Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional data analysis of sleeping energy expenditure

Adequate sleep is crucial during childhood for metabolic health, and physical and cognitive development. Inadequate sleep can disrupt metabolic homeostasis and alter sleeping energy expenditure (SEE). Functional data analysis methods were applied to SEE data to elucidate the population structure of SEE and to discriminate SEE between obese and non-obese children. Minute-by-minute SEE in 109 children, ages 5–18, was measured in room respiration calorimeters. A smoothing spline method was applied to the calorimetric data to extract the true smoothing function for each subject. Functional principal component analysis was used to capture the important modes of variation of the functional data and to identify differences in SEE patterns. Combinations of functional principal component analysis and classifier algorithm were used to classify SEE. Smoothing effectively removed instrumentation noise inherent in the room calorimeter data, providing more accurate data for analysis of the dynamics of SEE. SEE exhibited declining but subtly undulating patterns throughout the night. Mean SEE was markedly higher in obese than non-obese children, as expected due to their greater body mass. SEE was higher among the obese than non-obese children (p<0.01); however, the weight-adjusted mean SEE was not statistically different (p>0.1, after post hoc testing). Functional principal component scores for the first two components explained 77.8% of the variance in SEE and also differed between groups (p = 0.037). Logistic regression, support vector machine or random forest classification methods were able to distinguish weight-adjusted SEE between obese and non-obese participants with good classification rates (62–64%). Our results implicate other factors, yet to be uncovered, that affect the weight-adjusted SEE of obese and non-obese children. Functional data analysis revealed differences in the structure of SEE between obese and non-obese children that may contribute to disruption of metabolic homeostasis.
On speech coding in a perceptual domain

For speech coders which fall within the class of waveform coders, the reconstructed signal approaches the original with increasing bit rate. In such coders, the distortion criterion generally operates on the speech signal or a signal obtained by adaptive linear filtering of the speech signal. To satisfy computational and delay constraints, the distortion criterion must be reduced to a very simple approximation of the auditory system. This drawback of conventional approaches motivates a new speech coding paradigm in which the coding is performed in a domain where the single-letter squared-error criterion forms an accurate representation of perception. The new paradigm requires a model of the auditory periphery which is accurate, can be be inverted with relatively low computational effort, and which represents the signal with relatively few parameters. We develop such a model of the auditory periphery and discuss its suitability for speech coding. The results indicate that the new paradigm in general and our auditory model in particular form a promising basis for the coding of both speech and audio at low bit rates.
Pedogenesis in Mine Tailings

Although mine tailings dams are man-made deposits it is anticipated that soil forming (pedogenic) processes are active e.g. translocation and transformation. These two main groups of soil forming processes are controlled by environmental factors, also called soil forming factors; parent material, climate, topography, and biota. In the case of man made deposits, the anthropogenic factor could also be added. These factors operate and interact over time. Due to the infant condition of about all factors, the soil forming processes are also in an embriotic stage with poorly recognisable properties and diagnostic horizons, but the chemical and physical characteristics are clear and pronounced. Irrespective of the time since deposition or rehabilitation, well defined pedochemical transformation processes e.g. pH and changes in base saturation, took place in the platinum, gold, and kimberlite tailings. Other pedogenic processes such as leaching: eluviation-illuviation, oxidation and pseudo podzolization were also identified in analytical results in some of the tailings materials. Field observations also reveal other processes such as salination, crystalopedoturbation, erosion and crusting and to a lesser extent also horizon differentiation.
Spatially Distinct Seasonal Patterns and Forcings of the U.S. Warming Hole

We present a novel approach to characterize the spatiotemporal evolution of regional cooling across the eastern United States (commonly called the U.S. warming hole), by defining a spatially explicit boundary around the region of most persistent cooling. The warming hole emerges after a regime shift in 1958 where annual maximum (Tmax) and minimum (Tmin) temperatures decreased by 0.83°C and 0.46°C, respectively. The annual warming hole consists of two distinct seasonal modes, one located in the southeastern United States during winter and spring and the other in the midwestern United States during summer and autumn. A correlation analysis indicates that the seasonal modes differ in causation. Winter temperatures in the warming hole are significantly correlated with the Meridional Circulation Index, North Atlantic Oscillation, and Pacific Decadal Oscillation. However, the variability of ocean‐atmosphere circulation modes is insufficient to explain the summer temperature patterns of the warming hole.
Positive short-term effects of sheep grazing on the alpine avifauna

Abstract Grazing by large herbivores may negatively affect bird populations. This is of great conservation concern in areas with intensive sheep grazing. Sheep management varies substantially between regions, but no study has been performed in less intensively grazed systems. In a fully replicated, landscape scale experiment with three levels of sheep grazing, we tested whether the abundance and diversity of an assemblage of mountain birds were negatively affected by grazing or if grazing facilitated the bird assemblage. Density of birds was higher at high sheep density compared with low sheep density or no sheep by the fourth grazing season, while there was no clear effect on bird diversity. Thus, agricultural traditions and land use politics determining sheep density may change the density of avifauna in either positive or negative directions.
A Distributed Algorithm for Training Augmented Complex Adaptive IIR Filters

In this paper we consider the problem of decentralized (distributed) adaptive learning, where the aim of the network is to train the coefficients of a widely linear autoregressive moving average (ARMA) model by measurements collected by the nodes. Such a problem arises in many sensor network-based applications such as target tracking, fast rerouting, data reduction and data aggregation. We assume that each node of the network uses the augmented complex adaptive infinite impulse response (ACAIIR) filter as the learning rule, and nodes interact with each other under an incremental mode of cooperation. Since the proposed algorithm (incremental augmented complex IIR (IACA-IIR) algorithm) relies on the augmented complex statistics, it can be used to model both types of complex-valued signals (proper and improper signals). To evaluate the performance of the proposed algorithm, we use both synthetic and real-world complex signals in our simulations. The results exhibit superior performance of the proposed algorithm over the non-cooperative ACAIIR algorithm.
Diversity and community composition of marine mollusks fauna on a mainland island of the coast of Paraná, southern Brazil

A Ilha do Farol é uma ilha continental, no estado do Paraná, sul do Brasil. Devido à sua posição em relação ao continente, três ambientes distintos são observados nela: área de costão rochoso exposto ao mar aberto (A); área estuarina (B); área de praia arenosa (C). Considerando que as ilhas continentais são excelentes modelos de estudo que reproduzem as condições ambientais da zona costeira em menor escala, o estudo teve como objetivo levantar e pesquisar a malacofauna marinha na Ilha do Farol e comparar sua diversidade e composição. O método de amostragem foi baseado em coletas mensais nos três ambientes da ilha durante dois anos (2011-2012). O levantamento encontrou 91 espécies: 47 Gastropoda, 41 Bivalvia e três Scaphopoda. A maior riqueza e abundância de espécies prevaleceu no ambiente A. A maior equidade foi observada em B e o maior domínio em C. Houve predominância de Gastropoda e Bivalvia em A, enquanto a frequência de Scaphopoda não variou entre os ambientes. A composição de espécies das três classes variou entre as três áreas. A variação da diversidade e composição das espécies nos três ambientes podem estar relacionados com as características naturais de cada ambiente da ilha, como salinidade e ação de ondas.Palavras chave: Abundância, conservação, equitabililidade, levantamento, riqueza, Mollusca.Abstract: Farol Island is a continental island in the state of Paraná, southern Brazil. Due to its position in relation to the continent, three distinct environmental areas are observed: rocky shore area with open exposure to the sea (A) estuarine area (B); sandy beach area (C). Considering that the continental islands are excellent study models that reproduce the environmental conditions of the coastal zone in a smaller scale, the study aimed at surveying and researching the marine malacofauna on the Farol Island and comparing the diversity and shellfish composition. The sampling method was based on a monthly collection in three locations for two years (2011-2012). The survey found 91 species: 47 Gastropoda, 41 Bivalvia and three Scaphopoda. The highest abundance and species richness prevailed in environmental area A. The greatest equitability was observed in B and the highest dominance in C. There was a predominance of Gastropoda and Bivalvia in A, while the frequency of Scaphopoda did not vary among environments. The species composition of the three classes varied among the three areas. The variation of diversity and species composition in the three environments may be related to the natural characteristics of each side of the island, as salinity and wave action.Key words: Abundance, conservation, equitability, survey, richness, Mollusca.
Evidence for the Induction of Key Components of the NOTCH Signaling Pathway via Deltamethrin and Azamethiphos Treatment in the Sea Louse Caligus rogercresseyi

The extensive use of organophosphates and pyrethroids in the aquaculture industry has negatively impacted parasite sensitivity to the delousing effects of these antiparasitics, especially among sea lice species. The NOTCH signaling pathway is a positive regulator of ABC transporter subfamily C expression and plays a key role in the generation and modulation of pesticide resistance. However, little is known about the molecular mechanisms behind pesticide resistance, partly due to the lack of genomic and molecular information on the processes involved in the resistance mechanism of sea lice. Next-generation sequencing technologies provide an opportunity for rapid and cost-effective generation of genome-scale data. The present study, through RNA-seq analysis, determined that the sea louse Caligus rogercresseyi (C. rogercresseyi) specifically responds to the delousing drugs azamethiphos and deltamethrin at the transcriptomic level by differentially activating mRNA of the NOTCH signaling pathway and of ABC genes. These results suggest that frequent antiparasitic application may increase the activity of inhibitory mRNA components, thereby promoting inhibitory NOTCH output and conditions for increased resistance to delousing drugs. Moreover, data analysis underscored that key functions of NOTCH/ABC components were regulated during distinct phases of the drug response, thus indicating resistance modifications in C. rogercresseyi resulting from the frequent use of organophosphates and pyrethroids.
Systems biology Pathway analysis using random forests classification and regression

Motivation: Although numerous methods have been developed to better capture biological information from microarray data, commonly used single gene-based methods neglect interactions among genes and leave room for other novel approaches. For example, most classification and regression methods for microarray data are based on the whole set of genes and have not made use of pathway information. Pathway-based analysis in microarray studies may lead to more informative and relevant knowledge for biological researchers. Results: In this paper, we describe a pathway-based classification and regression method using Random Forests to analyze gene expression data. The proposed methods allow researchers to rank important pathways from externally available databases, discover important genes, find pathway-based outlying cases and make full use of a continuous outcome variable in the regression setting. We also compared Random Forests with other machine learning methods using several datasets and found that Random Forests classification error rates were either the lowest or the second-lowest. By combining pathway information and novel statistical methods, this procedure represents a promising computational strategy in dissecting pathways and can provide biological insight into the study of microarray data. Availability: Source code written in R is available from http:// bioinformatics.med.yale.edu/pathway-analysis/rf.htm Contact: hongyu.zhao@yale.edu Supplementary Information: Supplementary Data are available at http://bioinformatics.med.yale.edu/pathway-analysis/rf.htm
Fostering a Secure Framework for National Research and Education Network

In the context of management of network services, wide-spread deployment and security problems requiring considerable human efforts and involvement, secure and distributed management mechanism become a central concern. Considering both National and International indicators, there is a big inadequacy on secured networks in the developing countries compared to other countries. This important problem will definitely affect the collaborative efforts in research and education networking in Africa. In order to see to the improvement towards emerging networks and collaboration in Africa, the paper proposes a framework not exploited through the collaborative research and educational network by malicious interference of the shared resources. The paper tends to bridge the gap of insufficient ICT infrastructures using minimal hardware that demonstrated it can be used for building higher level security protocols. In order to tolerate the failure and provide uninterrupted services to network components, the work examined the behaviour and fault tolerance of the proposed framework.
On the Dynamics and Water Mass Transformation of a Boundary Current Connecting Alpha and Beta Oceans

A subpolar marginal sea, like the Nordic seas, is a transition zone between the temperature-stratified subtropics (the alpha ocean) and the salinity-stratified polar regions (the beta ocean). An inflow of Atlantic Water circulates these seas as a boundary current that is cooled and freshened downstream, eventually to outflow as Deep and Polar Water. Stratification in the boundary region is dominated by a thermocline over the continental slope and a halocline over the continental shelves, separating Atlantic Water from Deep and Polar Water, respectively. A conceptual model is introduced for the circulation and water mass transformation in a subpolar marginal sea to explore the potential interaction between the alpha and beta oceans. Freshwater input into the shelf regions has a slight strengthening effect on the Atlantic inflow, but more prominently impacts the water mass composition of the outflow. This impact of freshwater, characterized by enhancing Polar Water outflow and suppressing Deep Water outflow, is strongly determined by the source location of freshwater. Concretely, perturbations in upstream freshwater sources, like the Baltic freshwater outflow into the Nordic seas, have an order of magnitude larger potential to impact water mass transports than perturbations in downstream sources like the Arctic freshwater outflow. These boundary current dynamics are directly related to the qualitative stratification in transition zones and illustrate the interaction between the alpha and beta oceans.
Antiviral Efficacy and Host Immune Response Induction during Sequential Treatment with SB 9200 Followed by Entecavir in Woodchucks

SB 9200, an orally bioavailable dinucleotide, activates the viral sensor proteins, retinoic acid-inducible gene 1 (RIG-I) and nucleotide-binding oligomerization domain-containing protein 2 (NOD2) causing the induction of the interferon (IFN) signaling cascade for antiviral defense. The present study evaluated the overall antiviral response in woodchucks upon induction of immune response, first with SB 9200 followed by Entecavir (ETV) versus reduction of viral burden with ETV followed by SB 9200 immunomodulation. Woodchucks chronically infected with woodchuck hepatitis virus (WHV) were treated orally with SB 9200 (30 mg/kg/day) and ETV (0.5 mg/kg/day). Group 1 received ETV for 4 weeks followed by SB 9200 for 12 weeks. Group 2 received SB 9200 for 12 weeks followed by ETV for 4 weeks. At the end of treatment in Group 2, average reductions of 6.4 log10 in serum WHV DNA and 3.3 log10 in WHV surface antigen were observed whereas in Group 1, average reductions of 4.2 log10 and 1.1 log10 in viremia and antigenemia were noted. Both groups demonstrated marked reductions in hepatic WHV nucleic acid levels which were more pronounced in Group 2. Following treatment cessation and the 8-week follow-up, recrudescence of viral replication was observed in Group 1 while viral relapse in Group 2 was significantly delayed. The antiviral effects observed in both groups were associated with temporally different induction of IFN-α, IFN-β, and IFN-stimulated genes in blood and liver. These results suggest that the induction of host immune responses by pretreatment with SB 9200 followed by ETV resulted in antiviral efficacy that was superior to that obtained using the strategy of viral reduction with ETV followed by immunomodulation.
Coverage and Rate Analysis for Limited Information Cell Association in Stochastic-Layout Cellular Networks

The complexity and uncertainty inherent in large cellular networks make the acquisition of location and channel information of all but perhaps a few neighboring network nodes (base stations (BSs)) difficult for a given user. Therefore, a cell association policy must operate with sparse information. Thus, the serving BS is proposed to be the one that provides the highest instantaneous signal-to-interference ratio (SIR) from among all BSs providing average received signal power exceeding a predetermined minimum. This policy is evaluated for the downlink of single-tier (homogeneous) and two-tier (heterogeneous) networks, and for the latter, the key advantage of the proposed policy is its capability to enable traffic offloading. Two methods to determine the minimum average signal power are given. Coverage probabilities and average rates of mobile stations in coverage are derived, accounting for path loss, multipath fading, and random locations of BSs in each tier. Analysis is verified by Monte Carlo simulations. We observe that the instantaneous SIR and average received signal power of a few BSs are sufficient to achieve the coverage corresponding to the highest SIR association, which in general requires instantaneous SIR information of a larger subset of a network. We also observe that in a two-tier network, the effect of strong interference from high-power BSs, such as macro BSs, can be limited by proper choice of minimum average received signal power for low-power BSs.
PKBα is required for adipose differentiation of mouse embryonic fibroblasts

Protein kinase Bα (PKBα) is a key regulator of metabolism, proliferation and differentiation. We have explored the role of PKBα in adipogenesis using wild-type and PKBα-knockout mouse embryonic fibroblasts (MEFs) and show that lack of PKBα prevents MEF differentiation into adipocytes. Expression of ectopic PKBα in PKBα-deficient cells restores adipogenesis. We identified 80 genes whose expression was upregulated in wild-type MEFs during adipogenesis but whose expression was significantly reduced in PKBα-deficient MEFs under the same conditions. Significantly, the regulator of adipogenesis Krüppel-like transcription factor 15 gene expression was downregulated in PKBα-deficient MEFs but could be restored by expressing an active PKBα in the deficient cells. The level of lipocalin 2, renin 1 and receptor-activity-modifying protein 3 genes expressed by adipose cells was also decreased in PKBα-deficient MEFs, and are inhibited by LY294002 treatment during early adipocyte differentiation of 3T3-L1 cells. The results underscore an essential role for PKBα in the transcriptional program required for adipogenesis.
Filtering Nonlinear Turbulent Dynamical Systems through Conditional Gaussian Statistics

AbstractIn this paper, a general conditional Gaussian framework for filtering complex turbulent systems is introduced. Despite the conditional Gaussianity, such systems are nevertheless highly nonlinear and are able to capture the non-Gaussian features of nature. The special structure of the filter allows closed analytical formulas for updating the posterior states and is thus computationally efficient. An information-theoretic framework is developed to assess the model error in the filter estimates. Three types of applications in filtering conditional Gaussian turbulent systems with model error are illustrated. First, dyad models are utilized to illustrate that ignoring the energy-conserving nonlinear interactions in designing filters leads to significant model errors in filtering turbulent signals from nature. Then a triad (noisy Lorenz 63) model is adopted to understand the model error due to noise inflation and underdispersion. It is also utilized as a test model to demonstrate the efficiency of a nov.
Sum Multicoloring of Graphs

Scheduling dependent jobs on multiple machines is modeled by the graph multicoloring problem. In this paper we consider the problem of minimizing the average completion time of all jobs. This is formalized as the sum multicoloring problem: Given a graph and the number of colors required by each vertex, find a multicoloring which minimizes the sum of the largest colors assigned to the vertices. It reduces to the known sum coloring problem when each vertex requires exactly one color.This paper reports a comprehensive study of the sum multicoloring problem, treating three models: with and without preemptions, as well as co-scheduling where jobs cannot start while others are running. We establish a linear relation between the approximability of the maximum independent set problem and the approximability of the sum multicoloring problem in all three models, via a link to the sum coloring problem. Thus, for classes of graphs for which the independent set problem is ? -approximable, we obtain O(? )-approximations for preemptive and co-scheduling sum multicoloring and O(? logn)-approximation for nonpreemptive sum multicoloring. In addition, we give constant ratio approximations for a number of fundamental classes of graphs, including bipartite, line, bounded degree, and planar graphs.