Miracle-dz/UniFAR-FTUs huggingface dataset:
Microtubule retrograde flow retains neuronal polarization in a fluctuating state

In developing vertebrate neurons, a neurite is formed by more than a hundred microtubules. While individual microtubules are dynamic, the microtubule array itself has been regarded as stationary. Using live cell imaging in combination with photoconversion techniques and pharmacological manipulations, we uncovered that the microtubule array flows retrogradely within neurites to the soma. This microtubule retrograde flow drives cycles of microtubule density, a hallmark of the fluctuating state before axon formation. Shortly after axon formation, microtubule retrograde flow slows down in the axon, which stabilizes microtubule density cycles and thereby functions as a molecular wedge to enable axon extension. We propose microtubule retrograde flow and its specific slowdown in the axon to be the long-sought mechanism to single one neurite out to drive neuronal polarization.
Transition Between Sensitive Delusion of Reference and Mood Disorder: A Case Report

The Sensitive Delusion of Reference is a clinical entity described by Ernst Kretschmer and never integrated into mainstream nosographic systems. It represents the possibility of developing psychosis starting from a personality characterized by sensitivity, scrupulousness, and fear of judgment of others. The presentation of the following clinical case highlights how the overlap between this clinical entity and mood disorders leads to characteristic psychopathology, which has not been sufficiently detailed. In particular, the delusions, which always starts from the idea of reference and the shame in the face of the judgment of others, takes on characteristics of guilt during the depressive phases and persecutory themes during the activation phases. This clinical observation, which obviously needs to be confirmed on a larger scale, encourages a renewed interest in the concept of Kretschmer's Sensitive Delusion of Reference and creates the possibility of intersecting multiple psychopathological levels, for a more complete perspective on the individual case.
Delineating Conservation Areas for Cohabiting Species: An Example of Vernal Pond Conservation From Fort Stewart in Georgia, United States

Military installations are valuable in global biodiversity conservation as they secure representative ecosystems from land conversion and protect many threatened or endangered species. Selecting suitable areas for biodiversity conservation within military installations is a challenging problem as this must not impede military training activities. The issue gets more complicated when considering multiple cohabiting species in a metacommunity with species dependency. In this paper, we present an example for the conservation of two cohabiting species, Gopher Tortoise (GT) and Gopher Frog (GF), located within the boundaries of a military installation, Fort Stewart, Georgia, United States. The GF depends on both locations of GT habitat (burrows) and ephemeral vernal ponds (for breeding). We develop a model that identifies the cost-efficient areas for the conservation of these two species while taking into account the dependency of GF on GT burrows. The model selects a specified number of conservation areas for the two species, where each GF conservation area covers an adequate number of vernal ponds for the GFs to accommodate their reproduction, and each GT conservation area provides adequate habitat quality to sustain a viable GT population. The model also requires each GF site to be located close to GT sites so that the GFs could find refuge after they leave the water. We use the total distance of selected sites to the main roads in the military installation as a proxy for the conservation cost. We achieve contiguity of each conservation area by selecting sites that are adjacent to a central site of the conservation area to ensure undisrupted travel for both the GFs and the GTs. Using the model, we generated alternative configurations of conservation areas that could be considered by the land managers of Fort Stewart. Our methods are general and can be applied to other reserve site selection and land management problems with cohabiting interrelated species.
Application of Human Induced Pluripotent Stem Cell-Derived Cellular and Organoid Models for COVID-19 Research

The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its rapid international spread has caused the coronavirus disease 2019 (COVID-19) pandemics, which is a global public health crisis. Thus, there is an urgent need to establish biological models to study the pathology of SARS-CoV-2 infection, which not only involves respiratory failure, but also includes dysregulation of other organs and systems, including the brain, heart, liver, intestines, pancreas, kidneys, eyes, and so on. Cellular and organoid models derived from human induced pluripotent stem cells (iPSCs) are ideal tools for in vitro simulation of viral life cycles and drug screening to prevent the reemergence of coronavirus. These iPSC-derived models could recapitulate the functions and physiology of various human cell types and assemble the complex microenvironments similar with those in the human organs; therefore, they can improve the study efficiency of viral infection mechanisms, mimic the natural host-virus interaction, and be suited for long-term experiments. In this review, we focus on the application of in vitro iPSC-derived cellular and organoid models in COVID-19 studies.
Critical Influenza-Like Illness in a Nine-Year-Old Associated With a Poultry-Origin H9N2 Avian Influenza Virus: Risk Assessment and Zoonotic Potential

Subtype H9N2 avian influenza viruses (AIV), now the predominant avian influenza virus subtype in poultry in China, cause sporadic human infections manifesting as mild influenza-like illness. We isolated an H9N2 AIV from a critical case of respiratory illness in a 9-year-old with no underlying conditions. As this virus was associated with critical illness, we conducted a risk assessment to determine its mammalian pathogenicity. Clinical and laboratory data were collected from hospital records. A/Suzhou/GIRD01/2019 (H9N2) (GIRD01) was isolated from a throat swab and used in risk-assessment studies in comparison to prototypical and contemporary H9N2 AIVs and contemporary seasonal subtype H1N1 and H3N2 influenza viruses. The patient presented with fever, vomiting but rapidly declined to progressive wheezing followed by dyspnea. The patient was admitted to the intensive care unit and placed on mechanical ventilation. A diagnosis of pneumonia and type I respiratory failure was made. Viral RNA was detected in the bronchiolavelolar lavage and anal swab specimens, suggesting lower lung and extrapulmonary involvement. Respiratory syncytial virus was also detected by immunofluorescence in bronchiolavelolar lavage. Following an aggressive regimen of antiviral and antibacterial therapy, the patient recovered and was discharged from hospital after 13 days. GIRD01 was closely related to poultry-origin H9N2 AIVs in the area and contained several known markers of mammalian pathogenicity. GIRD01 also showed a strong affinity for mammalian-type over avian-type sialic acids. GIRD01 replicated more efficiently compared to older H9N2 viruses and contemporary seasonal viruses in vitro and produced asymptomatic infections in mice. In summary, GIRD01 was well-adapted to replication in in vitro and in vivo mammalian models but was not more pathogenic compared to similar contemporary strains of H9N2 AIVs. Therefore, these viruses may pose a risk of causing severe respiratory disease in humans.
Biomarkers for heart failure and prognostic prediction in patients with Fontan circulation.

A wide variety of pathologies are involved in heart failure in patients with congenital heart disease (CHD). Specific causes of heart failure after the Fontan procedure include not only single-ventricle circulation but also the function of the right ventricle as the systemic ventricle, atrioventricular or semilunar valve stenosis or regurgitation, pulmonary hypertension, and left ventricular dysfunction secondary to right ventricular enlargement or dysfunction. As post-Fontan heart failure can occur for a variety of reasons, clarification of pathophysiology is the first step in management and treatment. At the same time, it is important to understand each patient's current condition and treatment plan to make an accurate prognosis. Due to the wide variety of pathophysiologies in post-Fontan CHD patients, however, no single biomarker is useful in all situations. Relevant biomarkers must be selected according to each patient's disease state, and combinations of multiple biomarkers should also be considered. In this review, the author describes the clinical importance of various biomarkers for patients who have undergone a Fontan procedure.
Bidirectional relationship between cardiac extracellular matrix and cardiac cells in ischemic heart disease

Ischemic heart diseases (IHDs), including myocardial infarction and cardiomyopathies, are a leading cause of mortality and morbidity worldwide. Cardiac‐derived stem and progenitor cells have shown promise as a therapeutic for IHD but are limited by poor cell survival, limited retention, and rapid washout. One mechanism to address this is to encapsulate the cells in a matrix or three‐dimensional construct, so as to provide structural support and better mimic the cells' physiological microenvironment during administration. More specifically, the extracellular matrix (ECM), the native cellular support network, has been a strong candidate for this purpose. Moreover, there is a strong consensus that the ECM and its residing cells, including cardiac stem cells, have a constant interplay in response to tissue development, aging, disease progression, and repair. When externally stimulated, the cells and ECM work together to mutually maintain the local homeostasis by initially altering the ECM composition and stiffness, which in turn alters the cellular response and behavior. Given this constant interplay, understanding the mechanism of bidirectional cell‐ECM interaction is essential to develop better cell implantation matrices to enhance cell engraftment and cardiac tissue repair. This review summarizes current understanding in the field, elucidating the signaling mechanisms between cardiac ECM and residing cells in response to IHD onset. Furthermore, this review highlights recent advances in native ECM‐mimicking cardiac matrices as a platform for modulating cardiac cell behavior and inducing cardiac repair.
Parameter inference on brain network models with unknown node dynamics and spatial heterogeneity

Model-based data analysis of whole-brain dynamics links the observed data to model parameters in a network of neural masses. In recent years a special focus was placed on the role of regional variance of model parameters for the emergent activity. Such analyses however depend on the properties of the employed neural mass model, which is often obtained through a series of major simplifications or analogies. Here we propose a data-driven approach where the neural mass model needs not to be specified. Building on the recent progresses in identification of dynamical systems with neural networks, we propose a method to infer from the functional data both the neural mass model representing the regional dynamics as well as the region- and subject-specific parameters, while respecting the known network structure. We demonstrate on two synthetic data sets that our method is able to recover the original model parameters, and that the trained generative model produces dynamics resembling the training data both on the regional level and on the whole-brain level. We further apply the method to resting-state fMRI data from Human Connectome Project. We find that to achieve best fit, the model needs two dimensional state space and three regional parameters, one of which is strongly correlated with the map of genetic expression in human brain. The present approach opens a novel way to the analysis of resting-state fMRI with possible applications in understanding the changes of whole-brain dynamics during aging or in neurodegenerative diseases.
Intrapopulation variation in the diet of franciscana dolphin (Pontoporia blainvillei) off southern Brazil

Abstract The franciscana dolphin (Pontoporia blainvillei) is a coastal dolphin endemic to the western South Atlantic Ocean. The dolphin is listed as vulnerable in the IUCN Red List, with incidental catches in gillnet fisheries the greatest conservation concern for this species. Insights into the feeding habits of this dolphin are essential to understand its distribution, movements and use of habitat, which are fundamental for effective management of the species. The feeding habits of franciscana dolphins were investigated from analyses of stomach contents of animals incidentally caught by two fishing operations from southern and northern regions of the southern Brazilian coast. In this study we investigate the existence of intrapopulation (sexual maturity and sex-related) variation in the diet of the franciscana dolphin, evaluating the spatial (northern and southern geographic areas) and seasonal influences. The analyses were based on Linear and Generalized Linear Models (LM and GLM). The majority of identified prey species were bottom-dwelling teleosts and the squid Doryteuthis sanpaulensis. The most important prey differed spatially and seasonally between northern and southern regions of the study area, and our results revealed significant differences between sexes and sexual maturity stages, mainly related to prey species sizes. This variation might indicate differences in prey selection, availability or habitat use patterns among these groups. In any case, these dietary differences are likely to minimize intraspecific competition for food resources, and/or indicate spatio-temporal variation in prey availability.
Remote Ischemic Preconditioning Reduces Marathon-Induced Oxidative Stress and Decreases Liver and Heart Injury Markers in the Serum

Clinical studies continue to provide evidence of organ protection by remote ischemic preconditioning (RIPC). However, there is lack of insight into impact of RIPC on exercise-induce changes in human organs’ function. We here aimed to elucidate the effects of 10-day RIPC training on marathon-induced changes in the levels of serum markers of oxidative stress, and liver and heart damage. The study involved 18 male amateur runners taking part in a marathon. RIPC training was performed in the course of four cycles, by inflating and deflating a blood pressure cuff at 5-min intervals (RIPC group, n=10); the control group underwent sham training (n=8). The effects of RIPC on levels of oxidative stress, and liver and heart damage markers were investigated at rest after 10 consecutive days of training and after the marathon run. The 10-day RIPC training decreased the serum resting levels of C-reactive protein (CRP), alanine transaminase (ALT), γ-glutamyl transpeptidase (GGT), and malondialdehyde (MDA). After the marathon run, creatinine kinase MB (CK-MB), lactate dehydrogenase (LDH), cardiac troponin level (cTn), aspartate aminotransferase (AST), alkaline phosphatase (ALP), ALT, total bilirubin (BIL-T), and MDA levels were increased and arterial ketone body ratio (AKBR) levels were decreased in all participants. The changes were significantly diminished in the RIPC group compared with the control group. The GGT activity remained constant in the RIPC group but significantly increased in the control group after the marathon run. In conclusion, the study provides evidence for a protective effect of RIPC against liver and heart damage induced by strenuous exercise, such as the marathon.
Signal neutrality, scalar property, and collapsing boundaries as consequences of a learned multi-timescale strategy

We postulate that three fundamental elements underlie a decision making process: perception of time passing, information processing in multiple timescales and reward maximisation. We build a simple reinforcement learning agent upon these principles that we train on a random dot-like task. Our results, similar to the experimental data, demonstrate three emerging signatures. (1) Signal neutrality: insensitivity to the signal coherence in the interval preceding the decision. (2) Scalar property: the mean of the response times varies widely for different signal coherences, yet the shape of the distributions stays almost unchanged. (3) Collapsing boundaries: the “effective” decision-making boundary changes over time in a manner reminiscent of the theoretical optimal. Removing the perception of time or the multiple timescales from the model does not preserve the distinguishing signatures. Our results suggest an alternative explanation for signal neutrality. We propose that it is not part of motor planning. It is part of the decision-making process and emerges from information processing on multiple timescales.
An Integrated Approach to Determine the Stock Structure of Spinyhead Croaker Collichthys lucidus (Sciaenidae) in Chinese Coastal Waters

An integrated approach including analyses of different biological traits is a proven and powerful tool used to assess the population structures of fish species, which is vital for fishery stock conservation and management of wild resources. This study evaluates the use of three natural tags (i.e., microsatellites, parasites, and otolith nucleus chemistry) in order to describe the population structure of the spinyhead croaker, Collichthys lucidus, in the coastal waters of China, on evolutionary and ecological time scales. Spinyhead croaker was assigned with 86% accuracy to its regional origin (northern China vs. southern China) using all three natural tags. Accuracy decreased when incorporating only one type of natural tag (genetics: 19–69%; parasites: 30–60%; otolith chemistry: 51–86%) or when assigning the fish to a fine scale (sea areas: 44–64%; sampled estuaries: 19–66%). However, the overall accuracy assignment improved slightly compared with otolith chemistry (estuaries: 55 vs. 51%; sea areas: 66 vs. 64%; regions: 86 vs. 86%). Three natural tags and integrated results show that C. lucidus in Chinese coastal waters can be separated into distinct northern and southern Chinese stocks. Finally, this information should promote the development of effective conservation strategies and integrated fisheries management plans for this commercially important species.
Comparative Transcriptomics During Brown Rot Decay in Three Fungi Reveals Strain-Specific Degradative Strategies and Responses to Wood Acetylation

Brown rot fungi degrade wood in a two-step process in which enzymatic hydrolysis is preceded by an oxidative degradation phase. While a detailed understanding of the molecular processes during brown rot decay is mandatory for being able to better protect wooden products from this type of degradation, the underlying mechanisms are still not fully understood. This is particularly true for wood that has been treated to increase its resistance against rot. In the present study, the two degradation phases were separated to study the impact of wood acetylation on the behavior of three brown rot fungi commonly used in wood durability testing. Transcriptomic data from two strains of Rhodonia placenta (FPRL280 and MAD-698) and Gloeophyllum trabeum were recorded to elucidate differences between the respective decay strategies. Clear differences were found between the two decay stages in all fungi. Moreover, strategies varied not only between species but also between the two strains of the same species. The responses to wood acetylation showed that decay is generally delayed and that parts of the process are attenuated. By hierarchical clustering, we could localize several transcription factors within gene clusters that were heavily affected by acetylation, especially in G. trabeum. The results suggest that regulatory circuits evolve rapidly and are probably the major cause behind the different decay strategies as observed even between the two strains of R. placenta. Identifying key genes in these processes can help in decay detection and identification of the fungi by biomarker selection, and also be informative for other fields, such as fiber modification by biocatalysts and the generation of biochemical platform chemicals for biorefinery applications.
Editorial: Intact Forests

Global Conservation Program, Wildlife Conservation Society, Bronx, NY, United States, Department of Geography and Environmental Science, University of Dundee, Dundee, United Kingdom, 3 Environmental Change Institute, School of Geography and Environment, University of Oxford, Oxford, United Kingdom, 4 The School of Earth and Environmental Sciences, University of Queensland, Brisbane, QLD, Australia
Cacao (Theobroma cacao L.) Response to Water Stress: Physiological Characterization and Antioxidant Gene Expression Profiling in Commercial Clones

The increase in events associated with drought constraints plant growth and crop performance. Cacao (Theobroma cacao L.) is sensitive to water deficit stress (DS), which limits productivity. The aim of this research was to characterise the response of seven (CCN51, FEAR5, ICS1, ICS60, ICS95, EET8, and TSH565) commercially important cacao clones to severe and temporal water deficit stress. Ten-month-old cacao trees were submitted to two treatments: well-watered and water-stressed until the leaf water potential (Ψleaf) reached values between −3.0 and −3.5 MPa. The effects of hydric stress on water relations, gas exchange, photochemical activity, membrane integrity and oxidative stress-related gene expression were evaluated. All clones showed decreases in Ψleaf, but TSH565 had a higher capacity to maintain water homeostasis in leaves. An initial response phase consisted of stomatal closure, a general mechanism to limit water loss: as a consequence, the photosynthetic rate dropped by approximately 98% on average. In some clones, the photosynthetic rate reached negative values at the maximum stress level, evidencing photorespiration and was confirmed by increased intracellular CO2. A second and photosynthetically limited phase was characterized by a drop in PSII quantum efficiency, which affected all clones. On average, all clones were able to recover after 4 days of rewatering. Water deficit triggered oxidative stress at the early phase, as evidenced by the upregulation of oxidative stress markers and genes encoding ROS scavenging enzymes. The effects of water deficit stress on energy metabolism were deduced given the upregulation of fermentative enzyme-coding genes. Altogether, our results suggest that the EET8 clone was the highest performing under water deficit while the ICS-60 clone was more susceptible to water stress. Importantly, the activation of the antioxidant system and PSII repair mechanism seem to play key roles in the observed differences in tolerance to water deficit stress among clones.