Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring Genomic Variations in Nematode-Resistant Mutant Rice Lines

Rice (Oryza sativa) production is seriously affected by the root-knot nematode Meloidogyne graminicola, which has emerged as a menace in upland and irrigated rice cultivation systems. Previously, activation tagging in rice was utilized to identify candidate gene(s) conferring resistance against M. graminicola. T-DNA insertional mutants were developed in a rice landrace (acc. JBT 36/14), and four mutant lines showed nematode resistance. Whole-genome sequencing of JBT 36/14 was done along with the four nematode resistance mutant lines to identify the structural genetic variations that might be contributing to M. graminicola resistance. Sequencing on Illumina NovaSeq 6000 platform identified 482,234 genetic variations in JBT 36/14 including 448,989 SNPs and 33,245 InDels compared to reference indica genome. In addition, 293,238–553,648 unique SNPs and 32,395–65,572 unique InDels were found in the four mutant lines compared to their JBT 36/14 background, of which 93,224 SNPs and 8,170 InDels were common between all the mutant lines. Functional annotation of genes containing these structural variations showed that the majority of them were involved in metabolism and growth. Trait analysis revealed that most of these genes were involved in morphological traits, physiological traits and stress resistance. Additionally, several families of transcription factors, such as FAR1, bHLH, and NAC, and putative susceptibility (S) genes, showed the presence of SNPs and InDels. Our results indicate that subject to further genetic validations, these structural genetic variations may be involved in conferring nematode resistance to the rice mutant lines.
Effectiveness of Online-Delivered Project ImPACT for Children With ASD and Their Parents: A Pilot Study During the COVID-19 Pandemic

Objective During the COVID-19 pandemic, face-to-face intervention services for families of children with autism spectrum disorder (ASD) were limited. This study aimed to evaluate the effectiveness of an 8-week, online-delivered Project ImPACT program for children with ASD and their parents in China during the COVID-19 pandemic. Methods A pilot non-randomized study with a waitlist control group was conducted in 68 children with ASD and their parents in the Department of Developmental and Behavioral Pediatrics between April 15, 2020 and March 19, 2021. Participants were allocated to either the intervention (IG) or the waitlist group (WLG) according to their order of recruitment. Parents in the IG immediately received 8 weeks of the online-delivered Project ImPACT program, and the WLG received the same program with a delay when the IG had completed all sessions. Participants in both groups received treatment as usual during the research period. Results The online-delivered Project ImPACT program significantly improved the parent-reported social communication skills of children with ASD. Furthermore, parent's involvement in the training program produced a collateral reduction in parenting stress and an increase in perceived competence in the parental role. Parents rated the program acceptable in terms of curriculum schedule, session content, homework assignments, and therapist feedback. Conclusions The 8-week, online-delivered Project ImPACT program is a feasible and effective social skill training program for families of children with ASD in China during the COVID-19 pandemic. Due to the methodological limitations, randomized controlled studies with larger sample sizes are suggested to provide more solid evidence.
Applying Dimensionality Reduction Techniques in Source-Space Electroencephalography via Template and Magnetic Resonance Imaging-Derived Head Models to Continuously Decode Hand Trajectories

Several studies showed evidence supporting the possibility of hand trajectory decoding from low-frequency electroencephalography (EEG). However, the decoding in the source space via source localization is scarcely investigated. In this study, we tried to tackle the problem of collinearity due to the higher number of signals in the source space by two folds: first, we selected signals in predefined regions of interest (ROIs); second, we applied dimensionality reduction techniques to each ROI. The dimensionality reduction techniques were computing the mean (Mean), principal component analysis (PCA), and locality preserving projections (LPP). We also investigated the effect of decoding between utilizing a template head model and a subject-specific head model during the source localization. The results indicated that applying source-space decoding with PCA yielded slightly higher correlations and signal-to-noise (SNR) ratios than the sensor-space approach. We also observed slightly higher correlations and SNRs when applying the subject-specific head model than the template head model. However, the statistical tests revealed no significant differences between the source-space and sensor-space approaches and no significant differences between subject-specific and template head models. The decoder with Mean and PCA utilizes information mainly from precuneus and cuneus to decode the velocity kinematics similarly in the subject-specific and template head models.
Juxtaposing Medical Centers Using Different Questionnaires Through Score Predictors

Background Chronic tinnitus is a clinically multidimensional phenomenon that entails audiological, psychological and somatosensory components. Previous research has demonstrated age and female gender as potential risk factors, although studies to this regard are heterogeneous. Moreover, whilst recent research has begun to identify clinical “phenotypes,” little is known about differences in patient population profiles at geographically separated and specialized treatment centers. Identifying such differences might prevent potential biases in joint randomized controlled trials (RCTs) and allow for population-specific treatment adaptations. Method Two German tinnitus treatment centers were compared regarding pre-treatment data distributions of their patient population bases. To identify overlapping as well as center-specific factors, juxtaposition-, similarity-, and meta-data-based methods were applied. Results Between centers, significant differences emerged. One center demonstrated some predictive power of the patients of the other center with regard to questionnaire score after treatment, indicating similarities in treatment response across center populations. Furthermore, adherence to the completion of the questionnaires was found to be an important factor in predicting post-treatment data. Discussion Differential age and gender distributions per center should be considered as regards RCT design and individualized treatment planning.
A Pyramidal Feature Fusion Model on Swimming Crab Portunus trituberculatus Re-identification

Swimming crab Portunus trituberculatus is a vital crab species in coastal areas of China. In this study, an individual re-identification method based on Pyramidal Feature Fusion Model (PFFM) for P. trituberculatus was proposed. This method took the carapace texture of P. trituberculatus as a “biological fingerprint” and extracted carapace texture features, including global features and local features, to identify P. trituberculatus. Furthermore, this method utilized a weight adaptive module to improve re-identification (ReID) accuracy for the P. trituberculatus individuals with the incomplete carapace. To strengthen the discrimination of the extracted features, triplet loss was adopted in the model training process to improve the effectiveness of P. trituberculatus ReID. Furthermore, three experiments, i.e., PFFM on the effect of pyramidal model, P. trituberculatus features analysis, and comparisons to the State-of-the-Arts, were carried out to evaluate PFFM performance. The results showed that the mean average precision (mAP) and Rank-1 values of the proposed method reached 93.2 and 93% in the left half occlusion case, and mAP and Rank-1 values reached 71.8 and 75.4% in the upper half occlusion case. By using the experiments, the effectiveness and robustness of the proposed method were verified.
Metformin Protects Against Diabetes-Induced Cognitive Dysfunction by Inhibiting Mitochondrial Fission Protein DRP1

Objectives: Diabetes is an independent risk factor for dementia. Mitochondrial dysfunction is a critical player in diabetes and diabetic complications. The present study aimed to investigate the role of mitochondrial dynamic changes in diabetes-associated cognitive impairment. Methods: Cognitive functions were examined by novel object recognition and T-maze tests. Mice hippocampi were collected for electron microscopy and immunofluorescence examination. Neuron cell line HT22 and primary hippocampal neurons were challenged with high glucose in vitro. Mitotracker-Red CM-H2X ROS was used to detect mitochondrial-derived free radicals. Results: Diabetic mice exhibited memory loss and spatial disorientation. Electron microscopy revealed that diabetic mice had larger synaptic gaps, attenuated postsynaptic density and fewer dendritic spines in the hippocampus. More round-shape mitochondria were observed in hippocampal neurons in diabetic mice than those in control mice. In cultured neurons, high glucose induced a high phosphorylated level of dynamin-related protein 1 (DRP1) and increased oxidative stress, resulting in cell apoptosis. Inhibition of mitochondrial fission by Mdivi-1 and metformin significantly decreased oxidative stress and prevented cell apoptosis in cultured cells. Treatment of Mdivi-1 and metformin restored cognitive function in diabetic mice. Conclusion: Metformin restores cognitive function by inhibiting mitochondrial fission, reducing mitochondrial-derived oxidative stress, and mitigating neuron loss in hippocampi of diabetic mice. The protective effects of metformin shed light on the therapeutic strategy of cognitive impairment.
Quantitative Transcriptomic and Proteomic Analysis of Fruit Development and Ripening in Watermelon (Citrullus lanatus)

Fruit ripening is a highly complicated process, which is modulated by phytohormones, signal regulators and environmental factors playing in an intricate network that regulates ripening-related genes expression. Although transcriptomics is an effective tool to predict protein levels, protein abundances are also extensively affected by post-transcriptional and post-translational regulations. Here, we used RNA sequencing (RNA-seq) and tandem mass tag (TMT)-based quantitative proteomics to study the comprehensive mRNA and protein expression changes during fruit development and ripening in watermelon, a non-climacteric fruit. A total of 6,226 proteins were quantified, and the large number of quantitative proteins is comparable to proteomic studies in model organisms such as Oryza sativa L. and Arabidopsis. Base on our proteome methodology, integrative analysis of the transcriptome and proteome showed that the mRNA and protein levels were poorly correlated, and the correlation coefficients decreased during fruit ripening. Proteomic results showed that proteins involved in alternative splicing and the ubiquitin proteasome pathway were dynamically expressed during ripening. Furthermore, the spliceosome and proteasome were significantly enriched by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, suggesting that post-transcriptional and post-translational mechanisms might play important roles in regulation of fruit ripening-associated genes expression, which might account for the poor correlation between mRNAs and proteins during fruit ripening. Our comprehensive transcriptomic and proteomic data offer a valuable resource for watermelon research, and provide new insights into the molecular mechanisms underlying the complex regulatory networks of fruit ripening.
Influence of Controlled Stomatognathic Motor Activity on Sway, Control and Stability of the Center of Mass During Dynamic Steady-State Balance—An Uncontrolled Manifold Analysis

Multiple sensory signals from visual, somatosensory and vestibular systems are used for human postural control. To maintain postural stability, the central nervous system keeps the center of mass (CoM) within the base of support. The influence of the stomatognathic motor system on postural control has been established under static conditions, but it has not yet been investigated during dynamic steady-state balance. The purpose of the study was to investigate the effects of controlled stomatognathic motor activity on the control and stability of the CoM during dynamic steady-state balance. A total of 48 physically active and healthy adults were assigned to three groups with different stomatognathic motor conditions: jaw clenching, tongue pressing and habitual stomatognathic behavior. Dynamic steady-state balance was assessed using an oscillating platform and the kinematic data were collected with a 3D motion capturing system. The path length (PL) of the 3D CoM trajectory was used for quantifying CoM sway. Temporal dynamics of the CoM movement was assessed with a detrended fluctuation analysis (DFA). An uncontrolled manifold (UCM) analysis was applied to assess the stability and control of the CoM with a subject-specific anthropometric 3D model. The statistical analysis revealed that the groups did not differ significantly in PL, DFA scaling exponents or UCM parameters. The results indicated that deliberate jaw clenching or tongue pressing did not seem to affect the sway, control or stability of the CoM on an oscillating platform significantly. Because of the task-specificity of balance, further research investigating the effects of stomatognathic motor activities on dynamic steady-state balance with different movement tasks are needed. Additionally, further analysis by use of muscle synergies or co-contractions may reveal effects on the level of muscles, which were not visible on the level of kinematics. This study can contribute to the understanding of postural control mechanisms, particularly in relation to stomatognathic motor activities and under dynamic conditions.
A Comprehensive Approach to Evaluate Durum Wheat–Faba Bean Mixed Crop Performance

Plant breeding for intercropping is lagging because most varieties currently available in the market are selected for sole cropping systems. The present study analyzed the response of durum wheat (12 varieties) and faba bean (3 varieties) in pure and mixed cropping. Field trials were conducted in 2019 and 2020. The performance of each variety in mixed and pure cropping was evaluated using both univariate and multivariate analyses of the grain yield and land equivalent ratio (LER). For durum wheat, grain protein content was also evaluated. Durum wheat varieties were characterized by good performance in both years, whereas faba bean varieties were more affected by the growing season, suggesting that much breeding effort is warranted to improve the latter as a pure and mixed crop. Moreover, the relative performance of all varieties was affected by their combination in mixed cropping, as evaluated based on the ratio (LERratio) between LER for wheat (LERw) and LER for faba bean (LERfb). To further evaluate the overall performance of wheat and faba bean in mixed cropping, total yield, LERtotal (LERw + LERfb), and ln(LERratio) were subjected to principal component and cluster analyses. The first principal component combined the total yield and LERtotal in a single index of the overall performance of each mixed crop combination. The second principal component, based on ln(LERratio), highlighted the relative performance of varieties in each mixed crop combination. The proposed multivariate approach can be applied in the breeding programs for intercropping to identify variety combinations based on crop performance and the relative importance of the proportion of cereal and legume grains in the total harvest.
Community-Based Conservation and Management of Chelonians in the Amazon

Chelonians represent an important resource in the Amazon, either as a source of protein at the base of the food chain of aquatic and transition ecosystems, or in the dispersion of seeds of plants from floodplains and flooded forests. The consumption and predatory exploitation of their meat and eggs by local populations has been, and still is, one of the main threats to these animals. Community-based conservation projects allied to official protection programs have been restoring populations of chelonians of the genus Podocnemis throughout the Amazon since 1974. In this study, we analyzed the historical time series of protection data of Podocnemis expansa, P. unifilis, P. sextuberculata and P. erythrocephala in areas protected by the government and communities in the Amazonas state and northwest of Pará state. Between 1974 and 2019, 230,444 nests and 21,350,201 hatchlings of P. expansa, 170,076 nests and 3,229,821 hatchlings of P. unifilis, 647,715 nests and 6,410,092 hatchlings of P. sextuberculata and 24,617 nests and 168,856 hatchlings of P. erythrocephala were protected. Community protection schemes emerged in 1990, and covered 80.7% of the areas and produced 64.2% of P. unifilis hatchlings and 44.6% of P. sextuberculata hatchlings. The areas with the highest production of P. expansa remain under government protection (57.4%). Using the time series of production of nests and hatchlings per beach, logistic growth curves were estimated, and the values of r and K were compared between the two protection systems (government and community). Beaches controlled by the government showed higher support capacity in the production of nests (1,910.7 ± 1,035) and hatchlings (211,513 ± 93,031) of P. expansa and P. sextuberculata (81,160 ± 34,924 hatchlings). However, the communities were more efficient in protecting nests (r = 0.102 ± 0.2315) and hatchlings (r = 0.282 ± 0.166) of P. unifilis. Community-based protection and monitoring programs are an important component that should be incorporated by the government’s environmental agencies for the management and conservation of turtles in the Amazon.
Evaluation of Computational Methodologies for Accurate Prediction of Wall Shear Stress and Turbulence Parameters in a Patient-Specific Aorta

Background: Recent studies suggest that blood flow in main arteries is intrinsically disturbed, even under healthy conditions. Despite this, many computational fluid dynamics (CFD) analyses of aortic haemodynamics make the assumption of laminar flow, and best practices surrounding appropriate modelling choices are lacking. This study aims to address this gap by evaluating different modelling and post-processing approaches in simulations of a patient-specific aorta. Methods: Magnetic resonance imaging (MRI) and 4D flow MRI from a patient with aortic valve stenosis were used to reconstruct the aortic geometry and derive patient-specific inlet and outlet boundary conditions. Three different computational approaches were considered based on assumed laminar or assumed disturbed flow states including low-resolution laminar (LR-Laminar), high-resolution laminar (HR-Laminar) and large-eddy simulation (LES). Each simulation was ran for 30 cardiac cycles and post-processing was conducted on either the final cardiac cycle, or using a phase-averaged approach which utilised all 30 simulated cycles. Model capabilities were evaluated in terms of mean and turbulence-based parameters. Results: All simulation types, regardless of post-processing approach could correctly predict velocity values and flow patterns throughout the aorta. Lower resolution simulations could not accurately predict gradient-derived parameters including wall shear stress and viscous energy loss (largest differences up to 44.6% and 130.3%, respectively), although phase-averaging these parameters improved predictions. The HR-Laminar simulation produced more comparable results to LES with largest differences in wall shear stress and viscous energy loss parameters up to 5.1% and 11.6%, respectively. Laminar-based parameters were better estimated than turbulence-based parameters. Conclusion: Our findings suggest that well-resolved laminar simulations can accurately predict many laminar-based parameters in disturbed flows, but there is no clear benefit to running a HR-Laminar simulation over an LES simulation based on their comparable computational cost. Additionally, post-processing “typical” laminar simulation results with a phase-averaged approach is a simple and cost-effective way to improve accuracy of lower-resolution simulation results.
Application of MinION Amplicon Sequencing to Buccal Swab Samples for Improving Resolution and Throughput of Rumen Microbiota Analysis

The Illumina MiSeq platform has been widely used as a standard method for studying the rumen microbiota. However, the low resolution of taxonomic identification is the only disadvantage of MiSeq amplicon sequencing, as it targets a part of the 16S rRNA gene. In the present study, we performed three experiments to establish a high-resolution and high-throughput rumen microbial profiling approach using a combination of MinION platform and buccal swab sample, which is a proxy for rumen contents. In experiment 1, rumen contents and buccal swab samples were collected simultaneously from cannulated cattle (n = 6) and used for microbiota analysis using three different analytical workflows: amplicon sequencing of the V3–V4 region of the 16S rRNA gene using MiSeq and amplicon sequencing of near full-length 16S rRNA gene using MinION or PacBio Sequel II. All reads derived from the MinION and PacBio platforms were classified at the species-level. In experiment 2, rumen fluid samples were collected from beef cattle (n = 28) and used for 16S rRNA gene amplicon sequencing using the MinION platform to evaluate this sequencing platform for rumen microbiota analysis. We confirmed that the MinION platform allowed species-level taxa assignment for the predominant bacterial groups, which were previously identified at the family- and genus-level using the MiSeq platform. In experiment 3, buccal swab samples were collected from beef cattle (n = 30) and used for 16S rRNA gene amplicon sequencing using the MinION platform to validate the applicability of a combination of the MinION platform and buccal swab samples for rumen microbiota analysis. The distribution of predominant bacterial taxa in the buccal swab samples was similar to that in the rumen samples observed in experiment 2. Based on these results, we concluded that the combination of the MinION platform and buccal swab samples may be potentially applied for rumen microbial analysis in large-scale studies.
A Predicted Model for Refractory/Recurrent Cytomegalovirus Infection in Acute Leukemia Patients After Haploidentical Hematopoietic Stem Cell Transplantation

Objective We aimed to establish a model that can predict refractory/recurrent cytomegalovirus (CMV) infection after haploidentical donor (HID) hematopoietic stem cell transplantation (HSCT). Methods Consecutive acute leukemia patients receiving HID HSCT were enrolled (n = 289). We randomly selected 60% of the entire population (n = 170) as the training cohort, and the remaining 40% comprised the validation cohort (n = 119). Patients were treated according to the protocol registered at https://clinicaltrials.gov (NCT03756675). Results The model was as follows: Y = 0.0322 × (age) – 0.0696 × (gender) + 0.5492 × (underlying disease) + 0.0963 × (the cumulative dose of prednisone during pre-engraftment phase) – 0.0771 × (CD34+ cell counts in graft) – 1.2926. The threshold of probability was 0.5243, which helped to separate patients into high- and low-risk groups. In the low- and high-risk groups, the 100-day cumulative incidence of refractory/recurrent CMV was 42.0% [95% confidence interval (CI), 34.7%–49.4%] vs. 63.7% (95% CI, 54.8%–72.6%) (P < 0.001) for total patients and was 50.5% (95% confidence interval (CI), 40.9%–60.1%) vs. 71.0% (95% CI, 59.5%–82.4%) (P = 0.024) for those with acute graft-versus-host disease. It could also predict posttransplant mortality and survival. Conclusion We established a comprehensive model that could predict the refractory/recurrent CMV infection after HID HSCT. Clinical Trial Registration https://clinicaltrials.gov, identifier NCT03756675.