Miracle-dz/UniFAR-FTUs huggingface dataset:
Edge effects on fish associated with seagrass and sand patches

Seagrass beds form naturally patchy habitats with large areas of seagrass-sand inter- face, or edges. Fish were sampled at 3 sites in the temperate waters of Victoria, Australia, using small (0.5 m wide) push nets at 7 positions: unvegetated sand distant from the patch on the seaward side, the sand edge adjacent to the seagrass on the seaward side, the seagrass edge on the seaward side, the middle of the seagrass patch, the seagrass edge on the shore side of the patch, the sand adjacent to the seagrass on the shoreward side of the patch and unvegetated sand distant from the seagrass on the shoreward side. Samples were taken during the day and night, and seagrass variables were col- lected to describe structural complexity. As expected, more fish were caught in seagrass than over sand. Within seagrass, we found strong and consistent patterns at edges. Regardless of site, the total number of fish sampled was greater at the seaward seagrass edge (484 fish) than in the seagrass middle (231), but there was little difference between the seagrass middle and the shoreward seagrass edge (297). Two species of pipefish, Stigmatopora argus (193) and S. nigra (160), were much more abundant at the seaward seagrass edge than in the seagrass middle at all sites (54 and 46, respec- tively). The goby Nesogobius maccullochi showed a very different pattern. It was more abundant at the shoreward seagrass edge (127) than over the seagrass middle (31) at all sites, and tended to be more abundant over sand at the edge of seagrass patches than in any other sand positions. The weed- fish Cristiceps australis was significantly more abundant at the seaward seagrass edge (26) than in the middle (11), but only at night. Consistent patterns in fish distributions demonstrate clear edge effects both within and alongside seagrass at these sites in south-eastern Australia.
Inferring Motion Direction using Commodity Wi-Fi for Interactive Exergames

In-air interaction acts as a key enabler for ambient intelligence and augmented reality. As an increasing popular example, exergames, and the alike gesture recognition applications, have attracted extensive research in designing accurate, pervasive and low-cost user interfaces. Recent advances in wireless sensing show promise for a ubiquitous gesture-based interaction interface with Wi-Fi. In this work, we extract complete information of motion-induced Doppler shifts with only commodity Wi-Fi. The key insight is to harness antenna diversity to carefully eliminate random phase shifts while retaining relevant Doppler shifts. We further correlate Doppler shifts with motion directions, and propose a light-weight pipeline to detect, segment, and recognize motions without training. On this basis, we present WiDance, a Wi-Fi-based user interface, which we utilize to design and prototype a contactless dance-pad exergame. Experimental results in typical indoor environment demonstrate a superior performance with an accuracy of 92%, remarkably outperforming prior approaches.
Lactobacillus rhamnosus L34 Attenuates Gut Translocation-Induced Bacterial Sepsis in Murine Models of Leaky Gut

ABSTRACT Gastrointestinal (GI) bacterial translocation in sepsis is well known, but the role of Lactobacillus species probiotics is still controversial. We evaluated the therapeutic effects of Lactobacillus rhamnosus L34 in a new sepsis model of oral administration of pathogenic bacteria with GI leakage induced by either an antibiotic cocktail (ATB) and/or dextran sulfate sodium (DSS). GI leakage with ATB, DSS, and DSS plus ATB (DSS+ATB) was demonstrated by fluorescein isothiocyanate (FITC)-dextran translocation to the circulation. The administration of pathogenic bacteria, either Klebsiella pneumoniae or Salmonella enterica serovar Typhimurium, enhanced translocation. Bacteremia was demonstrated within 24 h in 50 to 88% of mice with GI leakage plus the administration of pathogenic bacteria but not with GI leakage induction alone or bacterial gavage alone. Salmonella bacteremia was found in only 16 to 29% and 0% of mice with Salmonella and Klebsiella administrations, respectively. Klebsiella bacteremia was demonstrated in 25 to 33% and 10 to 16% of mice with Klebsiella and Salmonella administrations, respectively. Lactobacillus rhamnosus L34 attenuated GI leakage in these models, as shown by the reductions of FITC-dextran gut translocation, serum interleukin-6 (IL-6) levels, bacteremia, and sepsis mortality. The reduction in the amount of fecal Salmonella bacteria with Lactobacillus treatment was demonstrated. In addition, an anti-inflammatory effect of the conditioned medium from Lactobacillus rhamnosus L34 was also demonstrated by the attenuation of cytokine production in colonic epithelial cells in vitro. In conclusion, Lactobacillus rhamnosus L34 attenuated the severity of symptoms in a murine sepsis model induced by GI leakage and the administration of pathogenic bacteria.
Eigenvector-Based Feature Extraction for Classification

This paper shows the importance of the use of class information in feature extraction for classification and inappropriateness of conventional PCA to feature extraction for classification. We consider two eigenvector-based approaches that take into account the class information. The first approach is parametric and optimizes the ratio of between-class variance to within-class variance of the transformed data. The second approach is a nonparametric modification of the first one based on local calculation of the between-class covariance matrix. We compare the two approaches with each other, with conventional PCA, and with plain nearest neighbor classification without feature extraction.
Nitrogen uptake by phytoplankton in the Atlantic sector of the Southern Ocean during late austral summer

As part of the Bonus-GoodHope (BGH) cam- paign, 15 N-labelled nitrate, ammonium and urea uptake mea- surements were made along the BGH transect from Cape Town to 60 S in late austral summer, 2008. Our results are categorised according to distinct hydrographic regions de- fined by oceanic fronts and open ocean zones. High regener- ated nitrate uptake rate in the oligotrophic Subtropical Zone (STZ) resulted in low f -ratios (f = 0.2) with nitrogen up- take being dominated by urea, which contributed up to 70 % of total nitrogen uptake. Size fractionated chlorophyll data showed that the greatest contribution (>50 %) of picophy- toplankton (<2 µm) were found in the STZ, consistent with a community based on regenerated production. The Sub- antarctic Zone (SAZ) showed the greatest total integrated ni- trogen uptake (10.3 mmol m 2 d 1 ), mainly due to enhanced nutrient supply within an anticyclonic eddy observed in this region. A decrease in the contribution of smaller size classes to the phytoplankton community was observed with increas- ing latitude, concurrent with a decrease in the contribution of regenerated production. Higher f -ratios observed in the SAZ (f = 0.49), Polar Frontal Zone (f = 0.41) and Antarc- tic Zone (f = 0.45) relative to the STZ (f = 0.24), indicate a higher contribution of NO 3 -uptake relative to total nitro- gen and potentially higher export production. High ambient regenerated nutrient concentrations are indicative of active regeneration processes throughout the transect and ascribed to late summer season sampling. Higher depth integrated
Causes of warm‐edge range limits: systematic review, proximate factors and implications for climate change

The factors that set species range limits underlie many patterns in ecology, evolution, biogeography and conservation. These factors have been the subject of several reviews, but there has been no systematic review of the causes of warm‐edge limits (low elevations and latitudes). Understanding these causes is urgent, given that the factors that set these limits might also drive extinction at warm edges as global climate changes. Many authors have suggested that warm‐edge limits are set by biotic factors (particularly competition) whereas others have stressed abiotic factors (particularly temperature). We synthesize the known causes of species' warm‐edge range limits, with emphasis on the underlying mechanisms (proximate causes).
Energy-Efficient Secure Transmission Design for the Internet of Things With an Untrusted Relay

In this paper, we investigate secure uplink transmission in a typical Internet of Things (IoT) deployment, where multiple sensors communicate with a controller via the assistance of an untrusted relay. By taking both the relay and direct links into account, three different scheduling schemes, e.g., optimal scheduling (OS) scheme, threshold-based scheduling (TS) scheme, and random scheduling (RS) scheme, are proposed to cope with the implementation complexity of user scheduling in IoT communications. For each scheduling scheme, we first derive the closed-form expressions for the secrecy outage probability and the secrecy throughput, as well as characterizing the secure energy efficiency to help facilitate an energy-efficient secure transmission design. Finally, numerical simulations demonstrate that increasing the number of sensors is an efficient method to boost the security and energy efficiency under the OS scheme. Moreover, the TS scheme provides a good tradeoff between implementation complexity and secrecy performance.
The Price Equation, Gradient Dynamics, and Continuous Trait Game Theory

A recent article convincingly nominated the Price equation as the fundamental theorem of evolution and used it as a foundation to derive several other theorems. A major section of evolutionary theory that was not addressed is that of game theory and gradient dynamics of continuous traits with frequency-dependent fitness. Deriving fundamental results in these fields under the unifying framework of the Price equation illuminates similarities and differences between approaches and allows a simple, unified view of game-theoretical and dynamic concepts. Using Taylor polynomials and the Price equation, I derive a dynamic measure of evolutionary change, a condition for singular points, the convergence stability criterion, and an alternative interpretation of evolutionary stability. Furthermore, by applying the Price equation to a multivariable Taylor polynomial, the direct fitness approach to kin selection emerges. Finally, I compare these results to the mean gradient equation of quantitative genetics and the canonical equation of adaptive dynamics.
A Comparative Study of Multi-SOM Algorithms for Determining the Optimal Number of Clusters

—The interpretation of the quality of clusters and the determination of the optimal number of clusters is still a crucial problem in clustering. We focus in this paper on multi-SOM clustering method which overcomes the problem of extracting the number of clusters from the SOM map through the use of a clustering validity index. We test the multi-SOM algorithm using real and artificial data sets with different evaluation criteria not used previously such as Davies Bouldin index, Dunn index and silhouette index. The multi-SOM algorithm is compared to k-means and Birch methods. Results show that it is more efficient than classical clustering methods.
Improved geometric variables for predicting disturbed flow at the normal carotid bifurcation

Recent work from our group has shown the primacy of the bifurcation area ratio and tortuosity in determining the amount of disturbed flow at the carotid bifurcation, believed to be a local risk factor for the carotid atherosclerosis. We have also presented fast and reliable methods of extraction of geometry from routine 3D contrast-enhanced magnetic resonance angiography, as the necessary step along the way for large-scale trials of such local risk factors. In the present study, we refine our original geometric variables to better reflect the underlying fluid mechanical principles. Flaring of the bifurcation, leading to flow separation, is defined by the maximum relative expansion of the common carotid artery (CCA), proximal to the bifurcation apex. The beneficial effect of curvature on flow inertia, via its suppression of flow separation, is now characterized by the tortuosity of CCA as it enters the flare region. Based on data from 50 normal carotid bifurcations, multiple linear regressions of these new independent geometric predictors against the dependent disturbed flow burden reveals adjusted R2 values approaching 0.5, better than the values closer to 0.3 achieved using the original variables. The excellent scan-rescan reproducibility demonstrated for our earlier geometric variables is shown to be preserved for the new definitions. Improved prediction of disturbed flow by robust and reproducible vascular geometry offers a practical pathway to large-scale studies of local risk factors in atherosclerosis.
Inflammasomes as therapeutic targets for Alzheimer's disease

Alzheimer's disease is the most common form of progressive dementia, typified initially by short term memory deficits which develop into a dramatic global cognitive decline. The classical hall marks of Alzheimer's disease include the accumulation of amyloid oligomers and fibrils, and the intracellular formation of neurofibrillary tangles of hyperphosphorylated tau. It is now clear that inflammation also plays a central role in the pathogenesis of the disease through a number of neurotoxic mechanisms. Microglia are the key immune regulators of the CNS which detect amyloidopathy through cell surface and cytosolic pattern recognition receptors (PRRs) and respond by initiating inflammation through the secretion of cytokines such as interleukin‐1β (IL‐1β). Inflammasomes, which regulate IL‐1β release, are formed following activation of cytosolic PRRs, and using genetic and pharmacological approaches, NLRP3 and NLRP1 inflammasomes have been found to be integral in pathogenic neuroinflammation in animal models of Alzheimer's disease. Therefore, the inflammasomes are very promising novel pharmacological targets which merit further research in the continued endeavor for efficacious therapeutics for Alzheimer's disease.
Genetic Diagnosis via Whole Exome Sequencing in Taiwanese Patients with Hypertriglyceridemia.

AIM Whole exome sequencing (WES) is a recently developed method for discovering rare mutations associated with hereditary disorders. However, the feasibility and utilization of this method in identifying familial hypertriglyceridemia is not well known. The purpose of the study was to identify the genetic locus that causes hypertriglyceridemia and assess its prevalence in Taiwanese subjects with hypertriglyceridemia. METHODS We performed WES among two individuals with hypertriglyceridemia and one control subject in an index family (22 members). Based on the WES findings, we extended the study to genotype 65 unrelated adult index patients with a fasting serum triglyceride level of ＞ 500 mg/dL and 125 normal controls using polymerase chain reaction. RESULTS Using WES alignment, variant calling and annotation, 15 presumptive causal variants were initially identified, including 13 cases by the autosomal dominant model and two cases by the autosomal recessive model. Only APOA5 c.553 G ＞ T (rs2075291), resulting in the amino acid mutation Gly185Cys, co-segregated well with hypertriglyceridemia in terms of autosomal recessive inheritance (homozygote TT: mean triglyceride level: 1,071 mg/dL vs non TT (GT and GG): mean triglyceride level: 118 mg/dL; p ＜ 0.001) in the index family. In the unrelated cohorts, the frequency of the TT genotype of rs2075291 was 12.3% in the hypertriglyceridemic group; however, no TT genotype was found in the control group. CONCLUSIONS Our results demonstrate that WES is feasible for identifying the genetic locus that causes hypertriglyceridemia. The TT genotype of APOA5 c.553G ＞ T acts as an important indicator of hypertriglyceridemia in patients in Taiwan.
The ten thousand

In Korean culture, the names of family members are recorded in special family books. This makes it possible to follow the distribution of Korean family names far back in history. It is shown here that these name distributions are well described by a simple null model, the random group formation (RGF) model. This model makes it possible to predict how the name distributions change and these predictions are shown to be borne out. In particular, the RGF model predicts that for married women entering a collection of family books in a certain year, the occurrence of the most common family name ‘Kim’ should be directly proportional to the total number of married women with the same proportionality constant for all the years. This prediction is also borne out to a high degree. We speculate that it reflects some inherent social stability in the Korean culture. In addition, we obtain an estimate of the total population of the Korean culture down to the year 500 AD, based on the RGF model, and find about ten thousand Kims. 4 Author to whom any correspondence should be addressed. New Journal of Physics 13 (2011) 073036 1367-2630/11/073036+12$33.00 © IOP Publishing Ltd and Deutsche Physikalische Gesellschaft
Coffee Intake Decreases Risk of Postmenopausal Breast Cancer: A Dose-Response Meta-Analysis on Prospective Cohort Studies

Aim: A dose-response meta-analysis was conducted in order to summarize the evidence from prospective cohort studies regarding the association between coffee intake and breast cancer risk. Methods: A systematic search was performed in electronic databases up to March 2017 to identify relevant studies; risk estimates were retrieved from the studies and linear and non-linear dose-response analysis modelled by restricted cubic splines was conducted. A stratified and subgroup analysis by menopausal and estrogen/progesterone receptor (ER/PR) status, smoking status and body mass index (BMI) were performed in order to detect potential confounders. Results: A total of 21 prospective studies were selected either for dose-response, the highest versus lowest category of consumption or subgroup analysis. The dose-response analysis of 13 prospective studies showed no significant association between coffee consumption and breast cancer risk in the non-linear model. However, an inverse relationship has been found when the analysis was restricted to post-menopausal women. Consumption of four cups of coffee per day was associated with a 10% reduction in postmenopausal cancer risk (relative risk, RR 0.90; 95% confidence interval, CI 0.82 to 0.99). Subgroup analyses showed consistent results for all potential confounding factors examined. Conclusions: Findings from this meta-analysis may support the hypothesis that coffee consumption is associated with decreased risk of postmenopausal breast cancer.
A Groupwise Multilinear Correspondence Optimization for 3D Faces

Multilinear face models are widely used to model the space of human faces with expressions. For databases of 3D human faces of different identities performing multiple expressions, these statistical shape models decouple identity and expression variations. To compute a high-quality multilinear face model, the quality of the registration of the database of 3D face scans used for training is essential. Meanwhile, a multilinear face model can be used as an effective prior to register 3D face scans, which are typically noisy and incomplete. Inspired by the minimum description length approach, we propose the first method to jointly optimize a multilinear model and the registration of the 3D scans used for training. Given an initial registration, our approach fully automatically improves the registration by optimizing an objective function that measures the compactness of the multilinear model, resulting in a sparse model. We choose a continuous representation for each face shape that allows to use a quasi-Newton method in parameter space for optimization. We show that our approach is computationally significantly more efficient and leads to correspondences of higher quality than existing methods based on linear statistical models. This allows us to evaluate our approach on large standard 3D face databases and in the presence of noisy initializations.
Simulation of synchronous reference frame PLL for grid synchronization using Simulink

The important problem in integration of grid and power converter is how to synchronize the inverter with the grid that is one is before connecting an inverter to the grid and other is during operation. The energy transfer between an inverter and grid is improved by proper design of synchronization techniques. The challenges associated with the design is how fast the voltage, phase angle and frequency are estimated and synchronized under ideal and non-ideal conditions. For effective estimation of above quantity, various synchronization methods have been proposed. In this paper, theory of single phase PLL is outlined and design and simulation of Synchronous Reference Frame Phase Locked Loop and the obtained simulation results for various non-ideal conditions like harmonics, voltage dip, phase jump and frequency variations are presented.
The Impact of Clostridium difficile Infection on Future Outcomes of Solid Organ Transplant Recipients

OBJECTIVE Clostridium difficile infection (CDI) is common in solid organ transplant (SOT) recipients, but few studies have examined long-term outcomes. We studied the impact of CDI after SOT on mortality and transplant organ complication-related hospitalizations (TOH). METHODS SOT recipients ≥18 years of age with at least 1 year of posttransplant data were analyzed using the MarketScan database for 2007–2014. Patients who died within one year of transplant were followed until death. Patients were grouped as early CDI (ie, first occurrence ≤90 days posttransplant), late CDI (ie, first occurrence >90 days posttransplant) and controls (ie, no CDI occurrence during follow-up). The risk of mortality or TOH after CDI was evaluated using Cox and logistic regressions, respectively. RESULTS Overall, 96 patients had early CDI, 97 patients had late CDI, and 5,913 patients were used as controls. The risk for death was significantly higher in the early CDI group than the control group (hazard ratio [HR],1.92; 95% confidence interval [CI], 1.12–3.29; P=.018); there was no significant difference between the late CDI group and the control group (HR, 0.86; 95% CI, 0.38–1.94; P=.717). Both the early CDI group (odds ratio [OR], 2.19; 95% CI, 1.45–3.31; P<.001) and the late CDI group (OR, 4.36; 95% CI, 2.84–6.71; P<.001) had higher risk for TOH than the control group. For those patients who survived >90 days posttransplant, both the early CDI group (n=89) and the late CDI group (n=97) had increased risk for death or TOH during follow-up than the control group (n=5,734). CONCLUSION Though our study could not prove causality, both early and late CDI occurrence in SOT recipients were associated with worse future outcomes than for SOT recipients without CDI. Infect Control Hosp Epidemiol 2018;39:563–570