gebhart/patrepeval huggingface dataset:
Microbial Degradation of Cycloparaffinic Hydrocarbons via Co-metabolism and Commensalism (1974)

Summary: Mineralization of a cycloparaffinic hydrocarbon in soil has been demonstrated. Addition of [U-14C]cyclohexane to marine mud, followed by incubation at 26 °C, resulted in the evolution of 14CO2. All attempts in our laboratory to isolate organisms from soil which utilize cycloparaffins as a sole source of carbon and energy have proved unsuccessful. However, several hydrocarbon-utilizing bacteria oxygenated cycloparaffins to ketone derivatives that serve as the energy and carbon source for numerous other soil micro-organisms. The concerted attack of a mixed microbial population on cyclohexane has been demonstrated, suggesting that both co-metabolism and commensalism are associated with microbial degradation of cycloparaffinic hydrocarbons.
Ti Plasmid Homologous Sequences Present in Tissues from Agrobacterium Plasmid-transformed Petunia Protoplasts (1982)

Suspension cell protoplasts of albino Petunia hybrida have been transformed by isolated Agrobacterium tumefaciens Ti plasmid. Uptake of octopine Ti plasmid (pTiACH5) into protoplasts was stimulated by poly-L-ornithine and polyethylene glycol (PEG). The frequency and efficiency of transformation of protoplasts to phytohormone autotrophy was compared using the two uptake agents with various concentrations of plasmid. Transformation was most efficient with PEG-mediated uptake, 5 μg of Ti plasmid per 106 protoplasts giving a frequency of 6×10−5. Octopine was not synthesised in any of the transformants after the second subculture on hormone-free medium. DNA-DNA hybridisation showed the presence of DNA homologous to the T-DNA region of pTiACH5 in all clones analysed.
Glucagon-like peptide 2 (GLP-2) accelerates the growth of colonic neoplasms in mice (2004)

The present results clearly indicate that GLP-2 promotes the growth of mucosal neoplasms. Our findings highlight the need for future investigations on the effects of GLP-2 in conditions needing long time treatment or with increased gastrointestinal cancer susceptibility.
Palladium-catalyzed regioselective C-2 arylation of 7-azaindoles, indoles, and pyrroles with arenes (2016)

A palladium-catalyzed regioselective C-2 arylation of 7-azaindoles, indoles, and pyrroles with arenes has been developed. This study unveils that a critical substrate dependent acid concentration is essential for achieving exclusive C-2 selectivity as well as mono-arylation in pyrroles. Incongruent to the literature, the protocol uses a reduced volume (at least 5 times) of arenes for workable access to C-2 arylated heterocycles.
GGSCRs: GGNMOS Triggered silicon controlled rectifiers for ESD protection in deep sub-micron CMOS processes (2001)

In this paper, design aspects, operation, protection capability and applications of SCRs in deep sub-micron CMOS are addressed. A novel Grounded-Gate NMOS Triggered SCR device (GGSCR) is introduced and compared to the LVTSCR. Experimental verification, including endurance testing, demonstrates that GGSCRs can fulfill all ESD protection requirements for todays IC applications in different 0.25 um, 0.18 um and 0.13 um CMOS processes.
Isolation and heterologous expression of a gene encoding 4-hydroxyphenylpyruvate dioxygenase from the wheat leaf-spot pathogen,Mycosphaerella graminicola (1998)

We describe the isolation and sequence of a gene encoding 4-hydroxyphenylpyruvate dioxygenase (HPPD) (EC 1.13.11.27)) from the wheat leaf-spot fungal pathogen Mycosphaerella graminicola (Septoria tritici), that directs the synthesis of 2,5-dihydroxyphenylacetate (homogentisic acid, HGA). The sequence of the deduced peptide showed homology to HPPDs from other organisms; the greatest identity was to a T-cell reactive protein, also identified as HPPD, from the human fungal pathogen Coccidioides immitis. As observed for HPPD from other sources, expression of the M. graminicola HPPD gene in Escherichia coli cells could be detected by the gradual development of a brown pigment in cultures as a result of the spontaneous oxidation and polymerisation of HGA. Pigment development in these cultures was prevented by the HPPD inhibitor sulcotrione.
A phase I radioimmunolocalization trial of humanized monoclonal antibody huA33 in patients with gastric carcinoma (2006)

In order to determine the in vivo characteristics of huA33, an open label dose escalation biopsy-based phase I clinical trial and radioimmunolocalization study were conducted with a complement determinant region-grafted humanized monoclonal antibody against the A33 antigen in patients with gastric carcinoma. Thirteen patients were entered onto one of four dose levels (1.0, 2.0, 5.0 or 10.0 mg/m(2)). Patients with locally advanced (UICC-TNM [International Union Against Cancer-tumor, node, metastasis] stage over 2 but resectable at clinical diagnosis) gastric carcinoma received a single infusion of (131)I-huA33 1 week prior to surgery. Adverse events were monitored, and imaging studies with gamma camera plus ex vivo scintigraphy of the resected specimen, biodistribution study by dosimetry analysis of the biopsied and resected tissues, and immunohistochemical analysis were carried out and evaluated. No dose-limiting toxicity was observed during the trial. Therefore, the maximum tolerated dose was not reached. Although cancer tissues with + intensity and <25% extent by immunostaining in biopsied frozen sections did not show positive imaging or postoperative dosimetry findings, cancers with ++ or +++ intensity or wide (>25%) extent by frozen and paraffin sections in the biopsied specimen showed positive ex vivo tumor images and positive antigen expression in resected gastric cancer specimens, and the biodistribution analysis showed tumor uptake of (131)I-huA33. In conclusion, humanized monoclonal antibody huA33 demonstrated selective localization to gastric cancer that expressed A33 antigen strongly. These excellent targeting characteristics of huA33 indicate potential for targeted therapy of advanced gastric cancer that is refractory to cytotoxic therapy, and could also be exploitable for curatively resected early gastric cancer in an adjuvant setting.
In Vitro Evaluation of Pluronic F127-Based Controlled-Release Ocular Delivery Systems for Pilocarpine (1998)

The overall objective of this study was to develop pluronic F127 (PF127)-containing formulations of pilocarpine hydrochloride (PHCL) suitable for controlled-release ocular delivery of PHCL. Various aqueous formulations were evaluated containing 1% w/v PHCL and 25% w/v PF127 alone or with one of the following additives present: poly(ethylene glycol) 4600 (PEG), poly(vinylpyrrolidone) 10,000 (PVP), poly(vinyl alcohol) 10,000 (PVA), methylcellulose 15 cP (MC), and hydroxypropyl methylcellulose 80-120 cP (HPMC). The in vitro dissolution of the PF127 formulations and the pilocarpine release profiles from them were obtained simultaneously at 34 degrees C and room temperature using a membraneless in vitro model. It was observed that the PEG- and PVP-containing PF127 formulations of PHCL dissolved the quickest and released the drug at a significantly faster rate than the control PF127 formulation, which had no additive present. The PF127 formulations of PHCL containing MC or HPMC exhibited the slowest dissolution rates and released the drug the slowest. The same rank order was observed at each temperature for the dissolution and PHCL release profiles of each formulation. On the basis of the in vitro results, the PF127 formulations of PHCL containing MC or HPMC as an additive showed potential for use as controlled-release ocular delivery systems for PHCL.
EL PRIMER REGLAMENTO DE PENSIONADOS DE LA ACADEMIA DE BELLAS ARTES EN ROMA (1976)

Revista especializada en la publicación de trabajos originales de investigación en Prehistoria y Arqueología. Es la publicación periódica más antigua de la UAM. Su enfoque abierto a cualquier temática y época pasada, hasta la más cercana, que sea objeto de la Ciencia arqueológica se abre a una decidida proyección internacional en la que quiere basar su futuro inmediato.
Challenges in the Discovery of Indoleamine 2,3-Dioxygenase 1 (IDO1) Inhibitors (2015)

Since the discovery of indoleamine 2,3-dioxygenase 1 (IDO1) as an attractive target for anticancer therapy in 2003, the search for inhibitors has been intensely pursued both in academia and in pharmaceutical companies. Many novel IDO1 inhibitor scaffolds have been described, and a few potent compounds have entered clinical trials. However, a significant number of the reported compounds contain problematic functional groups, suggesting that enzyme inhibition could be the result of undesirable side reactions instead of selective binding to IDO1. Here, we describe issues in the employed experimental protocols, review and classify reported IDO1 inhibitors, and suggest different approaches for confirming viable inhibitor scaffolds.
Expression of taurine transporter is regulated through the TonE (tonicity-responsive element)/TonEBP (TonE-binding protein) pathway and contributes to cytoprotection in HepG2 cells (2004)

In hypertonic environment, taurine accumulates in cells via activation of TauT (taurine transporter) as an adaptive regulation. Recent studies revealed that TonE (tonicity-responsive element)/TonEBP (TonE-binding protein) pathway regulated the expression of various molecules which protect cells against hypertonic stress. In the present study, we investigated the osmoregulatory mechanisms of TauT expression. TauT was up-regulated at both functional and transcriptional levels in HepG2 under hypertonic condition. The TonE site was identified in the promoter region of TauT gene. Reporter gene assay revealed that promoter activity was increased under hypertonic conditions, whereas deletion or mutation of TonE sequence abolished the induction of the promoter activity in response to hypertonicity. By using the reporter gene plasmids containing a TonE site of TauT promoter (p2xTonE-Luc), it was demonstrated that a TonE site was sufficient for the hypertonicity-mediated activation of TauT promoter. Importantly, co-transfection of TauT promoter gene plasmid with wild-type TonEBP expression vector enhanced promoter activity under isotonic conditions, whereas dominant-negative TonEBP abrogated the TauT promoter activity induced by hypertonicity. Finally, treatment with taurine prevented HepG2 cells from cell death induced by hypertonic medium. These findings suggested that induction of TauT by hypertonicity is mediated by the activation of the TonE/TonEBP pathway and confers resistance to hypertonic stress.
A Cyclic Voltammetry Method Suitable for Characterizing Antioxidant Properties of Wine and Wine Phenolics (2001)

Phenolic antioxidants are ranked by reducing strength and characterized for reversibility using cyclic voltammetry at a glassy carbon electrode. Phenolics with an ortho-diphenol group show a first oxidation peak close to 400 mV (vs. Ag/AgCl) in a model wine solution (12% ethanol, 0.033 M tartaric acid, adjusted to pH 3.6), with a linear concentration dependence below 0.01 mM. Dilution of white wines 10x, and red wines 400x, gave first oxidation peak currents in the 1.5 to 2.2 microA range and 1.9 to 3.4 microC of charge passed by 500 mV, producing values for the concentrations of phenolic antioxidants with low oxidation potentials in the wines. Further peaks in the cyclic voltammograms of the diluted wines correspond to classes of phenolics with higher oxidation potentials, providing a qualitative assessment of wine phenolics based on reducing strength.
Sensitization to Radiation and Alkylating Agents by Inhibitors of Poly(ADP-ribose) Polymerase Is Enhanced in Cells Deficient in DNA Double-Strand Break Repair (2010)

As single agents, chemical inhibitors of poly(ADP-ribose) polymerase (PARP) are nontoxic and have clinical efficacy against BRCA1- and BRCA2-deficient tumors. PARP inhibitors also enhance the cytotoxicity of ionizing radiation and alkylating agents but will only improve clinical outcomes if tumor sensitization exceeds effects on normal tissues. It is unclear how tumor DNA repair proficiency affects the degree of sensitization. We have previously shown that the radiosensitizing effect of PARP inhibition requires DNA replication and will therefore affect rapidly proliferating tumors more than normal tissues. Because many tumors exhibit defective DNA repair, we investigated the impact of double-strand break (DSB) repair integrity on the sensitizing effects of the PARP inhibitor olaparib. Sensitization to ionizing radiation and the alkylating agent methylmethane sulfonate was enhanced in DSB repair-deficient cells. In Artemis(-/-) and ATM(-/-) mouse embryo fibroblasts, sensitization was replication dependent and associated with defective repair of replication-associated damage. Radiosensitization of Ligase IV(-/-) mouse embryo fibroblasts was independent of DNA replication and is explained by inhibition of "alternative" end joining. After methylmethane sulfonate treatment, PARP inhibition promoted replication-independent accumulation of DSB, repair of which required Ligase IV. Our findings predict that the sensitizing effects of PARP inhibitors will be more pronounced in rapidly dividing and/or DNA repair defective tumors than normal tissues and show their potential to enhance the therapeutic ratio achieved by conventional DNA-damaging agents.
Intra- and Interspecific Variation in Primate Gene Expression Patterns (2002)

Although humans and their closest evolutionary relatives, the chimpanzees, are 98.7% identical in their genomic DNA sequences, they differ in many morphological, behavioral, and cognitive aspects. The underlying genetic basis of many of these differences may be altered gene expression. We have compared the transcriptome in blood leukocytes, liver, and brain of humans, chimpanzees, orangutans, and macaques using microarrays, as well as protein expression patterns of humans and chimpanzees using two-dimensional gel electrophoresis. We also studied three mouse species that are approximately as related to each other as are humans, chimpanzees, and orangutans. We identified species-specific gene expression patterns indicating that changes in protein and gene expression have been particularly pronounced in the human brain.
BIOMARKERS IN OIL SHALE: OCCURRENCE AND APPLICATIONS (1983)

Our study shows that incidental extra-spinal findings at conventional lumbar spine MRI are common but underestimated in radiological reports.
IL-11, a pleiotropic cytokine: exciting new effects of IL-11 on gastrointestinal mucosal biology. (1994)

Recombinant human interleukin 11 (rhIL-11) is a pleiotropic cytokine that stimulates bone marrow stem cells to proliferate and decreases intestinal mucosal injury produced by cytoablative drugs and radiation in animals. The effects of rhIL-11 were studied in a hamster model of oral mucositis and in two rat models of inflammatory bowel disease (IBD). Oral mucositis was induced in male Golden Syrian hamsters with 5-fluorouracil 60 mg/kg intraperitoneal, days 0 and 2. Peak mucositis occurred by day 10 in vehicle treated animals. rhIL-11, given twice daily subcutaneously, decreased the mucositis in a dose-dependent manner and increased animal survival at all doses tested. In two models of IBD, the acetic acid-induced acute colonic injury model in Sprague-Dawley rats and the transgenic Fischer 344 rats expressing human HLA-B27 and beta 2-microglobulin, rhIL-11 decreased the gross and microscopic damage in the colons of these animals. These data suggest that rhIL-11 exerts effects on the gastrointestinal mucosa which ameliorate responses to injurious stimuli.
Characterization of infectious molecular clones of equine infectious anaemia virus (1994)

We have recovered five infectious molecular clones of the lentivirus equine infectious anaemia virus (EIAV). The clones were recovered from fetal equine kidney (FEK) cells infected with a virulent, cell culture-adapted virus stock (designated PV) and have been characterized at a molecular level. Each clone has unique envelope and long terminal repeat (LTR) sequences. We further investigated LTR sequence variation in the PV stock using PCR amplification to obtain additional LTR clones from infected FEK cells and from peripheral blood mononuclear cells (PBMCs) from animals experimentally infected with PV. Sequence analysis of resulting clones indicates a selection for different LTR populations in pony PBMCs compared to FEK cells. Finally, we observed that the cloned EIAV proviruses did not remain infectious when maintained in a derivative of pBR322. However, two proviruses have been stably maintained in a low copy number vector (pLG338-SPORT).
Quantitative In Vitro Demonstration of Two‐Photon Photodynamic Therapy Using Photofrin® and Visudyne® (2007)

Photodynamic therapy (PDT), the combined action of a photosensitizer and light to produce a cytotoxic effect, is an approved therapy for a number of diseases. At present, clinical PDT treatments involve one-photon excitation of the photosensitizer. A major limitation is that damage may be caused to healthy tissues that have absorbed the drug and lie in the beam path. Two-photon excitation may minimize this collateral damage, as the probability of absorption increases with the square of the light intensity, enabling spatial confinement of the photosensitizer activation. A potential application is the treatment of the wet-form of age-related macular degeneration, the foremost cause of central vision loss in the elderly. Herein, the commercial photosensitizers Visudyne and Photofrin are used to demonstrate quantitative in vitro two-photon PDT. A uniform layer of endothelial cells (YPEN-1) was irradiated with a Ti:sapphire laser (300 fs, 865 nm, 90 MHz) using a confocal scanning microscope. Quantification of the two-photon PDT effect was achieved using the permeability stain Hoechst 33258 and a SYTOX Orange viability stain. Visudyne was found to be around seven times more effective as a two-photon photosensitizer than Photofrin under the conditions used, consistent with its higher two-photon absorption cross-section. We also demonstrate for the first time the quadratic intensity dependence of cellular two-photon PDT. This simple in vitro method for quantifying the efficacy of photosensitizers for two-photon excited PDT will be valuable to test specifically designed two-photon photosensitizers before proceeding to in vivo studies in preclinical animal models.
Segmentation of stained blood cell images measured at high scanning density with high magnification and high numerical aperture optics (1986)

In hematological morphology, it is necessary to resolve and analyze the smallest possible cellular details appearing in the light microscope. A prerequisite for computer-aided analysis of subtle morphological features is measuring the cells at a high scanning density with high magnification and high numerical aperture optics. Contrary to visual observations, the information content in a measured picture can be increased by setting the condensor's numerical aperture (NA) greater than the objective's NA. The complexity and heterogeneity of such cell images necessitate a new segmentation method that conserves the morphological information required in the subsequent image analysis, feature extraction, and cell classification. In our segmentation strategy, characteristic color difference thresholds for each nucleus and cytoplasm are combined with geometric operations, probability functions, and a cell model. All thresholds are repeatedly recalculated during the successive improvements of the image masks. None of the thresholds are fixed. This strategy segments blood cell images containing touching cells and large variations in staining, texture, size, and shape. Biological inconsistencies in the calculated cell masks are eliminated by comparing each mask with the cell model criteria integrated into the entire segmentation process. All 20,000 leukocyte images from 120 smears in our leukemia project were segmented with this method.
Induction of Neurite Outgrowth through Contactin and Nr-CAM by Extracellular Regions of Glial Receptor Tyrosine Phosphatase β (1997)

Receptor protein tyrosine phosphatase beta (RPTPbeta) is expressed as soluble and receptor forms with common extracellular regions consisting of a carbonic anhydrase domain (C), a fibronectin type III repeat (F), and a unique region called S. We showed previously that a recombinant Fc fusion protein with the C domain (beta C) binds to contactin and supports neuronal adhesion and neurite growth. As a substrate, betaCFS was less effective in supporting cell adhesion, but it was a more effective promoter of neurite outgrowth than betaCF. betaS had no effect by itself, but it potentiated neurite growth when mixed with betaCF. Neurite outgrowth induced by betaCFS was inhibited by antibodies against Nr-CAM and contactin, and these cell adhesion molecules formed a complex that bound betaCFS. NIH-3T3 cells transfected to express betaCFS on their surfaces induced neuronal differentiation in culture. These results suggest that binding of glial RPTPbeta to the contactin/Nr-CAM complex is important for neurite growth and neuronal differentiation.
Cloning and functional characterization of the Arabidopsis N‐acetylserotonin O‐methyltransferase responsible for melatonin synthesis (2015)

The N-acetylserotonin O-methyltransferase (ASMT) gene encodes the enzyme that catalyzes the conversion of N-acetylserotonin to melatonin as the last step in melatonin biosynthesis. The first plant ASMT gene to be cloned was from rice. An orthologous gene encoding a protein with ASMT activity and only 39.7% amino acid sequence identity to the rice ASMT protein was recently isolated from apple (Malus zumi). The low homology of the apple ASMT sequence prompted us to screen the Arabidopsis genome for a homologous ASMT gene. The At4g35160 gene exhibited the highest sequence identity (31%) to the rice ASMT gene, followed by the At1g76790 gene with 29% sequence identity. We purified recombinant proteins expressed from the two Arabidopsis genes. The At4g35160 recombinant protein exhibited ASMT enzyme activity, but the At1g76790 recombinant protein did not; thus, we designated At4g35160 as an Arabidopsis thaliana ASMT (AtASMT) gene. The AtASMT protein catalyzed the conversion of N-acetylserotonin to melatonin and serotonin to 5-methoxytryptamine with Vmax values of 0.11 and 0.29 pkat/mg protein, respectively. However, AtASMT exhibited no caffeic acid O-methyltransferase activity, suggesting that its function was highly specific to melatonin synthesis. AtASMT transcripts were induced by cadmium treatment in Arabidopsis followed by increased melatonin synthesis. Similar to other ASMT proteins, AtASMT was localized in the cytoplasm and its ectopic overexpression in rice resulted in increased ASMT enzyme activity and melatonin production, indicating the involvement of AtASMT in melatonin synthesis.