gebhart/patrepeval huggingface dataset:
REDD1 Is Essential for Optimal T Cell Proliferation and Survival (2015)

REDD1 is a highly conserved stress response protein that is upregulated following many types of cellular stress, including hypoxia, DNA damage, energy stress, ER stress, and nutrient deprivation. Recently, REDD1 was shown to be involved in dexamethasone induced autophagy in murine thymocytes. However, we know little of REDD1's function in mature T cells. Here we show for the first time that REDD1 is upregulated following T cell stimulation with PHA or CD3/CD28 beads. REDD1 knockout T cells exhibit a defect in proliferation and cell survival, although markers of activation appear normal. These findings demonstrate a previously unappreciated role for REDD1 in T cell function.
A single transient episode of hyperammonemia induces long-lasting alterations in protein kinase A (2007)

Hepatic encephalopathy in patients with liver disease is associated with poor prognosis. This could be due to the induction by the transient episode of hepatic encephalopathy of long-lasting alterations making patients more susceptible. We show that a single transient episode of hyperammonemia induces long-lasting alterations in signal transduction. The content of the regulatory subunit of the protein kinase dependent on cAMP (PKA-RI) is increased in erythrocytes from cirrhotic patients. This increase is reproduced in rats with portacaval anastomosis and in rats with hyperammonemia without liver failure, suggesting that hyperammonemia is responsible for increased PKA-RI in patients. We analyzed whether there is a correlation between ammonia levels and PKA-RI content in patients. All cirrhotic patients had increased content of PKA-RI. Some of them showed normal ammonia levels but had suffered previous hyperammonemia episodes. This suggested that a single transient episode of hyperammonemia could induce the long-lasting increase in PKA-RI. To assess this, we injected normal rats with ammonia and blood was taken at different times. Ammonia returned to basal levels at 2 h. However, PKA-RI was significantly increased in blood cells from rats injected with ammonia 3 wk after injection. In conclusion, it is shown that a single transient episode of hyperammonemia induces long-lasting alterations in signal transduction both in blood and brain. These alterations may contribute to the poor prognosis of patients suffering hepatic encephalopathy.
Conditions for continuous-wave operation of a 1.3-μm InGaAsP vertical-cavity laser (1993)

Long-wavelength InGaAsP/InP vertical-cavity surface-emitting lasers (VCSEL’s) are promising for optical communication systems. However, room-temperature continuous-wave (cw) operation has not yet been achieved because of the high temperature dependence of the Auger recombination, the low thermal conductivity of the materials, insufficient mirror reflectivity, and device structures with poor heat-dissipation capabilities. Therefore design optimization considering thermal-resistance and size-dependent cavity loss is very important.
An improved procedure for isolation of high-quality RNA from nematode-infected Arabidopsis roots through laser capture (2016)

Background: Cyst nematodes are biotrophs that form specialized feeding structures in the roots of host plants, which consist of a syncytial fusion of hypertrophied cells. The formation of syncytium is accompanied by profound transcriptional changes and active metabolism in infected tissues. The challenge in gene expression studies for syncytium has always been the isolation of pure syncytial material and subsequent extraction of intact RNA. Root fragments containing syncytium had been used for microarray analyses. However, the inclusion of neighbouring cells dilutes the syncytium-specific mRNA population. Micro-sectioning coupled with laser capture microdissection (LCM) offers an opportunity for the isolation of feeding sites from heterogeneous cell populations. But recovery of intact RNA from syncytium dissected by LCM is complicated due to extended steps of fixation, tissue preparation, embedding and sectioning. Results: In the present study, we have optimized the procedure of sample preparation for LCM to isolate high quality of RNA from cyst nematode induced syncytia in Arabidopsis roots which can be used for transcriptomic studies. We investigated the effect of various sucrose concentrations as cryoprotectant on RNA quality and morphology of syncytial sections. We also compared various types of microscopic slides for strong adherence of sections while removing embedding material. Conclusion: The use of optimal sucrose concentrations as cryoprotection plays a key role in RNA stability and morphology of sections. Treatment with higher sucrose concentrations minimizes the risk of RNA degradation, whereas longer incubation times help maintaining the morphology of tissue sections. Our method allows isolating high-quality RNA from nematode feeding sites that is suitable for downstream applications such as microarray experiments.
A call for comparing theories of consciousness and data sharing (2022)

Abstract Merker, Williford, and Rudrauf make several arguments against the integrated information theory of consciousness; whereas some have merit, their conclusion that the theory should be discarded is premature. Coming years promise advances in the empirical study of consciousness, and only after theories are independently tested with shared data can they be ruled in or out. We propose future research directions.
Kinetics of ASO Distribution and Pharmacodynamics in the CNS after an Intrathecal Bolus Dose in Rat (S38.008) (2016)

Objective: To characterize distribution kinetics, cellular uptake and pharmacodynamics of antisense oligonucleotides (ASOs) in the rat CNS following intrathecal injection. Background: ASOs in clinical development for CNS indications are administered via intrathecal bolus (ITB) injection. Understanding ASO distribution and pharmacodynamics following ITB is important to map which brain regions and cells may be targeted and how this changes as a function of dose and time. Methods: Time points ranged from 15 minutes to 16 weeks post-injection. Doses ranged from 10 ug to 700 ug. ASO distribution and kinetics of target protein reduction were determined by immunhistochemistry and fluorescent scanning. Distribution of 125I-labeled ASO was imaged in live rats by whole body SPECT/CT. ASO onset and duration of action in reducing mRNA was determined by qRT-PCR. Results: Distribution of ASO by immunohistochemistry was biphasic following ITB; early first order diffusion from CSF into brain parenchyma, followed by rapid redistribution from interstitial space into cells 8 h after injection. After 24 h, ASO distribution remained similar to week 16. SPECT/CT showed similar stable distribution from 24 h to 7 days post-ITB. ASO bound to leptomeninges with different kinetics and affinity than cellular uptake in brain parenchyma. Maximal mRNA reduction occurred 3 and 7 days post-injection in the spinal cord and cortex, respectively. > 50[percnt] mRNA reduction was sustained for 4 to 8 weeks, depending upon CNS region. Protein reductions peaked at 7 and 28 days in the cortex and deeper brain regions, respectively. Conclusions: The results show dose-dependent, diffusion-driven distribution of ASO in the rat CNS following ITB injection. All brain regions showed ASO uptake, with highest levels in structures close to the subdural space. Cellular uptake into neurons may involve active transport. The onset and duration of mRNA and protein reduction was rapid and sustained over an 8-week time course.
Variable Background Born Inversion by Wavefield Backpropagation (1988)

The inverse scattering problem for an acoustic medium is formulated by using the variable background Born approximation. A constant density acoustic medium is probed by a wide-band point source, and the scattered field is observed along a curved receiver array located outside the region where the medium velocity is different from the assumed background velocity function. The solution proposed relies on the introduction of a backpropagated field. This field is obtained by using a finite-difference scheme backward in time to backpropagate into the medium the scattered field observed along the receiver array. The backpropagated field is imaged at the source travel times, giving an image of the same type as obtained by reverse-time finite-difference migration techniques. The gradient of this image is then taken along rays linking the source to points in the medium and, after scaling, this gives the reconstructed potential. To relate the reconstructed potential to the true scattering potential, high frequency asymptotics and an additional approximation introduced by Beylkin [1] are used. These approximations reduce the validity of the reconstruction procedure to the high wavenumber region. With these approximations it is shown that, at a given point, the reconstructed potential corresponds to the convolution of the true potential with a weighting function obtained by partially reconstructing an impulse from its projections inside a cone. The angular range of this cone is totally determined by the geometry of the receiver array and by the relative location of the source with respect to the point considered. In the special case when the receiver array surrounds the domain where the scattering potential is located, it is found that, within the Born approximation, the reconstructed potential recovers exactly the high wavenumber part of the Fourier transform of the true potential. It is expected that, for a wide class of problems, the reconstruction technique described in this paper will be computationally more efficient than the generalized Radon transform (GRT) inversion method proposed by Beylkin [1] and Miller, Oristaglio, and Beylkin [2], [3].
Determining Wheat Dough Mixing Characteristics from Power Consumption Profile of a Conventional Mixer (2001)

ABSTRACT A Hobart mixer with a pin‐type attachment was used to mix soft wheat flour dough. Power consumption profiles were measured continuously during mixing for 20 min using a current transducer and a data logging system. Experimental variables were quantity of flour (500, 1,000, and 1,500 g of dry wheat flour), water content (43, 45, and 47%, wb), and mixer speed setting (low, medium, and high). The power consumption profiles were evaluated by moving average and spectral analysis. Peaks in the power consumption profiles were located to determine the optimal mixing time. The optimal mixing times were then compared with storage and viscous moduli measured using a dynamic rheometer to assure the maximum strength of wheat dough at the optimal mixing time. Tolerance was determined using the signal amplitude and phase angle data from spectral analysis. Optimal mixing times of various doughs at medium speed ranged from 510 to 850 sec; low and high flour quantities required longer mixing times than medium quantity of flour. The optimal mixing time increased when the moisture content was lowered. Tolerance was affected by mixing speed and moisture content of flour
Fine-grained transaction-level verification: using a variable transactor for improved coverage at the signal level (2005)

Maintaining coverage with increasing circuit scale has become a critical problem for logic-verification processes. While transaction-level verification (TLV) is an important step forward, fine-grained (FG) TLV provides better signal-level coverage by reactively changing transactors instead of transaction-level scenarios. Evaluations with a microprocessor design show the effectiveness of FGTLV; all design bugs at the signal level were to be detected, though many were not detected by plain TLV.
Optimum HDAF Relay-Assisted Combining Scheme with Relay Decision Information (2017)

For single-input multiple-output (SIMO) systems, Maximum Ratio Combining (MRC), employed at the receiver, achieves the best performance compared to other combining schemes in the literature, such as Selection Combining (SC) and Equal Gain Combining (EGC). However, for cooperative relay-based systems, MRC has limited performance due to the lack of relay decision information awareness at the destination combiner. To overcome this limitation, this paper proposes a new optimum combining scheme, which is being demonstrated for Hybrid-Decode-Amplify-Forward (HDAF) cooperative system. This scheme utilizes relay decision information in the form of the number of errors per received packet over the source-relay link. The derivation of the optimum combining scheme is based on a mathematical model that utilizes conditional error probability. The improved performance of the proposed optimum combining scheme is demonstrated through analytical results and Monte Carlo simulations.
Glutamine deprivation stimulates mTOR-JNK-dependent chemokine secretion (2014)

The non-essential amino acid, glutamine, exerts pleiotropic effects on cell metabolism, signalling and stress resistance. Here we demonstrate that short-term glutamine restriction triggers an endoplasmic reticulum (ER) stress response that leads to production of the pro-inflammatory chemokine, interleukin-8 (IL-8). Glutamine deprivation-induced ER stress triggers colocalization of autophagosomes, lysosomes and the Golgi into a subcellular structure whose integrity is essential for IL-8 secretion. The stimulatory effect of glutamine restriction on IL-8 production is attributable to depletion of tricarboxylic acid cycle intermediates. The protein kinase, mTOR, is also colocalized with the lysosomal membrane clusters induced by glutamine deprivation, and inhibition of mTORC1 activity abolishes both endomembrane reorganization and IL-8 secretion. Activated mTORC1 elicits IL8 gene expression via the activation of an IRE1-JNK signalling cascade. Treatment of cells with a glutaminase inhibitor phenocopies glutamine restriction, suggesting that these results will be relevant to the clinical development of glutamine metabolism inhibitors as anticancer agents.
Direct MRI detection of impending plaque development in multiple sclerosis (2015)

In some lesions, the abrupt opening of the blood-brain barrier, detected by contrast enhancement on MRI, can have directly visible antecedent MRI changes centered on the central vein. We propose that these findings might be the basis for prior reports of subtle pre-parenchymal enhancement changes in quantitative MRI indices. In line with the venulocentric model of lesion development, our findings are consistent with the centrality of early perivenular events in lesion formation in vivo.
Optical design of freeform lens for LED streetlight (2008)

2008-2009 > Academic research: refereed > Publication in refereed journal
Surface-tension-induced flattening of a nearly plane elastic solid (2012)

We report direct measurement of surface deformation in soft solids due to their surface tension. Gel replicas of poly(dimethysiloxane) masters with rippled surfaces are found to have amplitudes that decrease with decreasing gel modulus. Surface undulations of a thin elastomeric film are attenuated when it is oxidized by brief exposure to oxygen plasma. Surface deformation in both cases is modeled successfully as driven by surface tension and resisted by elasticity. Our results show that surface tension of soft solids drives significant deformation, and that the latter can be used to determine the former.
Blueberry polyphenols increase lifespan and thermotolerance in Caenorhabditis elegans (2006)

The beneficial effects of polyphenol compounds in fruits and vegetables are mainly extrapolated from in vitro studies or short-term dietary supplementation studies. Due to cost and duration, relatively little is known about whether dietary polyphenols are beneficial in whole animals, particularly with respect to aging. To address this question, we examined the effects of blueberry polyphenols on lifespan and aging of the nematode, Caenorhabditis elegans, a useful organism for such a study. We report that a complex mixture of blueberry polyphenols increased lifespan and slowed aging-related declines in C. elegans. We also found that these benefits did not just reflect antioxidant activity in these compounds. For instance, blueberry treatment increased survival during acute heat stress, but was not protective against acute oxidative stress. The blueberry extract consists of three major fractions that all contain antioxidant activity. However, only one fraction, enriched in proanthocyanidin compounds, increased C. elegans lifespan and thermotolerance. To further determine how polyphenols prolonged C. elegans lifespan, we analyzed the genetic requirements for these effects. Prolonged lifespan from this treatment required the presence of a CaMKII pathway that mediates osmotic stress resistance, though not other pathways that affect stress resistance and longevity. In conclusion, polyphenolic compounds in blueberries had robust and reproducible benefits during aging that were separable from antioxidant effects.
Cross sections and quantum yields of the 3 μm emission for Er3+ and Ho3+ dopants in crystals (1995)

We have measured the lifetimes of the 2.8 μm emission band for Er3+- and Ho3+-doped fluorides including LiYF4, BaY2F8, LaF3, and KY3F10, and for numerous oxides such as Y3Al5O12, YAlO3, La2Be2O5, and other crystals. Several quantum yields and branching ratios were experimentally evaluated as well, in order to determine the radiative lifetime of the upper laser level for the 2.8 μm transition. This information was employed to assess the cross sections of the 2.8 μm infrared emission band for several of these crystals, which involves the 4I11/2→4I13/2 transition for Er, and the 5I6→5I7 for Ho.
Tenascin-W Is a Novel Marker for Activated Tumor Stroma in Low-grade Human Breast Cancer and Influences Cell Behavior (2007)

This is the first report about human tenascin-W, the fourth and final member of the extracellular matrix protein family of tenascins. Sixty-three human breast tumor extracts were analyzed by Western blotting for the presence of tenascin-W and compared with tenascin-C, an established marker of tumor stroma. Interestingly, we found tenascin-W expression in the majority of the tumor tissues, but no detectable expression in the normal mammary parenchyma. Eighty-one percent of the breast tumor samples were tenascin-W positive and 86% showed expression of tenascin-C. However, tenascin-W and tenascin-C amounts varied greatly between tumors and some contained either tenascin-W or tenascin-C exclusively, indicating independent mechanisms regulating their expression. Although there was no difference between high- or low-grade tumors with respect to the presence of tenascin-C, tenascin-W was more prominent in low-grade tumors. For 42 of the breast cancer tissues, a frozen tumor microarray was available to confirm the Western blot data by immunohistochemistry. Similar to tenascin-C, tenascin-W was detected in the tumor stroma. Fibroblasts adhered to tenascin-W in a beta(1) integrin-dependent manner and spread with a distinctive morphology under conditions where they remained round on tenascin-C. CHOB2 cells expressing alpha(v)beta(1) or alpha4beta(1) integrins were able to spread on tenascin-W. Furthermore, addition of tenascin-W to the culture medium increased migration of breast cancer cells toward a fibronectin substratum in vitro. These data imply that tenascin-W expression in the activated tumor stroma facilitates tumorigenesis by supporting the migratory behavior of breast cancer cells.
Paper 237: An Allograft Based Tissue Engineered Meniscus Scaffold (2012)

Treatment options for irreparable meniscus injuries in the USA remain limited to partial or total meniscectomy and meniscus transplant. Current allograft meniscus transplants have been shown to lack complete cellular ingrowth. This may contribute to impaired long term incorporation and function. Increased porosity and interconnected pores may be able to improve the potential for cellular ingrowth. The objective of this study was to develop an allograft based 3-dimensional scaffold for use as a meniscus transplant.
Photoemission study ofLaAlO3/SrTiO3andLaAlO3/Nb:SrTiO3: Insulator-insulator versus insulator-semiconductor interfaces (2016)

By hard x-ray photoemission spectroscopy we have studied the electronic states of $\mathrm{LaAl}{\mathrm{O}}_{3}/\mathrm{SrTi}{\mathrm{O}}_{3}$(100) and ${\mathrm{LaAlO}}_{3}/\mathrm{Nb}$ : ${\mathrm{SrTiO}}_{3}$(100) heterostructures, where the polar $\mathrm{LaAl}{\mathrm{O}}_{3}$ layer is grown on the insulating and conducting substrates, respectively. The analysis of the valence band has shown that the electron affinity is as small as $+0.4\phantom{\rule{0.16em}{0ex}}\mathrm{eV}$ in both the $\mathrm{LaAl}{\mathrm{O}}_{3}/\mathrm{SrTi}{\mathrm{O}}_{3}$ and $\mathrm{LaAl}{\mathrm{O}}_{3}/\mathrm{Nb}:\mathrm{SrTi}{\mathrm{O}}_{3}$ heterostructures. The interface is ``staggered type'' (type II) in both of the heterostructures with the valence band maximum of $\mathrm{LaAl}{\mathrm{O}}_{3}$ above the valence band maximum of $\mathrm{SrTi}{\mathrm{O}}_{3}$. The valence band offset of 0.42 eV in the $\mathrm{LaAl}{\mathrm{O}}_{3}/\mathrm{SrTi}{\mathrm{O}}_{3}$ heterostructure has increased to 0.61 eV in the $\mathrm{LaAl}{\mathrm{O}}_{3}/\mathrm{Nb}:\mathrm{SrTi}{\mathrm{O}}_{3}$ as the $\mathrm{LaAl}{\mathrm{O}}_{3}$ component shifts towards the lower binding energy side. The electronic states of $\mathrm{LaAl}{\mathrm{O}}_{3}$ and $\mathrm{SrTi}{\mathrm{O}}_{3}$ have been merged with each other in the lower energy part of the valence band of the $\mathrm{LaAl}{\mathrm{O}}_{3}/\mathrm{Nb}:\mathrm{SrTi}{\mathrm{O}}_{3}$ heterostructures.
In Situ Scanning Electron Microscopy Detection of Carbide Nature of Dendrites in Li–Polymer Batteries (2018)

Li metal batteries suffer from dendrite formation which causes short circuit of the battery. Therefore, it is important to understand the chemical composition and growth mechanism of dendrites that limit battery efficiency and cycle life. In this study, in situ scanning electron microscopy was employed to monitor the cycling behavior of all-solid Li metal batteries with LiFePO<sub>4</sub> cathodes. Chemical analyses of the dendrites were conducted using a windowless energy dispersive spectroscopy detector, which showed that the dendrites are not metallic lithium as universally recognized. Our results revealed the carbide nature of the dendrites with a hollow morphology and hardness greater than that of pure lithium. These carbide-based dendrites were able to perforate through the polymer, which was confirmed by milling the polymer using focused ion beam. It was also shown that applying pressure on the battery can suppress growth of the dendrites.
How the Experts Do It (2018)

How should an AI-based explanation system explain an agent's complex behavior to ordinary end users who have no background in AI? Answering this question is an active research area, for if an AI-based explanation system could effectively explain intelligent agents' behavior, it could enable the end users to understand, assess, and appropriately trust (or distrust) the agents attempting to help them. To provide insights into this question, we turned to human expert explainers in the real-time strategy domain --"shoutcasters"-- to understand (1) how they foraged in an evolving strategy game in real time, (2) how they assessed the players' behaviors, and (3) how they constructed pertinent and timely explanations out of their insights and delivered them to their audience. The results provided insights into shoutcasters' foraging strategies for gleaning information necessary to assess and explain the players; a characterization of the types of implicit questions shoutcasters answered; and implications for creating explanations by using the patterns and abstraction levels these human experts revealed.