gebhart/patrepeval huggingface dataset:
Genotypic Variability of Soybean Response to Agrobacterium Strains Harboring the Ti or Ri Plasmids (1985)

Twenty four diverse cultivars of soybean (Glycine max [L.] Merrill) and three lines of its annual wild progenitor Glycine soja Sieb and Zucc. were tested for their response to Agrobacterium strains harboring either the Ti (tumor-inducing) plasmid (pTi) from Agrobacterium tumefaciens or the Ri (root-inducing) plasmid (pRi) from Agrobacterium rhizogenes following uniform wounding and inoculation. Based upon gall weight at 8 weeks postinfection, three G. max cultivars (Biloxi, Jupiter, and Peking) and one G. soja line, Plant Introduction (PI) 398.693B, were judged highly susceptible to A. tumefaciens strain A348 (pTiA6), ten genotypes moderately susceptible, 11 weakly susceptible, and two nonsusceptible. Of 26 genotypes inoculated with strain R1000 (pRiA4b), only seven responded in a clearly susceptible fashion by forming small, fleshy roots at internodal infection sites. Cotyledons excised from 1- or 3-day old seedlings of Peking and Biloxi cultivars also formed galls when infected in vitro with agrobacteria carrying either the Ti or Ri plasmid. Tumor lines established from cotyledon and stem galls induced by A. tumefaciens A348 (pTiA6) exhibited the T-DNA borne traits of phytohormone-independent growth and octopine synthesis. Additionally, DNA isolated from cultured tumors hybridized with labeled T-DNA probe.
A novel technique based on a PNA hybridization probe and FRET principle for quantification of mutant genotype in fibrous dysplasia/McCune-Albright syndrome (2004)

Somatic mutations are present in various proportions in numerous developmental pathologies. Somatic activating missense mutations of the GNAS gene encoding the Gs(alpha) protein have previously been shown to be the cause of fibrous dysplasia of bone (FD)/McCune-Albright syndrome (MAS). Because in MAS patients, tissues as diverse as melanocytes, gonads and bone are affected, it is generally accepted that the GNAS mutation in this disease must have occurred early in development. Interestingly, it has been shown that the development of an active FD lesion may require both normal and mutant cells. Studies of the somatic mosaic states of FD/MAS and many other somatic diseases need an accurate method to determine the ratio of mutant to normal cells in a given tissue. A new method for quantification of the mutant:normal ratio of cells using a PNA hybridization probe-based FRET technique was developed. This novel technique, with a linear sensitivity of 2.5% mutant alleles, was used to detect the percentage mutant cells in a number of tissue and cell culture samples derived from FD/MAS lesions and could easily be adapted for the quantification of mutations in a large spectrum of diseases including cancer.
Criteria And Scope Conditions For A Theory And Measure Of Social Presence (2001)

The need for a theory of social presence is more pressing as the Internet and virtual environments become increasing social. With time we can observe an increase in social interaction not only among users, but also between users and computer agents. A robust and detailed theory and measure of social presence could contribute to our understanding and explaining social behavior in mediated environments, allow researchers to predict and measure differences among media interfaces, and to guide the design of new social environments and interfaces. The article reviews, classifies, and critiques existing theories and measures of social presence. A set of criteria and scope conditions is proposed to address weaknesses in past theories and measures and to provide clear criteria for a measurement theory of social presence. DEFINITION OF THE PROBLEM
Protein Structure Prediction: A Practical Approach (1997)

1.: Protein structure prediction - principles and approaches. 2.: Protein sequence alignment and database scanning. 3.: Identification of protein sequence motifs. 4.: Prediction of secondary structure. 5.: Prediction of transmembrane protein topology. 6.: Comparative modelling of proteins. 7.: Antibody combining sites: structure and prediction. 8.: Protein folds and their recognition from sequence. 9.: The combinatorial approach. 10.: Modelling protein conformation by molecular mechanics and dynamics. 11.: Docking ligands to proteins. 12.: The prediction challenge
LED-Lit LCD TVs (2008)

Recent advances of LED-lit LCD TVs are reviewed. The influence of LED backlight on the color performance, electro-optic characteristics of the LCD TVs, and color-sequential LCDs are emphasized. The LED backlit LCDs not only exhibits a wider color gamut but also has a ∼ 1.3–2.5X smaller color shift than that of CCFL-BLU especially when there are no color filters used. Wide view angle of higher than 100:1 within the 85° viewing cone can be guaranteed with the optimal film compensation schemes. The LED light source as a 2D adaptive dimming backlight not only enhances the viewing angle but also lowers the power consumption. A thin twisted-nematic cell filled with a high birefringence exhibits a response time less than 2 ms, which is attractive for color sequential display using RGB LEDs.
High‐Performance Printed Transistors Realized Using Femtoliter Gravure‐Printed Sub‐10 μm Metallic Nanoparticle Patterns and Highly Uniform Polymer Dielectric and Semiconductor Layers (2012)

Using a novel high-speed, femtoliter-scale, micro-gravure printing with unprecedented scaling to the sub-10 μm regime and appropriately formulated, characterized, and optimized nanoparticle and polymer ink materials, highly scaled organic thin-film-transistors (OTFTs) are realized. They have excellent DC and AC characteristics and achieve record transition frequencies of 300 kHz, which opens up new classes of applications. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Establishment and characterization of conditionally immortalized cells from the mouse urogenital ridge (1996)

Cell cultures from the urogenital ridge have been established to facilitate the study of the regulation and downstream interactions of Sry in mammalian sex determination. Cells have been explanted from transgenic mice carrying a temperature sensitive SV40 large T-antigen, and established in ongoing cultures. Analysis of the cells in these cultures at the electron microscope level reveals multiple cell types that compare to the cell types found in vivo during this period of development. Primordial germ cells, that are simultaneously explanted in the course of these experiments, also survive in culture. The explants undergo a morphogenetic organization into branching cord-like structures when cells are trypsinized and plated in extracellular matrix (Matrigel). We analyzed the expression of a number of molecular markers of the fetal gonad during monolayer culture, during in vitro morphogenesis in Matrigel, and in clonal lines derived from the complex explants. This analysis included Sry which is found to be expressed in some cultures from XY urogenital ridges that have been maintained for as long as 8 months.
Correlated measurements of free and total intracellular calcium concentration in central nervous system neurons (1999)

Transient changes in the intracellular concentration of free calcium ([Ca2+])i) act as a trigger or modulator for a large number of important neuronal processes. Such transients can originate from voltage- or ligand-gated fluxes of Ca2+ into the cytoplasm from the extracellular space, or by ligand- or Ca2+(-)gated release from intracellular stores. Characterizing the sources and spatio-temporal patterns of [Ca2+]i transients is critical for understanding the role of different neuronal compartments in dendritic integration and synaptic plasticity. Optical imaging of fluorescent indicators sensitive to free Ca2+ is especially suited to studying such phenomena because this approach offers simultaneous monitoring of large regions of the dendritic tree in individual living central nervous system neurons. In contrast, energy-dispersive X-ray (EDX) microanalysis provides quantitative information on the amount and location of intracellular total, i.e., free plus bound, calcium (Ca) within specific subcellular dendritic compartments as a function of the activity state of the neuron. When optical measurements of [Ca2+]i transients and parallel EDX measurements of Ca content are used in tandem, and correlated simultaneously with electrophysiological measurements of neuronal activity, the combined information provides a relatively general picture of spatio-temporal neuronal total Ca fluctuations. To illustrate the kinds of information available with this approach, we review here results from our ongoing work aimed at evaluating the role of various Ca uptake, release, sequestration, and extrusion mechanisms in the generation and termination of [Ca2+]i transients in dendrites of pyramidal neurons in hippocampal slices during and after synaptic activity. Our observations support the long-standing speculation that the dendritic endoplasmic reticulum acts not only as an intracellular Ca2+ source that can be mobilized by a signal cascade originating at activated synapses, but also as a major intracellular Ca sink involved in active clearance mechanisms after voltage- and ligand-gated Ca2+ influx.
Temporal Detection And Processing Of Transparent Overlays For Video Indexing And Enhancement (2005)

Publication in the conference proceedings of EUSIPCO, Antalya, Turkey, 2005
Elevated BUBR1 Expression Is Associated with Poor Survival in Early Breast Cancer Patients (2013)

BUBR1 (budding uninhibited by benzimidazole-related 1) represents the component of a controlling complex in mitosis. Defects in mitotic control complex result in chromosomal instability and, as a result, disturb the mitotic process. This study was aimed at examining the prognostic value linked to the expression of BUBR1 in a group of patients with breast cancer. We analyzed the expression of BUBR1 in 98 stage II breast cancer patients with a median follow-up of 15 years. Immunohistochemical reactions were performed using monoclonal antibodies against BUBR1. We also studied the prognostic value of BUBR1 mRNA expression using the Kaplan-Meier (KM) plotter, which assessed the effect of 22,277 genes on survival in 2422 breast cancer patients. A background database was established using gene expression data and survival information on 2422 patients downloaded from the Gene Expression Omnibus (GEO; Affymetrix HGU133A and HGU133+2 microarrays). The median relapse-free survival was 6.43 years. Univariate and multivariate analyses showed that higher expression of BUBR1 was typical for cases of shorter overall survival, disease-free time, and disease-specific survival. KM plotter analysis showed that elevated BUBR1 mRNA expression had a negative impact on patients' relapse-free, distant metastases-free, and overall survival. Elevated BUBR1 expression was associated with poor survival in early stage breast cancer patients.
Discovery of OSI-906: A Selective and Orally Efficacious Dual Inhibitor of the IGF-1 Receptor and Insulin Receptor (2009)

OSI-906 is a novel, potent, selective and orally bioavailable dual IGF-1R/IR kinase inhibitor with favorable preclinical drug-like properties, which has demonstrated in vivo efficacy in tumor models and is currently in clinical testing.
A system of vectors for Bacillus subtilis spore surface display (2014)

Described system of vectors is a versatile tool for display of heterologous proteins on the surface of B. subtilis spores. Such recombinant spores can be further used as for example biocatalysts or antigen-carriers in vaccine formulations. The lack of antibiotic resistance genes in the system makes such spores an interesting option for applications in which a possible release to the environment can occur.
Person-to-Person Transmission of Andes Virus (2005)

Despite the fact that rodents are considered to be the infectious source of hantavirus for humans, another route of transmission was demonstrated. Andes virus (ANDV) has been responsible for most of the cases recorded in Argentina. Person-to-person transmission of ANDV Sout lineage was described during an outbreak of hantavirus pulmonary syndrome in southwest Argentina. In this study, we analyzed 4 clusters that occurred in 2 disease-endemic areas for different ANDV lineages. We found new evidence of interhuman transmission for ANDV Sout lineage and described the first event in which another lineage, ANDV Cent BsAs, was implicated in this mechanism of transmission. On the basis of epidemiologic and genetic data, we concluded that person-to-person spread of the virus likely took place during the prodromal phase or shortly after it ended, since close and prolonged contact occurred in the events analyzed here, and the incubation period was 15-24 days.
The Road for Nanomaterials Industry: A Review of Carbon Nanotube Production, Post‐Treatment, and Bulk Applications for Composites and Energy Storage (2013)

The innovation on the low dimensional nanomaterials brings the rapid growth of nano community. Developing the controllable production and commercial applications of nanomaterials for sustainable society is highly concerned. Herein, carbon nanotubes (CNTs) with sp(2) carbon bonding, excellent mechanical, electrical, thermal, as well as transport properties are selected as model nanomaterials to demonstrate the road of nanomaterials towards industry. The engineering principles of the mass production and recent progress in the area of CNT purification and dispersion are described, as well as its bulk application for nanocomposites and energy storage. The environmental, health, and safety considerations of CNTs, and recent progress in CNT commercialization are also included. With the effort from the CNT industry during the past 10 years, the price of multi-walled CNTs have decreased from 45 000 to 100 $ kg(-1) and the productivity increased to several hundred tons per year for commercial applications in Li ion battery and nanocomposites. When the prices of CNTs decrease to 10 $ kg(-1) , their applications as composites and conductive fillers at a million ton scale can be anticipated, replacing conventional carbon black fillers. Compared with traditional bulk chemicals, the controllable synthesis and applications of CNTs on a million ton scale are still far from being achieved due to the challenges in production, purification, dispersion, and commercial application. The basic knowledge of growth mechanisms, efficient and controllable routes for CNT production, the environmental and safety issues, and the commercialization models are still inadequate. The gap between the basic scientific research and industrial development should be bridged by multidisciplinary research for the rapid growth of CNT nano-industry.
Mechanism of Cleavage of Apurinic Sites by 9-Aminoellipticine (1989)

We have studied the kinetics of breakage of apurinic (AP) sites by the intercalating agent 9-aminoellipticine using fluorimetric methods with single (ss)- and double (ds)-stranded apurinic DNA. In order to understand the chemical process, high performance liquid chromatography was used to follow the reaction kinetics with the apurinic oligonucleotide model T(AP)T. The unstable intermediate, which is responsible for the beta-elimination step, is a Schiff base resulting from the interaction of the amino group of the aromatic amine with the aldehyde function of the deoxyribose moiety (AP site). Fluorescence occurs simultaneously with the breakage of both ss and ds DNA and of the oligonucleotide and arises from the formation of a conjugated double bond on the Schiff base through the beta-elimination reaction. In optimal conditions, the second order rate constant for the fluorescence build up is 15 x 10(3) min-1 M-1 for ds DNA and 0.105 x 10(3) min-1 M-1 for T(AP)T. The ability of 9-aminoellipticine to induce fluorescence and breakage of ss DNA and T(AP)T shows that intercalation is not essential for this reaction to occur. Nevertheless, the greater rate constant with DNA suggests that stacking is an important parameter for the reaction of the aromatic amine with the AP site.
Isolation and Culture of Murine Macrophages (2004)

The two most convenient sources of primary murine macrophages are the bone marrow and the peritoneal cavity. Resident peritoneal macrophages can readily be harvested from mice and purified by adherence to tissue culture plastic. The injection of Bio-Gel polyacrylamide beads or thioglycollate broth into the peritoneal cavity produces an inflammatory response allowing the purification of large numbers of elicited macrophages. The production of an activated macrophage population can be achieved by using Bacillus-Calmette-Guerin as the inflammatory stimulus. Resident bone marrow macrophages can be isolated following enzymatic separation of cells from bone marrow plugs and enrichment on 30% fetal calf serum containing medium or Ficoll-Hypaque gradients. Bone marrow-derived macrophages can be produced by differentiating nonadherent macrophage precursors with medium containing macrophage colony-stimulating factor.
Large-Scale Alignment of ABC Block Copolymer Microdomains via Solvent Vapor Treatment (2000)

We have studied the microdomain morphology of thin ABC triblock copolymer films supported by a solid substrate. The films were exposed to various solvent vapors, and the effect of the solvent removal speed on the resulting morphologies is investigated. Slow solvent extraction rates lead to a parallel alignment of lamellar microphases within the plane of the film. On fast drying, a perpendicular orientation of the lamellae is found. In the case of block copolymer samples with a highly anisotropic macroscopic shape, the microdomains can be aligned over large lateral areas. The results are discussed in view of the mechanical strain fields present during the drying process.
Dendritic Molecular Transporters Provide Control of Delivery to Intracellular Compartments (2007)

Novel biocompatible macromolecular vectors were developed that not only enable transport of bioactive cargo across the cell membrane but also control the delivery into defined intracellular compartments. This work describes the synthesis and design of two non-peptidic fluorescently labeled Newkome-type dendrimers, differentiated over a varied alkyl spacer with guanidine end moieties. The internalization of the fluorescein-labeled molecular transporter into mammalian cells showed strong subcellular localizations, evident with both live cells and fixed cells costained with DAPI, a nuclear stain. We observed that the subcellular distribution of these vectors varied significantly, as one of the vectors concentrates in the nucleus (FD-1) while the other (FD-2) concentrates in the cytosol. All experiments performed with NIH-3T3 fibroblasts and human microvascular endothelial cells (HMEC) showed similar results. The differential localization patterns of the two molecular transporters can be controlled through the variation of alkyl spacer length at the terminal generation of the dendrimer. Intracellular delivery of bioactive entities into specific subcellular locations, utilizing this practical approach, might overcome limitations in drug delivery and pioneer future technologies in drug transport.
Cancer statistics, 2015 (2015)

Each year the American Cancer Society estimates the numbers of new cancer cases and deaths that will occur in the United States in the current year and compiles the most recent data on cancer incidence, mortality, and survival. Incidence data were collected by the National Cancer Institute (Surveillance, Epidemiology, and End Results [SEER] Program), the Centers for Disease Control and Prevention (National Program of Cancer Registries), and the North American Association of Central Cancer Registries. Mortality data were collected by the National Center for Health Statistics. A total of 1,658,370 new cancer cases and 589,430 cancer deaths are projected to occur in the United States in 2015. During the most recent 5 years for which there are data (2007-2011), delay-adjusted cancer incidence rates (13 oldest SEER registries) declined by 1.8% per year in men and were stable in women, while cancer death rates nationwide decreased by 1.8% per year in men and by 1.4% per year in women. The overall cancer death rate decreased from 215.1 (per 100,000 population) in 1991 to 168.7 in 2011, a total relative decline of 22%. However, the magnitude of the decline varied by state, and was generally lowest in the South (∼15%) and highest in the Northeast (≥20%). For example, there were declines of 25% to 30% in Maryland, New Jersey, Massachusetts, New York, and Delaware, which collectively averted 29,000 cancer deaths in 2011 as a result of this progress. Further gains can be accelerated by applying existing cancer control knowledge across all segments of the population.
Macroion Attraction Due to Electrostatic Correlation between Screening Counterions. 1. Mobile Surface-Adsorbed Ions and Diffuse Ion Cloud (1996)

Highly charged macroion surfaces in solutions of multivalent electrolytes attract each other electrostatically through correlations in their counterion environment. We show that significant correlation occurs when the counterion distribution has a pseudo-two-dimensional character. This allows us to treat the electrostatic correlation attraction semianalytically by reducing the problem to interaction between layers of adsorbed but mobile counterions neutralizing surfaces of similar charge density. Both when the counterion distribution is in the two-dimensional limit, and when it has a more realistic three-dimensional character, Coulomb repulsion between counterions produces an alternation of positive and negative charges at the surface. Two such apposing patterns adjust complementarily to each other, resulting in electrostatic attraction of the surfaces. The magnitude of this attraction depends solely on the surface charge density and the solution dielectric constant, while its range is defined by the size of the planar correlation hole around each ion. The attraction is stable with respect to the disruptive influence of planar thermal motion of the ions. The theory enables construction of a universal function which, after being scaled with the appropriate parameters of the system, yields the attractive electrostatic correlation pressure.
Serine-cis-proline and Serine-trans-proline Isosteres:  Stereoselective Synthesis of (Z)- and (E)-Alkene Mimics by Still−Wittig and Ireland−Claisen Rearrangements (2003)

Two new amide isosteres of Ser-cis-Pro and Ser-trans-Pro dipeptides were designed and stereoselectively synthesized to be incorporated into potential inhibitors of the phosphorylation-dependent peptidylprolyl isomerase Pin1, an essential regulator of the cell cycle. The cis mimic, the (Z)-alkene isomer, was formed through the use of a Still-Wittig [2,3]-sigmatropic rearrangement, while the trans mimic, the (E)-alkene, was synthesized through the use of an Ireland-Claisen [3,3]-sigmatropic rearrangement. Starting from N-Boc-Ser(OBn)-N(OMe)Me, both mimics were synthesized in Boc-protected form suitable for peptide synthesis with an overall yield of 20% in 10 steps for the cis mimic and 13% in eight steps for the trans mimic.