Miracle-dz/UniFAR-FTUs huggingface dataset:
Increased Utilization of Storm Surge Barriers: A Research Agenda on Estuary Impacts

Rising coastal flood risk and recent disasters are driving interest in the construction of gated storm surge barriers worldwide, with current studies recommending barriers for at least 11 estuaries in the United States alone. Surge barriers partially block estuary‐ocean exchange with infrastructure across an estuary or its inlet and include gated areas that are closed only during flood events. They can alter the stratification and salt intrusion, change sedimentary systems, and curtail animal migration and ecosystem connectivity, with impacts growing larger with increasing gate closures. Existing barriers are being used with increasing frequency due to sea level rise. New barrier proposals typically come with maximum closure frequency recommendations, yet the future adherence to them is uncertain. Given that the broader environmental effects and coupled‐human dynamics of surge barriers are not well‐understood, we present an interdisciplinary research agenda for this increasingly prevalent modification to our coastal zone.
Melting Alpine Water Towers Aggravate Downstream Low Flows: A Stress‐Test Storyline Approach

Droughts can lead to extreme low flow situations in rivers, with resulting severe impacts. Upstream snow and ice melt in many of the world's mountain water towers can alleviate the hydrological consequences of drought, yet global warming threatens the cryosphere. To improve the understanding of melt water contributions during drought in the case of future glacier retreat, we developed stress‐test storyline scenarios to model streamflow and tested them in the European river Rhine basin. Meteorological conditions of past drought and low flow years in Europe, 1976, 2003, and 2018, were repeated at three future moments in time, representing nowadays, near future and far future conditions. The latter two conditions were obtained by climate projections under the RCP8.5 scenario. Results show that the low flow situations caused by the meteorological drought situations aggravate in future conditions, more so for the far future and for the year 2003 because of the relatively large glacier ice melt contribution in the past. Summer (July–September) streamflow may decline by 5%–25% far downstream and 30%–70% upstream and the duration of extreme low flow situations may double compared to the selected past drought events. These results are relevant for the Rhine as a major European river but stand exemplary for many other river basins and highlight the importance of cryospheric changes for downstream low flow situations in a changing climate. The stress‐test scenarios allow a glimpse into future extreme low flow events aiding adaptation planning, and might be adapted to include other important low flow drivers.
Stereotypical hippocampal clustering predicts navigational success in virtualized real-world environments

Structural differences along the long-axis of the hippocampus have long been believed to underlie meaningful functional differences, such as the granularity of information processing. Recent findings show that data-driven parcellations of the hippocampus sub-divide the hippocampus into a 10-cluster map with anterior-medial, anterior-lateral, and posteroanterior-lateral, middle, and posterior components. We tested whether task and experience could modulate this clustering using a spatial learning experiment where subjects were trained to virtually navigate a novel neighborhood in a Google Street View-like environment over a two-week period. Subjects were scanned while navigating routes early in training and at the end of their two-week training. Using the 10-cluster map as the ideal template, we find that subjects who eventually learn the neighborhood well have hippocampal cluster-maps consistent with the ideal—even on their second day of learning—and their cluster mappings do not change over the two week training period. However, subjects who eventually learn the neighborhood poorly begin with hippocampal cluster-maps inconsistent with the ideal, though their cluster mappings become more stereotypical by the end of the two week training. Interestingly this improvement seems to be route specific as even after some early improvement, when a new route is navigated participants’ hippocampal maps revert back to less stereotypical organization. We conclude that hippocampal clustering is not dependent solely on anatomical structure, and instead is driven by a combination of anatomy, task, and importantly, experience. Nonetheless, while hippocampal clustering can change with experience, efficient navigation depends on functional hippocampal activity clustering in a stereotypical manner, highlighting optimal divisions of processing along the hippocampal anterior-posterior and medial-lateral-axes.
Model-based concept to extract heart beat-to-beat variations beyond respiratory arrhythmia and baroreflex

Heart rate (HR) and its variability (HRV) reflect the autonomous nervous system (ANS) modulation, especially sympathovagal balance. This work aims to present concept of a personalizable HR model and an in silico system to identify the HR regulation parameters and subsequently capture residual heart beat-to-beat variations from individual psychophysiological recordings in humans. The model encompasses respiratory sinus arrhythmia (RSA) and baroreflex mechanisms, and uses respiration and blood pressure signals and the time instances of R peaks from an electrocardiogram as inputs. The system extracts the residual displacements of the modeled R peaks relative to the real R peaks. Three components – tonic, spontaneous, and 0.1 Hz changes – can be derived from these R peak residual displacements and can, therefore, enhance HRV analysis beyond RSA and baroreflex. Our model-based concept suggests that these residuals are not merely modeling errors. The proposed method could help to investigate additional neural regulation impulses from the higher-order brain and other influences.
Allosterically coupled conformational dynamics in solution prepare the sterol transfer protein StarD4 to release its cargo upon interaction with target membranes

Complex mechanisms regulate the cellular distribution of cholesterol, a critical component of eukaryote membranes involved in regulation of membrane protein functions directly and through the physiochemical properties of membranes. StarD4, a member of the steroidogenic acute regulator-related lipid-transfer (StART) domain (StARD)-containing protein family, is a highly efficient sterol-specific transfer protein involved in cholesterol homeostasis. Its mechanism of cargo loading and release remains unknown despite recent insights into the key role of phosphatidylinositol phosphates in modulating its interactions with target membranes. We have used large-scale atomistic Molecular dynamics (MD) simulations to study how the dynamics of cholesterol bound to the StarD4 protein can affect interaction with target membranes, and cargo delivery. We identify the two major cholesterol (CHL) binding modes in the hydrophobic pocket of StarD4, one near S136&S147 (the Ser-mode), and another closer to the putative release gate located near W171, R92&Y117 (the Trp-mode). We show that conformational changes of StarD4 associated directly with the transition between these binding modes facilitate the opening of the gate. To understand the dynamics of this connection we apply a machine-learning algorithm for the detection of rare events in MD trajectories (RED), which reveals the structural motifs involved in the opening of a front gate and a back corridor in the StarD4 structure occurring together with the spontaneous transition of CHL from the Ser-mode of binding to the Trp-mode. Further analysis of MD trajectory data with the information-theory based NbIT method reveals the allosteric network connecting the CHL binding site to the functionally important structural components of the gate and corridor. Mutations of residues in the allosteric network are shown to affect the performance of the allosteric connection. These findings outline an allosteric mechanism which prepares the CHL-bound StarD4 to release and deliver the cargo when it is bound to the target membrane.
Unravelling individual rhythmic abilities using machine learning

Humans can easily extract the rhythm of a complex sound, like music, and move to its regular beat, for example in dance. These abilities are modulated by musical training and vary significantly in untrained individuals. The causes of this variability are multidimensional and typically hard to grasp with single tasks. To date we lack a comprehensive model capturing the rhythmic fingerprints of both musicians and non-musicians. Here we harnessed machine learning to extract a parsimonious model of rhythmic abilities, based on the behavioral testing (with perceptual and motor tasks) of individuals with and without formal musical training (n = 79). We demonstrate that the variability of rhythmic abilities, and their link with formal and informal music experience, can be successfully captured by profiles including a minimal set of behavioral measures. These profiles can shed light on individual variability in healthy and clinical populations, and provide guidelines for personalizing rhythm-based interventions.
Environmental modulators of algae-bacteria interactions at scale

Photosynthetic microbes associated with non-photosynthetic, heterotrophic, bacteria play a key role in the global primary production. Understanding these phototroph-heterotroph associations is therefore important, but remains challenging because they reside in chemically complex aquatic and terrestrial environments. We do not understand how the myriad of environmental parameters from nutrient availability to pH impact interactions between phototrophs and their heterotrophic partners. Here, we leverage a massively parallel droplet microfluidic platform that enables us to interrogate algae-bacteria interactions in >100,000 communities across ∼525 environmental conditions with varying pH, carbon availability and phosphorous availability. By developing a statistical framework to dissect interactions in this complex dataset, we reveal that dependance of algae-bacteria interactions on nutrient availability is strongly modulated by pH and buffering capacity. Furthermore, we show that the chemical identity of the available organic carbon source controls how pH, buffering capacity, and nutrient availability modulate algae-bacteria interactions. By leveraging a high-throughput platform, our study reveals the previously underappreciated role of pH in modulating phototroph-heterotroph interactions.
Predicting future conservation areas while avoiding competition in two alpine urodele amphibians severely threatened by climate change

Climate change will cause important declines in species distributions, especially when living at high altitudes. The Critically Endangered Salamandra lanzai from SW Alps may be severely exposed to future climate change effects and its suitable climate may shrink or shift. Another Alpine salamander (S. atra) is present in the region, which in case of spatial overlap may represent a competitor for S. lanzai. It is urgent to estimate the effect of future climate change on these species and identify priority areas for conservation while accounting for competition between both species. With a Species Distribution Modelling (SDM) approach, we projected the current and future climate suitability of both salamander species. We accounted for uncertainty related to the methods (model replicates) and climate projections (data source, global circulation model and scenario) to provide a consensus map for practitioners. This map also takes into account potential competition with S. atra by penalizing the suitability scores of S. lanzai by the scores of S. atra. We predict a severe effect of climate change on both species. Most of the current habitats are projected to become largely unsuitable by 2070, regardless of the climatology and scenario. We identified important spatial disagreements between projections based on different data sources, mostly due to precipitation projections and daily temperature variation. This highlights the need to account for multiple climatologies in mountainous environments. Both species’ habitats are highly fragmented, which is expected to prevent distributional shifts through natural dispersion. We suggest to explore the possibility of translocation for the most threatened populations and simultaneously develop captive breeding programs. Biotic interactions are rarely accounted for in SDMs, and we encourage the documentation of species with similar ecological requirements to improve the relevance of SDMs for future conservation planning.
Point cloud registration based on concave hull association

ABSTRACT This letter presents a point cloud coarse registration method based on concave hull association. The assumption is that some internal points may be variable in different scans due to self-occlusion, but the hull vertices in overlap regions are consistent. Therefore, we only use the vertices of the concave hulls to find feature associations and reduce the number of wrong correspondences. Firstly, the method extracts the concave hulls and calculates the unique feature descriptors for each vertex of the hulls. Then, we use the sample consensus initial alignment algorithm to achieve feature matching and find the coarse registration parameters. The proposed method has been verified on different datasets and compared with state-of-the-art algorithms. The experiments demonstrate that the proposed algorithm eliminates unnecessary correspondences and obtains high efficiency and robustness.
Fast centromeric repeat turnover provides a glimpse into satellite DNA evolution in Nothobranchius annual killifishes

Satellite DNA (satDNA) is rapidly evolving class of tandem repeats with some motifs being involved in centromere organization and function. Rapid co-evolution of centromeric satDNA and associated proteins has been mostly attributed to the so-called centromere drive. To identify repeats associated with centromeric regions and test for the role of meiotic drive in their evolution, we investigated satDNA across Southern and Coastal clades of African annual killifishes of the genus Nothobranchius. C-banding showed expansion of (peri)centromeric heterochromatin regions in the Southern-clade killifishes. Molecular cytogenetic and bioinformatic analyses further revealed that two previously identified satellites, Nfu-SatA and Nfu-SatB, are associated with centromeres only in one lineage of the Southern clade. Nfu-SatB was, however, detected outside centromeres also in other members of the Coastal clade, which is consistent with the “library” hypothesis of satDNA evolution. We also identified a novel satDNA, Cl-36, associated with (peri)centromeres in N. foerschi, N. guentheri and N. rubripinnis from the Coastal clade. Our findings could be explained by centromere drive shaping karyotype change and centromeric repeat turnover in Nothobranchius species with possible reversal of spindle polarity within the Southern clade.
Editorial: Cryptosporidium, Giardia, Cyclospora, and Toxoplasma - Insights into their transmission

COPYRIGHT © 2023 Razakandrainibe, Ortega and La Carbona. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. TYPE Editorial PUBLISHED 27 March 2023 DOI 10.3389/fcimb.2023. 1175108
Microfluidic/HPLC combination to study carnosine protective activity on challenged human microglia: Focus on oxidative stress and energy metabolism

Carnosine (β-alanyl-L-histidine) is a naturally occurring endogenous peptide widely distributed in excitable tissues such as the brain. This dipeptide possesses well-demonstrated antioxidant, anti-inflammatory, and anti-aggregation properties, and it may be useful for treatment of pathologies characterized by oxidative stress and energy unbalance such as depression and Alzheimer’s disease (AD). Microglia, the brain-resident macrophages, are involved in different physiological brain activities such synaptic plasticity and neurogenesis, but their dysregulation has been linked to the pathogenesis of numerous diseases. In AD brain, the activation of microglia towards a pro-oxidant and pro-inflammatory phenotype has found in an early phase of cognitive decline, reason why new pharmacological targets related to microglia activation are of great importance to develop innovative therapeutic strategies. In particular, microglia represent a common model of lipopolysaccharides (LPS)-induced activation to identify novel pharmacological targets for depression and AD and numerous studies have linked the impairment of energy metabolism, including ATP dyshomeostasis, to the onset of depressive episodes. In the present study, we first investigated the toxic potential of LPS + ATP in the absence or presence of carnosine. Our studies were carried out on human microglia (HMC3 cell line) in which LPS + ATP combination has shown the ability to promote cell death, oxidative stress, and inflammation. Additionally, to shed more light on the molecular mechanisms underlying the protective effect of carnosine, its ability to modulate reactive oxygen species production and the variation of parameters representative of cellular energy metabolism was evaluated by microchip electrophoresis coupled to laser-induced fluorescence and high performance liquid chromatography, respectively. In our experimental conditions, carnosine prevented LPS + ATP-induced cell death and oxidative stress, also completely restoring basal energy metabolism in human HMC3 microglia. Our results suggest a therapeutic potential of carnosine as a new pharmacological tool in the context of multifactorial disorders characterize by neuroinflammatory phenomena including depression and AD.
Controversial role of ILC3s in intestinal diseases: A novelty perspective on immunotherapy

ILC3s have been identified as crucial immune regulators that play a role in maintaining host homeostasis and modulating the antitumor response. Emerging evidence supports the idea that LTi cells play an important role in initiating lymphoid tissue development, while other ILC3s can promote host defense and orchestrate adaptive immunity, mainly through the secretion of specific cytokines and crosstalk with other immune cells or tissues. Additionally, dysregulation of ILC3-mediated overexpression of cytokines, changes in subset abundance, and conversion toward other ILC subsets are closely linked with the occurrence of tumors and inflammatory diseases. Regulation of ILC3 cytokines, ILC conversion and LTi-induced TLSs may be a novel strategy for treating tumors and intestinal or extraintestinal inflammatory diseases. Herein, we discuss the development of ILCs, the biology of ILC3s, ILC plasticity, the correlation of ILC3s and adaptive immunity, crosstalk with the intestinal microenvironment, controversial roles of ILC3s in intestinal diseases and potential applications for treatment.
Optimal Cheating And Inspection Strategies Under A Chemical Weapons Treaty

AbstractA chemical weapons non-production agreement including limited numbers of shortnotice inspections at specified facilities is a definite future possibility. The verification aspects of such a treaty would present new and important strategic problems which are studied here for the case of a single production site. An inspector miist select when to inspect the facility, keeping in mind the length of time remaining in the treaty and the limited number of inspections permitted under it. The inspectee must determine and adjust the level of cheating — cheating more increases the inspectee’s gain if undetected but also increases the probability of detection in an inspection. These choices are modeled by a two-person zero-sum sequential game which has optimal strategies and a value that can be determined inductively. This model yields numerical and analytic results which have significant policy implications when interpreted in the context of chemical weapons treaties.
Editorial: The role of transcription factors in inborn errors of immunity

COPYRIGHT © 2023 Bogaert, Kuehn, Bordon and Haerynck. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. TYPE Editorial PUBLISHED 27 March 2023 DOI 10.3389/fimmu.2023. 1189312
Toward high-throughput engineering techniques for improving CAR intracellular signaling domains

Chimeric antigen receptors (CAR) are generated by linking extracellular antigen recognition domains with one or more intracellular signaling domains derived from the T-cell receptor complex or various co-stimulatory receptors. The choice and relative positioning of signaling domains help to determine chimeric antigen receptors T-cell activity and fate in vivo. While prior studies have focused on optimizing signaling power through combinatorial investigation of native intracellular signaling domains in modular fashion, few have investigated the prospect of sequence engineering within domains. Here, we sought to develop a novel in situ screening method that could permit deployment of directed evolution approaches to identify intracellular domain variants that drive selective induction of transcription factors. To accomplish this goal, we evaluated a screening approach based on the activation of a human NF-κB and NFAT reporter T-cell line for the isolation of mutations that directly impact T cell activation in vitro. As a proof-of-concept, a model library of chimeric antigen receptors signaling domain variants was constructed and used to demonstrate the ability to discern amongst chimeric antigen receptors containing different co-stimulatory domains. A rare, higher-signaling variant with frequency as low as 1 in 1000 could be identified in a high throughput setting. Collectively, this work highlights both prospects and limitations of novel mammalian display methods for chimeric antigen receptors signaling domain discovery and points to potential strategies for future chimeric antigen receptors development.