gebhart/patrepeval huggingface dataset:
Concordance among digital gene expression, microarrays, and qPCR when measuring differential expression of microRNAs (2010)

Profiling microRNA (miRNA) expression is of widespread interest given the critical role of miRNAs in many cellular functions. Profiling can be achieved via hybridization-based (microarrays), sequencing-based, or amplification-based (quantitative reverse transcription-PCR, qPCR) technologies. Among these, microarrays face the significant challenge of accurately distinguishing between mature and immature miRNA forms, and different vendors have developed different methods to meet this challenge. Here we measure differential miRNA expression using the Affymetrix, Agilent, and Illumina microarray platforms, as well as qPCR (Applied Biosystems) and ultra high-throughput sequencing (Illumina). We show that the differential expression measurements are more divergent when the three types of microarrays are compared than when the Agilent microarray, qPCR, and sequencing technology measurements are compared, which exhibit a good overall concordance.
Clustering Countries on Attitudinal Dimensions: A Review and Synthesis (1985)

Eight empirical studies using attitudinal data to cluster countries are reviewed. The major dimensions accounting for similarities among countries are discussed, and a final synthesis of clusters is presented.
A Dilution-Filtration System for Removing Cryoprotective Agents (2010)

In most cryopreservation applications, the final concentrations of cryoprotective agents (CPAs) must be reduced to biocompatible levels. However, traditional methods for removing CPAs usually have disadvantages of operation complexity, time consumption, and ease of contamination, especially for the applications involving large volumes of cell suspensions. A dilution-filtration system, which involves pure ultrafiltration for separation, was developed for continuous, automatic, and closed process of removing CPAs. To predict the optimal protocols under given experimental conditions, a theoretical model was established first. Cell-free experiments were then conducted to investigate the variation in CPA concentration during the process, and the experimental data were compared with the theoretical values for the validation of the model. Finally, ten units (212.9 ml/unit±9.5 ml/unit) of thawed human red blood cells (cryopreserved with 40% (w/v) glycerol) were deglycerolized using the theoretically optimal operation protocols to further validate the effectiveness and advantage of the system. In the cell-free experiments, glycerol was continuously removed and the concentration variations fitted the simulated results quite well. In the in-vitro experiments, glycerol concentration in RBC suspension was reduced to 5.57 g/l±2.81 g/l within an hour, and the cell count recovery rate was 91.19%±3.57%, (n=10), which proves that the system is not only safe for removing CPAs, but also particularly efficient for processing large-scale samples. However, the operation parameters must be carefully controlled and the optimal protocols should be specialized and various from case to case. The presented theoretical model provides an effective approach to find out the optimal operation protocols under given experimental conditions and constrains.
Edward-Wilkinson Behavior of Crystal Surfaces Grown By Sedimentation of Si<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">O</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math>Nanospheres (1996)

The surface of the solid structures obtained by natural sedimentation from aqueous solutions of monodisperse Si${\mathrm{O}}_{2}$ spheres is imaged by atomic force microscopy. The dynamic scaling method applied to these images leads to temporal and spatial logarithmic scalings of the surface width that is consistent with the Edward-Wilkinson interface motion equation. It suggests that the interface grows close to equilibrium by the aggregation of Si${\mathrm{O}}_{2}$ spheres which, after reaching the growing surface driven by gravity, relax to minimum potential energy sites without significant attractive particle-particle interactions.
Synthesis and antiulcer activity of (E)-5-[2-(3-pyridyl)ethenyl]-1H,7H-pyrazolo [1,5-a]pyrimidine-7-ones. (1986)

A series of (E)-5-[2-(3-pyridyl)ethenyl]-1H,7H-pyrazolo-[1,5-a]pyrimidine-7-ones were synthesized and evaluated for the inhibition of stress-induced gastric ulcers in the rat after oral administration. Several molecules were found to be very active. The particularly interesting compound (E)-1-(3-chlorophenyl)-5-[2-(3-pyridyl)ethenyl]-1H,7H-pyrazolo[1,5-a]- pyrimidine-7-one was chosen for wider pharmacological investigation.
Physical properties of dystrophin rod domain (1997)

We have prepared two fragments of the human dystrophin rod domain, each containing eight spectrin-like repeating units, by expression in Escherichia coli. The first corresponds to the central portion of the rod, the other to three repeats from the N-terminal end, fused to five repeats from the C-terminal end. The latter makes up the entire mutant rod, found in a patient with mild (Becker-type) muscular dystrophy. Both fragments were found to possess an ordered, stable structure, and had the form of short rod-like particles in the electron microscope. Molecular weight determinations by sedimentation equilibrium revealed that both polypeptides were monomeric in solution, suggesting that the dystrophin rod domain is incapable of forming an antiparallel homodimer. This supports the inference from sequence analyses [Winder et al., 1995: FEBS Lett. 369:27-33, 1996: Biochem. Soc. Trans. 24:2805] that the dystrophin rod domain lacks the arrangement of sites required for lateral self-association, and that dystrophin, unlike the other known proteins of the spectrin superfamily, may thus exist as a monomer.
Technetium-99m-labeled HL91 to identify tumor hypoxia: correlation with fluorine-18-FDG. (1998)

In this study, the use of 99mTc HL91 resulted in uptake in the majority of malignant tumors identified by 18F-FDG-PET. Technetium-99m HL91 exhibits good imaging characteristics, with imaging at 4 hr providing good lesion-to-normal tissue background ratios, that are further enhanced by SPECT.
Insulin-like growth factor I rapidly induces tyrosine phosphorylation of a Mr 150,000 and a Mr 160,000 protein in highly metastatic mouse colon carcinoma 26 NL-17 cells. (1991)

Insulin-like growth factor I (IGF-I) stimulates the proliferation of highly metastatic NL-17 cells to a greater extent than poorly metastatic NL-44 cells, both of which are derived from mouse colon carcinoma 26. The NL-17 cells have been compared with NL-44 cells for the signal transduction pathway of IGF-I. IGF-I receptors of both cell types were identified by affinity labeling, and there was no significant difference between the two cell types in the amount or the autophosphorylation activity of the IGF-I receptors. However, when IGF-I-dependent tyrosine phosphorylation of cellular components was examined, remarkable tyrosine phosphorylation of proteins with molecular weights of 150,000 (pp150) and 160,000 (pp160) was found in NL-17 cells. In contrast, this phosphorylation stayed at significantly lower levels in NL-44 cells than in NL-17 cells. The phosphorylation of pp150 and pp160 was induced within 10 s after the addition of IGF-I and reached its maximal level by 30 s. After the removal of IGF-I, the phosphorylation of pp150 and pp160 was reduced to the basal level within 30 min. This phosphorylation was not induced by platelet-derived or epidermal growth factor. The pp150 and pp160 were not absorbed by wheat germ agglutinin-agarose. They were found in the soluble fraction of cytoplasm but not in the membrane or the cytoskeleton. The pp150 and pp160 might be endogenous substrates of IGF-I receptor kinase. These results suggest that tyrosine phosphorylation of pp150 and pp160 mediates the higher proliferative response of NL-17 cells to IGF-I.
Hepatic perfusion in a tumor model using DCE-CT: an accuracy and precision study (2008)

In the current study we investigate the accuracy and precision of hepatic perfusion measurements based on the Johnson and Wilson model with the adiabatic approximation. VX2 carcinoma cells were implanted into the livers of New Zealand white rabbits. Simultaneous dynamic contrast-enhanced computed tomography (DCE-CT) and radiolabeled microsphere studies were performed under steady-state normo-, hyper- and hypo-capnia. The hepatic arterial blood flows (H(A)BF) obtained using both techniques were compared with ANOVA. The precision was assessed by the coefficient of variation (CV). Under normo-capnia the microsphere H(A)BF were 51.9 +/- 4.2, 40.7 +/- 4.9 and 99.7 +/- 6.0 ml min(-1) (100 g)(-1) while DCE-CT H(A)BF were 50.0 +/- 5.7, 37.1 +/- 4.5 and 99.8 +/- 6.8 ml min(-1) (100 g)(-1) in normal tissue, tumor core and rim, respectively. There were no significant differences between H(A)BF measurements obtained with both techniques (P > 0.05). Furthermore, a strong correlation was observed between H(A)BF values from both techniques: slope of 0.92 +/- 0.05, intercept of 4.62 +/- 2.69 ml min(-1) (100 g)(-1) and R(2) = 0.81 +/- 0.05 (P < 0.05). The Bland-Altman plot comparing DCE-CT and microsphere H(A)BF measurements gives a mean difference of -0.13 ml min(-1) (100 g)(-1), which is not significantly different from zero. DCE-CT H(A)BF is precise, with CV of 5.7, 24.9 and 1.4% in the normal tissue, tumor core and rim, respectively. Non-invasive measurement of H(A)BF with DCE-CT is accurate and precise. DCE-CT can be an important extension of CT to assess hepatic function besides morphology in liver diseases.
Automation of sample mounting for macromolecular crystallography (2006)

A standard sample holder and vial for cryocooled macromolecular crystals has been defined for use with robotic sample changers. This SPINE standard sample holder is a modified version, with added features and specifications, of sample holders in common use. In particular, the SPINE standard meets the precision required for automatic sample exchange and includes a cap that is identified by a two-dimensional datamatrix code as well as an optional vial. At the ESRF, the sample holder standard is in use with the EMBL/ESRF/BM14 robotic sample changer (SC3) which is installed on eight beamlines. The SC3 can hold up to 50 crystals stored in five baskets. A datamatrix reader in the SC3 ensures safe management of the sample flow and facilitates fully automatic screening and characterization of samples. Tools for handling and transporting 50 samples in a dry shipping dewar have been developed. In addition to the SC3, the SPINE sample holder is currently compatible with a number of other robotic sample changers.
Definition and evaluation of production test validation methods applied to Vx multiphase flow meters (2014)

Accurate flow rate measurements are very important in production testing. Originally small and insignificant deviations could propagate in subsequent applications where flow rate data is used as input parameter. Vx multiphase flow meters give much more information compared to conventional test separators. This extra data can be used for extra flow rate validation on the measurements, in order to find out whether it is possible to make sense of the data and if it is applicable on the long term and viable for further applications. Firstly, a comprehensive literature review has been done on current existing validation methods which gave a coherent overview. This work was used to define methods to detect measurement issues which can occur during a production test, defined by experts with considerable field experience. An adjusted choke model is presented which could be run in series with a Vx meter, which is able to detect: a drift in the differential pressure sensor; the under- or overestimation of the calculated gas rate or whether the meter is operating within the designed operation envelope or not. The choke model is tested on 96 data points from actual production tests with satisfactory results for fixed choke data. In addition, a methodology is developed to detect whether a production test has become stable or not. The method is translated into an algorithm which can be run on Vx meter output to decide in an automated fashion if a production test can be concluded, yielding representative production data. The method is tested on 700 production tests in order to define the model thresholds, which showed that the majority of the tests could have been concluded earlier. It has been found that by analyzing the statistical properties of the data it is possible to observe flow pattern transition. Furthermore, by representing certain parameters in the frequency domain, slug flow regimes can be detected and the corresponding slug flow periodicity can easily be subtracted from the data.
Intravascular 1320-nm Laser Closure of the Great Saphenous Vein (2004)

OBJECTIVE The objective was to determine the safety and efficacy of an intravascular laser with a novel wavelength to close the great saphenous vein. METHODS Twenty-four cases of an incompetent great saphenous vein (0.5–1.2 cm in diameter) associated with distal varicose veins were treated with a 1320-nm intravascular laser at 5 W with an automatic pullback mechanism at 1 mm/s. Patients were evaluated with duplex ultrasound to determine efficacy of treatment at various time periods to at least 6 months after the procedure. RESULTS All patients demonstrated complete closure of the incompetent great saphenous vein. In most cases, the treated great saphenous vein was not identifiable 6 months postoperatively. There was no recurrence of any varicose veins. All preoperative symptoms resolved after treatment, and no complications were noted. All patients were very pleased with the outcome of the procedure. CONCLUSIONS At 6 months or greater follow-up, a 5-W, 1320-nm intravascular laser with 1 mm/s automatic pullback, delivered through a diffusion-tip fiber, is safe and effective in treating an incompetent great saphenous vein up to 1.2 cm in diameter.
Results after replantation of avulsed permanent teeth. II. Periodontal healing and the role of physiologic storage and antiresorptive‐regenerative therapy (2005)

The status of the periodontal ligament (PDL) and of the pulp are decisive for the healing of avulsed and replanted teeth. A tooth rescue box was developed and distributed to offer optimal storage conditions for avulsed teeth. The therapy comprised extraoral endodontic treatment and applications of medicaments to enhance periodontal healing. In this long-term clinical study the healing results following avulsion and replantation were investigated. Twenty-eight permanent teeth in 24 patients were evaluated. The extraoral storage media and periods varied considerably. Soon after avulsion six teeth were stored in a cell culture medium (tooth rescue box Dentosafe) for 1-53 h; the PDL was defined as not compromised. Sixteen teeth were stored in a non-physiologic situation temporarily, the PDL was considered as compromised. Six teeth were stored in non-physiologic conditions for longer periods; the condition of the PDL was defined as hopeless. On 14 teeth antiresorptive-regenerative therapy (ART) with the local application of glucocorticoids and enamel matrix derivative and the systemic administration of doxycyclin was used. In all teeth extraoral endodontic treatment by retrograde insertion of posts was performed. The mean observation period was 31.2 months (+/-24.1; 5.1-100.2; median: 23.8). All six teeth rescued physiologically healed with a functional PDL (functional healing, FH) irrespective of the storage period. Of eight teeth with a compromised PDL on which ART was used, three teeth healed with a functional PDL. All other teeth showed replacement resorption, in three teeth additionally infection-related resorption was recorded. The predominant influence on the healing results was the immediate physiologic rescue of avulsed teeth (chi-square, P = 0.0001). The use of ART seemed to support FH (chi-square, P = 0.0547) in teeth with a compromised PDL. No other factors (maturity of roots, crown fractures, gender, age, antibiotics) were related to healing. In a linear regression analysis physiologic storage (P = 0.0013) and ART (P = 0.0421) were related to FH. For a good prognosis avulsed teeth should be stored immediately in a cell-compatible medium. Therefore the tooth rescue box should be distributed at places with higher risks of accidents, in families with children and in emergency facilities. The use of ART might have potential for enhancing the prognosis of teeth with a PDL that is compromised but not in a hopeless condition. Extraoral endodontic treatment reduces infection-related complications; this item was discussed in the first part of the publication.
Critical role of CD23 in allergen-induced bronchoconstriction in a murine model of allergic asthma (1999)

CD23-deficient and anti-CD23 monoclonal antibody-treated mice were used to investigate the role of the low-affinity receptor for IgE (CD23) in allergic airway inflammation and airway hyperresponsiveness (AHR). While there were no significant differences in ovalbumin (OVA)-specific IgE titers and tissue eosinophilia, evaluation of lung function demonstrated that CD23-/- mice showed an increased AHR to methacholine (MCh) when compared to wild-type mice but were completely resistant to the OVA challenge. Anti-CD23 Fab fragment treatment of wild-type mice did not affect the MCh-induced AHR but significantly reduced the OVA-induced airway constriction. These results imply a novel role for CD23 in lung inflammation and suggest that anti-CD23 Fab fragment treatment may be of therapeutic use in allergic asthma.
[Assurance of functional safety of electronics in cardiac pacemakers]. (2003)

The paper considers the causes of failure of electronics in pacemakers and actions made to reduce the likelihood of malfunction.
Twice‐daily compared with once‐daily insulin glargine in people with Type 1 diabetes using meal‐time insulin aspart (2006)

Blood glucose concentration rises in the late afternoon in association with falling plasma insulin levels towards the end of the 24-h period after insulin glargine injection in some people with Type 1 diabetes using once-daily glargine at dinner-time plus a rapid-acting insulin analogue at meal-times. This is prevented by twice-daily injection of insulin glargine.
Modeling the Morphology and Phase Stability of TiO<sub>2</sub>Nanocrystals in Water (2004)

The potential of titanium dioxide nanoparticles for advanced photochemical applications has prompted a number of studies to analyze the size, phase, and morphology dependent properties. Previously we have used a thermodynamic model of nanoparticles as a function of size and shape to predict the phase stability of titanium dioxide nanoparticles, with particular attention given to the crossover of stability between the anatase and rutile phases. This work has now been extended to titanium dioxide nanoparticles in water, to examine the effects of various adsorption configurations on the equilibrium shape and the phase transition. Density functional calculations have been used to accurately determine surface energies and surface tension of low index hydrated stoichiometric surfaces of anatase and rutile, which are presented along with a brief outline of the surface structure. We have shown that morphology of TiO2 nanocrystals is affected by the presence of water, resulting in variations in the size of the (001) and (001̄) truncation facets in anatase, and a reduction in the aspect ratio of rutile nanocrystals. Our results also highlight that the consideration of hydrated nanocrystal surfaces is necessary to accurately predict the correct size dependence of the anatase to rutile phase transition.
Microstructural Analysis for Si Wafer after CMG Process (2007)

The single crystal of Si is still one of the most important candidates among other materials including Single crystals of SiC, GaN, C(diamond) or compound semiconductors. The innovative process as called CMG(Chemo-Mechanical-Grinding) for Si wafer has been recently developed which is different from conventional CMP(Chemo-Mechanical-Polishing ) process. The CMG process can be done under dry conditions using CeO2 based solid bulk abrasives. The microstructures for surface and subsurface of Si single crystal after CMG process were analyzed using TEM/EDX, AFM, MFP-3D Microscope. The mechanism of CMG process was also investigated by X-ray diffraction and ICP chemical analysis using products by chemical reaction between Si and CeO2 abrasives. The results showed that Si single crystal after CMG had, 1) no defects even Si lattice revel or mechanical imperfections,2) better surface roughness as compared to CMP process. The CMG mechanism concluded that CeO2 reacted with Si producing Ce-Si-O amorphous phase.
The RING Finger Protein SNURF Is a Bifunctional Protein Possessing DNA Binding Activity (2001)

The small nuclear C(3)HC(4) finger protein (SNURF), RNF4, acts as transcriptional coactivator for both steroid-dependent and -independent promoters such as those driven by androgen response elements and GC boxes, respectively. However, SNURF does not possess intrinsic transcription activation function, and the precise molecular mechanism of its action is unknown. We have studied herein the interaction of SNURF with DNA in vitro. SNURF binds to linear double-stranded DNA with no apparent sequence specificity in a cooperative fashion that is highly dependent on the length of the DNA fragment used. SNURF interacts efficiently with both supercoiled circular and four-way junction DNA, and importantly, it also recognizes nucleosomes. An intact RING structure of SNURF is not mandatory for DNA binding, whereas mutations of specific positively charged residues in the N terminus (amino acids 8-11) abolish DNA binding. Interestingly, the ability of SNURF to interact with DNA is associated with its capability to enhance transcription from promoters containing GC box elements. Because SNURF can interact with both DNA and protein (transcription) factors, it may promote assembly of nucleoprotein structures.
Chemo-Enzymatic Synthesis of Ester-Linked Docetaxel-Monosaccharide Conjugates as Water-Soluble Prodrugs (2011)

Three new docetaxel prodrugs, i.e., 7-propionyldocetaxel 3''-O-β-D-glycopyranosides, which contain ester-linked monosaccharides, were synthesized by a chemo-enzymatic procedure involving enzymatic transglycosylations with lactase, β-galactosidase, or β-xylosidase. The water-solubility of 7-propionyldocetaxel 3''-O-β-D-glucopyranoside was 52-fold higher than that of docetaxel. 7-Propionyldocetaxel 3''-O-β-D-glucopyranoside and 7-propionyldocetaxel 3''-O-β-D-xylopyranoside were effectively hydrolyzed by the relevant enzyme(s) of human cancer cells to release docetaxel, whereas 7-propionyldocetaxel 3''-O-β-D-galactopyranoside was relatively resistant under similar conditions. 7-Propionyldocetaxel 3''-O-β-D-glucopyranoside and 7-propionyldocetaxel 3''-O-β-D-xylopyranoside showed in vitro cytotoxic activity against human cancer cells, whereas 7-propionyldocetaxel 3''-O-β-D-galactopyranoside exerted low cytotoxicity.
Assessment of Myocardial Viability by Using Newly Developed Myocardial SPECT Imaging. (1992)

Thallium myocardial imaging has been widely available for the detection of myocardial ischemia and assessment of myocardial viability in coronary artery diseases. However, myocardial imaging using SPECT and gamma-emitting radiopharmaceuticals has been developed for accurate evaluation of myocardial infarction and ischemia. The present study was undertaken to clinically evaluate myocardial necrosis, metabolism and sympathetic nerve activity. In this study, myocardial fatty acid metabolism was assessed using 123I-BMIPP, myocardial sympathetic neural activity was assessed using 123I-MIBG and myocardial necrosis was assessed using 111-In-antimyosin Fab. Dual energy SPECT using these new agents and thallium gives precise characterization of myocardial viability in coronary artery disease.