Miracle-dz/UniFAR-FTUs huggingface dataset:
2.3 Microscopic Representation of Solid-liquid-vapor Interactions

The microscopic aspects of solid-liquid-vapor interactions are usually crucial when we consider theories of phase change phenomena such as nucleation of bubbles and droplets and the heat transfer at the three-phase interface. For a microscopic system, we need to start from the verification of the well-known Young-Laplace equation [eq. 2.2-? ] and Young's equation [eq. 2.2-? ] for the contact angle. In addition, for the reliable theory of the dropwise condensation, the determination of the condensation coefficient would be necessary. Furthermore, only by the thickness of a molecular mono-layer, the oxidation layer on the solid surface or the surfactant layer in the gas-liquid interface will drastically change the surface phenomena. In general, experimental assignments of such problems are usually extremely difficult since the scale is too small to access so the individual measurement of surface energy is almost impossible. Thus, in this section the molecular dynamics studies are discussed in order to understand such molecular scale phenomena. 2.3. 1 Molecular Dynamics Method and Force between Molecules. Knowledge of statistical gas dynamics has been very helpful to understand the relationship between molecular motion and macroscopic gas dynamics phenomena. Recently, a direct simulation method using the Monte Carlo technique (DSMC) developed by Bird (1994) has been widely used for the practical simulations of rarefied gas dynamics. In the other extreme, statistical treatment of solid state matters has been well developed as the solid state physics [e.g. Kittel (1996)]. However, when we need to take care of liquid or inter-phase phenomena, which are inevitable for phase-change phenomena, neither gas-dynamics statistics nor the solid-state statistics are no longer valid at all. The most powerful tool for the investigation of the microscopic phenomena of solid-liquid-vapor interaction is the molecular dynamics method [e.g. Allen and Tildesley (1987)], where the classical equations of motion (Newton's equations) are solved for a set of molecules.
A Loop-Free Multi-Path Routing With QoS for Wireless Ad Hoc Network

Mobile ad hoc wireless network is a special network without any infrastructure. The routing path could be broken easily because every host in such network is able to move freely. If the routing path is broken, the source host must reconstruct another new route. This will increase higher network overhead and latency and cause a decrease in the data throughput. In this paper, AODV and DSR schemes are employed to design a simple loop-free multi-path routing (LFMPR) with QoS (Quality of Service) protocol. In the route request phase, intermediate nodes record multi-reverse links which is applied to construct multiple-paths during the route reply phase. Each path is assigned a unique flow identification (flow id) in order to prevent routing loop problems. The source host can choose a best path to achieve the QoS. Further, the LFMPR could help a node chooses another backup path to send data without performing route discovery when the routing path breaks which could increase network performance. The NS-2 is used to simulate the performance of the metrics
Synthesis of Differentially Driven Planar Cable Parallel Manipulators

In this paper, the idea of using cable differentials in the architecture of planar cable-driven parallel robots is introduced. Cable differentials are a type of mechanisms with several outputs driven by a single input. Using them in cable parallel manipulators can decrease their cost and control complexity. However, due to their kinematic constrains, cable differentials cannot be arbitrarily used in the design of these manipulators. Thus, a synthesis method is proposed to tackle this issue. First, the general requirements and characteristics of differentially driven planar cable mechanisms are reviewed. Then, the advantages of using these differentials instead of typically actuated cables are shown through a comparison between differentially actuated planar cable robots and fully actuated ones. The results reveal that with the same number of actuators, using differentials may lead to larger workspaces and improved kinetostatic properties. Subsequently, the systematic synthesis of differentially driven planar cable mechanisms is presented. For this, a method to find the different arrangements of q cables in a differential is proposed. Then, valid arrangements with 2, 3, and 4 cables are investigated. Finally, several differential actuation schemes are considered and all possible differentials with q=2, 3, and 4 cables are found.
Learning to recommend questions based on public interest

This paper is concerned with the problem of question recommendation in the setting of Community Question Answering (CQA). Given a question as query, our goal is to rank all of the retrieved questions according to their likelihood of being good recommendations for the query. In this paper, we propose a notion of public interest, and show how public interest can boost the performance of question recommendation. In particular, to model public interest in question recommendation, we build a language model to combine relevance score to the query and popularity score regarding question popularity. Experimental results on Yahoo! Answers dataset demonstrate the performance of question recommendation can be greatly improved with considering the public interest.
Evaluation of Protein A Gene Polymorphic Region DNA Sequencing for Typing of Staphylococcus aureus Strains

ABSTRACT Three hundred and twenty isolates of Staphylococcus aureus were typed by DNA sequence analysis of the X region of the protein A gene (spa). spa typing was compared to both phenotypic and molecular techniques for the ability to differentiate and categorize S. aureus strains into groups that correlate with epidemiological information. Two previously characterized study populations were examined. A collection of 59 isolates (F. C. Tenover, R. Arbeit, G. Archer, J. Biddle, S. Byrne, R. Goering, G. Hancock, G. A. Hébert, B. Hill, R. Hollis, W. R. Jarvis, B. Kreiswirth, W. Eisner, J. Maslow, L. K. McDougal, J. M. Miller, M. Mulligan, and M. A. Pfaller, J. Clin. Microbiol. 32:407–415, 1994) from the Centers for Disease Control and Prevention (CDC) was used to test for the ability to discriminate outbreak from epidemiologically unrelated strains. A separate collection of 261 isolates form a multicenter study (R. B. Roberts, A. de Lencastre, W. Eisner, E. P. Severina, B. Shopsin, B. N. Kreiswirth, and A. Tomasz, J. Infect. Dis. 178:164–171, 1998) of methicillin-resistant S. aureus in New York City (NYC) was used to compare the ability of spatyping to group strains along clonal lines to that of the combination of pulsed-field gel electrophoresis and Southern hybridization. In the 320 isolates studied, spa typing identified 24 distinct repeat types and 33 different strain types. spa typing distinguished 27 of 29 related strains and did not provide a unique fingerprint for 4 unrelated strains from the four outbreaks of the CDC collection. In the NYC collection, spa typing provided a clonal assignment for 185 of 195 strains within the five major groups previously described. spa sequencing appears to be a highly effective rapid typing tool for S. aureus that, despite some expense of specificity, has significant advantages in terms of speed, ease of use, ease of interpretation, and standardization among laboratories.
Award Playing with Cases : Rendering Expressive Music with Case-Based Reasoning

The simple rendering of a quantized score by a sequencer sounds monotonous and uninteresting. On the other hand, musicians make intentional deviations from the score to convey their own interpretation of the music. These deviations constitute what we call expressiveness and are mostly intended to clarify the musical structure of the composition. This includes the metrical structure (Sloboda 1983), the phrasing (Gabrielsson 1987), and harmonic structure (Palmer 1966). Besides clarifying the structure, expressiveness is also used as a way of communicating affective content (Juslin 2001; Lindström 1992; Gabrielsson 1995). But, why do we prefer listening to expressive music instead of nonexpressive synthesized music? There is a neurological explanation for that: The brain is interested in change. Indeed, auditory neurons, like most neurons in the brain, fire constantly even in silent environments. What really matters, therefore, is not the base firing rate but the changes in firing rate. There are auditory neurons whose firing rate changes only when the sound frequency or the sound intensity increases or decreases. Other neurons react similarly when a sound repeats. Conversely, most of the primary auditory neurons also exhibit what is known as habituation (Baars 1998), which means that when neurons repeatedly receive the same stimulus their firing rate decreases over time, which means that we deafen to a sound unless it manifests some sort of novelty or renewal in its characteristics. Therefore, it is not surprising that music becomes more interesting when it contains alterations in dynamics, timbre, pitch, rhythm, and others. This pack of alterations might at
Where were you while we were getting high policing? The consequences of co-location for broader partnership working in tackling organised crime and terrorism

ABSTRACT The Scottish Crime Campus (SCC) represents a significant financial and political investment in policing organised crime and terrorism in Scotland. The ethos of physically co-locating high-policing agencies and promoting partnership working has been central to the SCC; however, the consequences for those agencies and actors not permanently based here have hitherto been overlooked. Based on mixed methods research this study considers the range of ‘outside’ partners who work with the core SCC-based agencies, and explores the consequences of these co-location arrangements for broader partnership working across this ‘new network’ of high policing. It finds that these 'outside' partners report a range of positive benefits from engaging with the SCC: from improvements in the quality and depth of partnership working to enhanced service delivery in their own work. The SCC has deepened collaboration between the crime campus-based agencies and those partners who directly participate, albeit in a more limited fashion, in these co-location arrangements. Partnership working with agencies fully ‘beyond’ the crime campus, however, is better characterised as co-operative, not collaborative. Extending collaboration further across this network would bring further benefits, but requires the addressing of boundary issues, including challenges of insularity and isolation, that can result from co-location.
Learning Temporally Persistent Hierarchical Representations

A biologically motivated model of cortical self-organization is proposed. Context is combined with bottom-up information via a maximum likelihood cost function. Clusters of one or more units are modulated by a common contextual gating Signal; they thereby organize themselves into mutually supportive predictors of abstract contextual features. The model was tested in its ability to discover viewpoint-invariant classes on a set of real image sequences of centered, gradually rotating faces. It performed considerably better than supervised back-propagation at generalizing to novel views from a small number of training examples.
Cla4 kinase triggers destruction of the Rac1-GEF Cdc24 during polarized growth in Ustilago maydis

In the dimorphic fungus Ustilago maydis, Rac1 and its activator Cdc24 are essential for hyphal tip growth. Rac1 is shown to stimulate Cla4 kinase, which in turn triggers destruction of Cdc24. Expression of stabilized Cdc24 interferes with cell polarization, indicating that negative feedback regulation of Cdc24 is critical for tip growth.
Identifying Expertise Using Kinect Data

1. Introduction Project ​ based models of teaching and the use of maker spaces is becoming an important trend in modern education. But how to assess how well a student is doing on these activities? One hypothesis is that the set of gestures and time a student applies in solving tasks is a predictive of how much expertise he acquired. These kinetic and kinematic variables could suggest how long a student takes to solve a problem, how long he spends in analyses before testing a tactic or if he is trying a number of random strategies. When watching a student performing problem­solving tasks, an experienced teacher could infer the signs that his apprentice is evolving. This skill could be scaled if we were able to evaluate the performance of a student automatically, helping other teachers to identify the effectiveness of educational activities in several maker spaces. In this project, I apply machine learning to evaluate participants in a workshop organized in the Stanford's fablab, by comparing them with graduate engineering students (experts) using data from a Kinect sensor. The data consists of the coordinates from 30 body points, taken every 0.02 seconds. I used supervised learning algorithms (Logistic Regression, SVM) to evaluate the possibility of recognizing expertize using this data. et al, 2012). On these works, the authors aimed to distinguish young from old participants by their gait pattern. They reported good results using SVM, what motivated me to test these algorithms. In their study, Begg & Kamruzzaman extracted features like range of movement (kinect features) and angles for ankles and knee (kinematic features). The former had more positive influence on the results, indicating that kinematic analysis might be a good choice of features for these kind of data. ​ Zafrulla et al. (2011), who used data from a kinect to recognize sign language, used PCA to reduce the dimension of the dataset, though no impact on the learning efficacy was reported. Parajuli et al.(2012) reported using KPCA, an algorithm that performs PCA using a kernel, getting better results than using the usual PCA algorithm to select features for gait recognition. Those two last studies motivated me to test PCA on my dataset.
Near-optimal Nonmyopic Value of Information in Graphical Models

A fundamental issue in real-world systems, such as sensor networks, is the selection of observations which most effectively reduce uncertainty. More specifically, we address the long standing problem of nonmyopically selecting the most informative subset of variables in a graphical model. We present the first efficient randomized algorithm providing a constant factor (1 - 1/e – e) approximation guarantee for any e > 0 with high confidence. The algorithm leverages the theory of submodular functions, in combination with a polynomial bound on sample complexity. We furthermore prove that no polynomial time algorithm can provide a constant factor approximation better than (1 - 1/e) unless P = NP. Finally, we provide extensive evidence of the effectiveness of our method on two complex real-world datasets.
Toward a provably-correct implementation of the JVM bytecode verifier

This paper reports on our ongoing efforts to realize a provably-correct implementation of the Java Virtual Machine bytecode verifier. We take the perspective that bytecode verification is a data flow analysis problem, or more generally, a constraint-solving problem on lattices. We employ SPECWARE, a system available from Kestrel Institute that supports the development of programs from specifications, to formalize the bytecode verifier, and to formally derive an executable program from our specification.
Transcriptome Analysis of Beta macrocarpa and Identification of Differentially Expressed Transcripts in Response to Beet Necrotic Yellow Vein Virus Infection

Background Rhizomania is one of the most devastating diseases of sugar beet. It is caused by Beet necrotic yellow vein virus (BNYVV) transmitted by the obligate root-infecting parasite Polymyxa betae. Beta macrocarpa, a wild beet species widely used as a systemic host in the laboratory, can be rub-inoculated with BNYVV to avoid variation associated with the presence of the vector P. betae. To better understand disease and resistance between beets and BNYVV, we characterized the transcriptome of B. macrocarpa and analyzed global gene expression of B. macrocarpa in response to BNYVV infection using the Illumina sequencing platform. Results The overall de novo assembly of cDNA sequence data generated 75,917 unigenes, with an average length of 1054 bp. Based on a BLASTX search (E-value ≤ 10−5) against the non-redundant (NR, NCBI) protein, Swiss-Prot, the Gene Ontology (GO), Clusters of Orthologous Groups of proteins (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, there were 39,372 unigenes annotated. In addition, 4,834 simple sequence repeats (SSRs) were also predicted, which could serve as a foundation for various applications in beet breeding. Furthermore, comparative analysis of the two transcriptomes revealed that 261 genes were differentially expressed in infected compared to control plants, including 128 up- and 133 down-regulated genes. GO analysis showed that the changes in the differently expressed genes were mainly enrichment in response to biotic stimulus and primary metabolic process. Conclusion Our results not only provide a rich genomic resource for beets, but also benefit research into the molecular mechanisms of beet- BNYV Vinteraction.
X-rays from T Tauri: a test case for accreting T Tauri stars

Context. The generation of X-rays in accreting T Tauri stars (TTS) is thought to be predominantly due to energy dissipation in magnetic elds, but alternative X-ray generation mechanisms have been proposed, such as heating in accretion shocks near the stellar surface, or in shocks forming in jets. Aims. We test models and trends discussed in the literature using X-ray data from the classical TTS T Tau. Methods. High-resolution spectroscopy from the Reection Grating Spectrometers on XMM-Newton is used to infer electron densities, element abundances and the thermal structure of the X-ray source. We also discuss the ultraviolet light curve obtained by the Optical Monitor, and complementary ground-based photometry. A high-resolution image from Chandra constrains contributions from the two companions of T Tau N. Results. The X-ray grating spectrum is rich in emission lines, but shows an unusual mixture of features from very hot ( 30 MK) and very cool (1n3 MK) plasma, both emitted by similar amounts of emission measure. The cool plasma conrms the picture of a soft excess in the form of an enhanced O vii/O viii Ly ux ratio, similar to that previously reported for other accreting TTS. Diagnostics from lines formed by this plasma indicate low electron densities (< 10 10 cm 3 ). The Ne/Fe abundance ratio is consistent with a trend in pre-main sequence stars in which this ratio depends on spectral type, but not on accretion. Conclusions. On the basis of line density diagnostics, we conclude that the density of the cool isoft-excessi plasma is orders of magnitude below that predicted for an accretion shock, assuming previously determined accretion rates of (3 6) 10 8 M yr 1 . We argue that loading of magnetic eld lines with infalling material suppresses the heating process in a part of the corona. We thus suggest that the X-ray production of T Tau is inuenced by the accretion process although the X-rays may not form in the bulk of the accretion footpoints.
Adaptive Divergence in Experimental Populations of Pseudomonas fluorescens. V. Insight into the Niche Specialist Fuzzy Spreader Compels Revision of the Model Pseudomonas Radiation

Pseudomonas fluorescens is a model for the study of adaptive radiation. When propagated in a spatially structured environment, the bacterium rapidly diversifies into a range of niche specialist genotypes. Here we present a genetic dissection and phenotypic characterization of the fuzzy spreader (FS) morphotype—a type that arises repeatedly during the course of the P. fluorescens radiation and appears to colonize the bottom of static broth microcosms. The causal mutation is located within gene fuzY (pflu0478)—the fourth gene of the five-gene fuzVWXYZ operon. fuzY encodes a β-glycosyltransferase that is predicted to modify lipopolysaccharide (LPS) O antigens. The effect of the mutation is to cause cell flocculation. Analysis of 92 independent FS genotypes showed each to have arisen as the result of a loss-of-function mutation in fuzY, although different mutations have subtly different phenotypic and fitness effects. Mutations within fuzY were previously shown to suppress the phenotype of mat-forming wrinkly spreader (WS) types. This prompted a reinvestigation of FS niche preference. Time-lapse photography showed that FS colonizes the meniscus of broth microcosms, forming cellular rafts that, being too flimsy to form a mat, collapse to the vial bottom and then repeatably reform only to collapse. This led to a reassessment of the ecology of the P. fluorescens radiation. Finally, we show that ecological interactions between the three dominant emergent types (smooth, WS, and FS), combined with the interdependence of FS and WS on fuzY, can, at least in part, underpin an evolutionary arms race with bacteriophage SBW25Φ2, to which mutation in fuzY confers resistance.
Single-Cell Imaging of Bioenergetic Responses to Neuronal Excitotoxicity and Oxygen and Glucose Deprivation

Excitotoxicity is a condition occurring during cerebral ischemia, seizures, and chronic neurodegeneration. It is characterized by overactivation of glutamate receptors, leading to excessive Ca2+/Na+ influx into neurons, energetic stress, and subsequent neuronal injury. We and others have previously investigated neuronal populations to study how bioenergetic parameters determine neuronal injury; however, such experiments are often confounded by population-based heterogeneity and the contribution of effects of non-neuronal cells. Hence, we here characterized bioenergetics during transient excitotoxicity in rat and mouse primary neurons at the single-cell level using fluorescent sensors for intracellular glucose, ATP, and activation of the energy sensor AMP-activated protein kinase (AMPK). We identified ATP depletion and recovery to energetic homeostasis, along with AMPK activation, as surprisingly rapid and plastic responses in two excitotoxic injury paradigms. We observed rapid recovery of neuronal ATP levels also in the absence of extracellular glucose, or when glycolytic ATP production was inhibited, but found mitochondria to be critical for fast and complete energetic recovery. Using an injury model of oxygen and glucose deprivation, we identified a similarly rapid bioenergetics response, yet with incomplete ATP recovery and decreased AMPK activity. Interestingly, excitotoxicity also induced an accumulation of intracellular glucose, providing an additional source of energy during and after excitotoxicity-induced energy depletion. We identified this to originate from extracellular, AMPK-dependent glucose uptake and from intracellular glucose mobilization. Surprisingly, cells recovering their elevated glucose levels faster to baseline survived longer, indicating that the plasticity of neurons to adapt to bioenergetic challenges is a key indicator of neuronal viability.