gebhart/patrepeval huggingface dataset:
Advances in Treatment with Intensity-Modulated Conformal Radiotherapy (1998)

The modern practice of radiotherapy centres on the development of conformal radiotherapy, techniques to ensure the high-dose volume is tightly wrapped around the diseased tissue and excluded as far as possible from adjacent normal structures. The development of conformal radiotherapy is a chain of processes involving treatment planning, development of new methods to deliver radiation, verification of the accuracy of radiation delivery and improvement of biological outcome. This is an enormous field of activity. This invited review paper summarises some of the main elements of progress towards implementing intensity-modulated conformal radiotherapy. This is the newest and most exciting development and, when achieved clinically, will lead to a quantum leap in tumour control probability with a fixed level of normal tissue damage.
Cloning, sequencing, and expression of pyrophosphate-dependent phosphofructokinase from Propionibacterium freudenreichii. (1991)

Pyrophosphate-dependent 6-phosphofructo-1-kinase (PPi-PFK) from Propionibacterium freudenreichii is a non-allosteric enzyme with properties dissimilar to those of other described phosphofructokinases. The enzyme was cloned into pBluescript, sequenced, and expressed in Escherichia coli at levels 15 times higher than those observed in Propionibacterium. The gene consists of 1215 bases which code for a protein of 404 amino acids and a mass of 43,243 daltons. High G + C in the codon usage (66%) of the gene is consistent with the classification of Propionibacterium in the High-G + C subdivision of the Gram-positive bacteria. While showing no sequence identity to the non-allosteric ATP-dependent phosphofructokinase of E. coli, alignments of the amino acid sequence with other PFKs reveal degrees of identities among the amino halves of the proteins, from 26% between the Propionibacterium and potato PPi-PFKs, and 29% between Propionibacterium and E. coli ATP-PFKs. These levels of identities indicate that the amino halves of these proteins are homologous. Identities between the carboxyl half of Propionibacterium PFK and carboxyl halves of other sequences are below 20%, suggesting that the carboxyl half is not homologous. Despite the poor conservation, most of the residues that take part in the binding of fructose-6-P or Mg-PPi could be readily identified by analogy to the structure of the E. coli PFK. Both the fructose-6-P and ATP-binding sites are conserved, indicating that PPi binds to the homologous site of the E. coli ATP-binding site.
The fast affine projection algorithm (2002)

This paper discusses a new adaptive filtering algorithm called fast affine projections (FAP). FAP's key features include LMS like complexity and memory requirements (low), and RLS like convergence (fast) for the important case where the excitation signal is speech. Another of FAP's important features is that it causes no delay in the input or output signals. In addition, the algorithm is easily regularized resulting in robust performance even for highly colored excitation signals. The combination of these features make FAP an excellent candidate for the adaptive filter in the acoustic echo cancellation problem. A simple, low complexity numerical stabilization method for the algorithm is also introduced.
The reaction of α‐amino‐substituted diphenylphosphine oxide anions with elemental sulfur and selenium: A new route to thio‐ and selenoamides (1994)

Abstract The lithiated anions of α‐amino‐substituted diphenylphosphine oxides 1 , in which R can be hydrogen, aryl, alkyl and alkenyl, react with two equivalents of sulfur or selenium to form thio‐ and selenoamides, which can be isolated in good to excellent yields in most cases. The optimal reaction conditions (temperature and time) were found to depend both on the phosphine oxide used and on the chalcogene. A mechanism is presented which accounts for the stoichiometry of the reaction.
Inhibition of inducible nitric oxide synthase ameliorates cerebral ischemic damage (1995)

We sought to determine whether expression of the inducible, calcium-independent isoform of nitric oxide synthase (iNOS) contributes to the tissue damage produced by focal cerebral ischemia. The middle cerebral artery was occluded in halothane-anesthetized spontaneously hypertensive rats. Twenty-four hours later rats received intraperitoneal injections of the iNOS inhibitor aminoguanidine (100 mg/kg twice per day; n = 10) or of aminoguanidine + L-arginine (300 mg/kg four times per day; n = 7), aminoguanidine + D-arginine (n = 7), arginine alone (n = 6), or vehicle (n = 9). Drugs were administered for 3 consecutive days. Infarct volume was determined by image analysis in thionin-stained brain sections 4 days after induction of ischemia. Administration of aminoguanidine reduced infarct volume by 33 +/- 4% (P < 0.05 from vehicle; analysis of variance and Tukey's test), a reduction that was antagonized by coadministration of L- but not D-arginine. Administration of L-arginine alone did not affect infarct size (P > 0.05 vs. vehicle). In separate rats (n = 10), aminoguanidine attenuated calcium-independent NOS activity in the infarct (P < 0.05 vs. vehicle) without affecting calcium-dependent activity (P > 0.05). Aminoguanidine did not affect resting cerebral blood flow or the cerebrovascular vasodilation elicited by hypercapnia, as determined by laser-Doppler flowmetry (n = 4). We conclude that aminoguanidine selectively inhibits iNOS activity in the area of infarction and reduces the volume of the infarct produced by middle cerebral artery occlusion.(ABSTRACT TRUNCATED AT 250 WORDS)
Nitric Oxide Donors:  Chemical Activities and Biological Applications (2002)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNitric Oxide Donors: Chemical Activities and Biological ApplicationsPeng George Wang, Ming Xian, Xiaoping Tang, Xuejun Wu, Zhong Wen, Tingwei Cai, and Adam J. JanczukView Author Information Department of Chemistry, Wayne State University, Detroit, Michigan 48202 Cite this: Chem. Rev. 2002, 102, 4, 1091–1134Publication Date (Web):February 26, 2002Publication History Received4 June 2001Published online26 February 2002Published inissue 1 April 2002https://pubs.acs.org/doi/10.1021/cr000040lhttps://doi.org/10.1021/cr000040lresearch-articleACS PublicationsCopyright © 2002 American Chemical SocietyRequest reuse permissionsArticle Views14367Altmetric-Citations1100LEARN 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 SUBJECTS:Anions,Organic reactions,Peptides and proteins,Reaction products,Thiols Get e-Alerts
Palette Mode Coding in HEVC Screen Content Coding Extension (2016)

Palette mode is a new coding tool included in the HEVC screen content coding extension (SCC) to improve the coding efficiency for screen contents such as computer generated video with substantial amount of text and graphics. It is observed that a local area in screen content typically has a few colors separated by sharp edges. To exploit such characteristics, palette mode represents samples in a block with indexes pointing to the color entries in a palette table. This paper provides a detailed overview of the palette mode in HEVC SCC in terms of palette generation, coding of the palette, and coding of the palette indexes for the samples in the palette block. Several improvements to palette mode coding, which have been proposed but not included in HEVC SCC, are also described. Simulation results are presented to quantify the bitrate savings provided by the palette mode for equal distortions.
Associations of Diet with Albuminuria and Kidney Function Decline (2010)

Higher dietary intake of animal fat and two or more servings per week of red meat may increase risk for microalbuminuria. Lower sodium and higher beta-carotene intake may reduce risk for eGFR decline.
Drag-and-drop pasting (2006)

In this paper, we present a user-friendly system for seamless image composition, which we call drag-and-drop pasting. We observe that for Poisson image editing [Perez et al. 2003] to work well, the user must carefully draw a boundary on the source image to indicate the region of interest, such that salient structures in source and target images do not conflict with each other along the boundary. To make Poisson image editing more practical and easy to use, we propose a new objective function to compute an optimized boundary condition. A shortest closed-path algorithm is designed to search for the location of the boundary. Moreover, to faithfully preserve the object's fractional boundary, we construct a blended guidance field to incorporate the object's alpha matte. To use our system, the user needs only to simply outline a region of interest in the source image, and then drag and drop it onto the target image. Experimental results demonstrate the effectiveness of our "drag-and-drop pasting" system.
Endothelial Depletion of Acvrl1 in Mice Leads to Arteriovenous Malformations Associated with Reduced Endoglin Expression (2014)

Rare inherited cardiovascular diseases are frequently caused by mutations in genes that are essential for the formation and/or function of the cardiovasculature. Hereditary Haemorrhagic Telangiectasia is a familial disease of this type. The majority of patients carry mutations in either Endoglin (ENG) or ACVRL1 (also known as ALK1) genes, and the disease is characterized by arteriovenous malformations and persistent haemorrhage. ENG and ACVRL1 encode receptors for the TGFβ superfamily of ligands, that are essential for angiogenesis in early development but their roles are not fully understood. Our goal was to examine the role of Acvrl1 in vascular endothelial cells during vascular development and to determine whether loss of endothelial Acvrl1 leads to arteriovenous malformations. Acvrl1 was depleted in endothelial cells either in early postnatal life or in adult mice. Using the neonatal retinal plexus to examine angiogenesis, we observed that loss of endothelial Acvrl1 led to venous enlargement, vascular hyperbranching and arteriovenous malformations. These phenotypes were associated with loss of arterial Jag1 expression, decreased pSmad1/5/8 activity and increased endothelial cell proliferation. We found that Endoglin was markedly down-regulated in Acvrl1-depleted ECs showing endoglin expression to be downstream of Acvrl1 signalling in vivo. Endothelial-specific depletion of Acvrl1 in pups also led to pulmonary haemorrhage, but in adult mice resulted in caecal haemorrhage and fatal anaemia. We conclude that during development, endothelial Acvrl1 plays an essential role to regulate endothelial cell proliferation and arterial identity during angiogenesis, whilst in adult life endothelial Acvrl1 is required to maintain vascular integrity.
Growth and viability of secondary hair follicles of the Angora goat cultured in vitro. (1993)

The viability of isolated secondary anagen hair follicles from Angora goats was studied in an in vitro tissue culture system. Intact hair follicles were isolated from the dermal layer singly or in groups using watchmakers' forceps under a dissecting microscope following removal of both the epidermis at the basal layer and subcutaneous fat layers using a scalpel blade. The connective tissue sheath surrounding the follicle and the dermal papilla in the bulb were left intact. The isolated follicles were maintained floating in supplemented Williams E medium and showed significant increases in hair shaft length over 96 h. The viability of the cultured hair follicles was verified by the findings that (1) the rate of hair shaft elongation was similar to that occurring in vivo; (2) the pattern of DNA synthesis observed by autoradiography of [methyl-3H]thymidine uptake was maintained in the isolated follicles throughout culture; (3) the ATP content was significantly higher in growing follicles compared with that observed in freshly isolated follicles; and (4) Feulgen-stained preparations of fresh and maintained hair follicles confirmed the retention of mitotic activity in the matrix cells of the bulb for a maximum of 120 h of maintenance.
Genomic Survey of the Non-Cultivatable Opportunistic Human Pathogen, Enterocytozoon bieneusi (2009)

Enterocytozoon bieneusi is the most common microsporidian associated with human disease, particularly in the immunocompromised population. In the setting of HIV infection, it is associated with diarrhea and wasting syndrome. Like all microsporidia, E. bieneusi is an obligate, intracellular parasite, but unlike others, it is in direct contact with the host cell cytoplasm. Studies of E. bieneusi have been greatly limited due to the absence of genomic data and lack of a robust cultivation system. Here, we present the first large-scale genomic dataset for E. bieneusi. Approximately 3.86 Mb of unique sequence was generated by paired end Sanger sequencing, representing about 64% of the estimated 6 Mb genome. A total of 3,804 genes were identified in E. bieneusi, of which 1,702 encode proteins with assigned functions. Of these, 653 are homologs of Encephalitozoon cuniculi proteins. Only one E. bieneusi protein with assigned function had no E. cuniculi homolog. The shared proteins were, in general, evenly distributed among the functional categories, with the exception of a dearth of genes encoding proteins associated with pathways for fatty acid and core carbon metabolism. Short intergenic regions, high gene density, and shortened protein-coding sequences were observed in the E. bieneusi genome, all traits consistent with genomic compaction. Our findings suggest that E. bieneusi is a likely model for extreme genome reduction and host dependence.
Blood Glucose Measurement by Infrared Spectroscopy (1989)

For the development of an implantable artificial endocrine pancreas, a sensor for blood glucose measurement is needed providing a long-term stability. This goal can be achieved by the application of infrared spectroscopy which, unlike electrochemical sensors, responds directly to the glucose molecule. An investigation under physiological conditions revealed five glucose absorption bands in the near and middle infrared range. These are 1040, 1085, 1109, 1160 and 1365 cm-1. Only the 1040 cm-1 frequency coincides with none of the other infrared-active blood substances like proteins, lipids and urea. Nevertheless, the other absorption bands too, especially the 1109 cm-1 frequency, can be used for blood glucose measurement, if the superimposed absorptions are compensated. Methods for the compensation have been found. Technically feasible embodiments of an infrared glucose sensor are described.
A New Synthetic Method for the Synthesis of Hydroxylated Isoquinolines: Preparation of Methyl 6,7- and 7,8-Dihydroxyisoquinoline-3-carboxylates, Potential Protein-Tyrosine Kinase Inhibitors (1992)

Synthesis of potential protein-tyrosine kinase inhibitors (6c) and (6e) is presented as a general procedure for the preparation of polyhydroxylated iscquinolines.Key features of the method include selective hydroxyl protection of tenahydroisoquinolines by 0-acylation followed by ammatization using Mn02.Quantitative deprotection of resulting 0-acylisoquinolines is achieved using methanolic HCI.lscquinoline heterocycles are ubiquitous to a wide specrmmof natural products.lIt has recently been shown that the hydroxylated isoquinoline3-carboxyamide (2) posvsses significant inhibitory activity against platelet-derived growth factor (PDGF) protein tyrosine kinase (PTK)?This is of particular note in that inappropriate or aberrant expression of PDGF3 or other FTKs has been associated with a number of proliferative disorders, making inhibitors of FTKs potential candidates as anticancer therapeutics.43The 5.6-dihydroxyisoquinolineca~boxamide(2) can be viewed as a conformationally constrained analogue2 of the more general class of styryl-based PTK inhibitors exemplified by a-cyanocinnamamide (1).6In a like manner, the 7.8-dihydroxyisoquinolinecarboxamide (3) represents a confomlationally consnained mimetic of cinnamamide (1) having the phenyl ring rotated 180".Evidence suggests that this second orientation may be preferred for FTK inhibition.'
Evidence that phosphorylation of human Upf1 protein varies with intracellular location and is mediated by a wortmannin-sensitive and rapamycin-sensitive PI 3-kinase-related kinase signaling pathway (2001)

Human Upf1 protein (p), a group 1 RNA helicase, has recently been shown to function in nonsense-mediated mRNA decay (NMD) in mammalian cells. Here, we demonstrate that the estimated 3 x 10(6) copies of hUpf1 p per exponentially growing HeLa cell are essentially equally distributed among polysomal, subpolysomal, and ribosome-free fractions. We also demonstrate that hUpf1p binds RNA and is a phosphoprotein harboring phosphoserine and phosphothreonine. hUpf1p is phosphorylated to the highest extent when polysome-associated and to the lowest extent when ribosome free. We find that serum-induced phosphorylation of hUpf1p is inhibited by wortmannin at a concentration that selectively inhibits PI 3-kinase related kinases and, to a lesser extent, by rapamycin. These and other data suggest that phosphorylation is mediated by a wortmannin-sensitive and rapamycin-sensitive PI 3-kinase-related kinase signaling pathway. Comparisons are made of hUpf1p to Upf1p and SMG-2, which are the orthologs to hUpf1p in Saccharomyces cerevisiae and Caenorhabditis elegans, respectively.
Development of CpG-adjuvanted stable prefusion SARS-CoV-2 spike antigen as a subunit vaccine against COVID-19 (2020)

The COVID-19 pandemic is a worldwide health emergency which calls for an unprecedented race for vaccines and treatment. In developing a COVID-19 vaccine, we applied technology previously used for MERS-CoV to produce a prefusion-stabilized SARS-CoV-2 spike protein, S-2P. To enhance immunogenicity and mitigate the potential vaccine-induced immunopathology, CpG 1018, a Th1-biasing synthetic toll-like receptor 9 (TLR9) agonist was selected as an adjuvant candidate. S-2P in combination with CpG 1018 and aluminum hydroxide (alum) was found to be the most potent immunogen and induced high titer of neutralizing antibodies in sera of immunized mice against pseudotyped lentivirus reporter or live wild-type SARS-CoV-2. In addition, the antibodies elicited were able to cross-neutralize pseudovirus containing the spike protein of the D614G variant, indicating the potential for broad spectrum protection. A marked Th1 dominant response was noted from cytokines secreted by splenocytes of mice immunized with CpG 1018 and alum. No vaccine-related serious adverse effects were found in the dose-ranging study in rats administered single- or two-dose regimens of S-2P combined with CpG 1018 alone or CpG 1018 with alum. These data support continued development of CHO-derived S-2P formulated with CpG 1018 and alum as a candidate vaccine to prevent COVID-19 disease.
Preclinical efficacy evaluation of potential chemopreventive agents in animal carcinogenesis models: Methods and results from the NCI chemoprevention drug development program (1994)

In the NCI, Chemoprevention Branch drug development program, potential chemopreventive agents are evaluated for efficacy against chemical carcinogen-induced tumors in animal models. This paper summarizes the results of 144 agents in 352 tests using various animal efficacy models. Of these results, 146 were positive, representing 85 different agents. The target organs selected for the animals model are representative of high-incidence human cancers. The assays include inhibition of tumors induced by MNU in hamster trachea, DEN in hamster lung, AOM in rat colon (including inhibition of AOM-induced aberrant crypts), MAM in mouse colon, DMBA and MNU in rat mammary glands, DMBA promoted by TPA in mouse skin, and OH-BBN in mouse bladder. The agents tested may be classified into various pharmacological and chemical structural categories that are relevant to their chemopreventive potential. These categories include antiestrogens, antiinflammatories (e.g., NSAIDs), antioxidants, arachidonic acid metabolism inhibitors, GST and GSH enhancers, ODC inhibitors, protein kinase C inhibitors, retinoids and carotenoids, organosulfur compounds, calcium compounds, vitamin D3 and analogs, and phenolic compounds (e.g., flavonoids). The various categories of compounds have different spectra of efficacy in animal models. In hamster lung, GSH-enhancing agents and antioxidants appear to have high potential for inhibiting carcinogenesis. In the colon, NSAIDs and other antiinflammatory agents appear particularly promising. Likewise, NSAIDs are very active in mouse bladder. In rat mammary glands, retinoids and antiestrogens (as would be expected) are efficacious. Several of the chemicals evaluated also appear to be promising chemopreventive agents based on their activity in several of the animal models. Particularly, the ODC inhibitor DFMO was active in the colon, mammary glands, and bladder models, while the dithiolthione, oltipraz, was efficacious in all the models listed above (i.e., lung, colon, mammary glands, skin, and bladder).
Therapeutic Potential of Splice-Switching Oligonucleotides (2009)

Alternative splicing enables a single pre-messenger RNA transcript to yield multiple protein isoforms, making it a major contributor to the diversity of the proteome. While this process is essential for normal development, aberrations in alternative splicing are the cause of a multitude of human diseases. Methods for manipulating alternative splicing would thus be of therapeutic value. Chemically modified antisense oligonucleotides that alter alternative splicing by directing splice site selection have been developed to achieve this end. These splice-switching oligonucleotides (SSOs) have been applied to correct aberrant splicing, induce expression of a therapeutic splice variant, or induce expression of a novel therapeutic splice variant in a number of disease-relevant genes. Recently, in vivo efficacy of SSOs has been reported using animal disease models, as well as in results from the first clinical trial.