Miracle-dz/UniFAR-FTUs huggingface dataset:
Comprehensive analysis of structural variants in chickens using PacBio sequencing

Structural variants (SVs) are one of the main sources of genetic variants and have a greater impact on phenotype evolution, disease susceptibility, and environmental adaptations than single nucleotide polymorphisms (SNPs). However, SVs remain challenging to accurately type, with several detection methods showing different limitations. Here, we explored SVs from 10 different chickens using PacBio technology and detected 49,501 high-confidence SVs. The results showed that the PacBio long-read detected more SVs than Illumina short-read technology genomes owing to some SV sites on chromosomes, which are related to chicken growth and development. During chicken domestication, some SVs beneficial to the breed or without any effect on the genomic function of the breed were retained, whereas deleterious SVs were generally eliminated. This study could facilitate the analysis of the genetic characteristics of different chickens and provide a better understanding of their phenotypic characteristics at the SV level, based on the long-read sequencing method. This study enriches our knowledge of SVs in chickens and improves our understanding of chicken genomic diversity.
Fecal Lcn-2 level is a sensitive biological indicator for gut dysbiosis and intestinal inflammation in multiple sclerosis

Multiple Sclerosis (MS) has been reported to be associated with intestinal inflammation and gut dysbiosis. To elucidate the underlying biology of MS-linked gut inflammation, we investigated gut infiltration of immune cells during the development of spontaneous experimental autoimmune encephalomyelitis (EAE) in humanized transgenic (Tg) mice expressing HLA-DR2a and human T cell receptor (TCR) specific for myelin basic protein peptide (MBP87-99)/HLA-DR2a complexes. Strikingly, we noted the simultaneous development of EAE and colitis, suggesting a link between autoimmune diseases of the central nervous system (CNS) and intestinal inflammation. Examination of the colon in these mice revealed the infiltration of MBP-specific Th17 cells as well as recruitment of neutrophils. Furthermore, we observed that fecal Lipocalin-2 (Lcn-2), a biomarker of intestinal inflammation, was significantly elevated and predominantly produced by the gut-infiltrating neutrophils. We then extended our findings to MS patients and demonstrate that their fecal Lcn-2 levels are significantly elevated compared to healthy donors (HDs). The elevation of fecal Lcn-2 levels correlated with reduced bacterial diversity and increased levels of other intestinal inflammation markers including neutrophil elastase and calprotectin. Of interest, bacteria thought to be beneficial for inflammatory bowel disease (IBD) such as Anaerobutyricum, Blautia, and Roseburia, were reduced in fecal Lcn-2-high MS patients. We also observed a decreasing trend in serum acetate (a short-chain fatty acid) levels in MS Lcn-2-high patients compared to HDs. Furthermore, a decrease in the relative abundance of Blautia massiliensis was significantly associated with a reduction of acetate in the serum of MS patients. This study suggests that gut infiltration of Th17 cells and recruitment of neutrophils are associated with the development of gut dysbiosis and intestinal inflammation, and that fecal Lcn-2 level is a sensitive biological indicator for gut dysbiosis in multiple sclerosis.
Combining SAR images with land cover products for rapid urban flood mapping

Synthetic Aperture Radar (SAR) is an indispensable source of data for mapping and monitoring flood hazards, thanks to its ability to image the Earth’s surface in all weather conditions and at all times. Through cloud computing platforms such as Google Earth Engine (GEE), SAR imagery can be used in near-real time for rapid flood mapping. This has facilitated the disaster response community to make informed decisions in flood hazard interventions and management plans. However, rapid urban flood mapping using SAR is challenging, due to the complex land cover configuration in urban environments, coupled with complicated backscattering mechanisms. Here, we propose a novel method to utilise SAR imagery and land use-land cover (LULC) products for rapid urban flood mapping. Our approach uses a Land Cover Product to segment the study area into LULC types and differentiate each type with respect to whether double bounce is expected to occur during the flooding events. The normalised difference index was derived using a multi-temporal SAR image stack, and the threshold segmentation method was adopted for flood mapping. In addition, DEM and Surface Water datasets were employed to refine the flood extraction results using a morphological correction approach. We assessed the method quantitatively using two use cases: the 2017 Houston and 2022 Coraki flood events. Based on fine spatial resolution optical imagery, the proposed method achieved an accuracy of 92.7% for the August 2017 Houston flood mapping task and 89% for the March 2022 Coraki flood mapping task, which not only represents at least 13% in accuracy compared to non-LCP based flood extraction method, but also provides strong capability for rapid flood mapping in urban settings.
Integration of multi-omics technologies for crop improvement: Status and prospects

With the rapid development of next-generation sequencing (NGS), multi-omics techniques have been emerging as effective approaches for crop improvement. Here, we focus mainly on addressing the current status and future perspectives toward omics-related technologies and bioinformatic resources with potential applications in crop breeding. Using a large amount of omics-level data from the functional genome, transcriptome, proteome, epigenome, metabolome, and microbiome, clarifying the interaction between gene and phenotype formation will become possible. The integration of multi-omics datasets with pan-omics platforms and systems biology could predict the complex traits of crops and elucidate the regulatory networks for genetic improvement. Different scales of trait predictions and decision-making models will facilitate crop breeding more intelligent. Potential challenges that integrate the multi-omics data with studies of gene function and their network to efficiently select desirable agronomic traits are discussed by proposing some cutting-edge breeding strategies for crop improvement. Multi-omics-integrated approaches together with other artificial intelligence techniques will contribute to broadening and deepening our knowledge of crop precision breeding, resulting in speeding up the breeding process.
Association of Obstructive Sleep Apnea-Hypopnea Syndrome with hearing loss: A systematic review and meta-analysis

Objective This study seeks to investigate the relationship between Obstructive Sleep Apnea-Hypopnea Syndrome (OSAHS) and hearing impairment by meta-analysis. Methods Cochrane Library, PubMed, Embase, Web of Science and other databases are searched from their establishment to July 1st, 2022. Literature on the relationship between OSAHS and hearing loss is collected, and two researchers independently perform screening, data extraction and quality evaluation on the included literature. Meta-analysis is performed using RevMan 5.4. 1 software. According to the heterogeneity between studies, a random-effects model or fixed-effects model is used for meta-analysis. Results A total of 10 articles are included, with 7,867 subjects, 1,832 in the OSAHS group and 6,035 in the control group. The meta-analysis shows that the incidence of hearing impairment in the OSAHS group is higher than in the control group (OR = 1.38; 95% CI 1.18–1.62, Z = 4.09, P < 0.001), and the average hearing threshold of OSAHS patients is higher than that of the control group (MD = 5.89; 95% CI 1.87–9.91, Z = 2.87, P = 0.004). After stratifying the included studies according to hearing frequency, the meta-analysis shows that the OSAHS group has a higher threshold of 0.25, and the response amplitudes at frequencies 2, 4, 6, and 8 kHz are all higher than those of the control group. Conclusion Compared with the control group, the OSAHS group has a higher incidence of hearing loss, mainly high-frequency hearing loss. Thus, OSAHS is closely associated with and a risk factor for hearing loss.
The relationship between psychological resilience, neuroticism, attentional bias, and depressive symptoms in college Chinese students

In recent years, the incidence of depressive symptoms among Chinese college students has been increasing. Studies have shown that depressive symptoms are related to a variety of psychosocial factors, among which neuroticism, resilience, and attention bias are most notably related, but the correlation among the three is not clear. This study aimed to investigate the influence mechanisms of different degrees of resilience, attentional bias, and neuroticism in the formation of depressive symptoms. The college freshmen of this study were selected through stratified multi-stage cluster sampling. Students provided informed consent and then completed a general situation questionnaire and four scales: the Chinese version of the Connor–Davidson Resilience Scale, the Attention to Positive and Negative Information Scale, the Eysenck Personality Questionnaire, and the Zung Self-Rating Depressive Symptoms Scale. In total, 1,493 freshmen participated in the research group. Our results showed that low resilience, negative attention bias, and high neuroticism jointly increased the risk of depressive symptoms. There is a significant correlation between these three factors and depressive symptoms. Additionally, strength, tenacity, and attention bias all had more significant effects on the occurrence of depressive symptoms. These findings indicate that there may be an important psychological mechanism for the occurrence, development, and poor prognosis of depressive symptoms.
Integrated analysis of lncRNA-mediated ceRNA network involved in immune regulation in the spleen of Meishan piglets

Meishan pigs are a famous local pig breed in China, with high fertility and early sexual maturity, and stronger immunity compared to other breeds. The spleen is the largest lymphoid organ in pigs and performs essential functions, such as those relating to immunity and haematopoiesis. The invasion of many pathogenic microorganisms in pigs is associated with spleen damage. Long non-coding RNAs participate in a broad range of biological processes and have been demonstrated to be associated with splenic immune regulation. However, the expression network of mRNAs and lncRNAs in the spleen of Meishan pigs remains unclear. This study collected spleen tissues from Meishan piglets at three different ages as a model, and mRNA and lncRNA transcripts were profiled for each sample. Additionally, 1,806 differential mRNAs and 319 differential lncRNAs were identified. A complicated interaction between mRNAs and lncRNAs was identified via WGCNA, demonstrating that lncRNAs are a crucial regulatory component in mRNA. The results show that the modules black and red have similar mRNA and lncRNA transcription patterns and are mainly involved in the process of the immune defense response. The core genes (DHX58 and IFIT1) and key lncRNAs (TCONS-00002102 and TCONS-00012474) of piglet spleen tissue were screened using the ceRNA network. The expression of these genes is related to the immune response of pigs. Our research may contribute to a further understanding of mRNA and lncRNA expression in the spleen of piglets, and provide new ideas to improve the disease resistance of piglets.
Longitudinal bidirectional relations between children’s negative affectivity and maternal emotion expressivity

Although children’s negative affectivity is a temperamental characteristic that is biologically based, it is framed within and shaped by their emotional environments which are partly created by maternal emotion expressivity in the family. Children, in turn, play a role in shaping their family emotional context, which could lead to changes in mothers’ emotion expressivity in the family. However, these theorized longitudinal bidirectional relations between child negative affectivity and maternal positive and negative expressivity have not been studied from toddlerhood to early school-age. The current study utilized a cross-lagged panel model to examine the reciprocal relations between children’s negative affectivity and maternal expressivity within the family over the course of early childhood. Participants were 140 mother–child dyads (72 boys, mean age = 2.67 years, primarily White). Mothers reported the positive and negative expressivity in the family and children’s negative affectivity in toddlerhood (T1), preschool (T2), and school-age (T3). Maternal negative expressivity and child negative affectivity at T1 were significantly correlated. Maternal negative expressivity at T1 significantly predicted child negative affectivity at T3. Children’s negative affectivity at T2 significantly predicted mothers’ negative expressivity at T3. Mothers’ positive expressivity was not related to children’s negative affectivity at any of the three time points. The findings demonstrate the reciprocal relations between children’s negative affectivity and maternal negative expressivity in the family, suggesting the importance of the interplay between child temperament and maternal expressivity within the family emotional context.
Evaluating the adhesive potential of the newly isolated bacterial strains in research exploitation of plant microbial interaction

Bacterial adhesion potential constitutes the transition of bacteria from the planktonic to the static phase by promoting biofilm formation, which plays a significant role in plant-microbial interaction in the agriculture industry. In present study, the adhesion potential of five soil-borne bacterial strains belonging to different genera was studied. All bacterial strains were capable of forming colonies and biofilms of different levels of firmness on polystyrene. Significant variation was observed in hydrophobicity and motility assays. Among the five bacterial strains (SH-6, SH-8, SH-9, SH-10, and SH-19), SH-19 had a strong hydrophobic force, while SH-10 showed the most hydrophilic property. SH-6 showed great variability in motility; SH-8 had a swimming diffusion diameter of 70 mm, which was three times higher than that of SH-19. In the motility assay, SH-9 and SH-10 showed diffusion diameters of approximately 22 mm and 55 mm, respectively. Furthermore, among the five strains, four are predominately electron donors and one is electron acceptors. Overall, positive correlation was observed among Lewis acid base properties, hydrophobicity, and biofilm forming ability. However, no correlation of motility with bacterial adhesion could be found in present experimental work. Scanning electron microscopy images confirmed the adhesion potential and biofilm ability within extra polymeric substances. Research on the role of adhesion in biofilm formation of bacteria isolated from plants is potentially conducive for developing strategies such as plant–microbial interaction to mitigate the abiotic stress.
Functional connectivity impairment of thalamus-cerebellum-scratching neural circuits in pruritus of chronic spontaneous urticaria

Pruritus of chronic spontaneous urticaria (CSU) is one of the most common and irritating sensations that severely affects the quality of life. However, the changes in the functional connectivity (FC) between thalamic subregions and other brain regions have not been fully elucidated. This study aimed to explore the potential changes in brain neural circuits by focusing on various subregions of the thalamus in patients with CSU pruritus to contribute to the understanding of chronic pruritus from the perspective of central mechanisms. A total of 56 patients with CSU and 30 healthy controls (HCs) completed the data analysis. Urticaria Activity Score 7 (UAS7), pruritus visual analog score (VAS-P), Dermatological Life Quality Index (DLQI), and immunoglobulin E (IgE) values were collected to assess clinical symptoms. Seed-based resting-state functional connectivity (rs-FC) analysis was used to assess relevant changes in the neural circuits of the brain. Compared to HCs, seeds within the caudal temporal thalamus (cTtha) on the right side of patients with CSU showed increased rs-FC with the cerebellum anterior lobe (CAL). Seeds within the lateral prefrontal thalamus (lPFtha) on the right side showed increased rs-FC with both CAL and pons, while those within the medial prefrontal thalamus (mPFtha) on the right side showed increased rs-FC with both CAL and the dorsal lateral prefrontal cortex (dlPFC) on the right side. Seeds within the posterior parietal thalamus (PPtha) on the right side showed increased rs-FC with the cerebellum posterior lobe (CPL) on the left side. The UAS7 values and IgE levels were positively correlated with the rs-FC of the right dlPFC. Our results suggest that patients with CSU may exhibit stronger rs-FC alterations between certain thalamic subregions and other brain regions. These changes affect areas of the brain involved in sensorimotor and scratching. Trial registration number [http://www.chictr. org.cn], identifier [ChiCTR1900022994].
Towards Self-Consistent Modelling of the Sgr A* Accretion Flow: Linking Theory and Observation

The interplay between supermassive black holes (SMBHs) and their environments is believed to command an essential role in galaxy evolution. The majority of these SMBHs are in the radiative inefficient accretion phase where this interplay remains elusive, but suggestively important, due to few observational constraints. To remedy this, we directly fit 2-D hydrodynamic simulations to Chandra observations of Sgr A* with Markov Chain Monte Carlo sampling, self-consistently modelling the 2-D inflow-outflow solution for the first time. We find the temperature and density at flow onset are consistent with the origin of the gas in the stellar winds of massive stars in the vicinity of Sgr A*. We place the first observational constraints on the angular momentum of the gas and estimate the centrifugal radius, r$_c$ $\approx$ 0.056 r$_b$ $\approx8\times10^{-3}$ pc, where r$_b$ is the Bondi radius. Less than 1\% of the inflowing gas accretes onto the SMBH, the remainder being ejected in a polar outflow. For the first time, we decouple the quiescent point-like emission from the spatially extended flow. We find this point-like emission, accounting for $\sim4$\% of the quiescent flux, is spectrally too steep to be explained by unresolved flares, nor Bremsstrahlung, but is likely a combination of a relatively steep synchrotron powerlaw and the high energy tail of inverse-Compton emission. With this self-consistent model of the accretion flow structure, we make predictions for the flow dynamics and discuss how future X-ray spectroscopic observations can further our understanding of the Sgr A* accretion flow.
Exploring therapeutic potential of mitophagy modulators using Drosophila models of Parkinson’s disease

Parkinson’s disease (PD) is the second most popular age-associated neurodegenerative disorder after Alzheimer’s disease. The degeneration of dopaminergic neurons, aggregation of α-synuclein (α-syn), and locomotor defects are the main characteristic features of PD. The main cause of a familial form of PD is associated with a mutation in genes such as SNCA, PINK1, Parkin, DJ-1, LRKK2, and others. Recent advances have uncovered the different underlying mechanisms of PD but the treatment of PD is still unknown due to the unavailability of effective therapies and preventive medicines in the current scenario. The pathophysiology and genetics of PD have been strongly associated with mitochondria in disease etiology. Several studies have investigated a complex molecular mechanism governing the identification and clearance of dysfunctional mitochondria from the cell, a mitochondrial quality control mechanism called mitophagy. Reduced mitophagy and mitochondrial impairment are found in both sporadic and familial PD. Pharmacologically modulating mitophagy and accelerating the removal of defective mitochondria are of common interest in developing a therapy for PD. However, despite the extensive understanding of the mitochondrial quality control pathway and its underlying mechanism, the therapeutic potential of targeting mitophagy modulation and its role in PD remains to be explored. Thus, targeting mitophagy using chemical agents and naturally occurring phytochemicals could be an emerging therapeutic strategy in PD prevention and treatment. We discuss the current research on understanding the role of mitophagy modulators in PD using Drosophila melanogaster as a model. We further explore the contribution of Drosophila in the pathophysiology of PD, and discuss comprehensive genetic analysis in flies and pharmacological drug screening to develop potential therapeutic molecules for PD.
Superior visual rhythm discrimination in expert musicians is most likely not related to cross-modal recruitment of the auditory cortex

Training can influence behavioral performance and lead to brain reorganization. In particular, training in one modality, for example, auditory, can improve performance in another modality, for example, visual. Previous research suggests that one of the mechanisms behind this phenomenon could be the cross-modal recruitment of the sensory areas, for example, the auditory cortex. Studying expert musicians offers a chance to explore this process. Rhythm is an aspect of music that can be presented in various modalities. We designed an fMRI experiment in which professional pianists and non-musicians discriminated between two sequences of rhythms presented auditorily (series of sounds) or visually (series of flashes). Behavioral results showed that musicians performed in both visual and auditory rhythmic tasks better than non-musicians. We found no significant between-group differences in fMRI activations within the auditory cortex. However, we observed that musicians had increased activation in the right Inferior Parietal Lobe when compared to non-musicians. We conclude that the musicians’ superior visual rhythm discrimination is not related to cross-modal recruitment of the auditory cortex; instead, it could be related to activation in higher-level, multimodal areas in the cortex.