Miracle-dz/UniFAR-FTUs huggingface dataset:
Interpopulation variation in mating system and late‐stage inbreeding depression in Magnolia stellata

Inbreeding has the potential to cause evolutionary changes in populations, although these changes are likely to drive populations to extinction through inbreeding depression and reductions in genetic diversity. We investigated the mating system and late‐stage inbreeding depression (δ) in 10 populations of Magnolia stellata using nine microsatellite markers and evaluated the effects of population size and the degree of population isolation through inbreeding and inbreeding depression on the persistence of populations. The outcrossing rates were very similar (~0.7) among populations, but the correlations of paternity, fractions of biparental inbreeding and inbreeding coefficients at the seed stage (FS) varied among populations, suggesting that the level of outcrossing was similar among populations, while the quality of it was not. A significant negative correlation was detected between FS and population size. The average value of δ was 0.709, and the values in six of the 10 populations were significant. The values of δ differed among populations, although clear relationships with population size and the degree of population isolation were not detected. However, in one population, which was very small and located in the edge of the species’ range, we obtained a very low value of δ (–0.096), which may be indicative of purging or the fixation of deleterious alleles. Existing M. stellata populations that are small (and thus might be expected to have higher frequencies of inbreeding) and have large values of δ may be in danger of declining, even if the populations are located within the central region of the species’ range.
A Toolbox to Explore the Interaction of Adaptive Jamming and Anti-Jamming (demo)

Jamming has long been a problem in wireless communications. Recently, adaptive jamming and anti-jamming techniques have been proposed which aim to use feedback to better perform their task. For an anti-jamming receiver this means detecting jamming and adapting its protocol appropriately. For a jammer this means using feedback from the legitimate system to design a high-impact, low-power, hard-to-detect attack. In this work we introduce a toolbox to allow users to tests the performance of adaptive jamming and anti-jamming on the USRP2 radio platform. These test provide an important function by letting developers understand how well new protocols work against evolving jamming technologies.
Roundtrip Ticket for Secretory IgA: Role in Mucosal Homeostasis?1

An important activity of mucosal surfaces is the production of Ab referred to as secretory IgA (SIgA). SIgA serves as the first line of defense against microorganisms through a mechanism called immune exclusion. In addition, SIgA adheres selectively to M cells in intestinal Peyer’s patches, thus mediating the transepithelial transport of the Ab molecule from the intestinal lumen to underlying gut-associated organized lymphoid tissue. In Peyer’s patches, SIgA binds and is internalized by dendritic cells in the subepithelial dome region. When used as carrier for Ags in oral immunization, SIgA induces mucosal and systemic responses associated with production of anti-inflammatory cytokines and limits activation of dendritic cells. In terms of humoral immunity at mucosal surfaces, SIgA appears thus to combine properties of a neutralizing agent (immune exclusion) and of a mucosal immunopotentiator inducing effector immune responses in a noninflammatory context favorable to preserve local homeostasis of the gastrointestinal tract.
Further observations on the fine structure of freeze-cleaved tight junctions.

The fine structure of freeze-cleaved tight junctions has been examined in high-resolution replicas of rat small intestine. By carefully comparing the changes in the surface topography of the cleavage faces of specimens, which, before freezing, were either prefixed with glutaraldehyde and then infiltrated with glycerol, infiltrated with glycerol alone, or infiltrated with glycerol and then fixed with glutaraldehyde, a more precise definition of the tight-junction architecture at the supramolecular level has become possible. The results of this analysis suggest that the bilayer membranes contributing to a tight junction are held together along inter-connected lines of attachment that are arranged in the form of a continuous band-like mesh-work. Each line consists of 2 parallel rows, one in each membrane, of closely spaced adhesion particles. The sensitivity of these particles to glutaraldehyde and their cleaving behaviour under different experimental conditions indicate that they represent globular proteins which bridge the width of the adjoining membranes and are linked together in the plane of the inter-cellular space. Thus, the morphology of a tight-junction seal resembles a modified zipper with the locking units making head to head contact. Similarly, the presence of many open-ended sealing elements between crypt cells has been interpreted as suggesting that the formation of tight-junction seals could resemble a ‘zippering-up’ process. At the juncture of 3 cells the tight-junction meshwork is both modified and extended basally to produce a characteristic pattern. In the central area of such a triple junction, 3 parallel and very closely spaced vertical seals have been resolved, each joining a pair of adjacent plasma membranes. Small, regularly spaced, cross-bridging elements interlink pairs of central seals within the plane of each membrane. At different levels each individual central seal may further give rise to horizontal sealing elements which connect in a ladder-like fashion either to the major network or to vertical elements positioned at greater distances from the central axis. Evidence is presented suggesting that fragments of tight junctions can be internalized and broken down in lysosome-like vesicles.
Definitive Upfront Stereotactic Ablative Radiotherapy Combined with Image-Guided, Intensity Modulated Radiotherapy (IG-IMRT) or IG-IMRT Alone for Locally Advanced Non-Small Cell Lung Cancer

Background Image-guided (IG) intensity-modulated radiotherapy (IMRT) enables maximal tumor margin reduction for the sparing of organs at risk (OARs) when used to treat locally advanced non-small cell lung cancer (NSCLC) with definitive chemo-radiation. It also allows for the incorporation of stereotactic ablative radiotherapy (SABR) into the treatment regimen. Here, we describe our initial experience in combining definitive upfront SABR to the primary lesion with chemo-radiation delivered with conventionally fractionated IG-IMRT to the remaining regional disease; along with clinical outcome following chemo-radiation with conventionally fractionated IG-IMRT alone in the treatment of locally advanced NSCLC. Methods The clinical outcome of 29 patients with locally advanced NSCLC who underwent conventionally fractionated IG-IMRT, or definitive upfront SABR followed by IG-IMRT combined with chemotherapy (induction, concurrent, or both) was retrospectively reviewed. Results After a median follow up of 23.7 months, the median overall survival (OS) and progression-free survival (PFS) were 19.8 and 11.3 months, respectively. The 2 year local, regional, and distant control was 60%, 62%, and 38%, respectively. No local failure was observed in 3 patients following SABR + IG-IMRT while 6/26 patients failed locally following IG-IMRT alone. SABR + IG-IMRT was well tolerated. No ≥ grade 3 radiation-related toxicity was observed. Conclusion Definitive upfront SABR followed by IG-IMRT in selected patients with locally advanced NSCLC warrants further investigation in future clinical trials, while chemo-radiation with IG-IMRT alone was well tolerated.
Modeling the Observed Microwave Emission from Shallow Multi-Layer Tundra Snow Using DMRT-ML

The observed brightness temperatures (Tb) at 37 GHz from typical moderate density dry snow in mid-latitudes decreases with increasing snow water equivalent (SWE) due to volume scattering of the ground emissions by the overlying snow. At a certain point, however, as SWE increases, the emission from the snowpack offsets the scattering of the sub-nivean emission. In tundra snow, the Tb slope reversal occurs at shallower snow thicknesses. While it has been postulated that the inflection point in the seasonal time series of observed Tb V 37 GHz of tundra snow is controlled by the formation of a thick wind slab layer, the simulation of this effect has yet to be confirmed. Therefore, the Dense Media Radiative Transfer Theory for Multi Layered (DMRT-ML) snowpack is used to predict the passive microwave response from airborne observations over shallow, dense, slab-layered tundra snow. Airborne radiometer observations coordinated with ground-based in situ snow measurements were acquired in the Canadian high Arctic near Eureka, NT, in April 2011. The DMRT-ML was parameterized with the in situ snow measurements using a two-layer snowpack and run in two configurations: a depth hoar and a wind slab dominated pack. With these two configurations, the calibrated DMRT-ML successfully predicted the Tb V 37 GHz response (R correlation of 0.83) when compared with the observed airborne Tb footprints containing snow pits measurements. Using this calibrated model, the DMRT-ML was applied to the whole study region. At the satellite observation scale, observations from the Advanced Microwave Scanning Radiometer-Earth Observing System (AMSR-E) over the study area reflected seasonal differences between Tb V 37 GHz and Tb V 19 GHz that supports the hypothesis of the development of an early season volume scattering depth hoar layer, followed by the growth of the late season emission-dominated wind slab layer. This research highlights the necessity to consider the two-part emission characteristics of a slab-dominated tundra snowpack at 37 GHz Tb.
Measuring the Value of Information in NuVal Shelf Nutrition Label

July 2017 Abstract The objective of this study is to estimate the value of information provided by the NuVal shelf nutrition label―a prominent example of a new interpretive approach to front-of-package nutrition labeling that provides a multiple-level nutrition symbol. The rollout of NuVal at a supermarket in a Midwest town allowed us to estimate a mixed logit demand model for yogurt using household and barcode-level scanner data. We found the NuVal label promoted purchases of healthier yogurts. The average value of NuVal information in the yogurt category is estimated to be about 3% of total expenditures on yogurt. There is evidence suggesting that households who made less use of conventional nutrition labels prior to NuVal rollout may stand to benefit more from NuVal labels. Overall, our results indicate that there is a significant willingness to pay, on the part of consumers, for a universal adoption of an interpretive multiple-level shelf or front-of-package nutrition symbol.
Successful Aging: A Cross-National Study of Subjective Well-Being Later in Life

This paper aims to identify and analyze the life course and contextual factors that influence the subjective well-being (SWB) of individuals over 60 years of age. Our research is based on the results of the 5th wave of the World Value Survey. We have investigated the level of SWB for older people at both the individual and country level. The results of our research demonstrate that the strongest predictors of SWB later in life are satisfaction with one’s financial state, health, and a sense of control, meaning the belief that individuals are in control of their lives. Besides this, the important factors of SWB for older people are the ability to establish and maintain friendly relations with other people, such as family members and friends, and to invest their own resources in positive emotions and important relationships for themselves. Older people from ex-communist countries have the lowest level of SWB. Older people from English-speaking countries, such as the United States, Canada, New Zealand, and the United Kingdom, have, by contrast, the highest level of SWB. These results suggest that the degree of modernization influences SWB levels very strongly. For older people, the country in which they live, the level of democracy, GDP per capita, freedom, and tolerance are very important. In contemporary society, the later period of life is a time for self-realization, new activities, new leisure, and new emotions. If society understands the needs of older people and provides opportunities for their realization, society can overcome the challenges caused by population aging. Only then can we discuss the concept of ‘successful aging’
PCA-based walking engine using motion capture data

This paper aims to propose a novel approach to generate new generic human walking patterns using motion-captured data, leading to a real-time engine intended for virtual humans animation. The method applies the PCA (principal component analysis) technique on motion data acquired by an optical system to yield a reduced dimension space where not only interpolation, but also extrapolation are possible, controlled by quantitative speed parameter values. Moreover, with proper normalization and time warping methods, the generic presented engine can produce walking motions with continuously varying human height and speed with real-time reactivity
Exercising High-Level Parallel Programming on Streams: A Systems Biology Use Case

The stochastic modelling of biological systems, coupled with Monte Carlo simulation of models, is an increasingly popular technique in Bioinformatics. The simulation-analysis workflow may result into a computationally expensive task reducing the interactivity required in the model tuning. In this work, we advocate high-level software design as a vehicle for building efficient and portable parallel simulators for a variety of platforms, ranging from multi-core platforms to GPGPUs to cloud. In particular, the Calculus of Wrapped Compartments (CWC) parallel simulator for systems biology equipped with on-line mining of results, which is designed according to the Fast Flow pattern-based approach, is discussed as a running example. In this work, the CWC simulator is used as a paradigmatic example of a complex C++ application where the quality of results is correlated with both computation and I/O bounds, and where high-quality results might turn into big data. The Fast Flow parallel programming framework, which advocates C++ pattern-based parallel programming makes it possible to develop portable parallel code without relinquish neither run-time efficiency nor performance tuning opportunities. Performance and effectiveness of the approach are validated on a variety of platforms, inter-alia cache-coherent multi-cores, cluster of multi-core (Ethernet and Infiniband) and the Amazon Elastic Compute Cloud.
Functional Genomics Analysis of Singapore Grouper Iridovirus: Complete Sequence Determination and Proteomic Analysis

ABSTRACT Here we report the complete genome sequence of Singapore grouper iridovirus (SGIV). Sequencing of the random shotgun and restriction endonuclease genomic libraries showed that the entire SGIV genome consists of 140,131 nucleotide bp. One hundred sixty-two open reading frames (ORFs) from the sense and antisense DNA strands, coding for lengths varying from 41 to 1,268 amino acids, were identified. Computer-assisted analyses of the deduced amino acid sequences revealed that 77 of the ORFs exhibited homologies to known virus genes, 23 of which matched functional iridovirus proteins. Forty-two putative conserved domains or signatures were detected in the National Center for Biotechnology Information CD-Search database and PROSITE database. An assortment of enzyme activities involved in DNA replication, transcription, nucleotide metabolism, cell signaling, etc., were identified. Viruses were cultured on a cell line derived from the embryonated egg of the grouper Epinephelus tauvina, isolated, and purified by sucrose gradient ultracentrifugation. The protein extract from the purified virions was analyzed by polyacrylamide gel electrophoresis followed by in-gel digestion of protein bands. Matrix-assisted laser desorption ionization-time of flight mass spectrometry and database searching led to identification of 26 proteins. Twenty of these represented novel or previously unidentified genes, which were further confirmed by reverse transcription-PCR (RT-PCR) and DNA sequencing of their respective RT-PCR products.
Soluble leptin receptor represents the main leptin binding activity in human blood.

In human blood leptin circulates both free and bound to high molecular weight proteins. Hypothesising that these proteins may modulate ligand bioavailability and bioactivity of leptin, we investigated their molecular nature. Therefore, leptin binding activity was partially purified from human plasma using a leptin affinity column. Subjecting this preparation to size exclusion chromatography (SEC) we observed a coelution of leptin binding activity with levels of the soluble leptin receptor (sOB-R) determined by a newly developed ligand immunofunctional assay. In Western blot analysis the partially purified leptin binding activity exhibited sOB-R immunoreactivity in two bands of 110 and 140 kD. Following N-deglycosylation these bands were replaced by two bands with the molecular weight of 90 and 60 kD, suggesting two isoforms which are capable of leptin binding, as determined by cross-linking. Furthermore, different ratios of these isoforms were detectable in fractions of the leptin binding activity after separation by SEC. These findings indicate the formation of heterodimers and homodimers complexed with and without leptin. As the two sOB-R bands from Western blot analysis correspond to only two specific bands in cross-linking experiments with 125l-leptin, the role of both isoforms as leptin binding proteins appears to be exclusive. Therefore, our results indicate that sOB-R is the major leptin binding protein in the circulating human blood.
Perspective: Gluten-Free Products for Patients with Celiac Disease Should Not Contain Trace Levels.

Peter Makovicky, Pavol Makovicky, Iulia Lupan, Gabriel Samasca,* Genel Sur, and Hugh James Freeman Czech Centre for Phenogenomics and Laboratory of Transgenic Models of Diseases, Division BIOCEV, Institute of Molecular Genetics of the AS CR, Vestec, Czech Republic; Department of Biology, Faculty of Education, Janos Selye University, Komarno, Slovak Republic; Interdisciplinary Research Institute on Bio-Nano-Science, Cluj-Napoca, Romania; Departments of Immunology and Pediatrics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania; and Department of Medicine (Gastroenterology), Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
Exploitable Redirects on the Web: Identification, Prevalence, and Defense

Web sites on the Internet often use redirection. Unfortunately, without additional security, many of the redirection links can be manipulated and abused to mask phishing attacks. In this paper, we prescribe a set of heuristics to identify redirects that can be exploited. Using these heuristics, we examine the prevalence of exploitable redirects present in today's Web. Finally, we propose techniques for Web servers to secure their redirects and for clients to protect themselves from being misled by manipulated redirects.
Randomised controlled trial of early detection and cognitive therapy for preventing transition to psychosis in high-risk individuals

Background There is interest in the possibility of indicated prevention of psychosis. There is a strong case for using psychological approaches to prevent transition to psychosis in high-risk patients. Aims To identify individuals at high risk of transition to psychosis, and psychological characteristics relevant to the development of psychosis in this group. Method The design of a randomised controlled trial of cognitive therapy for the prevention of psychosis in people at high risk (meeting operational criteria of brief or attenuated psychotic symptoms, or first-degree family history with functional decline) is outlined. The first patients recruited are compared with non-patient samples on cognitive and personality factors; an interim analysis of transition rate is reported. Results Cases (n=31) were recruited mainly from primary care. Of the 23 high-risk patients monitored for 6–12 months, 5 (22%) made the transition to psychosis. The high-risk group scored significantly higher than non-patients on measures of schizotypy, metacognitive beliefs and dysfunctional self-schemas (sociotropy). Conclusions The findings validate the methods of identifying individuals at high risk of experiencing a psychotic episode. Compared with non-patient controls, the cases showed dysfunctional metacognitive beliefs and self-schemas.
Generalized list colourings of graphs

1. Introduction and NotationWe consider ﬁnite undirected graphs without loops and multiple edges. Thevertex set of a graph G is denoted by V(G) and the edge set by E(G). Thenotation H ⊆ G means that H is a subgraph of G. The vertex induced (wewill say brieﬂy: induced) subgraph H of G is denoted by H ≤G. We say thatG contains H whenever G contains a subgraph isomorphic to H. In general,we follow the notation and terminology of [5]. Let I denote the set of all mutually nonisomorphic graphs. If P is anonempty subset of I, then P will also denote the property that a graph is
Measuring Coverage in MNCH: Evaluation of Community-Based Treatment of Childhood Illnesses through Household Surveys

Community case management (CCM) is a strategy for training and supporting workers at the community level to provide treatment for the three major childhood diseases—diarrhea, fever (indicative of malaria), and pneumonia—as a complement to facility-based care. Many low- and middle-income countries are now implementing CCM and need to evaluate whether adoption of the strategy is associated with increases in treatment coverage. In this review, we assess the extent to which large-scale, national household surveys can serve as sources of baseline data for evaluating trends in community-based treatment coverage for childhood illnesses. Our examination of the questionnaires used in Demographic and Health Surveys (DHS) and Multiple Indicator Cluster Surveys (MICS) conducted between 2005 and 2010 in five sub-Saharan African countries shows that questions on care seeking that included a locally adapted option for a community-based provider were present in all the DHS surveys and in some MICS surveys. Most of the surveys also assessed whether appropriate treatments were available, but only one survey collected information on the place of treatment for all three illnesses. This absence of baseline data on treatment source in household surveys will limit efforts to evaluate the effects of the introduction of CCM strategies in the study countries. We recommend alternative analysis plans for assessing CCM programs using household survey data that depend on baseline data availability and on the timing of CCM policy implementation.
Camera self-calibration for sequential Bayesian structure from motion

Computer vision researchers have proved the feasibility of camera self-calibration —the estimation of a camera's internal parameters from an image sequence without any known scene structure. Various self-calibration algorithms have been published. Nevertheless, all of the recent sequential approaches to 3D structure and motion estimation from image sequences which have arisen in robotics and aim at real-time operation (often classed as visual SLAM or visual odometry) have relied on pre-calibrated cameras and have not attempted online calibration.