Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of finite scales of turbulence on dispersion estimates

The eddy-diffusion parameterization of turbulent transport is based on the assumption, often questionable for geophysical flows, of infinitesimal scales of turbulence. In this paper we quantitatively compute what are the consequences of this assumption on the estimates of dispersion for some simple flows with oceanographical scales. We compare the analytical results of two different models, one with infinitesimal turbulent time scale (corresponding to a model with eddy-diffusion) and the other with finite scale T. The difference between the two model results normalized with respect to the estimate of the eddy-diffusion model, called A, is computed and it is used as a measure of the accuracy of the eddy-diffusion parameterization. In the case of homogeneous turbulence, the eddy-diffusion model is accurate for asymptotic times t > T, as is known, whereas for small times it is characterized by an overestimate of the dispersion. A decreases asymptotically as T/t, with the overestimate less than 10% fort > lOT, so that the eddy-diffusion model is appropriate for the meso or global scales but it could be inadequate for short-term studies or for the interpretation of Lagrangian data. When a linear shear is superimposed on the turbulence, A still decreases as = T/t, which indicates that the range of applicability of the eddy-diffusion model is approximately the same for homogeneous and for linearly inhomogeneous flows. We then consider an oscillating linear shear with frequency o, and the results change drastically. A does not vanish asymptotically, but rather converges to an oscillating function with constant average and constant extrema. The values of A depend on the ratio between the turbulent time scale T and the period of oscillation l/w. When T and l/o are comparable, the eddy-diffusion model leads to an overestimate of order one even at asymptotic times. This result is a specific and analytically solvable example of a potentially much wider class of results valid for time-dependent flows with more complex spatial structure. A discussion of the possible generalizations and examples of applications to oceanographical flows are presented.
Missing arguments in earlier English clause structures

The purpose of this paper is to account for missing arguments in impersonal constructions in earlier English. Having examined all the proposals for accounting for the missing arguments in line with the discussion of such arguments in early child English, we saw that all of them had potential problems. I proposed a new view that the missing arguments were not missing, but simply did not exist in a given argument structure from the beginning, because the early clause is completely thematic ally constructed. Only arguments which are required by the meaning of the predicate have to be syntactically realized.
Coordinated Path-Following in the Presence of Communication Losses and Time Delays

This paper addresses the problem of steering a group of vehicles along given spatial paths while holding a desired time-varying geometrical formation pattern. The solution to this problem, henceforth referred to as the coordinated path-following (CPF) problem, unfolds in two basic steps. First, a path-following (PF) control law is designed to drive each vehicle to its assigned path, with a nominal speed profile that may be path dependent. This is done by making each vehicle approach a virtual target that moves along the path according to a conveniently defined dynamic law. In the second step, the speeds of the virtual targets (also called coordination states) are adjusted about their nominal values so as to synchronize their positions and achieve, indirectly, vehicle coordination. In the problem formulation, it is explicitly considered that each vehicle transmits its coordination state to a subset of the other vehicles only, as determined by the communications topology adopted. It is shown that the system that is obtained by putting together the PF and coordination subsystems can be naturally viewed as either the feedback or the cascade connection of the latter two. Using this fact and recent results from nonlinear systems and graph theory, conditions are derived under which the PF and the coordination errors are driven to a neighborhood of zero in the presence of communication losses and time delays. Two different situations are considered. The first captures the case where the communication graph is alternately connected and disconnected (brief connectivity losses). The second reflects an operational scenario where the union of the communication graphs over uniform intervals of time remains connected (uniformly connected in mean). To better root the paper in a nontrivial design example, a CPF algorithm is derived for multiple underactuated autonomous underwater vehicles (AUVs). Simulation results are presented and discussed.
A Genotypic Test for HIV-1 Tropism Combining Sanger Sequencing with Ultradeep Sequencing Predicts Virologic Response in Treatment-Experienced Patients

A tropism test is required prior to initiation of CCR5 antagonist therapy in HIV-1 infected individuals, as these agents are not effective in patients harboring CXCR4 (X4) coreceptor-using viral variants. We developed a clinical laboratory-based genotypic tropism test for detection of CCR5-using (R5) or X4 variants that utilizes triplicate population sequencing (TPS) followed by ultradeep sequencing (UDS) for samples classified as R5. Tropism was inferred using the bioinformatic algorithms geno2pheno[coreceptor] and PSSMx4r5. Virologic response as a function of tropism readout was retrospectively assessed using blinded samples from treatment-experienced subjects who received maraviroc (N = 327) in the MOTIVATE and A4001029 clinical trials. MOTIVATE patients were classified as R5 and A4001029 patients were classified as non-R5 by the original Trofile test. Virologic response was compared between the R5 and non-R5 groups determined by TPS, UDS alone, the reflex strategy and the Trofile Enhanced Sensitivity (TF-ES) test. UDS had greater sensitivity than TPS to detect minority non-R5 variants. The median log10 viral load change at week 8 was −2.4 for R5 subjects, regardless of the method used for classification; for subjects with non-R5 virus, median changes were −1.2 for TF-ES or the Reflex Test and −1.0 for UDS. The differences between R5 and non-R5 groups were highly significant in all 3 cases (p<0.0001). At week 8, the positive predictive value was 66% for TF-ES and 65% for both the Reflex test and UDS. Negative predictive values were 59% for TF-ES, 58% for the Reflex Test and 61% for UDS. In conclusion, genotypic tropism testing using UDS alone or a reflex strategy separated maraviroc responders and non-responders as well as a sensitive phenotypic test, and both assays showed improved performance compared to TPS alone. Genotypic tropism tests may provide an alternative to phenotypic testing with similar discriminating ability.
Rapid prototyping of location-based games with the multi-user publishing environment application platform

Location-Based Applications (LBA) react and adapt to changes in the environment of a user. Building LBAs, however, is a time consuming task, and a lot of effort needs to be put to the infrastructure supporting the development process. In this paper, a framework for rapid prototyping of location-based games (and applications) with the Multi-User Publishing Environment (MUPE) application platform is presented. The application platform allows developers to quickly prototype game ideas, and concentrate on the content of the games and game logic, rather than technology. The platform is further studied with a 24 hour development session, in which the developers were able to produce many functioning game applications in the given time frame.
A Combined Small-Angle X-ray and Neutron Scattering Study of the Structure of Purified Soluble Gastrointestinal Mucins

The structures of purified soluble porcine gastric (Muc5ac) and duodenal (Muc2) mucin solutions at neutral and acidic pH were examined using small‐angle X‐ray scattering and small‐angle neutron scattering experiments. We provide evidence for the morphology of the network above the semidilute overlap concentration and above the entanglement concentration. Furthermore, we investigated the gelation of both types of mucin solutions in response to a reduction in pH, where we observed the formation of large‐scale heterogeneities within the polymer solutions, typical of microphase‐separated gels. The concentration dependence of the inhomogeneity length scale (Ξ) and the amplitude of the excess scattering intensity [Iex(0)] are consistent with previously studied gelled synthetic polymeric systems. The persistence lengths of the chains were found to be similar for both Muc5ac and Muc2 from Kratky plots of the neutron data (8 ± 2 nm). © 2014 Wiley Periodicals, Inc. Biopolymers 101: 1154–1164, 2014.
8. Contextual acquisition of information categories: What has been done and what can be done automatically?

Semantic category acquisition and extension is a growing subfield in natural language processing (NLP) and information retrieval (IR), as the use of the Web increases demand for content-based access to textual data.1 We are both involved in (sub)language analysis for practical applications (Zweigenbaum & Consortium MENELAS 1994, Bourigault & Habert 1998). With J. Bouaud and A. Nazarenko, we developed software and methods for semantic category acquisition and extension (Nazarenko et al. 2001) which turned out to be akin to Harris’s approach.2 We were influenced as well by the work done on medical language by Naomi Sager and her team.3 Our aim in this paper is to try and appraise the Harrisian framework4 in contextual acquisition of information categories from a natural language processing (NLP) viewpoint. In our discussion of Harris’s analysis of sublanguages (Section 2), we put emphasis on the interplay between technical We thank B. Nevin and two anonymous referees as well as A. Borillo, D. Leeman, J.-M. Marandin, and N. Sager for their remarks on a draft version of this paper.
Detection of incoherent joint state due to inaccurate bone motion estimation

In biomechanical modelling and motion analysis, the use of personalised data such as bone geometry would provide more accurate and reliable results. However, there are still a limited number of tools used to measure the evolution of articular interactions. This paper proposes a coherence index to describe the articular status of contact surfaces during motion. The index relies on a robust estimation of the evolution of surfacic interactions between the joint surfaces. The index is first compared to distance maps on simulated motions. It is then used to compare two motion capture protocols (two different localisations of the markers for scapula tracking). The results show that the index detects progressive modifications in the joint and allows distinguishing the two protocols, in accordance with the literature. In the future, the index could, among other things, be used to compare/improve biomechanical models and motion analysis protocols.
Golgi-Disturbing Agents Lead to the Elimination of Intracellular Toxoplasma gondii

The Golgi apparatus is responsible for the genesis of secretory organelles of Toxoplasma gondii and lipid traffic to the vacuole. This study used anti-Golgi agents to demonstrate the importance of Golgi in Toxoplasma development. Monensin, Brefeldin A, Retinoic Acid and Okadaic Acid reduced the infection, leading to parasite elimination. Mon, BFA and RA affected secretory organelles and the Golgi Complex of the parasites, with faster parasite elimination in the presence of Monensin; in addition, the vesicular transit of host cell C6-NBD-ceramide metabolites was interrupted, but the GC of host cells was preserved. Our results suggest that several targets in the secretory pathway are affected in the intracellular Toxoplasma rather than in the host cells, resulting in interruption of parasite development and its elimination from the intracellular medium.
Temporal Connectives in a Discourse Context

We examine the role of temporal connectives in multi-sentence discourse. In certain contexts, sentences containing temporal connectives that are equivalent in temporal structure can fail to be equivalent in terms of discourse coherence. We account for this by offering a novel, formal mechanism for accommodating the presuppositions in temporal subordinate clauses. This mechanism encompasses both accommodation by discourse attachment and accomodation by temporal addition. As such, it offers a precise and systematic model of interactions between presupposed material, discourse context, and the reader's background knowledge. We show how the results of accommodation help to determine a discourse's coherence.
H.264 visual perceptual coding in uniform analyzing and encoding framework

The perception of Human Visual System (HVS) for the video scene is selective. Different regions in the video scene have distinctive levels of visual importance. In this study, we present a novel H.264 visual perceptual video coding (VPVC) method in a uniform analyzing and encoding framework, which can allocate bit and computation resources effectively. The framework presented in this work consists of a visual perception model, a H.264 perceptual encoder and a corresponding sharing channel of information. The visual perception model, composed of motion perception, texture perception and spatial position perception sub-models, can compute the visual perception map (VPM) by fusing these spatiotemporal visual features. Visual perception results of HVS for various regions can be simulated well by VPM. The side encoding information of H.264 encoder, including motion vectors (MVs) and sum of absolute differences (SADs), is applied as input features for motion perception sub-model. A novel VPVC method is proposed based on the VPM and the global motion type of video scene. Using an adaptive frequency coefficient suppression technique and a novel encoding strategy, the optimal bit resource allocation is achieved by classifying video scene based on the VPM. In order to allocate computation resource effectively in VPVC method, the relation between optimal encoding mode and image features at video scene level is experimentally analyzed. As a result, a fast and effective H.264 mode analysis algorithm is deduced. When compared with the conventional H.264 coding method, our results on four video sequences show that the proposed method can obtain a high PSNR gain up to about 2.0 dB for visual important regions and decrease about 38% of total encoding time on average.
HPP: A Reliable Causal Broadcast Protocol for Large-Scale Replication

This paper describes a fast, reliable, scalable and efficient broadcast protocol called HPP (hierarchical propagation protocol) for weak-consistency replica management. It is based on organizing the nodes in a network into a logical hierarchy and maintaining a limited amount of state information at each node. It ensures that messages are not lost due to failures or partitions and minimizes redundancy. Furthermore, the protocol allows messages to be diffused while nodes are down provided the parent and child nodes of a failed node are alive. Moreover, the protocol allows nodes to be moved in the logical hierarchy and the network to be restructured dynamically in order to improve performance, while still ensuring that no messages are lost while the switch takes place and without disturbing normal operation. A performance study of the protocol in terms of availability and propagation delay indicates that the protocol reduces the delay by a factor of four compared to a protocol that does not diffuse messages past failed nodes.
MicroRNA-155 Modulates Treg and Th17 Cells Differentiation and Th17 Cell Function by Targeting SOCS1

MicroRNA (miR)-155 is a critical player in both innate and adaptive immune responses. It can influence CD4+ T cell lineage choice. To clarify the role of miR-155 in CD4+ CD25+ regulatory T (Treg)/T helper (Th)17 cell differentiation and function, as well as the mechanism involved, we performed gain-and loss-of-function analysis by transfection pre-miR-155 and anti-miR-155 into purified CD4+ T cells. The results showed that miR-155 positively regulated both Treg and Th17 cell differentiation. It also induced the release of interleukin (IL)-17A by Th17 cells, but not the release of IL-10 and transforming growth factor (TGF)-β1 by Treg cells. Furthermore, we found that miR-155 reacted through regulating Janus kinase/signal transducer and activator of transcription (JAK/STAT) rather than TGF-β/mothers against decapentaplegic homolog (SMAD) signaling pathway in the process of Treg and Th17 cells differentiation. This may because suppressors of cytokine signaling (SOCS)1, the important negative regulator of JAK/STAT signaling pathway, was the direct target of miR-155 in this process, but SMAD2 and SMAD5 were not. Therefore, we demonstrated that miR-155 enhanced Treg and Th17 cells differentiation and IL-17A production by targeting SOCS1.
NUMERICAL SIMULATIONS OF WIND ACCRETION IN SYMBIOTIC BINARIES

About half of the binary systems are close enough to each other for mass to be exchanged between them at some point in their evolution, yet the accretion mechanism in wind accreting binaries is not well understood. We study the dynamical effects of gravitational focusing by a binary companion on winds from late-type stars. In particular, we investigate the mass transfer and formation of accretion disks around the secondary in detached systems consisting of an asymptotic giant branch (AGB) mass-losing star and an accreting companion. The presence of mass outflows is studied as a function of mass-loss rate, wind temperature, and binary orbital parameters. A two-dimensional hydrodynamical model is used to study the stability of mass transfer in wind accreting symbiotic binary systems. In our simulations we use an adiabatic equation of state and a modified version of the isothermal approximation, where the temperature depends on the distance from the mass losing star and its companion. The code uses a block-structured adaptive mesh refinement method that allows us to have high resolution at the position of the secondary and resolve the formation of bow shocks and accretion disks. We explore the accretion flow between the components and formation of accretion disks for a range of orbital separations and wind parameters. Our results show the formation of stream flow between the stars and accretion disks of various sizes for certain orbital configurations. For a typical slow and massive wind from an AGB star the flow pattern is similar to a Roche lobe overflow with accretion rates of 10% of the mass loss from the primary. Stable disks with exponentially decreasing density profiles and masses of the order 10−4 solar masses are formed when wind acceleration occurs at several stellar radii. The disks are geometrically thin with eccentric streamlines and close to Keplerian velocity profiles. The formation of tidal streams and accretion disks is found to be weakly dependent on the mass loss from the AGB star. Our simulations of gravitationally focused wind accretion in symbiotic binaries show the formation of stream flows and enhanced accretion rates onto the compact component. We conclude that mass transfer through a focused wind is an important mechanism in wind accreting interacting binaries and can have a significant impact on the evolution of the binary itself and the individual components.
South African Teachers Caught Between Nation Building and Global Demands: Is There a Way Out/Forward?

In this article, we explore the impact of the nation-building and global demands on teachers’ work and how they survive the pressure of, and reconcile, these various demands that impact their work. We draw on two separate data sets that emerged from studies undertaken in the Eastern Cape Province (EC), South Africa. Findings reveal a rift between the nation-building and global mandates. Most intended changes assumed that teachers are ready and prepared for whatever changes that are introduced. Consequently, teachers are in a constant struggle to come to terms with them, thus resulting in slow implementation or the nonimplementation of reforms in classrooms. We argue that recognition and acknowledgment of existing realities, classroom cultures, and implementation requirements or support should be the first step in improving education. Also, a strong visionary leadership becomes pivotal to achieve the desired reform success. Additionally, policy development and programs need to recognize the country's history and the murky terrain that still has to be navigated to ensure successful curriculum reform implementation.
SURVEY ON INFORMATION EXTRACTION FROM CHEMICAL COMPOUND LITERATURES : TECHNIQUES AND CHALLENGES

Chemical documents, especially those involving drug information, comprise a variety of types – the most common being journal articles, patents and theses. They typically contain large amounts of chemical information, such as PubMed-ID, activity classes and adverse or side effects. Techniques are used to extract information from a huge number of documents and it is presented in a useful structurally prepared format that can be applied to structured, semi-structured and unstructured texts. Numerous information extraction methods and techniques have been proposed and implemented. In principle, there are two main approaches to information extraction, the knowledge engineering approach and the learning approach. In this survey study, we first provide the historical background on information extraction approaches applied to chemical documents and discuss several kinds of information extraction tasks that have emerged in recent years. Then, we discuss the metrics used for evaluating information extraction systems, and finally the survey outlines the main issues that will shape future research in this area of study.
Experiences of Danish Business Expatriates in Russia: Power Distance in Organizational Communication

Abstract Rapid globalization of business processes stimulates many companies to dispatch their employees – business expatriates – on overseas assignments. Russia differs markedly from many other cultures in terms of specific communication norms and rules. Understanding such differences in organizational life is crucial for the success of business expatriates working there. This study employs in-depth interviews with eight Danish business expatriates who worked in Russia and examines the differences between the Danes and the Russians in terms of communication characteristics related to Hofstede’s cultural dimension power distance. This work enhances scholars’ empirical knowledge of power distance, which has rarely been investigated qualitatively.
Body mass index and survival in women with breast cancer—systematic literature review and meta-analysis of 82 follow-up studies

The current systematic literature review and meta-analysis extends and confirms the associations of obesity with an unfavourable overall and breast cancer survival in pre and postmenopausal breast cancer, regardless of when BMI is ascertained. Increased risks of mortality in underweight and overweight women and J-shape associations with total mortality were also observed. The recommendation of maintaining a healthy body weight throughout life is important as obesity is a pandemic health concern.