Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatio-temporal point processes as meta-models for population dynamics in heterogeneous landscapes

Landscape heterogeneity affects population dynamics, which determine species persistence, diversity and interactions. These relationships can be accurately represented by advanced spatially-explicit models (SEMs) allowing for high levels of detail and precision. However, such approaches are characterised by high computational complexity, high amount of data and memory requirements, and spatio-temporal outputs may be difficult to analyse. A possibility to deal with this complexity is to aggregate outputs over time or space, but then interesting information may be masked and lost, such as local spatio-temporal relationships or patterns. An alternative solution is given by meta-models and meta-analysis, where simplified mathematical relationships are used to structure and summarise the complex transformations from inputs to outputs. Here, we propose an original approach to analyse SEM outputs. By developing a meta-modelling approach based on spatio-temporal point processes (STPPs), we characterise spatio-temporal population dynamics and landscape heterogeneity relationships in agricultural contexts. A landscape generator and a spatially-explicit population model simulate hierarchically the pest-predator dynamics of codling moth and ground beetles in apple orchards over heterogeneous agricultural landscapes. Spatio-temporally explicit outputs are simplified to marked point patterns of key events, such as local proliferation or introduction events. Then, we construct and estimate regression equations for multi-type STPPs composed of event occurrence intensity and magnitudes. Results provide local insights into spatio-temporal dynamics of pest-predator systems. We are able to differentiate the contributions of different driver categories (i.e., spatio-temporal, spatial, population dynamics). We highlight changes in the effects on occurrence intensity and magnitude when considering drivers at global or local scale. This approach leads to novel findings in agroecology where the organisation of cultivated fields and semi-natural elements are known to play a crucial role for pest regulation. It aids to formulate guidelines for biological control strategies at global and local scale.
Quantitative Examination of Five Stochastic Cell-Cycle and Cell-Size Control Models for Escherichia coli and Bacillus subtilis

We examine five quantitative models of the cell-cycle and cell-size control in Escherichia coli and Bacillus subtilis that have been proposed over the last decade to explain single-cell experimental data generated with high-throughput methods. After presenting the statistical properties of these models, we test their predictions against experimental data. Based on simple calculations of the defining correlations in each model, we first dismiss the stochastic Helmstetter-Cooper model and the Initiation Adder model, and show that both the Replication Double Adder and the Independent Double Adder model are more consistent with the data than the other models. We then apply a recently proposed statistical analysis method and obtain that the Independent Double Adder model is the most likely model of the cell cycle. By showing that the Replication Double Adder model is fundamentally inconsistent with size convergence by the adder principle, we conclude that the Independent Double Adder model is most consistent with the data and the biology of bacterial cell-cycle and cell-size control. Mechanistically, the Independent Adder Model is equivalent to two biological principles: (i) balanced biosynthesis of the cell-cycle proteins, and (ii) their accumulation to a respective threshold number to trigger initiation and division.
Genome-Wide Reconstruction of Rediploidization Following Autopolyploidization across One Hundred Million Years of Salmonid Evolution

The long-term evolutionary impacts of whole genome duplication (WGD) are strongly influenced by the ensuing rediploidization process. Following autopolyploidization, rediploidization involves a transition from tetraploid to diploid meiotic pairing, allowing duplicated genes (ohnologues) to diverge genetically and functionally. Our understanding of autopolyploid rediploidization has been informed by a WGD event ancestral to salmonid fishes, where large genomic regions are characterized by temporally delayed rediploidization, allowing lineage-specific ohnologue sequence divergence in the major salmonid clades. Here, we investigate the long-term outcomes of autopolyploid rediploidization at genome-wide resolution, exploiting a recent ‘explosion’ of salmonid genome assemblies, including a new genome sequence for the huchen (Hucho hucho). We developed a genome alignment approach to capture duplicated regions across multiple species, allowing us to create 121,864 phylogenetic trees describing ohnologue divergence across salmonid evolution. Using molecular clock analysis, we show that 61% of the ancestral salmonid genome experienced an initial ‘wave’ of rediploidization in the late Cretaceous (85-106 Mya). This was followed by a period of relative genomic stasis lasting 17-39 My, where much of the genome remained in a tetraploid state. A second rediploidization wave began in the early Eocene and proceeded alongside species diversification, generating predictable patterns of lineage-specific ohnologue divergence, scaling in complexity with the number of speciation events. Finally, using gene set enrichment, gene expression, and codon-based selection analyses, we provide insights into potential functional outcomes of delayed rediploidization. Overall, this study enhances our understanding of delayed autopolyploid rediploidization and has broad implications for future studies of WGD events.
Carboxypeptidase E is efficiently secreted and internalized via lysosomes

Carboxypeptidase E (CPE) a key factor in the biosynthesis of most peptide hormones and neuropeptides, is predominantly expressed in endocrine tissues and the nervous system. This highly conserved enzyme cleaves the C-terminal basic residues of the peptide precursors to generate their bioactive form. CPE is a secreted protein; however, the Intracellular pathways leading to its secretion are still obscure. We combined live-cell microscopy and molecular analysis to examine the intracellular distribution and secretion dynamics of fluorescently tagged CPE. CPE was found to be a soluble luminal protein as it traffics from the ER via the Golgi apparatus to lysosomes. Moreover, CPE is efficiently secreted and reinternalized to lysosomes of neighboring cells. The C-terminal amphipathic helix of CPE is essential for its efficient targeting to, and secretion from lysosomes. Fluorescence resonance energy transfer demonstrated that CPE and its substrate neuropeptide Y (NPY) interact in the Golgi apparatus and Immunoprecipitation analysis demonstrated that both CPE and NPY are co-secreted. The implications of the well-defined CPE intra and extracellular routes are discussed.
The Relationship Between Perceived Teacher Support and School Burnout Among Males in Christian High Schools

Abstract Male students are especially susceptible to becoming disgruntled with high school and leaving school early. A quantitative correlational research study was conducted to explore whether teacher support can predict school burnout among Christian high school males. One hundred twenty-six male students from four private, Christian high schools in North Carolina and Virginia participated in this study which examined four sub-categories of teacher support (investedness, positive regard, expectations, and accessible). The Teacher Support Scale measured teacher support and the School Burnout Inventory measured participants’ level of school burnout. Multiple regression analysis revealed a statistically significant relationship between perceived teacher support and male students’ level of school burnout. The perception of Christian male students’ personal connection with teachers, specifically teachers’ positive regard, is believed to be a strong predictor of school burnout.
Ceramics, society and economy in the northern Levant

Contributions to the workshop One of the primary aims of the Computational Research on the Ancient Near East (CRANE), funded by the Social Sciences and Humanities Research Council of Canada, is to create a framework for the integration and analysis of data from multiple archaeological projects working in the Orontes River watershed (Harrison 2018). This workshop, held under the auspices of CRANE, focused on ceramics, a sub-field that, in Levantine archaeology at least, has often struggled to move beyond typological concerns to address research questions designed to improve our understanding of past social and economic organization (Badreshany et al. 2019). In keeping with the initial geographical focus of CRANE, material from sites in the Orontes watershed in western Syria lay at the heart of the workshop. However, it proved possible to extend our coverage to include data emerging from new projects in Lebanon. For the Early Bronze Age (EBA) at least, this has allowed us to compare developments in western Syria (extending roughly from Homs and Hama to the Amuq), to those in the central Levant, an area adjacent to the Orontes, but in which both the ceramic types, and modes of production, appear quite different. The contribution by Sowada et al. (2020), which deals with material of Levantine origin found in Egypt, was a late addition to the volume, included because we felt that the topic was closely aligned to our wider themes, and sheds light on the longer-distance connections of our region of interest, critical to the themes of the volume. Our workshop sought to close the gap between: 1. the detailed site-specific presentations of ceramic evidence which dominate the ceramic literature, 2. generalized inter-regional ceramic studies, which are often focused upon typo-chronological comparisons, and 3. high level region/period syntheses.
Constructive Alignment for Deep Learning in Undergraduate Civil Engineering Education

Attainment of competency is crucial for civil engineering students to solve socio-economic and environmental challenges and contribute to the development of a sustainable society by using engineering principles. Consequently, competency has become the measure of engineering graduates for which deep learning is essential. Constructive alignment has been argued to be vital for deep learning. The objective of the study was therefore to examine how constructive alignment could enforce deep learning among civil engineering students. The study was contextualised within an undergraduate civil engineering programme in a university of technology in South Africa. Mixed-methods research comprising student perceptions, focus group discussions and a case study was used for the study. Findings suggested that when the three components, namely, the intended learning outcomes, teaching and learning activities, and assessment tasks, are appropriately aligned, students learn deeply compared with the conventional form of learning. Furthermore, clear criteria to measure student performance, as well as structured written and oral feedback together are vital for deep learning.
Archaeometrical Characterization of Romanian Late Bronze Age Ceramic Fragments

Knowledge of the past can provide information to protect the future and the potential of the technological development in the analytical sciences can be successfully applied for the study and conservation of cultural objects. In this context, in the present paper we propose an analytical methodology to characterize seven samples of ancient ceramic objects (dating to the Late Bronze Age). The samples were analyzed using optical microscopy, and all the samples presented a strong inhomogeneity on the surface, as suggested by the different colors of the ceramics. X-ray fluorescence (XRF) results reveal a relatively heterogenous composition of the samples, as well as strong differences between the different surfaces of each sample. By comparative analysis of the diffractograms recorded for both sides of the same samples were observed some differences, especially in terms of relative concentration of the component minerals, and, in lesser content, in terms of new phases present in the samples. Corroborated results obtained by XRF and X-ray diffraction (XRD) offered information regarding mineralogical composition of the samples: for some of them illite/muscovite and plagioclase phases are present in higher quantities or a lower quartz content. The presence of these components was confirmed by Fourier-transform infrared spectroscopy (FTIR) analysis. The thermal analysis completes the analytical investigation of the ceramic samples. The thermal behavior of the sample conducted to some explanation regarding the observed differences, due to the raw materials (that the major clay mineral in the samples is represented by illite) or to environmental factors during their burial in the soil.
Genome-Wide Association Study of Motor Coordination

The ability to finely control our movement is key to achieving many of the educational milestones and life-skills we develop throughout our lives. Despite the centrality of coordination to early development, there is a vast gap in our understanding of the underlying biology. Like most complex traits, both genetics and environment influence motor coordination, however, the specific genes, early environmental risk factors and molecular pathways are unknown. Previous studies have shown that about 5% of school-age children experience unexplained difficulties with motor coordination. These children are said to have Developmental Coordination Disorder (DCD). For children with DCD, these motor coordination difficulties significantly impact their everyday life and learning. DCD is associated with poorer academic achievement, reduced quality of life, it can constrain career opportunities and increase the risk of mental health issues in adulthood. Despite the high prevalence of coordination difficulties, many children remain undiagnosed by healthcare professionals. Compounding under-diagnosis in the clinic, research into the etiology of DCD is severely underrepresented in the literature. Here we present the first genome-wide association study to examine the genetic basis of early motor coordination in the context of motor difficulties. Using data from the Avon Longitudinal Study of Parents and Children we generate a derived measure of motor coordination from four components of the Movement Assessment Battery for Children, providing an overall measure of coordination across the full range of ability. We perform the first genome-wide association analysis focused on motor coordination (N = 4542). No single nucleotide polymorphisms (SNPs) met the threshold for genome-wide significance, however, 59 SNPs showed suggestive associations. Three regions contained multiple suggestively associated SNPs, within five preliminary candidate genes: IQSEC1, LRCC1, SYNJ2B2, ADAM20, and ADAM21. Association to the gene IQSEC1 suggests a potential link to axon guidance and dendritic projection processes as a potential underlying mechanism of motor coordination difficulties. This represents an interesting potential mechanism, and whilst further validation is essential, it generates a direct window into the biology of motor coordination difficulties. This research has identified potential biological drivers of DCD, a first step towards understanding this common, yet neglected neurodevelopmental disorder.
Self-assembly of ultrathin mesoporous CoMoO4 nanosheet networks on flexible carbon fabric as a binder-free anode for lithium-ion batteries

Novel hierarchical CoMoO4 networks assembled by ultrathin mesoporous nanosheets were directly grown on flexible carbon fabric with robust adhesion by a facile hydrothermal method route and subsequent thermal annealing. The building block nanosheets of the as-prepared CoMoO4 nanoarchitectures show a mesoporous structure with pores of 2–5 nm, and the thickness as small as 3–5 nm. Based on the time-dependent experiments, a probable growth mechanism of the CoMoO4 nanosheet networks directly grown on the surface of carbon fabric is proposed. Benefitting from the unique structural features, the resultant CoMoO4/carbon fabric electrode exhibits excellent electrochemical performance with a high reversible capacity (1128.05 mA h g−1 at a current density of 100 mA g−1) and good cycling stability for highly reversible lithium storage (87.76% retention after 150 cycles). The superior electrochemical performance can be ascribed to the synergistic effect of charge transfer express way, high specific surface area and porous hierarchical structure for electrolyte penetration.
A Dynamical Generative Model of Social Interactions

The ability to make accurate social inferences makes humans able to navigate and act in their social environment effortlessly. Converging evidence shows that motion is one of the most informative cues in shaping the perception of social interactions. However, the scarcity of parameterized generative models for the generation of highly-controlled stimuli has slowed down both the identification of the most critical motion features and the understanding of the computational mechanisms underlying their extraction and processing from rich visual inputs. In this work, we introduce a novel generative model for the automatic generation of an arbitrarily large number of videos of socially interacting agents for comprehensive studies of social perception. The proposed framework, validated with three psychophysical experiments, allows generating as many as 15 distinct interaction classes. The model builds on classical dynamical system models of biological navigation and is able to generate visual stimuli that are parametrically controlled and representative of a heterogeneous set of social interaction classes. The proposed method represents thus an important tool for experiments aimed at unveiling the computational mechanisms mediating the perception of social interactions. The ability to generate highly-controlled stimuli makes the model valuable not only to conduct behavioral and neuroimaging studies, but also to develop and validate neural models of social inference, and machine vision systems for the automatic recognition of social interactions. In fact, contrasting human and model responses to a heterogeneous set of highly-controlled stimuli can help to identify critical computational steps in the processing of social interaction stimuli.
Plasma Markers of Disrupted Gut Permeability in Severe COVID-19 Patients

A disruption of the crosstalk between the gut and the lung has been implicated as a driver of severity during respiratory-related diseases. Lung injury causes systemic inflammation, which disrupts gut barrier integrity, increasing the permeability to gut microbes and their products. This exacerbates inflammation, resulting in positive feedback. We aimed to test whether severe Coronavirus disease 2019 (COVID-19) is associated with markers of disrupted gut permeability. We applied a multi-omic systems biology approach to analyze plasma samples from COVID-19 patients with varying disease severity and SARS-CoV-2 negative controls. We investigated the potential links between plasma markers of gut barrier integrity, microbial translocation, systemic inflammation, metabolome, lipidome, and glycome, and COVID-19 severity. We found that severe COVID-19 is associated with high levels of markers of tight junction permeability and translocation of bacterial and fungal products into the blood. These markers of disrupted intestinal barrier integrity and microbial translocation correlate strongly with higher levels of markers of systemic inflammation and immune activation, lower levels of markers of intestinal function, disrupted plasma metabolome and glycome, and higher mortality rate. Our study highlights an underappreciated factor with significant clinical implications, disruption in gut functions, as a potential force that may contribute to COVID-19 severity.
Ceremonial Ayahuasca in Amazonian Retreats—Mental Health and Epigenetic Outcomes From a Six-Month Naturalistic Study

Ayahuasca is a natural psychoactive brew, used in traditional ceremonies in the Amazon basin. Recent research has indicated that ayahuasca is pharmacologically safe and its use may be positively associated with improvements in psychiatric symptoms. The mechanistic effects of ayahuasca are yet to be fully established. In this prospective naturalistic study, 63 self-selected participants took part in ayahuasca ceremonies at a retreat centre in the Peruvian Amazon. Participants undertook the Beck Depression Inventory (BDI-II), State-Trait Anxiety Inventory (STAI), Self-compassion Scale (SCS), Clinical Outcomes in Routine Evaluation-Outcome Measure (CORE-OM), as well as secondary measures, pre- and post-retreat and at 6-months. Participants also provided saliva samples for pre/post epigenetic analysis. Overall, a statistically significant decrease in BDI-II (13.9 vs. 6.1, p < 0.001), STAI (44.4 vs. 34.3 p < 0.001) scores, and CORE-OM scores were observed (37.3 vs. 22.3 p < 0.001) at post-retreat, as well as a concurrent increase in SCS (3.1 vs. 3.6, p < 0.001). Psychometric improvements were sustained, and on some measures values further decreased at 6-month follow-up, suggesting a potential for lasting therapeutic effects. Changes in memory valence were linked to the observed psychometric improvements. Epigenetic findings were equivocal, but indicated that further research in candidate genes, such as sigma non-opioid intracellular receptor 1 (SIGMAR1), is warranted. This data adds to the literature supporting ayahuasca's possible positive impact on mental health when conducted in a ceremonial context. Further investigation into clinical samples, as well as greater analyses into the mechanistic action of ayahuasca is advised.
Genetic Polymorphisms in Enzymes Involved in One-Carbon Metabolism and Anti-epileptic Drug Monotherapy on Homocysteine Metabolism in Patients With Epilepsy

Aims: To investigate the effects of single nucleotide polymorphisms (SNPs) in genes of one-carbon metabolism (OCM) related enzymes and anti-epileptic drug (AED) monotherapy on homocysteine (Hcy) metabolism in patients with epilepsy, and to further explore specific SNPs that may increase patients' susceptibility to the effects of AEDs on the Hcy imbalance. Method: This case-control study analyzed 279 patients with epilepsy, including patients receiving monotherapy with valproate (VPA) (n = 53), oxcarbazepine (OXC) (n = 71), lamotrigine (LTG) (n = 55), or levetiracetam (LEV) (n = 35) and patients who had not taken any AEDs (controls, n = 65) for at least 6 months. Serum levels of vitamin B12 (vit B12), folate (FA) and Hcy were measured, and 23 SNPs in 13 genes of OCM-related enzymes were genotyped in all patients. Results: Methylenetetrahydrofolate reductase (MTHFR) rs1801133 was associated with elevated serum Hcy levels in patients with epilepsy (P < 0.001), and patients presenting the TT genotype exhibited higher serum Hcy levels than patients with the CC (P < 0.001) or CT (P < 0.001) genotype. A subsequent multiple linear regression analysis showed that AED monotherapy with VPA (vs. control: P = 0.023) or OXC (vs. control: P = 0.041), and genotypes of MTHFR rs1801133 TT (vs. CC: P < 0.001; vs. CT: P < 0.001), transcobalamin 2 (TCN2) rs1801198 CC (vs. GC: P = 0.039) and folate receptor 1 (FOLR1) rs2071010 AA (vs. GA: P = 0.031) were independent risk factors for higher Hcy levels. In the subgroup analysis of patients taking OXC, we found that patients with genotypes of MTHFR rs1801133 TT (vs. CC: P = 0.001; vs. CT: P < 0.001) and TCN2 rs1801198 CC (vs. GC: P = 0.021; vs. GG: P = 0.018) exhibited higher serum Hcy levels. Conclusions: VPA, OXC, and genotypes of MTHFR rs1801133 TT, TCN2 rs1801198 CC, and FOLR1 rs2071010 AA are all independent risk factors for elevated Hcy levels in patients with epilepsy. Moreover, genotypes of MTHFR rs1801133 TT and TCN2 rs1801198 CC may increase patients' susceptibility to the effect of OXC on disrupting Hcy homeostasis.