Miracle-dz/UniFAR-FTUs huggingface dataset:
Using landscape genomics to assess local adaptation and genomic vulnerability of a perennial herb Tetrastigma hemsleyanum (Vitaceae) in subtropical China

Understanding adaptive genetic variation of plant populations and their vulnerabilities to climate change are critical to preserve biodiversity and subsequent management interventions. To this end, landscape genomics may represent a cost-efficient approach for investigating molecular signatures underlying local adaptation. Tetrastigma hemsleyanum is, in its native habitat, a widespread perennial herb of warm-temperate evergreen forest in subtropical China. Its ecological and medicinal values constitute a significant revenue for local human populations and ecosystem. Using 30,252 single nucleotide polymorphisms (SNPs) derived from reduced-representation genome sequencing in 156 samples from 24 sites, we conducted a landscape genomics study of the T. hemsleyanum to elucidate its genomic variation across multiple climate gradients and genomic vulnerability to future climate change. Multivariate methods identified that climatic variation explained more genomic variation than that of geographical distance, which implied that local adaptation to heterogeneous environment might represent an important source of genomic variation. Among these climate variables, winter precipitation was the strongest predictor of the contemporary genetic structure. F ST outlier tests and environment association analysis totally identified 275 candidate adaptive SNPs along the genetic and environmental gradients. SNP annotations of these putatively adaptive loci uncovered gene functions associated with modulating flowering time and regulating plant response to abiotic stresses, which have implications for breeding and other special agricultural aims on the basis of these selection signatures. Critically, modelling revealed that the high genomic vulnerability of our focal species via a mismatch between current and future genotype-environment relationships located in central-northern region of the T. hemsleyanum’s range, where populations require proactive management efforts such as assistant adaptation to cope with ongoing climate change. Taken together, our results provide robust evidence of local climate adaption for T. hemsleyanum and further deepen our understanding of adaptation basis of herbs in subtropical China.
Niche models as a tool to inform restoration and conservation strategies: the case of Jubaea chilensis (palm, Arecaceae) and its seed disperser Octodon degus (rodent, Octodontidae)

Introduction Biotic interactions are a crucial component of the plant regeneration process, which has been traditionally studied at more local scales, providing the tools for planning and decision-making. Studies showing the signature of species interactions at coarser spatial scales contrasting with animal-plant interactions at fine scales have been scarce. This study aimed at integrating an approach, over both biogeographic and local scales, by testing two endemic species of Mediterranean central Chile: the relict and southernmost threatened Chilean palm Jubaea chilensis (Chilean palm; Molina; Baillón) and the caviomorph scatter-hoarding rodent Octodon degus (Degu; Molina), on which this palm currently relies for seed dispersal. Methods Integrating Geographic Information Systems and Ecological Niche Modeling, the intensity of seed-rodent interactions from a territorial perspective was evaluated in the range of the palm, at a biogeographic scale, identifying areas with greater or lesser potential for seed-rodent interactions; and in local populations, incorporating a variety of environmental factors that might affect palm regeneration. Results The present results show that the rodent (Octodon degus) may play a role in Chilean palm (Jubaea chilensis) seed dispersal and seed establishment, since; Chilean palm regeneration is higher in areas where both species co-occur. At a local scale, a prominent overlap between palm seedlings and degu burrows was also found, which, allied with other abiotic variables such as altitude and topographic humidity, are crucial for successful palm regeneration. Discussion Understanding the full extent of animal-plant interactions and how they are affected by habitat perturbation in a wide range will provide essential information for the design of effective conservation and management strategies, such as rewilding based on plant species.
Whole brain surface-based morphometry and tract-based spatial statistics in migraine with aura patients: difference between pure visual and complex auras

Background The migrainous aura has different clinical phenotypes. While the various clinical differences are well-described, little is known about their neurophysiological underpinnings. To elucidate the latter, we compared white matter fiber bundles and gray matter cortical thickness between healthy controls (HC), patients with pure visual auras (MA) and patients with complex neurological auras (MA+). Methods 3T MRI data were collected between attacks from 20 patients with MA and 15 with MA+, and compared with those from 19 HCs. We analyzed white matter fiber bundles using tract-based spatial statistics (TBSS) of diffusion tensor imaging (DTI) and cortical thickness with surface-based morphometry of structural MRI data. Results Tract-based spatial statistics showed no significant difference in diffusivity maps between the three subject groups. As compared to HCs, both MA and MA+ patients had significant cortical thinning in temporal, frontal, insular, postcentral, primary and associative visual areas. In the MA group, the right high-level visual-information-processing areas, including lingual gyrus, and the Rolandic operculum were thicker than in HCs, while in the MA+ group they were thinner. Discussion These findings show that migraine with aura is associated with cortical thinning in multiple cortical areas and that the clinical heterogeneity of the aura is reflected by opposite thickness changes in high-level visual-information-processing, sensorimotor and language areas.
The relationship of diverse leisure activities with flourishing

The relationship between leisure and wellbeing is of great interest in the field of leisure studies. Keyes (2002) developed a typology of flourishing vs. languishing that encompasses subjective, psychological, and social wellbeing and is linked with physical health and functioning. However, little research has been done to show how participation in various forms of leisure might be associated with this flourishing typology. Drawing on data from community data with over 5,000 adult participants, we assessed how leisure is associated with a flourishing typology. For the present analyses, we focus on scales that assessed social leisure (e.g., socializing with friends), cultural leisure (e.g., festival attendance), home-based leisure (e.g., reading books for pleasure), physically active leisure (e.g., moderate or vigorous), and media-based leisure (e.g., time spent playing computer games or watching TV). A flourishing typology was constructed from single-item ratings on life satisfaction (subjective wellbeing), psychological well-being (self-perceptions that one’s life activities are worthwhile), and social wellbeing (sense of belonging). Flourishing was linked to greater participation in cultural, social, home-based, and physically active leisure. Greater time spent playing computer games and watching TV was associated with languishing. Thus, certain forms of leisure reflect flourishing and others are linked with languishing. The nature of these associations remains to be explored, in particular, whether leisure contributes to flourishing or if flourishing facilitates certain forms of leisure participation.
The chemical neighborhood of cells in a diffusion-limited system

Microorganisms follow us everywhere, and they will be essential to sustaining long-term human space exploration through applications such as vitamin synthesis, biomining, and more. Establishing a sustainable presence in space therefore requires that we better understand how stress due to the altered physical conditions of spaceflight affects our companion organisms. In microgravity environments such as orbital space stations, microorganisms likely experience the change in gravity primarily through changes in fluid mixing processes. Without sedimentation and density-driven convection, diffusion becomes the primary process governing the movement of growth substrates and wastes for microbial cells in suspension culture. Non-motile cells might therefore develop a substrate-deficient “zone of depletion” and experience stress due to starvation and/or waste build-up. This would in turn impact the concentration-dependent uptake rate of growth substrates and could be the cause of the altered growth rates previously observed in microorganisms in spaceflight and in ground-simulated microgravity. To better understand the extent of these concentration differences and their potential influence on substrate uptake rates, we used both an analytical solution and finite difference method to visualize concentration fields around individual cells. We modeled diffusion, using Fick’s Second Law, and nutrient uptake, using Michaelis–Menten kinetics, and assessed how that distribution varies in systems with multiple cells and varied geometries. We determined the radius of the zone of depletion, within which cells had reduced the substrate concentration by 10%, to be 5.04 mm for an individual Escherichia coli cell in the conditions we simulated. However, we saw a synergistic effect with multiple cells near each other: multiple cells in close proximity decreased the surrounding concentration by almost 95% from the initial substrate concentration. Our calculations provide researchers an inside look at suspension culture behavior in the diffusion-limited environment of microgravity at the scale of individual cells.
Distribution and sources of particulate organic matter from the anthropogenically disturbed Iyidere River to the Black Sea coast

Understanding the biogeochemical processes of particulate organic matter occurring in the river under anthropogenic disturbances and its transport to the coastal system is important for environmental resource management. In this study, we investigated the sources and distribution of particulate organic matter (POM) from the upper reaches of the Iyidere River, Türkiye, to the coastal water of the Black Sea during the fall and spring seasons using the elemental (POC and PON (%), C/N), isotopic (δ13C and δ15N), and Bayesian mixing model (MixSIAR) analysis. The POC (%), PON (%), and C/N of POM varied seasonally, indicating that the composition of POM varied with river hydrology, which varies depending on the climate of the region. Both the mixing model and the isotopic and elemental ratios of POM have revealed that the organic matter sources contributing to the riverine of POM, during the fall season, when the precipitation is severe, exhibited a uniform distribution. Heavy rain increased soil erosion along the high-slope land, and as a result, soil and bacteria were identified as the main contributor of POM along the Iyidere River. The results showed that the organic matter sources contributing to POM in the spring season showed significant spatial variation. Terrestrial vegetation, soil OM, and bacteria were the main contributors of POM depending on sites, and these contributions did not show a regular trend along the river. δ15N of POM had significant spatial variation in both seasons that was likely caused by nitrogen inputs derived from anthropogenic activities along the river. The anthropogenic activities and cascade dams causing variations in the contribution of organic matter to the POM are the likely important driving factors in this river-coastal system.
Phospholamban R14del disease: The past, the present and the future

Arrhythmogenic cardiomyopathy affects significant number of patients worldwide and is characterized by life-threatening ventricular arrhythmias and sudden cardiac death. Mutations in multiple genes with diverse functions have been reported to date including phospholamban (PLN), a key regulator of sarcoplasmic reticulum (SR) Ca2+ homeostasis and cardiac contractility. The PLN-R14del variant in specific is recognized as the cause in an increasing number of patients worldwide, and extensive investigations have enabled rapid advances towards the delineation of PLN-R14del disease pathogenesis and discovery of an effective treatment. We provide a critical overview of current knowledge on PLN-R14del disease pathophysiology, including clinical, animal model, cellular and biochemical studies, as well as diverse therapeutic approaches that are being pursued. The milestones achieved in <20 years, since the discovery of the PLN R14del mutation (2006), serve as a paradigm of international scientific collaboration and patient involvement towards finding a cure.
Effects of daily static stretch training over 6 weeks on maximal strength, muscle thickness, contraction properties, and flexibility

Purpose Static stretch training (SST) with long stretching durations seems to be sufficient to increase flexibility, maximum strength (MSt) and muscle thickness (MTh). However, changes in contraction properties and effects on muscle damage remain unclear. Consequently, the objective of the study was to investigate the effects of a 6-week self-performed SST on MSt, MTh, contractile properties, flexibility, and acute response of creatine kinase (CK) 3 days after SST. Methods Forty-four participants were divided into a control (CG, n = 22) and an intervention group (IG, n = 22), who performed a daily SST for 5 min for the lower limb muscle group. While isometric MSt was measured in leg press, MTh was examined via sonography and flexibility by functional tests. Muscle stiffness and contraction time were measured by tensiomyography on the rectus femoris. Additionally, capillary blood samples were taken in the pretest and in the first 3 days after starting SST to measure CK. Results A significant increase was found for MSt (p < 0.001, η2 = 0.195) and flexibility in all functional tests (p < 0.001, η2 > 0.310). Scheffé post hoc test did not show significant differences between the rectus femoris muscle inter- and intragroup comparisons for MTh nor for muscle stiffness and contraction time (p > 0.05, η2 < 0.100). Moreover, CK was not significantly different between IG and CG with p > 0.05, η2 = 0.032. Discussion In conclusion, the increase in MSt cannot be exclusively explained by muscular hypertrophy or the increased CK-related repair mechanism after acute stretching. Rather, neuronal adaptations have to be considered. Furthermore, daily 5-min SST over 6 weeks does not seem sufficient to change muscle stiffness or contraction time. Increases in flexibility tests could be attributed to a stretch-induced change in the muscle–tendon complex.
Discrepancies of video head impulse test results in patients with idiopathic sudden sensorineural hearing loss with vertigo and vestibular neuritis

Objective Sudden sensorineural hearing loss with vertigo (SHLV) and vestibular neuritis (VN) remain frequent causes of acute vestibular syndrome (AVS). The aim of study was to compare the results of video head impulse test (vHIT) in patients with SHLV and VN. The characteristics of high-frequency vestibule-ocular reflex (VOR) and the differences of the pathophysiological mechanisms underlying these two AVS were explored. Methods Fifty-seven SHLV patients and 31 VN patients were enrolled. vHIT was conducted at the initial presentation. The VOR gains and occurrence of corrective saccades (CSs) of anterior, horizontal, and posterior semicircular canals (SCCs) in two groups were analyzed. Pathological vHIT results refer to impaired VOR gains and presence of CSs. Results In SHLV group, pathological vHIT results was most prevalent in the posterior SCC on the affected side (30/57, 52.63%), followed by horizontal (12/57, 21.05%) and anterior SCC (3/57, 5.26%). In VN group, pathological vHIT preferentially affected horizontal SCC (24/31, 77.42%), followed by anterior (10/31, 32.26%) and posterior SCC (9/31, 29.03%) on the affected side. As for anterior and horizontal SCC on the affected side, the incidences of pathological vHIT results in VN group were significantly higher than those in SHLV group (β = 2.905, p < 0.01; β = 2.183, p < 0.001). There were no significant differences in the incidence of pathological vHIT result in posterior SCC between two groups. Conclusion Comparison of vHIT results in patients with SHLV and VN revealed discrepancies in the pattern of SCCs impairments, which may be explained by different pathophysiological mechanisms underlying these two vestibular disorders presenting as AVS.
Hurricane GPROF: An Optimized Ocean Microwave Rainfall Retrieval for Tropical Cyclones

AbstractThe Goddard profiling algorithm (GPROF) is an operational passive microwave retrieval that uses a Bayesian scheme to estimate rainfall. GPROF 2014 retrieves rainfall and hydrometeor vertical profile information based upon a database of profiles constructed to be simultaneously consistent with Tropical Rainfall Measuring Mission (TRMM) precipitation radar (PR) and TRMM Microwave Imager (TMI) observations. A small number of tropical cyclones are in the current database constructed from one year of TRMM data, resulting in the retrieval performing relatively poorly for these systems, particularly for the highest rain rates. To address this deficiency, a new database focusing specifically on hurricanes but consisting of 9 years of TRMM data is created. The new database and retrieval procedure for TMI and GMI is called Hurricane GPROF. An initial assessment of seven tropical cyclones shows that Hurricane GPROF provides a better estimate of hurricane rain rates than GPROF 2014. Hurricane GPROF rain-rate .
SIXTEEN YEARS OF ULYSSES INTERSTELLAR DUST MEASUREMENTS IN THE SOLAR SYSTEM. III. SIMULATIONS AND DATA UNVEIL NEW INSIGHTS INTO LOCAL INTERSTELLAR DUST

Interstellar dust (ISD) in the solar system was detected in situ for the first time in 1993 by the Ulysses dust detector. The study of ISD is important for understanding its role in star and solar system formation. The goal of this paper is to understand the variability in the ISD observations from the Ulysses mission by using a Monte Carlo simulation of ISD trajectories, with the final aim to constrain the ISD particle properties from simulations and the data. The paper is part of a series of three: Strub et al. describe the variations of the ISD flow from the Ulysses data set, and Krüger et al. focus on its ISD mass distribution. We describe and interpret the simulations of the ISD flow at Ulysses orbit for a wide range of particle properties and discuss four open issues in ISD research: the existence of very big ISD particles, the lack of smaller ISD particles, the shift in dust flow direction in 2005, and particle properties. We conclude that the shift in the dust flow direction in 2005 can best be explained by Lorentz force in the inner heliosphere, but that an extra filtering mechanism is needed to fit the fluxes. A time-dependent filtering in the outer regions of the heliosphere is proposed for this. Also, the high charge-to-mass ratio values found for the heavier particles after 2003 indicate that these particles are lower in density than previously assumed. This method gives new insights into the ISD properties and paves the way toward getting a complete view on the ISD from the local interstellar cloud. We conclude that in combination with the data and simulations, also impact ionization experiments are necessary using low-density dust, in order to constrain the density of the particles.
Effect of paclobutrazol and summer pruning on yield and fruit quality of apple cv. ‘Red delicious’

The study was aimed to assess the effect of different levels of paclobutrazol and summer pruning on fruit quality of apple cv. ‘Red Delicious’. The experiment was conducted at SKUAST-K, Shalimar (J&K) during 2012 and 2013 on apple trees of >15 years age, spaced at 5.49 × 5.49 m distance. The experiment was laid in a completely randomized block design with paclobutrazol spray tested at 3 concentrations (250, 500 and 750 ppm) and summer pruning at 2 timings (8 and 12 weeks after full bloom) and their combinations. Highest yield of 101.0 kg tree−1 was obtained in treatment 750 ppm paclobutrazol + 2 summer prunings in comparison to control. In addition, it significantly improved fruit size (53.15 cm), weight (188.19 g), volume (188.12 cm3), colour change (3.40 score), firmness (11.98 kg cm−2), organoleptic rating in terms of taste (3.14 score), texture (3.24 score), flavour (3.12 score) and total soluble solids (14.47°B) whereas acidity (0.23%) was reduced in comparison to control and other treatments during both the years.
A unified bar–bend theory of river meanders

A two-dimensional model of flow and bed topography in sinuous channels with erodible boundaries is developed and applied in order to investigate the mechanism of meander initiation. By reexamining the problem recently tackled by Ikeda, Parker & Sawai (1981), a previously undiscovered ‘resonance’ phenomenon is detected which occurs when the values of the relevant parameters fall within a neighbourhood of certain critical values. It is suggested that the above resonance controls the bend growth, and it is shown that it is connected in some sense with bar instability. In fact, by performing a linear stability analysis of flow in straight erodible channels, resonant flow in sinuous channels is shown to occur when curvature ‘forces’ a ‘natural’ solution represented by approximately steady perturbations of the alternate bar type. A comparison with experimental observations appears to support the idea that resonance is associated with meander formation.
Studies in History and Philosophy of Modern Physics

Recently-discovered manuscripts throw new light on Poincare's discovery of the Lorentz group, and his ether-based interpretation of the Lorentz transformation. At first, Poincare postulated longitudinal contraction of bodies in motion with respect to the ether, and ignored time deformation. In April, 1909, he acknowledged time deformation due to translation, obtaining thereby a theory of relativity more compatible with those of Einstein and Minkowski.
Asymptotic results in gamma kernel regression

Abstract Based on the Gamma kernel density estimation procedure, this article constructs a nonparametric kernel estimate for the regression functions when the covariate are nonnegative. Asymptotic normality and uniform almost sure convergence results for the new estimator are systematically studied, and the finite performance of the proposed estimate is discussed via a simulation study and a comparison study with an existing method. Finally, the proposed estimation procedure is applied to the Geyser data set.