gebhart/patrepeval huggingface dataset:
Reciprocal regulation of distinct asparagine synthetase genes by light and metabolites inArabidopsis thaliana (1998)

In plants, the amino acid asparagine serves as an important nitrogen transport compound whose levels are dramatically regulated by light in many plant species, including Arabidopsis thaliana. To elucidate the mechanisms regulating the flux of assimilated nitrogen into asparagine, we examined the regulation of the gene family for asparagine synthetase in Arabidopsis. In addition to the previously identified ASN1 gene, we identified a novel class of asparagine synthetase genes in Arabidopsis (ASN2 and ASN3) by functional complementation of a yeast asparagine auxotroph. The proteins encoded by the ASN2/3 cDNAs contain a Pur-F type glutamine-binding triad suggesting that they, like ASN1, encode glutamine-dependent asparagine synthetase isoenzymes. However, the ASN2/3 isoenzymes form a novel dendritic group with monocot AS genes which is distinct from all other dicot AS genes including Arabidopsis ASN1. In addition to these distinctions in sequence, the ASN1 and ASN2 genes are reciprocally regulated by light and metabolites. Time-course experiments reveal that light induces levels of ASN2 mRNA while it represses levels of ASN1 mRNA in a kinetically reciprocal fashion. Moreover, the levels of ASN2 and ASN1 mRNA are also reciprocally regulated by carbon and nitrogen metabolites. The distinct regulation of ASN1 and ASN2 genes combined with their distinct encoded isoenzymes suggest that they may play different roles in nitrogen metabolism, as discussed in this paper.
Tc-99m MIBI Uptake in Breast Carcinoma and Axillary Lymph Node Metastases (1994)

Two female patients with breast cancer and axillary lymph node metastases had Tc-99m MIBI chest scintigraphy. The Tc-99m MIBI uptake in the primary breast cancer and metastatic lymph nodes were noted and discussed. The findings suggest that Tc-99m MIBI chest scintigraphy for palpable breast masses and axillary lymph nodes is a helpful test in detecting malignant breast masses and metastatic lymph nodes.
A fractal dimension feature extraction technique for detecting flaws in silicon wafers (2003)

The authors present a feature extraction method for detecting flaws in silicon wafers based on the idea of fractal dimension. They begin by discussing why fractal dimension is a good way to model wafer surface images. They then describe how to calculate the fractal dimension of a computer image of a wafer and how the results of such a calculation can be used for fault detection and image segmentation. The results of the application of this process to some wafer images are included.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
N-Glycosylation engineering of plants for the biosynthesis of glycoproteins with bisected and branched complex N-glycans (2011)

Glycoengineering is increasingly being recognized as a powerful tool to generate recombinant glycoproteins with a customized N-glycosylation pattern. Here, we demonstrate the modulation of the plant glycosylation pathway toward the formation of human-type bisected and branched complex N-glycans. Glycoengineered Nicotiana benthamiana lacking plant-specific N-glycosylation (i.e. β1,2-xylose and core α1,3-fucose) was used to transiently express human erythropoietin (hEPO) and human transferrin (hTF) together with modified versions of human β1,4-mannosyl-β1,4-N-acetylglucosaminyltransferase (GnTIII), α1,3-mannosyl-β1,4-N-acetylglucosaminyltransferase (GnTIV) and α1,6-mannosyl-β1,6-N-acetylglucosaminyltransferase (GnTV). hEPO was expressed as a fusion to the IgG-Fc domain (EPO-Fc) and purified via protein A affinity chromatography. Recombinant hTF was isolated from the intracellular fluid of infiltrated plant leaves. Mass spectrometry-based N-glycan analysis of hEPO and hTF revealed the quantitative formation of bisected (GnGnbi) and tri- as well as tetraantennary complex N-glycans (Gn[GnGn], [GnGn]Gn and [GnGn][GnGn]). Co-expression of GnTIII together with GnTIV and GnTV resulted in the efficient generation of bisected tetraantennary complex N-glycans. Our results show the generation of recombinant proteins with human-type N-glycosylation at great uniformity. The strategy described here provides a robust and straightforward method for producing mammalian-type N-linked glycans of defined structures on recombinant glycoproteins, which can advance glycoprotein research and accelerate the development of protein-based therapeutics.
Danazol Therapy for Autoimmune Hemolytic Anemia (1985)

We evaluated the use of danazol in 15 patients with autoimmune hemolytic anemia of the warm antibody type. Danazol, 600 to 800 mg/d, was added to previous regimens or given initially in conjunction with high-dose prednisone treatment. Twelve patients with autoimmune hemolytic anemia associated with nonmalignant disorders or idiopathic autoimmune hemolytic anemia and 1 of 3 patients with underlying neoplasms showed a rise in hematocrit within 1 to 3 weeks. Thereafter, glucocorticoid doses were tapered to a minimum requirement or stopped. Once remission was sustained, the dose of danazol was reduced to 200 to 400 mg/d. Although levels of erythrocyte-bound IgG antibody and C3 decreased with therapy, only the decrease in C3 was statistically significant (p less than 0.05) in this limited study. Danazol was effective regardless of the severity of the disorder and success or failure of previous treatments. Danazol is valuable in the treatment of autoimmune hemolytic anemia and may be better suited than glucocorticoids for long-term management.
Fast Control of Filter for Sensorless Vector Control SQIM Drive With Sinusoidal Motor Voltage (2007)

A pulsewidth-modulated (PWM) voltage applied to a squirrel-cage induction motor (SQIM) can cause high bearing currents, heating of rotor shaft, voltage spike across the motor terminals, etc. Filtering of this PWM voltage to obtain a sinusoidal output voltage can be a solution to this problem. However, a passive L-C filter makes the dynamic performance of the drive poor for high-performance control application. In this paper, a feed-forward control strategy for the L-C filter is proposed to have a good bandwidth for the filter output voltage. This filter control strategy is introduced along with a sensorless vector control strategy for the SQIM drive. This complete strategy retains the high dynamic performance of the drive even with the L-C filter. In this paper, a three-level converter is used as a voltage source inverter for the drive to have a less filter-size requirement. The control strategy is verified on a 7.5-hp SQIM drive with a three-level insulated-gate bipolar-transistor inverter and L-C filter. Experimental results validate the high dynamic performance of the drive with filter.
The Vibrio cholerae O139 serogroup antigen includes an O-antigen capsule and lipopolysaccharide virulence determinants. (1994)

Vibrio cholerae serogroup O139 emerged on the Indian subcontinent in October 1992 to become the first non-O1 V. cholerae serogroup documented to cause epidemic cholera. Although related to V. cholerae El Tor O1 strains, O139 strains have unique surface structures that include a capsular surface layer and lipopolysaccharide (LPS). Immunoblot analysis of either whole-cell lysates or LPS preparations revealed three electrophoretic forms of the O139 antigen: two slowly migrating forms and one rapidly migrating form that appeared identical to O139 LPS. All three forms of the antigen shared an epitope defined by an O139-specific monoclonal antibody. A serum-sensitive nonencapsulated mutant was isolated that lacks only the slow migrating forms. The slow migrating forms did not stain with silver whereas the rapidly migrating form did, suggesting that the former might constitute highly polymerized O-antigen side-chain molecules that were not covalently bound to core polysaccharide and lipid A (an "O-antigen capsule"). A single transposon insertion resulted in the loss of immunoreactivity of both the LPS and the O-antigen capsule, implying that there are genes common to the biosynthesis of both these macromolecules. The O139 LPS and O-antigen capsule were both important for colonization of the small intestine of the newborn mouse and for serum resistance, demonstrating that both of these forms of the O139 serogroup antigen are virulence factors.
Cetuximab for the Treatment of Colorectal Cancer (2007)

Cetuximab improves overall survival and progression-free survival and preserves quality-of-life measures in patients with colorectal cancer in whom other treatments have failed. (ClinicalTrials.gov number, NCT00079066 [ClinicalTrials.gov].).
EarlyCDT®-Lung test: improved clinical utility through additional autoantibody assays (2012)

Tumor-associated autoantibodies (AAbs) have been described in patients with lung cancer, and the EarlyCDT®-Lung test that measures such AAbs is available as an aid for the early detection of lung cancer in high-risk populations. Improvements in specificity would improve its cost-effectiveness, as well as reduce anxiety associated with false positive tests. Samples from 235 patients with newly diagnosed lung cancer and matched controls were measured for the presence of AAbs to a panel of six (p53, NY-ESO-1, CAGE, GBU4-5, Annexin I, and SOX2) or seven (p53, NY-ESO-1, CAGE, GBU4-5, SOX2, HuD, and MAGE A4) antigens. Data were assessed in relation to cancer type and stage. The sensitivity and specificity of these two panels were also compared in two prospective consecutive series of 776 and 836 individuals at an increased risk of developing lung cancer. The six-AAb panel gave a sensitivity of 39% with a specificity of 89 %, while the seven-AAb panel gave a sensitivity of 41 % with a specificity of 91 % which, once adjusted for occult cancers in the population, resulted in a specificity of 93 %. Analysis of these AAb assays in the at-risk population confirmed that the seven-AAb panel resulted in a significant increase in the specificity of the test from 82 to 90 %, with no significant change in sensitivity. The change from a six- to a seven-AAb assay can improve the specificity of the test and would result in a PPV of 1 in 8 and an overall accuracy of 92 %.
Regulation of ligand-receptor dynamics by guanine nucleotides. Real-time analysis of interconverting states for the neutrophil formyl peptide receptor. (1987)

Intact neutrophils exhibit interconverting active and inactive receptor states with half-times for dissociation of 10 s and 2 min, respectively. We examined the effect of guanine nucleotides on ligand-receptor dynamics at 37 degrees C in neutrophils permeabilized with digitonin using continuous fluorometric measurements. The permeabilized cells exhibit a single class of slowly dissociating receptors with a half-time similar to the inactive state. The slowly dissociating state is lengthened in the presence of 10 mM by Mg2+ about two-fold but is relatively insensitive to substitutions of Na+ or K+. When guanine nucleotide is added the receptors dissociate uniformly with a half-time similar to the active state but are sensitive to the substitution of Na+ or K+ (K+ or K+/Mg2+ approximately 10 s; Na+ or Na+/Mg2+ approximately 4 s). When receptors in permeabilized cells are ADP-ribosylated with pertussis toxin the rapidly dissociating state is detected. In the presence of nonsaturating nucleotide or incomplete ribosylation, complex rates of ligand dissociation intermediate between the active and inactive forms are observed. Micromolar concentrations of Ca2+ block the effect of guanine nucleotide on the receptor. The relationships between ligand-receptor dynamics in intact neutrophils and interconverting states regulated by guanine nucleotides and ions in permeabilized cells are discussed.
Functions and devices of Mitsubishi active safety ASV (2002)

The Advanced Safety Vehicle (ASV) project, advocated by Japan's Ministry of Transport, was carried out from 1991 to March 1996 to promote developing safety measures for the 21st century mainly by intellectualizing vehicles. This paper introduces the main functions and devices of Mitsubishi's Active Safety ASV which employs many state-of-the-art technologies to support the driver under various traffic situations. The ASV is equipped with a multi-eye system which consists of two lane-detecting cameras, two scanning laser radar, six passive trigonometric-type sensors, and three stereo cameras, to detect surrounding traffic situations. The friendly man-machine interface consists of sophisticated indicators, warning systems, and indirect visual field systems using small video cameras. The collision avoidance system assesses the situational risk and warns the driver or performs an automatic collision avoidance if necessary.
Computational adaptive optics for broadband optical interferometric tomography of biological tissue (2012)

Aberrations in optical microscopy reduce image resolution and contrast, and can limit imaging depth when focusing into biological samples. Static correction of aberrations may be achieved through appropriate lens design, but this approach does not offer the flexibility of simultaneously correcting aberrations for all imaging depths, nor the adaptability to correct for sample-specific aberrations for high-quality tomographic optical imaging. Incorporation of adaptive optics (AO) methods have demonstrated considerable improvement in optical image contrast and resolution in noninterferometric microscopy techniques, as well as in optical coherence tomography. Here we present a method to correct aberrations in a tomogram rather than the beam of a broadband optical interferometry system. Based on Fourier optics principles, we correct aberrations of a virtual pupil using Zernike polynomials. When used in conjunction with the computed imaging method interferometric synthetic aperture microscopy, this computational AO enables object reconstruction (within the single scattering limit) with ideal focal-plane resolution at all depths. Tomographic reconstructions of tissue phantoms containing subresolution titanium-dioxide particles and of ex vivo rat lung tissue demonstrate aberration correction in datasets acquired with a highly astigmatic illumination beam. These results also demonstrate that imaging with an aberrated astigmatic beam provides the advantage of a more uniform depth-dependent signal compared to imaging with a standard gaussian beam. With further work, computational AO could enable the replacement of complicated and expensive optical hardware components with algorithms implemented on a standard desktop computer, making high-resolution 3D interferometric tomography accessible to a wider group of users and nonspecialists.
Immunoinformatics and epitope prediction in the age of genomic medicine (2015)

Immunoinformatics involves the application of computational methods to immunological problems. Prediction of B- and T-cell epitopes has long been the focus of immunoinformatics, given the potential translational implications, and many tools have been developed. With the advent of next-generation sequencing (NGS) methods, an unprecedented wealth of information has become available that requires more-advanced immunoinformatics tools. Based on information from whole-genome sequencing, exome sequencing and RNA sequencing, it is possible to characterize with high accuracy an individual's human leukocyte antigen (HLA) allotype (i.e., the individual set of HLA alleles of the patient), as well as changes arising in the HLA ligandome (the collection of peptides presented by the HLA) owing to genomic variation. This has allowed new opportunities for translational applications of epitope prediction, such as epitope-based design of prophylactic and therapeutic vaccines, and personalized cancer immunotherapies. Here, we review a wide range of immunoinformatics tools, with a focus on B- and T-cell epitope prediction. We also highlight fundamental differences in the underlying algorithms and discuss the various metrics employed to assess prediction quality, comparing their strengths and weaknesses. Finally, we discuss the new challenges and opportunities presented by high-throughput data-sets for the field of epitope prediction.
Cloning, sequence, and expression of the pantothenate permease (panF) gene of Escherichia coli (1990)

Pantothenate permease, the product of the panF gene, catalyzes the sodium-dependent uptake of extracellular pantothenate. The panF gene was isolated from an Escherichia coli genomic DNA library and subcloned into multicopy plasmids. Increased copy number of the panF+ allele resulted in increased rates of pantothenate uptake and a significant increase in the steady-state intracellular pantothenate concentration. Despite the higher levels of pantothenate, the utilization of pantothenate for coenzyme A formation was not elevated, indicating that pantothenate kinase activity is the dominant regulator of coenzyme A biosynthesis. DNA sequencing of the panF gene revealed the presence of a single open reading frame that encoded a hydrophobic protein with a molecular weight of 51,992. Sequence analysis predicts that pantothenate permease is an integral membrane protein possessing 12 hydrophobic membrane-spanning domains connected by short hydrophilic sequences. The predicted topological profile of pantothenate permease is similar to that of other membrane carriers that catalyze cation-dependent symport.
Cationic antimicrobial protein of Mr 37 kDa: a multifunctional inflammatory protein. (2001)

Our studies strongly suggest that CAP37 plays a pivotal role in monocyte-endothelial interactions and the transmigration of monocytes from the vasculature into extravascular tissues.
Expansion of an osteopontin‐expressing T follicular helper cell subset correlates with autoimmunity in B6.Sle1b mice and is suppressed by the H1‐isoform of the Slamf6 receptor (2013)

The costimulatory receptor Slamf6 partially controls lupus-related autoimmunity in congenic Sle1b mice; for instance, the presence of the protein isoform Slamf6-H1 in Sle1b.Slamf6-H1 mice mitigates disease. Here, we report that young Sle1b mice, but not Sle1b.Slamf6-H1 or B6 mice, contain a memory T-helper cell subset identified by ]mt]2-fold increase in expression of 17 genes, chief among which is Spp1, encoding the cytokine osteopontin (OPN). These T follicular helper (TFH) cells, including OPN(+) TFH cells, expand concomitantly with severity of the disease. By contrast, Sle1b.Slamf6-H1 or Sle1b.SAP(-)/(-) mice do not develop autoantibodies and the number of T(FH) cells is 5 times lower than in age-matched Sle1b mice. By comparing Sle1b and Sle1b.OPN(-)/(-) mice, we find that the lack of OPN expression impedes early autoantibody production. Furthermore, on the adoptive transfer of Sle1b.OPN(-)/(-) CD4(+) T cells into bm12 recipients autoantibody production and germinal center formation is reduced compared to recipients of Sle1b.OPN(+/+) CD4(+) T cells. We propose a model in which OPN provides a survival signal for a precursor T(FH) cell subset, which is a key factor in autoimmunity.
Long‐term genome diploidization in allopolyploidNicotianasectionRepandae(Solanaceae) (2005)

Here, we analyze long-term evolution in Nicotiana allopolyploid section Repandae (the closest living diploids are N. sylvestris, the maternal parent, and N. obtusifolia, the paternal parent). We compare data with other more recently formed Nicotiana allopolyploids. We investigated 35S and 5S nuclear ribosomal DNA (rDNA) chromosomal location and unit divergence. A molecular clock was applied to the Nicotiana phylogenetic tree to determine allopolyploid ages. N. tabacum and species of Repandae were c. 0.2 and 4.5 Myr old, respectively. In all Repandae species, the numbers of both 35S and 5S rDNA loci were less than the sum of those of the diploid progenitors. Trees based on 5S rDNA spacer sequences indicated units of only the paternal parent. In recent Nicotiana allopolyploids, the numbers of rDNA loci equal the sum of those of their progenitors. In the Repandae genomes, diploidization is associated with locus loss. Sequence analysis indicates that 35S and 5S units most closely resemble maternal and paternal progenitors, respectively. In Nicotiana, 4.5 Myr of allopolyploid evolution renders genomic in situ hybridization (GISH) unsuitable for the complete resolution of parental genomes.
The human antimicrobial and chemotactic peptides LL-37 and α-defensins are expressed by specific lymphocyte and monocyte populations (2000)

We identified antibacterial components in human T and natural killer (NK) cells by using freshly isolated lymphocytes enriched for T and NK cells as starting material. After growing these lymphocytes for 5 days in the presence of interleukin (IL)-2, we isolated and characterized several antibacterial peptides/proteins from the supernatant-alpha-defensins (HNP 1-3), LL-37, lysozyme, and a fragment of histone H2B-although other active components were also present. We then used reverse transcriptase-polymerase chain reaction to search for expression of the gene coding for LL-37 in several B-cell lines, gammadelta T-cell lines, NK clones, and one monocytic cell line, with positive results, but found no expression in several alphabeta T-cell lines. The alpha-defensins (HNP 1-3) were also found to be expressed in several of these cell lines. To confirm the presence of these antibacterial peptides in lymphocytes, we localized them to NK, gammadelta T cells, B cells, and monocytes/macrophages by using double-staining immunohistochemical analysis of freshly isolated lymphocytes. We also found that primary cultures of lymphocytes transcribe and secrete LL-37 and that these processes are affected by IL-6 and interferon-gamma. In addition, we demonstrated that LL-37 has chemotactic activity for polymorphonuclear leukocytes and CD4 T lymphocytes, whereas others have shown chemotactic activity for human alpha-defensins (HNP 1-2). These findings suggest that microbicidal peptides are effector molecules of lymphocytes and that antibacterial activity previously shown to be derived from T and NK cells may be partly mediated by the antibacterial peptides LL-37 and HNP 1-3.
Microchip Electrophoretic Immunoassay for Serum Cortisol (1996)

An immunoassay performed using a microchip electrophoretic system is described. Separation and quantitation of free and bound labeled antigen in a competitive assay are carried out in channels micromachined into fused silica substrates. Such microchips are attractive because of their small size, ruggedness, and amenability to automated handling. The assay achieves the determination of cortisol in blood serum over the range of clinical interest (1-60 micrograms/dL) without the need for extraction or other sample preparation steps. The separation is performed in less than 30 s. Very high throughput is possible by operating the assay in multiple channels in parallel. These characteristics make microchip electrophoretic systems a promising technology for the rapid analysis of clinical samples.
Ultra-High-Speed DNA Sequencing Using Capillary Electrophoresis Chips (1995)

DNA sequencing has been performed on microfabricated capillary electrophoresis chips. DNA separations were achieved in 50 x 8 microns cross-section channels microfabricated in a 2 in. x 3 in. glass sandwich structure using a denaturing 9% T, 0% C polyacrylamide sieving medium. DNA sequencing fragment ladders were produced and fluorescently labeled using the recently developed energy transfer dye-labeled primers. Sequencing extension fragments were separated to approximately 433 bases in only 10 min using a one-color detection system and an effective separation distance of only 3.5 cm. Using a four-color labeling and detection format, DNA sequencing with 97% accuracy and single-base resolution to approximately 150 bases was achieved in only 540 s. A resolution of greater than 0.5 was obtained out to 200 bases for both the one- and four-color separations. The prospects for enhancing the resolution and sensitivity of these chip separations are discussed. This work establishes the feasibility of high-speed, high-throughput DNA sequencing using capillary array electrophoresis chips.