Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-Wide Analysis of the Cytochrome P450 Gene Family Involved in Salt Tolerance in Gossypium hirsutum

Plant cytochrome P450 (P450) participates in a wide range of biosynthetic reactions and targets a variety of biological molecules. These reactions lead to various fatty acid conjugates, plant hormones, secondary metabolites, lignin, and various defensive compounds. In our previous research, transcriptome analysis was performed on the salt-tolerant upland cotton “Tongyan No. 1. ” Many differentially expressed genes (DEGs) belong to the P450 family, and their domains occur widely in plants. In this current research, P450 genes were identified in Gossypium hirsutum with the aid of bioinformatics methods for investigating phylogenetic relations, gene structure, cis-elements, chromosomal localization, and collinearity within a genome. qRT-PCR was conducted to analyze P450 gene expression patterns under salt stress. The molecular weights of the 156 P450 genes were in the range of 5,949.6–245,576.3 Da, and the length of the encoded amino acids for all the identified P450 genes ranged from 51 to 2,144. P450 proteins are divided into four different subfamilies based on phylogenetic relationship, gene structure, and chromosomal localization of gene replication. The length of P450 genes in upland cotton differs greatly, ranging from 1,500 to 13,000 bp. The number of exons in the P450 family genes ranged from 1 to 9, while the number of introns ranged from 0 to 8, and there were similar trends within clusters. A total of 31 cis-acting elements were identified by analyzing 1,500 bp promoter sequences. Differences were found in cis-acting elements among genes. The consistency between qRT-PCR and previous transcriptome analysis of salt tolerance DEGs indicated that they were likely to be involved in the salt tolerance of cotton seedlings. Our results provide valuable information on the evolutionary relationships of genes and functional characteristics of the gene family, which is beneficial for further study of the cotton P450 gene family.
Active Life for Brain Health: A Narrative Review of the Mechanism Underlying the Protective Effects of Physical Activity on the Brain

A growing body of evidence clearly indicates the beneficial effects of physical activity (PA) on cognition. The importance of PA is now being reevaluated due to the increase in sedentary behavior in older adults during the COVID-19 pandemic. Although many studies in humans have revealed that PA helps to preserve brain health, the underlying mechanisms have not yet been fully elucidated. In this review, which mainly focuses on studies in humans, we comprehensively summarize the mechanisms underlying the beneficial effects of PA or exercise on brain health, particularly cognition. The most intensively studied mechanisms of the beneficial effects of PA involve an increase in brain-derived neurotrophic factor (BDNF) and preservation of brain volume, especially that of the hippocampus. Nonetheless, the mutual associations between these two factors remain unclear. For example, although BDNF presumably affects brain volume by inhibiting neuronal death and/or increasing neurogenesis, human data on this issue are scarce. It also remains to be determined whether PA modulates amyloid and tau metabolism. However, recent advances in blood-based biomarkers are expected to help elucidate the beneficial effects of PA on the brain. Clinical data suggest that PA functionally modulates cognition independently of neurodegeneration, and the mechanisms involved include modulation of functional connectivity, neuronal compensation, neuronal resource allocation, and neuronal efficiency. However, these mechanisms are as yet not fully understood. A clear understanding of the mechanisms involved could help motivate inactive persons to change their behavior. More accumulation of evidence in this field is awaited.
Genome-Wide Association and Mendelian Randomization Analysis Reveal the Causal Relationship Between White Blood Cell Subtypes and Asthma in Africans

Background: White blood cell (WBC) traits and their subtypes such as basophil count (Bas), eosinophil count (Eos), lymphocyte count (Lym), monocyte count (Mon), and neutrophil counts (Neu) are known to be associated with diseases such as stroke, peripheral arterial disease, and coronary heart disease. Methods: We meta-analyze summary statistics from genome-wide association studies in 17,802 participants from the African Partnership for Chronic Disease Research (APCDR) and African ancestry individuals from the Blood Cell Consortium (BCX2) using GWAMA. We further carried out a Bayesian fine mapping to identify causal variants driving the association with WBC subtypes. To access the causal relationship between WBC subtypes and asthma, we conducted a two-sample Mendelian randomization (MR) analysis using summary statistics of the Consortium on Asthma among African Ancestry Populations (CAAPA: n cases = 7,009, n control = 7,645) as our outcome phenotype. Results: Our metanalysis identified 269 loci at a genome-wide significant value of (p = 5 × 10−9) in a composite of the WBC subtypes while the Bayesian fine-mapping analysis identified genetic variants that are more causal than the sentinel single-nucleotide polymorphism (SNP). We found for the first time five novel genes (LOC126987/MTCO3P14, LINC01525, GAPDHP32/HSD3BP3, FLG-AS1/HMGN3P1, and TRK-CTT13-1/MGST3) not previously reported to be associated with any WBC subtype. Our MR analysis showed that Mon (IVW estimate = 0.38, CI: 0.221, 0.539, p < 0.001), Neu (IVW estimate = 0.189, CI: 0.133, 0.245, p < 0.001), and WBCc (IVW estimate = 0.185, CI: 0.108, 0.262, p < 0.001) are associated with increased risk of asthma. However, there was no evidence of causal relationship between Lym and asthma risk. Conclusion: This study provides insight into the relationship between some WBC subtypes and asthma and potential route in the treatment of asthma and may further inform a new therapeutic approach.
Association Between 2D- and 3D-Speckle-Tracking Longitudinal Strain and Cardiovascular Magnetic Resonance Evidence of Diffuse Myocardial Fibrosis in Heart Transplant Recipients

Objective: This study aimed to: (1) evaluate the association between myocardial fibrosis (MF) quantified by extracellular volume fraction (ECV) and myocardial strain measured by two-dimensional (2D)- and three-dimensional speckle-tracking echocardiography (3D-STE) and (2) further investigate which strain parameter measured by 2D- and 3D-STE is the more robust predictor of MF in heart transplant (HT) recipients. Methods: A total of 40 patients with HT and 20 healthy controls were prospectively enrolled. Left ventricular (LV)-global longitudinal strain (GLS), global circumferential strain (GCS), and global radial strain (GRS) were measured by 2D- and 3D-STE. LV diffuse MF was defined by cardiovascular magnetic resonance (CMR)-ECV. Results: The HT recipients had a significantly higher native T1 and ECV than healthy controls (1043.8 ± 34.0 vs. 999.7 ± 19.7 ms, p < 0.001; 26.6 ± 2.7 vs. 24.3 ± 1.8%, p = 0.02). The 3D- and 2D-STE-LVGLS and LVGCS were lower (p < 0.005) in the HT recipients than in healthy controls. ECV showed a moderate correlation with 2D-LVGLS (r = 0.53, p = 0.002) and 3D-LVGLS (r = 0.60, p < 0.001), but it was not correlated with 2D or 3D-LVGCS, or LVGRS. Furthermore, 3D-LVGLS and 2D-LVGLS had a similar correlation with CMR-ECV (r = 0.60 vs. 0.53, p = 0.670). A separate stepwise multivariate linear analysis showed that both the 2D-LVGLS (β = 0.39, p = 0.019) and 3D-LVGLS (β = 0.54, p < 0.001) were independently associated with CMR-ECV. Conclusion: CMR marker of diffuse MF was present in asymptomatic patients with HT and appeared to be associated with decreased myocardial strain by echocardiography. Both the 2D- and 3D-LVGLS were independently correlated with diffuse LVMF, which may provide an alternative non-invasive tool for monitoring the development of adverse fibrotic remodeling during the follow-up of HT recipients.
Mutual Skill Learning and Adaptability to Others via Haptic Interaction

When learning a new skill through an unknown environment, should we practice alone, or together with another beginner, or learn from the expert? It is normally helpful to have an expert guiding through unknown environmental dynamics. The guidance from the expert is fundamentally based on mutual interactions. From the perspective of the beginner, one needs to face dual unknown dynamics of the environment and motor coordination of the expert. In a cooperative visuo-haptic motor task, we asked novice participants to bring a virtual mass onto the specified target location under an unknown external force field. The task was completed by an individual or with an expert or another novice. In addition to evaluation of the motor performance, we evaluated the adaptability of the novice participants to a new partner while attempting to achieve a common goal together. The experiment was set in five phases; baseline for skill transfer and adaptability, learning and evaluation for adaptability and skill transfer respectively. The performance of the participants was characterized by using the time to target, effort index, and length of the trajectory. Experimental results suggested that (1) peer-to-peer interactions among paired beginners enhanced the motor learning most, (2) individuals practicing on their own (learning as a single) showed better motor learning than practicing under the expert's guidance, and (3) regarding the adaptability, peer-to-peer interactions induced higher adaptability to a new partner than the novice-to-expert interactions while attempting to achieve a common goal together. Thus, we conclude that the peer-to-peer interactions under a collaborative task can realize the best motor learning of the motor skills through the new environmental dynamics, and adaptability to others in order to achieve a goal together. We suggest that the peer-to-peer learning can induce both adaptability to others and learning of motor skills through the unknown environmental dynamics under mutual interactions. On the other hand, during the peer-to-peer interactions, the novice can learn how to coordinate motion with his/her partner (even though one is a new partner), and thus, is able to learn the motor skills through new environmental dynamics.
Non-linear Methods Predominant in Fetal Heart Rate Analysis: A Systematic Review

The analysis of fetal heart rate variability has served as a scientific and diagnostic tool to quantify cardiac activity fluctuations, being good indicators of fetal well-being. Many mathematical analyses were proposed to evaluate fetal heart rate variability. We focused on non-linear analysis based on concepts of chaos, fractality, and complexity: entropies, compression, fractal analysis, and wavelets. These methods have been successfully applied in the signal processing phase and increase knowledge about cardiovascular dynamics in healthy and pathological fetuses. This review summarizes those methods and investigates how non-linear measures are related to each paper's research objectives. Of the 388 articles obtained in the PubMed/Medline database and of the 421 articles in the Web of Science database, 270 articles were included in the review after all exclusion criteria were applied. While approximate entropy is the most used method in classification papers, in signal processing, the most used non-linear method was Daubechies wavelets. The top five primary research objectives covered by the selected papers were detection of signal processing, hypoxia, maturation or gestational age, intrauterine growth restriction, and fetal distress. This review shows that non-linear indices can be used to assess numerous prenatal conditions. However, they are not yet applied in clinical practice due to some critical concerns. Some studies show that the combination of several linear and non-linear indices would be ideal for improving the analysis of the fetus's well-being. Future studies should narrow the research question so a meta-analysis could be performed, probing the indices' performance.
Examining the Associations Between Online Interactions and Momentary Affect in Depressed Adolescents

Concern has been raised over parallel increases in youth depression and online interactive media use over the past two decades. The aim of this study was to determine whether online interactions are associated with users’ affective states. Using ecological momentary assessment, we measured depressed adolescents’ momentary affect during and residual feelings following online interactions with offline friends and family, online friends, and acquaintances/strangers. We found that depressed adolescents use texting services and social networking sites to interact online, most frequently with offline friends and family, followed by online friends. Results of generalized estimating equations showed associations between negative affect and digital interactions with offline friends and family. Participants were less likely to report feeling better after interacting with online friends than after interacting with any other relationship type. Our findings highlight the heterogeneity of depressed adolescents’ online interactions and suggest that their affective experience varies depending on the nature of the relationships they have with those with whom they interact.
The Role of Estrogen Receptor α in Response to Longitudinal Bone Growth in ob/ob Mice

The absence of leptin results in contrasting growth pattern of appendicular and axial bone growth in ob/ob mice. Endochondral bone formation is an important procedure of growth plate determining the bone growth, where this procedure is also regulated by estrogen and its receptor (ER) signaling pathway. The present study is undertaken to explore the roles of ERs in regulating the different growth patterns in ob/ob mice. In this study, C57BL/6 female mice were used as wild-type (WT) mice; ob/ob mice and WT mice were age-matched fed, and bone length is analyzed by X-ray plain film at the 12 weeks old. We confirm that ob/ob mice have shorter femoral length and longer spine length than WT mice (p < 0.05). The contrasting expression patterns of chondrocyte proliferation proteins and hypertrophic marker proteins are also observed from the femur and spinal growth plate of ob/ob mice compared with WT mice (p < 0.01). Spearman’s analysis showed that body length (axial and appendicular length) is positively related to the expression level of ERα in growth plate. Three-week-old female ob/ob mice are randomized divided into three groups: 1) ob/ob + ctrl, 2) ob/ob + ERα antagonist (MPP), and 3) ob/ob + ERβ antagonist (PHTPP). Age-matched C57BL/6 mice were also divided into three groups, same as the groups of ob/ob mice. MPP and PHTPP were administered by intraperitoneal injection for 6 weeks. However, the results of X-ray and H&E staining demonstrate that leptin deficiency seems to disturb the regulating effects of ER antagonists on longitudinal bone growth. These findings suggested that region-specific expression of ERα might be associated with contrasting phenotypes of axial and appendicular bone growth in ob/ob mice. However, ER signaling on longitudinal bone growth was blunted by leptin deficiency in ob/ob mice, and the underlying association between ERs and leptin needs to be explored in future work.
The Global Epidemic of the SARS-CoV-2 Delta Variant, Key Spike Mutations and Immune Escape

During the COVID-19 pandemic, SARS-CoV-2 variants have emerged and spread worldwide. The Delta (B.1.617.2) variant was first reported in India in October 2020 and was classified as a “variant of concern (VOC)” by the WHO on 11 May, 2021. Compared to the wild-type strain, several studies have shown that the Delta variant is more transmissible and has higher viral loads in infected samples. COVID-19 patients infected with the Delta variant have a higher risk of hospitalization, intensive care unit (ICU) admission, and mortality. The Delta variant is becoming the dominant strain in many countries around the world. This review summarizes and analyses the biological characteristics of key amino acid mutations, the epidemic characteristics, and the immune escape of the Delta variant. We hope to provide scientific reference for the monitoring and prevention measures of the SARS-CoV-2 Delta variant and the development strategy of a second-generation vaccine.
Concurrent Validity of the Adult Eating Behavior Questionnaire in a Canadian Sample

The current study aimed to test the factor structure of the Adult Eating Behavior Questionnaire (AEBQ), its construct validity against the Three-Factor Eating Questionnaire (TFEQ-R18) and its associations with body mass index (BMI) in Canadian adults (n = 534, 76% female). Confirmatory factor analysis (CFA) revealed that a seven-factor AEBQ model, with the Hunger subscale removed, had better fit statistics than the original eight-factor structure. Cronbach’s alpha was used to assess the internal reliability of each subscale and resulted with α > 0.70 for all subscales except for Hunger (α = 0.68). Pearson’s correlations were used to inform the convergent and discriminant validation of AEBQ against the TFEQ-R18 and to examine the relationship between AEBQ and BMI. All AEBQ Food Approach subscales positively correlated with that of the TFEQ-R18 Emotional Eating and Uncontrolled Eating subscales. Similarly, BMI correlated positively with Food Approach subscales (except Hunger) and negatively with Food Avoidance subscales (except Food Fussiness). These results support the use of a seven-factor AEBQ for adults self-reporting eating behaviors, construct validity of the AEBQ against TFEB-R18, and provide further evidence for the association of these traits with BMI.
Kinematic Boundary Conditions Favouring Subduction Initiation at Passive Margins Over Subduction at Mid-oceanic Ridges

We perform numerical modelling to simulate the shortening of an oceanic basin and the adjacent continental margins in order to discuss the relationship between compressional stresses acting on the lithosphere and the time dependent strength of the mid-oceanic ridges within the frame of subduction initiation. We focus on the role of stress regulating mechanisms by testing the stress–strain-rate response to convergence rate, and the thermo-tectonic age of oceanic and continental lithospheres. We find that, upon compression, subduction initiation at passive margin is favoured for thermally thin (Palaeozoic or younger) continental lithospheres (<160 km) over cratons (>180 km), and for oceanic basins younger than 60 Myr (after rifting). The results also highlight the importance of convergence rate that controls stress distribution and magnitudes in the oceanic lithosphere. Slow convergence (<0.9 cm/yr) favours strengthening of the ridge and build-up of stress at the ocean-continent transition allowing for subduction initiation at passive margins over subduction at mid-oceanic ridges. The results allow for identifying geodynamic processes that fit conditions for subduction nucleation at passive margins, which is relevant for the unique case of the Alps. We speculate that the slow Africa–Europe convergence between 130 and 85 Ma contributes to the strengthening of the mid-oceanic ridge, leading to subduction initiation at passive margin 60–70 Myr after rifting and passive margin formation.
CCR5 and Biological Complexity: The Need for Data Integration and Educational Materials to Address Genetic/Biological Reductionism at the Interface of Ethical, Legal, and Social Implications

In the age of genomics, public understanding of complex scientific knowledge is critical. To combat reductionistic views, it is necessary to generate and organize educational material and data that keep pace with advances in genomics. The view that CCR5 is solely the receptor for HIV gave rise to demand to remove the gene in patients to create host HIV resistance, underestimating the broader roles and complex genetic inheritance of CCR5. A program aimed at providing research projects to undergraduates, known as CODE, has been expanded to build educational material for genes such as CCR5 in a rapid approach, exposing students and trainees to large bioinformatics databases and previous experiments for broader data to challenge commitment to biological reductionism. Our students organize expression databases, query environmental responses, assess genetic factors, generate protein models/dynamics, and profile evolutionary insights into a protein such as CCR5. The knowledgebase generated in the initiative opens the door for public educational information and tools (molecular videos, 3D printed models, and handouts), classroom materials, and strategy for future genetic ideas that can be distributed in formal, semiformal, and informal educational environments. This work highlights that many factors are missing from the reductionist view of CCR5, including the role of missense variants or expression of CCR5 with neurological phenotypes and the role of CCR5 and the delta32 variant in complex critical care patients with sepsis. When connected to genomic stories in the news, these tools offer critically needed Ethical, Legal, and Social Implication (ELSI) education to combat biological reductionism.
What’s “up”? Impaired Spatial Preposition Processing in Posterior Cortical Atrophy

This study seeks to confirm whether lesions in posterior regions of the brain involved in visuo-spatial processing are of functional relevance to the processing of words with spatial meaning. We investigated whether patients with Posterior Cortical Atrophy (PCA), an atypical form of Alzheimer’s Disease which predominantly affects parieto-occipital brain regions, is associated with deficits in working memory for spatial prepositions. Case series of patients with PCA and matched healthy controls performed tests of immediate and delayed serial recall on words from three lexico-semantic word categories: number words (twelve), spatial prepositions (behind) and function words (e.g., shall). The three word categories were closely matched for a number of psycholinguistic and semantic variables including length, bi-/tri-gram frequency, word frequency, valence and arousal. Relative to controls, memory performance of PCA patients on short word lists was significantly impaired on spatial prepositions in the delayed serial recall task. These results suggest that lesions in posterior parieto-occipital regions specifically impair the processing of spatial prepositions. Our findings point to a pertinent role of posterior cortical regions in the semantic processing of words with spatial meaning and provide strong support for modality-specific semantic theories that recognize the necessary contributions of sensorimotor regions to conceptual semantic processing.