Miracle-dz/UniFAR-FTUs huggingface dataset:
MiRNA Regulatory Functions in Photoreceptors

MicroRNAs (miRNAs) are important regulators of gene expression. These small, non-coding RNAs post-transcriptionally silence messenger RNAs (mRNAs) in a sequence-specific manner. In this way, miRNAs control important regulatory functions, also in the retina. If dysregulated, these molecules are involved in several retinal pathologies. For example, several miRNAs have been linked to essential photoreceptor functions, including light sensitivity, synaptic transmission, and modulation of inflammatory responses. Mechanistic miRNA knockout and knockdown studies further linked their functions to degenerative retinal diseases. Of note, the type and timing of genetic manipulation before, during, or after retinal development, is important when studying specific miRNA knockout effects. Within this review, we focus on miR-124 and the miR-183/96/182 cluster, which have assigned functions in photoreceptors in health and disease. As a single miRNA can regulate hundreds of mRNAs, we will also discuss the experimental validation and manipulation approaches to study complex miRNA/mRNA regulatory networks. Revealing these networks is essential to understand retinal pathologies and to harness miRNAs as precise therapeutic and diagnostic tools to stabilize the photoreceptors’ transcriptomes and, thereby, function.
Alterations of Iron Level in the Bilateral Basal Ganglia Region in Patients With Middle Cerebral Artery Occlusion

Background and Purpose: The purpose of this study was to explore the changes of iron level using quantitative susceptibility mapping (QSM) in the bilateral basal ganglia region in middle cerebral artery occlusion (MCAO) patients with long-term ischemia. Methods: Twenty-seven healthy controls and nine patients with MCAO were recruited, and their QSM images were obtained. The bilateral caudate nucleus (Cd), putamen (Pt), and globus pallidus (Gp) were selected as the regions of interest (ROIs). Susceptibility values of bilateral ROIs were calculated and compared between the affected side and unaffected side in patients with MCAO and between patients with MCAO and healthy controls. In addition, receiver operating characteristic (ROC) curves were performed to evaluate the diagnostic capability of susceptibility values in differentiating healthy controls and patients with MCAO by the area under the curve (AUC). Results: The susceptibility values of bilateral Cd were asymmetric in healthy controls; however, this asymmetry disappeared in patients with MCAO. In addition, compared with healthy controls, the average susceptibility values of the bilateral Pt in patients with MCAO were increased (P < 0.05), and the average susceptibility value of the bilateral Gp was decreased (P < 0.05). ROC curves showed that the susceptibility values of the Pt and Gp had a larger AUC (AUC = 0.700 and 0.889, respectively). Conclusion: As measured by QSM, the iron levels of the bilateral basal ganglia region were significantly changed in patients with MCAO. Iron dyshomeostasis in the basal ganglia region might be involved in the pathophysiological process of middle cerebral artery stenosis and occlusion. These findings may provide a novel insight to profoundly address the pathophysiological mechanisms of MCAO.
The Price of the Induced Defense Against Pests: A Meta-Analysis

Plants and phytophagous arthropods have co-evolved for millions of years. During this long coexistence, plants have developed defense mechanisms including constitutive and inducible defenses. In an effort to survive upon herbivore attack, plants suffer a resource reallocation to facilitate the prioritization of defense toward growth. These rearrangements usually end up with a penalty in plant growth, development or reproduction directly linked to crop losses. Achieving the balance to maximize crop yield requires a fine tune regulation specific for each host-arthropod combination, which remains to be fully elucidated. The purpose of this work is to evaluate the effects of induced plant defenses produced upon pest feeding on plant fitness and surrogate parameters. The majority of the studies are focused on specific plant-pest interactions based on artificial herbivory damage or simulated defoliation on specific plant hosts. In this meta-analysis, the relevance of the variables mediating plant-pest interactions has been studied. The importance of plant and pest species, the infestation conditions (plant age, length/magnitude of infestation) and the parameters measured to estimate fitness (carbohydrate content, growth, photosynthesis and reproduction) in the final cost have been analyzed through a meta-analysis of 209 effects sizes from 46 different studies. Herbivore infestation reduced growth, photosynthesis and reproduction but not carbohydrate content. When focusing on the analyses of the variables modulating plant-pest interactions, new conclusions arise. Differences on the effect on plant growth and photosynthesis were observed among different feeding guilds or plant hosts, suggesting that these variables are key players in the final effects. Regarding the ontogenetic stage of a plant, negative effects were reported only in infestations during the vegetative stage of the plant, while no effect was observed during the reproductive stage. In addition, a direct relation was found between the durability and magnitude of the infestation, and the final negative effect on plant fitness. Among the parameters used to estimate the cost, growth and photosynthesis revealed more differences among subgroups than reproduction parameters. Altogether, this information on defense-growth trade-offs should be of great help for the scientific community to design pest management strategies reducing costs.
Tomato Rootstocks Mediate Plant-Water Relations and Leaf Nutrient Profiles of a Common Scion Under Suboptimal Soil Temperatures

Environments with short growing seasons and variable climates can have soil temperatures that are suboptimal for chilling-sensitive crops. These conditions can adversely affect root growth and physiological performance thus impairing water and nutrient uptake. Four greenhouse trials and a field study were conducted to investigate if rootstocks can enhance tomato performance under suboptimal soil temperatures (SST). In a controlled greenhouse environment, we exposed four commercial rootstocks (Estamino, Maxifort, RST-04-106-T, and Supernatural) grafted with a common scion (cv. BHN-589) to optimal (mean: 24°C) and SST (mean: 13.5°C) and compared their performance with the non-grafted BHN-589 cultivar. Several root and shoot physiological traits were evaluated: root hydraulic conductivity and conductance, root anatomy, leaf gas exchange, leaf δ13C, shoot C and N, and biomass. Under field conditions, the same five phenotypes were evaluated for canopy growth, normalized difference vegetation index (NDVI), leaf nutrients, biomass, and yield. Under SST, root hydraulic conductivity (Lp) and conductance (KR), stomatal conductance (gs), and plant biomass decreased. Hydrostatic Lp decreased more than osmotic Lp (Lp∗hyd: 39–65%; Lp∗os: 14–40%) and some of the reduced conductivity was explained by the increased cortex area of primary roots observed under SST (67–140%). Under optimal soil temperatures, all rootstocks conferred higher gs than the non-grafted cultivar, but only two rootstocks maintained higher gs under SST. All phenotypes showed greater reductions in shoot biomass than root biomass resulting in greater (∼20%) root-to-shoot ratios. In the field, most grafted phenotypes increased early canopy cover, NDVI, shoot biomass, and fruit yield. Greenhouse results showed that Lp∗os may be less affected by SST than Lp∗hyd and that reductions in Lp may be offset by enhanced root-to-shoot ratios. We show that some commercial rootstocks possess traits that maintained better rates of stomatal conductance and shoot N content, which can contribute toward better plant establishment and improved performance under SST.
Deep Learning-Based Classification and Voxel-Based Visualization of Frontotemporal Dementia and Alzheimer’s Disease

Frontotemporal dementia (FTD) and Alzheimer’s disease (AD) have overlapping symptoms, and accurate differential diagnosis is important for targeted intervention and treatment. Previous studies suggest that the deep learning (DL) techniques have the potential to solve the differential diagnosis problem of FTD, AD and normal controls (NCs), but its performance is still unclear. In addition, existing DL-assisted diagnostic studies still rely on hypothesis-based expert-level preprocessing. On the one hand, it imposes high requirements on clinicians and data themselves; On the other hand, it hinders the backtracking of classification results to the original image data, resulting in the classification results cannot be interpreted intuitively. In the current study, a large cohort of 3D T1-weighted structural magnetic resonance imaging (MRI) volumes (n = 4,099) was collected from two publicly available databases, i.e., the ADNI and the NIFD. We trained a DL-based network directly based on raw T1 images to classify FTD, AD and corresponding NCs. And we evaluated the convergence speed, differential diagnosis ability, robustness and generalizability under nine scenarios. The proposed network yielded an accuracy of 91.83% based on the most common T1-weighted sequence [magnetization-prepared rapid acquisition with gradient echo (MPRAGE)]. The knowledge learned by the DL network through multiple classification tasks can also be used to solve subproblems, and the knowledge is generalizable and not limited to a specified dataset. Furthermore, we applied a gradient visualization algorithm based on guided backpropagation to calculate the contribution graph, which tells us intuitively why the DL-based networks make each decision. The regions making valuable contributions to FTD were more widespread in the right frontal white matter regions, while the left temporal, bilateral inferior frontal and parahippocampal regions were contributors to the classification of AD. Our results demonstrated that DL-based networks have the ability to solve the enigma of differential diagnosis of diseases without any hypothesis-based preprocessing. Moreover, they may mine the potential patterns that may be different from human clinicians, which may provide new insight into the understanding of FTD and AD.
Latent Heat Storage Materials and Systems: A Review

The use of a latent heat storage system using Phase Change Materials (PCM) is an effective way of storing thermal energy (solar energy, off-peak electricity, industrial waste heat) and has the advantages of high storage density and the isothermal nature of the storage process. It has been demonstrated that, for the development of a latent heat storage system, choice of the PCM plays an important role in addition to heat transfer mechanism. The information on the latent heat storage materials and systems is enormous and published widely in the literatures. In this paper, we make an effort to gather the information from the previous works on PCMs and latent heat storage systems. This review will help to find a suitable PCM for various purposes a suitable heat exchanger with ways to enhance the heat transfer, and it will also help to provide a variety of designs to store the heat using PCMs for different applications, i.e. space heating & cooling, solar cooking, greenhouses, solar water heating and waste heat recovery systems. Measurement techniques of thermophysical properties, studies on thermal cycles for long term stability, corrosion of the PCMs and enhancement of heat transfer in PCM are discussed. New PCM innovations are also included for the awareness of new applications. This paper contains a list of about 250 PCMs and more than 250 references.
Novel Targets of SARS-CoV-2 Spike Protein in Human Fetal Brain Development Suggest Early Pregnancy Vulnerability

Pregnant women are at greater risk of infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), because of their altered immunity and strained cardiovascular system. Emerging studies of placenta, embryos, and cerebral organoids suggest that fetal organs including brain could also be vulnerable to coronavirus disease 2019 (COVID-19). Additionally, a case study from Paris has reported transient neurological complications in neonates born to pregnant mothers. However, it remains poorly understood whether the fetal brain expresses cellular components that interact with Spike protein (S) of coronaviruses, which facilitates fusion of virus and host cell membrane and is the primary protein in viral entry. To address this question, we analyzed the expression of known (ACE2, TMPRSS2, and FURIN) and novel (ZDHHC5, GOLGA7, and ATP1A1) S protein interactors in publicly available fetal brain bulk and single cell RNA sequencing datasets. Bulk RNA sequencing analysis across multiple regions of fetal brain spanning 8 weeks post conception (wpc)−37wpc indicates that two of the known S protein interactors are expressed at low levels with median normalized gene expression values ranging from 0.08 to 0.06 (ACE2) and 0.01–0.02 (TMPRSS2). However, the third known S protein interactor FURIN is highly expressed (11.1–44.09) in fetal brain. Interestingly, all three novel S protein interactors are abundantly expressed throughout fetal brain development with median normalized gene expression values ranging from 20.38–21.60 (ZDHHC5), 92.47–68.35 (GOLGA7), and 65.45–194.5 (ATP1A1). Moreover, the peaks of expression of novel interactors is around 12–26wpc. Using publicly available single cell RNA sequencing datasets, we further show that novel S protein interactors show higher co-expression with neurons than with neural progenitors and astrocytes. These results suggest that even though two of the known S protein interactors are present at low levels in fetal brain, novel S protein interactors are abundantly present and could play a direct or indirect role in SARS-CoV-2 fetal brain pathogenesis, especially during the 2nd and 3rd trimesters of pregnancy.
Near-Field Body-Wave Extraction From Ambient Seafloor Noise in the Nankai Subduction Zone

Ambient noise correlation is capable of retrieving waves propagating between two receivers. Although waves retrieved using this technique are primarily surface waves, the retrieval of body waves, including direct, refracted, and reflected waves, has also been reported from land-based observations. The difficulty of body wave extraction may be caused by large amplitudes and little attenuation of surface waves excited by microseisms, indicating that body wave extraction using seafloor records is very challenging because microseisms are generated in ocean areas and large amplitudes of surface waves are presumably observed at the seafloor. In this study, we used a unique dataset acquired by dense arrays deployed in the Nankai subduction zone, including a permanent cabled-network of 49 stations, a borehole sensor, and 150 temporary stations, to attempt to extract near-field body waves from ambient seafloor noise observed by multivariate sensors of broadband and short-period seismometers, differential pressure gauges (DPGs), and hydrophones. Our results show that P waves are extracted only in the DPG-record correlations at a frequency of 0.2–0.5 Hz, which can be seen up to a separation distance of two stations of 17 km with an apparent velocity of 3.2 km/s. At 1–3 Hz, P waves are observed only in the vertical-record correlations up to a separation distance of 11 km with an apparent velocity of 2.0 km/s. These velocity differences reflect the vertical velocity gradient of the accretionary prism, because the P waves at low frequencies propagate at relatively long distances and therefore the turning depth is greater. Moreover, the long-period and short-period P waves are observed at the slope and flat regions on the accretionary prism, respectively. To investigate the retrieved wavefield characteristics, we conducted a two-dimensional numerical simulation for wave propagations, where we located single sources at the sea surface above the flat and slope bathymetry regions. Based on our observations and simulations, we suggest that the retrieval of near-field body waves from ambient seafloor noises depends on the relative amplitudes of P and other surface waves in the ambient noise wavefield, and those are controlled by the subseafloor velocity structure, seafloor topography, and water depth.
QseC Inhibition as a Novel Antivirulence Strategy for the Prevention of Acute Hepatopancreatic Necrosis Disease (AHPND)-Causing Vibrio parahaemolyticus

Acute hepatopancreatic necrosis disease (AHPND) caused by Vibrio parahaemolyticus resulted in great economic losses in global shrimp aquaculture. There is an urgent need for development of novel strategies to combat AHPND-causing V. parahaemolyticus (Vp AHPND), given that one of the greatest challenges currently is the widespread use of antibiotics and subsequent emergence of multidrug-resistant bacteria. Here, we proposed a broad-spectrum antivirulence approach targeting a conserved histidine kinase, QseC, which has been demonstrated to activate virulence expression in several Gram-negative pathogens. Our results showed that QseC mediated the catecholamine stimulated effects on growth and flagellar motility of Vp AHPND. Transcriptome analysis revealed that QseC was involved in the global regulation of the virulence of Vp AHPND as the ΔqseC mutant exhibited a decreased expression of genes related to type IV pilin, flagellar motility, and biofilm formation, while an overexpression of type VI secretion system and cell wall biosynthesis. Subsequently, the bacterial catecholamine receptor antagonist LED209 not only neutralized the stimulatory effects of host catecholamines on the growth and motility of Vp AHPND in vitro, but also attenuated the virulence of Vp AHPND towards brine shrimp larvae and white shrimp in vivo. Additionally, LED209 presented no interference with pathogen growth, nor the toxicity to the experimental animals. These results suggest that QseC can be an attractive antivirulence therapy target, and LED209 is a promising candidate for development of broad-spectrum antivirulence agents. This is the first study that demonstrated the role of QseC in the global regulation of Vp AHPND infection and demonstrated the antivirulence potential of LED209, which provides insight into the use of an antivirulence approach for targeting not only Vp AHPND, but also a much larger collection of pathogenic bacteria.
RNA-Binding Protein MSI2 Binds to miR-301a-3p and Facilitates Its Distribution in Mitochondria of Endothelial Cells

Numerous miRNAs have been detected in mitochondria, which play important roles in many physiological and pathophysiological processes. However, the dynamic changes of miRNA distribution in mitochondria and their mechanisms in reactive oxygen species (ROS)-induced endothelial injury remain unclear. Therefore, miRNA levels in whole cells and mitochondria of H2O2-treated endothelial cells were analyzed by small RNA sequencing in the present study. The results showed that H2O2 significantly reduced the relative mitochondrial distribution of dozens of miRNAs in human umbilical vein endothelial cells (HUVECs). Among the high-abundance miRNAs, miR-301a-3p has the most significant changes in the redistribution between cytosol and mitochondria confirmed by absolute quantitative polymerase chain reaction (qPCR). To unravel the mechanism of miR-301a-3p distribution in mitochondria, RNA pull-down followed by label-free quantitative proteomic analysis was performed, and RNA-binding protein Musashi RNA binding protein 2 (MSI2) was found to specifically bind to miR-301a-3p. Western blotting and immunofluorescence colocalization assay showed that MSI2 was located in mitochondria of various cell types. H2O2 significantly downregulated MSI2 expression in whole endothelial cells, promoted the distribution of MSI2 in cytosol and decreased its distribution in the mitochondria. Moreover, overexpression of MSI2 increased the mitochondrial distribution of miR-301a-3p, whereas inhibition of MSI2 decreased its distribution in mitochondria. Thus, MSI2 might be responsible for the distribution of miR-301a-3p between cytosol and mitochondria in endothelial cells. Our findings revealed for the first time that MSI2 was involved in the regulation of miRNA distribution in mitochondria and provided valuable insight into the mechanism of mitochondrial distribution of miRNAs.
Sodium and Potassium in the Canadian Total Diet Study

Sodium (Na) and potassium (K) are essential nutrients. We investigated Na and K content of foods collected from the 2007 Vancouver Total Diet Study (TDS). Our food nutrient content data showed that processed foods and soups had a high Na content while fluid milk, unprocessed meats and several fruits and vegetables had a high K content. The Na/K ratio indicated, with few exceptions, a segregation of the foods high in Na from ones high in K. Based on this data, new Na and K intakes were generated using Canadian Community Health Survey (CCHS2.2), cycle 2.2 Nutrition dietary recall. In general, the results showed a lower Na intake than indicated by CCHS2.2, but still higher than the Tolerable Upper Level of Intake (UL). K intakes were similar to CCHS2.2 data showing an intake lower than the AI. %%%%Le sodium (Na) ainsi que le potassium (K) sont des nutriments essentiels. Nous avons examine le contenu de Na et de K d'aliments collectes pour l'Etude Canadienne sur l'alimentation totale de Vancouver conduite en 2007. Notre base de donnees sur le contenu nutritionnel des aliments a demontre que les aliments traites et les soupes ont un haut niveau de Na alors que le lait, les viandes non-traitees ainsi que plusieurs fruits et legumes detiennent un niveau eleve de K. Bases sur ces donnees, de nouvelles prises ont ete generees en utilisant l'Enquete sur la sante dans les collectivites canadiennes (ESCC 2.2), cycle 2.2, Nutrition. En general, les resultats ont demontre un niveau d'ingestion de Na moins que CCHS mais plus eleve que l'apport maximum tolerable (AMT). Les ingestions de K etaient similaires aux donnees contenues dans l'ESCC 2.2, demontrant une ingestion inferieure a l'apport suffisant (AS).