gebhart/patrepeval huggingface dataset:
A simple approach to using an amorphous silicon EPID to verify IMRT planar dose maps (2009)

A simplified method of verifying intensity modulated radiation therapy (IMRT) fields using a Varian aS500 amorphous silicon electronic portal imaging device (EPID) is demonstrated. Unlike previous approaches, it does not involve time consuming or complicated analytical processing of the data. The central axis pixel response of the EPID, as well as the profile characteristics obtained from images acquired with a 6 MV photon beam, was examined as a function of field size. Ion chamber measurements at various depths in a water phantom were then collected and it was found that at a specific depth d(ref), the dose response and profile characteristics closely matched the results of the EPID analysis. The only manipulation required to be performed on the EPID images was the multiplication of a matrix of off axis ratio values to remove the effect of the flood field calibration. Similarly, d(ref) was found for 18 MV. Planar dose maps at d(ref) in a water phantom for a bar pattern, a strip pattern, and 14 clinical IMRT fields from two patient cases each being from a separate anatomical region, i.e., head and neck as well as the pelvis, for both energies were generated by the Pinnacle planning system (V7.4). EPID images of these fields were acquired and converted to planar dose maps and compared directly with the Pinnacle planar dose maps. Radiographic film dosimetry and a MapCHECK dosimetry device (Sun Nuclear Corporation, Melbourne, FL) were used as an independent verification of the dose distribution. Gamma analysis of the EPID, film, and Pinnacle planar dose maps generated for the clinical IMRT fields showed that approximately 97% of all points passed using a 3% dose/3 mm DTA tolerance test. Based on the range of fields studied, the author's results appear to justify using this approach as a method to verify dose distributions calculated on a treatment planning system, including complex intensity modulated fields.
PPNEMA: A Resource of Plant-Parasitic Nematodes Multialigned Ribosomal Cistrons (2008)

Plant-parasitic nematodes are important pests of crop plants worldwide, and also among the most difficult animals to identify. Their identification based on nuclear ribosomal DNA (rDNA) cistron (18S, 28S, and 5.8S RNA genes, and internal transcribed spacers, ITS1 and ITS2) is becoming a popular tool. Sequences from nuclear ribosomal RNA repeats have been used to demonstrate the identity of isolates from various hosts and to unravel the relationships of cryptic and complex species. In addition, the availability of RNA sequences allows study of phylogenetic relationships between nematodes, also for more complete understanding of their biology as agricultural pests. PPNEMA is a plant-parasitic nematode bioinformatic resource. It consists of a database of ribosomal cistron sequences from various species grouped according to nematode genera, and a search system allowing data to be extracted according to both text and pattern searching. PPNEMA offers to the scientific community a preprocessed archive of plant parasitic nematode sequences useful for nematologists. It is a tool to retrieve plant nematode multialigned sequences for phylogenetic studies or to recognize a nematode by comparing its rDNA sequence with the PPNEMA available genus specific multialignments.
CRISPR‐Cas9 Genome Editing in <i>Drosophila</i> (2015)

The CRISPR-Cas9 system has transformed genome engineering of model organisms from possible to practical. CRISPR-Cas9 can be readily programmed to generate sequence-specific double-strand breaks that disrupt targeted loci when repaired by error-prone non-homologous end joining (NHEJ) or to catalyze precise genome modification through homology-directed repair (HDR). Here we describe a streamlined approach for rapid and highly efficient engineering of the Drosophila genome via CRISPR-Cas9-mediated HDR. In this approach, transgenic flies expressing Cas9 are injected with plasmids to express guide RNAs (gRNAs) and positively marked donor templates. We detail target-site selection; gRNA plasmid generation; donor template design and construction; and the generation, identification, and molecular confirmation of engineered lines. We also present alternative approaches and highlight key considerations for experimental design. The approach outlined here can be used to rapidly and reliably generate a variety of engineered modifications, including genomic deletions and replacements, precise sequence edits, and incorporation of protein tags.
[Simultaneous determination of total flavone and total saponin in Gynostemma pentaphyllum by signal multiplier spectrophotometry]. (2006)

Important chemical constituents analysis for the total flavone and total saponin in Gynostemma pentaphyllum is described. The colour reactions of flavones and saponines with vanillin-perchloric acid in acetic acid produced the good absorptions at 451 and 547 nm, but the absorption peaks too overlapped to be determined simultaneously. A new method for the total flavone and the total saponin in Gynostemma pentaphyllum to be determined by signal multiplier spectrophotometry simultaneously without any preliminary separation was proposed. For quantitative analysis, the rutinum as a standard of the total flavone and the ginsenoside Rb1 as standard of the total saponin were applied. The experiment results showed that the regression equations of concentration and deltaA were obtained: deltaAflavone = 0.0133+4.417 0Cflavone, relation coefficient rflavone = 0.9994, and the total flavone concentrations were in 0-0. 16 microg x mI(-1) with deltaA obeying linear relation; deltaAsaporin = 2.775 5Csaponin -0.8881 x 10(-2), relation coefficient rsaponin = 0.9991, and the total saponin concentrations were in 0-0.30 microg x mL(-1) with deltaA obeying linear relation respectively. The recovery ratio was 104.0%-113.0% and 86.8%-94.6% respectively. The RSDflavone was less than 0.58% (n = 9) and RSDsaponin was less than 0. 35% (n=9) respectively. The proposed method is simple, rapid accurate and feasible.
A Study of Methods for Constructing Photographic Emulsion Characteristic Curves (1948)

The purpose of this discussion will be to study various techniques that have been developed for the construction of emulsion characteristic curves, with special emphasis of the Two Line Method.
Cystine-Glutamate Transporter <i>SLC7A11</i> in Cancer Chemosensitivity and Chemoresistance (2005)

SLC7A11 (xCT), together with SLC3A2 (4F2hc), encodes the heterodimeric amino acid transport system x(c)-, which mediates cystine-glutamate exchange and thereby regulates intracellular glutathione levels. We used microarrays to analyze gene expression of transporters in 60 human cancer cell lines used by the National Cancer Institute for drug screening (NCI-60). The expression of SLC7A11 showed significant correlation with that of SLC3A2 (r = 0.66), which in turn correlated with SLC7A5 (r = 0.68), another known partner for SLC3A2, and with T1A-2 (r = 0.60; all P < 0.0001). Linking expression of SLC7A11 with potency of 1,400 candidate anticancer drugs identified 39 showing positive correlations, e.g., amino acid analogue, L-alanosine, and 296 with negative correlations, e.g., geldanamycin. However, no significant correlation was observed with the geldanamycin analogue 17-allylamino, 17-demethoxygeldanamycin (17-AAG). Inhibition of transport system x(c)- with glutamate or (S)-4-carboxyphenylglycine in lung A549 and HOP-62, and ovarian SK-OV-3 cells, reduced the potency of L-alanosine and lowered intracellular glutathione levels. This further resulted in increased potency of geldanamycin, with no effect on 17-AAG. Down-regulation of SLC7A11 by small interfering RNA affected drug potencies similarly to transport inhibitors. The inhibitor of gamma-glutamylcysteine synthetase, buthionine sulfoximine, also decreased intracellular glutathione levels and enhanced potency of geldanamycin, but did not affect L-alanosine. These results indicate that SLC7A11 mediates cellular uptake of L-alanosine but confers resistance to geldanamycin by supplying cystine for glutathione maintenance. SLC7A11 expression could serve as a predictor of cellular response to L-alanosine and glutathione-mediated resistance to geldanamycin, yielding a potential target for increasing chemosensitivity to multiple drugs.
A moist, odour-free environment. A multicentred trial of a foamed gel and a hydrocolloid dressing. (1992)

Exuding wounds such as leg ulcers present special problems. A clinical trial of a new foamed gel dressing showed that it provides a moist healing environment without unacceptable odour, and improves the condition of the wound when compared to a hydrocolloid dressing.
Unsaturated Flow through a Small Fracture-Matrix Network: Part 1. Experimental Observations (2004)

The behavior of unsaturated flow was investigated in a laboratory model. A constant and uniform supply of chemically equilibrated water was introduced to the upper surface of three artificial fractures in a surrogate fracture network consisting of a thin wall of uncemented limestone blocks. Water was collected from the lower boundary via fiberglass wicks placed at the bottom of each artificial fracture. Eight experiments were conducted to evaluate the repeatability of flow under nearly identical conditions and to characterize general patterns in flow behavior. Collected data revealed that flow generally converged to a single fracture in the bottom row of blocks. Periods of pathway switching were observed to be more common than periods with steady, constant flow pathways. We noted the importance of fracture intersections for integrating uniform flow and discharging a cascade, where water advances rapidly to the next capillary barrier creating a stop and start advance of water through the network. Under very similar initial moisture and boundary conditions, flow in the system was less repeatable than expected. The results of this simple experiment suggest that the interaction of multiple fracture intersections in a network creates flow behavior not generally recognized in popular conceptual and numerical models, (i.e., convergence of flow, pathway switching, and fluid cascades).
[The specificity of the mechanisms regulating hematopoiesis under different extreme exposures]. (1991)

The reactions of the hematopoietic tissue and the mechanisms of their development were studied in rats during blood loss and when they were suspended on the neck fold. The mechanisms of hematopoiesis regulation were found to be similar in principle in exposure to different stresses: activation of the erythropoietin system and increase of blood serum colony-stimulating activity occurred in both cases.
Continuous Wave Laser Damage On Optical Components (1983)

Continuous wave laser damage on optical components is a major problem encountered in the operation of high energy chemical lasers. Although the damage phenomena on cooled and uncooled optical components are very similar to those on pulsed laser devices, mechanisms of damage are different. Unlike pulsed laser systems, maintenance of optical figure due to thermal distortion becomes an important aspect of the complete optical train for a device that may be required to operate for a number of seconds. This paper deals with damage mechanisms on cooled and uncooled optical components and how the damage may be predicted. Further, predictive tools for determining the thermal and mechanical forces that operate on optical components to induce distortions in the optical train are evaluated.
REACT - A Process for Improving Open-Source Software Reuse (2018)

Software reuse is a popular practice, which is constantly gaining ground among practitioners. The main reason for this is the potential that it provides for reducing development effort and increasing the end-product quality. At the same time, Open-Source Software (OSS) repositories are nowadays flourishing and can facilitate the reuse process, through the provision of a variety of software artifacts. However, up-to-date OSS reuse processes have mostly been opportunistic, leading to not fully capitalizing existing reuse potentials. In this study we propose a process (namely REACT) for improving planned OSS reuse practices, i.e., we define the activities that a software engineer can perform to reuse OSS artifacts. To illustrate the applicability of REACT, we provide an example, in which a mobile application is developed based upon the reuse of OSS artifacts. To validate the proposed process we compared the effort required to develop the application with and without adapting REACT process. Our preliminary results suggest that REACT may reduce up to 50% the effort required to build an application from scratch.
Clinical application of a new endoscopic technique for detection of in situ bronchial carcinoma. (1979)

Hematoporphyrin is preferentially concentrated by cancer tissue and therefore is a potentially useful chemical marker. This report demonstrates the effectiveness of a photoelectric hematoporphyrin fluorescence detector used simultaneously with flexible fiberoptic bronchoscopy as a means of detecting and localizing bronchogenic carcinoma. The detector generates an audio signal when fluorescence is within the visual field of the bronchoscope. Of interest is that an audio signal was generated which indicated hematoporphyrin fluorescence in areas where no mucosal abnormality had been seen. These areas proved to be carcinoma in situ.
Reactions of the xenon(3P1) and krypton(3P1) resonance states with halogen donor molecules (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReactions of the xenon(3P1) and krypton(3P1) resonance states with halogen donor moleculesH. C. Brashears Jr. and D. W. SetserCite this: J. Phys. Chem. 1980, 84, 2, 224–226Publication Date (Print):January 1, 1980Publication History Published online1 May 2002Published inissue 1 January 1980https://pubs.acs.org/doi/10.1021/j100439a020https://doi.org/10.1021/j100439a020research-articleACS PublicationsRequest reuse permissionsArticle Views37Altmetric-Citations31LEARN 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 options Get e-Alerts
Cell-Type Specific Posttranslational Processing of Peptides by Different Pituitary Cell Lines* (1990)

In order to compare prohormone processing in two distinct pituitary cell types, somatomammotrope cells (GH3) and corticotrope cells (AtT-20) were stably transfected with vectors encoding preproneuropeptide Y (preproNPY) containing four different pairs of basic amino acids at the single endoproteolytic cleavage site: wildtype or KR (lysine-arginine), RR, RK, and KK. The GH-NPY cell lines cleaved proNPY to a similar extent, regardless of the sequence of the basic amino acids at the cleavage site (KR = RR = RK = KK). AtT-20-NPY cells are known to exhibit a strong hierarchy of cleavage site preference when processing wildtype and mutated proNPY forms (KR = RR greater than RK much greater than KK). All four types of GH-NPY and AtT-NPY cells faithfully produced NPY (1-36) NH2 from proNPY (1-69), regardless of the amino acid sequence at the cleavage site. All four types of GH-NPY cells produced some of the expected proNPY-COOH-terminal peptide with Ser40 at its NH2-terminal [proNPY (40-69)]. GH3 cells expressing the RR, RK, and KK forms of proNPY yielded in addition some proNPY-COOH-terminal peptide retaining the amino terminals Lys39 or Arg39 residue. In contrast, AtT-NPY-RK cells produced only the Lys39 form of proNPY-COOH-terminal peptide while the other three AtT-NPY lines (KR, RR, and KK) produced only the Ser40 form of proNPY-COOH-terminal peptide. The residence time of proNPY and NPY in GH3 cells was dramatically increased by treatment with insulin, estradiol, and epidermal growth factor, in concert with the expected increase in PRL synthesis and decrease in GH synthesis; increased residence time in the cells did not result in an increase in the extent of cleavage of proNPY to NPY. AtT-20 cells did not respond to the somatomammotrope-specific set of hormones. Thus, there are several important differences in the posttranslational processing and storage of peptide hormones in corticotropes and somatomammotropes.
Copolymerization of vinyl acetate with 1‐octene and ethylene by cobalt‐mediated radical polymerization (2007)

Abstract The cobalt‐mediated radical polymerization of vinyl acetate was extended to copolymerization with 1‐alkenes (ethylene or 1‐octene). In agreement with the low amount of 1‐alkene that could be incorporated into the copolymer, a gradient structure was predictable, but a rather low polydispersity was observed. A poly(vinyl acetate)‐ b ‐poly(octene) copolymer was also successfully synthesized, leading to a poly (vinyl alcohol)‐ b ‐poly(octene) amphiphilic copolymer upon the methanolysis of the poly (vinyl acetate) block. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 2532–2542, 2007
Chromogenic and fluorogenic indicators and substrates in diagnostic microbiology (1993)

Summary The biochemical activity of bacteria can be detected by a change in the light absorption of product/substrate or the reaction of either with an indicator. Microbiology can make use of the advances in inorganic chemistry applied to other specialities for the development of novel indicators. Compounds have been developed that yield brightly coloured or fluorescent products when acted on by bacterial enzymes or when reacted with specific bacterial metabolites. The new compounds produce rapid results which are clearly seen and which are often more specific than previous methods. Improvement in the heat stability of reagents and their use in simple tests is bringing the greater use of these newer indicators into the clinical microbiology laboratory, although their chemical structure may be retained by the manufacturer. The aim of this review is to give a brief overview of the expanding chemistry currently available and highlight areas where developments are to be expected.
Influence of the Lactose Plasmid on the Metabolism of Galactose by <i>Streptococcus lactis</i> (1979)

Streptococcus lactis strain DR1251 was capable of growth on lactose and galactose with generation times, at 30 degrees C, of 42 and 52 min, respectively. Phosphoenolpyruvate-dependent phosphotransferase activity for lactose and galactose was induced during growth on either substrate. This activity had an apparent K(m) of 5 x 10(-5) M for lactose and 2 x 10(-2) M for galactose. beta-d-Phosphogalactoside galactohydrolase activity was synthesized constitutively by these cells. Strain DR1251 lost the ability to grow on lactose at a high frequency when incubated at 37 degrees C with glucose as the growth substrate. Loss of ability to metabolize lactose was accompanied by the loss of a 32-megadalton plasmid, pDR(1), and Lac(-) isolates did not revert to a Lac(+) phenotype. Lac(-) strains were able to grow on galactose but with a longer generation time. Galactose-grown Lac(-) strains were deficient in beta-d-phosphogalactoside galactohydrolase activity and phosphoenolpyruvate phosphotransferase activity for both lactose and galactose. There was also a shift from a predominantly homolactic to a heterolactic fermentation and a fivefold increase in galactokinase activity, relative to the Lac(+) parent strain grown on galactose. These results suggest that S. lactis strain DR1251 metabolizes galactose primarily via the tagatose-6-phosphate pathway, using a lactose phosphoenolpyruvate phosphotransferase activity to transport this substrate into the cell. Lac(-) derivatives of strain DR1251, deficient in the lactose phosphoenolpyruvate phosphotransferase activity, appeared to utilize galactose via the Leloir pathway.
Clear Cell Renal Cell Carcinoma is linked to Epithelial-to-Mesenchymal Transition and to Fibrosis (2017)

Clear cell renal cell carcinoma (ccRCC) represents the most common type of kidney cancer with high mortality in its advanced stages. Our study aim was to explore the correlation between tumor epithelial-to-mesenchymal transition (EMT) and patient survival. Renal biopsies of tumorous and adjacent nontumorous tissue were taken with a 16 g needle from our patients (<i>n</i> = 26) undergoing partial or radical nephrectomy due to ccRCC RNA sequencing libraries were generated using Illumina TruSeq<sup>®</sup> Access library preparation protocol and TruSeq Small RNA library preparation kit. Next generation sequencing (NGS) was performed on Illumina HiSeq2500. Comparative analysis of matched sample pairs was done using the Bioconductor Limma/voom R-package. Liquid chromatography-tandem mass spectrometry and immunohistochemistry were applied to measure and visualize protein abundance. We detected an increased generic EMT transcript score in ccRCC Gene expression analysis showed augmented abundance of <i>AXL</i> and <i>MMP14</i>, as well as down-regulated expression of <i>KL</i> (klotho). Moreover, microRNA analyses demonstrated a positive expression correlation of miR-34a and its targets <i>MMP14</i> and <i>AXL</i> Survival analysis based on a subset of genes from our list EMT-related genes in a publicly available dataset showed that the EMT genes correlated with ccRCC patient survival. Several of these genes also play a known role in fibrosis. Accordingly, recently published classifiers of solid organ fibrosis correctly identified EMT-affected tumor samples and were correlated with patient survival. EMT in ccRCC linked to fibrosis is associated with worse survival and may represent a target for novel therapeutic interventions.
Age Determination in Dogs (1939)

In the same manner as in other domestic animals, the age of dogs can be ascertained mainly on the basis of an examination of the teeth. Ordinarily, the adult dog has forty-two teeth: twenty in the upper jaw and twenty in the lower, which are designated as incisors, canines, premolars and molars.