Miracle-dz/UniFAR-FTUs huggingface dataset:
Exposure to sounds during sleep impairs hippocampal sharp wave ripples and memory consolidation

Sleep is critical for the consolidation of recent experiences into long-term memories. As a key underlying neuronal mechanism, hippocampal sharp-wave ripples (SWRs) occurring during sleep define periods of hippocampal reactivation of recent experiences and have been causally linked with memory consolidation. Hippocampal SWR-dependent memory consolidation during sleep is often referred to as occurring during an “offline” state, dedicated to processing internally generated neural activity patterns rather than external stimuli. However, the brain is not fully disconnected from the environment during sleep. In particular, sounds heard during sleep are processed by a highly active auditory system which projects to brain regions in the medial temporal lobe, reflecting an anatomical pathway for sound modulation of hippocampal activity. While neural processing of salient sounds during sleep, such as those of a predator or an offspring, is evolutionarily adaptive, whether ongoing processing of environmental sounds during sleep interferes with SWR-dependent memory consolidation remains unknown. To address this question, we used a closed-loop system to deliver non-waking sound stimuli during or following SWRs in sleeping rats. We found that exposure to sounds during sleep suppressed the ripple power and reduced the rate of SWRs. Furthermore, sounds delivered during SWRs (On-SWR) suppressed ripple power significantly more than sounds delivered 2 seconds after SWRs (Off-SWR). Next, we tested the influence of sound presentation during sleep on memory consolidation. To this end, SWR-triggered sounds were applied during sleep sessions following learning of a conditioned place preference paradigm, in which rats learned a place-reward association. We found that On-SWR sound pairing during post-learning sleep induced a complete abolishment of memory retention 24 h following learning, while leaving memory retention immediately following sleep intact. In contrast, Off-SWR pairing weakened memory 24 h following learning as well as immediately following learning. Notably, On-SWR pairing induced a significantly larger impairment in memory 24 h after learning as compared to Off-SWR pairing. Together, these findings suggest that sounds heard during sleep suppress SWRs and memory consolidation, and that the magnitude of these effects are dependent on sound-SWR timing. These results suggest that exposure to environmental sounds during sleep may pose a risk for memory consolidation processes.
Neural patterns associated with mixed valence feelings differ in consistency and predictability throughout the brain

Mixed valence feelings, defined by the simultaneous presence of positive and negative affect, remain understudied in neuroscience. We used functional magnetic resonance imaging to investigate subjects watching an animated short film known to induce mixed feelings. These same subjects were asked to identify the time periods during which they had experienced positive, negative, and mixed feelings. Using Hidden-Markov models, we found that activity in the insula, amygdala, nucleus accumbens, and anterior cingulate allowed us to predict the onset of new feeling states as determined by individual self-report. Further analyses found spatiotemporally unique and consistent neural patterns in the insular cortex for univalent states, but not for mixed valence states. However, ventromedial prefrontal cortex and anterior cingulate exhibited unique neural consistency for both univalent and mixed valence states. This study is the first to reveal direct evidence for a neurally consistent representation of mixed feelings in the central nervous system.
QTL analysis of floral morphology polymorphisms between Gilia yorkii and G. capitata

Speciation is a complex process typically accompanied by significant genetic and morphological differences between sister populations. In plants, this can result in divergent floral morphologies causing pollinator differences and reproductive isolation between populations. Here, we explore floral trait differences between two recently diverged species, Gilia yorkii and G. capitata. The distributions of floral traits in parental, F1, and F2 populations are compared, and groups of correlated traits are identified. We describe the genetic architecture of floral traits through a quantitative trait locus (QTL) analysis using an F2 population of 187 individuals. While all identified QTLs were of moderate (10-25%) effect, interestingly, many QTL intervals colocalized on Chromosomes 6 and 9, suggesting that sets of traits may share a common genetic basis. Our results provide a framework for future identification of genes involved in the evolution of floral morphology.
Compact deep neural network models of visual cortex

A powerful approach to understanding the computations carried out in visual cortex is to develop models that predict neural responses to arbitrary images. Deep neural network (DNN) models have worked remarkably well at predicting neural responses [1, 2, 3], yet their underlying computations remain buried in millions of parameters. Have we simply replaced one complicated system in vivo with another in silico? Here, we train a data-driven deep ensemble model that predicts macaque V4 responses ∼50% more accurately than currently-used task-driven DNN models. We then compress this deep ensemble to identify compact models that have 5,000x fewer parameters yet equivalent accuracy as the deep ensemble. We verified that the stimulus preferences of the compact models matched those of the real V4 neurons by measuring V4 responses to both ‘maximizing’ and adversarial images generated using compact models. We then analyzed the inner workings of the compact models and discovered a common circuit motif: Compact models share a similar set of filters in early stages of processing but then specialize by heavily consolidating this shared representation with a precise readout. This suggests that a V4 neuron’s stimulus preference is determined entirely by its consolidation step. To demonstrate this, we investigated the compression step of a dot-detecting compact model and found a set of simple computations that may be carried out by dot-selective V4 neurons. Overall, our work demonstrates that the DNN models currently used in computational neuroscience are needlessly large; our approach provides a new way forward for obtaining explainable, high-accuracy models of visual cortical neurons.
Adherent reformed islets: a long-term primary cell-based platform for exploring mouse and human islet biology

Pancreatic islets are 3-dimensional micro-organs that maintain β-cell functionality via cell-cell and cell-matrix communication. Isolated primary islets are the gold standard for in vitro models. However, native islets present experimental challenges for long-term mechanistic studies owing to their short culture life (approximately 1 week). We developed a novel long-term protocol to study the function of primary islets. The protocol employed reformed islets following dispersion and a fine-tuned culture environment. Reformed islets are highly similar to their primary counterparts across various physiological characteristics. Long-term culture of reformed islets enables high-resolution imaging, repeated functional assessment, and the study of cell-cell communication. Unlike other platforms such as stem cell-derived organoids, reformed islets retain their resident immune populations, making them ideal for studying both resident and infiltrating immune cells and their interactions with hormone-producing islet cells. Qualitative and quantitative analyses revealed that the composition and cytoarchitecture of the reformed islets mimicked those found in primary islets, including the presence of macrophages and CD4+ and CD8+ T cells, which are the key resident immune cell types. Reformed islets secrete insulin and are glucose-responsive, and their β-cells can be stimulated to proliferate using GLP-1 receptor agonism. Furthermore, a comparison of the transcriptomic landscape of isolated human islets and reformed islets generated from the same donor demonstrated a high degree of similarity. Our reformed islets provide an ideal platform to study diabetes pathology. We recapitulated both the T1DM and T2DM disease milieu and validated our model for studying islet immune trafficking and invasion using activated macrophages and T cells. Our data illustrates that reformed islets are an anatomical and functional alternative to native human and mouse islets. Moreover, reformed islets have an advantage over mouse and human β-cell lines, including MIN6 and EndoC-βH1cells, that lack the signalling input of non-β-endocrine cells and immune cell crosstalk. In this study, we showed that reformed islets are a durable paradigm (cell-based model) for islet-based exploration and a means of target discovery/validation for diabetes research. Graphical Abstract
An unmanned aerial vehicle pipeline to estimate body volume at scale for ecological monitoring

Demographic data are essential to construct mechanistic models to understand how populations change over time and in response to global threats like climate change. Existing demographic data are either lacking or insufficient for many species, particularly those that are challenging to study, such as marine mammals. A pipeline for collecting accurate demographic data to construct robust demographic models at scale would fill this knowledge gap for many species, including marine mammals like pinnipeds (seals, sea lions, and walruses). We introduce a non-invasive pipeline to estimate the 3D body size (volume) of species that will allow monitoring at high spatial and temporal scales. Our pipeline integrates 3D structure-from-motion photogrammetry data collected via planned flight missions using off-the-shelf, multirotor unmanned aerial vehicles (UAVs). We apply and validate this pipeline on the grey seal Halichoerus grypus, a marine species that spends much of its time at sea but is predictably observable during its annual breeding season. We investigate the optimal ground sampling distance (GSD) for surveys by calculating the success rates and accuracy of volume estimates of individuals at different elevations. We establish an optimal GSD of 0.8 cm px-1 for animals similar in size to UK grey seals (∼1.4 - 2.5 m length), making our pipeline reproducible and applicable to a broad range of organisms. Volume estimates were accurate and could be made for up to 68% of hauled-out seals in the study areas. Finally, we highlight six key traits that make a species well-suited to estimating body volume following this pipeline. Good candidates include large reptiles like crocodiles, large mammals such as hippopotamus, and shrubs or bushes in deserts and Mediterranean habitats. Our pipeline accurately estimates individual body volume of marine macrovertebrates in a time-and cost-effective manner whilst minimising disturbance. Whilst the approach is applied to pinnipeds here, the pipeline is adaptable to many different taxa that are otherwise challenging to study. Our proposed approach therefore opens up previously inaccessible areas of the Tree of Life to demographic studies, which will improve our ability to protect and conserve these species into the future.
Transmission dynamics of MERS-CoV in a transgenic human DPP4 mouse model

Since 2002, three novel coronavirus outbreaks have occurred: severe acute respiratory syndrome coronavirus (SARS-CoV-1), Middle East respiratory syndrome coronavirus (MERS-CoV), and SARS-CoV-2. A better understanding of the transmission potential of coronaviruses will result in adequate infection control precautions and an early halt of transmission within the human population. Experiments on the stability of coronaviruses in the environment, as well as transmission models, are thus pertinent. Here, we show that transgenic mice expressing human DPP4 can be infected with MERS-CoV via the aerosol route. Exposure to 5×106 TCID50 and 5×104 TCID50 MERS-CoV per cage via fomites resulted in transmission in 15 out of 20 and 11 out of 18 animals, respectively. Exposure of sentinel mice to donor mice one day post inoculation with 105 TCID50 MERS-CoV resulted in transmission in 1 out of 38 mice via direct contact and 4 out of 54 mice via airborne contact. Exposure to donor mice inoculated with 104 TCID50 MERS-CoV resulted in transmission in 0 out of 20 pairs via direct contact and 0 out of 5 pairs via the airborne route. Our model shows limited transmission of MERS-CoV via the fomite, direct contact, and airborne routes. The hDPP4 mouse model will allow assessment of the ongoing evolution of MERS-CoV in the context of acquiring enhanced human-to-human transmission kinetics and will inform the development of other transmission models.
Cyclic and pseudo-cyclic electron pathways play antagonistic roles during nitrogen deficiency in Chlamydomonas reinhardtii

Nitrogen (N) scarcity is a frequently encountered situation that constrains global biomass productivity. In response to N deficiency, cell division stops and photosynthetic electron transfer is downregulated, while carbon storage is enhanced. However, the molecular mechanism downregulating photosynthesis during N deficiency and its relationship with carbon storage are not fully understood. The Proton Gradient Regulator-like 1 (PGRL1) controlling cyclic electron flow (CEF) and Flavodiiron proteins involved in pseudo-(CEF) are major players in the acclimation of photosynthesis. To determine the role of PGRL1 or FLV in photosynthesis under N deficiency, we measured photosynthetic electron transfer, oxygen gas exchange and carbon storage in Chlamydomonas pgrl1 and flvB knockout mutants. Under N deficiency, pgrl1 maintains higher net photosynthesis and O2 photoreduction rates, while flvB shows a similar response compared to control strains. Cytochrome b6f and PSI are maintained at a higher abundance in pgrl1. The photosynthetic activity of flvB and pgrl1 flvB double mutants decreases in response to N deficiency similar to the control strains. Furthermore, the preservation of photosynthetic activity in pgrl1 is accompanied by an increased accumulation of triacylglycerol depending on the genetic background. Taken together, our results suggest that in the absence of PGRL1-controlled CEF, FLV-mediated PCEF maintains net photosynthesis at a high level and that CEF and PCEF play antagonistic roles during N deficiency. It further illustrates how nutrient status and genetic makeup of a strain can affect the regulation of photosynthetic energy conversion in relation to carbon storage and provides new strategies for improving lipid productivity in algae. Significance statement Nitrogen (N) deficiency, an often-encountered phenomenon in nature, results in growth arrest, downregulation of photosynthesis and massive carbon storage in microalgae. However, more mechanistic insights involved in tuning photosynthetic electron transfer during N deficiency are required. Here, we provide evidence that a well-conserved protein in chlorophytes, the Proton Gradient Regulator-like 1 (PGRL1), is a key regulator of photosynthesis during N deficiency. In its absence, cells exhibited sustained photosynthesis thanks to the Flavodiiron (FLV) proteins. We propose that both PGRL1 and FLV, by having antagonistic roles in N deficiency, manage the redox landscape, carbon storage and biomass production. Our work revolves around the current paradigm of photosynthesis regulation during N deficiency and provides a new framework for improving biomass production and carbon storage in microalgae for biotechnological purposes.
Interacting at a distance: a critical review of the role of ICT in developing the learner–context interface in a university language programme

Abstract This article examines the introduction of new online technologies to support distance language learning in a higher education institution in the UK, charting the development from using telephone conferencing in the 1990s to the implementation of Moodle and videoconferencing more recently. It uses the sociocultural concept of the learner–context interface to emphasise the centrality of both learners and context in the design and delivery of technology-supported language courses rather than making the development of computer-mediated learning opportunities the main focus. Building on research and evaluation work carried out over more than 15 years, the authors of this article analyse the issues that have arisen and that have affected change regarding technology and pedagogy. Central areas of investigation in terms of the learners were found to be interaction, learning communities, metacognition, literacy, affect and learner support; in terms of context they include task design, teacher roles and teacher skills. In the conclusion, limitations of the research and new developments are outlined.
Interacting at a distance: a critical review of the role of ICT in developing the learner–context interface in a university language programme

Interacting at a distance: a critical review of the role of ICT in developing the learner–context interface in a university language programme Journal Item How to cite: Hampel, Regine and de los Arcos, Beatriz (2013). Interacting at a distance: a critical review of the role of ICT in developing the learner–context interface in a university language programme. Innovation in Language Learning and Teaching, 7(2) pp. 158–178.
IMAGE DEHAZING TO ENHANCE IMAGE QUALITY USING DCP AND GUIDED FILTER BASED HYBRID ALGORITHM

: Image dehazing is a critical task in computer vision and image processing that aims to restore clear visibility in hazy or foggy images. In recent years, significant advancements have been made in image dehazing algorithms, leading to improved results and enhanced visual quality. This paper presents a comprehensive review and comparative analysis of state-of-the-art image dehazing techniques. We categorize the existing methods into different groups based on their underlying principles and analyze their strengths and limitations. Additionally, we provide a comparative evaluation of these techniques based on various metrics, including visual quality, computational complexity, and robustness to different hazing conditions. This analysis aims to assist researchers and practitioners in understanding the current landscape of image dehazing methods and identifying avenues for future research.
A Study of Soil Heavy Metal Pollution in the Manganese Mining in Drama, Greece

 Abstract — The release of heavy metals into the environment has increased over the last years. In this study, 25 soil samples (0-15 cm) from the fields near the mining area in Drama region were selected. The samples were analyzed in the laboratory for their physicochemical properties and for seven “pseudo-total’’ heavy metals content, namely Pb, Zn, Cd, Cr, Cu, Ni, and Mn. The total metal concentrations (Pb, Zn, Cd, Cr, Cu, Ni and Mn) in digests were determined by using the atomic absorption spectrophotometer. According to the results, the mean concentration of the listed heavy metals in 25 soil samples are Cd 1.1 mg/kg, Cr 15 mg/kg, Cu 21.7 mg/kg, Ni 30.1 mg/kg, Pd 50.8 mg/kg, Zn 99.5 mg/kg and Mn 815.3 mg/kg. The results show that the heavy metals remain in the soil even if the mining closed many years ago.
LOWER TRIASSIC ICHNOFOSSILS AND SEDIMENTARY ENVIRONMENTS IN THE DENGFENG AREA,WESTERN HENAN PROVINCE

The Lower Triassic Liujiagou and Heshanggou formations in the Dengfeng area consist of fluvial and lacustrine deposits.On the basis of sedimentary characteristics,8types of sedimentary sequence were established.Additionally,many continental ichnofossils,including at least 8ichnogenera and 10 ichnospecies,have been recovered.Three ichnoassemblages have been recognized including,1)the Scoyeniaichnoassemblage in very shallow and periodically exposed flood plains land and overbank environments,2)the Arenicolites ichnoassemblage in lakeshore environment where water levels fluctuated frequently,and 3)the Taenidium-Planolites ichnoassemblage in the relatively calm shallow lacustrine environment.Based on a comprehensive analysis of sedimentary and ichnofossil data,a sedimentary environment model of ichnoassemblages is proposed for the Early Triassic strata in the study area.
Methane production, consumption and its carbon isotope ratios in the Southern Ocean during the austral summer

Abstract The distribution of dissolved CH 4 in the Southern Ocean at 140 ◦ E was measured dur-ing the austral summer. Surface CH 4 was supersaturated on average, and the calcu-lated mean sea-air ﬂux rate was 0. 32µmolm −2 d −1 . The vertical distributions exhibited 5 a CH 4 maximum at approximately 125 m (∆CH 4 , 2.94nM) below the chlorophyll-richlayer, suggesting a relationship between CH 4 production and plankton dynamics in thisarea. CH 4 oxidation and ocean movement characteristics in the deep layer led to theenrichment and ﬂuctuation of δ 13 C CH 4 . We estimated the inﬂuence of Southern OceanCH 4 , a source of isotopically heavy CH 4 to the atmosphere, on the global CH 4 budgetto be approximately 0.19Ggd −1 . 10 1 Introduction Considerable attention has recently been focused on biogenic trace gases in ecosys-tems because they include a signiﬁcant amount of greenhouse gases. Methane (CH 4 )is an eﬀective greenhouse gas that is approximately 20 times more eﬀective in radiative 15 forcing than CO
Climate change and its influence on plant species and terrestrial habitats

Several scenarios regarding the effects of climate change on the spatial distribution of plant species are proposed, highlighting the problems of bioclimatic envelop models (BEM) that have recently proliferated. Distortions of these models may be due to natural or anthropic causes, and all in all these might have a significant effect on the estimated projections. It is essential to include the ecosystem concept when estimating the effects of climate change, which implies the implementation of habitat (as defined by the European Union) studies. Climate change poses a series of challenges related to conservation, since the change in species distributions and ecosystems has a substantial impact on the functionality of protected areas networks and ecological corridors currently in use. Biodiversity collections such as gene banks become more relevant, and the role of ecological restoration increases in importance. For the measures to be effective, the emphasis should be on a programme that addresses the consequences of climate change taking into account the ecosystem concept and acting at habitat and landscape levels, rather than at species level.