gebhart/patrepeval huggingface dataset:
Structural Analysis of Arabidopsis thaliana Chromosome 3. II. Sequence Features of the 4,251,695 bp Regions Covered by 90 P1, TAC and BAC Clones (2000)

To deduce the entire sequence of the top arm of the Arabidopsis thaliana chromosome 3, the sequence determination was performed on a total of 90 P1, TAC and BAC clones chosen according to our sequencing strategy. Sequence features of the resulting 4,251,695 bp regions were analyzed with various computer programs for similarity search and gene modeling. As a result, a total of 941 potential protein-coding genes were identified. The average density of the genes identified was 1 gene per 4210 bp. Introns were observed in 73% of the genes, and the average number per gene and the average length of the introns were 3.6 and 159 bp, respectively. These sequence features are essentially identical to those of chromosomes 3 and 5 in our previous reports. The regions also contained 14 tRNA genes when searched by similarity to reported tRNA genes and the tRNA scan-SE program. The sequence data and information on the potential genes are available through the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http://www.kazusa.or.jp/kaos/.
Efficacy and Safety of Endovascular Cooling After Cardiac Arrest (2006)

Endovascular cooling improved survival and short-term neurological recovery compared with standard treatment in comatose adult survivors of cardiac arrest. Temperature control was effective and safe with this device.
Preparation of an Amphiphilic Resin‐Supported BINAP Ligand and Its Use for Rhodium‐Catalyzed Asymmetric 1,4‐Addition of Phenylboronic Acid in Water. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Extraction of genomic DNA from yeasts for PCR-based applications (2011)

We have developed a quick and low-cost genomic DNA extraction protocol from yeast cells for PCR-based applications. This method does not require any enzymes, hazardous chemicals, or extreme temperatures, and is especially powerful for simultaneous analysis of a large number of samples. DNA can be efficiently extracted from different yeast species (Kluyveromyces lactis, Hansenula polymorpha, Schizosaccharomyces pombe, Candida albicans, Pichia pastoris, and Saccharomyces cerevisiae). The protocol involves lysis of yeast colonies or cells from liquid culture in a lithium acetate (LiOAc)-SDS solution and subsequent precipitation of DNA with ethanol. Approximately 100 nanograms of total genomic DNA can be extracted from 1 × 10(7) cells. DNA extracted by this method is suitable for a variety of PCR-based applications (including colony PCR, real-time qPCR, and DNA sequencing) for amplification of DNA fragments of ≤ 3500 bp.
Understanding supercapacitors based on nano-hybrid materials with interfacial conjugation (2013)

The recent fast development of supercapacitors, also known scientifically as electrochemical capacitors, has benefited significantly from synthesis, characterisations and electrochemistry of nanomaterials. Herein, the principle of supercapacitors is explained in terms of performance characteristics and charge storage mechanisms, i.e. double layer (or interfacial) capacitance and pseudo-capacitance. The semiconductor band model is applied to qualitatively account for the pseudo-capacitance in association with rectangular cyclic voltammograms (CVs) and linear galvanostatic charging and discharging plots (GCDs), aiming to differentiate supercapacitors from rechargeable batteries. The invalidity of using peak shaped CVs and non-linear GCDs for capacitance measurement is highlighted. A selective review is given to the nano-hybrid materials between carbon nanotubes and redox active materials such as electronically conducting polymers and transition metal oxides. A new concept, “interfacial conjugation”, is introduced to reflect the capacitance enhancement resulting from π–π stacking interactions at the interface between two materials with highly conjugated chemical bonds. The prospects of carbon nanotubes and graphenes for supercapacitor applications are briefly compared and discussed. Hopefully, this article can help readers to understand supercapacitors and nano-hybrid materials so that further developments in materials design and synthesis, and device engineering can be more efficient and objective.
Arginine-Rich Anti-Vascular Endothelial Growth Factor (Anti-VEGF) Hexapeptide Inhibits Collagen-Induced Arthritis and VEGF-Stimulated Productions of TNF-α and IL-6 by Human Monocytes (2005)

Vascular endothelial growth factor (VEGF) has been suggested to play a critical role in the pathogenesis of rheumatoid arthritis (RA). We previously identified a novel RRKRRR hexapeptide that blocked the interaction between VEGF and its receptor through the screening of peptide libraries. In this study, we investigated whether anti-VEGF peptide RRKRRR (dRK6) could suppress collagen-induced arthritis (CIA) and regulate the activation of mononuclear cells of RA patients. A s.c. injection of dRK6 resulted in a dose-dependent decrease in the severity and incidence of CIA and suppressed synovial infiltration of inflammatory cells in DBA/1 mice. In these mice, the T cell responses to type II collagen (CII) in lymph node cells and circulating IgG Abs to CII were also dose-dependently inhibited by the peptides. In addition, VEGF directly increased the production of TNF-alpha and IL-6 from human PBMC. Synovial fluid mononuclear cells of RA patients showed a greater response to VEGF stimulation than the PBMC of healthy controls. The major cell types responding to VEGF were monocytes. Moreover, anti-VEGF dRK6 inhibited the VEGF-induced production of TNF-alpha and IL-6 from synovial fluid mononuclear cells of RA patients and decreased serum IL-6 levels in CIA mice. In summary, we observed first that dRK6 suppressed the ongoing paw inflammation in mice and blocked the VEGF-induced production of proinflammatory cytokines. These data suggest that dRK6 may be an effective strategy in the treatment of RA, and could be applied to modulate various chronic VEGF-dependent inflammatory diseases.
Drug and neurotransmitter receptors. New perspectives with clinical relevance (1989)

Our understanding of drug and neurotransmitter receptors has been greatly advanced by receptor binding techniques. The theme of multiple-receptor subtypes with clinical relevance is highlighted by calcium antagonist and benzodiazepine receptors. Numerous drugs may exert therapeutic and untoward effects via calcium channels. Examples include effects of loperamide hydrochloride on diarrhea, the phenothiazine thioridazine hydrochloride on cardiac and ejaculatory function, and the neuromuscular toxicity of aminoglycosides. Elevated numbers of calcium antagonist receptors in hypertrophic cardiomyopathy may be involved in the pathophysiology of this disease. Benzodiazepines act via discrete central and peripheral receptors. At central receptors, benzodiazepines facilitate the inhibitory effects of the neurotransmitter -y-aminobutyric acid. Peripheral benzodiazepine receptors are localized to mitochondria and enriched in several endocrine glands where they are influenced by therapeutic blood levels of benzodiazepines such as diazepam. (<i>JAMA</i>. 1989;261:3126-3129)
Pharmaceutical development of a parenteral lyophilized formulation of the novel antitumor agent aplidine. (2000)

Aplidine is a naturally occurring cyclic depsipeptide isolated from the Mediterranean tunicate Aplidium albicans. Aplidine displays promising in vitro and in vivo antitumor activities against various solid human tumor xenografts and is therefore developed now for clinical testing. The aim of this study was to develop a stable parenteral pharmaceutical dosage form for clinical Phase I testing. Aplidine raw material was characterized by using several chromatographic and spectrometric techniques. These experiments showed that aplidine exists as two isomers. A stability-indicating HPLC assay was developed. Solubility testing showed that aplidine exhibits very poor aqueous solubility. Because solubilized aplidine showed substantial degradation under heat and light stress testing conditions, it was decided to develop a lyophilized dosage form. Freeze-drying was carried out with a 500 micrograms/mL solution of aplidine in 40% (v/v) tert-butanol in Water for Injection (WfI) containing 25 mg/mL D-mannitol as a bulking agent. Differential scanning calorimetry was applied to determine the optimal freeze-drying cycle parameters. The prototype, containing 500 micrograms aplidine and 25 mg D-mannitol per vial, was found to be the optimal formulation in terms of solubility, length of lyophilization cycle, and dosage requirements in the forthcoming Phase I clinical studies. Quality control of the freeze-dried formulation demonstrates that the manufacturing process does not affect the integrity of aplidine. The optimal reconstitution solution was found to be 15/15/70% (v/v/v) Cremophor EL/ethanol/WfI (CEW). Both reconstituted product and dilutions of the reconstituted product with normal saline (up to 1:100 v/v) appeared to be stable for at least 24 hours after preparation. Shelf-life data, available thus far, show that the lyophilized formulation is stable for at least 1 year when stored at +2-8 degrees C in the dark.
Multimodal Biometrics: An Overview (2004)

Publication in the conference proceedings of EUSIPCO, Viena, Austria, 2004
Directed evolution of a -glycosidase from Agrobacterium sp. to enhance its glycosynthase activity toward C3-modified donor sugars (2012)

Glycans bearing modified hydroxyl groups are common in biology but because these modifications are added after assembly, enzymes are not available for the transfer and coupling of hydroxyl-modified monosaccharide units. Access to such enzymes could be valuable, particularly if they can also introduce 'bio-orthogonal tags'. Glycosynthases, mutant glycosidases that synthesize glycosides using glycosyl fluoride donors, are a promising starting point for creation of such enzymes through directed evolution. Inspection of the active site of a homology model of the GH1 Agrobacterium sp. β-glycosidase, which has both glucosidase and galactosidase activity, identified Q24, H125, W126, W404, E411 and W412 as amino acids that constrain binding around the 3-OH group, suggesting these residues as targets for mutation to generate an enzyme capable of handling 3-O-methylated sugars. Site-directed saturation mutagenesis at these positions within the wild-type β-glycosidase gene and screening via an on-plate assay yielded two mutants (Q24S/W404L and Q24N/W404N) with an improved ability to hydrolyze 4-nitrophenyl 3-O-methyl-β-D-galactopyranoside (3-MeOGal-pNP). Translation of these mutations into the evolved glycosynthase derived from the same glucosidase (2F6) yielded glycosynthases (AbgSL-T and AbgNN-T, where T denotes transferase) capable of forming 3-O-methylated glucosides on multi-milligram scales at rates approximately 5 and 40 times greater, respectively, than the parent glycosynthase.
Naturally Processed Non-canonical HLA-A*02:01 Presented Peptides (2014)

Human leukocyte antigen (HLA) class I molecules generally present peptides (p) of 8 to 11 amino acids (aa) in length. Although an increasing number of examples with lengthy (>11 aa) peptides, presented mostly by HLA-B alleles, have been reported. Here we characterize HLA-A*02:01 restricted, in addition to the HLA-B*0702 and HLA-B*4402 restricted, lengthy peptides (>11 aa) arising from the B-cell ligandome. We analyzed a number of 15-mer peptides presented by HLA-A*02:01, and confirmed pHLA-I formation by HLA folding and thermal stability assays. Surprisingly the binding affinity and stability of the 15-mer epitopes in complex with HLA-A*02:01 were comparable with the values observed for canonical length (8 to 11 aa) HLA-A*02:01-restricted peptides. We solved the structures of two 15-mer epitopes in complex with HLA-A*02:01, within which the peptides adopted distinct super-bulged conformations. Moreover, we demonstrate that T-cells can recognize the 15-mer peptides in the context of HLA-A*02:01, indicating that these 15-mer peptides represent immunogenic ligands. Collectively, our data expand our understanding of longer epitopes in the context of HLA-I, highlighting that they are not limited to the HLA-B family, but can bind the ubiquitous HLA-A*02:01 molecule, and play an important role in T-cell immunity.
Polysaccharide strong and weak gels (1993)

Small deformation oscillatory shear measurements have enabled a distinction to be made between so-called "strong" and "weak" gels, in particular those formed from biologically significant polysaccharides. At small enough strains, both systems give essentially the same mechanical spectrum, with G' > G", and with both moduli largely independent of frequency. However, the deformation dependence of the two classes of materials is very different. Strong gels are essentially strain independent (linearly viscoelastic) for strains of greater than about 0.25, whereas weak gels show such a response only for strains of less than about 0.05. At large deformations strong gels will rupture and fail, and will never "heal" without melting and resetting. Conversely, weak gels will recover and can flow without fracture, giving a power law response, with an exponent approaching -1, so-called "yield stress" behavior. The rheological properties of a strong gel, agarose, derived from the Rhodophyceae (marine algae) and a weak gel xanthan, an exocellular slime exuded by bacteria of the genus Xanthomonas, are measured in vitro, and related to in vivo requirements.
Monolithic 3D integration of logic and memory: Carbon nanotube FETs, resistive RAM, and silicon FETs (2014)

We demonstrate monolithic 3D integration of logic and memory in arbitrary vertical stacking order with the ability to use conventional inter-layer vias to connect between any layers of the 3D IC. We experimentally show 4 vertically-stacked layers (logic layer followed by two memory layers followed by another logic layer), enabled by the integration of traditional silicon-FETs (on the bottom-most layer) with low-processing-temperature emerging nanotechnologies: metal-oxide resistive random-access memory (RRAM), and carbon nanotube-FETs (CNFETs). As a demonstration, we show a routing element of a switchbox for a field-programmable gate array (FPGA), with each component of the routing element (involving both logic and memory elements) on their own vertical layer.
Lung Cancer Adjuvant Therapy (2007)

Lung cancer is the most common cause of cancer-related mortality in North America with non-small cell lung cancer representing the majority of cases. Despite advances in treatment, the prognosis remains poor with recurrence rates as high as 50% after surgical resection alone. In this article, we review the rationale and evidence for neoadjuvant and adjuvant therapy with chemotherapy, radiation therapy, and combined modality therapy in patients with resected non-small cell lung cancer.
Palladium-Catalyzed Intermolecular Coupling of Aryl Halides and Amides (2000)

[formula: see text] The first general intermolecular C-N bond-forming reactions between aryl halides and amides were realized using a palladium catalyst with Xantphos as the ligand. Aryl triflates, carbamates, and sulfonamides are also viable substrates for the amidations, which proceed at 45-110 degrees C with 1-4 mol% of Pd catalyst in 66-99% yields and exhibit good functional group compatibility.
Effects of indol-3-butyric acid (IBA), plant growth promoting rhizobacteria (PGPR) and carbohydrates on rooting of hardwood cutting of MM106 Apple rootstock (2009)

This investigation was conducted to evaluate the effects of a range of indole-3-butyric acid (IBA) concentrations (1000, 2000 and 4000 ppm), two strains ofAgrobacterium rubi (A-18) and Bacillus subtilis (OSU-142) and four carbohydrates (Glucose, Sucrose, Sorbitol and Mannitol) alone, in combination with two and three treatments on the rooting capacity of the hardwood cuttings of MM106 apple rootstock in greenhouse conditions. No rooting was obtained from control treatments but only low callus formation (10%). Single treatments did not induce rooting, except IBA-1000 ppm, OSU-142 and A-18, but induced better callus formation (20%) compared to control. Double and the three combinations were more successful in terms of rooting and callus formation. A-18+sorbitol, OSU-142+sorbitol+IBA-2000, A-18+sorbitol+IBA-2000 and A-18+sorbitol+IBA-4000 treatments were obtained from the highest rooting formation (30%) and OSU-142+sorbitol treatment had the highest callus rate (70%), that may be a precursor of adventitious root formation. IBA-1000 ppm treatment had the highest adventitious root number (16.5). A-18 treatment had the highest average adventitious root thickness (1.61 mm). The results indicate that double and triple combination of IBA, bacteria and carbohydrates are more effective in increasing rooting capacity and more quality rooting when compared to control, or carbohydrate, IBA and bacteria alone.

	 

	Key words: Apple rootstock, hardwood cutting, IBA, bacteria, carbohydrate.
Bone Cell Proliferation on Carbon Nanotubes (2006)

We explored the use of carbon nanotubes (CNTs) as suitable scaffold materials for osteoblast proliferation and bone formation. With the aim of controlling cell growth, osteosarcoma ROS 17/2.8 cells were cultured on chemically modified single-walled (SW) and multiwalled (MW) CNTs. CNTs carrying neutral electric charge sustained the highest cell growth and production of plate-shaped crystals. There was a dramatic change in cell morphology in osteoblasts cultured on MWNTs, which correlated with changes in plasma membrane functions.
Blue-Noise Multitone Dithering (2008)

The introduction of the blue-noise spectra-high-frequency white noise with minimal energy at low frequencies-has had a profound impact on digital halftoning for binary display devices, such as inkjet printers, because it represents an optimal distribution of black and white pixels producing the illusion of a given shade of gray. The blue-noise model, however, does not directly translate to printing with multiple ink intensities. New multilevel printing and display technologies require the development of corresponding quantization algorithms for continuous tone images, namely multitoning. In order to define an optimal distribution of multitone pixels, this paper develops the theory and design of multitone, blue-noise dithering. Here, arbitrary multitone dot patterns are modeled as a layered superposition of stack-constrained binary patterns. Multitone blue-noise exhibits minimum energy at low frequencies and a staircase-like, ascending, spectral pattern at higher frequencies. The optimum spectral profile is described by a set of principal frequencies and amplitudes whose calculation requires the definition of a spectral coherence structure governing the interaction between patterns of dots of different intensities. Efficient algorithms for the generation of multitone, blue-noise dither patterns are also introduced.
Deletion of purE attenuates Brucella melitensis 16M for growth in human monocyte-derived macrophages (1995)

We constructed a defined purine-auxotrophic mutant of Brucella melitensis 16M by chromosomal gene replacement. We electroporated B. melitensis 16M with suicide plasmids containing a kanamycin resistance cassette that replaced 226 bp at the carboxyl end of purE, the intergenic region, and 18 bases of the purK open reading frame. Recombinant B. melitensis delta purE201 required exogenous purines for growth on minimal media. Purine auxotrophy was complemented by electroporation of B. melitensis delta purE201 failed to grow in human monocyte-derived macrophages, while the growth of wild-type 16M and the complemented strain, delta purE201 (pSD5), increased by nearly two logs. These results suggest that B. melitensis delta purE201 will be attenuated in animals and humans and thus may be useful as a live attenuated vaccine.
Mouse limb muscle is determined in the absence of the earliest myogenic factor myf-5. (1994)

myf-5 is the only member of the MyoD family of myogenic regulatory genes to be expressed in the mouse embryo prior to muscle cell differentiation. We have used the developing limb as a model in which to follow the formation of peripheral muscle, to address the question of whether myogenic precursor cells are already present in the limb bud before expression of myf-5. The lacZ reporter gene has been introduced into the myf-5 gene by homologous recombination so that its expression is under the control of the endogenous myf-5 locus. beta-Galactosidase (beta-gal) coloration provides a sensitive assay for myf-5+ cells. Embryos were generated from embryonic stem cells carrying this mutation, and the appearance of beta-gal+ (myf-5+) cells was followed during limb development in vivo. Limb buds, at a stage when they are beta-gal-, were cultured in vitro. After several days, beta-gal+ cells accumulated in the premuscle mass. We conclude that determined muscle precursor cells in the limb bud do not initially express any member of the MyoD family. Furthermore, myogenic precursor cells in the somite, which, according to the avian model, migrate from the ventral/lateral edge of the dermomyotome to form peripheral muscle masses, are also negative for these factors.
Epinephrine absorption after different routes of administration in an animal model (1999)

In this model, absorption of epinephrine was significantly faster after intramuscular injection than after subcutaneous injection or inhalation. The extent of absorption was satisfactory after both intramuscular and subcutaneous injections. Neither the rate nor the extent of absorption was satisfactory after administration by inhalation.
Inhibitory effect of angiogenesis inhibitor TNP-470 on tumor growth and metastasis of human cell lines in vitro and in vivo. (1993)

Antitumor activity of angiogenesis inhibitor TNP-470 was evaluated in eight human cultured cell lines derived from choriocarcinoma: SCH, NUC-1, and GCH-1(m); ovarian cancer; TYK and Nakajima; and uterine endometrial cancer: HEC-6, HEC-50, and HEC-1-A. After 7-day culture with TNP-470, in medium at the concentration of 10(1) to 10(-2) micrograms/ml, the inhibition of growth was observed in all of the eight cell lines. The 50% inhibitory concentration of choriocarcinona cell lines was at an extremely low level compared to that of epithelial ovarian cancer and uterine endometrial cancer. In addition, the antitumor effect of this compound was studied in in vivo experiments using nude mice with tumors of GCH-1(m), NUC-1, or Nakajima cells. When the size of the transplanted tumor reached 100-200 mm3 in volume, 3, 10, or 30 mg/kg of TNP-470 was injected s.c. every other day. The inhibitory effect of TNP-470 was obtained by the administration of 10 and 30 mg/kg in GCH-1(m) and NUC-1 cells, respectively, while in Nakajima cells no significant effect was observed. In nude mice treated with 30 mg/kg of TNP-470, lung metastasis of GCH-1(m) cells was strongly inhibited both in the number and in the size of tumor nodules, indicating that the capillary growth in the originally developed tumor was also significantly reduced. These results suggest that the clinical setting using TNP-470 may be one of the promising treatments for the metastasis of tumor cells.