRD), is metrically tetragonal and can be refined in the P4bm space group. XRD data show an increased splitting of hk0 00l reflections with decreasing R cation size indicating an increasing tetragonal distortion (measured by tetragonality c/a). Dielectric data and ferroelectric measurements indicate that the ferroelectric Curie temperature, T(C), increases with decreasing R size and so a direct correlation between T(C) and tetragonality/ionic radius of R is demonstrated. Rietveld refinements show that the large A2-site is fully occupied by Ba(2+) and, in addition to the R cation size, the presence of vacancies at the A1-site (perovskite-like site) is also shown to strongly affect the stability of ferroelectricity in this structure type.
Polysaccharide production in batch process of Neisseria meningitidis serogroup C comparing Frantz, modified Frantz and Cartlin 6 cultivation media (2003)

Polysaccharide of N. meningitidis serogroup C constitutes the antigen for the vaccine against meningitis. The goal of this work was to compare three cultivation media for production of this polysaccharide: Frantz, modified Frantz medium (with replacement of glucose by glycerol), and Catlin 6 (a synthetic medium with glucose). The comparative criteria were based on the final polysaccharide concentrations and the yield coefficient cell/polysaccharide (Y P/X). The kinetic parameters: pH, substrate consumption and cell growth were also determined. For this purpose, 9 cultivation runs were carried out in a 80 L New Brunswick bioreactor, under the following conditions: 42 L of culture medium, temperature 35ºC, air flow 5 L/min, agitation frequency 120 rpm and vessel pressure 6 psi, without dissolved oxygen or pH controls. The cultivation runs were divided in three groups, with 3 repetitions each. The cultivation using the Frantz medium presented the best results: average of final polysaccharide concentration = 0.134 g/L and Y P/X=0.121, followed by Catlin 6 medium, with results of 0.095 g/L and 0.067 respectively. Considering the principal advantages in the use of the synthetic medium, i.e. facilitation of a cultivation and purification steps of the polysaccharide production process, there is a possibility that in the near future, Catlin 6 will replace the traditional Frantz medium.
Epigallocatechin Gallate Remodels Overexpressed Functional Amyloids in Pseudomonas aeruginosa and Increases Biofilm Susceptibility to Antibiotic Treatment (2016)

Epigallocatechin-3-gallate (EGCG) is the major polyphenol in green tea. It has antimicrobial properties and disrupts the ordered structure of amyloid fibrils involved in human disease. The antimicrobial effect of EGCG against the opportunistic pathogen Pseudomonas aeruginosa has been shown to involve disruption of quorum sensing (QS). Functional amyloid fibrils in P. aeruginosa (Fap) are able to bind and retain quorum-sensing molecules, suggesting that EGCG interferes with QS through structural remodeling of amyloid fibrils. Here we show that EGCG inhibits the ability of Fap to form fibrils; instead, EGCG stabilizes protein oligomers. Existing fibrils are remodeled by EGCG into non-amyloid aggregates. This fibril remodeling increases the binding of pyocyanin, demonstrating a mechanism by which EGCG can affect the QS function of functional amyloid. EGCG reduced the amyloid-specific fluorescent thioflavin T signal in P. aeruginosa biofilms at concentrations known to exert an antimicrobial effect. Nanoindentation studies showed that EGCG reduced the stiffness of biofilm containing Fap fibrils but not in biofilm with little Fap. In a combination treatment with EGCG and tobramycin, EGCG had a moderate effect on the minimum bactericidal eradication concentration against wild-type P. aeruginosa biofilms, whereas EGCG had a more pronounced effect when Fap was overexpressed. Our results provide a direct molecular explanation for the ability of EGCG to disrupt P. aeruginosa QS and modify its biofilm and strengthens the case for EGCG as a candidate in multidrug treatment of persistent biofilm infections.
Conjugated linoleic acid does not inhibit development of aberrant crypt foci in colons of male Sprague-Dawley rats. (2001)

Conjugated linoleic acid (CLA) is a potent inhibitor of the initiation and promotion of mammary carcinogenesis in animal models, but its role in colon carcinogenesis remains unclear. The objective of this study was to determine whether CLA inhibits the promotion of colon carcinogenesis. Forty male Sprague-Dawley rats were given a single dose of azoxymethane (20 mg/kg body wt i.p.). After 1 wk, the animals were randomized into two groups (n = 20) and fed a control AIN-93G diet or the control diet supplemented with 1% CLA at the expense of the soybean oil. After 12 wk, the animals were killed, and their colons were stained with methylene blue for aberrant crypt foci (ACF) analysis by light microscopy. The total number of ACF per animal did not differ between the control (174 +/- 11) and CLA (170 +/- 10) groups. Furthermore, CLA did not affect the average crypt multiplicity (crypts/ACF) or the average number of ACF in any size category. However, rats fed the 1% CLA diet had significantly higher serum insulin levels at the time of sacrifice than those fed the control diet. Thus it is possible that the promoting effects of elevated serum insulin on colon carcinogenesis may have counteracted an inhibitory effect of CLA.
Nolz1 promotes striatal neurogenesis through the regulation of retinoic acid signaling (2010)

Nolz1 promotes RA signaling in the LGE, contributing to the striatal neurogenesis during development.
Building Trust in History Matching: The Role of Multidimensional Projection (2012)

Abstract Assisted history matching frameworks powered by stochastic population-based sampling algorithms have been a popular choice for real-life reservoir management problems for the past decade. These methods provide an ensemble of history-matched models which can be used to quantify the uncertainty of future field performance. As a critique, population-based algorithms are generally considered black-boxes with little knowledge of their performance during history matching. In most cases, the misfit value is used as the only criteria to monitor the sampling algorithms and assess their quality. This paper applies three recently developed multidimensional projection schemes as a novel interactive, exploratory visualization tool for gaining insights to the sampling performance of population-based algorithms and comparing multiple runs in history matching. We use Least Square Projection (LSP), Projection by Clustering (ProjClus) and Principle Component Analysis (PCA) to examine the relationship between exploration of search space and the uncertainty in predictions of reservoir production. These projection techniques provide a mapping of the high dimensional search space into a 2D space by trying to maintain the distance relationships between sampled points. The application of multidimensional projection is illustrated for history matching of the benchmark PUNQ-S3 model using ant colony, differential evolution, particle swarm and the neighbourhood algorithms. We conclude that multi-dimensional projection algorithms are valuable diagnostic tools that should accompany assisted history matching workflows in order to evaluate their performance and compare ensembles of history-matched models. Using the projection tools, we show that misfit value - as an indicator of match quality - is not the only important factor in making reliable predictions. We demonstrate that exploration of the search space is also a critical element in the uncertainty quantification workflow which can be monitored with multidimensional projection schemes.
NVMalloc: Exposing an Aggregate SSD Store as a Memory Partition in Extreme-Scale Machines (2012)

DRAM is a precious resource in extreme-scale machines and is increasingly becoming scarce, mainly due to the growing number of cores per node. On future multi-petaflop and exaflop machines, the memory pressure is likely to be so severe that we need to rethink our memory usage models. Fortunately, the advent of non-volatile memory (NVM) offers a unique opportunity in this space. Current NVM offerings possess several desirable properties, such as low cost and power efficiency, but suffer from high latency and lifetime issues. We need rich techniques to be able to use them alongside DRAM. In this paper, we propose a novel approach for exploiting NVM as a secondary memory partition so that applications can explicitly allocate and manipulate memory regions therein. More specifically, we propose an NVMalloc library with a suite of services that enables applications to access a distributed NVM storage system. We have devised ways within NVMalloc so that the storage system, built from compute node-local NVM devices, can be accessed in a byte-addressable fashion using the memory mapped I/O interface. Our approach has the potential to re-energize out-of-core computations on large-scale machines by having applications allocate certain variables through NVMalloc, thereby increasing the overall memory capacity available. Our evaluation on a 128-core cluster shows that NVMalloc enables applications to compute problem sizes larger than the physical memory in a cost-effective manner. It can bring more performance/efficiency gain with increased computation time between NVM memory accesses or increased data access locality. In addition, our results suggest that while NVMalloc enables transparent access to NVM-resident variables, the explicit control it provides is crucial to optimize application performance.
Aminobenzoic acid diuretics. 3. 4-Substituted 5-sulfamylanthranilic acid derivatives (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAminobenzoic acid diuretics. 3. 4-Substituted 5-sulfamylanthranilic acid derivativesPeter W. Feit and Ole B. Tvaermose NielsenCite this: J. Med. Chem. 1972, 15, 1, 79–83Publication Date (Print):January 1, 1972Publication History Published online1 May 2002Published inissue 1 January 1972https://pubs.acs.org/doi/10.1021/jm00271a021https://doi.org/10.1021/jm00271a021research-articleACS PublicationsRequest reuse permissionsArticle Views146Altmetric-Citations9LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Assessment of a 3D neural spheroid model to detect pharmaceutical-induced neurotoxicity (2022)

Drug-induced neurotoxicity is a leading cause of safety-related attrition for therapeutics in clinical trials, often driven by poor predictivity of preclinical in vitro and in vivo models of neurotoxicity. Over a dozen different iPSC-derived 3D spheroids have been described in recent years, but their ability to predict neurotoxicity in patients has not been evaluated nor compared with the predictive power of nonclinical species. To assess the predictive capabilities of human iPSC-derived neural spheroids (microBrains), we used 84 structurally diverse pharmaceuticals with robust clinical and pre-clinical datasets with varying degrees of seizurogenic and neurodegenerative liability. Drug-induced changes in neural viability and phenotypic calcium bursts were assessed using 7 endpoints based on calcium oscillation profiles and cel-lular ATP levels. These endpoints, normalized by therapeutic exposure, were used to build logistic regression models to establish endpoint cutoffs and evaluate probability for clinical neurotoxicity. The neurotoxicity score calculated from the logistic regression model could distinguish neurotoxic from non-neurotoxic clinical molecules with a specificity as high as 93.33% and a sensitivity of 53.49%, demonstrating a very low false positive rate for the prediction of seizures, convulsions, and neurodegeneration. In contrast, nonclinical species showed a higher sensitivity (75%) but much lower specificity (30.4%). The neural spheroids demonstrated higher likelihood ratio positive and inverse likelihood ratio neg-ative values compared with nonclinical safety studies. This assay has the potential to be used as a predictive assay to detect neurotoxicity in early drug discovery, aiding in the early identification of compounds that eventually may fail due to neurotoxicity.
Pattern Formation And Rhythm Generation In The Ventral Respiratory Group (2000)

1. There is increasing evidence that the kernel of the rhythm-generating circuitry for breathing is located within a discrete subregion of a column of respiratory neurons within the ventrolateral medulla referred to as the ventral respiratory group (VRG). It is less clear how this rhythm is transformed into the precise patterns appearing on the varied motor outflows. 2. Two different approaches were used to test whether subregions of the VRG have distinct roles in rhythm or pattern generation. In one, clusters of VRG neurons were activated or inactivated by pressure injection of small volumes of neuroactive agents to activate or inactivate groups of respiratory neurons and the resulting effects on respiratory rhythm and pattern were determined. The underlying assumption was that if rhythm and pattern are generated by neurons in different VRG subregions, then we should be able to identify regions where activation of neurons predominantly alters rhythm with little effect on pattern and other regions where pattern is altered with little effect on rhythm. 3. Based on the pattern of phrenic nerve responses to injection of an excitatory amino acid (DL-homocysteate), the VRG was divided into four subdivisions arranged along the rostrocaudal axis. Injections into the three rostral regions elicited changes in both respiratory rhythm and pattern. From rostral to caudal the regions included: (i) a rostral bradypnoea region, roughly associated with the Bötzinger complex; (ii) a dysrhythmia/tachypnoea area, roughly associated with the pre-Bötzinger complex (PBC); (iii) a second caudal bradypnoea area; and, most caudally, (iv) a region from which no detectable change in respiratory motor output was elicited. 4. In a second approach, the effect of unilateral lesions of one subregion, the PBC, on the Breuer-Hering reflex changes in rhythm were determined. Activation of this reflex by lung inflation shortens inspiration and lengthens expiration (TE). 5. Unilateral lesions in the PBC attenuated the reflex lengthening of TE, but did not change baseline respiratory rhythm. 6. These findings are consistent with the concept that the VRG is not functionally homogenous, but consists of rostrocaudally arranged subregions. Neurons within the so-called PBC appear to have a dominant role in rhythm generation. Nevertheless, neurons within other subregions contribute to both rhythm and pattern generation. Thus, at least at an anatomical level resolvable by pressure injection, there appears to be a significant overlap in the circuitry generating respiratory rhythm and pattern.
Video‐enhanced microscopy of organelle movement in an intact epithelium (1992)

Digitally enhanced video microscopy has provided improved optical resolution in the study of intracellular organelle/particle movement, particularly in extruded axoplasm and certain thin single cell systems. We report here, for the first time, particle movement in an intact, isolated epithelium, the killifish proximal convoluted tubule. Cytoplasmic particles exhibited predominantly unidirectional linear movement approaching several microns in length, sometimes with multiple turns. The velocities of 34 particles measured in 11 cells averaged 0.29 microns/sec (range, 0.007-3.1 microns/sec). Microtubules--the well-established basis for organelle movement in cells--were present but were sparsely represented in electron micrographs of these cells. Video-enhanced microscopic techniques can now be applied to the study of organelle/particle movement in an intact epithelium.
Vacuum-processed small molecule solar cells based on terminal acceptor-substituted low-band gap oligothiophenes (2011)

Novel A-D-A type oligothiophenes incorporating benzothiadiazole (BTDA) and thiadiazolopyridine (TDAPy) as terminal acceptor groups have been developed for small molecule organic solar cells (SMSC). In vacuum-processed planar heterojunction solar cells the TDAPy-based oligomer showed a power conversion efficiency of 3.15% and a high fill factor of 0.67.
Effects of sewage sludge compost and chemical fertilizer application on microbial biomass and N mineralization rates (2002)

Abstract To determine the effect of sewage sludge compost and chemical fertilizer application on the soil chemical properties, net N mineralization rates, CO2 evolution rates, microbial biomass C and N, a non-leaching experiment was conducted under controlled conditions of temperature (25°C) and moisture content (80% wHC) using 2 types of soils that had been previously treated with sewage sludge composts or chemical fertilizer during short or long periods of time. The incubation lasted for 90 d. The treatments included: soils samples taken from 3 plots, each receiving sewage sludge compost with rice husk (RH), sewage sludge compost with sawdust (SD), and chemical fertilizer (CF), each applied at the rate of 200 kg N ha−1 biannually for 22 years (Tama farm) and 2 years (Chiba farm). The application of SD and RH led to a significant increase in the total N and C and soluble organic C reservoirs of the two soil types regardless of the application history. Soil pH was always higher in the sludge-treated soils than in the CF-treated soils. The SD- and RH-treated soils at the Tama farm showed significantly higher emission rates of CO2, cumulative CO2, and microbial biomass C and N than the CF-treated soils and SD- and RH-treated soils at the Chiba farm. The metabolic quotients of the soils treated with sewage sludge compost were significantly higher than those of the CF-treated soils. However the soils treated with sewage sludge compost of both Tama and Chiba farms exhibited a mixed response during the incubation period. Net N mineralization rates were significantly higher in the soils treated with SD followed by RH at the Mama farm; while the SD, RH, and CF-treated soils of the Chiba farm and CF soils of the Tama farm exhibited a negative N mineralization rate (immobilization). These results showed that the soils amended with sewage sludge composts displayed larger and more active microbial biomass than those treated with CF, which has implications for current interests in shifting from chemical fertilizer application to organic wastes for promoting efficient nutrient cycling in agro-ecosystems.
Enabling Multiple Conjugation to Oligonucleotides Using “Click Cycles” (2016)

An efficient method for the synthesis of multiply functionalized oligonucleotides (ONs) utilizing a novel H-phosphonate alkyne-based linker for multiple functionalization (LMF) is developed. The strategy allows for the conjugation of various active entities to oligonucleotide through the postsynthetic attachment of LMF at the 5'-terminus of ONs using H-phosphonate chemistry followed by conjugation of various entities via [3 + 2] copper(I) catalyzed cycloaddition in a stepwise manner. Each cycle is composed of attachment of the LMF followed by a click reaction with azido-containing units. Sequential solid-phase synthesis of oligonucleotide conjugates containing three attached entities was performed using an acetylated form of MIF peptide conjugated to azido linker, achieving high conversions at each unit addition. In addition, to show the versatility of the method, oligonucleotide conjugates with several different classes of compounds were synthesized. Each conjugate containing three different entities, whose structure and function varied (e.g., sugars, peptides, fluorescent labels, and m<sub>3</sub>G-Caps).