gebhart/patrepeval huggingface dataset:
PTEN regulates AMPA receptor-mediated cell viability in iPS-derived motor neurons (2014)

Excitatory transmission in the brain is commonly mediated by the α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) receptors. In amyotrophic lateral sclerosis (ALS), AMPA receptors allow cytotoxic levels of calcium into neurons, contributing to motor neuron injury. We have previously shown that oculomotor neurons resistant to the disease process in ALS show reduced AMPA-mediated inward calcium currents compared with vulnerable spinal motor neurons. We have also shown that PTEN (phosphatase and tensin homolog deleted on chromosome 10) knockdown via siRNA promotes motor neuron survival in models of spinal muscular atrophy (SMA) and ALS. It has been reported that inhibition of PTEN attenuates the death of hippocampal neurons post injury by decreasing the effective translocation of the GluR2 subunit into the membrane. In addition, leptin can regulate AMPA receptor trafficking via PTEN inhibition. Thus, we speculate that manipulation of AMPA receptors by PTEN may represent a potential therapeutic strategy for neuroprotective intervention in ALS and other neurodegenerative disorders. To this end, the first step is to establish a fibroblast-iPS-motor neuron in vitro cell model to study AMPA receptor manipulation. Here we report that iPS-derived motor neurons from human fibroblasts express AMPA receptors. PTEN depletion decreases AMPA receptor expression and AMPA-mediated whole-cell currents, resulting in inhibition of AMPA-induced neuronal death in primary cultured and iPS-derived motor neurons. Taken together, our results imply that PTEN depletion may protect motor neurons by inhibition of excitatory transmission that represents a therapeutic strategy of potential benefit for the amelioration of excitotoxicity in ALS and other neurodegenerative disorders.
Site-Specific Differentiation of Fibroblasts in Normal and Scleroderma Skin (2008)

Abstract : The central hypothesis of this research is that the site-specific differentiation of fibroblasts plays an important role in the anatomic specificity of systemic sclerosis (SSc). During the funding period, (i) we identified appropriate markers and technologies for systematic investigation of the positional identity of fibroblasts, both in normal and diseased tissues. (ii) We found that long noncoding RNAs are the predominant position specific output of the HOX loci, and their misexpression in systemic sclerosis suggests that altered fibroblast positional identity is involved. (iii) Ongoing studies suggest that some long noncoding RNAs are being mis-expressed in activated fibroblasts from SSc.
System Dynamics Modeling of Nitrogen Removal in a Stormwater Infiltration Basin with Biosorption‐Activated Media (2013)

Stormwater infiltration basins, one of the typical stormwater best management practices, are commonly constructed for surface water pollution control, flood mitigation, and groundwater restoration in rural or residential areas. These basins have soils with better infiltration capacity than the native soil; however, the ever-increasing contribution of nutrients to groundwater from stormwater due to urban expansion makes existing infiltration basins unable to meet groundwater quality criteria related to environmental sustainability and public health. This issue requires retrofitting current infiltration basins for flood control as well as nutrient control before the stormwater enters the groundwater. An existing stormwater infiltration basin in north-central Florida was selected, retrofitted, and monitored to identify subsurface physiochemical and biological processes during 2007-2010 to investigate nutrient control processes. This implementation in the nexus of contaminant hydrology and ecological engineering adopted amended soil layers packed with biosorption activated media (BAM; tire crumb, silt, clay, and sand) to perform nutrient removal in a partitioned forebay using a berm. This study presents an infiltration basin-nitrogen removal (IBNR) model, a system dynamics model that simulates nitrogen cycling in this BAM-based stormwater infiltration basin with respect to changing hydrologic conditions and varying dissolved nitrogen concentrations. Modeling outputs of IBNR indicate that denitrification is the biogeochemical indicator in the BAM layer that accounted for a loss of about one third of the total dissolved nitrogen mass input.
Complete list of tight Bell inequalities for two parties with four binary settings (2019)

We give the complete list of 175 facets of the local polytope for the case where Alice and Bob each choose their measurements from a set of four binary outcome measurements. For each inequality we compute the maximum quantum violation for qubits, the resistance to noise, and the minimal detection efficiency required for closing the detection loophole with maximally entangled qubit states, in the case where both detectors have the same efficiency (symmetric case).
Effect of Surface Alignment on the Stability and Electro-Optical Properties of Blue Phase Liquid Crystals (2014)

さまざまな配向膜を用いて界面配向がブルー相液晶の安定性および電気光学特性に与える影響について調査した．その結果，垂直配向膜の混合比率が上昇するにしたがい，ブルー相の温度範囲が拡大した．さらに，水平ポリイミド配向膜を塗布したサンプルにおいて，プレートレットがほとんど見えない完璧なモノドメインのテクスチャを得ることができた．しかしながら，電気光学特性において界面からの影響を確認することはできなかった．
Novel therapeutic approaches for hepatitis B virus covalently closed circular DNA (2015)

Hepatitis B virus (HBV) infection is a major global health problem. Although current therapies, such as the use of nucleos(t)ide analogs, inhibit HBV replication efficiently, they do not eliminate covalently closed circular DNA (cccDNA), which persists in hepatocyte nuclei. As HBV cccDNA is a viral transcription template, novel therapeutic approaches to directly target HBV cccDNA are necessary to completely eradicate persistent HBV infections. HBV cccDNA levels in HBV-infected human liver cells are extremely low; thus, more reliable and simple measurement methods are needed to correctly monitor their levels during therapeutic treatment. Although reverse transcription-polymerase chain reaction or Southern blot procedures are currently used in research studies, these methods are not completely reliable and are also time-consuming and labor-intensive. Genome editing technologies, such as zinc finger nucleases, transcription activator-like effector nucleases, and the clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas9) system, which are designed to target specific DNA sequences, represent highly promising potential therapeutic tools. In particular, the CRISPR/Cas9 system is an easily customizable sequence-specific nuclease with high flexibility and may be the most feasible approach to target HBV cccDNA. Further research to develop easier, safer, and more effective protocols should be pursued.
Hydrogenation of semiconductor surfaces: Si and Ge (111) (1988)

The relaxations of hydrogenated Si and Ge (111) surfaces are determined using ab initio self-consistent calculations in a slab configuration. The Si-H and Ge-H bonds are found to be considerably larger than the sum of covalent radii. The substrate relaxations are small and their physical origin can be explained in terms of electronic charge transfer which eliminates the surface dipole moment. The calculated frequencies of the hydrogen vibrational modes are in excellent agreement with experiment. A surface-atom vibrational mode is compared to similar modes in the amorphous hydrogenated materials. The comparison predicts that internal surfaces (microvoids) in the amorphous network are locally much softer than the corresponding crystalline surface configuration.
Measurement of Herceptin uptake in vivo using a novel fluoresence sensor (2005)

3846 An in vivo sensor that can detect the uptake of fluorescently labeled antibodies has been tested in a mouse model of human breast cancer. The fluorescence sensor was used to probe human tumor xenografts implanted in nude mice. A MCF7Her2 cell line that overexpresses clinically relevant levels of Her2 was used. The mice were implanted with MCF7Her2 cells in either the flank or the mammary pad and estrogen pellets were implanted in the scapular region to facilitate tumor growth. The tumors were allowed to grow until they reached approximately 5 mm in diameter. Herceptin (Trastuzumab) was fluorescently labeled (Alexa Fluor 647, Molecular Probes) and introduced into the tail vein of the animals (n=8) at a concentration of 4 mg/Kg. A control group (n=5) was injected with a fluorescently labeled, isotype-matched IgG antibody. The sensor was then used to record relative fluorescence signal levels in the tumor and in the flank over time. The mice were not anesthetized and were allowed to go back into their cages between time points. The ratio of the signals from the tumor and normal tissue was seen to be higher in the mice treated with Herceptin versus the control antibody. Whereas the signals in the tumors exposed to Herceptin rose over time, peaking between 24-48 hours, signals in the flank and in both regions of the control animals simply decayed over time. There was variation in the tumor/normal ratio in the animals receiving Herceptin that seemed to correlate with IHC grading of the excised tumors (performed at the end of the study period). These preliminary findings are summarized in the Table below: It is proposed that the fluorescence sensor could be a useful tool for the study of in vivo pharmacokinetics of some therapeutic molecules of interest.
Real-time 3D face tracking based on active appearance model constrained by depth data (2014)

Active Appearance Model (AAM) is an algorithm for fitting a generative model of object shape and appearance to an input image. AAM allows accurate, real-time tracking of human faces in 2D and can be extended to track faces in 3D by constraining its fitting with a linear 3D morphable model. Unfortunately, this AAM-based 3D tracking does not provide adequate accuracy and robustness, as we show in this paper. We introduce a new constraint into AAM fitting that uses depth data from a commodity RGBD camera (Kinect). This addition significantly reduces 3D tracking errors. We also describe how to initialize the 3D morphable face model used in our tracking algorithm by computing its face shape parameters of the user from a batch of tracked frames. The described face tracking algorithm is used in Microsoft's Kinect system.
Monocyte activation in rheumatoid arthritis (RA): increased integrin, Fcγ and complement receptor expression and the effect of glucocorticoids (1999)

The aim of this work was to study the expression of beta 1- and beta 2-integrins, CR1, CD44 and Fc gamma receptors on peripheral blood monocytes in RA. The expression of these receptors was measured by flow cytometry, before and after treatment with low-dose prednisolone. Expression of the same receptors was also measured before and after treatment with metyrapone, a substance that inhibits the synthesis of cortisol in the adrenals. The expression of the beta 2-integrins CD11a, CD11b and CD18, of CD35 (CR1), and of Fc gamma RII and Fc gamma RI (CD32 and CD64) on monocytes was elevated in the RA patients compared with healthy controls, while the expression of the beta 1-integrins (CD29, CD49d, CD49f) was unaffected. A significant correlation between monocyte expression of CD64 and C-reactive protein (CRP), and blood platelet count, respectively, was found in the group of patients with RA. After 4-6 weeks of treatment with low-dose prednisolone, the expression on the monocytes of CD11a, CD11b, CD18, CD35, CD32 and CD64 was normalized. A significant correlation (r = 0.64, P = 0.02) was found between the decrease in expression of CD11b and clinical improvement after prednisolone treatment. Two days of metyrapone treatment, which significantly lowered the serum cortisol levels, elevated the expression of CD35 and CD49f. Priming of peripheral monocytes seems to be one of the mechanisms behind the recruitment of monocytes to the rheumatoid synovium. One reason for the good clinical effects of prednisolone in RA could be a down-regulation of adhesion and phagocytosis receptors on monocytes.
Liver chimeric mice with tupaia hepatocyte transplantation as an animal model for hepatitis B virus infection and antiviral therapy (2019)

The human liver chimeric mouse is a milestone animal model for hepatitis B virus (HBV) infection. Such mice with primary human hepatocyte (PHH) transplantation are adequate to support chronic HBV infection for several weeks and to evaluate antiviral drugs. However, the drawbacks of PHHs include lack of available donors, poor expansion in vitro and ethical issues that limit the application of human liver chimeric mice, necessitating the search for alternatives. Here, we transplanted primary tupaia hepatocytes (PTHs) into the livers of immunodeficient mice and achieved high liver chimerism within six weeks. These tupaia liver chimeric mice are adequate to support chronic infection of the four common HBV genotypes A, B, C and D for 36 weeks, as well as evaluate of antiviral drugs, including hepatitis B immune globulin (HBIG), monoclonal antibody and nucleoside analogues (NAs), for preventative therapy and treatment post infection. In conclusion, the tupaia liver chimeric mouse model provides a convenient, efficient and stable animal model for chronic HBV infection and long-term drug evaluation.
Residues of cymiazole in honey and honey bees (1994)

SUMMARYTen honey bee (Apis mellifera ligustica) colonies were treated with the acaricide cymiazole hydrochloride (Apitol) at the dose recommended for controlling Varroa jacobsoni: 2 g Apitol (17.5% a.i.) in 100 ml of 20% sugar syrup sprinkled on to the combs of each colony. Samples of honey and dead honey bees were collected for up to 112 and 15 days respectively after treatment and analysed using a liquid Chromatograph. Cymiazole residues in unsealed honey decreased from an average of 2.45 ppm 1 day after treatment to 0.14 ppm 112 days after treatment: in bees residues were 84.12 ppm after 1 day but decreased quickly and were 0.07 ppm after 15 days. The results suggest that honey bees can rapidly degrade this compound, but that levels higher than the permitted 0.01 ppm (in Italy) can easily occur in honey from treated colonies.
Bandwidth enhancement in multimode fibers (2009)

We report on a substantial improvement in the bandwidth of graded index multimode fibers caused by a controlled intentional mode coupling. Scattering from micron size core inclusions induce the mode coupling with minimum power loss.
An Implicit Harmonic Balance Method in Graphics Processing Units for Vibrating Blades (2015)

An implicit harmonic balance method for modeling the unsteady non-linear periodic flow about vibrating airfoils in turbomachinery is presented. As departing point, an implicit edge-based three-dimensional Reynolds Averaged Navier-Stokes equations solver for unstructured grids that runs both on central processing units (CPUs) and graphics processing units (GPUs) is used. The harmonic balance method performs a spectral discretization of the time derivatives and marches in pseudo-time a new system of equations where the unknowns are the variables at different time samples. The application of the method to vibrating airfoils is discussed. It is shown that a time spectral scheme may achieve the same temporal accuracy at a much lower computational cost than a Backward Finite Difference method at the expense of using more memory. The performance of the implicit solver has been assessed with several application examples. A speed-up factor of 10 is obtained between the spectral and finite difference version of the code whereas and an additional speed-up factor of 10 is obtained when the code is ported to GPUs, totalizing a speed factor of 100. The performance of the solver in GPUs has been assessed using the 10th standard aeroelastic configuration and a transonic compressor.
A receiver model for optical fiber communication systems with arbitrarily polarized noise (2005)

The authors have derived a receiver model that provides an explicit relationship between the Q factor and the optical signal-to-noise ratio (OSNR) in optical fiber communication systems for arbitrary pulse shapes, realistic receiver filters, and arbitrarily polarized noise. It is shown how the system performance depends on both the degree of polarization of the noise and the angle between the Stokes' vectors of the signal and the noise. The results demonstrate that the relationship between the OSNR and the Q factor is not unique when the noise is partially polarized. This paper defines the enhancement factor and three other parameters that explicitly quantify the relative performance of different modulation formats in a receiver. The theoretical and experimental results show that the performance of the return-to-zero format is less sensitive to variations in the receiver characteristics than is the performance of the nonreturn-to-zero format. Finally, a validation of the formula is presented for computing the Q factor from the OSNR and the Stokes vectors of the signal and the noise by comparison with both experiments and Monte Carlo simulations.
Visualization of peptide presentation following oral application of antigen in normal and Peyer's patches‐deficient mice (2003)

Orally applied antigens generate systemic unresponsiveness by induction of anergy and deletion of specific T cells at high antigen doses, and induction of regulatory T cells at low doses of antigen. These different immune reactions have been attributed to different types of antigen-presenting cells (APC) and/or different secondary lymphoid organs participating in the induction of the immune response. We used high-sensitivity immunofluorescence to directly identify for the first time the cells presenting orally applied antigen in vivo. At low peptide doses (<1 mg) peptide presentation was exclusively detected on dendritic cells (DC) of the Peyer's patches (PP) and mesenteric lymph nodes (mLN). At high doses (>1 mg) peptides were presented systemically and by all types of APC but presentation was still maximal on DC of the PP (up to 65%). Nevertheless, at limiting antigen doses T cell activation in the gut-associated lymphoid tissue occurs preferentially in the mLN but not in PP. PP-deficient mice have the same frequencies of peptide-presenting cells in mLN, peripheral lymph nodes and spleen and activation of naive T cells in vivo is not affected. Therefore, PP are not critical for antigen presentation as well as for T cell activation in response to orally applied soluble antigens.
Simultaneous teleportation of multiple single-photon degrees of freedom (2011)

We report how quantum information encoded into multiple photonic degrees of freedom may be simultaneously teleported using a single, common physical process. The application of teleportation to the complete quantum state of a photon, i.e. the spectral, spatial, and polarization component states, permits the full photonic Hilbert space to be used for encoding information while simultaneously enabling subspaces to be addressed individually, e.g. for quantum information processing. We analyze the feasibility of teleporting the full quantum state through numerical analysis of the fidelity under nominal experimental conditions and for different types of input states, e.g. single-photon states that are separable or entangled in the physical degrees of freedom.
All Solid State High Average Power Ti:Sapphire CPA Laser (2001)

In recent years, high repetition rate Ti:sapphire chirped pulse amplification (CPA) lasers have been used in the fields such as X-ray laser study1), electron acceleration study2), micromachining3,4), medical treatment5), etc. In these studies, high repetition rate and high energy ultra-short-pulse CPA is strongly desired, especially in former two fields.
Low-Cost Wind Generator for Supplying Isolated DC loads (2007)

The present paper deals with a low-cost wind power generator. The proposed generator is very suitable and cost-effective for supplying isolated DC loads in remote areas where extension of grid is economically not feasible. The dynamic flux model of the self-excited induction generator used in the wind power-generator is given. This model, known to account for magnetic saturation is validated by experimental results. Performance of the generator under variable wind speed and/or variable load is discussed.
The E3‐ubiquitin ligase TRIM2 regulates neuronal polarization (2010)

The establishment of a polarized morphology with a single axon and multiple dendrites is an essential step during neuronal differentiation. This cellular polarization is largely depending on changes in the dynamics of the neuronal cytoskeleton. Here, we show that the tripartite motif (TRIM)-NHL protein TRIM2 is regulating axon specification in cultured mouse hippocampal neurons, where one of several initially indistinguishable neurites is selected to become the axon. Suppression of TRIM2 by RNA interference results in the loss of neuronal polarity while over-expression of TRIM2 induces the specification of multiple axons. TRIM2 conducts its function during neuronal polarization by ubiquitination of the neurofilament light chain. Together, our results imply an important function of TRIM2 for axon outgrowth during development.
Frailty in older adults: insights and interventions. (2005)

Frailty is a state of vulnerability that carries an increased risk of poor outcomes in older adults. Common signs and symptoms are fatigue, weight loss, muscle weakness, and progressive decline in function. Frail older adults are among the most challenging for medical management. However, awareness of this syndrome and its risks can help us care for these patients more confidently and decrease their risk for adverse outcomes.
A Potent, Selective and Cell-Active Allosteric Inhibitor of Protein Arginine Methyltransferase 3 (PRMT3) (2020)

PRMT3 catalyzes the asymmetric dimethylation of arginine residues of various proteins. It is essential for maturation of ribosomes, may have a role in lipogenesis, and is implicated in several diseases. A potent, selective, and cell- active PRMT3 inhibitor would be a valuable tool for further investigating PRMT3 biology. Here we report the discovery of the first PRMT3 chemical probe, SGC707, by structure-based optimization of the allosteric PRMT3 inhibitors we reported previously, and thorough characterization of this probe in biochemical, biophysical, and cellular assays. SGC707 is a potent PRMT3 inhibitor (IC50 = 31 ± 2 nm, KD = 53 ± 2 nm) with outstanding selectivity (selective against 31 other methyltransferases and more than 250 non-epigenetic targets). The mechanism of action studies and crystal structure of the PRMT3-SGC707 complex confirm the allosteric inhibition mode. Importantly, SGC707 engages PRMT3 and potently inhibits its methyltransferase activity in cells. It is also bioavailable and suitable for animal studies. This well- characterized chemical probe is an excellent tool to further study the role of PRMT3 in health and disease.
Assessment of corticospinal tract dysfunction and disease severity in\n amyotrophic lateral sclerosis (2016)

The upper motor neuron dysfunction in amyotrophic lateral sclerosis was\nquantified using triple stimulation and more focal transcranial magnetic\nstimulation techniques that were developed to reduce recording variability.\nThese measurements were combined with clinical and neurophysiological data to\ndevelop a novel random forest based supervised machine learning prediction\nmodel. This model was capable of predicting cross-sectional ALS disease\nseverity as measured by the ALSFRSr scale with 97% overall accuracy and 99%\nprecision. The machine learning model developed in this research provides a\nnew, unique and objective diagnostic method for quantifying disease severity\nand identifying subtle changes in disease progression in ALS.\n
Silencing Survivin Splice Variant 2B Leads to Antitumor Activity in Taxane-Resistant Ovarian Cancer (2011)

These data identify survivin 2B as an important target in ovarian cancer and provide a translational path forward for developing new therapies against this target.