Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of Support Compliance on the Resonant Behavior of Microcantilever-Based Sensors in Viscous Fluids

EFFECT OF SUPPORT COMPLIANCE ON THE RESONANT BEHAVIOR OF MICROCANTILEVER-BASED SENSORS IN VISCOUS FLUIDS Rabin Maharjan, B.E. , M.S. Marquette University, 2013 Resonant microcantilevers are often considered for use in chemical sensing and biosensing applications. However, when excited in the conventional transverse flexural mode, their performance in liquids is severely compromised. Theoretical and experimental studies have shown that the detrimental effects of the liquid may be mitigated by operating the microcantilever in lateral flexure, especially for microbeams having smaller length-to-width (L/b) ratios. However, for these most promising geometries the predictions of existing models tend to diverge from experimental data for resonant frequency (fres) and quality factor (Q). A likely reason for these discrepancies is support compliance, which has been neglected in existing models. Thus, the derivation of an analytical model for the lateral-mode dynamic response of a microcantilever in a viscous fluid, including the effects of support compliance, is warranted and is the focus of this dissertation. Analytical solutions for natural frequency and Q are first obtained for the freevibration case, followed by solutions for the forced-vibration response when the cantilever is excited by an imposed harmonic relative rotation near the support (simulating electrothermal actuation). Values of fres and Q are extracted from the response spectra for the tip deflection and the bending strain near the support. The support compliance (required as model input) is analytically related to device dimensions by employing dimensional analysis and 3-D FEA. The analytical results for the resonant characteristics are also related to sensor performance metrics (sensitivity and limit of detection), thus permitting one to exploit the potential of lateral-mode microcantileverbased liquid-phase sensors. The impact of support compliance, fluid resistance, and beam dimensions on the freeand forced-vibration response are explored, as are the differences associated with the two output signals. Comparisons of results with experimental data show a marked improvement over the previous rigid-support models for smaller L/b values. For the practical ranges of parameters considered the model indicates that, at smaller L/b values, support compliance may reduce Q by up to ~14% and fres and mass sensitivity (Sm) by up to ~21%. Conversely, for L/b>15 the support compliance effects are no more than 2% on Q and 4% on fres and Sm.
Modelling financial time series with switching state space models

The deficiencies of stationary models applied to financial time series are well documented. A special form of non-stationarity, where the underlying generator switches between (approximately) stationary regimes, seems particularly appropriate for financial markets. We use a dynamic switching (modelled by a hidden Markov model) combined with a linear dynamical system in a hybrid switching state space model (SSSM) and discuss the practical details of training such models with a variational EM algorithm due to Z. Ghahramani and G.E. Hinton (1998). The performance of the SSSM is evaluated on several financial data sets and it is shown to improve on a number of existing benchmark methods.
New results on disturbance rejection for energy-shaping controlled port-Hamiltonian systems

In this paper we present a method to robustify energy-shaping controllers for port-Hamiltonian (pH) systems by adding an integral action that rejects unknown additive disturbances. The proposed controller preserves the pH structure and, by adding to the new energy function a suitable cross term between the plant and the controller coordinates, it avoids the unnatural coordinate transformation used in the past. This paper extends our previous work by relaxing the requirement that the systems Hamiltonian is strictly convex and separable, which allows the controller to be applied to a large class of mechanical systems, including underactuated systems with non-constant mass matrix. Furthermore, it is shown that the proposed integral action control is robust against unknown damping in the case of fully-actuated systems.
Interaction of human peripheral blood monocytes with apoptotic polymorphonuclear cells

Macrophages have the potential to recognize apoptotic neutrophils and phagocytose them while the same function for monocytes is uncertain. In fact, early findings indicated that monocytes started to phagocytose neutrophils on the third day of differentiation to macrophages. Here we show, using flow cytometry and confocal microscopy, that peripheral blood monocytes phagocytose apoptotic but not freshly isolated granulocytes. Recognition of apoptotic cells is predominantly connected with CD16+ monocytes (CD14high CD16+ and CD14dim CD16+) and requires CD36. Clearance of apoptotic polymorphonuclear leucocytes appears to be independent of the CD14 mechanism. Uptake of apoptotic Jurkat T cells by monocytes is CD14 and CD36 dependent. Liposomes containing phosphatidyl‐l‐serine reduce binding of apoptotic polymorphonuclear leucocytes. Lipopolysaccharide‐activated subpopulations of monocytes while in contact with apoptotic cells produce more anti‐inflammatory cytokine interleukin‐10 whereas the production of pro‐inflammatory cytokines, tumour necrosis factor‐α and interleukin‐1β is reduced.
Scheduling real-time applications in an open environment

This paper extends the two-level hierarchical scheme in (Deng et al., 1997) for scheduling independently developed real-time applications with non-real-time applications in an open environment. The environment allows the schedulability of each real-time application to be validated independently of other applications in the system. The extended scheme removes the following two restrictions of the scheme: real-time applications that are scheduled preemptively must consist solely of periodic tasks; and applications must not share global resources (i.e., resources used by more than one application). Consequently, the extended scheme can accommodate a much broader spectrum of real-time applications.
Is it Now Time to Establish Visualization Science as a Scientific Discipline?

It is now time to establish visualization science as a scientific discipline. The proposed deadline to achieve this is 2010. Today, research areas in visualization are isolated. What is missing is the big picture and mutual agendas. To establish visualization science as a discipline, researchers need to agree on the origins and areas of visualization research; then on the long-term (e.g., 2020) research goals. The benefit of an established discipline is more impact, both in teaching (curricula) and research (e.g., framework programmes of the European Union). This article aims to start the discussion on a synthesis through extended definitions and a big picture. It provides an example for a sharp and extended definition of a field that today is vaguely defined: information architecture. Finally, it proposes a draft of the big picture of the fields, the visualization science fingerprint, thus a step towards an established visualization science
A Comparative User Study of Web Search Interfaces: HotMap, Concept Highlighter, and Google

Users of traditional Web search engines commonly find it difficult to evaluate the results of their Web searches. We suggest the use of information visualization and interactive visual manipulation as methods for improving the ability of users to evaluate the results of a Web search. In this paper, we present the results of a user study that compared the search results interface provided by Google to that of two systems we have developed: HotMap and Concept Highlighter. We found that users were able to perform their searches faster with HotMap, were able to find more relevant documents with Concept Highlighter, and generally ranked these interfaces higher than Google with respect to subjective measures. When given a choice between these interfaces, participants ranked HotMap the highest, followed by Google and Concept Highlighter. These results indicate that even though the list-based representation of search results are common among search engines, visual and interactive interfaces to Web search results can be more efficient, effective, and satisfying to the users
Performance Bounds for Bidirectional Coded Cooperation Protocols

In coded bidirectional cooperation, two nodes wish to exchange messages over a shared half-duplex channel with the help of a relay. In this correspondence, we derive performance bounds for this problem for each of three decode-and-forward protocols. The first protocol is a two phase protocol where both users simultaneously transmit during the first phase and the relay alone transmits during the second. In this protocol, our bounds are tight. The second protocol considers sequential transmissions from the two users followed by a transmission from the relay while the third protocol is a hybrid of the first two protocols and has four phases. In the latter two protocols the bounds are not identical. Numerical evaluation shows that in some cases of interest our bounds do not differ significantly. Finally, in the Gaussian case with path loss, we derive achievable rates and compare the relative merits of each protocol. This case is of interest in cellular systems. Surprisingly, we find that in some cases, the achievable rate region of the four phase protocol contains points that are outside the outer bounds of the other two protocols.
Body composition and hydration status changes in male and female open-water swimmers during an ultra-endurance event

Abstract Body mass changes during ultra-endurance performances have been described for running, cycling and for swimming in a heated pool. The present field study of 20 male and 11 female open-water swimmers investigated the changes in body composition and hydration status during an ultra-endurance event. Body mass, both estimated fat mass and skeletal muscle mass, haematocrit, plasma sodium concentration ([Na+]) and urine specific gravity were determined. Energy intake, energy expenditure and fluid intake were estimated. Males experienced significant reductions in body mass (−0.5 %) and skeletal muscle mass (−1.1 %) (P < 0.05) during the race compared to females who showed no significant changes with regard to these variables (P > 0.05). Changes in percent body fat, fat mass, and fat-free mass were heterogeneous and did not reach statistical significance (P > 0.05) between gender groups. Fluid intake relative to plasma volume was higher in females than in males during the ultra-endurance event. Compared to males, females' average increase in haematocrit was 3.3 percentage points (pp) higher, urine specific gravity decrease 0.1 pp smaller, and plasma [Na+] 1.3 pp higher. The observed patterns of fluid intake, changes in plasma volume, urine specific gravity, and plasma [Na+] suggest that, particularly in females, a combination of fluid shift from blood vessels to interstitial tissue, facilitated by skeletal muscle damage, as well as exercise-associated hyponatremia had occurred. To summarise, changes in body composition and hydration status are different in male compared to female open-water ultra-endurance swimmers.
A recommendation system for software function discovery

Since some application software provides users with too many functions, it is often difficult to find those that are useful. This paper proposes a recommendation system based on a collaborative filtering approach to let users discover useful functions at low cost for the purpose of improving productivity when using application software. The proposed system automatically collects histories of software function execution (usage histories) from many users through the Internet. Based on the collaborative filtering approach, collected histories are used for recommending a set of candidate functions that may be useful to the individual user. This paper illustrates conventional filtering algorithms and proposes a new algorithm suitable for recommendation of software functions. The result of an experiment with a prototype recommendation system showed that the average ndpm of our algorithm was smaller than that of conventional algorithms, and it also showed that the standard deviation of ndpm of our algorithm was smaller than that of conventional algorithms. Furthermore, while every conventional algorithm had a case whose recommendation was worse than the random algorithm, our algorithm did not.
Food-Related Compounds That Modulate Expression of Inducible Nitric Oxide Synthase May Act as Its Inhibitors

Natural compounds commonly found in foods may contribute to protect cells against the deleterious effects of inflammation. These anti-inflammatory properties have been linked to the modulation of transcription factors that control expression of inflammation-related genes, including the inducible nitric oxide synthase (iNOS), rather than a direct inhibitory action on these proteins. In this study, forty two natural dietary compounds, known for their ability to exert an inhibitory effect on the expression of iNOS, have been studied in silico as docking ligands on two available 3D structures for this protein (PDB ID: 3E7G and PDB ID: 1NSI). Natural compounds such as silibinin and cyanidin-3-rutinoside and other flavonoids showed the highest theoretical affinities for iNOS. Docking affinity values calculated for several known iNOS inhibitors significatively correlated with their reported half maximal inhibitory concentrations (R = 0.842, P < 0.0001), suggesting the computational reliability of the predictions made by our docking simulations. Moreover, docking affinity values for potent iNOS inhibitors are of similar magnitude to those obtained for some studied natural products. Results presented here indicate that, in addition to gene expression modulation of proteins involved in inflammation, some chemicals present in food may be acting by direct binding and possible inhibiting actions on iNOS.
Inducing Word Sense with Automatically Learned Hidden Concepts

Word Sense Induction (WSI) aims to automatically induce meanings of a polysemous word from unlabeled corpora. In this paper, we first propose a novel Bayesian parametric model to WSI. Unlike previous work, our research introduces a layer of hidden concepts and view senses as mixtures of concepts. We believe that concepts generalize the contexts, allowing the model to measure the sense similarity at a more general level. The Zipf’s law of meaning is used as a way of pre-setting the sense number for the parametric model. We further extend the parametric model to non-parametric model which not only simplifies the problem of model selection but also brings improved performance. We test our model on the benchmark datasets released by Semeval-2010 and Semeval-2007. The test results show that our model outperforms state-of-theart systems.
EP24.15 is associated with lipid rafts

Metalloendopeptidase EC 3.4. 24.15 (EP24.15, thimet oligopeptidase) is a neuropeptide‐metabolizing peptidase expressed throughout the body, but primarily in the brain, gonads, and pituitary. For EP24.15 to have its greatest effect upon peptides in the periphery, it must be targeted and released into the extracellular space. Western blot analysis of fractions taken from discontinuous sucrose density gradients carried out on crude plasma membrane fractions from AtT‐20 cells reveals colocalization of EP24.15 and flotillin‐1, a known lipid raft marker. Further analysis revealed that an intracellular membrane marker and non‐lipid raft, plasma membrane marker, failed to colocalize, supporting EP24.15/lipid raft association. Furthermore, EP24.15 immunoreactivity in lipid raft fractions generated from cells treated with methyl β‐cyclodextrin (MβCD) was greatly reduced. Finally, treatment with MβCD resulted in the accumulation of EP24.15 in the media of drug‐treated cells over vehicle‐treated cells, suggesting that a large percentage of EP24.15 associating with lipid rafts resides on the extracellular surface of the plasma membrane. With this exofacial localization, EP24.15 could have ample access to neuropeptides not only in the immediate microenvironment, but the ability to degrade or modify peptides bound for receptor interaction. © 2003 Wiley‐Liss, Inc.
Atherosclerotic Plaque Stability Is Affected by the Chemokine CXCL10 in Both Mice and Humans

Background. The chemokine CXCL10 is specifically upregulated during experimental development of plaque with an unstable phenotype. In this study we evaluated the functional consequences of these findings in mice and humans. Methods and Results. In ApoE−/− mice, we induced unstable plaque with using a flow-altering device around the carotid artery. From week 1 to 4, mice were injected with a neutralizing CXCL10 antibody. After 9 weeks, CXCL10 inhibition resulted in a more stable plaque phenotype: collagen increased by 58% (P = 0.002), smooth muscle cell content increased 2-fold (P = 0.03), while macrophage MHC class II expression decreased by 50% (P = 0.005). Also, the size of necrotic cores decreased by 41% (P = 0.01). In 106 human carotid endarterectomy specimens we found that increasing concentrations of CXCL10 strongly associate with an increase in atheromatous plaque phenotype (ANOVA, P = 0.003), with high macrophage, low smooth muscle cell, and low collagen content. Conclusions. In the present study we showed that CXCL10 is associated with the development of vulnerable plaque in human and mice. We conclude that CXCL10 might provide a new lead towards plaque-stabilizing therapy.
Low Complexity Message Passing Algorithm for SCMA System

Sparse code multiple access (SCMA) is a novel non-orthogonal air-interface technology in which several users share a same frequency resource simultaneously. The SCMA decoder is based on a message passing algorithm (MPA) for the sparsity of codeword. In the original MPA, all the users update a message until the maximum number of iterations is reached, resulting in high computational complexity. This letter puts forward a threshold-based MPA, where a belief threshold is applied to control the algorithm process. Simulation results show that the proposed scheme obtains a low computational complexity with only a slight performance degradation when the threshold is set appropriately.
Myxoma Virus M11L Blocks Apoptosis through Inhibition of Conformational Activation of Bax at the Mitochondria

ABSTRACT Many viruses inhibit or retard apoptosis, a strategy that subverts one of the most ancient antiviral mechanisms. M11L, a myxoma virus-encoded antiapoptotic protein, has been previously shown to localize to mitochondria and block apoptosis of virus-infected cells (H. Everett, M. Barry, S. F. Lee, X. J. Sun, K. Graham, J. Stone, R. C. Bleackley, and G. McFadden, J. Exp. Med. 191:1487-1498, 2000; H. Everett, M. Barry, X. Sun, S. F. Lee, C. Frantz, L. G. Berthiaume, G. McFadden, and R. C. Bleackley, J. Exp. Med. 196:1127-1139, 2002; and G. Wang, J. W. Barrett, S. H. Nazarian, H. Everett, X. Gao, C. Bleackley, K. Colwill, M. F. Moran, and G. McFadden, J. Virol. 78:7097-7111, 2004). This protection from apoptosis involves constitutive-forming inhibitory complexes with the peripheral benzodiazepine receptor and Bak on the outer mitochondrial membrane. Here, we extend the study to investigate the interference of M11L with Bax activation during the process of apoptosis. Myxoma virus infection triggers an early apoptotic signal that induces rapid Bax translocation from cytoplasm to mitochondria, despite the existence of various viral antiapoptotic proteins. However, in the presence of M11L, the structural activation of Bax at the mitochondrial membrane, which is characterized by the occurrence of a Bax conformational change, is blocked in both M11L-expressing myxoma-infected cells and M11L-transfected cells under apoptotic stimulation. In addition, inducible binding of M11L to the mitochondrially localized Bax is detected in myxoma virus-infected cells and in M11L/Bax-cotransfected cells as measured by immunoprecipitation and tandem affinity purification analysis, respectively. Importantly, this inducible Bax/M11L interaction is independent of Bak, demonstrated by the complete block of Bax-mediated apoptosis in myxoma-infected cells that lack Bak expression. Our findings reveal that myxoma M11L modulates apoptosis by multiple independent strategies which all contribute to the blockade of apoptosis at the mitochondrial checkpoint.
Structure formation and dynamics in molecularly thin smectic liquid crystal films

This doctoral thesis presents a study of thin films of smectic liquid crystals. This class of material shows the property to form stable films of only a few molecules thickness both on substrates and freely suspended in air. This feature together with the anisotropy of the material offers the possibility to prepare and investigate samples that cannot be formed by other materials. As the dimensions of the films are reduced, the physical properties are expected to change with respect to the observed surface structures and the dynamics in the film. For freely suspended films, the presented work analyses the translational dynamics in films with a thicknesses ranging from 22 down to only 2 smectic layers, using single molecule tracking. For all the studied compounds it was observed that thinner films show a faster diffusion. The measured effect is quantitatively larger than predicted from theory. However, molecular dynamics simulations support the finding of drastic changes for ultrathin films. Within the smectic A phase (i.e. not close to phase transitions), the temperature dependence is observed to show the classical Arrhenius behaviour. Contrary to that, in the vicinity of the phase transition to a smectic phase with in-plane ordering, the diffusion coefficient scales similarly to the one of a glass transition. Also heterogeneous free-standing film are studied concerning the molecular behaviour. It is shown that the molecules have a strong tendency to avoid crossing phase boundaries. For liquid crystal films on substrates, this work presents thin films of 8CB on silicon wafers. Despite the numerous studies of this material-substrate combination, no controlled creation of films with a small number of layers was reported so far. Such homogeneous films are created and studied with respect their inner structure using atomic force microscopy and ellipsometry. The dynamics is analysed using single molecule tracking, showing a slowdown of the diffusion when going to thinner films. These homogeneous films can also be used to create droplets with a volume below 10 femtolitres, which in turn can be used to study smectic layering on the surface with the main volume of the droplet in the nematic phase. It is also shown how the homogeneous films can be employed as a base material for the writing of stable structures on the nanoscale.
Data Biased Robust Counter Strategies

The problem of exploiting information about the environment while still being robust to inaccurate or incomplete information arises in many domains. Competitive imperfect information games where the goal is to maximally exploit an unknown opponent’s weaknesses are an example of this problem. Agents for these games must balance two objectives. First, they should aim to exploit data from past interactions with the opponent, seeking a best-response counter strategy. Second, they should aim to minimize losses since the limited data may be misleading or the opponent’s strategy may have changed, suggesting an opponent-agnostic Nash equilibrium strategy. In this paper, we show how to partially satisfy both of these objectives at the same time, producing strategies with favourable tradeoffs between the ability to exploit an opponent and the capacity to be exploited. Like a recently published technique, our approach involves solving a modified game; however the result is more generally applicable and even performs well in situations with very limited data. We evaluate our technique in the game of two-player, Limit Texas Hold’em.