gebhart/patrepeval huggingface dataset:
Microdilution antifungal susceptibility testing of Candida albicans and Cryptococcus neoformans with and without agitation: an eight-center collaborative study (1996)

The growth patterns observed in the trailing wells when fluconazole is being tested may give rise to readings that suggest resistance or increased MICs for known susceptible strains. We conducted a multicenter study to evaluate the intralaboratory and interlaboratory reproducibilities of a method that uses agitation to disperse these types of growth. Ten strains of Candida albicans and five strains of Cryptococcus neoformans were tested against fluconazole, flucytosine, and amphotericin B by using a microdilution adaptation of the proposed reference method of the National Committee for Clinical Laboratory Standards for yeasts (M27-T). The endpoint criterion used before agitation was consistent with the M27-T recommendation, while a criterion of 50% or more reduction of growth compared with the control was used after agitation. The results of this study showed that use of agitation and the modified endpoint criterion both improved intralaboratory and inter-laboratory agreement and increased the frequency of interpretable MICs. The MICs obtained by this method were comparable to those obtained by the broth macrodilution M27-T method. Like M27-T, this method was not able to definitely distinguish amphotericin B-susceptible from -resistant strains, although the MICs for the resistant strains were consistently higher than those for the susceptible ones. The findings imply that agitation should be seriously considered when antifungal agents, particularly fluconazole, are tested in a microdilution format.
Azaphilones, Furanoisophthalides, and Amino Acids from the Extracts of <i>Monascus pilosus</i>-Fermented Rice (Red-Mold Rice) and Their Chemopreventive Effects (2005)

Six azaphilones, monascin (1), ankaflavin (2), rubropunctatin (3), monascorburin (4), rubropunctamine (5), and monascorburamine (6), two furanoisophthalides, xanthomonasin A (7) and xanthomonasin B (8), and two amino acids, (+)-monascumic acid (9) and (-)-monascumic acid (10), isolated from the extracts of Monascus pilosus-fermented rice (red-mold rice) were evaluated for their inhibitory effects on 12-O-tetradecanoylphorbol-13-acetate (TPA)-induced inflammation in mice, on the induction of Epstein-Barr virus early antigen (EBV-EA) by TPA in Raji cells, and on the activation of (+/-)-(E)-methyl-2[(E)-hydroxy-imino]-5-nitro-6-methoxy-3-hexemide (NOR 1), a nitric oxide (NO) donor. Among the compounds tested, seven compounds (1-6 and 10) on TPA-induced inflammation, and six compounds (1, 3-5, 9, and 10) on EBV-EA activation, exhibited potent inhibitory effects. All of the compounds tested showed moderate inhibitory effects on NOR 1 activation.
Measurement of the Cyanophycin Granule Polypeptide Contained in the Blue-Green Alga <i>Anabaena cylindrica</i> (1973)

An assay was developed to determine the amount of cyanophycin granules in blue-green algae. The amount of this polypeptide in cells of Anabaena cylindrica was measured as a function of culture age and was compared with changes in other proteinaceous cellular components. The data presented support the notion that the cyanophycin granule is a cellular nitrogen reserve.
Antiproliferative and Antiangiogenic Activities of Smenospongine, a Marine Sponge Sesquiterpene Aminoquinone (2011)

We previously reported that smenospongine, a sesquiterpene aminoquinone isolated from the marine sponge Dactylospongia elegans, showed antiproliferative or cytotoxic activities on leukemia cells. In this study, we investigated the effect of smenospongine on solid tumors. Since angiogenesis is well known to be closely involved in growth and metastasis of solid tumors, the antiangiogenic effect of smenospongine was determined. We found that smenospongine inhibited proliferation, migration and tube formation of human umbilical vein endothelial cells (HUVEC). Moreover, the inhibitory activity of smenospongine on growth of solid tumor cells was investigated. Smenospongine inhibited the growth of 39 human solid cancer cells in vitro, with a mean Log GI(50) value of -5.55. In conclusion, smenospongine exhibits antitumor activity on solid tumors via two mechanisms, an antiangiogenic effect on endothelial cells and direct inhibition of growth of tumor cells.
Variable-PRI processing for meteorologic Doppler radars (2002)

In this communication we described how, with nonuniform sampling, the concept of bandlimited extrapolation can be used to obtain unambiguous Doppler velocity estimates in the supra-Nyquist region. The proposed method coherently processes a multi-PRI sample using a generalized form of periodogram analysis. The work is described in the context of meteorologic Doppler processing and includes a discussion of effective suppression for stationary ground clutter when multi-PRI schemes are used.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Hydration of carboxamides. Evaluation of the free energy change for addition of water to acetamide and formamide derivatives (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHydration of carboxamides. Evaluation of the free energy change for addition of water to acetamide and formamide derivativesJ. Peter GuthrieCite this: J. Am. Chem. Soc. 1974, 96, 11, 3608–3615Publication Date (Print):May 1, 1974Publication History Published online1 May 2002Published inissue 1 May 1974https://pubs.acs.org/doi/10.1021/ja00818a039https://doi.org/10.1021/ja00818a039research-articleACS PublicationsRequest reuse permissionsArticle Views565Altmetric-Citations82LEARN 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
The timing of TCRα expression critically influences T cell development and selection (2005)

Sequential rearrangement of the T cell receptor for antigen (TCR) beta and alpha chains is a hallmark of thymocyte development. This temporal control is lost in TCR transgenics because the alpha chain is expressed prematurely at the CD4- CD8- double negative (DN) stage. To test the importance of this, we expressed the HY alpha chain at the physiological CD4+ CD8+ double positive (DP) stage. The reduced DP and increased DN cellularity typically seen in TCR transgenics was not observed when the alpha chain was expressed at the appropriate stage. Surprisingly, antigen-driven selection events were also altered. In male mice, thymocyte deletion now occurred at the single positive or medullary stage. In addition, no expansion of CD8 alpha alpha intestinal intraepithelial lymphocytes (IELs) was observed, despite the fact that HY transgenics have been used to model IEL development. Collectively, these data establish the importance of proper timing of TCR expression in thymic development and selection and emphasize the need to use models that most accurately reflect the physiologic process.
Survival of GacS/GacA Mutants of the Biological Control Bacterium <i>Pseudomonas aureofaciens</i> 30-84 in the Wheat Rhizosphere (2002)

GacS/GacA comprises a two-component regulatory system that controls the expression of secondary metabolites required for the control of plant diseases in many pseudomonads. High mutation frequencies of gacS and gacA have been observed in liquid culture. We examined whether gacS/gacA mutants could competitively displace the wild-type populations on roots and thus pose a threat to the efficacy of biological control. The survival of a gac mutant alone and in competition with the wild type on roots was examined in the biological control strain Pseudomonas aureofaciens 30-84. In this bacterium, GacS/GacA controls the expression of phenazine antibiotics that are inhibitory to plant pathogenic fungi and enhance the competitive survival of the bacterium. Wheat seedlings were inoculated with strain 30-84, and bacteria were recovered from roots after 21 days in sterile or nonsterile soil to check for the presence of gacS or gacA mutants. Although no mutants were detected in the inoculum, gacS/gacA mutants were recovered from 29 out of 31 roots and comprised up to 36% of the total bacterial populations. Southern hybridization analysis of the recovered gacA mutants did not indicate a conserved mutational mechanism. Replacement series analysis on roots utilizing strain 30-84 and a gacA mutant (30-84.gacA) or a gacS mutant (30-84.A2) demonstrated that although the mutant population partially displaced the wild type in sterile soil, it did not do so in natural soil. In fact, in natural soil final rhizosphere populations of wild-type strain 30-84 starting from mixtures were at least 1.5 times larger than would be predicted from their inoculation ratio and generally were greater than or equal to the population of wild type alone despite lower inoculation rates. These results indicate that although gacS/gacA mutants survive in natural rhizosphere populations, they do not displace wild-type populations. Better survival of wild-type populations in mixtures with mutants suggests that mutants arising de novo or introduced within the inoculum may be beneficial for the survival of wild-type populations in the rhizosphere.
A Robust Automatic Dip Picking Technique to Improve Geological Interpretation and Post-Drill Formation Evaluation of Azimuthal Wellbore Image Logs (2015)

Abstract Automatic dip picking avoids the disadvantages of hand picking (subjective, time-consuming, and ergonomically unfriendly); in particular, it reduces dip uncertainty for low-resolution borehole images. Many automatic dip picking methods have been developed since the 1950's. Each of these methods is tied to a specific type of tool (e.g., dipmeter tools or partial-wellbore-coverage pad-type imagers), and they are unreliable to process high-angle and horizontal (HAHz) wellbore azimuthal image data. This article presents a new method to detect dips in HAHz borehole images. Although this method was originally designed for full wellbore azimuthal images, it is applicable to any dipmeter and pad-type image logs. The proposed automatic dip picking method is simple, yet robust. It consists of the following three main steps: first, determine an optimal sinusoidal trend on the image at each depth using a minimum-variance technique; second, compute the contrast at each depth along the optimal sinusoidal line on the gradient (or first-derivative) image; and finally, locate bedding surface boundaries at depths with the highest contrasts. This method emulates the human pattern recognition process by first observing overall global image sinusoidal trends, and then examining detailed local bed contrasts to locate the bed boundaries. Conventional pattern fitting methods using edge detection and Hough transform (or sinewave fitting) can be unreliable and greatly affected by the noise and artifacts on the image, as these methods focus immediately on detailed and localized image features, and often overlook global image patterns. Although other correlation techniques have been tested, the minimum-variance method is the preferred approach, for it generates the most consistent sinewaves. It correlates all azimuthal bins simultaneously and is much more reliable than two-curve correlation methods. Since the variances are calculated along sinusoidal lines, there is no need to perform individual sinewave fitting. The minimum-variance method combines the conventional, complicated, two-step dipmeter processing methodology (first curve correlation, then sinewave fitting) into one single step to determine an optimal local sinewave. With fewer steps, there are fewer scenarios and problems to consider and fewer parameters to adjust. Moreover, at each depth, the minimum-variance method can find the optimal sinewave within a full range of search parameters (sinusoid amplitude and phase). It can identify faults if visible, as well as reversed sinewaves in “bulls-eye” sections where the wellbore axis is almost parallel to the bedding planes. The proposed method has been applied to many logging-while-drilling density images and dipmeter data from fields worldwide. It has substantially reduced the interpretational time in building earth models from image logs for logging tool response modeling in petrophysical evaluation.
Regulatory Networks Revealed by Transcriptional Profiling of Damaged <i>Saccharomyces cerevisiae</i> Cells: Rpn4 Links Base Excision Repair with Proteasomes (2000)

Exposure to carcinogenic alkylating agents, oxidizing agents, and ionizing radiation modulates transcript levels for over one third of Saccharomyces cerevisiae's 6,200 genes. Computational analysis delineates groups of coregulated genes whose upstream regions bear known and novel regulatory sequence motifs. One group of coregulated genes contain a number of DNA excision repair genes (including the MAG1 3-methyladenine DNA glycosylase gene) and a large selection of protein degradation genes. Moreover, transcription of these genes is modulated by the proteasome-associated protein Rpn4, most likely via its binding to MAG1 upstream repressor sequence 2-like elements, that turn out to be almost identical to the recently identified proteasome-associated control element (G. Mannhaupt, R. Schnall, V. Karpov, I. Vetter, and H. Feldmann, FEBS Lett. 450:27-34, 1999). We have identified a large number of genes whose transcription is influenced by Rpn4p.
Absence of Fer protein tyrosine kinase exacerbates endotoxin induced intestinal epithelial barrier dysfunction in vivo (2005)

Fer plays a role in regulating LPS induced epithelial barrier dysfunction in vivo through both neutrophil dependent and neutrophil independent mechanisms.
Study on Machine Learning Based Intelligent Defect Detection System (2018)

In the paper, it is proposed to develop a machine learning based intelligent defect detection system for metal products. The common machine vision system has the surface (stain, shallow pit, shallow tumor, scratches, Edge defects, pattern defects) detection, or for the processing of the size, diameter, diameter, eccentricity, height, thickness and other parts of the non-contact numerical parameters of detection. Considering the quality of the work piece and the defects of the standard, so for the quality of customized testing requirements, the study is the development of machine vision and machine learning metal products defect detection system, mainly composed of three procedures: Image preprocessing, training procedures and testing procedures. The system architecture consists of three parts: (1) Image preprocessing: we first use the machine vision. OPENCV to carry out the image pre-processing part of the product before the detection. (2) Training procedures: The algorithm of the machine learning includes the convolution neural network (CNN), chunk-max pooling is used to train the program, and the generative adversarial network (GAN) based architecture is used to solve the problem of small datasets for surface defects. (3) Testing procedures：The Python language is used to write the program and implement the testing procedures with the GPU-Based embedded hardware In industries, collecting training dataset is usually costly and related methods are highly dataset-dependent. So most companies cannot provide Big-data to be analyzed or applied. By the experimental results, the recognition accuracy can be obviously improved as increasing data augmentation by GAN-Based samples maker. Manual inspection is labor intensive, costly and less in efficiency. Therefore, this study will contribute to technological innovation, industry, national development and other applications. (1) The use of intelligent machine learning technology will make the industry 4.0 technology more sophisticated. (2) It will make the development of equipment industry be better by the machine learning applications. (3) It will increase the economics and productivity of countries for the aging of the population by machine learning.
An Outsider's View (2007)

An Outsider's View looks at magazines from the point of view of someone who does not enjoy magazines.
A Freeze Frame View of Vesicular Stomatitis Virus Transcription Defines a Minimal Length of RNA for 5′ Processing (2011)

The RNA synthesis machinery of vesicular stomatitis virus (VSV) comprises the genomic RNA encapsidated by the viral nucleocapsid protein (N) and associated with the RNA dependent RNA polymerase, the viral components of which are a large protein (L) and an accessory phosphoprotein (P). The 241 kDa L protein contains all the enzymatic activities necessary for synthesis of the viral mRNAs, including capping, cap methylation and polyadenylation. Those RNA processing reactions are intimately coordinated with nucleotide polymerization such that failure to cap results in termination of transcription and failure to methylate can result in hyper polyadenylation. The mRNA processing reactions thus serve as a critical check point in viral RNA synthesis which may control the synthesis of incorrectly modified RNAs. Here, we report the length at which viral transcripts first gain access to the capping machinery during synthesis. By reconstitution of transcription in vitro with highly purified recombinant polymerase and engineered templates in which we omitted sites for incorporation of UTP, we found that transcripts that were 30-nucleotides in length were uncapped, whereas those that were 31-nucleotides in length contained a cap structure. The minimal RNA length required for mRNA cap addition was also sufficient for methylation since the 31-nucleotide long transcripts were methylated at both ribose-2'-O and guanine-N-7 positions. This work provides insights into the spatial relationship between the active sites for the RNA dependent RNA polymerase and polyribonucleotidyltransferase responsible for capping of the viral RNA. We combine the present findings with our recently described electron microscopic structure of the VSV polymerase and propose a model of how the spatial arrangement of the capping activities of L may influence nucleotide polymerization.
B Cell–Intrinsic and –Extrinsic Regulation of Antibody Responses by PARP14, an Intracellular (ADP-Ribosyl)Transferase (2013)

The capacity to achieve sufficient concentrations of Ag-specific Ab of the appropriate isotypes is a critical component of immunity that requires efficient differentiation and interactions of Ag-specific B and Th cells along with dendritic cells. Numerous bacterial toxins catalyze mono(ADP-ribosyl)ation of mammalian proteins to influence cell physiology and adaptive immunity. However, little is known about biological functions of intracellular mammalian mono(ADP-ribosyl)transferases, such as any ability to regulate Ab responses. poly-(ADP-ribose) polymerase 14 (PARP14), an intracellular protein highly expressed in lymphoid cells, binds to STAT6 and encodes a catalytic domain with mammalian mono(ADP-ribosyl)transferase activity. In this article, we show that recall IgA as well as the STAT6-dependent IgE Ab responses are impaired in PARP14-deficient mice. Whereas PARP14 regulation of IgE involved a B cell-intrinsic process, the predominant impact on IgA was B cell extrinsic. Of note, PARP14 deficiency reduced the levels of Th17 cells and CD103⁺ DCs, which are implicated in IgA regulation. PARP14 enhanced the expression of RORα, Runx1, and Smad3 after T cell activation, and, importantly, its catalytic activity of PARP14 promoted Th17 differentiation. Collectively, the findings show that PARP14 influences the class distribution, affinity repertoire, and recall capacity of Ab responses in mice, as well as provide direct evidence of the requirement for protein mono-ADP-ribosylation in Th cell differentiation.
<title>Design and implementation issues in VPL: visual language for image processing</title> (1992)

VPL 1.0 is a visual programming language for image processing. It uses a lazy functional programming paradigm, expressed with a box-and-arc representation. In the current version of the system, the image processing functionality is provided by VIEW-Station, an image processing library developed in one of Canon's Japanese laboratories. Some of the notable features of the system are: the program is always 'live'; higher-order functions are allowed; and the visual language interface and evaluation modules are designed to connect easily to (most) C++ or ANSI-C image processing libraries. This paper discusses the advantages and disadvantages of these design decisions. It also discusses some of the resulting implementation issues, and the solutions adopted. Specific topics covered include: the use of higher-order functions in image processing; what type-checking would be desirable for image processing in a visual language environment; what type-checking is feasible when the visual language environment is used as a front-end to a C++ library; and the advantages and disadvantages of having the image processing sub-system fully integrated.
Practically realizable digital transmission significantly below the Nyquist bandwidth (1995)

Proposes a practically realizable digital signaling scheme that requires a bandwidth significantly below the Nyquist limit, and at the same time achieves the same asymptotic performance as memoryless PAM. A five-step iterative procedure for constructing such schemes is presented, and examples that occupy down to about 60 percent of the Nyquist bandwidth are demonstrated using this simple procedure. Practical receiver structures are also briefly discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Prostasin, A Potential Tumor Marker in Ovarian Cancer- A Pilot Study (2009)

These findings indicate that prostasin is overexpressed in many epithelial ovarian cancers. Further studies of prostasin as a potential biomarker for this disease are warranted.