gebhart/patrepeval huggingface dataset:
Effect of Yam ( <i>Dioscorea alata</i> Compared to <i>Dioscorea japonica</i> ) on Gastrointestinal Function and Antioxidant Activity in Mice (2006)

ABSTRACT: Effects of Chinese yam ( Dioscorea alata) and Japanese yam ( Dioscorea japonica ) on gastrointestinal functions including intestinal microflora and intestinal enzymes' activities, as well as antioxidant protection against lipopolysaccharide (LPS)‐induced oxidative damage, in Balb/cA mice were examined. In part I, mice were fed yam‐supplemented diet for 4 or 8 wk, and killed with carbon dioxide. In part II, mice were fed yam‐supplemented diet for 4 wk, and followed by intraperitoneal LPS treatment (i.p. 4 mg/kg bodyweight). The intake of Chinese yam and Japanese yam significantly changed intestinal microflora, in which the colony numbers of Bifidobacterium and Lactobacillus were increased and the colony numbers of Clostridium perfringens were decreased ( P < 0.05). The intake of both Chinese and Japanese yams also significantly elevated the activity of leucine aminopeptidase and lipase ( P < 0.05), and the activities of sucrase and maltase were increased only in 20% yam‐treated groups ( P < 0.05). The preintake of yam significantly alleviated subsequent LPS‐induced oxidative injury by decreasing lipid oxidation level and fibronectin production and elevating superoxide dismutase activity ( P < 0.05). Both Chinese and Japanese yams contained dietary fibers, polyphenols, and flavonoids, which may contribute to the observed gastrointestinal function and antioxidant protection. These results suggest that both Chinese yam and Japanese yam were beneficial for intestinal health and oxidation prevention.
Fabrication of flexible piezoelectric PMN-PT based composite films for energy harvesting (2017)

Flexible piezoelectric composite films of lead magnesium niobate and lead titanate (PMN-PT) ceramic and multiwalled carbon nanotube (MW-CNT) in the matrix of polyvinyldene fluoride (PVDF) were fabricated for green energy harvesting and self-powered sensing. Compositions of PMN-PT was varied from 10-50 volume (vol. %) in PVDF matrix while a constant concentration of MW-CNT was maintained (1vol. %). Phase purity of the synthesized composites was confirm by X-ray diffraction (XRD) analysis. PMN-PT powder was found to be in single phase without the presence of any additional peak, which generally arises due to crystallization of another pyrochlore phase. Surface morphology study by scanning electron microscopy (SEM) revealed a well dispersed PMN-PT/CNT in PVDF matrix. The maximum measured output voltage and current during mechanical pressing and releasing conditions were found to be ∼ 3 volt and 30 nA, respectively in 30 vol. % PMN-PT composite.
Immunohistochemical localization of candidates for vesicular glutamate transporters in the rat brain (2002)

Vesicular glutamate transporter 1 (VGluT1) is one of the best markers for glutamatergic neurons, because it accumulates transmitter glutamate into synaptic vesicles. Differentiation-associated Na(+)-dependent inorganic phosphate cotransporter (DNPI) shows 82% amino acid identity to VGluT1, and is another candidate for vesicular glutamate transporters. Here, we report the immunocytochemical localization of DNPI and compare it with that of VGluT1 in the adult rat brain. Both DNPI and VGluT1 immunoreactivities were found mostly in neuropil, presumably in axon terminals, throughout the brain. In the telencephalic regions, intense DNPI immunoreactivity was observed in the glomeruli of the olfactory bulb, layer IV of the neocortex, granular layer of the dentate gyrus, presubiculum, and postsubiculum. In contrast, VGluT1 immunoreactivity was intense in the olfactory tubercle, layers I-III of the neocortex, piriform cortex, entorhinal cortex, hippocampus, dentate gyrus, and subiculum. In the thalamic nuclei, DNPI-immunoreactive terminal-like profiles were much larger than VGluT1-immunoreactive ones, suggesting that DNPI immunoreactivity was subcortical in origin. DNPI immunoreactivity was much more intense than VGluT1 immunoreactivity in many brainstem and spinal cord regions, except the pontine nuclei, interpeduncular nucleus, cochlear nuclei, and external cuneate nucleus. In the molecular layer of the cerebellar cortex, climbing-like fibers showed intense DNPI immunoreactivity, whereas neuropil contained dense VGluT1-immnoreactive deposits. Both DNPI and VGluT1 immunoreactivities were observed as mossy fiber terminal-like profiles in the cerebellar granular layer. DNPI and VGluT1 immunoreactivities appeared associated with synaptic vesicles in the axon terminals forming asymmetric synapses in several regions examined electron microscopically. The present results indicate that DNPI and VGluT1 are used by different neural components in most, if not all, brain regions, suggesting the complementary functions of DNPI and VGluT1.
Radiation Exposure of Patients by Cone Beam CT during Endobronchial Navigation - A Phantom Study (2014)

Due to this low level of radiation exposure Cone Beam Computed Tomography is expected to attract interventionists interested in using and guiding endobronchial or transcutaneous ablative procedures to peripheral endobronchial and other lung lesions.
TIM Lecture Series – Using Risk to Drive a Security Service (2013)

Overview The fourth TIM lecture of 2013 was presented by Paul Card, Director of R&D at Seccuris. Card drew upon his experience as a programmer, entrepreneur, and professor to reflect upon the importance of leveraging uncertainty and managing risk when developing a technology platform in a small company. The event was held at Carleton University in Ottawa, Canada, on May
Comparison of model‐based arterial input functions for dynamic contrast‐enhanced MRI in tumor bearing rats (2009)

When using tracer kinetic modeling to analyze dynamic contrast-enhanced MRI (DCE-MRI) it is necessary to identify an appropriate arterial input function (AIF). The measured AIF is often poorly sampled in both clinical and preclinical MR systems due to the initial rapid increase in contrast agent concentration and the subsequent large-scale signal change that occurs in the arteries. However, little work has been carried out to quantify the sensitivity of tracer kinetic modeling parameters to the form of AIF. Using a preclinical experimental data set, we sought to measure the effect of varying model forms of AIF on the extended Kety compartmental model parameters (K(trans), v(e), and v(p)) through comparison with the results of experimentally acquired high temporal resolution AIFs. The AIF models examined have the potential to be parameterized on lower temporal resolution data to predict the form of the true, higher temporal resolution AIF. The models were also evaluated through application to the population average AIF. It was concluded that, in the instance of low temporal resolution or noisy data, it may be preferable to use a bi-exponential model applied to the raw data AIF, or when individual measurements are not available a bi-exponential model of the average AIF.
Research progress of islet β cell regeneration in the treatment of diabetes (2018)

Progressive function failure of islet β cells and insulin resistance are the main causes of the occurrence and development of diabetes mellitus.Islet transplantation and human embryonic stem cell transplantation are effective methods for the treatment of diabetes. However, the lack of donor sources, immune rejection and canceration limit their clinical applications. The regeneration of endogenous islet β cells provides a new way to treat diabetes. At present, common methods of endogenous regeneration include self-replication of β cells, differentiation of adult stem cells and embryonic stem cells into insulin-positive cells, and differentiation of terminal differentiated cells into insulin-secreting cells.


Key words: 
Diabetes mellitus; βcell regeneration; Replication; Neogenesis; Transdifferentiation
Spot indole test: evaluation of four reagents (1982)

Kovacs indole reagent, p-dimethylaminobenzaldehyde, Ehrlich indole reagent and p-dimethylaminocinnamaldehyde were used as spot indole reagents to test 359 strains of gram-negative rods growing on 5% sheep blood agar, Trypticase soy agar (BBL Microbiology Systems), and MacConkey agar. The p-dimethylaminocinnamaldehyde reagent was the most sensitive of those tested and provided results that were easiest to interpret. The p-dimethylaminocinnamaldehyde reagent was able to detect providencia alcalifaciens indole production because of the red-violet color unique to that organism. All reagents tested were accurate in detecting indole produced by members of the Enterobacteriaceae family, with the exception of P. alcalifaciens.
Real-Time Bioluminescence Imaging of Glycans on Live Cells (2010)

Cell-surface glycans are attractive targets for molecule imaging due to their reflection of cellular processes associated with development and disease progression. In this paper, we describe the design, synthesis, and biological application of a new phosphine probe for real-time imaging of cell-surface glycans using bioluminescence. To accomplish this goal, we took advantage of the bioorthogonal chemical reporter technique. This strategy uses a two-step labeling procedure in which an unnatural sugar analogue containing a functional handle is (1) incorporated into sugar-bearing proteins via the cell's own biosynthetic machinery and then (2) detected with an exogenously added probe. We designed phosphine-luciferin reagent 1 to activate bioluminescence in response to Staudinger ligation with azide-labeled glycans. We chose to use a phosphine probe because, despite their slow reaction kinetics, they remain the best-performing reagents for tagging azidosugars in mice. Given the sensitivity and negligible background provided by bioluminescence imaging (BLI), we reasoned that 1 might be able to overcome some of the limitations encountered with fluorescent phosphine probes. In this work, we synthesized the first phosphine-luciferin probe for use in real-time BLI and demonstrated that azide-labeled cell-surface glycans can be imaged with 1 using concentrations as low as single digit nanomolar and times as little as 5 min, a feat that cannot be matched by any previous fluorescent phosphine probes. Even though we have only demonstrated its use in visualizing glycans, it can be envisioned that this probe could also be used for bioluminescence imaging of any azide-containing biomolecule, such as proteins and lipids, since azides have been previously incorporated into these molecules. The phosphine-luciferin probe is therefore poised for many applications in real-time imaging in cells and whole animals. These studies are currently in progress in our laboratory.
In Vitro Microtumors Provide a Physiologically Predictive Tool for Breast Cancer Therapeutic Screening (2015)

Many anti-cancer drugs fail in human trials despite showing efficacy in preclinical models. It is clear that the in vitro assays involving 2D monoculture do not reflect the complex extracellular matrix, chemical, and cellular microenvironment of the tumor tissue, and this may explain the failure of 2D models to predict clinical efficacy. We first optimized an in vitro microtumor model using a tumor-aligned ECM, a tumor-aligned medium, MCF-7 and MDA-MB-231 breast cancer spheroids, human umbilical vein endothelial cells, and human stromal cells to recapitulate the tissue architecture, chemical environment, and cellular organization of a growing and invading tumor. We assayed the microtumor for cell proliferation and invasion in a tumor-aligned extracellular matrix, exhibiting collagen deposition, acidity, glucose deprivation, and hypoxia. We found maximal proliferation and invasion when the multicellular spheroids were cultured in a tumor-aligned medium, having low pH and low glucose, with 10% fetal bovine serum under hypoxic conditions. In a 7-day assay, varying doses of fluorouracil or paclitaxel had differential effects on proliferation for MCF-7 and MDA-MB-231 tumor spheroids in microtumor compared to 2D and 3D monoculture. The microtumors exhibited a tumor morphology and drug response similar to published xenograft data, thus demonstrating a more physiologically predictive in vitro model.
A Nonlinear Stein-Based Estimator for Multichannel Image Denoising (2008)

The use of multicomponent images has become widespread with the improvement of multisensor systems having increased spatial and spectral resolutions. However, the observed images are often corrupted by an additive Gaussian noise. In this paper, we are interested in multichannel image denoising based on a multiscale representation of the images. A multivariate statistical approach is adopted to take into account both the spatial and the intercomponent correlations existing between the different wavelet subbands. More precisely, we propose a new parametric nonlinear estimator which generalizes many reported denoising methods. The derivation of the optimal parameters is achieved by applying Stein's principle in the multivariate case. Experiments performed on multispectral remote sensing images clearly indicate that our method outperforms conventional wavelet denoising techniques.
Signal Transduction by Vascular Endothelial Growth Factor Receptors (2012)

Vascular endothelial growth factors (VEGFs) are master regulators of vascular development and of blood and lymphatic vessel function during health and disease in the adult. It is therefore important to understand the mechanism of action of this family of five mammalian ligands, which act through three receptor tyrosine kinases (RTKs). In addition, coreceptors like neuropilins (NRPs) and integrins associate with the ligand/receptor signaling complex and modulate the output. Therapeutics to block several of the VEGF signaling components have been developed with the aim to halt blood vessel formation, angiogenesis, in diseases that involve tissue growth and inflammation, such as cancer. In this review, we outline the current information on VEGF signal transduction in relation to blood and lymphatic vessel biology.
Thermotolerance and the Heat-shock Response in Candida albicans (1989)

At elevated temperatures, yeast cells of Candida albicans synthesized nine heat-shock proteins (HSPs) with apparent molecular masses of 98, 85, 81, 76, 72, 54, 34, 26 and 18 kDa. The optimum temperature for the heat-shock response was 45 degrees C although HSPs were detected throughout the range 41-46 degrees C. Protein synthesis was not observed in cells kept at 48 degrees C. Yeast cells survived exposure to an otherwise lethal temperature of 55 degrees C when they had previously been exposed to 45 degrees C. The thermotolerance induced during incubation at 45 degrees C required protein synthesis, since protection was markedly reduced by trichodermin. Mercury ions induced a set of three stress proteins, one of which corresponded in size to an HSP, and cadmium ions evoked one stress protein seemingly unrelated to the HSPs observed after temperature shift.
Channel density and efficiency optimization of spectral beam combining systems based on volume Bragg gratings in sequential and multiplexed arrangements (2015)

Spectral-beam-combining (SBC) systems utilizing multiple volume Bragg gratings must be carefully analyzed to maximize channel density and efficiency, and thus output radiance. This analysis grows increasingly difficult as the number of channels in the system increases, and heuristic optimization techniques are useful tools for exploring the limits of these systems. We explore three classes of multigrating SBC systems: cascaded, where each grating adds a new channel to the system in sequence; sandwiched, where several individual gratings are placed together and all channels enter the system at the same facet; and multiplexed, where all of the gratings occupy the same holographic optical element (HOE). Loss mechanisms differ among these three basic classes, and our optimization algorithm shows that the highest channel density for a given minimum efficiency and fixed operating bandwidth is achieved for a cascaded grating system. The multiplexed grating system exhibits the lowest channel density under the same constraints but has the distinct advantage of being realized by a single HOE. For a particular application, one must weigh channel density and efficiency versus system complexity when choosing among these basic classes of SBC systems. Additionally, one may need to consider the effects of finite-width input beams. As input beam radius is reduced, angular clipping effects begin to dominate over spectral interference and crosstalk effects, limiting all three classes of SBC systems in a similar manner.
CBFEM-MPI: A Parallelized Version of Characteristic Basis Finite Element Method for Extraction of 3-D Interconnect Capacitances (2009)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> In this paper, we present a novel, non-iterative domain decomposition method, which has been parallelized by using the message passing interface (MPI) library, and used to efficiently extract the capacitance matrixes of 3-D interconnect structures, by employing characteristic basis functions (CBFs) in the context of the finite element method (FEM). In this method, which is called CBFEM-MPI, the computational domain is partitioned into a number of nonoverlapping subdomains in which the CBFs are constructed by employing a procedure that is different from what has been used in the past for generating them. Specifically, the CBFs for the problem at hand are determined by calculating the potentials due to a finite number of point charges located hypothetically along the boundaries of the conductors. Two major advantages of the method are substantial reduction of the matrix size—enabling the use of direct solvers—and the utilization of parallel processing techniques that provide a substantial decrease in the overall computation time. Numerical examples are included to illustrate the application of the proposed approach to a number of representative problems. </para>
VR-Goggles for Robots: Real-to-Sim Domain Adaptation for Visual Control (2019)

In this letter, we deal with the reality gap from a novel perspective, targeting transferring deep reinforcement learning (DRL) policies learned in simulated environments to the real-world domain for visual control tasks. Instead of adopting the common solutions to the problem by increasing the visual fidelity of synthetic images output from simulators during the training phase, we seek to tackle the problem by translating the real-world image streams back to the synthetic domain during the deployment phase, to make the robot feel at home. We propose this as a lightweight, flexible, and efficient solution for visual control, as first, no extra transfer steps are required during the expensive training of DRL agents in simulation; second, the trained DRL agents will not be constrained to being deployable in only one specific real-world environment; and third, the policy training and the transfer operations are decoupled, and can be conducted in parallel. Besides this, we propose a simple yet effective shift loss that is agnostic to the downstream task, to constrain the consistency between subsequent frames which is important for consistent policy outputs. We validate the shift loss for artistic style transfer for videos and domain adaptation, and validate our visual control approach in indoor and outdoor robotics experiments.
Small-molecule agonists for the thyrotropin receptor stimulate thyroid function in human thyrocytes and mice (2009)

Seven-transmembrane-spanning receptors (7TMRs) are prominent drug targets. However, small-molecule ligands for 7-transmembrane-spanning receptors for which the natural ligands are large, heterodimeric glycoprotein hormones, like thyroid-stimulating hormone (TSH; thyrotropin), have only recently been reported, and none are approved for human use. We have used quantitative high-throughput screening to identify a small-molecule TSH receptor (TSHR) agonist that was modified to produce a second agonist with increased potency. We show that these agonists are highly selective for human TSHR versus other glycoprotein hormone receptors and interact with the receptor's serpentine domain. A binding pocket within the transmembrane domain was defined by docking into a TSHR homology model and was supported by site-directed mutagenesis. In primary cultures of human thyrocytes, both TSH and the agonists increase mRNA levels for thyroglobulin, thyroperoxidase, sodium iodide symporter, and deiodinase type 2, and deiodinase type 2 enzyme activity. Moreover, oral administration of the agonist stimulated thyroid function in mice, resulting in increased serum thyroxine and thyroidal radioiodide uptake. Thus, we discovered a small molecule that activates human TSHR in vitro, is orally active in mice, and could be a lead for development of drugs to use in place of recombinant human TSH in patients with thyroid cancer.
Single-molecule sensing of peptides and nucleic acids by engineered aerolysin nanopores (2019)

Nanopore sensing is a powerful single-molecule approach for the detection of biomolecules. Recent studies have demonstrated that aerolysin is a promising candidate to improve the accuracy of DNA sequencing and to develop novel single-molecule proteomic strategies. However, the structure-function relationship between the aerolysin nanopore and its molecular sensing properties remains insufficiently explored. Herein, a set of mutated pores were rationally designed and evaluated in silico by molecular simulations and in vitro by single-channel recording and molecular translocation experiments to study the pore structural variation, ion selectivity, ionic conductance and capabilities for sensing several biomolecules. Our results show that the ion selectivity and sensing ability of aerolysin are mostly controlled by electrostatics and the narrow diameter of the double β-barrel cap. By engineering single-site mutants, a more accurate molecular detection of nucleic acids and peptides has been achieved. These findings open avenues for developing aerolysin nanopores into powerful sensing devices.
A novel indoor localization system for healthcare environments (2012)

This paper proposes a novel indoor localization system, specifically designed for use in healthcare environments. The challenge for this indoor localization project is to decide in which room or in which area of a corridor the blindfolded node is situated, and this with a 100% guarantee that the determined location complies with the actual location of the blindfolded node. We propose a decentralized localization algorithm which uses Received Signal Strength information between the beacons and blindfolded nodes, combined with a smart beacon addressing scheme which is used by the localization algorithm. These beacons are existing access points to a backbone network equipped with a wireless interface. By using a proximity-based approach, we are able to decide where a blindfolded node is situated on a low resource and decentralized basis.