gebhart/patrepeval huggingface dataset:
Development of virus vectors for gene therapy of β chain hemoglobinopathies: flanking with a chromatin insulator reduces γ-globin gene silencing in vivo (2002)

We have previously described the development of oncoretrovirus vectors for human gamma-globin using a truncated beta-globin promoter, modified gamma-globin cassette, and alpha-globin enhancer. However, one of these vectors is genetically unstable, and both vectors exhibit variable expression patterns in cultured cells, common characteristics of oncoretrovirus vectors for globin genes. To address these problems, we identified and removed the vector sequences responsible for genetic instability and flanked the resultant vector with the chicken beta-globin HS4 chromatin insulator to protect expression from chromosomal position effects. After determining that flanking with the cHS4 element allowed higher, more uniform levels of gamma-globin expression in MEL cell lines, we tested these vectors using a mouse bone marrow transduction and transplantation model. When present, the gamma-globin cassettes from the uninsulated vectors were expressed in only 2% to 5% of red blood cells (RBCs) long term, indicating they are highly sensitive to epigenetic silencing. In contrast, when present the gamma-globin cassette from the insulated vector was expressed in 49% +/- 20% of RBCs long term. RNase protection analysis indicated that the insulated gamma-globin cassette was expressed at 23% +/- 16% per copy of mouse alpha-globin in transduced RBCs. These results demonstrate that flanking a globin vector with the cHS4 insulator increases the likelihood of expression nearly 10-fold, which in turn allows for gamma-globin expression approaching the therapeutic range for sickle cell anemia and beta thalassemia.
Monitoring the stage of diagonalization in Jacobi-type methods (2002)

Since the stage of diagonalization of Jacobi-type methods is difficult to monitor in a parallel environment, it is usually proposed to execute a predetermined number of sweeps (iterations) on a parallel processor array. A possibility for monitoring the stage of diagonalization is essential in order to avoid the execution of a significant number of unnecessary sweeps. Based on a Lemma used for a generalized proof of the quadratic convergence of the Jacobi EVD and SVD methods a new criteria for monitoring the stage of diagonalization is derived. Using this criteria it can easily be monitored when the stage of quadratic convergence is reached (only one bit yields this information). Therefore, only the (small) number of quadratically convergent sweeps must be predetermined. A further similar criteria particularly useful for Jacobi-type methods using CORDIC-based approximate rotations is also given.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A robust dynamic niching genetic clustering approach for image segmentation (2011)

In this paper, a novel genetic clustering algorithm based on dynamic niching (DNGA) for image segmentation is proposed. It is an effective and robust approach to image segmentation on the basis of a total similarity function relating to the approximate density shape estimation. In the new algorithm, a dynamic identification of the niches is performed at each generation to automatically evolve the proper number of clusters and appropriate cluster centers of the data set. Moreover, a local search method is embeded in the evolutionary process which makes the dynamic niching method insensitive to the radius of the niche. Compared to existing methods, DNGA algorithm does not need to pre-specify the number of segmentation. Several images are used to demonstrate its superiority. The experimental results show that DNGA algorithm has high performance, effectiveness and flexibility.
One-Pot Silver-Catalyzed and PIDA-Mediated Sequential Reactions: Synthesis of Polysubstituted Pyrroles Directly from Alkynoates and Amines (2009)

The addition/oxidative cyclization of alkynes with amines in the presence of AgBF(4) catalyst and PIDA oxidant leads to polysubstituted pyrroles. The reaction corresponds to the construction of a pyrrole fragment, which also provides a new way to the formation of C-C bonds.
Microstructure and field-emission characteristics of boron-doped Si nanoparticle chains (2001)

One-dimensional boron-doped Si nanoparticle chains synthesized in bulk quantity using laser ablating SiO powder mixed with B2O3 powder have been investigated by transmission electron microscopy and measured by electron field emission. Transmission electron microscopy showed that the outer diameters of the nanoparticles in the chains were around 15 nm. High-resolution transmission electron microscopy showed that the nanoparticles had perfect lattices with an 11 nm crystalline core and a 2 nm amorphous oxide outerlayer while the distance of the interparticles was 4 nm. Field-emission measurement showed that the turn-on field of Si nanoparticle chains was 6 V/μm, which was much lower than that of undoped Si nanowires (9 V/μm). X-ray photoelectron spectroscopy confirmed that the Si nanoparticles had been heavily doped by boron.
Improved interface stability of phase-change recording media (2003)

During writing, the phase-change layer in a medium for optical recording is heated to above its melting temperature of typically 600 °C. Although this situation lasts for only 10–100 ns, it is repeated many times during consecutive overwrite cycles. As a result, the phase-change layer gradually reacts with the adjacent ZnS:SiO2 isolation layers, which deteriorates the overwrite performance. Applying Rutherford backscattering spectrometry, we observed that thin caplayers of AlOxNy, HfOxNy, Si3N4, or In–SnOx, introduced at both interfaces of the phase-change layer, suppress this reaction adequately. Such layers appear also very beneficial for the inherently unstable interface between the Ag mirror and the ZnS:SiO2 dielectric layer.
Treatment-Response Models for Counterfactual Reasoning with Continuous-time, Continuous-valued Interventions (2017)

Treatment effects can be estimated from observational data as the difference in potential outcomes. In this paper, we address the challenge of estimating the potential outcome when treatment-dose levels can vary continuously over time. Further, the outcome variable may not be measured at a regular frequency. Our proposed solution represents the treatment response curves using linear time-invariant dynamical systems---this provides a flexible means for modeling response over time to highly variable dose curves. Moreover, for multivariate data, the proposed method: uncovers shared structure in treatment response and the baseline across multiple markers; and, flexibly models challenging correlation structure both across and within signals over time. For this, we build upon the framework of multiple-output Gaussian Processes. On simulated and a challenging clinical dataset, we show significant gains in accuracy over state-of-the-art models.
Lymphocyte Proliferation Response During Eimeria tenella Infection Assessed by a New, Reliable, Nonradioactive Colorimetric Assay (2002)

The application of a tetrazolium salt, WST-8, 2-(2-methoxy-4-nitrophenyl)-3-(4-nitrophenyl)-5-(2,4-disulfophenyl)-2H tetrazolium, monosodium salt to the lymphocyte proliferation assay in the chicken system was evaluated. Proliferation of concanavalin (Con A)-induced splenic lymphocytes and peripheral blood lymphocytes (PBL) was evaluated with WST-8 and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT). Coefficients of correlation (r) between these two reagents were 0.98 and 0.97 in splenic lymphocytes and PBL, respectively. In general, the sensitivity of the WST-8 assay was significantly higher than that of the MTT assay, and the standard deviations of the WST-8 assay were significantly lower than those of the MTT assay. The WST-8 assay was fast and highly reproducible and provided a good indication of mitogen-induced proliferation of spleen cells induced by Con A. With the use of the WST-8 assay, splenic mitogenic response of chickens infected with Eimeria decreased transiently at 7 days but increased significantly at 10 days after primary infection compared with that of uninfected chickens. Additionally, the measurement of interleukin (IL)-2 production with WST-8 was highly reproducible and showed a significant increase in IL-2 production upon stimulation of Eimeria tenella-immune spleen cells with Con A. After E. tenella infection, splenic IL-2 production increased significantly at 7 days post-primary and at 2 days post-secondary infection. The WST-8 assay is fast, simple, and more reproducible and sensitive than the MTT assay. This study demonstrates the effectiveness of the WST-8 assay to assess cell-mediated immune response of chickens in normal and disease states.
Research on customer-oriented shopping guide system of suit-dress with intelligent characteristics (2009)

Suit-dress dealing via network is soaring in recent years and its commercial potential is enormous. Based on the analysis of the limitation of existing shopping guide Web sites, this paper proposes a customer-oriented shopping assistant system of suit-dress with intelligent characteristics. In this article, the shopping assistant system is composed of three functional modules: quantified and classified suit-dress database module, consumer individual database module and the dress recommendation module. A few of objective attributes, such as fabric, price and brand, are used to classify the dresses and some adjective gradable antonym pairs are chosen to quantify the style of clothing. These information about dresses are stored in the quantified and classified suit-dress database. Compared with the customer's requirement put in her individual database, the third module decides the sequence of recommendations. In addition, we illustrate the customer's purchasing process while using the system and discuss the possibility and the crucial issues to realize it.
Time delay spread measurements at 850 MHz and 1.7 GHz inside a metropolitan office building (1989)

Time delay spread and signal level measurements were made in a multistoried office building in New York City at 850 MHz and 1.7 GHz. No significant statistical difference in time delay spread was found at the two frequencies. The maximum root-mean-square time delay spread at both frequencies did not exceed 100 ns. Attenuation was very nearly the same at the two frequencies, within the limits of the experiment's accuracy.
Bispecific multivalent antibody studied by real-time interaction analysis for the development of an antigen-inhibition enzyme-linked immunosorbent assay (1996)

A bispecific antibody with specificities for both 7-hydroxycoumarin (7-OHC) and alkaline phosphatase (AP) was produced by chemically cross-linking two parental polyclonal antibodies. Real-time interaction analysis of the bispecific multivalent antibody (bsMAb) was performed using BIAcore, a surface plasmon resonance (SPR)-based biosensor, in order to confirm its bispecific nature. A 7-OHC-BSA conjugate was covalently immobilized to a dextran matrix to serve as the reaction surface and unconjugated bovine serum albumin (BSA) was immobilized on to a separate dextran matrix as a control surface. Immunoaffinity-purified bsMAb, parental anti-7-OHC antibody and AP were injected over both surfaces. The bsMAb was shown to bind both antigens, 7-OHC and AP, simultaneously. Comparison of the ratio of mass bound for bsMAb and AP (5:1) with the ratio of the molecular masses of bsMAb (approximately 300 kDa) and AP (85 kDa) (3.5:1) suggests that most of the bsMAb species possess both specificities. The bsMAb was employed in a one-step antigen-inhibition ELISA for the detection of 7-OHC. The assay was compared with a conventional ELISA approach employing an AP-labelled secondary antibody. The bispecific antibody approach proved to be faster and more sensitive, with a detection limit of 6 ng ml-1 as compared with approximately 50 ng ml-1 for the conventional approach. The assay was used for the quantification of free and total 7-OHC in urine samples from two healthy volunteers who had been administered coumarin. The accuracy and precision of the assay were assessed. The bispecific antibody-based assay gave similar results, accuracy and precision, but proved to be far more sensitive (limit of determination 6 ng ml-1 for total 7-OHC). It is concluded that real-time interaction analysis using BIAcor provides a rapid method for the evaluation of the bsMAb and it was verified that the bispecific product formed by chemical cross-linking of two parental antibodies offers a simple alternative for the development of a highly sensitive ELISA.
Carbohydrate antigen sialyl Lewis a--its pathophysiological significance and induction mechanism in cancer progression. (2007)

Carbohydrate antigen sialyl Lewis a (CA19-9) is the most frequently applied serum tumor marker for diagnosis of cancers in the digestive organs. Recent progress disclosed the presence of a normal counterpart of the determinant, namely disialyl Lewis a, which is predominantly expressed in non-malignant epithelial cells of the digestive organs, while sialyl Lewis a is preferentially expressed in cancers. The disialyl Lewis a determinant carries one extra sialic residue attached through a 2 --> 6 linkage to the GlcNAc moiety compared to cancer-associated sialyl Lewis a, which carries only one 2 --> 3 linked sialic acid residue (monosialyl Lewis a). Disialyl Lewis a in normal epithelial cells serves as a ligand for immunosuppressive receptors such as sialic acid binding immunoglobulin (Ig)-like lectins (siglec-7) and -9 expressed on resident monocytes/macrophages and maintains immunological homeostasis of mucosal membranes in digestive organs. Epigenetic silencing of a gene for a 2 --> 6 sialyl-transferase in the early stages of carcinogenesis results in an impairment of 2 --> 6 sialylation, leading to incomplete synthesis and accumulation of sialyl Lewis a, which lacks the 2 --> 6 linked sialic acid residue, in cancer cells. Simultaneous determination of serum levels of sialyl- and disialyl Lewis a, and calculation of the monosialyl/disialyl Lewis a ratio provide information useful for excluding a false-positive serum diagnosis, and also for averting the undesired influence of the Lewis blood group of patients on serum antigen levels. During the course of cancer progression in locally advanced cancers, tumor hypoxia induces transcription of several glycogenes involved in sialyl Lewis a synthesis. Expression of the determinant, consequently, is further accelerated in more malignant hypoxia-resistant cancer cell clones, which become predominant clones in advanced stage cancers and frequently develop hematogenous metastasis. Sialyl Lewis a, as well as its positional isomer sialyl Lewis x, serves as a ligand for vascular cell adhesion molecule E-selectin and facilitates hematogenous metastasis through mediating adhesion of circulating cancer cells to vascular endothelium. Patients having both strong sialyl Lewis a expression on cancer cells and enhanced E-selectin expression on vascular beds are at a greater risk of developing distant hematogenous metastasis.
Effects of Extended Feeding of Decocainized Erythroxylon Coca Leaves on Growth and Selected Organs in Rats and Rabbits (1988)

Erythroxylon coca leaves from the Trujillo area of Peru were extracted with methylene chloride to remove most cocaine-like alkaloids. The decocainized leaves were formulated in a honey-water vehicle and fed on a chronic basis to female rats for 32 weeks and female rabbits for 13 weeks. Rabbits fed decocainized leaves at doses of 21 or 210 mg demonstrated no significant change in growth (weight gain) when compared with those receiving vehicle. Histological findings were unremarkable except for fatty islands in the myocardium. Rats fed the decocainized leaves at doses of 1.5 and 15 mg demonstrated no significant changes in weight, whereas those receiving 150 mg had a significant decrease in weight gain when compared with control animals receiving vehicle. Necropsy findings in rats demonstrated pyometra in all groups receiving decocainized leaves as well as in some of the controls. Those rats with pyometra often exhibited endometrial metaplasia. Renal tubular calcification and proteinaceous material were consistently noted at all dose levels. Portal triaditis was also found in the livers of most rats.
Compensatory <b> <i>ahp</i> </b> C Gene Expression in Isoniazid-Resistant <b> <i>Mycobacterium tuberculosis</i> </b> (1996)

Mutations that eliminate KatG catalase-peroxidase activity prevent activation of isoniazid and are a major mechanism of resistance to this principal drug for the treatment of Mycobacterium tuberculosis infections. However, the loss of KatG activity in clinical isolates seemed paradoxical because KatG is considered an important factor for the survival of the organism. Expression of either KatG or the recently identified alkyl hydroperoxidase AhpC was sufficient to protect bacilli against the toxic effects of organic peroxides. To survive during infection, isoniazid-resistant KatG mutants have apparently compensated for the loss of KatG catalase-peroxidase activity by a second mutation, resulting in hyperexpression of AhpC.
Properties of epitaxial SrRuO3 thin films (1993)

SrRuO3 thin films were deposited on (100) LaAlO3 using pulsed laser deposition. The films were (001) oriented normal to the substrate surface with a high degree of in-plane orientation with respect to the substrate’s major axes. An ion beam minimum yield of 2.5% was obtained for the films, indicating high crystallinity. The films exhibited metallic behavior with a room temperature resistivity of ∼200 mW cm. A kink in the resistivity, corresponding to a ferromagnetic phase transition, was observed at ∼160 K. It was found that SrRuO3 is structurally and chemically compatible with the YaB2Cu3O7−d (YBCO) superconductors. High quality YBCO films were obtained on SrRuO3 LaAlO3. Multilayers of YBCO/SrRuO3 were successfully fabricated.
[The prevention of hypertension]. (1989)

The instability is shown of some types of hemodynamics in the course of 24 hours in healthy persons. Healthy persons with initial hyper- and normokinetic types of blood circulation are characterized by a disposition to inadequate reaction of the vascular tone in response to diurnal changes of the minute blood volume. Periodic elevation of the peripheral vascular resistance above permissible levels makes it necessary to carry out prophylactic measures against hypertensive disease.
MBE growth optimization of InAs (001) homoepitaxy (2013)

The optimal conditions for growth of homoepitaxial InAs layers by molecular beam epitaxy were investigated over a wide range of substrate temperatures and As2/In flux ratios at a growth rate of 0.66 monolayer/s. Material quality was investigated using a variety of techniques: differential interference contrast microscopy, scanning electron microscopy, and atomic force microscopy. The results indicated that the InAs layer grown at a temperature between 430 and 450 °C with an As2/In flux ratio of about 15:1 yielded the highest quality, with a defect density of 2 × 104 cm−2 and a root mean square roughness of 0.19 nm. The quality can be further improved by growth at a lower growth rate of 0.22 monolayer/s. The morphology of large oval hillock defects on the InAs layers suggested that these defects originated at the substrate surface.
Elimination of transducer bond corrections in accurate ultrasonic-wave velocity measurements by use of capacitive transducers (1977)

A capacitive-driver–capacitive-detector system for generation and detection of ultrasonic waves has been developed. This eliminates the necessity of bonding piezoelectric transducers to solid samples. With the capacitive-driver–capacitive-detector system, free–free boundary conditions exist at the sample surfaces and longitudinal ultrasonic-wave velocities in solids can be measured accurately without correcting for ultrasonic-wave phase shifts due to sample-bonded transducer interfaces. The capacitive driver has a mica dielectric which increases the breakdown potential, but maintains the free–free boundary conditions at the solid specimen surfaces. This allows for a larger-amplitude ultrasonic signal to be generated in the sample than is possible with an air-gap capacitive driver. This improves the precision of the measurement. The accuracy of the method is comparable with that of bonded-transducer methods, after bond corrections are made.
PIK3CA Mutations Frequently Coexist with RAS and BRAF Mutations in Patients with Advanced Cancers (2011)

PIK3CA, RAS (KRAS, NRAS), and BRAF mutations are frequent in diverse tumors. In a wide variety of tumors, PIK3CA mutations coexist with RAS (KRAS, NRAS) and BRAF mutations.
Cloning, expression, and nucleotide sequence of rat liver sterol carrier protein 2 cDNAs. (1991)

The structure and expression of rat sterol carrier protein 2 (SCP2) were studied by cloning and sequencing SCP2 cDNAs and by hybridizing the SCP2 cDNA to RNA from a variety of rat tissues. Initial screening of a rat liver cDNA library with an oligonucleotide probe derived from the rat SCP2 protein sequence revealed an 825-base pair cDNA clone coding for the complete SCP2 protein sequence. Our results suggest that rat liver SCP2 is 143 amino acid residues long, including a 20-amino acid residue prepeptide (pre-SCP2). Using the rat SCP2 cDNA as a probe for Northern blot hybridization analyses under high stringency conditions with rat liver poly(A) RNA, four mRNA species differing in their sizes and levels of expression are detected. The lengths of the corresponding mRNAs are 0.8, 1.4, 2.1, and 2.7 kilobases (kb), respectively. In all other tissues analyzed mRNAs hybridizing to the SCP2 cDNA probe were detected in levels much lower than in the liver. In these tissues the vast majority of the expressed SCP2 mRNAs consists of the 0.8-kb mRNA. Results from Southern blotting hybridization analyses with rat genomic DNA suggest that the four different mRNA species are products of a single gene. Extensive screening of rat liver cDNA libraries using rat liver SCP2 cDNA probes led to the isolation of 10 additional clones, all of them containing cDNA insertions longer than 0.8 kb. Restriction mapping and nucleotide sequencing analyses of these cDNAs indicate that eight extend upstream of the SCP2 cDNA, and two extend 5' as well as 3'. Translation of the sequence extending most upstream suggests that this cDNA is a nearly full-length cDNA coding for a protein of 547 amino acids (SCP chi). SCP chi contains a 404-amino acid amino-terminal extension as compared with pre-SCP2 whereas its carboxyl-terminal part is identical with pre-SCP2. Sequencing of the 3' extension cDNAs suggests that polyadenylation had occurred 651 nucleotides downstream as compared with the remaining cDNAs. A probe from this region hybridizes to the 1.4- and 2.7-kb mRNAs. From our data we conclude that the 1.4- and 2.7-kb mRNA species are generated by alternative polyadenylation of the 0.8- and 2.1-kb mRNAs, respectively. In contrast, the 2.1- and 2.7-kb mRNAs contain an approximately 1300-nucleotide extension upstream of the 0.8- and 1.4-kb mRNAs, suggesting differential splicing of the primary SCP2 gene transcript leading to expression of pre-SCP2 and SCP chi from a single gene.