Miracle-dz/UniFAR-FTUs huggingface dataset:
Phenomics and Genomics Reveal Adaptation of Virgibacillus dokdonensis Strain 21D to Its Origin of Isolation, the Seawater-Brine Interface of the Mediterranean Sea Deep Hypersaline Anoxic Basin Discovery

The adaptation of sporeformers to extreme environmental conditions is frequently questioned due to their capacity to produce highly resistant endospores that are considered as resting contaminants, not representing populations adapted to the system. In this work, in order to gain a better understanding of bacterial adaptation to extreme habitats, we investigated the phenotypic and genomic characteristics of the halophile Virgibacillus sp. 21D isolated from the seawater-brine interface (SBI) of the MgCl2-saturated deep hypersaline anoxic basin Discovery located in the Eastern Mediterranean Sea. Vegetative cells of strain 21D showed the ability to grow in the presence of high concentrations of MgCl2, such as 14.28% corresponding to 1.5 M. Biolog phenotype MicroArray (PM) was adopted to investigate the strain phenotype, with reference to carbon energy utilization and osmotic tolerance. The strain was able to metabolize only 8.4% of 190 carbon sources provided in the PM1 and PM2 plates, mainly carbohydrates, in accordance with the low availability of nutrients in its habitat of origin. By using in silico DNA-DNA hybridization the analysis of strain 21D genome, assembled in one circular contig, revealed that the strain belongs to the species Virgibacillus dokdonensis. The genome presented compatible solute-based osmoadaptation traits, including genes encoding for osmotically activated glycine-betaine/carnitine/choline ABC transporters, as well as ectoine synthase enzymes. Osmoadaptation of the strain was then confirmed with phenotypic assays by using the osmolyte PM9 Biolog plate and growth experiments. Furthermore, the neutral isoelectric point of the reconstructed proteome suggested that the strain osmoadaptation was mainly mediated by compatible solutes. The presence of genes involved in iron acquisition and metabolism indicated that osmoadaptation was tailored to the iron-depleted saline waters of the Discovery SBI. Overall, both phenomics and genomics highlighted the potential capability of V. dokdonensis 21D vegetative cells to adapt to the environmental conditions in Discovery SBI.
Antithrombotic/Antiplatelet Treatment in Transcatheter Structural Cardiac Interventions—PFO/ASD/LAA Occluder and Interatrial Shunt Devices

Transcatheter interventions enable safe and efficient treatment of various structural heart diseases. However, therapy does not finished with the end of the procedure. Device thrombosis is a possible serious complication. Therefore, careful patient management should include optimal antiplatelet or antithrombotic medication to enhance safe and complete endothelial coverage of the implanted device. In case of thrombus formation careful diagnostic evaluation and prompt treatment is crucial. This paper provides an update to current knowledge and understanding of prevention and management of device related thrombosis.
Asymptotic Guarantees for Learning Generative Models with the Sliced-Wasserstein Distance

Minimum expected distance estimation (MEDE) algorithms have been widely used for probabilistic models with intractable likelihood functions and they have become increasingly popular due to their use in implicit generative modeling (e.g. Wasserstein generative adversarial networks, Wasserstein autoencoders). Emerging from computational optimal transport, the Sliced-Wasserstein (SW) distance has become a popular choice in MEDE thanks to its simplicity and computational benefits. While several studies have reported empirical success on generative modeling with SW, the theoretical properties of such estimators have not yet been established. In this study, we investigate the asymptotic properties of estimators that are obtained by minimizing SW. We first show that convergence in SW implies weak convergence of probability measures in general Wasserstein spaces. Then we show that estimators obtained by minimizing SW (and also an approximate version of SW) are asymptotically consistent. We finally prove a central limit theorem, which characterizes the asymptotic distribution of the estimators and establish a convergence rate of $\sqrt{n}$, where $n$ denotes the number of observed data points. We illustrate the validity of our theory on both synthetic data and neural networks.
Calicivirus RNA-Dependent RNA Polymerases: Evolution, Structure, Protein Dynamics, and Function

The Caliciviridae are viruses with a positive-sense, single-stranded RNA genome that is packaged into an icosahedral, environmentally stable protein capsid. The family contains five genera (Norovirus, Nebovirus, Sapovirus, Lagovirus, and Vesivirus) that infect vertebrates including amphibians, reptiles, birds, and mammals. The RNA-dependent RNA polymerase (RdRp) replicates the genome of RNA viruses and can speed up evolution due to its error-prone nature. Studying calicivirus RdRps in the context of genuine virus replication is often hampered by a lack of suitable model systems. Enteric caliciviruses and RHDV in particular are notoriously difficult to propagate in cell culture; therefore, molecular studies of replication mechanisms are challenging. Nevertheless, research on recombinant proteins has revealed several unexpected characteristics of calicivirus RdRps. For example, the RdRps of RHDV and related lagoviruses possess the ability to expose a hydrophobic motif, to rearrange Golgi membranes, and to copy RNA at unusually high temperatures. This review is focused on the structural dynamics, biochemical properties, kinetics, and putative interaction partners of these RdRps. In addition, we discuss the possible existence of a conserved but as yet undescribed structural element that is shared amongst the RdRps of all caliciviruses.
Downregulation of Orco and 5-HTT Alters Nestmate Discrimination in the Subterranean Termite Odontotermes formosanus (Shiraki)

Nestmate discrimination allows social insects to recognize nestmates from non-nestmates using colony-specific chemosensory cues, which typically evoke aggressive behavior toward non-nestmates. Functional analysis of genes associated with nestmate discrimination has been primarily focused on inter-colonial discrimination in Hymenopterans, and parallel studies in termites, however, are grossly lacking. To fill this gap, we investigated the role of two genes, Orco and 5-HTT, associated with chemosensation and neurotransmission respectively, in nestmate discrimination in a highly eusocial subterranean termite, Odontotermes formosanus (Shiraki). We hypothesized that knocking down of these genes will compromise the nestmate recognition and lead to the antagonistic behavior. To test this hypothesis, we carried out (1) an in vivo RNAi to suppress the expression of Orco and 5-HTT, respectively, (2) a validation study to examine the knockdown efficiency, and finally, (3) a behavioral assay to document the phenotypic impacts/behavioral consequences. As expected, the suppression of either of these two genes elevated stress level (e.g., vibrations and retreats), and led to aggressive behaviors (e.g., biting) in O. formosanus workers toward their nestmates, suggesting both Orco and 5-HTT can modulate nestmate discrimination in termites. This research links chemosensation and neurotransmission with nestmate discrimination at the genetic basis, and lays the foundation for functional analyses of nestmate discrimination in termites.
Modeling the Relationships Between Metacognitive Beliefs, Attention Control and Symptoms in Children With and Without Anxiety Disorders: A Test of the S-REF Model

In the metacognitive model, attentional control and metacognitive beliefs are key transdiagnostic mechanisms contributing to psychological disorder. The aim of the current study was to investigate the relative contribution of these mechanisms to symptoms of anxiety and depression in children with anxiety disorders and in non-clinical controls. In a cross-sectional design, 351 children (169 children diagnosed with a primary anxiety disorder and 182 community children) between 7 and 14 years of age completed self-report measures of symptoms, attention control and metacognitive beliefs. Clinically anxious children reported significantly higher levels of anxiety, lower levels of attention control and higher levels of maladaptive metacognitive beliefs than controls. Across groups, lower attention control and higher levels of maladaptive metacognitive beliefs were associated with stronger symptoms, and metacognitions were negatively associated with attention control. Domains of attention control and metacognitions explained unique variance in symptoms when these were entered in the same model within groups, and an interaction effect between metacognitions and attention control was found in the community group that explained additional variance in symptoms. In conclusion, the findings are consistent with predictions of the metacognitive model; metacognitive beliefs and individual differences in self-report attention control both contributed to psychological dysfunction in children and metacognitive beliefs appeared to be the strongest factor.
Tests of acoustic scale shifts in halo-based mock galaxy catalogues

We utilize mock catalogues from high-accuracy cosmological N-body simulations to quantify shifts in the recovery of the acoustic scale that could potentially result from galaxy clustering bias. The relationship between galaxies and dark matter haloes presents a complicated source of systematic errors in modern redshift surveys, particularly when aiming to make cosmological measurements to sub-per cent precision. Apart from a scalar, linear bias parameter accounting for the density contrast ratio between matter tracers and the true matter distribution, other types of galaxy bias, such as assembly and velocity biases, may also significantly alter clustering signals from small to large scales. We create mocks based on generalized halo occupation populations of 36 periodic boxes from the abacus cosmosrelease, and test various biased models along with an unbiased base case in a total volume of $48 \, h^{-3} \, {\rm Gpc}^{3}$. Two reconstruction methods are applied to galaxy samples and the apparent acoustic scale is derived by fitting the two-point correlation function multipoles. With respect to the baseline, we find a 0.3 per cent shift in the line-of-sight acoustic scale for one variation in the satellite galaxy population, and we find a 0.7 per cent shift for an extreme level of velocity bias of the central galaxies. All other bias models are consistent with zero shift at the 0.2 per cent level after reconstruction. We note that the bias models explored are relatively large variations, producing sizeable and likely distinguishable changes in small-scale clustering, the modelling of which would further calibrate the baryon acoustic oscillations standard ruler.
DCASE 2019: CNN depth analysis with different channel inputs for Acoustic Scene Classification

The objective of this technical report is to describe the framework used in Task 1, Acoustic scene classification (ASC), of the DCASE 2019 challenge. The presented approach is based on Log-Mel spectrogram representations and VGG-based Convolutional Neural Networks (CNNs). Three different CNNs, with very similar architectures, have been implemented. Themain difference is the number of filters in their convolutional blocks. Experiments show that the depth of the network is not the most relevant factor for improving the accuracy of the results.The performance seems to be more sensitive to the input audio representation. This conclusion is important for the implementation of real-time audio recognition and classification systemon edge devices. In the presented experiments the best audio representation is the Log-Mel spectrogram of the harmonic andpercussive sources plus the Log-Mel spectrogram of the difference between left and right stereo-channels. Also, in order to improve accuracy, ensemble methods combining different model predictions with different inputs are explored. Besides geometric and arithmetic means, ensembles aggregated with the Orness Weighted Averaged (OWA) operator have shown interesting andnovel results. The proposed framework outperforms the baseline system by 14.34 percentage points. For Task 1a, the obtained development accuracy is 76.84 percent, being 62.5 percent the baseline, whereas the accuracy obtained in public leaderboard is 77.33 percent,being 64.33 percent the baseline.
Effects of Replanting and Retention of Mature Oil Palm Riparian Buffers on Ecosystem Functioning in Oil Palm Plantations

Oil palm plantations are a major agricultural land use in Southeast Asia. In the coming decades large areas of mature oil palm will be cleared and replanted. To inform more sustainable long-term production in this globally important crop, it is crucial we understand how replanting impacts ecosystem functions and services. We investigated whether several production-relevant ecosystems functions (dung removal, soil mesofauna feeding activity, herbivory, herbivore predation, and seed predation), and the simultaneous delivery of all functions (ecosystem multifunctionality), vary between recently-replanted oil palm (1-4 yr) and mature oil palm (23-30 yr) areas. Following new in-country and Roundtable on Sustainable Palm Oil (RSPO) guidelines, riparian buffers of mature oil palm, in which subsequent natural regrowth is allowed, are being preserved during the replanting cycle in plantations that lack natural forest reserves. We investigated whether or not mature oil palm riparian buffers maintain levels of ecosystem functioning beneficial for palm oil production. Only one function (herbivory) differed between mature and replanted areas, with higher levels of herbivory found in recently replanted oil palm. There was no difference in ecosystem multifunctionality between mature and recently-replanted oil palm. Mature oil palm riparian buffers were found to be valuable for maintaining lower levels of herbivory than recently-replanted oil palm. However, no other functions, nor ecosystem multifunctionality, differed between the mature oil palm riparian buffers and recently-replanted oil palm. The results of this study suggest that replanting has limited impacts on the ecosystem functions we considered. Furthermore, they suggest mature oil palm riparian buffers do not have negative impacts on production-relevant ecosystem functions in oil palm landscapes.
Investigating the Efficacy of the Hand Selection Complexity Task Across the Lifespan

There is inconsistent evidence demonstrating a relationship between task complexity and hand preference. However, analyzing the point at which task complexity overrides the decision to demonstrate a biomechanically efficient movement can enable complexity to be quantified. Young children (ages 3–7), adolescents (ages 8–12), young adults (ages 18–25), and older adults (ages 65+) performed a newly developed Hand Selection Complexity Task (HSCT) and completed the Waterloo Handedness Questionnaire (WHQ). The HSCT included a reciprocal Fitts’ tapping task performed in the contralateral space (i.e., same side as preferred hand), followed by ipsilateral space (i.e., opposite side of preferred hand). An alternating contralateral-ipsilateral pattern enabled the participant to progress through six levels of difficulty in three conditions (manipulating target amplitude, width, and combined factors). As participants were free to perform with whichever hand (i.e., preferred, non-preferred) they deemed most appropriate, the level of difficulty where a hand switch occurred was identified. HSCT completion time and error scores were also computed. Findings revealed age to be a significant predictor of dependent measures when considering significant effects and interactions. Combined with the covariate WHQ score as a significant predictor of HSCT time and errors (in some, but not all cases), it can be argued that age-related effects reflect the development of handedness, and changes in strength of handedness across the lifespan. Together, findings suggest that task complexity plays an important role in hand selection when performing a task of increasing difficulty. It appears that task complexity will take precedent over object proximity and biomechanical efficiency, at a certain point, in order to complete the movement with the preferred hand. This point ultimately changes throughout the lifespan.
Marine Bacterial Diversity in Coastal Sichang Island, the Upper Gulf of Thailand, in 2011 Wet Season

Tha Wang coast in Sichang island, Chonburi province, Thailand, serves a major pier, cargo transportation and is populated with anthropogenic activities. Hence, monitoring of environmental status, in part by microbial diversity, is essential. Previously, the coastal marine microbiota of this area in a dry season (February 2011) had been reported, but the database for a wet season is none. As marine microbiota in several sites were reported fluctuate between dry and wet seasons, specifically in the 2011 that one of the largest flood in Thailand history even occurred from July 2011 to January 2012; the present study thereby first revealed the coastal Sichang water microbiota in the 2011 wet season (July 2011) using metagenomic derived 16S rRNA gene sequencing. Wet and dry seasons showed differences in prokaryotic community richness and evenness: community similarity indices by Jaccard, Lennon, and Yue & Clayton were 2.06-58.28%. This resulted in differences in metabolic potentials, for instances the lower metabolisms for energy and nutrient cycling but the greater in pathogenesis in wet season. Our data were also compared against the flooding water microbiota nearby to Chonburi province to observe any possible correlation; and the coastal Sichang was found distinct given diverse sources of flooding water and local contamination might affect the diversity. In conclusion, this wet-season microbiota supported the better knowledge on the seasonal microbiota of coastal Sichang island.
On the Vector Space in Photoplethysmography Imaging

We study the vector space of visible wavelength intensities from face videos widely used as input features in Photoplethysmography Imaging (PPGI). Based upon theoretical principles of group invariance in the Euclidean space, we derive a change of the topology where the corresponding distance between successive measurements is defined as geodesic on a Riemannian manifold. This lower dimensional embedding of the sensor signal unifies the invariance properties with respect to translation of the features as discussed by several former approaches. The resulting operator acts implicitly on the feature space without requiring any kind of prior knowledge and parameter tuning. The resulting feature's time varying quasi-periodic shaping naturally occurs in form of the canonical state space representation according to the known diffusion process of blood volume changes. This reduces drastically computational complexity and consequently simplifies the implementation. Experiments from face videos on two public databases have shown a competitive estimation performances of heart rate and robustness in comparison with already available methods.
Managing Recovery Resilience in Coral Reefs Against Climate-Induced Bleaching and Hurricanes: A 15 Year Case Study From Bonaire, Dutch Caribbean

Coral reefs are among the world's most endangered ecosystems. Coral mortality can result from ocean warming or other climate-related events such as coral bleaching and intense hurricanes. While resilient coral reefs can recover from these impacts as has been documented in coral reefs throughout the tropical Indo-Pacific, no similar reef-wide recovery has ever been reported for the Caribbean. Climate change-related coral mortality is unavoidable, but local management actions can improve conditions for regrowth and for the establishment of juvenile corals thereby enhancing the recovery resilience of these ecosystems. Previous research has determined that coral reefs with sufficient herbivory limit macroalgae and improve conditions for coral recruitment and regrowth. Management that reduces algal abundance increases the recovery potential for both juvenile and adult corals on reefs. Every other year on the island of Bonaire, Dutch Caribbean, we quantified patterns of distribution and abundance of reef fish, coral, algae, and juvenile corals along replicate fixed transects at 10 m depth at multiple sites from 2003 to 2017. Beginning with our first exploratory study in 2002 until 2007 coral was abundant (45% cover) and macroalgae were rare (6% cover). Consecutive disturbances, beginning with Hurricane Omar in October 2008 and a coral bleaching event in October 2010, resulted in a 22% decline in coral cover and a sharp threefold increase in macroalgal cover to 18%. Juvenile coral densities declined to about half of their previous abundance. Herbivorous parrotfishes had been declining in abundance but stabilized around 2010, the year fish traps were phased out and fishing for parrotfish was banned. The average parrotfish biomass from 2010 to 2017 was more than twice that reported for coral reefs of the Eastern Caribbean. During this same period, macroalgae declined and both juvenile coral density and total adult coral cover returned to pre-hurricane and bleaching levels. To our knowledge, this is the first example of a resilient Caribbean coral reef ecosystem that fully recovered from severe climate-related mortality events.
Re-exploring Molecular Complexity with ALMA (ReMoCA): interstellar detection of urea

Context. Urea, NH2C(O)NH2, is a molecule of great importance in organic chemistry and biology. Two searches for urea in the interstellar medium have been reported in the past, but neither were conclusive. Aims. We want to take advantage of the increased sensitivity and angular resolution provided by the Atacama Large Millimeter/submillimeter Array (ALMA) to search for urea toward the hot molecular cores embedded in the high-mass-star-forming region Sgr B2(N). Methods. We used the new spectral line survey named ReMoCA (Re-exploring Molecular Complexity with ALMA) that was performed toward Sgr B2(N) with ALMA in its observing cycle 4 between 84 and 114 GHz. The spectra were analyzed under the local thermodynamic equilibrium approximation. We constructed a full synthetic spectrum that includes all the molecules identified so far. We used new spectroscopic predictions for urea in its vibrational ground state and first vibrationally excited state to search for this complex organic molecule in the ReMoCA data set. We employed the gas-grain chemical kinetics model MAGICKAL to interpret the astronomical observations. Results. We report the secure detection of urea toward the hot core Sgr B2(N1) at a position called N1S slightly offset from the continuum peak, which avoids obscuration by the dust. The identification of urea relies on nine clearly detected transitions. We derive a column density of 2.7 × 1016 cm−2 for urea, two orders of magnitude lower than the column density of formamide, and one order of magnitude below that of methyl isocyanate, acetamide, and N-methylformamide. The latter molecule is reliably identified toward N1S with 60 clearly detected lines, confirming an earlier claim of its tentative interstellar detection. We report the first interstellar detections of NH2CH18O and 15NH2CHO. We also report the nondetection of urea toward the secondary hot core Sgr B2(N2) with an abundance relative to the other four species at least one order of magnitude lower than toward the main hot core. Our chemical model roughly reproduces the relative abundances of formamide, methyl isocyanate, acetamide, and N-methylformamide, but it overproduces urea by at least one order of magnitude. Conclusions. Urea is clearly detected in one of the hot cores. Comparing the full chemical composition of Sgr B2(N1S) and Sgr B2(N2) may help understand why urea is at least one order of magnitude less abundant in the latter source.