gebhart/patrepeval huggingface dataset:
Diagnostic Accuracy of Canine Scent Detection in Early- and Late-Stage Lung and Breast Cancers (2006)

Training was efficient and cancer identification was accurate; in a matter of weeks, ordinary household dogs with only basic behavioral "puppy training" were trained to accurately distinguish breath samples of lung and breast cancer patients from those of controls. This pilot work using canine scent detection demonstrates the validity of using a biological system to examine exhaled breath in the diagnostic identification of lung and breast cancers. Future work should closely examine the chemistry of exhaled breath to identify which chemical compounds can most accurately identify the presence of cancer.
Identification of a novel isoform of the cyclic-nucleotide phosphodiesterase PDE3A expressed in vascular smooth-muscle myocytes (2000)

We have identified a new cyclic-nucleotide phosphodiesterase isoform, PDE3A, and cloned its cDNA from cultured aortic myocytes. The nucleotide sequence of its coding region is similar to that of the previously cloned myocardial isoform except for the absence of the initial 300–400nt that are present in the latter, as confirmed by reverse-transcriptase-mediated PCR, 5′ rapid amplification of cDNA ends and a ribonuclease protection assay. Expression in Spodoptera frugiperda (Sf9) cells yields a protein with catalytic activity and inhibitor sensitivity typical of the PDE3 family. The recombinant protein's molecular mass of approx. 131kDa is compatible with translation from an ATG sequence corresponding to nt 436–438 of the myocardial PDE3A coding region. Antibodies against residues 424–460 (nt 1270–1380) and 1125–1141 (nt 3373–3423) of the myocardial isoform react with an approx. 118kDa band in Western blots of homogenates of human aortic myocytes, whereas antibodies against residues 29–42 (nt 85–126) do not react with any bands in these homogenates. Our results suggest that a vascular smooth-muscle isoform (‘PDE3A2’) is a product of the same gene as the longer myocardial (‘PDE3A1’) and the shorter placental (‘PDE3A3’) isoforms and is generated pre-translationally in a manner that results in the absence of the 145 N-terminal amino acids of PDE3A1.
The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity (2017)

The improved high quality peach genome assembly (Peach v2.0) represents a valuable tool for the analysis of the genetic diversity, domestication, and as a vehicle for genetic improvement of peach and related Prunus species. Moreover, the important phylogenetic position of peach and the absence of recent whole genome duplication (WGD) events make peach a pivotal species for comparative genomics studies aiming at elucidating plant speciation and diversification processes.
Physical unclonable functions for device authentication and secret key generation (2007)

Physical Unclonable Functions (PUFs) are innovative circuit primitives that extract secrets from physical characteristics of integrated circuits (ICs). We present PUF designs that exploit inherent delay characteristics of wires and transistors that differ from chip to chip, and describe how PUFs can enable low-cost authentication of individual ICs and generate volatile secret keys for cryptographic operations.
Antitumor effects of L6, an IgG2a antibody that reacts with most human carcinomas. (1986)

Mouse monoclonal antibody L6 (IgG2a subtype) recognizes a ganglioside antigen expressed at the surface of cells from human non-small-cell lung carcinomas, breast carcinomas, and colon carcinomas. We now show that this antibody can lyse L6 antigen-positive human tumor cells in the presence of Leu-11b-positive human lymphocytes (i.e., mediate antibody-dependent cellular cytotoxicity) or human serum (mediate complement-dependent cytotoxicity) and that it can inhibit the outgrowth of an L6 antigen-positive human tumor transplanted onto nude mice.
Thrombin-induced endothelial barrier disruption in intact microvessels: role of RhoA/Rho kinase-myosin phosphatase axis (2008)

Endothelial hyperpermeability is regulated by a myosin light chain-2 (MLC2) phosphorylation-dependent contractile mechanism. Thrombin is a potent inducer of hyperpermeability of cultured monolayers of endothelial cells (ECs) via Rho kinase-mediated MLC2-phosphorylation. The aim of the present study was to investigate the effects of thrombin on in situ endothelial morphology and barrier integrity. Cytoskeletal dynamics, regions of paracellular flux, and MLC2-phosphorylation of ECs were visualized by digital three-dimensional imaging microscopy of pressurized rat kidney arterioles. Myosin phosphatase targeting subunit (MYPT1)-phosphorylation was used as a surrogate marker for Rho kinase activity. Thrombin induced the formation of F-actin filaments in ECs in situ and rounding of the ECs in the absence of obvious formation of gaps between ECs. These changes were accompanied by an increase in MLC2 phosphorylation and a decrease in barrier integrity. In vitro analysis revealed that Rho kinase activity on F-actin filaments was associated with a contractile response that enhanced opening of the barrier. Rho kinase activity was not detectable on F-actin filaments induced by histamine, an inducer of a more transient hyperpermeability response. Inhibition of the myosin phosphatase mimicked the effects of thrombin on barrier function. The thrombin-induced changes in in situ MLC2 phosphorylation and barrier function were Rho kinase dependent. These data demonstrate a direct effect of thrombin on EC morphology and barrier integrity in intact microvessels. Furthermore, they establish an important contribution of enhanced Rho kinase activity to the development of prolonged but not transient types of endothelial barrier dysfunction.
Virus‐induced gene silencing in tomato (2002)

We have previously demonstrated that a tobacco rattle virus (TRV)-based vector can be used in virus-induced gene silencing (VIGS) to study gene function in Nicotiana benthamiana. Here we show that recombinant TRV infects tomato plants and induces efficient gene silencing. Using this system, we suppressed the PDS, CTR1 and CTR2 genes in tomato. Suppression of CTR1 led to a constitutive ethylene response phenotype and up-regulation of an ethylene response gene, CHITINASE B. This phenotype is similar to Arabidopsis ctr1 mutant plants. We have constructed a modified TRV vector based on the GATEWAY recombination system, allowing restriction- and ligation-free cloning. Our results show that tomato expressed sequence tags (ESTs) can easily be cloned into this modified vector using a single set of primers. Using this vector, we have silenced RbcS and an endogenous gene homologous to the tomato EST cLED3L14. In the future, this modified vector system will facilitate large-scale functional analysis of tomato ESTs.
From Hierarchical to Open Access Electric Power Systems (2007)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> In this paper the modeling, monitoring, and control of electric power systems are presented from the point of view of large-scale dynamic systems. First a summary of current hierarchical operations is given, together with an assessment of the underlying assumptions. Next, the challenge of operating electric power systems over very broad ranges of system conditions is presented as an open sensing, estimation, and control problem. The latter part of this paper is motivated by fundamental technological and organizational changes. These are requiring a shift from hierarchical to multilayered open access modeling, monitoring, and control paradigms for large complex electric power systems. A vision of a novel information-based multilayered Dynamic Energy Control Protocols (DECPs) framework for facilitating evolution into open access just-in-time (JIT) and just-in-place (JIP) electricity services of the future is presented. </para>
Tracers and contrast agents in cardiovascular imaging: present and future. (1996)

This brief article addresses the current status and future potential of nuclear medicine, X-ray computed tomography (CT), ultrasound (US), and magnetic resonance (MR) imaging in the diagnosis of cardiovascular diseases. The currently perceived advantages and disadvantages, as well as the possible future roles, of each of the modalities with regard to the evaluation of coronary artery disease are delineated. The certain advent of MR and US myocardial contrast agents, combined with the inexorable pressures of health care reform, will alter the future usage patterns of all four modalities. Future debates about which modality should be used in which clinical situation will be based not on "anatomy vs function", nor on which specialty owns which "turf", but rather on the issues of cost effectiveness and patient outcomes.
Optimization of the Capsid of Recombinant Adeno-Associated Virus 2 (AAV2) Vectors: The Final Threshold? (2013)

The ubiquitin-proteasome pathway plays a critical role in the intracellular trafficking of AAV2 vectors, and phosphorylation of certain surface-exposed amino acid residues on the capsid provides the primary signal for ubiquitination. Removal of several critical tyrosine (Y) and serine (S) residues on the AAV2 capsid has been shown to significantly increase transduction efficiency compared with the wild-type (WT) vectors. In the present study, site-directed mutagenesis of each of the 17 surface-exposed threonine (T) residues was conducted, and the transduction efficiency of four of these mutants, T455V, T491V, T550V, and T659V, was observed to increase up to 4-fold in human HEK293 cells in vitro. The most critical Y, S, and T mutations were subsequently combined, and the quadruple-mutant (Y444+500+730F+T491V) AAV2 vector was identified as the most efficient. This vector increased the transduction efficiency ∼24-fold over the WT AAV2 vector, and ∼2-3-fold over the previously described triple-mutant (Y444+500+730F) vector in a murine hepatocyte cell line, H2.35, in vitro. Similar results were obtained in murine hepatocytes in vivo following tail vein injection of the Y444+500+730F+T491V scAAV2 vector, and whole-body bioluminescence imaging of C57BL/6 mice. The increase in the transduction efficiency of the Y-T quadruple-mutant over that of the Y triple-mutant correlated with an improved nuclear translocation of the vectors, which exceeded 90%. These observations suggest that further optimization of the AAV2 capsid by targeting amino acid residues involved in phosphorylation may not be possible. This study has thus led to the generation of a novel Y444+500+730F+T491V quadruple-mutant AAV2 vector with potential for use in liver-directed human gene therapy.
Garage Virtual Reality (1993)

This book/disk combination explains the latest developments in new computer graphics technology. The focus of the book, however, is the disk, which allows the reader to use existing software and experiment with the fascinating world of virtual reality on the computer screen. Users will learn about the history, state of the art and the future directions of virtual reality.
Composition-Tunable ZnxCd1-xSe Nanocrystals with High Luminescence and Stability (2003)

High-quality Zn(x)Cd(1-x)Se nanocrystals have been successfully prepared at high temperature by incorporating stoichiometric amounts of Zn and Se into pre-prepared CdSe nanocrystals. With increasing Zn content, a composition-tunable emission across most of the visible spectrum has been demonstrated by a systematic blue-shift in emission wavelength. The photoluminescence (PL) properties for the obtained Zn(x)Cd(1-x)Se nanocrystals (PL efficiency of 70-85%, fwhm = 22-30 nm) are comparable to those for the best reported CdSe-based QDs. In particular, they also have good PL properties in the blue spectral range. Moreover, the alloy nanocrystals can retain their high luminescence (PL efficiency of over 40%) when dispersed in aqueous solutions and maintain a symmetric peak shape and spectral position under rigorous experimental conditions. A rapid alloying process was observed at a temperature higher than "alloying point". The mechanism of the high luminescence efficiency and stability of Zn(x)Cd(1-x)Se nanocrystals is explored.
Analysis of the ReSuMe Learning Process For Spiking Neural Networks (2008)

Analysis of the ReSuMe Learning Process For Spiking Neural Networks In this paper we perform an analysis of the learning process with the ReSuMe method and spiking neural networks (Ponulak, 2005; Ponulak, 2006b). We investigate how the particular parameters of the learning algorithm affect the process of learning. We consider the issue of speeding up the adaptation process, while maintaining the stability of the optimal solution. This is an important issue in many real-life tasks where the neural networks are applied and where the fast learning convergence is highly desirable.
Regulation of theBacillus subtilis furandperRGenes by PerR: Not All Members of the PerR Regulon Are Peroxide Inducible (2002)

PerR is a ferric uptake repressor (Fur) homolog that functions as the central regulator of the inducible peroxide stress response in Bacillus subtilis. PerR has been previously demonstrated to regulate the mrgA, katA, ahpCF, hemAXCDBL, and zosA genes. We now demonstrate that PerR also mediates both the repression of its own gene and that of fur. Whereas PerR-mediated repression of most target genes can be elicited by either manganese or iron, repression of perR and fur is selective for manganese. Genetic studies indicate that repression of PerR regulon genes by either manganese or iron requires PerR and is generally independent of Fur. Indeed, in a fur mutant, iron-mediated repression is enhanced. Unexpectedly, repression of the fur gene by manganese appears to require both PerR and Fur, but only PerR binds to the fur regulatory region in vitro. The fur mutation appears to act indirectly by affecting cellular metal ion pools and thereby affecting PerR-mediated repression. While many components of the perR regulon are strongly induced by hydrogen peroxide, little, if any, induction of fur and perR could be demonstrated. Thus, not all components of the PerR regulon are components of the peroxide stimulon. We suggest that PerR exists in distinct metallated forms that differ in DNA target selectivity and in sensitivity to oxidation. This model is supported by the observation that the metal ion composition of the growth medium can greatly influence the transcriptional response of the various PerR regulon genes to hydrogen peroxide.
Increased expression of Fc receptors on neutrophils and monocytes may reflect ongoing bacterial infection (1996)

The Fc gammaR receptors for IgG, Fc gammaRI, Fc gammaRII and Fc gammaRIII were measured on neutrophils and monocytes from 36 patients suspected of systemic infection. These results were compared with 30 blood donor controls to assess the level of expression as an early indicator of bacterial infection. Fc gammaRI expression on neutrophils was found to be significantly increased from patients with systemic or localised infections, when compared to non-infected patient group, i.e., patients with no cultural evidence of bacterial infections, (p=0.02, p=0.04) or normal controls (p<0.0001, p=0.0005). Fc gammaRI expression on monocytes was also significantly increased in both of the infected groups compared to normal controls (p<0.0001, p=0.001); however, no significant difference could be seen when compared with the non-infected patients. Fc gammaRIII was found to be significantly increased on a subset of monocytes in patients with systemic or localised infections compared to the non-infected group (p=0.009, p=0.006) and compared to the normal controls (p=0.009, p=0.003). Infections caused by gram-negative bacilli induced a higher Fc gammaR response than infection with either streptococci or staphylococci. These data suggest that the measurement of Fc gammaRI on neutrophils and Fc gammaRIII on monocytes may be a useful rapid indicator of bacterial infection.
Structural and Functional Characterization of Monomeric EphrinA1 Binding Site to EphA2 Receptor (2012)

The EphA2 receptor is overexpressed in glioblastoma multiforme and has been to shown to contribute to cell transformation, tumor initiation, progression, and maintenance. EphrinA1 (eA1) is a preferred ligand for the receptor. Treatment with monomeric eA1, the form of eA1 found in the extracellular environment, causes receptor phosphorylation, internalization, and down-regulation with subsequent anti-tumor effects. Here, we investigated the structure-function relationship of a monomeric eA1 focusing on its G-H loop ((108)FQRFTPFTLGKEFKE(123)G), a highly conserved region among eAs that mediates binding to their receptors. Alanine substitution mutants of the G-H loop amino acids were transfected into U-251 MG glioblastoma multiforme cells, and functional activity of each mutant in conditioned media was assessed by EphA2 down-regulation, ERK and AKT activation and cellular response assays. Alanine substitutions at positions Pro-113 Thr-115, Gly-117, Glu-122, and also Gln-109 enhanced the EphA2 receptor down-regulation and decreased p-ERK and p-AKT. Substitution mutants of eA1 at positions Phe-108, Arg-110, Phe-111, Thr-112, Phe-114, Leu-116, Lys-118, Glu-119, and Phe-120 had a deleterious effect on EphA2 down-regulation when compared with eA1-WT. Mutants at positions Phe-108, Lys-18, Lys-121, Gly-123 retained similar properties to eA1-WT. Recombinant eA1-R110A, -T115A, -G117A, and -F120A have been found to exhibit the same characteristics as the ligands contained in the conditioned media mainly due to the differences in their binding to the receptor. Thus, we have identified variants of eA1 that possess either superagonistic or antagonistic properties. These new findings will be important in the understanding of the receptor/ligand interactions and in further design of anti-cancer therapies targeting the eA/EphA system.
Rapid Differentiation of a Rare Subset of Adult Human Lin−CD34−CD38− Cells Stimulated by Multiple Growth Factors In Vitro (1999)

Recently, several reports of lineage-negative (lin(-)) CD34(-) cells with in vivo hematopoietic activity have focused interest on the properties and growth factor response characteristics of these cells. We have now identified a combination of 5 growth factors that are necessary and sufficient to stimulate a marked mitogenic and differentiation response by a subset of human lin(-)CD34(-)CD38(-) cells present in normal adult human marrow and granulocyte colony-stimulating factor (G-CSF)-mobilized blood. Less than 0.1% of the cells in highly purified (including doubly sorted) lin(-)CD34(-)CD38(-) cells from these 2 sources formed colonies directly in semisolid medium or generated such cells after 6 weeks in long-term culture. Nevertheless, approximately 1% of the same lin(-)CD34(-)CD38(-) cells were able to proliferate rapidly in serum-free liquid suspension cultures containing human flt-3 ligand, Steel factor, thrombopoietin, interleukin-3 (IL-3), and hyper-IL-6 to produce a net 28- +/- 8-fold increase in total cells within 10 days. Of the cells present in these 10-day cultures, 5% +/- 2% were CD34(+) and 2.5% +/- 0.9% were erythroid, granulopoietic, megakaryocytopoietic, or multilineage colony-forming cells (CFC) (13 +/- 7 CFC per lin(-)CD34(-)CD38(-) pre-CFC). In contrast to lin(-)CD34(+)CD38(-) cells, this response of lin(-)CD34(-)CD38(-) cells required exposure to all of the 5 growth factors used. Up to 1.7 x 10(5) lin(-)CD34(-) adult marrow cells failed to engraft sublethally irradiated NOD/SCID-beta(2)M(-/-) mice. These studies demonstrate unique properties of a rare subset of lin(-)CD34(-)CD38(-) cells present in both adult human marrow and mobilized blood samples that allow their rapid proliferation and differentiation in vitro within an overall period of 3 to 4 weeks. The rapidity of this response challenges current concepts about the normal duration and coordinated control of these processes in adults.
Cloned mice derived from somatic cell nuclei. (2000)

In 1997, a cloned sheep "Dolly" was produced by nuclear transfer of somatic cell. The first birth of cloned mice derived from some somatic cells were succeeded in 1998. At present, it is shown that somatic cells, cumulus cells, fibroblasts and Sertoli cells can be used to the study of cloned animal as nuclear donor. In this study investigation was designed to compare with efficiency on the production of cloned embryos by using the microinjection and the electrofusion methods for nuclear transfer. Oocyte enucleation was performed with a micromanipulator. The oocyte was held by holding pipette, and was enucleated using a beveled pipette. Microinjection method: Cell's nucleus injection was carried out by piezo-micromanipulator. Cytochalasin B treated cumulus cell was aspirated into a injection pipette, and was broken its plasma membrane using the injection pipette. Then, the cumulus cell was injected into the enucleated ooplasm directly. Electrofusion method: The cell was aspirated into a beveled pipette, and then an aspirated cell was inserted into perivitelline space. Then, the pair of enucleated oocyte and cell was fused using electrical cell fusion apparatus. The reconstituted embryos were activated after nuclear transfer using St2+. Reconstituted embryos had been produced by the microinjection showed the embryonic development to over 8-cell stages. But, the rate of fragmentation of reconstituted embryos by the microinjection showed a little high rate in comparison with the electrofusion. When some reconstituted embryos by the microinjection were transplanted to pseudopregnant females' oviduct, 9 fetuses were observed at 14 days post coitum.
Developmental Transcript Profiling of Cyst Nematode Feeding Cells in Soybean Roots (2007)

Cyst nematodes of the genus Heterodera are obligate, sedentary endoparasites that have developed highly evolved relationships with specific host plant species. Successful parasitism involves significant physiological and morphological changes to plant root cells for the formation of specialized feeding cells called syncytia. To better understand the molecular mechanisms that lead to the development of nematode feeding cells, transcript profiling was conducted on developing syncytia induced by the soybean cyst nematode Heterodera glycines in soybean roots by coupling laser capture microdissection with high-density oligonucleotide microarray analysis. This approach has identified pathways that may play intrinsic roles in syncytium induction, formation, and function. Our data suggest interplay among phytohormones that likely regulates synchronized changes in the expression of genes encoding cell-wall-modifying proteins. This process appears to be tightly controlled and coordinately regulated with cell wall rigidification processes that may involve lignification of feeding cell walls. Our data also show local downregulation of jasmonic acid biosynthesis and responses in developing syncytia, which suggest a local suppression of plant defense mechanisms. Moreover, we identified genes encoding putative transcription factors and components of signal transduction pathways that may be important in the regulatory processes governing syncytium formation and function. Our analysis provides a broad mechanistic picture that forms the basis for future hypothesis-driven research to understand cyst nematode parasitism and to develop effective management tools against these pathogens.
Biochemistry of oxidative stress (2007)

The terms 'antioxidant', 'oxidative stress' and 'oxidative damage' are widely used but rarely defined. This brief review attempts to define them and to examine the ways in which oxidative stress and oxidative damage can affect cell behaviour both in vivo and in cell culture, using cancer as an example.