gebhart/patrepeval huggingface dataset:
Diet and Habitat Requirements of the Philippine Endemic Frugivorous Monitor Lizard Varanus bitatawa (2018)

&lt;p&gt;Little is known about the ecology and diet of Varanus bitatawa, a recently discovered monitor lizard endemic to the Sierra Madre Mountains of Northern Luzon. Here we present data that show that it has a seasonal omnivorous diet comparable to its southern congener Varanus olivaceus. Consumption of fruits from Pandanus sp., Canarium sp. and Microcos stylocarpa was evident in fecal samples, from spool and line tracking observations, and from camera trap images. The frugivorous diet was supplemented with snails and insects belonging to the orders Orthoptera, Phasmatodea and Coleoptera. Habitat of V. bitatawa was studied in lowland disturbed dipterocarp forest at an elevation below 300 m. In three sampled sites basal area of dipterocarp trees ranged from 16.23 to 84.14 m2 ha-1, total tree density from 624.6 to 1021.4 trees per ha-1 and density of Pandanus from 115.15 to 222.30 trees per ha-1. Predominantly arboreal, V. bitatawa showed reliance on large sentinel trees. Of trees utilized, 47.4% were estimated at over 30 m tall with a mean circumference at breast height (CBH) of 176.28 cm and were significantly larger than the mean CBH of trees in sampled habitats. Shy and reclusive, V. bitatawa is likely to be vulnerable to disturbance. Illegal selective logging further degrades remaining habitat threatening the large dipterocarp trees on which they rely. Continued and improved protection of the forests within the Sierra Madre Mountain Range is imperative to safeguard the future of this restricted range species.&lt;br /&gt;&lt;/p&gt;
Antibiotic-free bacterial strain selection using antisense peptide nucleic acid. (2003)

Antibiotics are widely useful in medicine, agriculture, and industrial fermentations. However, increasing problems with resistant strains call for restrained use and alternative strategies. Antisense peptide nucleic acids (PNAs) show potent bactericidal effects when targeted against the essential Escherichia coli acpP gene. Aside from attractive antimicrobial therapeutic possibilities for such antisense PNAs, we considered that they could be used as a substitute for antibiotics in bacterial strain selection. Here, treatment of a mixture of E. coli wild-type cells and cells carrying a binding-site altered copy of acpP (acpP-1) with anti-acpP PNA completely killed wild-type cells within 2 h, whereas cells carrying acpP-1 proliferated. Furthermore, electrotransformation of E. coli cells with the plasmid carrying acpP-1 followed by PNA selection gave rise to only true transformants. Unlike previous antibiotic-free selection strategies, this procedure does not require special growth environments or special host strains. Also, the PNA-selected cells grow at a near normal rate. The results open possibilities to use antisense PNAs for strain selection and construction in research and industrial application.
Graft rescue for haemodialysis arterio-venous grafts: is it worth doing and which factors predict a good outcome? (1998)

Arterio-venous grafts in patients with end-stage renal failure are used when the patients have inadequate native veins or where there is an urgent need for permanent vascular access. Complications include thrombosis, bleeding, infection and pseudoaneurysm formation. The factors causing thrombosis can be divided into patient-related and graft-related factors. In this study 47 graft rescues in 24 patients were analysed. Polytetrafluoroethylene (PTFE) and polyurethane grafts were used. A successful graft rescue was defined as one in which a thrill was felt after surgical thrombectomy and the graft was subsequently used for haemodialysis. Eighteen grafts were PTFE and 10 were polyurethane; there were 15 women and nine men. There were 20 successful and 27 unsuccessful rescues, the overall success rate being 42.6% (20/47 rescues). Evidence of underlying stenoses was found in 14 graft rescues: 11 were at the venous end, two at the arterial end and one at the apex. A vein patch was used in these patients. In successful graft rescues an identifiable structural cause was found in only seven (25.9%) of the failed graft rescues. In spite of the common belief that graft rescue is unproductive, this study has shown that graft rescue was successful in 42.6% of cases. This was especially so when there was a surgically correctable underlying graft stenosis.
Molecular Cloning and Expression of Megakaryocyte Potentiating Factor cDNA (1995)

The human megakaryocyte potentiating factor (hMPF) has been previously purified from a culture supernatant of human pancreatic cancer cells HPC-Y5 (Yamaguchi, N., Hattori, K., Oh-eda, M., Kojima, T., Imai, N., and Ochi, N. (1994) J. Biol. Chem. 269, 805-808). We have now isolated hMPF cDNA from a HPC-Y5 cDNA library using polymerase chain reaction and plaque hybridization methods. The hMPF cDNA encodes a polypeptide consisting of 622 amino acids, including a signal peptide of 33 amino acids, and with a deduced molecular mass of 68 kDa, although HPC-Y5 cells secrete a 33-kDa form of hMPF. Human MPF does not show any significant homology with other previously described sequences. The cDNA was expressed in COS-7 and Chinese hamster ovary (CHO) cells, and megakaryocyte potentiating activity was detected in their culture supernatant. The COS-7 cells secreted only a 33-kDa recombinant hMPF, whereas an additional 30-kDa form was detected in the culture medium of CHO cells. The 33-kDa rhMPF purified from CHO cells showed megakaryocyte potentiating activity, but not the purified 30-kDa rhMPF. The difference in structure and activity between the 33- and 30-kDa forms of hMPF was ascribed to the existence in the 33-kDa form of the C-terminal 25 amino acid residues.
Acute antinociceptive responses in single and combinatorial opioid receptor knockout mice: distinct mu, delta and kappa tones (2003)

We have examined responses of mice lacking mu, delta and kappa opioid receptor (MOR, DOR and KOR, respectively) genes, as well as combinatorial mutants, in several pain models. This is the first truly comparative study of all three opioid receptor-deficient mice, with genotypes and gender analysis using mice on the hybrid 50% 129/SV : 50% C57BL/6 genetic background. In the tail-immersion test, only KOR-/- females showed decreased withdrawal latencies. This modification was also found in MOR/KOR and MOR/DOR/KOR, but not MOR/DOR mutants. The hotplate test revealed increased nociceptive sensitivity for MOR-/-, a phenotype which was also observed in double mutants involving the MOR deletion, and in the triple mutants. The tail-pressure test showed increased response for both MOR-/- and DOR-/- mutants, a modification which was enhanced in the triple-mutant mice. In the formalin test, MOR-/- and DOR-/- mice showed increased responses in the early and late phases, respectively, while the triple mutant tended to show enhanced nociception in both phases. Finally, the enhanced response of KOR-/- mice in the writhing test, which we have demonstrated previously, was confirmed in double MOR/KOR- and triple-mutant mice. Together, the data support the existence of an antinociceptive opioid tone. Each receptor presents a distinct pattern of activities, with mu receptors influencing responses to mechanical, chemical and thermal nociception at a supraspinal level, kappa receptors involved in spinally mediated thermal nociception and chemical visceral pain, and delta receptors modulating mechanical nociception and inflammatory pain. Phenotypes of mutant mice were subtle, suggesting a low endogenous opioid tone in the regulation of physiological pain.
Overlapping and enzyme-specific contributions of matrix metalloproteinases-9 and -12 in IL-13–induced inflammation and remodeling (2002)

IL-13 potently stimulates eosinophilic and lymphocytic inflammation and alveolar remodeling in the lung, effects that depend on the induction of various matrix metalloproteinases (MMPs). Here, we compared the remodeling and inflammatory effects of an IL-13 transgene in lungs of wild-type, MMP-9-deficient, or MMP-12-deficient mice. IL-13-induced alveolar enlargement, lung enlargement, compliance alterations, and respiratory failure and death were markedly decreased in the absence of MMP-9 or MMP-12. Moreover, IL-13 potently induced MMPs-2, -12, -13, and -14 in the absence of MMP-9, while induction of MMPs-2, -9, -13, and -14 by IL-13 was diminished in the absence of MMP-12. A deficiency in MMP-9 did not alter eosinophil, macrophage, or lymphocyte recovery, but increased the recovery of total leukocytes and neutrophils in bronchoalveolar lavage (BAL) fluids from IL-13 transgenic mice. In contrast, a deficiency in MMP-12 decreased the recovery of leukocytes, eosinophils, and macrophages, but not lymphocytes or neutrophils. These studies demonstrate that IL-13 acts via MMPs-9 and -12 to induce alveolar remodeling, respiratory failure, and death and that IL-13 induction of MMPs-2, -9, -13, and -14 is mediated at least partially by an MMP-12-dependent pathway. The also demonstrate that MMPs-9 and -12 play different roles in the generation of IL-13-induced inflammation, with MMP-9 inhibiting neutrophil accumulation and MMP-12 contributing to the accumulation of eosinophils and macrophages.
Molecular Cytogenetics of the Genus Arabidopsis: In situ Localization of rDNA Sites, Chromosome Numbers and Diversity in Centromeric Heterochromatin (1993)

We have used in situ hybridization to determine the number of sites of rDNA in species in the genus Arabidopsis. A. wallichii (2n = 16) has one major pair of sites and one minor pair of sites, while A. pumila and A. griffithiana (both 2n = 32) have six major and two minor rDNA sites. A. thaliana (2n = 10) is known to have two pairs of rDNA sites. a highly repeated para-centromeric sequence from A. thaliana, pAL1, is absent in the other three species. Hence the A.thaliana genome is not present (or the centromeric DNA has evolved substantially) in the polyploid species A. pumila and A. griffithiana. Analysis of Arabidopsis species is a valuable complement to the large programmes for genetic analysis of A. thaliana.Copyright 1993, 1999 Academic Press
Peptides fused to the amino-terminal end of diphtheria toxin are translocated to the cytosol. (1991)

Diphtheria toxin belongs to a group of toxic proteins that enter the cytosol of animal cells. We have here investigated the effect of NH2-terminal extensions of diphtheria toxin on its ability to become translocated to the cytosol. DNA fragments encoding peptides of 12-30 amino acids were fused by recombinant DNA technology to the 5'-end of the gene for a mutant toxin. The resulting DNA constructs were transcribed and translated in vitro. The translation products were bound to cells and then exposed to low pH to induce translocation across the cell membrane. Under these conditions all of the oligopeptides tested, including three viral peptides and the leader peptide of diphtheria toxin, were translocated to the cytosol along with the enzymatic part (A-fragment) of the toxin. Neither hydrophobic nor highly charged sequences blocked translocation. The results are compatible with a model in which the COOH-terminus of the A-fragment first crosses the membrane, whereas the NH2-terminal region follows behind. The possibility of using nontoxic variants of diphtheria toxin as vectors to introduce peptides into the cytosol to elicit MHC class I-restricted immune response and clonal expansion of the relevant CD8+ cytotoxic T lymphocytes is discussed.
DNA Cross-Linker–Induced G2/M Arrest in Group C Fanconi Anemia Lymphoblasts Reflects Normal Checkpoint Function (1998)

Cells from individuals with Fanconi anemia (FA) arrest excessively in the G2/M cell cycle compartment after exposure to low doses of DNA cross-linking agents. The relationship of this abnormality to the fundamental genetic defect in such cells is unknown, but many investigators have speculated that the various FA genes directly regulate cell cycle checkpoints. We tested the hypothesis that the protein encoded by the FA group C complementing gene (FAC) functions to control a cell cycle checkpoint and that cells from group C patients (FA[C]) have abnormalities of cell cycle regulation directly related to the genetic mutation. We found that retroviral transduction of FA(C) lymphoblasts with wild-type FAC cDNA resulted in normalization of the cell cycle response to low-dose mitomycin C (MMC). However, when DNA damage was quantified in terms of cytogenetic damage or cellular cytotoxicity, we found similar degrees of G2/M arrest in response to equitoxic amounts of MMC in FA(C) cells as well as in normal lymphoblasts. Similar results were obtained using isogenic pairs of uncorrected, FAC- or mock-corrected (neo only) FA(C) cell lines. To test the function of other checkpoints we examined the effects of hydroxyurea (HU) and ionizing radiation on cell cycle kinetics of FA(C) and normal lymphoblasts as well as with isogenic pairs of uncorrected, FAC-corrected, or mock-corrected FA(C) cell lines. In all cases the cell cycle response of FA(C) and normal lymphoblasts to these two agents were identical. Based on these studies we conclude that the aberrant G2/M arrest that typifies the response of FA(C) cells to low doses of cross-linking agents does not represent an abnormal cell cycle response but instead represents a normal cellular response to the excessive DNA damage that results in FA(C) cells following exposure to low doses of cross-linking agents.
An Antifungal Agent Inhibits an Aminoacyl-tRNA Synthetase by Trapping tRNA in the Editing Site (2007)

Aminoacyl-transfer RNA (tRNA) synthetases, which catalyze the attachment of the correct amino acid to its corresponding tRNA during translation of the genetic code, are proven antimicrobial drug targets. We show that the broad-spectrum antifungal 5-fluoro-1,3-dihydro-1-hydroxy-2,1-benzoxaborole (AN2690), in development for the treatment of onychomycosis, inhibits yeast cytoplasmic leucyl-tRNA synthetase by formation of a stable tRNA(Leu)-AN2690 adduct in the editing site of the enzyme. Adduct formation is mediated through the boron atom of AN2690 and the 2'- and 3'-oxygen atoms of tRNA's3'-terminal adenosine. The trapping of enzyme-bound tRNA(Leu) in the editing site prevents catalytic turnover, thus inhibiting synthesis of leucyl-tRNA(Leu) and consequentially blocking protein synthesis. This result establishes the editing site as a bona fide target for aminoacyl-tRNA synthetase inhibitors.
First-principle derivation of gain in high-index-contrast waveguides (2008)

From first principles we develop figures of merit to determine the gain experienced by the guided mode and the lasing threshold for devices based on high-index-contrast waveguides. We show that as opposed to low-index-contrast systems, this quantity is not equivalent to the power confinement since in high-index-contrast structures the electric and magnetic field distributions cannot be related by proportionality constant. We show that with a slot waveguide configuration it is possible to achieve more gain than one would expect based on the power confinement in the gain media. Using the figures of merit presented here we optimize a slot waveguide geometry to achieve low-threshold lasing and discuss the fabrication tolerances of such a design.
FFT and sparse FFT techniques and applications (2017)

Currently, the FFT is used in different areas, starting from identification of frequency on mechanical vibration to image enhancement. Real-time computation by interpret the acquired data can be easily possible by Fast Fourier Transform (FFT). The best with an efficient algorithm is FFT so it is the foundation for analyzing, monitoring, and controlling various systems. Many applications like digital signal processing, partial differential equation solvers, communications, image processing, all most all Fourier coefficients are very small and known as sparse. In this paper we present different impact of fft and sparse fft in the areas of medical imaging, wireless communication.
Antiviral Activity of Constituents ofTamus communis (1991)

The antiviral activity of the phenanthrene derivatives 1-6, of the spyrostane triglycosides dioscin (7) and gracillin (8), of the furostanol tetraglycosides methylprotodioscin (9), its (25S) epimer methylprotoneodioscin (10), and methylprotogracillin 11, have been tested towards two RNA viruses: vesicular stomatitis virus and human rhinovirus type 1B. All these products were extracted from the rizomes of Tamus communis L; compound 11 was isolated also from Asparagus cochinchinesis, together with pseudoprotodioscin (12), a 20 (22)-unsaturated furostanoside, which was also investigated for antiviral activity. The results were of some interest mainly for the phenanthrene derivatives.
Neural Network Training-Data Selection Using Memory-Reduced Cluster Analysis for Field Model Development (2003)

This paper is related to neural network processing of near well bore geological logging data. The paper has been prepared to address the increased use and interest in artificial intelligence technologies in the interpretation of open-hole and/or casedhole formation evaluation data.A typical neural network model is developed from a training well or wells where measurements are available. The model is tested on a validation well or wells before it is applied to a specific field /reservoir. Quite often models are developed with limited data: for example single well data should be retrained with multi well data to improve its scope and applicability. Unfortunately, some efforts to upgrade can result in choosing to use sub-optimal training algorithms because of the need to deal with an extensively increased data size. The consequence is a reduction in predictive accuracy. To improve accuracy, it is wise to have ways (1) remove faulty, redundant and insignificant data, (2) detect inconsistent data, (3) have the ability to
Characterizing Acoustic Attenuation of Homogeneous Media Using Focused Impulsive Acoustic Radiation Force (2006)

A new method to characterize a material's attenuation using acoustic radiation force is proposed. Comparison of displacement magnitudes generated in a homogeneous material by acoustic radiation force excitations can be used to estimate the material's attenuation when the excitations are applied over a range of focal depths while maintaining a constant lateral focal configuration. Acoustic attenuations are related to the inverse of the excitation focal depth that yields the greatest focal zone displacement for this protocol. Experimental studies in calibrated tissue-mimicking phantoms are presented to demonstrate the feasibility of this method. Attenuations ranging from 0.3-1.5 dB/cm/MHz were characterized over excitation focal depths ranging from 5-30 mm, with an accuracy of 0.1 +/- 0.15 dB/cm/MHz. As currently implemented, this method is limited to characterizing materials that have homogeneous material properties and acoustic attenuations. This method for characterizing acoustic attenuation can be performed using conventional diagnostic scanners without any additional hardware and could also be performed concurrently with acoustic radiation force-based imaging modalities to generate images of mechanical properties and attenuation that are spatially co-registered with B-mode images.
Superoxide dismutase ameliorates TNBS-induced colitis by reducing oxidative stress, adhesion molecule expression, and leukocyte recruitment into the inflamed intestine (2004)

Oxidant stress has been implicated in the pathogenesis of inflammatory bowel disease. Antioxidant enzymes, such as superoxide dismutase (SOD), are candidate drugs for modulating this pathogenic factor. This study was designed to determine the therapeutic value of SOD in an experimental model of colitis and to study the mechanisms underlying its effects on intestinal inflammation. For that purpose, colitic (trinitrobenzene sulfonic acid-induced) and control rats were studied. Groups of colitic animals were treated with different doses of SOD (1, 4, or 13 mg/kg/day) or vehicle, starting after induction of colitis and during 7 days. Clinical and pathological markers of colitis severity and lipid peroxidation in colonic tissue were measured. Leukocyte-endothelial cell interactions in colonic venules and expression of vascular cell adhesion molecule 1 (VCAM-1) were determined. Development of colitis was associated with a significant loss in body weight, an increase in macroscopic and microscopic damage scores, and colonic myeloperoxidase activity. Administration of SOD significantly attenuated these changes in a dose-dependent manner and reduced lipid peroxidation in colonic tissue. The increase in leukocyte rolling and adhesion in colonic venules of colitic rats were significantly reduced by administration of SOD, 13 mg/kg/day. Development of colitis was associated with a marked increase in endothelial VCAM-1 expression, which was significantly reduced by treatment with SOD. In conclusion, treatment with SOD significantly reduces peroxidation reactions in the inflamed colon and affords significant amelioration of colonic inflammatory changes in experimental colitis. This effect is related to a reduction in VCAM-1 expression and leukocyte recruitment into the inflamed intestine.
Prospective Evaluation of Amplification‐Boosted ELISA for Heat‐Denatured p24 Antigen for Diagnosis and Monitoring of Pediatric Human Immunodeficiency Virus Type 1 Infection (1999)

The performance in pediatric human immunodeficiency virus type 1 (HIV-1) infection of a signal-amplification boosted ELISA for HIV-1 p24 antigen in plasma after heat-mediated immune complex dissociation was prospectively compared with polymerase chain reaction-based procedures. Diagnostic sensitivity and specificity of the p24 antigen test were 100% and 99.2%, respectively. Quantification revealed RNA in 85.7% and p24 antigen in 87.4% of 230 samples from 25 infected children. Concentrations of these indices in individual samples correlated (P<.0001). Introduction or modification of antiretroviral treatment showed concordant responses of RNA and p24 antigen in 39 (90.7%) of 43 instances. The treatment-induced changes in concentrations of RNA were higher than those of p24 antigen in 11 instances. In 1 instance, however, the concentration change of p24 antigen was greater than that of RNA (P=. 002). Variation of RNA concentrations was more marked than that of p24 antigen (P=.002). The p24 antigen test was equivalent to PCR for diagnosing and monitoring pediatric HIV-1 infection.
Dominant Th2 Differentiation of Human Regulatory T Cells upon Loss of FOXP3 Expression (2011)

CD4(+)CD25(+)FOXP3(+) regulatory T cells (Treg) are pivotal for peripheral self-tolerance. They prevent immune responses to auto- and alloantigens and are thus under close scrutiny as cellular therapeutics for autoimmune diseases and the prevention or treatment of alloresponses after organ or stem cell transplantation. We previously showed that human Treg with a memory cell phenotype, but not those with a naive phenotype, rapidly downregulate expression of the lineage-defining transcription factor FOXP3 upon in vitro expansion. We now compared the transcriptomes of stable FOXP3(+) Treg and converted FOXP3(-) ex-Treg by applying a newly developed intranuclear staining protocol that permits the isolation of intact mRNA from fixed, permeabilized, and FACS-purified cell populations. Whole-genome microarray analysis revealed strong and selective upregulation of Th2 signature genes, including GATA-3, IL-4, IL-5, and IL-13, upon downregulation of FOXP3. Th2 differentiation of converted FOXP3(-) ex-Treg occurred even under nonpolarizing conditions and could not be prevented by IL-4 signaling blockade. Thus, our studies identify Th2 differentiation as the default developmental program of human Treg after downregulation of FOXP3.