gebhart/patrepeval huggingface dataset:
Classification of Fusarium-Infected Korean Hulled Barley Using Near-Infrared Reflectance Spectroscopy and Partial Least Squares Discriminant Analysis (2017)

The purpose of this study is to use near-infrared reflectance (NIR) spectroscopy equipment to nondestructively and rapidly discriminate <i>Fusarium</i>-infected hulled barley. Both normal hulled barley and <i>Fusarium</i>-infected hulled barley were scanned by using a NIR spectrometer with a wavelength range of 1175 to 2170 nm. Multiple mathematical pretreatments were applied to the reflectance spectra obtained for <i>Fusarium</i> discrimination and the multivariate analysis method of partial least squares discriminant analysis (PLS-DA) was used for discriminant prediction. The PLS-DA prediction model developed by applying the second-order derivative pretreatment to the reflectance spectra obtained from the side of hulled barley without crease achieved 100% accuracy in discriminating the normal hulled barley and the <i>Fusarium</i>-infected hulled barley. These results demonstrated the feasibility of rapid discrimination of the <i>Fusarium</i>-infected hulled barley by combining multivariate analysis with the NIR spectroscopic technique, which is utilized as a nondestructive detection method.
A 3D model of the voltage‐dependent anion channel (VDAC) (2002)

Eukaryotic porins are a group of membrane proteins whose best known role is to form an aqueous pore channel in the mitochondrial outer membrane. As opposed to the bacterial porins (a large family of protein whose 3D structure has been determined by X-ray diffraction), the structure of eukaryotic porins (also termed VDACs, voltage-dependent anion-selective channels) is still a matter of debate. We analysed the secondary structure of VDAC from the yeast Saccharomyces cerevisiae, the fungus Neurospora crassa and the mouse with different types of neural network-based predictors. The predictors were able to discriminate membrane beta-strands, globular alpha-helices and membrane alpha-helices and localised, in all three VDAC sequences, 16 beta-strands along the chain. For all three sequences the N-terminal region showed a high propensity to form a globular alpha-helix. The 16 beta-strand VDAC motif was thus aligned to a bacterial porin-derived template containing a similar 16 beta-strand motif. The alignment of the VDAC sequence with the bacterial porin sequence was used to compute a set of 3D coordinates, which constitutes the first 3D prediction of a eukaryotic porin. All the predicted structures assume a beta-barrel structure composed of 16 beta-strands with the N-terminus outside the membrane. Loops are shorter in this side of the membrane than in the other, where two long loops are protruding. The shape of the pore varies between almost circular for Neurospora and mouse and slightly oval for yeast. Average values between 3 and 2.5 nm at the C-carbon backbone are found for the diameter of the channels. In this model VDAC shows large portions of the structure exposed on both sides of the membrane. The architecture we determine allows speculation about the mechanism of possible interactions between VDAC and other proteins on both sides of the mitochondrial outer membrane. The computed 3D model is consistent with most of the experimental results so far reported.
A novel type of congenital hypochromic anemia associated with a nonsense mutation in the STEAP3/TSAP6 gene (2011)

STEAP3/TSAP6 encodes a ferrireductase that is involved in the acquisition of iron by developing erythroblasts and steap3/tsap6 null-mice display severe microcytic anemia. We report a family in which 3 siblings born to healthy parents display transfusion-dependent hypochromic anemia. A nonsense STEAP3/TSAP6 was identified in the siblings at the heterozygous state. This mutation was inherited from their father while no mutation was found in their mother. A large variability of expression was found between normal alleles in a control population, confirming a previous report that STEAP3/TSAPS6 is an expressed quantitative trait locus (e-QTL). Determination of the relative allele expression showed that the "normal" allele was expressed at a significantly higher level in the father than in the affected siblings relative to the shared mutated allele. The blood level of STEAP3/TSAP6 mRNA was severely reduced in the siblings, while both parents were in the lower range of normal controls. The STEAP3/TSAP6 protein was also reduced in lymphocytic cell lines from the patients. Collectively, our data support the hypothesis that STEAP3/TSAP6 deficiency leads to severe anemia in the affected siblings and results from the combination of a mutated allele inherited from their father and a weakly expressed allele inherited from their mother.
Estimation of Surface Oxide on Surfactant-Free Gold Nanoparticles Laser-Ablated in Water (2007)

Surfactant-free gold nanoparticles were prepared by laser ablation of a gold metal plate in water. The nanoparticles were characterized by absorption spectroscopy, ζ-potential measurements, and XPS spectroscopy. The nanoparticles are negatively charged because the surface atoms are partially oxidized to Au−O-, according to the literature by Sacher and co-workers (J. Phys. Chem. B, 2004, 108, 16864). We further examined electrostatic interactions between nanoparticle and cationic surfactants. It was found that the surfactant cations attach to the particle surface, neutralizing the particle charge. Taking advantage of the electrostatic interactions, we estimated that 3.3−6.6% of the surface gold atoms was oxidized in water.
Partition Enrichment of Nucleotide Sequences (PINS) - A Generally Applicable, Sequence Based Method for Enrichment of Complex DNA Samples (2014)

The dwindling cost of DNA sequencing is driving transformative changes in various biological disciplines including medicine, thus resulting in an increased need for routine sequencing. Preparation of samples suitable for sequencing is the starting point of any practical application, but enrichment of the target sequence over background DNA is often laborious and of limited sensitivity thereby limiting the usefulness of sequencing. The present paper describes a new method, Probability directed Isolation of Nucleic acid Sequences (PINS), for enrichment of DNA, enabling the sequencing of a large DNA region surrounding a small known sequence. A 275,000 fold enrichment of a target DNA sample containing integrated human papilloma virus is demonstrated. Specifically, a sample containing 0.0028 copies of target sequence per ng of total DNA was enriched to 786 copies per ng. The starting concentration of 0.0028 target copies per ng corresponds to one copy of target in a background of 100,000 complete human genomes. The enriched sample was subsequently amplified using rapid genome walking and the resulting DNA sequence revealed not only the sequence of a the truncated virus, but also 1026 base pairs 5' and 50 base pairs 3' to the integration site in chromosome 8. The demonstrated enrichment method is extremely sensitive and selective and requires only minimal knowledge of the sequence to be enriched and will therefore enable sequencing where the target concentration relative to background is too low to allow the use of other sample preparation methods or where significant parts of the target sequence is unknown.
Inducing apoptosis in chemotherapy‐resistant B‐lineage acute lymphoblastic leukaemia cells by targeting HSPA5, a master regulator of the anti‐apoptotic unfolded protein response signalling network (2011)

We present previously unknown evidence that the immunoglobulin heavy chain binding protein BIP/HSPA5, also known as glucose regulated protein (GRP)78, serving as a pivotal component of the pro-survival axis of the unfolded protein response (UPR) signalling network, is abundantly expressed in relapsed B-lineage acute lymphoblastic leukaemia (ALL) and contributes to chemotherapy resistance of leukaemic B-cell precursors. The resistance of B-lineage ALL cells to the standard anti-leukaemic drug vincristine was overcome by the HSPA5 inhibitor epigallocatechin gallate, which inhibits the anti-apoptotic function of HSPA5 by targeting its ATP-binding domain. Notably, chemotherapy-resistant B-lineage ALL cells underwent apoptosis within 48 h of exposure to a doxorubicin-conjugated cell-penetrating cyclic anti-HSPA5 peptide targeting surface-expressed HSPA5 molecules on leukaemia cells. The identification of the HSPA5 as a chemoresistance biomarker and molecular target for B-lineage ALL may lead to new anti-leukaemic treatment strategies that are much needed.
Silica Nanoparticles and Polyethyleneimine (PEI)-Mediated Functionalization: A New Method of PEI Covalent Attachment for siRNA Delivery Applications (2013)

Small-interfering RNA (siRNA) is a synthetic double-stranded RNA that consists of approximately 21 nucleotides (nts). It induces degradation of target mRNAs in a sequence-specific manner by the RNA interference (RNAi) mechanism. Thus, siRNAs offer a potential strategy for silencing mutated or defective genes that cause a variety of human diseases. The main obstacles of harnessing siRNAs as drugs are their inefficient delivery to cells and off-target effect making clinical applications very challenging. To address these issues, researchers have studied a variety of nanocarrier systems for siRNA delivery. This study presents the design, fabrication, and full characterization of innovative polyethyleneimine (PEI)-decorated polycationic 34.2 ± 4.2 nm silica (SiO2) NPs for siRNA-mediated gene silencing. More specifically, a new means of introduction (covalent mode of attachment) of the polycationic 25 kDa PEI polymer onto the SiO2 NP surface has been developed that makes use of an effective electrophilic double Michäel acceptor, divinyl sulfone (DVS). The resulting novel SiO2-PEI nanoparticles (SPEI NPs) have been fully characterized using a wide range of analytical, spectroscopic, and microscopic methods (TEM, DLS, ζ potential, elemental analysis (EA), XPS, TGA, and FTIR). Disclosing quite low cytotoxicity due to this unique mode of PEI covalent grafting, SPEI NPs/siRNA polyplexes have been successfully tested for the induction of gene silencing using dual-reporter luciferase transfected human osteosarcoma U2OS cells. The corresponding gene silencing data showed a clear correlation between PEI/siRNA ratios, siRNA concentration(s), and the level of gene silencing. Moreover, these SPEI NPs have been demonstrated to be thermodynamically stable with an ability to efficiently bind siRNAs and induce silencing for at least a one-year-long storage.
Discovery of siRNA Lipid Nanoparticles to Transfect Suspension Leukemia Cells and Provide In Vivo Delivery Capability (2013)

As a powerful research tool, siRNA's therapeutic and target validation utility with leukemia cells and long-term gene knockdown is severely restricted by the lack of omnipotent, safe, stable, and convenient delivery. Here, we detail our discovery of siRNA-containing lipid nanoparticles (LNPs) able to effectively transfect several leukemia and difficult-to-transfect adherent cell lines also providing in vivo delivery to mouse spleen and bone marrow tissues through tail-vein administration. We disclose a series of novel structurally related lipids accounting for the superior transfection ability, and reveal a correlation between expression of Caveolins and successful transfection. These LNPs, bearing low toxicity and long stability of >6 months, are ideal for continuous long-term dosing. Our discovery represents the first effective siRNA-containing LNPs for leukemia cells, which not only enables high-throughput siRNA screening with leukemia cells and difficult-to-transfect adherent cells but also paves the way for the development of therapeutic siRNA for leukemia treatment.
Remote Building Monitoring and Control (1996)

This project is intended to develop a prototype system which would permit remote monitoring and control of multiple commercial buildings across the Internet from a single control center. Such a system would be used by operators of multiple buildings, such as school districts, governments, universities, large retailers, utility companies, building management firms, et al. We anticipate that such a system would reduce the labor costs of building monitoring and control and thereby permit more extensive monitoring and control of building HVAC and lighting systems. We estimate that this will generate improvements in building energy efficiency of 15 percent on average. Phase I of the project involves the following components: ffl A gateway between the building energy monitoring and control system (EMCS) and the Internet. This gateway is intended to present a common interface to the remote building monitoring control system via the Common Object Request Broker Architecture (CORBA) protocols....
E Protein Function in Lymphocyte Development (2002)

Lymphocytes arise from hematopoietic stem cells through the coordinated action of transcription factors. The E proteins (E12, E47, HEB and E2-2) have emerged as key regulators of both B and T lymphocyte differentiation. This review summarizes the current data and examines the various functions of E proteins and their antagonists, Id2 and Id3, throughout lymphoid maturation. Beyond an established role in B and T lineage commitment, E proteins continue to be essential at subsequent stages of development. E protein activity regulates the expression of surrogate and antigen receptor genes, promotes Ig and TCR rearrangements, and coordinates cell survival and proliferation with developmental progression in response to TCR signaling. Finally, this review also discusses the role of E47 as a tumor suppressor.
A multi-color fast-switching microfluidic droplet dye laser (2009)

We describe a multi-color microfluidic dye laser operating in whispering gallery mode based on a train of alternating droplets containing solutions of different dyes; this laser is capable of switching the wavelength of its emission between 580 nm and 680 nm at frequencies up to 3.6 kHz-the fastest among all dye lasers reported; it has potential applications in on-chip spectroscopy and flow cytometry.
Recruitment of IRAK to the interleukin 1 receptor complex requires interleukin 1 receptor accessory protein (1997)

The proinflammatory cytokine interleukin 1 (IL-1) activates the transcription of many genes encoding acute phase and proinflammatory proteins, a function mediated primarily by the transcription factor NF-kappaB. An early IL-1 signaling event is the recruitment of the Ser/Thr kinase IRAK to the type I IL-1 receptor (IL-1RI). Here we describe the function of a previously identified IL-1 receptor subunit designated IL-1 receptor accessory protein (IL-1RAcP). IL-1 treatment of cells induces the formation of a complex containing both IL-1RI and IL-1RAcP. IRAK is recruited to this complex through its association with IL-1RAcP. Overexpression of an IL-1RAcP mutant lacking its intracellular domain, the IRAK-binding domain, prevented the recruitment of IRAK to the receptor complex and blocked IL-1-induced NF-kappaB activation.
Prognostic value of cadherin-associated molecules (alpha-, beta-, and gamma-catenins and p120cas) in bladder tumors. (1996)

Loss of E-cadherin-mediated adhesion is an important step in the progression of many carcinomas. In model systems, it has been shown that cadherin function requires not only proper E-cadherin expression but also its linkage to the cytoskeleton through catenins. Hence, defects in catenins may cause defective E-cadherin function, and catenins as well as E-cadherin might constitute prognostic indicators. Here, we extend our previous study on E-cadherin in bladder cancer (Cancer Res., 53: 3241-3245, 1993). We have evaluated the expression of E-cadherin-associated cytoplasmic molecules (alpha-, beta-, and gamma-catenins and p120cas) to clarify whether or not the pattern of their expression could provide additional prognostic information beyond that from E-cadherin alone. Forty-eight frozen bladder tumor specimens and 9 samples of normal urothelium were studied by immunohistochemistry. A discrepancy between the E-cadherin and catenin expression pattern was seen in 20.8% of cases. Abnormal expression of each molecule is significantly correlated with tumor grade (P < 0.01) and stage (P < 0.01). Reduced expression of all of the molecules correlates with poor survival (P < 0.01 for each variable). Proportional hazard regression analysis showed that beta-catenin, E-cadherin, and alpha-catenin have strong predictive value, whereas plakoglobin and p120cas have a somewhat lower predictive value. Within patients with invasive tumors, those with a normal staining for either E-cadherin, alpha-catenin, or beta-catenin show a trend toward better survival. However, the difference in survival is significant only for E-cadherin (P < 0.05). Thus, beta-catenin, E-cadherin, and alpha-catenin have similar prognostic values. Therefore, from a practical point of view, the expression of any of these proteins can be of prognostic value for patients with bladder cancer.
Genetic structure of Neisseria meningitidis populations in relation to serogroup, serotype, and outer membrane protein pattern (1987)

The genetic structure of populations of Neisseria meningitidis was examined by an analysis of electrophoretically demonstrable allelic variation at 15 genes encoding enzymes in 650 isolates of eight serogroups (A, B, C, W135, X, Y, Z, and 29E) and 38 nonserogroupable isolates. A total of 331 distinctive multilocus genotypes (electrophoretic types, ETs) was identified, among which mean genetic diversity per locus (H = 0.547) was greater than in Escherichia coli and other bacterial species thus far studied. The intercontinental distribution of some ETs and the recovery of organisms of identical genotype over periods of many years strongly suggest that the genetic structure of N. meningitidis is basically clonal as a consequence of low rates of recombination of chromosomal genes. Variation among strains in serogroup, serotype, and the electrophoretic pattern of the major outer membrane proteins has little relationship to the complex structure of populations revealed by enzyme electrophoresis, which involves 14 major lineages of clones diverging from one another at genetic distances greater than 0.50. Genetic diversity among ETs of isolates of the same serogroup was, on average, 84% of that in the total sample. Clones of serogroup A were unusual in being genotypically less heterogeneous than those of other serogroups and in forming a single phylogenetic group. Isolates of the same serotype or outer membrane protein pattern were also highly heterogeneous; on average, 87 and 97%, respectively, of the total species diversity was represented by ETs of the same serotype or outer membrane protein.
Real Time Dynamic Simulation of Power System Using Multiple Microcomputers (1990)

Recent developments in the design and manufacture of microcomputers together with improved simulation techniques make it possible to achieve the speed and accuracy required for the dynamic simulation of power systems in real time. This paper presents some experimental results and outlines new ideas on hardware architecture, mathematical algorithms and software development for this purpose. The results of power system studies are discussed, and a new system formulation is proposed in which the State equations and electrical network equations are partitioned; the network equations being solved separately on a host processor while the state equations of each generating unit are solved on slave units. A transputer based, parallel processing system connected to micro VAX computer is proposed for the simulation of the dynamics of a power system in realtime. Such a simulator can be used for the evaluation of instability over a long period of time resulting from persisting faults and for the study of voltage collapse phenomena in power systems.
Discovery and Preclinical Studies of (R)-1-(4-(4-Fluoro-2-methyl-1H-indol-5-yloxy)-5- methylpyrrolo[2,1-f][1,2,4]triazin-6-yloxy)propan- 2-ol (BMS-540215), an In Vivo Active Potent VEGFR-2 Inhibitor (2006)

A series of substituted 4-(4-fluoro-1H-indol-5-yloxy)pyrrolo[2,1-f][1,2,4]triazine-based inhibitors of vascular endothelial growth factor receptor-2 kinase is reported. Structure-activity relationship studies revealed that a methyl group at the 5-position and a substituted alkoxy group at the 6-position of the pyrrolo[2,1-f][1,2,4]triazine core gave potent compounds. Biochemical potency, kinase selectivity, and pharmacokinetics of the series were optimized and in vitro safety liabilities were minimized to afford BMS-540215 (12), which demonstrated robust preclinical in vivo activity in human tumor xenograft models. The l-alanine prodrug of 12, BMS-582664 (21), is currently under evaluation in clinical trials for the treatment of solid tumors.
Bone-Marrow Transplantation in a Patient with Sickle-Cell Anemia (1984)

SICKLE-CELL anemia affects 1 in 600 of the U.S. black population and accounts for 80,000 deaths annually throughout the world.1 , 2 Current therapy is designed to prevent sickle-cell crises, but supportive care remains the only treatment available once they occur. Attempts to alter the expression of hemoglobin genes in β-thalassemia and sickle-cell anemia with the use of azacytidine have produced only transient effects.3 This report describes the conversion of sickle-cell anemia to sickle-cell trait by marrow transplantation (done for treatment of leukemia) in a child with both sickle-cell anemia and acute myeloblastic leukemia. It raises the possibility of using marrow transplantation . . .
Super‐Hydrophobic Surfaces: From Natural to Artificial (2002)

Abstract Super‐hydrophobic surfaces, with a water contact angle (CA) greater than 150°, have attracted much interest for both fundamental research and practical applications. Recent studies on lotus and rice leaves reveal that a super‐hydrophobic surface with both a large CA and small sliding angle (α) needs the cooperation of micro‐ and nanostructures, and the arrangement of the microstructures on this surface can influence the way a water droplet tends to move. These results from the natural world provide a guide for constructing artificial super‐hydrophobic surfaces and designing surfaces with controllable wettability. Accordingly, super‐hydrophobic surfaces of polymer nanofibers and differently patterned aligned carbon nanotube (ACNT) films have been fabricated.
Urine Detection of Survivin and Diagnosis of Bladder Cancer (2001)

Highly sensitive and specific determination of urine survivin appears to provide a simple, noninvasive diagnostic test to identify patients with new or recurrent bladder cancer.
The response of leptin, interleukin-6 and fat oxidation to feeding in weight-losing patients with pancreatic cancer (2004)

At baseline, weight-losing pancreatic cancer patients (n=7) had lower leptin (P<0.05) but higher cortisol, interleukin-6, resting energy expenditure and fat oxidation than healthy subjects (n=6, P<0.05). Over a 4 h feeding period, the areas under the curve for glucose, cortisol and interleukin-6 were greater (P<0.05), but less for leptin in the cancer group (P<0.05). Therefore, it would appear that low leptin concentrations, increased fat oxidation and insulin resistance are associated with increased concentrations of cortisol and interleukin-6 in weight-losing patients with pancreatic cancer.