gebhart/patrepeval huggingface dataset:
The management of respiratory motion in radiation oncology report of AAPM Task Group 76a) (2006)

This document is the report of a task group of the AAPM and has been prepared primarily to advise medical physicists involved in the external-beam radiation therapy of patients with thoracic, abdominal, and pelvic tumors affected by respiratory motion. This report describes the magnitude of respiratory motion, discusses radiotherapy specific problems caused by respiratory motion, explains techniques that explicitly manage respiratory motion during radiotherapy and gives recommendations in the application of these techniques for patient care, including quality assurance (QA) guidelines for these devices and their use with conformal and intensity modulated radiotherapy. The technologies covered by this report are motion-encompassing methods, respiratory gated techniques, breath-hold techniques, forced shallow-breathing methods, and respiration-synchronized techniques. The main outcome of this report is a clinical process guide for managing respiratory motion. Included in this guide is the recommendation that tumor motion should be measured (when possible) for each patient for whom respiratory motion is a concern. If target motion is greater than 5 mm, a method of respiratory motion management is available, and if the patient can tolerate the procedure, respiratory motion management technology is appropriate. Respiratory motion management is also appropriate when the procedure will increase normal tissue sparing. Respiratory motion management involves further resources, education and the development of and adherence to QA procedures.
Nonresponsiveness to Hepatitis B Vaccine in Health Care Workers (1986)

Twenty-eight health care workers who had a poor antibody response when initially vaccinated with hepatitis B vaccine were revaccinated with three additional 20-microgram doses. Eight of the twenty nonresponders, who had levels of antibody to hepatitis B surface antigen (anti-HBs) of less than 8 estimated radioimmunoassay (RIA) units, and all 8 of the hyporesponders, who had anti-HBs levels of 8 or 16 RIA units, attained anti-HBs levels of 36 RIA units or more after revaccination. Tests for HLA-A, B, C, and DR; for complement proteins C2, C4A, C4B, and BF; and for the erythrocyte enzyme glyoxalase I were done in 17 nonresponders and 3 hyporesponders. Nine (45%) had HLA-DR7 and 8 (40%) had HLA-DR3, compared with an expected rate of 23% in the general population. At least one of two extended haplotypes (B44, DR7, FC31 or B8, DR3, SCO1) were detected in 6 of the 9 who did not respond to revaccination, compared with 2 of 11 who responded to a second course of vaccine. Poor responders to vaccine may benefit from revaccination, and genetic factors may modulate the immune response to vaccination.
Extracellular Matrix Molecules and their Receptors: Functions in Neural Development (1991)

The brain's default mode network consists of discrete, bilateral and symmetrical cortical areas, in the medial and lateral parietal, medial prefrontal, and medial and lateral temporal cortices of the human, nonhuman primate, cat, and rodent brains. Its ...Read More
Patchwork‐structure serpins from silkworm (Bombyx mori) larval hemolymph (1991)

A new serpin (serine proteinase inhibitor), having antichymotryptic activity, was isolated from silkworm, Bombyx mori, larval hemolymph and was named silkworm antichymotrypsin II (sw-AchyII). Amino-acid-sequence analysis of sw-AchyII revealed that it consisted of 375 amino acids without cysteine or glycosylated residues. sw-AchyII formed an SDS-undissociable complex with alpha-chymotrypsin, but this complex was broken down at pH 12.5 into alpha-chymotrypsin and sw-AchyII in which the reactive site was cleaved. Amino-acid-sequence analysis after cleavage identified in P1-P1' residue at the reactive site of sw-AchyII as Phe340-Met341. The amino acid sequence from the amino terminus to residue 336 was completely identical to the corresponding region of sw-AT [Takagi, H., Narumi, H., Nakamura, K. & Sasaki, T. (1990) J. Biochem. (Tokyo) 108, 372-378]. The degree of similarity between sw-AchyII and silkworm antitrypsin (sw-AT) from residue 337 to the carboxy terminus was only 46%. Reactive sites of both serpins were in the variable regions.
A Sequence-Independent Strategy for Detection and Cloning of Circular DNA Virus Genomes by Using Multiply Primed Rolling-Circle Amplification (2004)

The discovery of novel viruses has often been accomplished by using hybridization-based methods that necessitate the availability of a previously characterized virus genome probe or knowledge of the viral nucleotide sequence to construct consensus or degenerate PCR primers. In their natural replication cycle, certain viruses employ a rolling-circle mechanism to propagate their circular genomes, and multiply primed rolling-circle amplification (RCA) with phi29 DNA polymerase has recently been applied in the amplification of circular plasmid vectors used in cloning. We employed an isothermal RCA protocol that uses random hexamer primers to amplify the complete genomes of papillomaviruses without the need for prior knowledge of their DNA sequences. We optimized this RCA technique with extracted human papillomavirus type 16 (HPV-16) DNA from W12 cells, using a real-time quantitative PCR assay to determine amplification efficiency, and obtained a 2.4 x 10(4)-fold increase in HPV-16 DNA concentration. We were able to clone the complete HPV-16 genome from this multiply primed RCA product. The optimized protocol was subsequently applied to a bovine fibropapillomatous wart tissue sample. Whereas no papillomavirus DNA could be detected by restriction enzyme digestion of the original sample, multiply primed RCA enabled us to obtain a sufficient amount of papillomavirus DNA for restriction enzyme analysis, cloning, and subsequent sequencing of a novel variant of bovine papillomavirus type 1. The multiply primed RCA method allows the discovery of previously unknown papillomaviruses, and possibly also other circular DNA viruses, without a priori sequence information.
Cationic domain 141-150 of apoE covalently linked to a class A amphipathic helix enhances atherogenic lipoprotein metabolism in vitro and in vivo (2001)

We previously showed 1 that a peptide, Ac-hE18A-NH(2), in which the arginine-rich heparin-binding domain of apolipoprotein E (apoE) [residues 141;-150] (LRKLRKRLLR), covalently linked to 18A (DWLKAFYDKVAEKLKEAF; a class A amphipathic helix with high lipid affinity), enhanced LDL uptake and clearance. Because VLDL and remnants contain more cholesterol per particle than LDL, enhanced hepatic clearance of VLDL could lead to an effective lowering of plasma cholesterol. Therefore, in the present article we compared the ability of this peptide to mediate/facilitate the uptake and degradation of LDL and VLDL in HepG2 cells. The peptide Ac-hE18A-NH(2), but not Ac-18A-NH(2), enhanced the uptake of LDL by HepG2 cells 5-fold and its degradation 2-fold. The association of the peptides with VLDL resulted in the displacement of native apoE; however, only Ac-hE18A-NH(2) but not Ac-18A-NH(2) caused markedly enhanced uptake (6-fold) and degradation (3-fold) of VLDL. Ac-hE18A-NH(2) also enhanced the uptake (15-fold) and degradation (2-fold) of trypsinized VLDL Sf 100;-400 (containing no immuno-detectable apoE), indicating that the peptide restored the cellular interaction of VLDL in the absence of its essential native ligand (apoE). Pretreatment of HepG2s with heparinase and heparitinase abrogated all peptide-mediated enhanced cellular activity, implicating a role for cell-surface heparan sulfate proteoglycans (HSPG). Intravenous administration of Ac-hE18A-NH(2) into apoE gene knockout mice reduced plasma cholesterol by 88% at 6 h and 30% at 24 h after injection. We conclude that this dual-domain peptide associates with LDL and VLDL and results in rapid hepatic uptake via a HSPG-facilitated pathway.
HSV-2: in pursuit of a vaccine (2011)

Herpes simplex virus type 2 (HSV-2) is one of the most prevalent sexually transmitted infections worldwide. In addition to recurrent genital ulcers, HSV-2 causes neonatal herpes, and it is associated with a 3-fold increased risk for HIV acquisition. Although many HSV-2 vaccines have been studied in animal models, few have reached clinical trials, and those that have been tested in humans were not consistently effective. Here, we review HSV-2 pathogenesis, with a focus on novel understanding of mucosal immunobiology of HSV-2, and vaccine efforts to date, in an attempt to stimulate thinking about future directions for development of effective prophylactic and therapeutic HSV-2 vaccines.
Teratogenic compounds of Veratrum californicum (Durand). V. Comparison of cyclopian effects of steroidal alkaloids from the plant and structurally related compounds from other sources (1968)

Abstract Cyclopamine, and its glycoside alkaloid X, along with jervine and veratrosine, induced cyclopian malformations in offspring born to ewes ingesting these compounds on the fourteenth day of gestation. Other steroidal alkaloids with somewhat similar structures and various other steroidal compounds including certain hormones and steroidal sapogenins did not induce the malformation.
Association between exercise-induced pulmonary hemorrhage and performance in Thoroughbred racehorses (2005)

Results suggest that EIPH is associated with impaired performance in Thoroughbred racehorses not medicated with furosemide and not using nasal dilator strips.
Site‐specific recombinases: from tag‐and‐target‐ to tag‐and‐exchange‐based genomic modifications (2011)

Site-specific recombinases (SSRs) enable novel tag-and-target as well as tag-and-exchange strategies for tailoring mammalian genomes. If used in combination with homologous recombination, which per se is inefficient but can serve to introduce SSR sites, the tagged locus lends itself to repeated modification at largely increased efficiency and specificity. The more conventional SSR-based genetic modifications enable straightforward integration of a transgene with efficiencies depending on both the target locus and the vector composition. Only the more recent tag-and-exchange strategies in conjunction with advanced selection principles enable the clean replacement of a genomically anchored cassette by a donor cassette with the related architecture. Meanwhile this recombinase-mediated cassette exchange (RMCE) concept could be verified for two classes of SSRs, belonging to either the Tyr or the Ser family. Certain members of these open different fields of application that will be discussed with reference to the molecular properties of the respective enzymes. A major aim of our review is to characterize the RMCE-relevant components and describe their optimal utilization in the fields of gene therapy and molecular genomics. Early contributions to the field of experimental animal models will be mentioned considering in vivo modifications enabled by microinjection into oocytes.
Complex Objects In Knowledge-based Requirement Engineering (1991)

An Object Relationship Model is proposed as part of a project to develop a knowledge-based requirement engineering assistant. This paper describes the basic data model of the ORM and then concentrates on the use of complex objects as a knowledge representation platform for requirement engineering. Different kinds of dependency and exclusiveness in a complex object are discussed. Three special type of roles: emergent, derived, and inherited roles are also investigated. A number of ways to provide knowledge-based support for the modelling of complex objects are then discussed: consistency and completeness checking, design history recording, and partial reuse of design.
Design, Synthesis, Molecular Modeling Studies, and Calpain Inhibitory Activity of Novel α-Ketoamides Incorporating Polar Residues at the P1‘-Position (2003)

A series of novel alpha-ketoamides incorporating stereoisomeric residues with different electronic properties at the P(1)'-position were synthesized to study the electronic requirements for inhibitor binding to the S(1)'-subsite of calpain I. The results of the study suggested the presence of an acidic amino acid residue at the S(1)'-subsite of calpain I. For example, ester 1a (Cbz-l-Leu-l-Phe-CO-d-Phe-OMe) was over 450-fold more potent than its carboxylic acid derivative 2a (Cbz-l-Leu-l-Phe-CO-d-Phe-OH). Additionally, amidino derivative 3a (Cbz-l-Leu-l-Phe-CONH-d-CH[C(NH)NH(2)]Bn) was about 6000-fold more potent than 2a. Furthermore, 4a (Cbz-l-Leu-l-Phe-CONHCH(2)Bn) was 12-fold less potent than its aza analogue 4b (Cbz-l-Leu-l-Phe-CONHNHBn). The results are consistent with the presence of an acidic amino acid residue at the S(1)'-subsite of calpain I. The acidic amino acid residue was found to be Glu261 via molecular modeling studies.
Behavioral Responses and Sublethal Effects of Spruce Budworm (Lepidoptera: Tortricidae) and Fall Webworm (Lepidoptera: Arctiidae) Larvae to Bacillus thuringiensis Cry1A(a) Toxin in Diet (1993)

Journal Article Behavioral Responses and Sublethal Effects of Spruce Budworm (Lepidoptera: Tortricidae) and Fall Webworm (Lepidoptera: Arctiidae) Larvae to Bacillus thuringiensis Cry1A(a) Toxin in Diet Get access R. Ramachandran, R. Ramachandran 1 1Current address: Sandoz (India), Sandoz House, Worli, Bombay 400018 India. Search for other works by this author on: Oxford Academic PubMed Google Scholar K. F. Raffa, K. F. Raffa 1 1Current address: Sandoz (India), Sandoz House, Worli, Bombay 400018 India. Search for other works by this author on: Oxford Academic PubMed Google Scholar M. J. Miller, M. J. Miller 2Agracetus Incorporated, Middleton, WI 53562 Search for other works by this author on: Oxford Academic PubMed Google Scholar D. D. Ellis, D. D. Ellis 3Department of Horticulture, University of Wisconsin, Madison, WI 53706 Search for other works by this author on: Oxford Academic PubMed Google Scholar B. H. McCown B. H. McCown 3Department of Horticulture, University of Wisconsin, Madison, WI 53706 Search for other works by this author on: Oxford Academic PubMed Google Scholar Environmental Entomology, Volume 22, Issue 1, 1 February 1993, Pages 197–211, https://doi.org/10.1093/ee/22.1.197 Published: 01 February 1993 Article history Received: 28 April 1992 Accepted: 14 August 1992 Published: 01 February 1993
Down regulation of the receptors for tumor necrosis factor by interleukin 1 and 4 beta-phorbol-12-myristate-13-acetate. (1987)

Binding of radiolabeled tumor necrosis factor (TNF) to cell surface receptors was markedly reduced in human foreskin fibroblasts and cells from SV-80 and HeLa cell lines subsequent to treatment with interleukin 1 (IL-1) or 4 beta-phorbol-12-myristate-13-acetate (PMA). The decrease in TNF binding was initiated within minutes of application of IL-1 or PMA and could not be blocked by cycloheximide, suggesting that it is independent of protein synthesis. Scatchard plot analysis of TNF binding to the SV-80 cells indicated that its decrease in response to IL-1 and PMA reflects a reduced amount of TNF receptors, with no change in their affinity. IL-1 and PMA together had an additive effect on TNF binding. Treatment with TNF did not result in decreased binding of IL-1 to its receptors nor did TNF and IL-1 compete directly for their respective receptors. Human U937 cells on which receptors for IL-1 were below detectable levels exhibited no decrease in TNF binding when treated with IL-1, but did so in response to PMA. In addition to a decrease in TNF receptors, cells treated with IL-1 or PMA exhibited a lesser vulnerability to the cytolytic effect of TNF. The two kinds of changes were not completely correlated. A particularly notable dissimilarity was evident when comparing the rate of their reversal: the TNF receptor level was fully recovered within a few hours of removal of IL-1 or of the water-soluble analogue of PMA, 4 beta-phorbol-12,13-dibutyrate, from pretreated SV-80 cells; yet at that time resistance to the cytotoxicity of TNF was still prominent. These findings indicate that IL-1 as well as tumor-promoting phorbol diesters can down regulate cellular response to TNF by inducing a decrease in the number of receptors for TNF, and apparently through some other effect(s) as well.
The Use of Olaparib (AZD2281) Potentiates SN-38 Cytotoxicity in Colon Cancer Cells by Indirect Inhibition of Rad51-Mediated Repair of DNA Double-Strand Breaks (2014)

Potent application of topoisomerase I inhibitor plus PARP inhibitor has been suggested to be an effective strategy for cancer therapy. Reportedly, mismatch repair (MMR)-deficient colon cancer cells are sensitive to topoisomerase I inhibitor, presumably due to microsatellite instability (MSI) of the MRE11 locus. We examined the synergy of SN-38, an active metabolite of irinotecan, in combination with the PARP inhibitor olaparib in colon cancer cells showing different MMR status, such as MSI or microsatellite stable (MSS) phenotype. Treatment with SN-38 and olaparib in combination almost halved the IC50 of SN-38 for a broad spectrum of colon cancer cells independent of the MMR status. Furthermore, olaparib potentiated S-phase-specific double-strand DNA breaks (DSB) induced by SN-38, which is followed by Rad51 recruitment. siRNA-mediated knockdown of Rad51, but not Mre11 or Rad50, increased the sensitivity to olaparib and/or SN-38 treatment in colon cancer cells. In vivo study using mouse xenograft demonstrated that olaparib was effective to potentiate the antitumor effect of irinotecan. In conclusion, olaparib shows a synergistic effect in colon cancer cells in combination with SN-38 or irinotecan, potentiated by the Rad51-mediated HR pathway, irrespective of the Mre11-mediated failure of the MRN complex. These results may contribute to future clinical trials using PARP inhibitor plus topoisomerase I inhibitor in combination. Furthermore, the synergistic effect comprising topoisomerase I-mediated DNA breakage-reunion reaction, PARP and Rad51-mediated HR pathway suggests the triple synthetic lethal pathways contribute to this event and are applicable as a potential target for future chemotherapy.
SemperWiki: a semantic personal wiki (2005)

Wikis are collaborative authoring environments, and are very popular. The original concept has recently been extended in two directions: semantic Wikis and personal Wikis. Semantic Wikis focus on better retrieval and querying facilities, by using semantic annotations of pages. Personal Wikis focus on improving usability and on providing an easy-to-use personal information space. We combine these two developments and present a semantic personal Wiki. Our application SemperWiki o#ers the usability of personal Wikis and the improved retrieval and querying of semantic Wikis. Users can annotate pages with RDF together with their normal text.The system is extremely easy-touse, provides intelligent navigation based on semantic annotations, and responds instantly to all changes.
ArabidopsisNAC1 transduces auxin signal downstream of TIR1 to promote lateral root development (2000)

Auxin plays a key role in lateral root formation, but the signaling pathway for this process is poorly understood. We show here that NAC1, a new member of the NAC family, is induced by auxin and mediates auxin signaling to promote lateral root development. NAC1 is a transcription activator consisting of an N-terminal conserved NAC-domain that binds to DNA and a C-terminal activation domain. This factor activates the expression of two downstream auxin-responsive genes, DBP and AIR3. Transgenic plants expressing sense or antisense NAC1 cDNA show an increase or reduction of lateral roots, respectively. Finally, TIR1-induced lateral root development is blocked by expression of antisense NAC1 cDNA, and NAC1 overexpression can restore lateral root formation in the auxin-response mutant tir1, indicating that NAC1 acts downstream of TIR1.
The 3' untranslated region of satellite tobacco necrosis virus RNA stimulates translation in vitro. (1993)

The RNA of satellite tobacco necrosis virus (STNV) is a monocistronic messenger that lacks both a 5' cap structure and a 3' poly(A) tail. We show that in a cell-free translation system derived from wheat germ, STNV RNA lacking the 600-nucleotide trailer is translated an order of magnitude less efficiently than full-size RNA. Deletion analyses positioned the translational enhancer domain (TED) within a conserved hairpin structure immediately downstream from the coat protein cistron. TED enhances translation when fused to a heterologous mRNA, but the level of enhancement depends on the nature of the 5' untranslated sequence and is maximal in combination with the STNV leader. The STNV leader and TED have two regions of complementarity. One of the complementary regions in TED resembles picornavirus box A, which is involved in cap-independent translation but which is located upstream of the coding region.
Deletion ofPlasmodium berghei-specific CD4+T cells adoptively transferred into recipient mice after challenge with homologous parasite (1998)

The immune response to malaria parasites includes T cell responses that reduce parasites by effector T cell responses and by providing help for antibody responses. Some parasites are more sensitive to antibody and others are more sensitive to cell-mediated immunity. We demonstrate that cultured CD4(+) T cells that produce interferon gamma and interleukin 2, but not interleukin 4, in response to stimulation with the rodent parasite Plasmodium berghei can reduce but not eliminate parasites in vivo after adoptive transfer. Although cells can persist in vivo for up to 9 months in uninfected mice, infection results in elimination of up to 99% of specific T cells in different tissues, as judged by tracking T cells labeled with the fluorescent dye 5-(and -6)-carboxyfluorescein diacetate succinimidyl ester. T cells specific for ovalbumin are unaffected. In vivo activation and division of transferred T cells per se are not responsible for deletion because T cells positive for 5-(and -6)-carboxyfluorescein diacetate succinimidyl ester divide up to six times within 7 days in uninfected mice and are not deleted. Understanding the factors responsible for parasite-mediated specific deletion of T cells would enhance our knowledge of parasite immunity.