gebhart/patrepeval huggingface dataset:
Development of a fluorogenic matrix metalloproteinase 9 screening assays (MMP-9) (2022)

Matrix metalloproteinase 9, is a member of the MMP family of transmembrane zinc-dependent endopeptidase enzymes responsible for both physiological and pathophysiological tissue remodeling. In pathophysiological conditions, MMP-9 is upregulated and plays a key role in promoting the progression of various disease pathologies, including disorders during wound healing and inflammatory processes, such as arthritis, diabetes, and cancer. Subsequently, MMP-9 is an important target for inhibitor screening and led to an increased research interest in natural MMP-9 inhibitors, with a frequent focus on polyphenols [1], [2]. A broad range of different substrate and enzyme types and concentrations is described in the literature, using a fluorescence detection mode. Fluorescence measurement by assessing its increase after preincubation with a test compound is basically trivial and a successful technique, yet our recent findings show that this detection mode may have some pitfalls. Natural products containing high intrinsic fluorescence may lead to unreliable inhibition constants of polyphenols such as caffeates and stilbene monomers, which can be classified as false positive inhibitors. In this study, we investigated the inhibitory potential of 32 Vietnames extracts and 37 natural products, including compounds previously reported as MMP-9 inhibitors, at a test concentration of 30 µg/ml and 25 µM, respectively. IC50 values of cyperusphenol B (15.8 µM), cyperusphenol D (18.3 µM) and porphyra-334 (28.0 µM) were determined by concentration-response curves and their inhibitory effects were confirmed by molecular docking experiments. These results will aid in the search for new natural MMP-9 inhibitors and contribute to a better understanding of the screening assay.
PROCION YELLOW AND CATECHOLAMINE DERIVATIVES CHEMICAL RELATIONSHIPS (1973)

The use of Procion Yellow (M-4RS, ICI America, Inc.) as a fluorochrome in conjunction with catecholamine-derived isoquinoline fluorescence is examined by chemical techniques. From a series of chemical studies it has been found that: (a) Procion Yellow does not interfere with the formation of isoquinoline derivatives of catecholamine; (b) commercially available Procion Yellow is a composite of four species, all of whose emission-excitation maxima are distinguishable from that of catecholamine-derived isoquinohines; and (c) the emission-excitation maxima of Procion Yellow and of the catecholamine-derived isoquinolines are distinguishable one from another in solution. It is suggested that Procion Yellow can be a valuable fluorochrome to use in conjunction with the histofluorometric method. The data support the possibility that single adrenergic neuronal cells after being tagged with Procion Yellow can subsequently be shown to contain biogenic amines.
Faster and Cheaper: Parallelizing Large-Scale Matrix Factorization on GPUs (2016)

Matrix factorization (MF) is employed by many popular algorithms, e.g., collaborative filtering. The emerging GPU technology, with massively multicore and high intra-chip memory bandwidth but limited memory capacity, presents an opportunity for accelerating MF much further when appropriately exploiting the GPU architectural characteristics. This paper presents cuMF, a CUDA-based matrix factorization library that implements memory-optimized alternate least square (ALS) method to solve very large-scale MF. CuMF uses a variety set of techniques to maximize the performance on either single or multiple GPUs. These techniques include smart access of sparse data leveraging GPU memory hierarchy, using data parallelism in conjunction with model parallelism, minimizing the communication overhead between computing units, and utilizing a novel topology-aware parallel reduction scheme. With only a single machine with four Nvidia GPU cards, cuMF can be 6-10 times as fast, and 33-100 times as cost-efficient, compared with the state-of-art distributed CPU solutions. Moreover, this cuMF can solve the largest matrix factorization problem ever reported yet in current literature, while maintaining impressively good performance.
Aporphines. 20. Chemically induced fragmentation of nitrobenzylisoquinolinium salts (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAporphines. 20. Chemically induced fragmentation of nitrobenzylisoquinolinium saltsJohn L. Neumeyer and Werner DafeldeckerCite this: J. Org. Chem. 1977, 42, 4, 751–752Publication Date (Print):March 1, 1977Publication History Published online1 May 2002Published inissue 1 March 1977https://doi.org/10.1021/jo00424a038RIGHTS & PERMISSIONSArticle Views65Altmetric-Citations2LEARN 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 InReddit PDF (295 KB) Get e-Alerts Get e-Alerts
Lack of direct DNA damage in human blood leukocytes and lymphocytes after in vitro exposure to high power microwave pulses (2005)

Currently, the potential genotoxicity of high power microwave pulses (HPMP) is not clear. Using the alkaline single cell gel electrophoresis assay, also known as the alkaline comet assay, we studied the effects of HPMP (8.8 GHz, 180 ns pulse width, peak power 65 kW, pulse repetition frequency 50 Hz) on DNA of human whole-blood leukocytes and isolated lymphocytes. The cell suspensions were exposed to HPMP for 40 min in a rectangular waveguide. The average SAR calculated from the temperature kinetics was about 1.6 kW/kg (peak SAR was about 300 MW/kg). The steady-state temperature rise in the 50 microl samples exposed to HPMP was 3.5 +/- 0.1 degrees C. In independent experiments, we did not find any statistically significant DNA damage manifested immediately after in vitro HPMP exposure of human blood leukocytes or lymphocytes or after HPMP exposure of leukocytes subsequently incubated at 37 degrees C for 30 min. Our results indicate that HPMP under the given exposure conditions did not induce DNA strand breaks, alkali-labile sites, and incomplete excision repair sites, which could be detected by the alkaline comet assay.
The Electro Magnetic Response of Human Skin in Submellimeter Frequency Range (2007)

Summary form only given. For more than 50 years a number of phenomena of nonthermal effects (high Q factor resonances) of extremely high frequency microwaves (MMW) on biological systems have been reported. Intriguingly the reported resonant frequencies are virtually absent in natural biological surroundings, making these effect all the more unusual. While some insight has been gained their interpretation has remained controversial. Theoretical ideas discussed in earlier papers in connection with experimental observations have largely proved to be inconclusive, with poor reproducibility and several confounding results. Furthermore there is ample experimental evidence of the beneficiary effects of low power (less than 20 mW/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ) MMW electromagnetic radiation in a number of therapeutic avenues such as coronary artery disease, various cancers, pain relief, wound regeneration and hyper tension. In short, while there has been extensive documentation and some serious theoretical consideration, the true cause of these phenomena remain a mystery. Clearly a more solid indication of the main biophysical mechanism(s) of the observed effects would offer the possibility to truly exploit these beneficial aspects, in a systematic fashion. In current presentation the other possible mechanisms are proposed and there validity is illustrated by experimental data.
Estimation of Phase Shifts in Structured Illumination for High Resolution Imaging (2007)

The application of structured illumination for enhanced resolution requires accurate knowledge of phase shifts in the sinusoidal illumination. This work proposes a method to estimate random, unknown phase shifts and subsequent image reconstruction.
Effect of cytosine arabinoside on the growth and phenotypic expression of GI-ME-N, a new human neuroblastoma cell line. (1988)

Cytosine-arabinoside (ARA-C) effects on a new human neuroblastoma cell line (GI-ME-N), recently established in our laboratory, have been extensively tested. Low doses of ARA-C allowing virtually 100% cell viability induce morphological differentiation and growth inhibition; differentiated cells appear larger and flattened with elongated dendritic processes; such cells appeared within 48 hours after a dose of ARA-C as low as 0.1 microgram/ml. The new morphological aspect reached the maximum expression after 5-6 days of culture being independent of the addition of extra drug to the culture. A decrease in (3H)-thymidine incorporation was also observed within 48 hours being the cell growth completely inhibited at the 6th day. Membrane immunofluorescence with specific monoclonal antibodies showed several dramatic changes in NB-specific antigen expression after 5 days of treatment with ARA-C. These findings suggest that low ARA-C doses promote the differentiation of GI-ME-N neuroblastoma cells resulting in an altered expression of the malignant phenotype.
Comparative shelf life and efficacy of LDPE and PVC degrading bacterial consortia under bioformulation (2011)

The present study elucidates the development of the talc-based formulation for long-term sustenance / storage of bacterial consortia, pertains to degrade polymer (LDPE and PVC). Four potential bacterial consortia were employed which consisted of Microbacterium sp., Pseudomonas putida, P. aeruginosa, P. otitidis, Bacterium Te68R, Bacillus aerius, B. cereus and Acanthopleurobacter pedis. The viability of consortia was ascertained by measuring the colony forming units per mL besides assuring the polymer biodegradation potential after formulation in talc by carrying out in vitro assays. The analysis was done by determination of λ-max shifts and scanning electron microscopy for changes in polymer composition and surface dissolution, respectively. It reveals that using the described formulations, all the consortia were able to successfully retain their characteristic biodegradation property even after 70 days of storage at ambient conditions. Furthermore, the SEM micrographs documented significant disruption of surface texture of polymer (LDPE and PVC) film by respective consortia recovered after storage. Thus, the talc-based formulation may be useful for the storage and handling of polymer-degrading consortia for large-scale applications to minimize the solid waste disposal.

Keywords: biodegradation, bioformulation, talc, consortia, shelf life, LDPE, PVC, SEM
Satellite Lines in the 59Co Resonance in Cobalt-Nickel Alloys (1968)

The distribution of effective field at the 59Co nucleus in alloys of composition CocNi1−c has been studied for c[similar or greater-than]0.93 using an automatic swept frequency spin-echo NMR spectrometer at 4.2°K. Three satellite lines were observed displaced approximately 7.5 MHz, 15 MHz, and 22 MHz below the main line at 217.4 MHz. The intensities of the satellite lines relative to the main line are in good agreement with the probabilities of configurations with one, two, and three nickela toms respectively in the near-neighbor shell. A further partially resolved satellite 2 MHz below the main line was also observed and attributed to nuclei with one nickel atom in the next-nearest neighbor shell and none in the first-neighbor shell. From these measurements it is concluded that the magnetic disturbance produced by a nickel atom in the cobalt lattice is well localized, in agreement with the neutron-diffraction measurements.
Anode hole injection versus hydrogen release: the mechanism for gate oxide breakdown (2002)

Recent studies have shown that post-metallization anneal in deuterium can improve transistor lifetime by one order of magnitude or more. In this paper, we show that the gate oxide reliability of devices annealed in deuterium is similar to that of devices annealed in hydrogen. This finding suggests that a model for gate oxide breakdown which involves release of interfacial hydrogen may not be accurate.
RT-PCR detection of tyrosinase, gp100, MART1/Melan-A, and TRP-2 gene transcripts in peripheral blood of melanoma patients. (2001)

The results we obtained support the use of RT-PCR assay for indirect detection of melanoma cells in peripheral blood of melanoma patients. As the transcripts for the tyrosinase gene and MART-1/Melan A gene were not detected, additional optimization experiments of RT-PCR assay are required.
Compressive Origin-Destination Matrix Estimation (2014)

The paper presents an approach to estimate Origin-Destination (OD) flows and their path splits, based on traffic counts on links in the network. The approach called Compressive Origin-Destination Estimation (CODE) is inspired by Compressive Sensing (CS) techniques. Even though the estimation problem is underdetermined, CODE recovers the unknown variables exactly when the number of alternative paths for each OD pair is small. Noiseless, noisy, and weighted versions of CODE are illustrated for synthetic networks, and with real data for a small region in East Providence. CODE's versatility is suggested by its use to estimate the number of vehicles and the Vehicle-Miles Traveled (VMT) using link counts.
Integrating a Facebook Group with the Open Wonderland environment (2013)

Although broad research has been done on virtual learning environments and the role of communities in social networks, few studies exist which sufficiently support the relationship between these two domains. In this paper, the authors demonstrate the effectiveness of integrating these two environments by creating a novel prototype and conducting a preliminary pilot\nevaluation session. For the prototype system, a Facebook Group was utilised as a repository for learning content and the Open Wonderland platform was selected as a mixed reality intelligent environment for 3D virtual collaborative activities. Finally, this prototype was evaluated by means of a two-hour task-based assessment and user-satisfaction questionnaire.
How many different clonotypes do immune repertoires contain? (2019)

Immune repertoires rely on diversity of T-cell receptors and immunoglobulins to protect us against foreign threats. The ability to recognize a wide variety of pathogens is linked to the number of different clonotypes expressed by an individual. Out of the estimated ∼1012 different B and T cells in humans, how many of them express distinct receptors? We review current and past estimates for these numbers. We point out a fundamental limitation of current methods, which ignore the tail of small clones in the distribution of clone sizes. We show that this tail strongly affects the total number of clones, but it is impractical to access experimentally. We propose that combining statistical models with mechanistic models of lymphocyte clonal dynamics offers possible new strategies for estimating the number of clones.
UTILIZATION OF PLASMA-CELL ENERGY CONVERSION IN NUCLEAR REACTORS (1960)

Our work reveals the mechanisms underlying the enhanced buccal delivery of IPC-DNVs: the DNVs facilitate penetration through the main barrier, and the deposition of IPC enhances buccal absorption. Our results and proposed mechanisms could be an important reference to understand other nanocarriers based on protein (peptide)-phospholipid complexes that penetrate the mucosa and provide a theoretical basis for the future development of buccal delivery systems for insulin.
Platinum Oxoboryl Complexes as Substrates for the Formation of 1:1, 1:2, and 2:1 Lewis Acid–Base Adducts and 1,2‐Dipolar Additions (2015)

The oxoboryl complex trans-[(Cy3 P)2 BrPt(B≡O)] (2) reacts with the Group 13 Lewis acids EBr3 (E=Al, Ga, In) to form the 1:1 Lewis acid-base adducts trans-[(Cy3 P)2 BrPt(B≡OEBr3 )] (6-8). This reactivity can be extended by using two equivalents of the respective Lewis acid EBr3 (E=Al, Ga) to form the 2:1 Lewis acid-base adducts trans-[(Cy3 P)2 (Br3 Al-Br)Pt(B≡OAlBr3 )] (18) and trans-[(Cy3 P)2 (Br3 Ga-Br)Pt(B≡OGaBr3 )] (15). Another reactivity pattern was demonstrated by coordinating two oxoboryl complexes 2 to InBr3 , forming the 1:2 Lewis acid-base adduct trans-[{(Cy3 P)2 BrPt(B≡O)}2 InBr3 ] (20). It was also possible to functionalize the B≡O triple bond itself. Trimethylsilylisothiocyanate reacts with 2 in a 1,2-dipolar addition to form the boryl complex trans-[(Cy3 P)2 BrPt{B(NCS)(OSiMe3 )}] (27).
The cholesterol‐lowering effect of guar gum is not the result of a simple diversion of bile acids toward fecal excretion (1997)

The effects of partially hydrolyzed, nonviscous, guar gum (PHGG) on cholesterol metabolism and digestive balance have been compared with those of native guar gum (GUAR) in rats adapted to 0.4% cholesterol diets. Both types of guar gum elicited acidic fermentations in the large intestine, but only GUAR effectively lowered plasma cholesterol (P < 0.001), chiefly in the triglyceride-rich lipoprotein fraction. The biliary bile acid excretion was significantly enhanced in rats fed GUAR (P < 0.05), as well as the intestinal and cecal bile acid pool (P < 0.001). In rats fed GUAR and to a lesser extent in those fed PHGG, the fecal excretion of bile acids and neutral sterol was higher than in controls (P < 0.01). The digestive balance (cholesterol intake-steroid excretion) was positive in control rats (+47 mumol/d), whereas it was negative in rats fed GUAR (-20 mumol/d), which could involve a higher rate of endogenous cholesterol synthesis. In rats fed PHGG, the steroid balance remained slightly positive. Liver 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) reductase activity was very low (22 pmol/min/mg protein), owing to cholesterol supplementation, in control rats or in rats fed PHGG, whereas it was markedly higher (+463%) in rats fed GUAR. In conclusion, even if PHGG does alter some parameters of the enterohepatic cycle of cholesterol and bile acids, its effects are not sufficient to elicit a significant cholesterol-lowering effect. The intestinal (ileal or cecal) reabsorption of bile acids was not reduced, but rather increased, by GUAR; nevertheless the intestinal capacities of reabsorption were overwhelmed by the enlargement of the digestive pool of bile acids. In the present model, induction of HMG-CoA reductase probably takes place in the presence of elevated portal bile acid concentrations.
True vasculitis in lupus nephritis (2010)

Vascular lesions are encountered frequently in renal biopsy specimens of patients with systemic lupus erythematosus (SLE) and can present in a variety of morphologic forms. True renal lupus vasculitis (TRLV) is one of the rare vascular lesions associated with lupus nephritis that has been infrequently reported in the medical literature. The primary focus on glomerular pathology and collective classification of the vascular lesions under lupus vasculopathy is one of the reasons why this form of inflammatory vasculitis has been under-recognized as a separate disease entity. Here we have comprehensively reviewed the literature on renal vascular involvement in SLE for a better understanding of the epidemiology, morphologic features, pathogenesis, clinical course and treatment of TRLV. It can be morphologically differentiated from other forms of renal vascular lesions in lupus nephritis, i.e. arteriosclerosis, uncomplicated vascular immune deposits, non-inflammatory necrotizing vasculopathy, and thrombotic microangiopathy. Despite close similarities with antineutrophil cytoplasmic autoantibody associated vasculitis (AASV), there are certain morphological differences that warrant a thorough investigation of the possible pauci-immune mechanism of pathogenesis. The vasculitis follows a severe clinical course in general with rapid progression to renal failure, although favorable outcomes have been reported in certain cases. The standard use of steroids and cytotoxic drugs has yielded variable results in the treatment of TRLV. Current treatment modalities being used in lupus nephritis and AASV have been compared in this article with focus on drugs acting on the inflammatory cells implicated in TRLV pathogenesis.
P28.09: Novel automatic method for measuring fetal arm adipose tissue in 2D ultrasound images across gestation (2012)

To develop and evaluate a new clinical tool to automatically measure fetal arm adipose tissue area in a transverse section at mid-humeral level on 2D ultrasound images across a range of gestational ages. Fetal arm adipose tissue was automatically measured on 20 cross-sectional ultrasound images at mid-humeral level from optimally healthy fetuses between 21 and 31 weeks of gestation using a novel image analysis measurement tool. The measurement tool is based on a feature-based strategy, which makes use of structural and edge information to delineate the tissue boundaries. A shape-based strategy is used to complete the missing information in the shadowed area under the humerus bone. The final estimation of the adipose tissue layer is obtained after a contour smoothing step. The new methodology was compared to manual delineations, measured twice by the same expert on each of the 20 images. The differences between automatic and the first set of manual measurements were assessed using a Bland-Altman plot obtaining a mean of − 39.27 mm2 (−20.46%) and a standard deviation of 32.32 mm2. Compared to the second set of manual measurements the mean error was − 25.85 mm2 (−10.24%) with a standard deviation of 28.70 mm2. Good correlation of the automatic method with respect to manual delineations was observed across gestation. This method has the potential as an automated quantitative tool for assessment of fetal arm fat thickness. Supporting information can be found in the online version of this abstract. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.