Miracle-dz/UniFAR-FTUs huggingface dataset:
A meta-analysis of operational interactions between pinnipeds and fisheries

The global recovery of pinniped populations is a conservation success. However, pinniped population recovery has increased human-wildlife conflict with fisheries, an issue often reported and requiring management, but one that lacks global synthesis. We conduct a meta-analysis to estimate the impacts of operational interactions (specifically, lost catch) between pinnipeds and fisheries. Where quantifiable interactions are reported (n = 36), on average fishers have a 33.7% chance of interacting with pinnipeds on any given fishing day, and 13.8% lost catch. We find a large degree of heterogeneity between studies, with some fisheries experiencing much more negative interactions than others. Specifically, smaller-scale fisheries using nets are up to twice as likely to have negative interactions and lose up to five times more catch compared to large-scale fisheries. We conclude that pinniped-fishery conflict is a substantial global issue, but its impacts are not uniform. To successfully manage long-term coexistence between pinnipeds and humans, explicit data quantifying operational interactions is required. Population recoveries can have unintended consequences for fisheries, and management of ecological, social and economic outcomes is needed for long-term coexistence. Teaser Pinniped population recoveries have led to significant impacts on fisheries, but small-scale fisheries lose out most.
Thermal stress analysis of functionally graded material structures using analytical expressions in radial integration BEM

This paper presents a new approach using analytical expressions in the radial integration boundary element method (RIBEM) for 2D thermal stress analysis of structures consisting of functionally graded materials. This approach can improve the computational efficiency considerably and can overcome the timeconsuming deficiency of RIBEM in computing involved radial integrals. Using this equation together with the three-step multi-domain BEM technique, thermal stress analysis can be carried out for complicated structures comprised of, arbitrarily, many numbers of media with varying material properties. The Kelvin fundamental solutions independent of elastic modulus are used in this paper. As a result, the resulting integral equations include domain integrals due to the nonhomogeneity and temperature variations of the material. All these domain integrals are transformed into equivalent boundary integrals using the radial integration method (RIM), resulting in a pure boundary element analysis algorithm. Numerical examples are given to demonstrate the efficiency of the presented approach.
Hepatic WDR23 proteostasis mediates insulin clearance by regulating insulin-degrading enzyme

Clearance of circulating insulin is critical for metabolic homeostasis. In the liver, insulin is degraded by the activity of the insulin-degrading enzyme (IDE). Here we establish a hepatic regulatory axis for IDE through WDR23-proteostasis. Wdr23KO mice have increased IDE expression, reduced circulating insulin, and defective insulin responses. Genetically engineered human cell models lacking WDR23 also increase IDE expression and display dysregulated phosphorylation of insulin signaling cascade proteins, IRS-1, AKT2, MAPK, FoxO, and mTOR, similar to cells treated with insulin, which can be mitigated by chemical inhibition of IDE. Mechanistically, the cytoprotective transcription factor NRF2, a direct target of WDR23-Cul4 proteostasis, mediates the enhanced transcriptional expression of IDE when WDR23 is ablated. Moreover, an analysis of human genetic variation in WDR23 across a large naturally aging human cohort in the US Health and Retirement Study reveals a significant association of WDR23 with altered hemoglobin A1C (HbA1c) levels in older adults, supporting the use of WDR23 as new molecular determinant of metabolic health in humans.
Ethylene-mediated phosphorylation of ORESARA1 induces sequential leaf death during flooding in Arabidopsis

Outline The volatile phytohormone ethylene is a major regulator of plant adaptive responses to flooding. In flooded plant tissues, it quickly increases to high concentrations due to its low solubility and diffusion rates in water. The passive, quick and consistent accumulation of ethylene in submerged plant tissues makes it a reliable cue for plants to trigger flood-acclimative responses. However, persistent ethylene accumulation can also have negative effects, notably accelerated leaf senescence. Ethylene is a well-established positive regulator of senescence which is a natural element of plant ageing. However stress-induced senescence hampers the photosynthetic capacity and stress recovery of plants. In submerged Arabidopsis shoots, senescence follows a strict age-dependent pattern starting with the older leaves. Although mechanisms underlying ethylene-mediated senescence have been uncovered, it is unclear how submerged plants avoid an indiscriminate breakdown of leaves despite high systemic accumulation of ethylene. Here we demonstrate in Arabidopsis plants that even though submergence triggers a leaf-age independent activation of ethylene signaling via EIN3, senescence was initiated only in the old leaves. This EIN3 stabilization also led to the overall transcript and protein accumulation of the senescence-promoting transcription factor ORESARA1 (ORE1). ORE1 protein accumulated in both old and young leaves during submergence. However, leaf age-dependent senescence could be explained by ORE1 activation via phosphorylation only in old leaves. Our results unravel a mechanism by which plants regulate the speed and pattern of senescence during environmental stresses like flooding. Such an age-dependent phosphorylation of ORE1 ensures that older expendable leaves are dismantled first, thus prolonging the life of younger leaves and meristematic tissues vital to whole plant survival.
A multi-layer mean-field model for the cerebellar cortex: design, validation, and prediction

Mean-field (MF) models can be used to summarize in a few statistical parameters the salient properties of an inter-wired neuronal network incorporating different types of neurons and synapses along with their topological organization. MF are crucial to efficiently implement the modules of large-scale brain models maintaining the specificity of local microcircuits. While MFs have been generated for the isocortex, they are still missing for other parts of the brain. Here we have designed and simulated a multi-layer MF of the cerebellar network (including Granule Cells, Golgi Cells, Molecular Layer Interneurons, and Purkinje Cells) and validated it against experimental data and the corresponding spiking neural network (SNN) microcircuit model. The cerebellar MF was built using a system of equations, where properties of neuronal populations and topological parameters are embedded in inter-dependent transfer functions. The model time constant was optimised using local field potentials recorded experimentally from acute mouse cerebellar slices as a template. The MF satisfactorily reproduced the average dynamics of the different neuronal populations in response to various input patterns and predicted the modulation of Purkinje Cells firing depending on cortical plasticity, which drives learning in associative tasks, and the level of feedforward inhibition. The cerebellar MF provides a computationally efficient tool that will allow to investigate the causal relationship between microscopic neuronal properties and ensemble brain activity in virtual brain models addressing both physiological and pathological conditions.
Kinetic control in amyloid polymorphism: Different agitation and solution conditions promote distinct amyloid polymorphs of alpha-synuclein

Aggregation of neuronal protein α-synuclein is implicated in synucleinopathies, including Parkinson’s disease. Despite abundant in vitro studies, the mechanism of α-synuclein assembly process remains ambiguous. In this work, α-synuclein aggregation was induced by its constant mixing in two separate modes, either by agitation in a 96-well microplate reader (MP) or in microcentrifuge tubes using a shaker incubator (SI). Aggregation in both modes occurred through a sigmoidal growth pattern with a well-defined lag, growth, and saturation phase. The end-stage MP- and SI-derived aggregates displayed distinct differences in morphological, biochemical, and spectral signatures as discerned through AFM, proteinase-K digestion, FTIR, Raman, and CD spectroscopy. The MP-derived aggregates showed irregular morphology with a significant random coil conformation, contrary to SI-derived aggregates, which showed typical β-sheet fibrillar structures. The end-stage MP aggregates convert to β-rich SI-like aggregates upon 1) seeding with SI-derived aggregates and 2) agitating in SI. We conclude that end-stage MP aggregates were in a kinetically trapped conformation, whose kinetic barrier was bypassed upon either seeding by SI-derived fibrils or shaking in SI. We further show that MP-derived aggregates that form in the presence of sorbitol, an osmolyte, displayed a β-rich signature, indicating that the preferential exclusion effect of osmolytes helped overcome the kinetic barrier. Our findings help in unravelling the kinetic origin of different α-synuclein aggregated polymorphs (strains) that encode diverse variants of synucleinopathies. We demonstrate that kinetic control shapes the polymorphic landscape of α-synuclein aggregates, both through de novo generation of polymorphs, and by their interconversion.
Three-magnon splitting controlled by temperature

A nonlinear magnon interaction has been investigated in an yttrium iron garnet/Pt film. In the bilayer film, multiple microwave absorption signals due to the excitation of magnetostatic spin waves, including magnoetostatic surface waves and backward volume magnetostatic spin waves, were observed at room temperature. The microwave absorption spectrum was found to be changed drastically by decreasing temperature. This drastic change in the microwave absorption spectrum is attributed to the appearance of the three-magnon splitting process; the spin-wave dispersion calculated by taking into account the temperature variation of the saturation magnetization indicates that the change in the microwave absorption spectrum appears when the lowest frequency of the spin-wave dispersion becomes lower than a half of the microwave excitation frequency. At this condition, the energy and momentum conservation laws can be fulfilled in the process where a pumped magnon splits into two magnons. These results demonstrate that the nonlinear magnon interaction can be controlled not only by excitation frequency but also by temperature.
Natural genetic variation in the pheromone production of C. elegans

From bacterial quorum sensing to human language, communication is essential for social interactions. Nematodes produce and sense pheromones to communicate among individuals and respond to environmental changes. These signals are encoded by different types and mixtures of ascarosides, whose modular structures further enhance the diversity of this nematode pheromone language. Interspecific and intraspecific differences in this ascaroside pheromone language have been described previously, but the genetic basis and molecular mechanisms underlying the variation remain largely unknown. Here, we analyzed natural variation in the production of 44 ascarosides across 95 wild Caenorhabditis elegans strains using high-performance liquid chromatography coupled to high-resolution mass spectrometry (HPLC-HRMS). By cross-analyzing genomes and exo-metabolomes of wild strains, we discovered quantitative trait loci (QTL) that underlie the natural differences in pheromone bouquet composition. Fine mapping of the QTL further uncovered associations between mitochondrial metabolism and pheromone production. Our findings demonstrate how natural genetic variation in core metabolic pathways can affect the production of social signals.
Development of tools for Data Management

With the large volumes of data currently being produced, the scientiﬁc community is posed with the challenge of how to manage large quantities of data. Data management aids researchers with the tasks of analysing, searching, and storing data. In order to push for better data management, and compliance with the open science principles, most funding agencies and research institutions are now requiring that grant applications be accompanied by a Data Management Plan (DMP). A DMP is a document that details how data is to be created, shared, published and preserved. However, not all researchers have the necessary expertise or time to create a DMP and subsequently apply its recommendations. Additionally the existence of multiple DMP templates leads to a generalized lack of standardization in existing DMP documents. The objective of this project is to tackle the challenge posed by the multitude of DMP templates created by funding agencies and research institutes. To achieve this objective the proposed approach is to collect DMP documents with the assistance of the Data Management service of ELIXIR Portugal and store a machine-actionable representation in a triplestore repository. Simultaneously the knowledge that is expressed in the stored DMP documents will be veriﬁed that covers what is required in the DMP template.
Event Transformer FlowNet for optical flow estimation

Event cameras are bioinspired sensors that produce asynchronous and sparse streams of events at image locations where intensity change is detected. They can detect fast motion with low latency, high dynamic range, and low power consumption. Over the past decade, efforts have been conducted in developing solutions with event cameras for robotics applications. In this work, we address their use for fast and robust computation of optical flow. We present ET-FlowNet, a hybrid RNN-ViT architecture for optical flow estimation. Visual transformers (ViTs) are ideal candidates for the learning of global context in visual tasks, and we argue that rigid body motion is a prime case for the use of ViTs since long-range dependencies in the image hold during rigid body motion. We perform end-to-end training with self-supervised learning method. Our results show comparable and in some cases exceeding performance with state-of-the-art coarse-to-fine event-based optical flow estimation.
Real Time Hybrid Rendering Techniques

Ray tracing has long been the holy grail of real time rendering. This technique, commonly used for photo realism, simulates the physical behavior of light, at the cost of being computationally heavy. With the introduction of Nvidia RTX graphic card family, which provides hardware support for ray tracing, this technique started to look like a reality for real time. However, the same problems that afﬂicted the usage of this technique remain, and even with specialized hardware it is still extremely expensive. To account for these drawbacks, researchers and developers pair this technique with rasterization and denoising. This results in a hybrid system that tries to join the best of both worlds, having both photo realistic quality and real time performance. In this work we intend on further exploring hybrid render systems, offering a review of the state of the art with a special focus on real time ray tracing and our own hybrid implementation with photo realistic quality and real time performance ( > 30 fps), implemented using the Vulkan API. In this project, we highlight the detailed analysis of the impacts of History Rectiﬁcation (Variance Color Clamping) on the temporal ﬁlter component of the denoising system and how to overcome the introduced artifacts. Additionally, we also highlight the analysis of the introduction of a separable blur on the spatial ﬁlter and the introduction of Reinhard Tone Mapping prior to denoising, consequently improving this procedure.
S1742170521000119jra 633..643

Despite continuous growth in demand for organic food and farm products, US domestic supply is not keeping pace. Increasing domestic supply requires, in part, that more farms transition to certified organic production. This in turn requires a better understanding of the transition process. This paper reports on a national survey of farmers transitioning to organic certification through participation in the United States Department of Agriculture’s (USDA) Natural Resources Conservation Service (NRCS) Environmental Quality Incentives Program Organic Initiative (EQIP-OI). Our analysis focuses on what motivates farmers to undertake transition to organic certification and what obstacles they confront in the process. The survey population included farmers in the midst of the transition process and farmers who began transition but decided not to pursue organic farming, allowing us to compare both groups to farmers who successfully transitioned to certified organic. Because farmers do not control all of the factors that influence their success, we use a ‘spheres of influence’ framework to analyze obstacles at four levels: the farm, local and regional infrastructure, the marketplace and policy. Our results improve our understanding of the transition process and apply to a wide range of stakeholders and service providers who support farmers in different ways, through crop research, infrastructure development, market development and policy.
A Toolbox for Ef ﬁ cient Proximity-Dependent Biotinylation in Zebra ﬁ sh Embryos

Understanding how proteins are organized in compart-ments is essential to elucidating their function. While proximity-dependent approaches such as BioID have enabled a massive increase in information about organelles, protein complexes, and other structures in cell culture, to date there have been only a few studies on living vertebrates. Here, we adapted proximity labeling for protein discovery in vivo in the vertebrate model organism, zebra ﬁ sh. Using lamin A (LMNA) as bait and green ﬂ uorescent protein (GFP) as a negative control, we developed, optimized, and benchmarked in vivo TurboID and miniTurbo labeling in early zebra ﬁ sh embryos. We developed both an mRNA injection protocol and a transgenic system in which transgene expression is controlled by a heat shock promoter. In both cases, biotin is provided directly in the egg water, and we demonstrate that 12 h of labeling are suf ﬁ cient for biotinylation of prey proteins, which should permit time-resolved analysis of development. After statistical scoring, we found that the proximal partners of LMNA detected in each system were enriched for nuclear envelope and nuclear membrane proteins and included many orthologs of human proteins identi ﬁ ed as proximity partners of lamin A in mammalian cell culture. The tools and protocols developed here will allow zebra- ﬁ sh researchers to complement genetic tools with powerful proteomics approaches.
Comparative efficacy and safety of prophylactic norepinephrine and phenylephrine in spinal anesthesia for cesarean section: A systematic review and meta-analysis with trial sequential analysis

Background: Phenylephrine is the first-line drug used to maintain blood pressure in cesarean delivery. However, it poses a high risk of bradycardia and depression of cardiac activity in pregnant women. Consequently, norepinephrine has gained popularity over the recent years, as an alternative to Phenylephrine because it is thought that prophylactic use of vasopressors may reduce the incidence of hypotension after spinal anesthesia. This systematic review compared the efficacy of both treatments. Methods: We searched the following databases; CNKI, PubMed, Embase, Web of science, clinicaltrials.gov, Medline and Cochrane Library, for randomized controlled trials comparing the prophylactic efficacy of norepinephrine and phenylephrine on elective cesarean delivery under spinal anesthesia. The search period was from inception to July 2022, and the primary outcome indicator was incidence of bradycardia. Statistical analysis was conducted on Rev manager 5.4, and the Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) framework was used to evaluate the quality of evidence from each main finding. Results: A total of 12 papers were included in the analysis. The incidence of bradycardia (RR = 0.37, 95% CI: 0.28 to 0.49, p < 0.00001) and reactive hypertension (RR = 0.58, 95% CI 0.40 to 0.83, p = 0.003) was significantly lower in the norepinephrine (NE) group compared with the phenylephrine (PE) category. In contrast, there were no statistical differences in the umbilical cord blood gas analysis pH values between the groups (arterial: MD = 0.00, 95% CI −0.00 to 0.01, p = 0.22, vein: MD = 0.01, 95% CI −0.00 to 0.02, p = 0.06). The incidence of hypotension, nausea, and vomiting did not differ significantly between the NE and PE groups (hypotension: 23% vs. 18%; nausea: 14% vs. 18%; vomiting: 5% vs. 7%, respectively). Conclusion: Prophylactic use of norepinephrine is safe and effective in maintaining maternal hemodynamics without causing adverse events to either the pregnant woman or fetus. Systematic Review Registration: website https://www.crd. york.ac. uk/prospero/, identifier CRD42022347095
Hepatocellular carcinoma risk-stratification based on ASGR1 in circulating epithelial cells for cancer interception

Purpose: Lack of diagnostic and prognostic biomarkers in hepatocellular carcinoma impedes stratifying patients based on their risk of developing cancer. The aim of this study was to evaluate phenotypic and genetic heterogeneity of circulating epithelial cells (CECs) based on asialoglycoprotein receptor 1 (ASGR1) and miR-122-5p expression as potential diagnostic and prognostic tools in patients with hepatocellular carcinoma (HCC) and liver cirrhosis (LC). Methods: Peripheral blood samples were extracted from LC and HCC patients at different disease stages. CECs were isolated using positive immunomagnetic selection. Genetic and phenotypic characterization was validated by double immunocytochemistry for cytokeratin (CK) and ASGR1 or by in situ hybridization with miR-122-5p and CECs were visualized by confocal microscopy. Results: The presence of CECs increased HCC risk by 2.58-fold, however, this was only significant for patients with previous LC (p = 0.028) and not for those without prior LC (p = 0.23). Furthermore, the number of CECs lacking ASGR1 expression correlated significantly with HCC incidence and absence of miR-122-5p expression (p = 0.014; r = 0.23). Finally, overall survival was significantly greater for patients at earlier cancer stages (p = 0.018), but this difference was only maintained in the group with the presence of CECs (p = 0.021) whereas progression-free survival was influenced by the absence of ASGR1 expression. Conclusion: Identification and characterization of CECs by ASGR1 and/or miR-122-5p expression may be used as a risk-stratification tool in LC patients, as it was shown to be an independent prognostic and risk-stratification marker in LC and early disease stage HCC patients.