Miracle-dz/UniFAR-FTUs huggingface dataset:
Nerve growth factor- and epidermal growth factor-stimulated phosphorylation of a PC12 cytoskeletally associated protein in situ

Nerve growth factor (NGF) and epidermal growth factor (EGF) produce stable alterations in PC12 cells that persist in the detergent- insoluble cytoskeleton, resulting in the phosphorylation of a 250,000- mol-wt cytoskeletally associated protein in situ. Treatment of PC12 cells with NGF or EGF, followed by detergent lysis of the cells and incubation of the resulting cytoskeletons with gamma-32P-ATP, permitted detection of hormonally stimulated, energy-dependent events, which result in the enhanced phosphorylation of a cytoskeletally associated protein as an immediate consequence of receptor occupancy. These events were elicited only upon treatment of intact cells at physiological temperatures. The NGF- and EGF-stimulated events occurred rapidly; however, they were a transient effect of hormone action. NGF and EGF were found to act through independent mechanisms to stimulate the in situ phosphorylation of the 250,000-mol-wt protein, as the effects of NGF, but not EGF, were blocked by methyltransferase inhibitors. The 250,000-mol-wt protein was phosphorylated on serine and threonine residues in response to both NGF and EGF although in somewhat different proportions. The data suggest that the hormone-stimulated labeling of the 250,000-mol-wt protein may be the result of either the direct activation of a protein kinase, the redistribution of the kinase relative to its substrates as a consequence of hormone action, or the coincident occurrence of these events.
Hierarchical Bayesian Language Models for Conversational Speech Recognition

Traditional n -gram language models are widely used in state-of-the-art large vocabulary speech recognition systems. This simple model suffers from some limitations, such as overfitting of maximum-likelihood estimation and the lack of rich contextual knowledge sources. In this paper, we exploit a hierarchical Bayesian interpretation for language modeling, based on a nonparametric prior called Pitman-Yor process. This offers a principled approach to language model smoothing, embedding the power-law distribution for natural language. Experiments on the recognition of conversational speech in multiparty meetings demonstrate that by using hierarchical Bayesian language models, we are able to achieve significant reductions in perplexity and word error rate.
An architecture for high-throughput and improved-quality stereo vision processor

This paper presents the VLSI architecture to achieve high-throughput and improved-quality stereo vision for real applications. The stereo vision processor generates gray-scale output images with depth information from input images taken by two CMOS Image Sensors (CIS). The depth estimator using the sum of absolute differences (SAD) algorithm as stereo matching technique is implemented on hardware by exploiting pipelining and parallelism. To produce depth maps with improved-quality at real-time, pre-and post-processing units are adopted, and to enhance the adaptability of the system to real environments, special function registers (SFRs) are assigned to vision parameters. The design using 0.18um standard CMOS technology can operate at 120MHz clock, achieving over 140 frames/sec depth maps with 320 by 240 image size and 64 disparity levels. Experimental results based on images taken in real world and the Middlebury data set will be presented. Comparison data with existing hardware systems and hardware specifications of the proposed processor will be given. ii To my parents and brother iii Acknowledgments I would like to thank Dr. Gang Qu for advising and supporting me. He has always been considerate to me, and encouraging me to find better ways on the degree course. I could complete this work with his help and understanding. I also would like to thank the members of the committee, Dr. Shuvra S. Bhattacharyya and Dr. Ankur Srivastava. Their interests and constructive discussions on my research were helpful to me. It is my pleasure to thank the Korea Institute of Science and Technology (KIST). The work experience in the KIST deepened my knowledge and competence in the field of stereo vision systems. I would like to give my deepest gratitude to my parents and brother. Their endless support and love have motivated me not to give up in my life. The life in the University of Maryland was the most painful time I have ever gone through. However, I would like to believe that it is a present from the God, and I am convinced that to open the present in the future will become delight.
Estrogen Enhances Angiogenesis through a Pathway Involving Platelet-Activating Factor-Mediated Nuclear Factor-κB Activation

In this study, we investigated the molecular events involved in estrogen-induced angiogenesis. Treatment of the human endometrial adenocarcinoma cells, HEC-1A, with estrogen up-regulated mRNA expression and protein synthesis of various angiogenic factors such as tumor necrosis factor-α, interleukin-1, basic fibroblast growth factor, and vascular endothelial growth factor. The estrogen-dependent induction of the expression was blocked by the platelet-activating factor (PAF) antagonists, WEB 2170. Estrogen treatment caused the activation of nuclear factor (NF)-κB in HEC-1A cells and was also blocked by PAF antagonist. Inhibitors of NF-κB activation inhibited estrogen-induced mRNA expression and protein synthesis of the angiogenic factors. Estrogen led to a pronounced angiogenesis as assessed by a mouse Matrigel model in vivo and endothelial cell sprouting in vitro. PAF antagonists or NF-κB inhibitors significantly inhibited this estrogen-dependent angiogenesis. Estrogen caused phospholipase A2 (PLA2) gene and protein expression. Estrogen-induced vascular endothelial growth factor mRNA expression and sprouting were significantly inhibited by PLA2 inhibitors, suggesting PLA2 expression is the upstream pathway in the estrogen-induced angiogenesis. Taken together, these results suggest that estrogen induces the production of angiogenic factors via a mechanism involving PAF-mediated NF-κB activation.
Ultraviolet Mutagenesis in Bacteriophage T4 I. Irradiation of Extracellular Phage Particles

Drake, John W. (University of Illinois, Urbana). Ultraviolet mutagenesis in bacteriophage T4. I. Irradiation of extracellular phage particles. J. Bacteriol. 91:1775–1780. 1966. —Ultraviolet (UV) irradiation of extracellular T4 phage particles induces about 2 × 10−4r mutations per lethal hit. The mutants largely escape detection unless the irradiated phages are plated with very soft overlay agar. Multiplicity reactivation is not a prerequisite for mutagenesis. A much higher frequency of base pair substitution-type mutants is induced than is found in the spontaneous background, but sign mutants are also induced. Nearly half of the mutants map into previously identified UV hot spots. The rII mutants induced extracellularly are very similar to those induced intracellularly. The mutants also appear to result from direct radiation effects upon the bacteriophage deoxyribonucleic acid.
RF MEMS and NEMS technology, devices, and applications

Will RF MEMS deliver on its promise to be one of the major MEMS businesses in the future? RF MEMS has now entered its second generation; high-volume production of both contacting and non-contacting switches and filters (based on bulk acoustic waves) was ramped up worldwide starting in 2003. In first-generation RF MEMS, discrete components were developed to demonstrate RF performance and reliability, and low-cost, high-volume chip- and wafer-scale packaging eliminated the final barriers to high-volume production of discrete replacement components with MEMS. In this paper, we review the RF MEMS industry and the commercialization status of RF MEMS components. We also provide a detailed case study of mobile telephone basestations, demonstrating how RF MEMS can impact telecommunications. Finally, we look at research into third-generation RF MEMS and NEMS, in which integration, active devices, and new functionality will create opportunities for disruptive changes in RF subsystems, enabling such things as software-defined radio.
Towards more efficient generic semantic authoring for adaptive hypermedia

Personalization of delivery has always been important in any consumer industry. With the growth of the WWW into our everyday life, information has become increasingly a consumer commodity. For instance, in educational domain, today's learners expect high quality, relevant educational materials, delivered to them in a timely and appropriate manner. Adaptive hypermedia (AH) systems aim to personalise the delivery of materials to the needs of the user -- both to their stated requirements as well as to their less obvious desires. This paper describes steps taken towards creating more efficient generic semantic authoring for adaptive hypermedia, starting from an existing framework, LAOS, an existing system, MOT, and evaluation results thereof. This system is to make use of existing appropriate Semantic Web techniques to ensure the level of generality and convertibility to different adaptive (educational) hypermedia delivery engines. Some improvements were implemented and a preliminary pilot usability study was performed, as reported in this paper.
Dynamic clustering algorithm design for ultra dense small cell networks in 5G

Ultra dense networks are a promising technology enabling high power and spectrum efficiencies in future wireless systems. It is well-known that for ultra dense networks inter-cell interference is one of the main bottlenecks prohibiting achieving the promised performance gains. In order to effectively coordinate or mitigate interference in paper, we propose a graph-based low complexity dynamic clustering algorithm. The key idea behind the proposed algorithm is that dividing the whole network into a number of clusters under size constraint and the maximum intra-cluster interference and minimum inter-cluster interference. The logic is maximum intra-cluster can be effectively controlled by the coordination within each cluster. Meanwhile, graph-based algorithm is exploited to further reduce implementation complexity and make the proposed algorithm suitable for practical implementation. Finally, simulation results numerically demonstrate that the proposed low complexity algorithm has almost the same performance compared to the existing high performance algorithm but the complexity is much lower.
HERITABILITY OF PREFERENCES FOR MULTIPLE CUES OF MATE QUALITY IN HUMANS

Human mate preferences have received a great deal of attention in recent decades because of their centrality to sexual selection, which is thought to play a substantial role in human evolution. Most of this attention has been on universal aspects of mate preferences, but variation between individuals is less understood. In particular, the relative contribution of genetic and environmental influences to variation in mate preferences is key to sexual selection models but has barely been investigated in humans, and results have been mixed in other species. Here, we used data from over 4000 mostly female twins who ranked the importance of 13 key traits in a potential partner. We used the classical twin design to partition variation in these preferences into that due to genes, family environment, and residual factors. In women, there was significant variability in the broad‐sense heritability of individual trait preferences, with physical attractiveness the most heritable (29%) and housekeeping ability the least (5%). Over all the trait preferences combined, broad‐sense heritabilities were highly significant in women and marginally significant in men, accounting for 20% and 19% of the variation, respectively; family environmental influences were much smaller. Heritability was a little higher in reproductive aged than in nonreproductive aged women, but the difference was not significant.
Mining Wikipedia for Large-scale Repositories of Context-Sensitive Entailment Rules

This paper focuses on the central role played by lexical information in the task of Recognizing Textual Entailment. In particular, the usefulness of lexical knowledge extracted from several widely used static resources, represented in the form of entailment rules, is compared with a method to extract lexical information from Wikipedia as a dynamic knowledge resource. The proposed acquisition method aims at maximizing two key features of the resulting entailment rules: coverage (i.e. the proportion of rules successfully applied over a dataset of TE pairs), and context sensitivity (i.e. the proportion of rules applied in appropriate contexts). Evaluation results show that Wikipedia can be effectively used as a source of lexical entailment rules, featuring both higher coverage and context sensitivity with respect to other resources.
PLD of high-k dielectric films on silicon

Thin films of high-k materials praseodymium oxide (PrxOy) and hafnium oxide (HfOx) were deposited on silicon (100) surfaces by pulsed laser deposition (PLD), using the third harmonic of a Nd:YAG laser. The two materials are compared with respect to their morphology, in dependence on the substrate temperature during deposition, and their chemical composition and crystalline structure, in particular at the interface. The films of both oxides exhibit a grainy structure when deposited at substrate temperatures below 750°C, with the grain size increasing from ≈ 40 nm at room temperature to ≈ 100 nm at 750°C. However, the PrxOy films are much more uniform than hafnia, the latter exhibiting increasingly larger holes, reaching several nm into the silicon substrate. For a substrate temperature of 900°C, the film morphology for PrxOy completely changes to much larger crystalline areas, while for HfOx the role of holes in the film becomes substantial. Also, the interface chemistry is significantly different for both materials: a silicate formation for PrxOy and a rich abundance of SiO2 and a silicide for hafnia. Finally, our PrxOy-films exert compressive stress on the substrate, for HfOx-films tensile stress is observed which, however, may also result from interfacial SiO2.
Example-based dynamic skinning in real time

In this paper we present an approach to enrich skeleton-driven animations with physically-based secondary deformation in real time. To achieve this goal, we propose a novel, surface-based deformable model that can interactively emulate the dynamics of both low-and high-frequency volumetric effects. Given a surface mesh and a few sample sequences of its physical behavior, a set of motion parameters of the material are learned during an off-line preprocessing step. The deformable model is then applicable to any given skeleton-driven animation of the surface mesh. Additionally, our dynamic skinning technique can be entirely implemented on GPUs and executed with great efficiency. Thus, with minimal changes to the conventional graphics pipeline, our approach can drastically enhance the visual experience of skeleton-driven animations by adding secondary deformation in real time.
3D Wavefield Extrapolation In Laterally-varying Tilted TI Media

A new wavefield extrapolation method has been developed that allows the propagation of waves in an anisotropic medium. The anisotropic medium considered here is transversely isotropic (TI) with an axis of symmetry. Our method applies an asymmetric explicit correction filter after the normal isotropic extrapolation operator. It is stable and suitable for laterally varying TI media. This new scheme is useful to extrapolate wavefields in a vertical transversely isotropic (VTI) medium in tilted coordinates. The explicit correction operator, designed by a weighted least-square method, is stable and accurate for the desired wavenumbers. Impulse responses from this scheme and the anisotropic phase-shift method are compared to illustrate the algorithm.
Calcium‐activated potassium channels and endothelial dysfunction: therapeutic options?

The three subtypes of calcium‐activated potassium channels (KCa) of large, intermediate and small conductance (BKCa, IKCa and SKCa) are present in the vascular wall. In healthy arteries, BKCa channels are preferentially expressed in vascular smooth muscle cells, while IKCa and SKCa are preferentially located in endothelial cells. The activation of endothelial IKCa and SKCa contributes to nitric oxide (NO) generation and is required to elicit endothelium‐dependent hyperpolarizations. In the latter responses, the hyperpolarization of the smooth muscle cells is evoked either via electrical coupling through myo‐endothelial gap junctions or by potassium ions, which by accumulating in the intercellular space activate the inwardly rectifying potassium channel Kir2.1 and/or the Na+/K+‐ATPase. Additionally, endothelium‐derived factors such as cytochrome P450‐derived epoxyeicosatrienoic acids and under some circumstances NO, prostacyclin, lipoxygenase products and hydrogen peroxide (H2O2) hyperpolarize and relax the underlying smooth muscle cells by activating BKCa. In contrast, cytochrome P450‐derived 20‐hydroxyeicosatetraenoic acid and various endothelium‐derived contracting factors inhibit BKCa. Aging and cardiovascular diseases are associated with endothelial dysfunctions that can involve a decrease in NO bioavailability, alterations of EDHF‐mediated responses and/or enhanced production of endothelium‐derived contracting factors. Because potassium channels are involved in these endothelium‐dependent responses, activation of endothelial and/or smooth muscle KCa could prevent the occurrence of endothelial dysfunction. Therefore, direct activators of these potassium channels or compounds that regulate their activity or their expression may be of some therapeutic interest. Conversely, blockers of IKCa may prevent restenosis and that of BKCa channels sepsis‐dependent hypotension.
Hierarchical propagation of geometric constraints for full-custom physical design of ICs

In industrial environments, full-custom layout design of analog and mixed-signal ICs is done hierarchically. In order to increase design efficiency, cell layouts are reused in the design hierarchy. Constraints forming relations between instances in different hierarchical contexts are of critical importance. While implementing a cell layout, these constraints have to be available in the cell's context. In this paper, a general definition of hierarchical constraints for a constraint-driven design flow is given. Furthermore it is shown, how top-down declared constraints can be propagated into another hierarchical context. Only by propagation they become visible and verifiable for bottom-up cell design. The feasibility of our proposed methodology is shown by applying it to a modular Smart Power IC of the automotive industry.
Sparse Approximation via Penalty Decomposition Methods

In this paper we consider sparse approximation problems, that is, general $l_0$ minimization problems with the $l_0$-"norm" of a vector being a part of constraints or objective function. In particular, we first study the first-order optimality conditions for these problems. We then propose penalty decomposition (PD) methods for solving them in which a sequence of penalty subproblems are solved by a block coordinate descent (BCD) method. Under some suitable assumptions, we establish that any accumulation point of the sequence generated by the PD methods satisfies the first-order optimality conditions of the problems. Furthermore, for the problems in which the $l_0$ part is the only nonconvex part, we show that such an accumulation point is a local minimizer of the problems. In addition, we show that any accumulation point of the sequence generated by the BCD method is a saddle point of the penalty subproblem. Moreover, for the problems in which the $l_0$ part is the only nonconvex part, we establish that such an accumulation point is a local minimizer of the penalty subproblem. Finally, we test the performance of our PD methods by applying them to sparse logistic regression, sparse inverse covariance selection, and compressed sensing problems. The computational results demonstrate that our methods generally outperform the existing methods in terms of solution quality and/or speed.
A MICROFABRICATION APPROACH TO MULTICELLULAR MECHANICS

To address the question of how cell-generated forces regulate the organization and function of endothelial cells, I investigated the mechanical forces in a simple model of cell-cell contact: paired cells contacting each other via a single cell-cell junction. To study the responsiveness of AJs to force, I adapted a system of microfabricated force sensors to quantitatively report both the cell-cell tugging force and the size of adherens junctions (AJ). I observed that AJ size was modulated by tugging force: AJs and tugging force grew or decayed with myosin activation or inhibition, respectively. This myosin-dependent regulation operated in concert with a Rac1, force-independent control of AJ size, and was illustrated by showing that effects of vascular permeability agents (S1P, thrombin) on junctional stability are reversed by changing the extent to which these agents coupled to the Rac and myosin-dependent pathways. Furthermore, I showed that direct application of mechanical tugging force, rather than myosin activity per se, is sufficient to trigger AJ growth. Inspired by the study of mechanical force on the junctions between two cells, I further extended our tools to measure mechanical force in a more complicated multicellular system involving more cells and more than one type of cells. I investigated the role of mechanical force in a model system of monocytes transmigrating across an endothelial monolayer. Using our force measurement system, I first found that the average traction force in the whole endothelial monolayer increased during monocyte firm adhesion and transmigration. By specifically look at traction forces at the cellular level, I found that the endothelial cell with the monocyte firmly adhered on it showed a much larger traction forces, with the direction of the traction force aligned more centripetally toward the monocyte. Moreover, the sub-cellular and pan-cellular analysis of the traction forces in the monolayer revealed an increase of traction force in local zones vicinity to the monocyte. Finally, engagement of endothelial adhesion molecules could increase traction forces in the endothelial cells. Taken together, this study implicates mechanical forces in firm adhesion and transmigration. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Bioengineering First Advisor Christopher Chen
Crossing the phantom divide with parametrized post-Friedmann dark energy

Dark energy models with a single scalar field cannot cross the equation of state divide set by a cosmological constant. More general models that allow crossing require additional degrees of freedom to ensure gravitational stability. We show that a parameterized post-Friedmann description of cosmic accelerzation provides a simple but accurate description of multiple scalar field crossing models. Moreover the prescription provides a well-controlled approximation for a wide range of smooth dark energy models. It conserves energy and momentum and is exact in the metric evolution on scales well above and below the transition scale to relative smoothness. Standard linear perturbation tools have been altered to include this description and made publicly available for studies of the dark energy involving cosmological structure out to the horizon scale.