Miracle-dz/UniFAR-FTUs huggingface dataset:
The Implicit and Explicit a-# Schemes

Artificial numerical dissipation is an important issue in large Reynolds number computations. In such computations, the artificial dissipation inherent in traditional numerical schemes can overwhelm the physical dissipation and yield inaccurate results on meshes of practical size. In the present work, the space-time conservation element and solution element method is used to construct new and accurate numerical schemes such that artificial numerical dissipation will not overwhelm physical dissipation. Specifically, these schemes have the property that numerical dissipation vanishes when the physical viscosity goes to zero. These new schemes therefore accurately model the physical dissipation even when it is extremely small. The method of space-time conservation element and solution element, currently under development, is a nontraditional numerical method for solving conservation laws. The method is developed on the basis of local and global flux conservation in a spacetime domain, in which space and time are treated in a unified manner. Exphcit solvers for model and fluid dynamic conservation laws have previously been investigated. In this paper, we introduce a new concept in the design of implicit schemes, and use it to construct two highly accurate solvers for a convection-diffusion equation. The two schemes become identical in the pure convection case, and in the pure diffusion case. The implicit schemes are apphcable over the whole Reynolds number range, from purely diffusive equations to purely inviscid (convective) equations. The stabihty and consistency of the schemes are analysed, and some numerical results are presented. It is shown that, in the inviscid case, the new schemes become explicit and their amplification factors are identical to those of the Leapfrog scheme. On the other hand, in the pure diffusion case, their principal amplification factor becomes the amplification factor of the Crank-Nicolson scheme. We also construct an explicit solver with the treatment of diffusion being based on that in the imphcit solvers. The explicit solver has only a CFL stability hmitation on the Courant number, yet it retains the second-order spatial accuracy of the imphcit schemes.
Motivation in service-learning: An improvement over traditional instructional methods

This paper aims at exploring the motivation of university students who participated in service-learning projects as part of their coursework, and to determine whether their level of motivation is higher for the service-learning project as compared to performing more traditional academic tasks and assignments. The Service-Learning project carried out during the ICT in Education course intended to support the development of digital literacy in a Maasai school in Kenya. The instrument used to evaluate motivation of the university students is the motivation scale called Motivated Strategies for Learning Questionnaire (MSLQ) proposed by Pintrich and his collaborators (1991) adapted to the Spanish population by Roces Montero (1996). The results of the research indicate that there are significant differences in favor of service-learning in relation to motivation in general for the completion of the activities and specifically in relation to the utility of the activity as seen at the present moment and in the future, as well as promoting creativity, the interest in the task which includes the perception of the importance of the project, the need to work hard and thoroughly and willingness to face challenges and difficulties in order to achieve the set objective. No significant differences have been observed in relation to the desire to obtain a better grade for completing the activity or need to prove personal value to others, as well as to broaden the information to complete the activity.
Analysis and computation of some tumor growth models with nutrient: From cell density models to free boundary dynamics

In this paper, we study the tumor growth equation along with various models for the nutrient component, including the \emph{in vitro} model and the \emph{in vivo} model. At the cell density level, the spatial availability of the tumor density $n$ is governed by the Darcy law via the pressure $p(n)=n^{\gamma}$. For finite $\gamma$, we prove some a priori estimates of the tumor growth model, such as boundedness of the nutrient density, and non-negativity and growth estimate of the tumor density. As $\gamma \rightarrow \infty$, the cell density models formally converge to Hele-Shaw flow models, which determine the free boundary dynamics of the tumor tissue in the incompressible limit. We derive several analytical solutions to the Hele-Shaw flow models, which serve as benchmark solutions to the geometric motion of tumor front propagation. Finally, we apply a conservative and positivity preserving numerical scheme to the cell density models, with numerical results verifying the link between cell density models and the free boundary dynamical models.
Chemical defense against predators and bacterial fouling in the Mediterranean sponges Axinella polypoides and A. verrucosa

The diverse natural products found within sponges mediate many of their ecological interactions, including predator feeding deterrence and defense against fouling. Pyrrole-imidazole compounds, often involved in such ecological interactions, are exclusively found in marine sponges, mainly from the genera Axinella and Agelas. Employing field and laboratory assays, we studied the chemical defense of 2 co-occurring Mediterranean sponges, Axinella polypoides and A. verrucosa, collected from the Gulf of Naples, Italy, against microbial fouling, as well as their feeding deterrence against the generalist shrimp Palaemon elegans. These assays revealed no activity in the extracts of A. polypoides, while the n-butanol part of the A. verrucosa extract showed activity in all assays at natural concentrations. This fraction of the extract contains the bromopyrrole hymenidin, and our assays revealed antibacterial and feeding deterrence activity for this pure compound. 1H nuclear magnetic resonance quantification confirmed the presence of hymenidin and debromo-carteramine A, another previously isolated antibacterial compound, at ecologically relevant concentrations in the n-butanol part of the A. verrucosa extract. Our results indicate different antimicrobial and feeding deterrence defense strategies in the 2 examined sympatric sponge species, and multiple defensive roles of hymenidin in the defense of A. verrucosa, similar to those of other bromopyrroles isolated from taxonomically related Caribbean sponges.
Improved Detection of Dengue Virus Serotypes from Serum Samples - Evaluation of Single-Tube Multiplex RT-PCR with Cell Culture

Serological assays commonly used for the diagnosis of dengue are feasible only five or six days after the onset of illness; moreover, they involve antigenic cross-reactivity between four serotypes. However, viraemia present during the acute phase of the illness can be detected by cell culture. Being a complicated and time-consuming procedure, it cannot be used as routine diagnostic assay. In this study, the efficacy of multiplex RT-PCR (mRT-PCR) for serotypic characterization of dengue virus was evaluated using serum samples directly. The sensitivity of the assay was compared with the gold standard method of virus isolation by cell culture with serotypic characterization by indirect immunofluorescent antibody test (IFAT). Serum samples collected within 5–7 days of illness from 240 patients, clinically suspected of having dengue infection, were processed directly by mRT-PCR. An aliquote of each of these samples was simultaneously inoculated in C6/36 cell culture for the propagation of virus for serotypic characterization by IFAT as well as mRT-PCR. ELISA/rapid immunochromatography test was performed to find out the presence of anti-dengue IgM antibodies. 44 patients were found to be positive for one of the four serotypes by mRT-PCR and 39 by IFAT on examination of culture fluid and infected cells respectively. However, 76 patients were found positive for dengue virus serotypes by mRT-PCR performed directly on serum samples, thus indicating significantly higher sensitivity of this method. The most predominant serotype detected during this study period was DENV-2, followed by DENV-3.This study proposed mRT-PCR as a method of choice for rapid, cost-effective and sensitive confirmatory diagnosis in the early phase of dengue infection.
The Challenge of Measuring Hunger through Survey

There is widespread interest in estimating the number of hungry people in the world as well as trends in hunger. Current global counts rely on combining each country’s total food balance with information on distribution patterns from household consumption expenditure surveys. Recent research has advocated for calculating hunger numbers directly from these same surveys, which are increasingly available in low-income countries. For either approach, embedded in this effort are a number of important details about how household surveys are designed and how these data are then used. Using a survey experiment in Tanzania, this study finds great fragility in hunger counts stemming from alternative survey designs. As such, caution should be taken in drawing inferences on hunger over time and space on the basis of household surveys.
Autophagic Flux Failure in Neurodegeneration: Identifying the Defect and Compensating Flux Offset

Protein degradation through autophagy is one of the key pathways that maintain proteostasis and neuronal viability. Dysregulation in autophagy has been associated with a number of major protein aggregation storage disorders that are characterized by increased cellular vulnerability and susceptibility to undergo cell death. Although the molecular machinery, the proteome, and the regulation of the autophagy system are becoming increasingly clear, the specific nature of its dysfunction in the context of neuronal disease pathogenesis remains largely unclear. Moreover, although the intricate network of autophagy regulatory proteins with key metabolic checkpoints is increas‐ ingly being revealed, the relationship between autophagy dysfunction, the changing rate of protein degradation in the specific pathology, and the aggregate prone behavior of specific candidate proteins remains less understood. Many questions remain and deserve urgent attention. When does a neuron respond with heightened autophagic activity and When does the system fail to degrade autophagy cargo? This book chapter will focus on some of the main challenges in the field of autophagy research, the identity, and nature of autophagic flux failure in neurodegeneration, current means to discern and measure autophagic flux dysfunction in neuronal tissue, and recent advances in compensating the flux offset. Specifically, the role of both macroautophagy and chaperone‐mediated autophagy in neuronal function and dysfunction and the spatiotemporal changes in their rates of protein degradation will be discussed and their molecular interplay highlighted. Finally, current advances in the use of autophagy modulators to better control autophagy activity will be stressed and contextualized within the framework of re‐establishing neuronal proteostasis to favorably control cellular fate.
Parameters for the Collapse of Turbulence in the Stratified Plane Couette Flow

We perform direct numerical simulation of the Couette flow as a model for the stable boundary layer. The flow evolution is investigated for combinations of the (bulk) Reynolds number and the imposed surface buoyancy flux. First, we establish what the similarities and differences are between applying a fixed buoyancy difference (Dirichlet) and a fixed buoyancy flux (Neumann) as boundary conditions. Moreover, two distinct parameters were recently proposed for the turbulent-to-laminar transition: the Reynolds number based on the Obukhov length and the “shear capacity,” a velocity-scale ratio based on the buoyancy flux maximum. We study how these parameters relate to each other and to the atmospheric boundary layer. The results show that in a weakly stratified equilibrium state, the flow statistics are virtually the same between the different types of boundary conditions. However, at stronger stratification and, more generally, in nonequilibrium conditions, the flow statistics do depend on the type of boundary condition imposed. In the case of Neumann boundary conditions, a clear sensitivity to the initial stratification strength is observed because of the existence of multiple equilibriums, while for Dirichlet boundary conditions, only one statistically steady turbulent equilibrium exists for a particular set of boundary conditions. As in previous studies, we find that when the imposed surface flux is larger than the maximum buoyancy flux, no turbulent steady state occurs. Analytical investigation and simulation data indicate that this maximum buoyancy flux converges for increasing Reynolds numbers, which suggests a possible extrapolation to the atmospheric case.
Iterative Language Model Adaptation for Indo-Aryan Language Identification

This paper presents the experiments and results obtained by the SUKI team in the Indo-Aryan Language Identification shared task of the VarDial 2018 Evaluation Campaign. The shared task was an open one, but we did not use any corpora other than what was distributed by the organizers. A total of eight teams provided results for this shared task. Our submission using a HeLI-method based language identifier with iterative language model adaptation obtained the best results in the shared task with a macro F1-score of 0.958.
Reproductive biology of the introduced sailfin catfish Pterygoplichthys pardalis (Pisces: Loricariidae) in peninsular Malaysia

Reproductive biology of the introduced sailfin cat fish Pterygoplichthys pardalis in the Langat River of peninsular Malaysia was studied. Fish samples were collected monthly from Langat River during March 2003 - June 2004. The sex ratio observed for P. pardalis was female-biased with 1: 2. Gonadal maturity stage is achieved at 12.5 cm standard length (SL) for males and 13.0 cm SL for females. This species appeared to have continuous spawning that peaked when water levels were high between September and January. Egg sizes were found to reach as large as 3.3 mm in dia in the ovary; suggesting that they spawn in batches. Fecundity varied from 1297 to 18791 numbers per brood, proportional to individual size. Data obtained from this study indicate that the introduced sailfin cat fish has successfully colonised in Langat River in Malaysia.
The origin of the limuloids

from the basal Namurian of England. Analysis of the nature of segment reduction from the more primitive to the advanced xiphosurids indicates that in the bellinuroid (limulicine) line caudal fusion was dominant, and supports the notion that the limuloids arose from an early bellinuroid in the late Devonian or earliest Carboniferous, from such as the late Devonian
The Dynamics of Crises and the Equity Premium

It is a major challenge for asset pricing models to generate a high equity premium and a low risk-free rate while imposing realistic consumption dynamics. To address this issue, our paper proposes a novel pricing channel: we allow for consumption drops that can spark an economic crisis. This new feature generates a large equity premium even if possible consumption drops are of moderate size. In turn, our model also matches the consumption data of 42 countries along several dimensions. In particular, our approach generates a realistic number of crises that have realistic durations and involve clustering of moderate consumption drops. Received October 17, 2014; accepted August 18, 2015 by Editor Pietro Veronesi.
CuO Nanoparticles Supported on TiO2 with High Efficiency for CO2 Electrochemical Reduction to Ethanol

Non-noble metal oxides consisting of CuO and TiO2 (CuO/TiO2 catalyst) for CO2 reduction were fabricated using a simple hydrothermal method. The designed catalysts of CuO could be in situ reduced to a metallic Cu-forming Cu/TiO2 catalyst, which could efficiently catalyze CO2 reduction to multi-carbon oxygenates (ethanol, acetone, and n-propanol) with a maximum overall faradaic efficiency of 47.4% at a potential of −0.85 V vs. reversible hydrogen electrode (RHE) in 0.5 M KHCO3 solution. The catalytic activity for CO2 electroreduction strongly depends on the CuO contents of the catalysts as-prepared, resulting in different electrochemistry surface areas. The significantly improved CO2 catalytic activity of CuO/TiO2 might be due to the strong CO2 adsorption ability.
Psychophysical Neuroeconomics of Decision Making: Nonlinear Time Perception Commonly Explains Anomalies in Temporal and Probability Discounting

Anomalies in decision over time (e.g., “hyperbolic time discounting”) and under risk (e.g., Allais paradox and hyperbolic probability discounting) have been attracting attention in behavioral and neuroeconomics. We have proposed that psychophysical time commonly explains anomalies in both decisions (Takahashi, 2011, Physica A; Takahashi et al., 2012, J Behav Econ & Finance). By adopting the q-exponential time and probability discounting models, our psychophysical and behavioral economic experiment confirmed that nonlinear distortion of psychophysical time is a common cause of the anomalies in decision both over time and under risk (i.e., intertemporal choice and decision under risk). Implications for psychophysical neuroeconomics and econophysics are discussed.
Reconstruction of sea level around the Korean Peninsula using cyclostationary empirical orthogonal functions

Abstract. Since the advent of the modern satellite altimeter era, the understanding of the sea level has increased dramatically. The satellite altimeter record, however, dates back only to the 1990s. The tide gauge record, on the other hand, extends through the 20th century but with poor spatial coverage when compared to the satellites. Many studies have been conducted to create a dataset with the spatial coverage of the satellite datasets and the temporal length of the tide gauge records by finding novel ways to combine the satellite data and tide gauge data in what is known as sea level reconstruction. However, most of the reconstructions of sea level were conducted on a global scale, leading to reduced accuracy on regional levels, especially when there are relatively few tide gauges. The seas around the Korean Peninsula are one such area with few tide gauges before 1960. In this study, new methods are proposed to reconstruct past sea level around the Korean Peninsula. Using spatial patterns obtained from a cyclostationary empirical orthogonal function decomposition of satellite data, we reconstruct sea level over the period from 1900 to 2014. Sea surface temperature data and altimeter data are used simultaneously in the reconstruction process, leading to an elimination of reliance on tide gauge data. Although we did not use the tide gauge data in the reconstruction process, the reconstructed sea level has a better agreement with the tide gauge observations in the region than previous studies that incorporated the tide gauge data. This study demonstrates a reconstruction technique that can potentially be used at regional levels, with particular emphasis on areas with poor tide gauge coverage.
Biological sludge liquor treatment at municipal wastewater treatment plants – a review

Separate biological treatment of sludge liquor, produced when dewatering digested sludge at wastewater treatment plants, can be favourable in achieving sufficient nitrogen removal. The treatment has the potential to decrease volume requirements and electrical energy and external carbon consumption. The characteristics of sludge liquor (high temperature, high ammonium concentration, low COD:N ratio) support high autotrophic growth rates. These conditions also favour nitrite accumulation, which makes a short-cut nitrification-denitrification process, i.e. nitritation-denitritation, possible, e.g. in an SBR or in a chemostat. As there is no need for external carbon dosage to achieve around 89 % nitrogen reduction in the nitritation-anammox process, it provides an interesting alternative to the nitritation-denitritation process. However, the very slow-growing anammox bacteria require long start-up periods, sufficient inoculum from other plants and extra knowledge for operators. The nitritation-anammox process can be configured in a oneor two-reactor system in floc-type suspended growth, granular or moving-bed biofilm systems. Today, the floc-based systems in SBRs are the most widely used nitritation-anammox systems in full-scale applications, possibly because most old sludge liquor treatment plants are SBRs. Furthermore, the floc-based system has the lowest electrical energy consumption and the start-up period can be very short because of the use of inoculation.
Observed Atmospheric Responses to Global SST Variability Modes: A Unified Assessment Using GEFA*

The authors present a comprehensive assessment of the observed atmospheric response to SST variability modes in a unified approach using the Generalized Equilibrium Feedback Analysis (GEFA). This study confirms a dominant atmospheric response to the tropical SST variability associated with ENSO. A further analysis shows that the classical response to ENSO consists of two parts, one responding to the tropical Pacific ENSO mode and the other to the tropical Indian Ocean monopole (IOM) mode. The Pacific ENSO generates a significant baroclinic Rossby wave response locally over the tropical Pacific as well as equivalent barotropic wave train responses remotely into the extratropics. The IOM mode forces a strongly zonally symmetric response throughout the tropics and the extratropics. Furthermore, modest atmospheric responses to other oceanic modes were identified. For example, the North Pacific SST variability mode appears to generate an equivalent barotropic warm SST-ridge response locally over the Aleutian low with significant downstream influence on the North Atlantic Oscillation (NAO), whereas the North Atlantic tripole SST mode tends to force a local response on NAO. Finally, this pilot study serves as a demonstration of the potential utility of GEFA in identifying multiple surface feedbacks to the atmosphere in the observation.
Do geographic distribution, niche property and life form explain plants' vulnerability to global change?

We modelled the future distribution in 2050 of 975 endemic plant species in southern Africa distributed among seven life forms, including new methodological insights improving the accuracy and ecological realism of predictions of global changes studies by: (i) using only endemic species as a way to capture the full realized niche of species, (ii) considering the direct impact of human pressure on landscape and biodiversity jointly with climate, and (iii) taking species' migration into account. Our analysis shows important promises for predicting the impacts of climate change in conjunction with land transformation. We have shown that the endemic flora of Southern Africa on average decreases with 41% in species richness among habitats and with 39% on species distribution range for the most optimistic scenario. We also compared the patterns of species' sensitivity with global change across life forms, using ecological and geographic characteristics of species. We demonstrate here that species and life form vulnerability to global changes can be partly explained according to species' (i) geographical distribution along climatic and biogeographic gradients, like climate anomalies, (ii) niche breadth or (iii) proximity to barrier preventing migration. Our results confirm that the sensitivity of a given species to global environmental changes depends upon its geographical distribution and ecological proprieties, and makes it possible to estimate a priori its potential sensitivity to these changes.