Miracle-dz/UniFAR-FTUs huggingface dataset:
Autophagy-Associated Proteins Control Ebola Virus Internalization Into Host Cells

Abstract Ebola virus (EBOV) enters host cells by macropinocytosis, a poorly understood process. Recent studies have suggested that cell factors involved in autophagy, an evolutionally conserved pathway leading to the lysosomal degradation of protein aggregates and organelles during cellular stress, also have roles in macropinocytosis. Here, we demonstrate that autophagy-associated proteins are required for trafficking of EBOV into the cell body. Depleting cells of beclin 1, autophagy-related protein 7, or microtubule-associated protein 1A/B light chain 3B (LC3B) abolished EBOV uptake, owing to a block in vesicle formation at the cell surface. Both LC3B-I and LC3B-II interacted with macropinocytic structures. Our work indicates that, although various forms of LC3B possess an inherent ability to associate with forming macropinosomes, LC3B-II is critical for internalization of macropinocytic vesicles and, therefore, EBOV from the cell surface.
The Enduring Appeal of ‘Learning Styles’

Individualism is the dominant value system in Western cultures and, as such, it affects the conduct of every aspect of human endeavour, including education. One of the most enduring effects on education has been the search for individual differences that can explain and predict variation in student achievement, with the hope that pedagogical methods can be designed that will capitalise on these. ‘Learning styles’ remain a popular choice for filling this role and the number of models of learning styles on offer continues to proliferate. Research conducted over the last 40 years has failed to show that individual attributes can be used to guide effective teaching practice. That ‘learning styles’ theory appeals to the underlying culture's model of the person ensures the theory's continued survival, despite the evidence against its utility. Rather than being a harmless fad, learning styles theory perpetuates the very stereotyping and harmful teaching practices it is said to combat.
Microbial Community Shifts in Response to Acid Mine Drainage Pollution Within a Natural Wetland Ecosystem

Natural wetlands are known to play an important role in pollutant remediation, such as remediating acid mine drainage (AMD) from abandoned mine sites. However, many aspects of the microbiological mechanisms underlying AMD remediation within wetlands are poorly understood, including the role and composition of associated microbial communities. We have utilized an AMD-polluted river-wetland system to perform rRNA sequence analysis of microbial communities that play a role in biogeochemical activities that are linked to water quality improvement. Next-generation sequencing of bacterial 16S rRNA gene amplicons from river and wetland sediment samples identified variation in bacterial community structure and diversity on the basis of dissolved and particulate metal concentrations, sediment metal concentrations and other water chemistry parameters (pH and conductivity), and wetland plant presence. Metabolic reconstruction analysis allowed prediction of relative abundance of microbial metabolic pathways and revealed differences between samples that cluster on the basis of the severity of AMD pollution. Global metabolic activity was predicted to be significantly higher in unpolluted and wetland sediments in contrast to polluted river sediments, indicating a metabolic stress response to AMD pollution. This is one of the first studies to explore microbial community structure dynamics within a natural wetland exposed to AMD and our findings indicate that wetland ecosystems play critical roles in maintaining diversity and metabolic structure of sediment microbial communities subject to high levels of acidity and metal pollution. Moreover, these microbial communities are predicted to be important for the remediation action of the wetland.
Helicon normal modes in Proto-MPEX

The Proto-MPEX helicon source has been operating in a high electron density ‘helicon-mode’. Establishing plasma densities and magnetic field strengths under the antenna that allow for the formation of normal modes of the fast-wave are believed to be responsible for the ‘helicon-mode’. A 2D finite-element full-wave model of the helicon antenna on Proto-MPEX is used to identify the fast-wave normal modes responsible for the steady-state electron density profile produced by the source. We also show through the simulation that in the regions of operation in which core power deposition is maximum the slow-wave does not deposit significant power besides directly under the antenna. In the case of a simulation where a normal mode is not excited significant edge power is deposited in the mirror region.
Mimic and Classify : A meta-algorithm for Conditional Independence Testing

Given independent samples generated from the joint distribution $p(\mathbf{x},\mathbf{y},\mathbf{z})$, we study the problem of Conditional Independence (CI-Testing), i.e., whether the joint equals the CI distribution $p^{CI}(\mathbf{x},\mathbf{y},\mathbf{z})= p(\mathbf{z}) p(\mathbf{y}|\mathbf{z})p(\mathbf{x}|\mathbf{z})$ or not. We cast this problem under the purview of the proposed, provable meta-algorithm, "Mimic and Classify", which is realized in two-steps: (a) Mimic the CI distribution close enough to recover the support, and (b) Classify to distinguish the joint and the CI distribution. Thus, as long as we have a good generative model and a good classifier, we potentially have a sound CI Tester. With this modular paradigm, CI Testing becomes amiable to be handled by state-of-the-art, both generative and classification methods from the modern advances in Deep Learning, which in general can handle issues related to curse of dimensionality and operation in small sample regime. We show intensive numerical experiments on synthetic and real datasets where new mimic methods such conditional GANs, Regression with Neural Nets, outperform the current best CI Testing performance in the literature. Our theoretical results provide analysis on the estimation of null distribution as well as allow for general measures, i.e., when either some of the random variables are discrete and some are continuous or when one or more of them are discrete-continuous mixtures.
Interactive Computing for Engineering Applications

This study presents an integration framework for simulation codes that supports distributed computations as well as visualisation data access on demand in order to reduce latency and enable a high degree of interactivity based on a ‘minimal invasion’ principle, i.e. with only a few code changes necessary. Furthermore, we address the problem of rigid coupling / communication patterns of simulation back-ends with visualisation front-ends which, in case of huge data advent, leads, due to long response times, to a complete loss of the connection between cause and effect.
MCTS-Minimax Hybrids with State Evaluations (Extended Abstract)

Monte-Carlo Tree Search (MCTS) has been found to show weaker play than minimax-based search in some tactical game domains. In order to combine the tactical strength of minimax and the strategic strength of MCTS, MCTS-minimax hybrids have been proposed in prior work. This article continues this line of research for the case where heuristic state evaluation functions are available. Three different approaches are considered, employing minimax in the rollout phase of MCTS, as a replacement for the rollout phase, and as a node prior to bias move selection. The latter two approaches are newly proposed. Results show that the use of enhanced minimax for computing node priors results in the strongest MCTS-minimax hybrid in the three test domains of Othello, Breakthrough, and Catch the Lion. This hybrid also outperforms enhanced minimax as a standalone player in Breakthrough, demonstrating that at least in this domain, MCTS and minimax can be combined to an algorithm stronger than its parts.
Preoperative Diagnosis and Treatment Outcomes of Incarcerated Inferiorly Displaced Flap Tear of the Medial Meniscus: Comparison between Flap Tears with and without Incarcerated Fragment

The purpose of this study was to compare preoperative variables and postoperative outcomes between flap tears with and without incarceration of inferiorly displaced fragments of medial meniscus and find distinct features of incarcerated flap tear of medial meniscus to improve preoperative diagnosis. 79 patients who underwent partial meniscectomy for flap tear of medial meniscus were classified into two groups: group U, usual flap tear without incarcerated fragment; group I, flap tear with incarcerated inferiorly displaced fragment. Patient characteristics and preoperative variables including duration of symptom aggravation were investigated. A comprehensive physical examination including joint line tenderness was performed. Magnetic resonance imaging (MRI) examination was carried out on all patients. Clinical assessments were performed with functional scores including visual analogue scale (VAS), and radiologic evaluation was conducted. Preoperative values and postoperative outcomes measured at the minimum follow-up duration of 2 years were compared between the groups. The groups did not differ significantly regarding postoperative outcomes by functional and radiological evaluations (p > 0.05). In making preoperative diagnosis, sensitivity of diagnosis based solely on MR images was significantly lower in group I (68.8%) than that in group U (90.5%) (p = 0.040). The following clinical features differed significantly between the groups: Patients in group I had higher scores in preoperative VAS (group U = 6.6; group I = 7.7) (p = 0.011) and shorter duration of symptom aggravation (group U = 13.8 weeks; group I = 3.9 weeks) (p < 0.001). Joint line tenderness was positive more distinctly in group I (100%) than in group U (74.6%). If displaced flap tear was properly resected, improved outcomes did not differ regardless of incarceration of flap tear. In diagnosing incarcerated inferiorly displaced flap tear, sensitivity of diagnosis based solely on MR images could be low. Distinguishing clinical findings would be helpful in obtaining a more appropriate diagnosis.
Linoleic Acid in Adipose Tissue and Development of Ischemic Stroke: A Danish Case‐Cohort Study

Background We investigated the association between the content of linoleic acid in adipose tissue, a biomarker of long‐term intake of linoleic acid, and the risk of ischemic stroke and its subtypes. Methods and Results The Danish cohort study Diet, Cancer and Health included 57 053 patients aged 50 to 65 years at enrollment. All participants had an adipose tissue biopsy performed at enrollment, while information on ischemic stroke during follow‐up was obtained from the Danish National Patient Register. Stroke diagnoses were all validated and classified according to the Trial of Org 10172 in Acute Stroke Treatment (TOAST) classification. Cases and a randomly drawn subcohort of 3500 patients had their fatty acid composition in adipose tissue determined by gas chromatography. Hazard ratios with 95% confidence intervals were calculated using weighted Cox proportional hazard regression. During 13.5 years of follow‐up, 1879 ischemic stroke cases were identified, for which 1755 adipose biopsies were available, while adipose biopsies were available for 3203 participants in the subcohort. When comparing the highest and the lowest quartiles of adipose tissue content of linoleic acid there was a negative association with the rate of total ischemic stroke (hazard ratio, 0.78; 95% confidence interval, 0.65–0.93) and large artery atherosclerosis (hazard ratio, 0.61; 95% confidence interval, 0.43–0.88), while there was an indication of a negative association with small‐vessel occlusion (hazard ratio, 0.87; 95% confidence interval, 0.69–1.11). There was no clear association with the rate of cardioembolism. Conclusions The content of linoleic acid in adipose tissue was inversely associated with the risk of total ischemic stroke and stroke caused by large artery atherosclerosis.
Platforms for Investigating LncRNA Functions

Prior to the sequencing of the human genome, it was presumed that most of the DNA coded for proteins. However, with the advent of next-generation sequencing, it has now been recognized that most complex eukaryotic genomes are in fact transcribed into noncoding RNAs (ncRNAs), including a family of transcripts referred to as long noncoding RNAs (lncRNAs). LncRNAs have been implicated in many biological processes ranging from housekeeping functions such as transcription to more specialized functions such as dosage compensation or genomic imprinting, among others. Interestingly, lncRNAs are not limited to a defined set of functions but can regulate varied activities such as messenger RNA degradation, translation, and protein kinetics or function as RNA decoys or scaffolds. Although still in its infancy, research into the biology of lncRNAs has demonstrated the importance of lncRNAs in development and disease. However, the specific mechanisms through which these lncRNAs act remain poorly defined. Focused research into a small number of these lncRNAs has provided important clues into the heterogeneous nature of this family of ncRNAs. Due to the complex diversity of lncRNA function, in this review, we provide an update on the platforms available for investigators to aid in the identification of lncRNA function.
Diode laser therapy in the management of chronic periodontitis – A clinico-microbiological study

Introduction Chronic periodontitis (CP) is an infectious disease resulting in inflammation of the supporting tissues of the teeth with progressive attachment loss and bone loss. This study aimed to evaluate the effect of 980-nm diode laser, as an adjunct to scaling and root planing (SRP) in the management of CP. Methodology A total of 40 systemically healthy subjects diagnosed with CP were randomly assigned into two groups G1 (SRP and sham application of laser) and G2 (SRP and laser irradiation) with equal numbers in each. The levels of Porphyromonas gingivalis (Pg) were estimated from plaque samples using real-time polymerase chain reaction. Clinical and microbiological parameters were assessed at baseline, 4–6, and 12–14 weeks posttreatment in both groups. Results A gradual reduction in the levels of Pg and improvement in clinical parameters were observed from baseline to 4–6 and 12–14 weeks in both groups. However, the comparison between groups, although clinically relevant, was not found to be statistically significant. Conclusion Although a 980-nm diode laser may not have any added benefit compared with SRP, it may emerge as an effective non-surgical treatment option in advanced periodontitis with complex inaccessible subgingival niches where comprehensive periodontal care may not be feasible.
Charge-Then-Forward: Wireless-Powered Communication for Multiuser Relay Networks

This paper studies a relay-assisted wireless-powered communication network consisting of multiple source-destination pairs and a hybrid relay node (HRN). We consider a “charge-then-forward” protocol at the HRN, in which the HRN with constant energy supply first acts as an energy transmitter to charge the sources, and then forwards the information from the sources to their destinations through time division multiple access (TDMA) or frequency division multiple access (FDMA). Processing costs at the wireless-powered sources are taken into account. Our goal is to maximize the sum rate of all transmission pairs by jointly optimizing the time, frequency, and power resources. The formulated optimization problems for both TDMA and FDMA are non-convex. For the TDMA scheme, by appropriate transformation, the problem is reformulated as a convex problem and be optimally solved. For the FDMA case, we find the asymptotically optimal solution in the dual domain. Furthermore, suboptimal algorithms are proposed for both schemes to tradeoff the complexity and performance. Finally, the simulation results validate the effectiveness of the proposed schemes.
Characterization of a cdc14 null allele in Drosophila melanogaster

ABSTRACT Cdc14 is an evolutionarily conserved serine/threonine phosphatase. Originally identified in Saccharomyces cerevisiae as a cell cycle regulator, its role in other eukaryotic organisms remains unclear. In Drosophila melanogaster, Cdc14 is encoded by a single gene, thus facilitating its study. We found that Cdc14 expression is highest in the testis of adult flies and that cdc14 null flies are viable. cdc14 null female and male flies do not display altered fertility. cdc14 null males, however, exhibit decreased sperm competitiveness. Previous studies have shown that Cdc14 plays a role in ciliogenesis during zebrafish development. In Drosophila, sensory neurons are ciliated. We found that the Drosophila cdc14 null mutants have defects in chemosensation and mechanosensation as indicated by decreased avoidance of repellant substances and decreased response to touch. In addition, we show that cdc14 null mutants have defects in lipid metabolism and resistance to starvation. These studies highlight the diversity of Cdc14 function in eukaryotes despite its structural conservation. Summary: The Cdc14 phosphatase has been implicated in cell cycle regulation in S. cerevisiae. We show that Drosophila cdc14 mutants are viable, but exhibit defects in sperm competition, chemosensation, and mechanosensation.
A collection of marginalized two-part random-effects models for analyzing medical expenditure panel data: Impact of the New Cooperative Medical Scheme on healthcare expenditures in China

Marginalized two-part random-effects generalized Gamma models have been proposed for analyzing medical expenditure panel data with excessive zeros. While these models provide marginal inference on expected healthcare expenditures, the usual unilateral specification of heteroscedastic variance on one of the two shape parameters for the generalized Gamma distribution in these models fails to encompass important special cases within the generalized gamma modeling framework. In this article, we construct marginalized two-part random-effects models that employ the log-normal, log-skew-normal, generalized Gamma, Weibull, Gamma, and inverse Gamma distributions to delineate the spectrum of nonzero healthcare expenditures in the second part of the models. These marginalized models supply additional choices for analyzing healthcare expenditure panel data with excessive zeros. We review the concepts of marginal effect and incremental effect, and summarize how these effects are estimated. For studies whose primary goal is to make inference on marginal effect or incremental effect of an independent variable with respect to healthcare expenditures, we advocate empirical mean square error criterion and information criteria to choose among candidate models. Then, we use the proposed models in an empirical analysis to examine the impact of the New Cooperative Medical Scheme on healthcare expenditures among older adults in rural China.
Convergence rates and structure of solutions of inverse problems with imperfect forward models

The goal of this paper is to further develop an approach to inverse problems with imperfect forward operators that is based on partially ordered spaces. Studying the dual problem yields useful insights into the convergence of the regularised solutions and allow us to obtain convergence rates in terms of Bregman distances—as usual in inverse problems, under an additional assumption on the exact solution called the source condition. These results are obtained for general absolutely one-homogeneous functionals. In the special case of -based regularisation we also study the structure of regularised solutions and prove convergence of their level sets to those of an exact solution. Finally, using the developed theory, we adapt the concept of debiasing to inverse problems with imperfect operators and propose an approach to pointwise error estimation in -based regularisation.
DIVISION OF THE HUMANITIES AND SOCIAL SCIENCES CALIFORNIA INSTITUTE OF TECHNOLOGY PASADENA , CALIFORNIA 91125 APPROXIMATE EXPECTED UTILITY RATIONALIZATION

We propose a new measure of deviations from expected utility, given data on economic choices under risk and uncertainty. In a revealed preference setup, and given a positive number e, we provide a characterization of the datasets whose deviation (in beliefs, utility, or perceived prices) is within e of expected utility theory. The number e can then be used as a distance to the theory. We apply our methodology to three recent large-scale experiments. Many subjects in those experiments are consistent with utility maximization, but not expected utility maximization. The correlation of our measure with demographics is also interesting, and provides new and intuitive findings on expected utility. ∗Echenique: Division of the Humanities and Social Sciences, California Institute of Technology, fede@hss.caltech.edu. Imai: Department of Economics, LMU Munich, taisuke.imai@econ.lmu. de. Saito: Division of the Humanities and Social Sciences, California Institute of Technology, saito@caltech.edu. We are very grateful to Nicola Persico, who posed questions to us that led to some of the results in this paper, and to Dan Friedman and Yves Le Yaouanq for very helpful comments on an early draft. This research is supported by Grant SES1558757 from the National Science Foundation. Echenique also thanks the NSF for its support through the grant CNS-1518941.
Oxytocin receptor signaling contributes to olfactory avoidance behavior induced by an unpleasant odorant

ABSTRACT Oxytocin (OXT) and its receptor (OXTR) regulate reproductive physiology (i.e. parturition and lactation), sociosexual behavior, learned patterns of behavior and olfactory behavior in social contexts. To characterize the function of OXTR in basic olfactory behavior, the present study compared the behavioral responses of homozygous, heterozygous and wild-type mice when these mice were confronted with an unpleasant odorant (butyric acid) in a custom-made Y-maze in the absence of a social context. Wild-type mice avoided the first encounter with the butyric acid odorant, whereas homozygous and heterozygous mice did not. However, both heterozygous and wild-type mice habituated when confronted with the butyric odorant again on the following 2 days. By contrast, homozygous mice failed to habituate and instead avoided the location of the odorant for at least 3 days. These data suggest that homozygous and heterozygous mice display abnormal olfactory responses to the presentation of an unpleasant odorant. Our studies demonstrate that OXTR plays a critical role in regulating olfactory behavior in the absence of a social context. Summary: Homozygous mice exhibited abnormal olfactory behaviors, namely failure in the acute avoidance of butyric acid and in habituation behavior, in the absence of a social context.
External progress report 13 th October 2015 Forest carbon change in Uganda 2000-2012 estimated with InSAR

A novel approach for forest carbon monitoring is demonstrated wall-to-wall for Uganda. Forest height changes over time are used to estimate change in forest carbon stock. The height changes are derived from two data sets covering Uganda, i.e. the SRTM in 2000 and Tandem-X around 2012. These heights are derived from interferometric SAR, i.e. an advanced radar sensor system. Both forest height decreases from logging and forest height increases from growth are seen over Uganda. On average the height decreased by 2.6 cm per year during 2000-2012. This decrease corresponds to an annual CO2 emission of 20.7 million t. The uncertainty of this estimate is given by a 95% confidence interval of ±8.5 million t. If this is used as a Reference Emission Level it means that if Uganda reduced its forests carbon stock change to zero, Uganda might claim a REDD credit of 105 million US$ per year from a donor country.