gebhart/patrepeval huggingface dataset:
[11] Using hydroxyl radical to probe DNA structure (1992)

This chapter describes the application of the hydroxyl radical as a reagent for elucidating the structural details of DNA. The hydroxyl radical cleaves DNA by abstracting a hydrogen atom from a deoxyribose residue in the DNA backbone. Subsequently, the sugar breaks down, leaving a single-nucleoside gap with predominantly 5´- and 3´-phosphate ends. A small amount of 3´-phosphoglycolate is formed as well. This product migrates faster than the corresponding 3´-phosphate and can be seen when high percentage polyacrylamide gels are used to separate the products of hydroxyl radical cleavage of 5´-radiolabeled DNA. The examples presented in the chapter show that the hydroxyl radical cleavage experiment yields high resolution, reproducible structural data for DNA in solution. Adenine tracts in both a bent restriction fragment and a short oligonucleotide duplex have a characteristic pattern of hydroxyl radical cleavage that is related to the unusual conformation adopted by these tracts. The four strands of an immobile Holliday junction show distinctive hydroxyl radical protections that report on the crossover configuration of the molecule. Not only does this technique provide structural data at the nucleotide level, it can easily be performed by any laboratory that is experienced in the methods of molecular biology.
A Novel Proximity Assay for the Detection of Proteins and Protein Complexes: Quantitation of HER1 and HER2 Total Protein Expression and Homodimerization in Formalin-fixed, Paraffin-Embedded Cell Lines and Breast Cancer Tissue (2009)

The availability of drugs targeting the EGFR/HER/erbB signaling pathway has created a need for diagnostics that accurately predict treatment responses. We have developed and characterized a novel assay to provide sensitive and quantitative measures of HER proteins and homodimers in formalin-fixed, paraffin-embedded (FFPE) cell lines and breast tumor tissues, to test these variables. In the VeraTag assay, HER proteins and homodimers are detected through the release of fluorescent tags conjugated to specific HER antibodies, requiring proximity to a second HER antibody. HER2 protein quantification was normalized to tumor area, and compared to receptor numbers in 12 human tumor cell lines determined by fluorescence-activated cell sorting (FACS), and with HER immunohistochemistry (IHC) test categories and histoscores in cell lines and 170 breast tumors. HER1 and HER2 expression levels determined by the VeraTag assay are proportional to receptor number over more than a 2 log10 range, and HER homodimer levels are consistent with crosslinking and immunoprecipitation results. VeraTag HER2 measurements of breast tumor tissue and cell lines correlate with standard IHC test categories (P<0.001). VeraTag HER2 levels also agree with IHC histoscores at lower HER2 protein levels, but are continuous and overlapping between IHC test categories, extending the dynamic range 5-fold to 10-fold at higher HER2 levels. The VeraTag assay specifically and reproducibly measures HER1 and HER2 protein and homodimers in FFPE tissues. The continuous measure of HER2 protein levels over a broad dynamic range, and the novel HER2 homodimer measure, are presently being assessed as predictive markers for responses to targeted HER2 therapy.
Effects of Docosahexaenoic and Eicosapentaenoic Acid on Lipid Metabolism, Eicosanoid Production, Platelet Aggregation and Atherosclerosis in Hypercholesterolemic Rats (1999)

Exogenously hypercholesterolemic (ExHC) rats were fed on an atherogenic diet supplemented with 1% each of either ethyl ester docosahexaenoic acid [EE-DHA, 22:6(n-3)], ethyl ester eicosapentaenoic acid [EE-EPA, 20:5(n-3)] or safflower oil (SO) for 6 months. The rats fed on the diets containing EE-EPA or EE-DHA, compared with those fed on SO, had lower serum cholesterol and triacylglycerol levels, less aggregation of platelets and slower progress of intimal thickening in the ascending aorta. Relative to the SO-fed rats, both of the (n-3) fatty acid-fed rats had a significantly reduced proportion of arachidonic acid in the platelet and aortic phospholipids, and lower production of thromboxane A2 by platelets and of prostacyclin by the aorta. These results suggest that EPA and DHA are similarly involved in preventing atherosclerosis development by reducing hypercholesterolemia and modifying the platelet functions.
Triple inhalers for obstructive airways disease: will they be useful? (2011)

Keywords:: asthmaCOPDcorticosteroidindacaterollong-acting β2-agonistlong-acting muscarinic antagonisttiotropium
Scanning Probe Contact Printing (2003)

This paper reports a scanning probe contact printing (SP-CP) method for generating submicron patterns. It uses a novel scanning probe with an integrated elastomeric tip to transfer chemical materials onto a substrate. The SP-CP method combines the advantages of microcontact printing and dip-pen nanolithography to generate monolayer features chemisorbed on a gold surface. Arbitrary, connected features such as lines or blocks can be formed by connecting multiple dots, analogous to dot-matrix printing. We discuss the design and fabrication of the novel probes for SP-CP and how they can be used to generate sub-500-nm dots and lines of 1-octadecanethiol on a gold surface.
cis- and trans-acting regulation of gene expression of equine infectious anemia virus (1988)

Deletion analysis of the equine infectious anemia virus long terminal repeat revealed that sequences responsive to virus-specific transactivation are located within the region spanning the transcriptional start site (-31 to +22). In addition, an active exon of a trans-acting factor (tat) was identified downstream of pol and overlapping env (nucleotides 5264 to 5461). Activation by tat is accompanied by an increase in the steady-state levels of mRNA directed by the equine infectious anemia virus long terminal repeat.
Three dimensional statics for continuum robotics (2009)

This paper introduces a method for computing the shape of a continuously-flexible (continuum) robot in 3-D space which includes gravity loading by applying Cosserat rod theory to a continuum robot. With this theory, the shape of the rod can be determined using force-torque balance equations obtained from a simple free body diagram that represents the continuum robot. Real-time performance of 125 Hz makes this approach viable for the control of a continuum robot, enabled by avoiding boundary-value conditions in the solution.
Loss and gain of distinct regions of chromosome 1q in primary breast cancer. (1995)

Alterations of the long arm of chromosome 1 are the most frequent cytogenetic abnormalities found in human breast carcinoma. We examined genetic alterations on chromosome 1q in 124 human breast tumors, using restriction fragment length polymorphism markers mapping to the long arm (13 markers) and short arm (4 markers). Imbalance of heterozygosity at one or more loci on the long arm was observed in 80 (65%) of the 124 tumors. Among these 80 tumor DNAs, 38 showed an allele gain, 16 a loss of heterozygosity, and 1 both allele gain and loss of heterozygosity at each locus on the long arm, indicating that 55 tumor DNAs had a gain and/or loss of the entire long arm of chromosome 1. Detailed alteration mapping of the other 25 tumors showing partial alterations of chromosome 1q identified two distinct altered regions: a smallest common deleted region at 1q21-31 and a smallest common overrepresented region at 1q41-q44. The results suggest that both oncogenes and tumor suppressor genes are present on chromosome 1q and are associated with breast tumorigenesis.
GPD1, Which Encodes Glycerol-3-Phosphate Dehydrogenase, Is Essential for Growth under Osmotic Stress in Saccharomyces cerevisiae, and Its Expression Is Regulated by the High-Osmolarity Glycerol Response Pathway (1994)

The yeast Saccharomyces cerevisiae responds to osmotic stress, i.e., an increase in osmolarity of the growth medium, by enhanced production and intracellular accumulation of glycerol as a compatible solute. We have cloned a gene encoding the key enzyme of glycerol synthesis, the NADH-dependent cytosolic glycerol-3-phosphate dehydrogenase, and we named it GPD1. gpd1 delta mutants produced very little glycerol, and they were sensitive to osmotic stress. Thus, glycerol production is indeed essential for the growth of yeast cells during reduced water availability. hog1 delta mutants lacking a protein kinase involved in osmostress-induced signal transduction (the high-osmolarity glycerol response [HOG] pathway) failed to increase glycerol-3-phosphate dehydrogenase activity and mRNA levels when osmotic stress was imposed. Thus, expression of GPD1 is regulated through the HOG pathway. However, there may be Hog1-independent mechanisms mediating osmostress-induced glycerol accumulation, since a hog1 delta strain could still enhance its glycerol content, although less than the wild type. hog1 delta mutants are more sensitive to osmotic stress than isogenic gpd1 delta strains, and gpd1 delta hog1 delta double mutants are even more sensitive than either single mutant. Thus, the HOG pathway most probably has additional targets in the mechanism of adaptation to hypertonic medium.
Development of a Novel, Low-Cost, Disposable Wooden Pencil Graphite Electrode for Use in the Determination of Antioxidants and Other Biological Compounds (2015)

The development of portable sensors that can be used outside the lab is an active area of research in the electroanalytical field. A major focus of such research is the development of low-cost electrodes for use in these sensors. Current electrodes, such as glassy-carbon electrodes (GCEs), are costly and require time-consuming preparation. Alternatives have been proposed, including mechanical pencil-lead electrodes (MPEs). However, MPEs themselves possess numerous drawbacks, particularly structural fragility. In this paper, we present a novel pencil-graphite electrode (PGE) fabricated from a regular HB#2 pencil. This PGE is a simple, disposable, extremely low-cost alternative to GCEs ($0.30 per PGE, vs. $190 + per GCE), and possesses the structural stability that MPEs lack. PGEs were characterized by square-wave voltammetry of ferricyanide, gallic acid, uric acid, dopamine, and several foodstuffs. In all cases, PGEs demonstrated sensitivities comparable or superior to those of the GCE and MPE (LOD = 5.62 × 10(-4) M PGE, 4.80 × 10(-4) M GCE, 2.93 × 10(-4) M MPE). Signal areas and peak heights were typically four to ten times larger for the PGE relative to the GCE.
Liposomal formulation of a self lymphoma antigen induces potent protective antitumor immunity. (1998)

We developed a liposome carrier for a model nonimmunogenic, self Ag. This carrier reproducibly converted lymphoma Ig into a potent tumor rejection Ag in mice. A single immunization induced protection against challenges representing 20 to 100 times the minimum lethal dose of parental tumor. This protective effect required minimal amounts of incorporated Ag and IL-2 and elicited specific Abs (compared with free Ag or liposomal control Ig which did not elicit any specific Abs); depletion experiments demonstrated a requirement for effector CD4+ and CD8+ T cells. Head-to-head comparisons, indicating superior potency and induction of specific T cell activation, distinguished liposomal from prototype, carrier-conjugated Ag. These results provide a strategy for formulating weak tumor or other clinically important Ags into vaccines.
Doses to nuclear technicians in a dedicated PET/CT centre utilising 18F fluorodeoxyglucose (FDG) (2006)

The first dedicated PET/CT centre in Norway was established at the Norwegian Radiumhospital in Oslo in 2005. Knowing that the introductions of PET-isotopes in nuclear medicine give increased occupational radiation dose to the technicians, a study was carried out in order to map the doses to staff members during different working operations and to see if any dose reducing measures were needed. The results of the study are in good agreement with other studies, and a technician dose of 20-25 nSv per injected MBq of 18F seems to be representative for such centres. For an average injected activity of 350 MBq per patient, the dose limit is reached after handling around 3000 patients annually. For an annual number of less than 500 patients at the centre and rotation of the staff, an annual individual dose for the technicians would realistically be less than 2-3 mSv. Even a major increase in the number of patients will not result in individual doses near the ICRP dose limit.
Aerosol Delivery Devices in the Treatment of Asthma (2008)

Nebulizers convert solutions or suspensions into aerosols with a particle size that can be inhaled into the lower respiratory tract. There are pneumatic jet nebulizers, ultrasonic nebulizers, and mesh nebulizers. Newer nebulizer designs are breath-enhanced, breath-actuated, or have aerosol-storage bags to minimize aerosol loss during exhalation. Nebulizers can be used with helium-oxygen mixture and can be used for continuous aerosol delivery. Increased attention has recently been paid to issues related to the use of a facemask with a nebulizer. The pressurized metered-dose inhaler (pMDI) is a very commonly used device for aerosol delivery. There are press-and-breathe and breath-actuated pMDI designs. Issues related to pMDIs that have received increasing attention are the conversion to hydrofluoroalkane propellant and the use of dose counters. Many patients have poor pMDI technique. Valved holding chambers and spacers are used to improve pMDI technique and to decrease aerosol deposition in the upper airway. In recent years increasing attention has been paid to the issues of electrostatic charge and facemasks related to valved holding chambers. Many newer formulations for inhalation have been released in dry-powder inhalers, which are either unit-dose or multi-dose inhalers. Systematic reviews and meta-analyses have suggested that each of these aerosol delivery devices can work equally well in patients who can use them correctly. However, many patients use these devices incorrectly, so proper patient education in their use is critical.
Comparative genome analysis: selection pressure on the Borrelia vls cassettes is essential for infectivity (2006)

The complete genome sequences of a B. garinii and a B. afzelii strain facilitate further comparative studies within the genus Borrellia. Our study shows that loss of infectivity can be traced back to only one single event in B. garinii PBi: the loss of the vls cassettes possibly due to error prone gene conversion. Similar albeit extended losses in B. afzelii PKo support the hypothesis that infectivity of Borrelia species depends heavily on the evasion from the host response.
Long-Term Outcomes in Rheumatoid Arthritis (1995)

Long-term outcomes in the majority of patients with established rheumatoid arthritis (RA) include radiographic progression, severe functional declines, work disability and premature mortality. These outcomes have been recognized primarily in long-term clinical observational studies, which also indicate that most courses of traditional therapies are discontinued within 2 yr. Severe long-term outcomes in RA are predicted more effectively by sustained inflammatory activity than by any measure of baseline activity at a single point in time. Aggressive efforts to control inflammatory activity prior to irreversible damage would appear to be a reasonable strategy for treatment of RA.
Determination of multielements by neutron activation analysis using a coincidence counting method. (2000)

放射化分析におけるγ線測定において,壊変時にカスケード状にγ線を同時に放出する核種を高感度に測定するために,コンプトンバックグラウンドを低減できる同時計数法の検討を行った。同軸型Ge検出器とその周りをコンプトン散乱γ線検出用の井戸型NaI(Tl)検出器で囲んで同時計数法で測定し,マルチパラメーターMCAを用いた同時計数スペクトルと同軸型Ge検出器のみの通常計数法のスペクトルを同時に得た。この方法により3種類の標準物質(河川底質,Typical Japanese Diet,耳石)と鉄遺物中の7元素(Se,Hf,Ba,Cs,Co,Sb,Sc)の分析を行った。標準物質については認証値とよく一致した結果が得られた。同時計数法では,通常計数法に比べてほかの妨害核種によるγ線が除去でき,微弱なγ線が検出できるため,微量な元素まで定量できた。
Effects of substrate stiffness on cell morphology, cytoskeletal structure, and adhesion (2004)

The morphology and cytoskeletal structure of fibroblasts, endothelial cells, and neutrophils are documented for cells cultured on surfaces with stiffness ranging from 2 to 55,000 Pa that have been laminated with fibronectin or collagen as adhesive ligand. When grown in sparse culture with no cell-cell contacts, fibroblasts and endothelial cells show an abrupt change in spread area that occurs at a stiffness range around 3,000 Pa. No actin stress fibers are seen in fibroblasts on soft surfaces, and the appearance of stress fibers is abrupt and complete at a stiffness range coincident with that at which they spread. Upregulation of α5 integrin also occurs in the same stiffness range, but exogenous expression of α5 integrin is not sufficient to cause cell spreading on soft surfaces. Neutrophils, in contrast, show no dependence of either resting shape or ability to spread after activation when cultured on surfaces as soft as 2 Pa compared to glass. The shape and cytoskeletal differences evident in single cells on soft compared to hard substrates are eliminated when fibroblasts or endothelial cells make cell-cell contact. These results support the hypothesis that mechanical factors impact different cell types in fundamentally different ways, and can trigger specific changes similar to those stimulated by soluble ligands. Cell Motil. Cytoskeleton 60:24–34, 2005. © 2004 Wiley-Liss, Inc.
A yeast gene product, Fob1 protein, required for both replication fork blocking and recombinational hotspot activities (1996)

The pleiotropic effect of the fob1 mutation suggests that homologous recombination at HOT1 is closely linked with DNA replication fork blocking event at RFB.
Diagnosis in Autism (1997)

The results of a survey of almost I300 parent members of autistic societies in the UK are described. The ages of their children ranged from 2 to 49 years. The survey focused on parents' views of the diagnostic process and data were collected on the age at which diagnosis was made, the time taken to obtain a diagnosis and the professionals involved. Differences in geographical area were also assessed. Overall, the results indicate that children are now being diagnosed earlier than in previous decades, but the average age of diagnosis is still around 6 years. There are also wide regional variations in diagnosis. The survey indicates that many parents continue to experience lengthy and often frustrating delays before they finally receive a diagnosis. Moreover, even when this process is completed, the amount of practical help subsequently provided is generally very limited. Factors related to parental satisfaction with the diagnostic process are discussed in detail.
Network coding‐based multi‐path routing algorithm in two‐layered satellite networks (2017)

Satellite networks are capable of contenting a variety of data transmission needs of users in geographically diverse locations throughout the world. Multi‐layered satellite networks (MLSNs) can construct efficient communications networks due to their extensive coverage and high network capacity. However, throughput degradation and severe end‐to‐end delay could occur in MLSNs because of the traffic congestion. To resolve these problems, the authors first propose a novel MEO/LEO satellite network architecture that construct effective inter‐satellite links. Then the authors present a network coding‐based multi‐path routing algorithm to deliver traffic through the hybrid satellite network. The analysis of characteristics of the proposed scheme are addressed by performance evaluations in simulation.
In vitro exposure of acute promyelocytic leukemia cells to arsenic trioxide (As2O3) induces the solitary expression of CD66c (NCA‐50/90), a member of the CEA family (1999)

Arsenic trioxide (As2O3) is a useful drug for the treatment of acute promyelocytic leukemia (APL), acting through a complex mechanism involving the induction of apoptosis. We investigated by flow cytometry whether in vitro treatment of APL leukemic cells with As2O3 determined specific surface membrane changes. Twelve APL bone marrow aspirates were analyzed following 7 days of in vitro treatment with As2O3 (0.25, 0.5 and 2.5 microM) with regard to the expression of a series of differentiation antigens. Twelve acute myeloid leukemia (AML) samples of non-APL morphotype were analyzed as controls. Exposure of APL as well as non-APL samples to any concentration of As2O3 did not affect the expression of beta2 integrins (CD11a and CD11b), CD45 isoforms (RA, RB and R0), CD44/H-CAM, CD33 and the CEA-related antigen family members CD66ade and CD66b, thus failing to disclose any maturating effect. Of interest, in all APL samples (but not in AML) every tested dose of As2O3 determined a dramatic upregulation of CD66c display; intermediate concentration (0.5 microM) of As2O3 increased the median percentage of CD66c+ cells from 5% in control cultures (25th-75th percentile 2-12%) to 80% in drug-exposed cultures (25th-75th percentile 58-90%) (P<0.001). The induction of solitary expression of CD66c is a new finding which demonstrates As2O3 capability of generating phenotypic changes absolutely restricted to APL cells Moreover, these results provide experimental basis for considering the involvement of the newly described CD66 signalling pathway in As2O3-driven programmed cell death.
Two receptor interacting domains in the nuclear hormone receptor corepressor RIP13/N-CoR. (1996)

The thyroid hormone receptor (TR) and the retinoic acid receptor (RAR) act as transcriptional repressors when they are not occupied by their cognate ligands. This repressor function is mediated by proteins called corepressors. One of the nuclear hormone receptor corepressors, N-CoR, was originally isolated as a retinoid X receptor-interacting protein called RIP13. We have isolated a new potential variant of RIP13/N-CoR that is missing previously described transcriptional repressor domains but is similar in structure to the related corepressor termed SMRT or TRAC-2. Detailed analysis of the interaction with TR and RAR demonstrates that RIP13/N-CoR contains a new receptor interaction domain, termed ID-II, in addition to the previously described domain, referred to here as ID-I. Both ID-I and ID-II are capable of interacting independently with either TR or RAR, as assessed by the yeast two-hybrid system, by a mammalian two-hybrid system, or by direct in vitro binding. Results with all three approaches confirm that RIP13/N-CoR also interacts with retinoid X receptor, but this interaction is weaker than that with TR or RAR. Together, these results demonstrate that RIP13/N-CoR can interact with several different nuclear hormone receptors via two separate receptor interaction domains. Differences between the interactions observed in the different systems suggest that corepressor function may be modified by additional factors present in various cell types.
Quantitative multi-detector emission computerized tomography using iterative attenuation compensation. (1982)

An iterative procedure to correct for attenuation has been developed for a multidetector, single-photon emission tomographic scanner. The difference between measured and estimated data projections is used at each iteration to form an error image which is used, in turn, to correct the image. A damping factor that minimizes chi2 is applied after each iteration to speed convergence. Several phantoms of different size, with various concentration distributions, have been used to compare this method with a first-order multiplicative attenuation correction used previously with this scanner. The first-order correction is inadequate for most of the phantoms studied, whereas relative and absolute quantitative capability is demonstrated for the iterative attenuation correction. The reconstructed average number of counts per pixel is a linear function of activity concentration up to 5 muCi/ml for all regions of uniform activity whose size is greater than or equal to 5 cm. The importance of using an accurate attenuation distribution with this method is demonstrated with a torso-like phantom.