gebhart/patrepeval huggingface dataset:
Integrated multi-omics analysis of RB-loss identifies widespread cellular programming and synthetic weaknesses (2021)

Inactivation of RB is one of the hallmarks of cancer, however gaps remain in our understanding of how RB-loss changes human cells. Here we show that pRB-depletion results in cellular reprogramming, we quantitatively measured how RB-depletion altered the transcriptional, proteomic and metabolic output of non-tumorigenic RPE1 human cells. These profiles identified widespread changes in metabolic and cell stress response factors previously linked to E2F function. In addition, we find a number of additional pathways that are sensitive to RB-depletion that are not E2F-regulated that may represent compensatory mechanisms to support the growth of RB-depleted cells. To determine whether these molecular changes are also present in RB1<sup>-/-</sup> tumors, we compared these results to Retinoblastoma and Small Cell Lung Cancer data, and identified widespread conservation of alterations found in RPE1 cells. To define which of these changes contribute to the growth of cells with de-regulated E2F activity, we assayed how inhibiting or depleting these proteins affected the growth of RB1<sup>-/-</sup> cells and of Drosophila E2f1-RNAi models in vivo. From this analysis, we identify key metabolic pathways that are essential for the growth of pRB-deleted human cells.
Performance Analysis of a Packet Switch Based on SingleBuffered Banyan Network (2009)

Banyan networks are being proposed for interconnecting memory and processor modules in multiprocessor systems as well as for packet switching in communication networks. This paper describes an analysis of the performance of a packet switch based on a single-buffered Banyan network. A model of a single-buffered Banyan network provides results on the throughput, delay, and internal blocking. Results of this model are combined with models of the buffer controller (finite and infinite buffers). It is shown that for balanced loads, the switching delay is low for loads below maximum throughput (about 45 percent per input link) and the blocking at the input buffer controller is low for reasonable buffer sizes.
Nikon F2 exposure tool development (2003)

Present status of development of F2 (157nm) exposure tool in Nikon is described. Key points of F2 exposure tool are reported; low aberration projection optics, CaF2 quality, coating durability and gas purging of the pellicle space. We also report the measurement of refractive index inhomogeneity inside CaF2 crystals, which is suspected as the cause of local flare. Characteristics of high NA optics over 0.9 are investigated by imaging simulations for both 193nm and 157nm wavelengths, which are compared NA=0.85 imaging.
Methionine Metabolism: Major Pathways and Enzymes Involved and Strategies for Control and Diversification of Volatile Sulfur Compounds in Cheese (2011)

For economical reasons and to accommodate current market trends, cheese manufacturers and product developers are increasingly interested in controlling cheese flavor formation and developing new flavors. Due to their low detection threshold and diversity, volatile sulfur compounds (VSCs) are of prime importance in the overall flavor of cheese and make a significant contribution to their typical flavors. Thus, the control of VSCs formation offers considerable potential for industrial applications. This paper gives an overview of the main VSCs found in cheese, along with the major pathways and key enzymes leading to the formation of methanethiol from methionine, which is subsequently converted into other sulfur-bearing compounds. As these compounds arise primarily from methionine, the metabolism of this amino acid and its regulation is presented. Attention is focused in the enzymatic potential of lactic acid bacteria (LAB) that are widely used as starter and adjunct cultures in cheese-making. In view of industrial applications, different strategies such as the enhancement of the abilities of LAB to produce high amounts and diversity of VSCs are highlighted as the principal future research trend.
Measurement of the Doppler effect in uranium-238. [24 and 144 keV, 38 to 1100 K] (1979)

The Doppler effect of /sup 238/U metal and /sup 238/U in U/sub 3/O/sub 8/ was studied by using beams of filtered neutrons at 24 +- 0.9 keV and 144 +- 12 keV from the University of Missouri Research Reactor (MURR) Facility. The Doppler effect is the broadening of the widths of the nuclear resonances in the total cross section due to the thermal motion of the nuclei. The effective average total cross sections (EATCS) for both kinds of samples were measured with good geometry transmission measurements as functions of sample thickness and temperature to show the Doppler effect. The temperature of the samples ranged from 38 to 1100 K. Temperature-related density effects were removed by simultaneously measuring the attenuation of gamma rays passing through the samples. The EATCS data as function of sample thickness at room temperature were fit with a nuclear cross section calculated from a ladder of resonances in the center-of-mass system. This ladder was generated from a set of synthesized nuclear parameters. The best fits to the cross sections when extrapolated to zero thickness, give 13.5 +- 0.2 b at 24 keV and 11.9 +- 0.2 b at 144 keV. The value at 24 keV agrees withmore » the ENDF/B-IV, while the value at 144 keV is approx. 4% greater.An ideal gas model including an effective mass, M/sub eff/, and an effective temperature, T/sub eff/, was used to Doppler broaden the calculated nuclear cross sections. With this model, good agreement was obtained with the EATCS data for all sample thickness at all temperatures with an M/sub eff/ of 238 amu for the /sup 238/U metal and 400 amu for /sup 238/U in U/sub 3/O/sub 8/. The temperature dependence of t/sub eff/ was determined by calculating the total energy by use of Debye frequency theta/sub v/ distributions. In these calculations, the Debye temperatures, theta/sub D/, that provided the best fits were theta/sub D/ = 260 K for the metal and theta/sub D/ = 545 K for U/sub 3/O/sub 8/. 9 figures, 1 table.« less
Water-soluble HPMA copolymer—prostaglandin E1conjugates containing a cathepsin K sensitive spacer (2006)

A novel bone targeting, N-(2-hydroxypropyl)methacrylamide (HPMA) copolymer based, prostaglandin E1 (PGE1) delivery system was designed, synthesized and characterized. PGE1 was bound to the polymer backbone via a spacer, composed of a cathepsin K sensitive tetrapeptide (Gly-Gly-Pro-Nle) and a self-eliminating 4-aminobenzyl alcohol structure. The HPMA copolymer conjugates were prepared by photo-initiated free radical copolymerization of HPMA, PGE1-containing macromonomer, and optionally a comonomer containing a reactive p-nitrophenyl ester group. The latter group was used as attachment points for the D-aspartic acid octapeptide targeting moieties. Incubation of the PGE1-containing macromonomer and HPMA copolymer-PGE1 conjugates with cathepsin K resulted in release of unmodified PGE1. The rate of release depended on the composition of the conjugate. The higher the PGE1 content in the conjugate, the slower the PGE1 release. This appeared to be the result of association of hydrophobic side-chains in aqueous media, which rendered the formation of the enzyme substrate complex more difficult. The data seems to indicate that HPMA copolymer-PGE1 conjugates have a potential in the treatment of osteoporosis and other bone diseases.
Evaluation of toxicological and teratogenic effects of carbosilane glucose glycodendrimers in zebrafish embryos and model rodent cell lines (2018)

Glycodendrimers (Glyco-DDMs) represent a rapidly growing class of nanoparticles with promising properties for biomedical applications but concerns regarding the impact on human health and environment are still justified. Here we report, for the first time, the comparative study of in vivo developmental toxicity of carbosilane Glyco-DDMs and their cytotoxicity in vitro. Carbosilane Glyco-DDMs (generation 1-3) containing 4, 8, and 16 β-d-glucopyranosyl units at the periphery (DDM<sub>1</sub>Glu, DDM<sub>2</sub>Glu, and DDM<sub>3</sub>Glu) were synthesized and characterized by <sup>1</sup>H, <sup>13</sup>C and <sup>29</sup>Si NMR, mass spectrometry, dynamic light scattering, atomic force microscopy (AFM), and computer modeling. In vitro cytotoxicity assay (MTT) of DDM<sub>1-3</sub>Glu was performed on three different rodent cell lines (Cricetulus griseus) - B14 (ATCC, CCL-14.1), BRL 3A (ATCC, CRL-1442), and NRK 52E (ATCC, CRL-1571). Overall, very low cytotoxicity was observed with calculated IC<sub>50</sub> in mM range with slight difference between each cell line and DDM generation investigated. Modified fish embryo test (FET) was further used for DDM<sub>3</sub>Glu developmental toxicity testing on zebrafish (Danio rerio) embryos. While seemingly harmless to intact embryos, adverse effects of DDMs on the embryonic development become evident after chorion removal (LD<sub>50</sub>=2.78 µM at 96 hpe). We summarized that the modified FET test showed a two to three orders of magnitude difference between the in vitro cytotoxicity and in vivo developmental toxicity of DDM<sub>3</sub>Glu. While, in general, the Glyco-DDMs show great promises as efficient vectors in targeted drug delivery or as therapeutic molecules itself, we suggest that their developmental toxicity should be thoroughly investigated to exclude safety risks associated with their potential biomedical use.
The Aptly Named Phoenix Dwarf Galaxy (2007)

The Local Group galaxy Phoenix has the properties of a dwarf spheroidal galaxy, but an adjacent HI cloud has been found to be at the same radial velocity as the stars. The proximity suggests that this cloud is associated with the most recent ($\le 100$ Myr) star formation in Phoenix. We have obtained relatively high sensitivity and high resolution HI imaging with the VLA with the goal of distinguishing between different processes for displacing the gas from the galaxy. Due to the outer curvature of the HI cloud, it appears that expulsion from the galaxy by winds from supernovae is more likely than ram-pressure stripping. The isolation of the galaxy makes tidal stripping highly unlikely. Using a star formation history constructed from HST imaging, we construct a simple kinematic model which implies that the HI cloud is still gravitationally bound to the galaxy. Gas which is expelled from the centers of dwarf galaxies but which remains gravitationally bound may explain the episodic star formation observed in several dwarfs. In the specific case of Phoenix, there may be future star formation in this currently dSph-like galaxy.
High Rate Shear Insult Delivered to Cortical Neurons Produces Heterogeneous Membrane Permeability Alterations (2006)

Traumatic brain injury (TBI) occurs when brain tissue is subjected to stresses and strains at high rates and magnitudes, yet the mechanisms of injury and cellular thresholds are not well understood. The events that occur at the time of and immediately after an insult are hypothesized to initiate cell dysfunction or death following a critical cell strain and strain rate. We analyzed neuronal plasma membrane disruption in two in vitro injury models-fluid shear stress delivered to planar cultures and shear strain induction of 3-D neural cultures. We found that insult severity positively correlated with the degree of membrane disruptions in a heterogeneous fashion in both cell configurations. Furthermore, increased membrane permeability led to increases in electrophysiological disturbance. Specifically, cells that exhibited increased membrane permeability did not fire random action potentials, in contrast to neighboring cells that had intact plasma membranes. This approach provides an experimental framework to investigate injury tolerance criteria as well as mechanistically driven therapeutic strategies.
Optimal Identical Binary Quantizer Design for Distributed Estimation (2012)

We consider the design of identical one-bit probabilistic quantizers for distributed estimation in sensor networks. We assume the parameter-range to be finite and known and use the maximum Crameŕ-Rao lower bound (CRB) over the parameter-range as our performance metric. We restrict our theoretical analysis to the class of antisymmetric quantizers and determine a set of conditions for which the probabilistic quantizer function is greatly simplified. We identify a broad class of noise distributions, which includes Gaussian noise in the low-SNR regime, for which the often used threshold-quantizer is found to be minimax-optimal. Aided with theoretical results, we formulate an optimization problem to obtain the optimum minimax-CRB quantizer. For a wide range of noise distributions, we demonstrate the superior performance of the new quantizer-particularly in the moderate to high-SNR regime.
PointPoseNet: Point Pose Network for Robust 6D Object Pose Estimation (2020)

In this paper, we propose a novel pipeline to estimate 6D object pose from RGB-D images of known objects present in complex scenes. The pipeline directly operates on raw point clouds extracted from RGB-D scans. Specifically, our method takes the point cloud as input and regresses the point-wise unit vectors pointing to the 3D keypoints. We then use these vectors to generate keypoint hypotheses from which the 6D object pose hypotheses are computed. Finally, we select the best 6D object pose from the hypotheses based on a proposed scoring mechanism with geometry constraints. Extensive experiments show that the proposed method is robust against the variety in object shape and appearance as well as occlusions between objects, and that our method outperforms the state-of-the-art methods on the LINEMOD and Occlusion LINEMOD datasets.
Pulse Echo Ultrasonic Techniques for Underwater Inspection of Steel Waterfront Structures. (1983)

Abstract : Laboratory tests were made to: (1) determine the measurement accuracy using three different methods of acquiring and interpreting the ultrasonic data, (2) identify operator training requirements and optimum information feedback techniques for the diver, and (3) analyze the electrical power transmission characteristics of the ultrasonic system and identify any potential safety hazards to the diver. Due to the problems associated with multiple front surface echoes, digital ultrasonic thickness gages should not be used as the only means of inspecting steel structures in areas found to have irregular front surface conditions or where the thickness readings are found to fluctuate rapidly over a small area. Field tests of the ultrasonic scanner and surface milling adapter have confirmed that results comparable to those obtained during laboratory tests are attainable during in-situ inspection of steel pilings; since the ultrasonic scanner and milling adapter technique is not truly nondestructive in nature, however, it should be considered an interim inspection procedure. Investigation of alternative inspection techniques that do not require material removal should be continued. A power system test circuit should be incorporated into any 100-VAC circuit used to power underwater ultrasonic test equipment. As an additional safety precaution, inspection divers should be required to wear neoprene wetsuit gloves and should be instructed not to reach through the air/water interface while holding any grounded electronic equipment in their hands.
Power optimization for VLSI circuits and systems (2010)

Low power design can be exploited at various levels, e.g., system level, architecture level, circuit level, and device level. This paper gives a brief overview of low power design principals, then focuses discussion on circuit level methods specifically state-of-the-art low power design techniques of clocking systems. Finally we discuss low power optimization techniques at system and architecture level.
Estimating loss rates in an integrated services network by neural networks (2002)

Loss rate is one of the most important quality of service (QoS) requirements in a packet communication network carrying multimedia traffic. This paper presents a method for estimating loss rates as a function of a feature vector, x, based on a maximum likelihood principle. Two backpropagation networks, a multi-layer perceptron (MLP) network and a radial basis function (RBF) network, are applied to samples of simulated M/M/1 queue data, as well as to samples of simulated combinations of constant bit rate (CBR) and Poisson traffic data, at different x. Our results show that a) this method is superior to earlier methods since it properly treats the samples, eliminating nuisance parameters, b) it gives a direct measure of QoS that can be used in higher level communication network decision functions, and c) RBF networks give more accurate loss rate estimates than MLP networks do.
Identification of Mechanisms Underlying Transporter Associated with Antigen Processing Deficiency in Metastatic Murine Carcinomas (2005)

Expression of transporter associated with antigen processing (TAP) is often lost in metastatic carcinomas, resulting in defective antigen processing and presentation and escape of the cancer cells from immune surveillance. In this study, the nature of TAP deficiencies in tumors was investigated. By chromatin immunoprecipitation assay, we showed that the recruitment of RNA polymerase II to the TAP-1 gene was impaired in TAP-deficient cells derived from murine melanoma, prostate, and lung carcinomas, compared with TAP-expressing fibroblasts and lymphoma cells. This suggested that the deficiency in TAP-1 expression resulted, at least partially, from a relatively low level of transcription of the TAP-1 gene. Furthermore, levels of TAP-1 promoter activity, as assessed by stable transfections with a reporter construct containing the TAP-1 promoter, were relatively low in TAP-deficient cells. To examine genetic heritability of regulators of TAP-1 promoter activity, TAP- and MHC class I-deficient cells of H-2b origin were fused with wild-type fibroblasts of H-2k origin. Fusion with TAP-expressing cells complemented the low levels of TAP-1 promoter activity in TAP-deficient cells. However, these fused cells exhibited lower levels of TAP-1 mRNA and H-2k than unfused fibroblasts. Further analysis showed that TAP-1 mRNA stability was lower in fused carcinoma fibroblasts than in unfused fibroblasts. Based on these results, we propose that TAP deficiency in many carcinomas is caused by a decrease in activity/expression of trans-acting factors regulating TAP-1 promoter activity, as well as a decrease in TAP-1 mRNA stability. These results have significant implications for understanding immune evasion mechanisms in tumors.
Association of heat-shock protein 70 with lipid rafts is required for Japanese encephalitis virus infection in Huh7 cells (2011)

Japanese encephalitis virus (JEV) is an enveloped flavivirus and the most common agent of viral encephalitis. It enters cells through receptor-mediated endocytosis and low pH-triggered membrane fusion. Although lipid rafts, cholesterol-enriched lipid-ordered membrane domains, have been shown to participate in JEV entry, the mechanisms of the early events of JEV infection, including the cellular receptors of JEV, remain largely unknown. In the current study, it was demonstrated that heat-shock protein 70 (HSP70), rather than other members of the HSP70 family, was required for JEV entry into a human cell line. Cell-surface expression of HSP70 and a direct interaction between JEV envelope (E) protein and HSP70 were observed. Biochemical fractionation showed that HSP70 clearly migrated into the raft fraction after virus infection and co-fractioned with E protein. Depletion of cholesterol shifted the E protein and HSP70 to a non-raft membrane and decreased JEV entry without affecting virus binding to host cells. Notably, recruitment of HSP70 into lipid rafts was required for activation of the phosphoinositide 3-kinase/Akt signalling pathway in the early stage of JEV infection. These results indicate that lipid rafts facilitate JEV entry, possibly by providing a convenient platform to concentrate JEV and its receptors on the host-cell membrane.
High Resolution Photography with an RGB-Infrared Camera (2015)

A convenient solution to RGB-Infrared photography is to extend the basic RGB mosaic with a fourth filter type with high transmittance in the near-infrared band. Unfortunately, applying conventional demosaicing algorithms to RGB-IR sensors is not possible for two reasons. First, the RGB and near-infrared image are differently focused due to different refractive indices of each band. Second, manufacturing constraints introduce crosstalk between RGB and IR channels. In this paper we propose a novel image formation model for RGB-IR cameras that can be easily calibrated, and propose an efficient algorithm that jointly addresses three restoration problems--channel deblurring, channel separation and pixel demosaicing--using quadratic image regularizers. We also extend our algorithm to handle more general regularizers and pixel saturation. Experiments show that our method produces sharp, full-resolution images of pure RGB color and IR.
Neurodevelopmental Functioning in Very Young Children Undergoing Treatment for Non-CNS Cancers (2012)

This study identifies deficits as well as spared functions in children with non-CNS cancers; the results suggest ways parents and healthcare professionals may plan specific remediations to enhance quality of life in young cancer survivors.
Dynamics of Interlayer Na-Ions in Ga-Substituted Na2Zn2TeO6 (NZTO) Studied by Variable-Temperature Solid-State 23Na NMR Spectroscopy and DFT Modeling (2023)

Local Na-coordination and dynamics of Na<sub>2-<i>x</i></sub>Zn<sub>2-<i>x</i></sub>Ga<i><sub>x</sub></i>TeO<sub>6</sub>; <i>x</i> = 0.00 (NZTO), 0.05, 0.10, 0.15, 0.20, were studied by variable-temperature, <sup>23</sup>Na NMR methods and DFT AIMD simulations. Structure and dynamics were probed by NMR in the temperature ranges of 100-293 K in a magnetic field of 18.8 T and from 293 up to 500 K in a magnetic field of 11.7 T. Line shapes and <i>T</i><sub>1</sub> relaxation constants were analyzed. At 100 K, the otherwise dynamic Na-ions are frozen out on the NMR time scale, and a local structure characterization was performed for Na-ions at three interlayer sites. On increasing the temperature, complex peak shape coalescences occurred, and at 293 K, the Na NMR spectra showed some averaging due to Na-ion dynamics. A further increase to 500 K did not reveal any new peak shape variations until the highest temperatures, where an apparent peak splitting was observed, similar to what was observed in the 18.8 T experiments at lower temperatures. A three-site exchange model coupled with reduced quadrupolar couplings due to dynamics appear to explain these peak shape observations. The Ga substitution increases the Na-jumping rate, as proved by relaxation measurements and by a decrease in temperature for peak coalescence. The estimated activation energy for Na dynamics in the NZTO sample, from relaxation measurements, corresponds well to results from DFT AIMD simulations. Upon Ga substitution, measured activation energies are reduced, which is supported, in part, by DFT calculations. Addressing the correlated motion of Na-ions appears important for solid-state ion conductors since benefits can be gained from the decrease in activation energy upon Ga substitution, for example.
High-speed SiGe:C bipolar technology (2002)

A SiGe:C bipolar technology with a narrow base integrated into a double-polysilicon self-aligned transistor has been developed. A transit frequency of 106 GHz at a collector emitter breakdown voltage of 2.3 V, a maximum oscillation frequency of 145 GHz, and 6.5 ps gate delay demonstrate balanced transistor performance. State-of-the-art results for high-speed digital, analog, and low-power circuits are achieved.