Miracle-dz/UniFAR-FTUs huggingface dataset:
Chromosome-Level Genome Assembly Provides Insights into the Evolution of the Special Morphology and Behaviour of Lepturacanthus savala

Savalani hairtail Lepturacanthus savala is a widely distributed fish along the Indo-Western Pacific coast, and contributes substantially to trichiurid fishery resources worldwide. In this study, the first chromosome-level genome assembly of L. savala was obtained by PacBio SMRT-Seq, Illumina HiSeq, and Hi-C technologies. The final assembled L. savala genome was 790.02 Mb with contig N50 and scaffold N50 values of 19.01 Mb and 32.77 Mb, respectively. The assembled sequences were anchored to 24 chromosomes by using Hi-C data. Combined with RNA sequencing data, 23,625 protein-coding genes were predicted, of which 96.0% were successfully annotated. In total, 67 gene family expansions and 93 gene family contractions were detected in the L. savala genome. Additionally, 1825 positively selected genes were identified. Based on a comparative genomic analysis, we screened a number of candidate genes associated with the specific morphology, behaviour-related immune system, and DNA repair mechanisms in L. savala. Our results preliminarily revealed mechanisms underlying the special morphological and behavioural characteristics of L. savala from a genomic perspective. Furthermore, this study provides valuable reference data for subsequent molecular ecology studies of L. savala and whole-genome analyses of other trichiurid fishes.
Construction of a Diagnostic Model and a lncRNA-Associated ceRNA Network Based on Apoptosis-Related Genes for Schizophrenia

Methods Gene expression profiles and apoptosis-related data were downloaded from the Gene Expression Omnibus and Molecular Signature databases, respectively. Apoptosis-related differentially expressed mRNAs (DEGs) and miRNAs (DEMs) from blood samples between the schizophrenia and healthy control individuals were screened. A diagnostic model was developed using the data from univariate and least absolute shrinkage and selection operator (LASSO) regression analyses, followed by validation using the GSE38485 dataset. Cases were divided into low-risk (LR) and high-risk (HR) groups based on the risk score of the model, and differences in immune gene sets and pathways between these two groups were compared. Finally, a ceRNA network was constructed by integrating long non-coding RNAs (lncRNAs), DEMs, and DEGs. Results A diagnostic model containing 15 apoptosis-related genes was developed and its diagnostic efficiency was found to be robust. The HR group was correlated with higher immune scores of chemokines, cytokines, and interleukins; it was also significantly involved in pathways such as pancreatic beta cells and early estrogen response. A ceRNA network composed of 2 lncRNAs, 14 miRNAs, and 5 mRNAs was established. Conclusions The established model is a potential tool to improve the diagnostic efficiency of patients with schizophrenia, and the nodes included in the ceRNA network might serve as biomarkers and therapeutic targets for schizophrenia.
IL18 Gene Polymorphism Is Associated with Total IgE in Adult Subjects with Asthma

The allergic asthma phenotype is characterized by a T helper type 2 (Th2) immune response, based on Immunoglobulin E (IgE)-mediated type 1 hypersensitivity reactions. Total IgE is the sum of all IgE types produced by the human body and is used as a biomarker of inflammation in asthma. We analysed data collected in 143 asthma cases (median age 42.1 years) from the general Italian population (GEIRD survey; 2008–2010) to identify single nucleotide polymorphisms (SNPs) in candidate genes that are associated with total IgE in adult subjects with asthma. These patients reported respiratory symptoms in response to perennial allergens and provided data on 166 SNPs tagging 50 candidate genes or gene regions. Replication of the statistically significant results was performed in 842 asthma cases from other European countries (ECRHS II survey; 1998–2002). SNP rs549908 in interleukin 18 (IL18) gene was significantly associated with total IgE in GEIRD, and this result was replicated in ECRHS II. SNP rs1063320 in the human leukocyte antigen G (HLA-G) gene was identified in GEIRD, but this association was not replicated in ECRHS II. Further investigating IL18 and its biological pathways could be important for developing new therapeutic targets, due to its involvement in inflammatory response processes.
Synergy of Regenerative Periodontal Surgery and Orthodontics Improves Quality of Life of Patients with Stage IV Periodontitis: 24-Month Outcomes of a Multicenter RCT

In stage IV periodontitis patients with pathologic tooth migration (PTM), interdisciplinary treatment includes regenerative periodontal surgery (RPS) with an application of biomaterials and orthodontic therapy (OT) to restore function, esthetics and thereby quality of life (QoL). In a 24-month randomized trial we explored the synergy between regenerative medicine and biomechanical force application. The following methods were used: Forty-three patients had been randomized to a combined treatment comprising RPS and subsequent OT starting either 4 weeks (early OT) or 6 months (late OT) post-operatively. Clinical periodontal parameters and oral health-related QoL (GOHAI) were recorded up to 24 months. We obtained the following results: Mean clinical attachment gain (∆CAL ± SD) was significantly higher with early OT (5.96 ± 2.1 mm) versus late OT (4.65 ± 1.76 mm) (p = 0.034). Pocket closure (PPD ≤ 4 mm) was obtained in 91% of defects with early OT compared to 90% with late OT. GOHAI-scores decreased significantly from 26.1 ± 7.5 to 9.6 ± 4.7 (early OT) and 25.1 ± 7.1 to 12.7 ± 5.6 (late OT). Inconclusion, teeth severely compromised by intrabony defects and PTM can be treated successfully by RPS followed by early OT with the advantage of an overall reduced treatment time. As a result of the combined periodontal-orthodontic therapy, the oral health-related QoL of patients was significantly improved. Early stimulation of wound healing with orthodontic forces had a favorable impact on the outcomes of regenerative periodontal surgery.
The Influence of Urban Gardening Activities on Participants’ Perceived Restorativeness, Resilience, Sense of Community and Stress

This study aimed to investigate the influence of urban garden activities on participants’ perceived restorativeness, resilience, sense of community, and stress reduction. A total of ninety individuals who agreed to participate in the experiment were divided into experimental and control groups. To collect data, 16 sessions of urban garden activities were conducted every two weeks from May to November 2022. Perceived Restorativeness Scale, Connor–Davidson Resilience Scale, Sense of Community Index, and Brief Encounter Psychosocial Instrument were employed to measure participants’ psychological effects. To evaluate physiological effects, salivary cortisol tests were performed. The results of the study revealed that urban gardening activities influenced on participants’ physiological and psychological reactions in positive ways.
Effect of Cross-Linking Density on Non-Linear Viscoelasticity of Vulcanized SBR: A MD Simulation and Experimental Study

In recent years, there has been a growing interest in changes in dynamic mechanical properties of mixed rubber during dynamic shear, yet the influence of vulcanized characteristics on the dynamic shear behavior of vulcanized rubber, particularly the effect of cross-linking density, has received little attention. This study focuses on styrene–butadiene rubber (SBR) and aims to investigate the impact of different cross-linking densities (Dc) on dynamic shear behavior using molecular dynamics (MD) simulations. The results reveal a remarkable Payne effect, where the storage modulus experiences a significant drop when the strain amplitude (γ0) exceeds 0.1, which can be attributed to the fracture of the polymer bond and the decrease in the molecular chain’s flexibility. The influence of various Dc values mainly resides at the level of molecular aggregation in the system, where higher Dc values impede molecular chain motion and lead to an increase in the storage modulus of SBR. The MD simulation results are verified through comparisons with existing literature.
In Utero Exposure to Hormonal Contraception and Mortality in Offspring with and without Cancer: A Nationwide Cohort Study

Simple Summary Hormonal contraception is widely used among reproductive-aged women. In spite of the high effectiveness of hormonal contraception, some users become pregnant, probably due to irregular use. We previously reported an increased morbidity of childhood cancer in a nationwide cohort of offspring exposed in utero to maternal use of hormonal contraception. However, it remains unknown if mortality is increased in offspring with and without cancer after in utero exposure to hormonal contraception. The present study indicates that in utero exposure to hormonal contraception has an influence on long-term child mortality and survival after a diagnosis of leukemia. These novel findings have potential use in guidelines for hormonal contraception use in relation to pregnancy and expand our understanding of the etiology and prognosis of childhood leukemia. Abstract Approximately 400 million women of reproductive age use hormonal contraceptives worldwide. Eventually, pregnancy sometimes occurs due to irregular use. Use in early pregnancy is found to be associated with child morbidities including cancer, the main reason for disease-related death in children. Here, we add the missing piece about in utero exposure to hormonal contraception and mortality in offspring, including assessments of prognosis in children with cancer. In utero exposure to hormonal contraception may be associated with death since we found a hazard ratio (HR) of 1.22 (95% confidence interval (CI) 1.01–1.48) compared to children of mothers with previous use. The HRs were 1.22 (95% CI 0.99–1.13) for oral combined products and 2.92 (95% CI 1.21–7.04) for non-oral progestin-only products. A poorer prognosis was also found in exposed children with leukemia (3.62 (95% CI: 1.33–9.87)). If causal, hormonal contraception in pregnancy seems detrimental for offspring health and a marker of poorer prognosis in children with leukemia.
The effects of pulmonary rehabilitation on inflammatory biomarkers in patients with chronic obstructive pulmonary disease: Protocol for a systematic review and meta-analysis

Introduction Chronic obstructive pulmonary disease (COPD) is a common, preventable lung disease which affects more than 300 million people worldwide. People with COPD have elevated levels of inflammatory biomarkers, which are linked to physiological alterations in the respiratory system and extrapulmonary manifestations. Pulmonary rehabilitation (PR) is one of the strategies used in the management of individuals with COPD irrespective of severity, however its effect on systemic inflammation is poorly understood. We report the protocol of a systematic review on the effects of PR on systemic inflammation in patients with COPD. Materials and methods Using the search terms “chronic obstructive pulmonary disease”, “pulmonary rehabilitation”, and “inflammatory biomarkers” and their synonyms, five databases (AMED, CINAHL, Ovid MEDLINE, MEDLINE (Pubmed), EMBASE) will be searched from their inception to identify primary literature evaluating the effects of PR on systemic inflammation. Two reviewers will independently screen titles, abstracts, and full texts for eligibility using the Covidence web-based software. Eligible studies must be published in a peer-reviewed journal and include: (1) participants with COPD undergoing PR with an exercise component of at least 4 weeks in length and (2) a measure of systemic inflammation (e.g., bloodwork or sputum sample) as an outcome of interest. We will use the Cochrane Risk of Bias Tools (ROB2 and ROBINS-I) and will rate the quality of the evidence using the Grading of Recommendations, Assessment, Development and Evaluations (GRADE) tool. This protocol has followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Protocols (PRISMA-P) guidelines and is registered with the International Prospective Register of Systematic Reviews (PROSPERO). Conclusion The results of this systematic review will summarize the status of the evidence highlighting the effect of PR on systemic inflammation. A manuscript will be drafted and submitted to a peer-reviewed journal and shared at conferences.
SheepFaceNet: A Speed–Accuracy Balanced Model for Sheep Face Recognition

Simple Summary The use of computer vision technology has improved the effectiveness of individual sheep identification, but existing methods face challenges such as large parameter sizes, slow recognition speeds, and difficult deployment. To address this issue, we have made improvements and optimizations based on the Retinaface face recognition model to create a balanced speed-accuracy sheep face recognition model. The optimized model has fewer parameters, simpler computations, faster inference speeds, and higher recognition accuracy, making it well-suited for deployment on resource-constrained edge devices. This research is expected to promote the application of deep learning-based sheep face recognition methods in production. Abstract The recognition of sheep faces based on computer vision has improved the efficiency and effectiveness of individual sheep identification, providing technical support for the development of smart farming. However, current recognition models have problems such as large parameter sizes, slow recognition speed, and difficult deployment. Therefore, this paper proposes an efficient and fast basic module called Eblock and uses it to build a lightweight sheep face recognition model called SheepFaceNet, which achieves the best balance between speed and accuracy. SheepFaceNet includes two modules: SheepFaceNetDet for detection and SheepFaceNetRec for recognition. SheepFaceNetDet uses Eblock to construct the backbone network to enhance feature extraction capability and efficiency, designs a bidirectional FPN layer (BiFPN) to enhance geometric location ability, and optimizes the network structure, which affects inference speed, to achieve fast and accurate sheep face detection. SheepFaceNetRec uses Eblock to construct the feature extraction network, uses ECA channel attention to improve the effectiveness of feature extraction, and uses multi-scale feature fusion to achieve fast and accurate sheep face recognition. On our self-built sheep face dataset, SheepFaceNet recognized 387 sheep face images per second with an accuracy rate of 97.75%, achieving an advanced balance between speed and accuracy. This research is expected to further promote the application of deep-learning-based sheep face recognition methods in production.
Peripheral Complement Factor-Based Biomarkers for Patients with First-Episode Schizophrenia

Objective Schizophrenia (SCZ) is a severe, protracted neurological disorder that causes disruptive conduct in millions of individuals globally. Discovery of potential biomarkers in clinical settings would lead to the development of efficient diagnostic techniques and an awareness of the disease’s pathogenesis and prognosis. The aim of the present study was to discover and identify serum complement factor-based biomarkers in discriminating patients with first-episode SCZ from healthy controls. Methods Eighty-nine patients with first-episode SCZ and 89 healthy controls were included in this study. Psychiatric symptom severity of patients with SCZ was measured with the Brief Psychiatric Rating Scale-18 Item Version (BPRS) and the Scales for the Assessment of Negative/Positive Symptoms (SANS/SAPS). A total of 5 complement factors including complement component 1 (C1), C2, C3, C4, and 50% hemolytic complement (CH50) were measured using commercially available enzyme-linked immunosorbent assay (ELISA) kits. The levels of serum complement factors in the SCZ and control groups were compared, and the receiver operating characteristic (ROC) curve method was used to assess the diagnostic values of various complement factors for separating SCZ patients from healthy controls. Pearson’s correlation test was used to assess the relationships between serum complement factor concentrations and the psychiatric symptom severity. Results There was an increase in serum levels of C1, C2, C3, C4, and CH50 among patients with SCZ. Moreover, based on ROC curve analysis, the AUC value of a combined panel of C1, C2, C3, C4, and CH50 was 0.857 when used to discriminate patients with SCZ from healthy controls. Furthermore, serum C2, C3, and CH50 levels were positively correlated to the scores of SANS, SAPS, and BPRS in patients with SCZ, respectively. Conclusion These results suggested that circulating complement factors including C1, C2, C3, C4, and CH50 may have potential in discovering biomarkers for diagnosing first-episode SCZ.
Tree Root-Associated Microbial Communities Depend on Various Floor Management Systems in an Intensive Apple (Malus × domestica Borkh.) Orchard

Regenerative 3agriculture prioritizes soil health to build up organic soil carbon and nitrogen stocks while supporting the active and diverse soil biota that is a prerequisite for maintaining crop productivity and quality in sustainable food production. This study aimed at unravelling the impact of organic and inorganic soil maintenance systems in a ‘Red Jonaprince’ apple (Malus × domestica Borkh.) orchard on soil microbiota biodiversity and soil physico-chemical properties. During our study, we compared seven floor management systems in terms of microbial community diversity. Fungal and bacterial communities on all taxonomic levels differed largely between systems that augmented organic matter (organic) and other tested inorganic regimes. The dominant phylum of the soil in all management systems was Ascomycota. The operational taxonomic units (OTUs) within the Ascomycota were largely identified as members of Sordariomycetes, followed by Agaricomycetes, and both dominated in organic systems versus inorganic. The most prominent phyla, Proteobacteria, accounted for 43% of all assigned bacteria OTUs. Gammaproteobacteria, Bacteroidia, and Alphaproteobacteria were predominant in organic samples, while Acidobacteriae, Verrucomicrobiae, and Gemmatimonadetes were more abundant in inorganic mulches.
Oreocharis oriolus, a new species of Gesneriaceae in a sclerophyllous oak community from Yunnan, Southwest China

Abstract Oreocharis oriolus, a new species of Gesneriaceae in a sclerophyllous oak community from Yunnan, Southwest China, is described and illustrated. Morphologically, it resembles both O. forrestii and O. georgei, while it is distinct in combined characters of wrinkled leaves, peduncle and pedicel covered with whitish and egladular villous hairs, bract lanceolate and nearly glabrescent adaxially, and staminode absent. Molecular phylogenetic analysis based on nuclear ribosomal internal transcribed spacer (nrITS) and chloroplast DNA fragment (trnL‐F) of 61 congeneric species also supported O. oriolus as a new species while it was nested with O. delavayi. It was currently assessed as ‘Critically Endangered’ (CR) regarding to its small‐sized population and narrow distribution following the IUCN categories and criteria.
Nuclear Delivery of Nanoparticle-Based Drug Delivery Systems by Nuclear Localization Signals

Nanomedicine 2.0 refers to the next generation of nanotechnology-based medical therapies and diagnostic tools. This field focuses on the development of more sophisticated and precise nanoparticles (NPs) for targeted drug delivery, imaging, and sensing. It has been established that the nuclear delivery of NP-loaded drugs can increase their therapeutic efficacy. To effectively direct the NPs to the nucleus, the attachment of nuclear localization signals (NLSs) to NPs has been employed in many applications. In this review, we will provide an overview of the structure of nuclear pore complexes (NPCs) and the classic nuclear import mechanism. Additionally, we will explore various nanoparticles, including their synthesis, functionalization, drug loading and release mechanisms, nuclear targeting strategies, and potential applications. Finally, we will highlight the challenges associated with developing nucleus-targeted nanoparticle-based drug delivery systems (NDDSs) and provide insights into the future of NDDSs.
Development of an Automated Online Flow Cytometry Method to Quantify Cell Density and Fingerprint Bacterial Communities

Cell density is an important factor in all microbiome research, where interactions are of interest. It is also the most important parameter for the operation and control of most biotechnological processes. In the past, cell density determination was often performed offline and manually, resulting in a delay between sampling and immediate data processing, preventing quick action. While there are now some online methods for rapid and automated cell density determination, they are unable to distinguish between the different cell types in bacterial communities. To address this gap, an online automated flow cytometry procedure is proposed for real-time high-resolution analysis of bacterial communities. On the one hand, it allows for the online automated calculation of cell concentrations and, on the other, for the differentiation between different cell subsets of a bacterial community. To achieve this, the OC-300 automation device (onCyt Microbiology, Zürich, Switzerland) was coupled with the flow cytometer CytoFLEX (Beckman Coulter, Brea, USA). The OC-300 performs the automatic sampling, dilution, fixation and 4′,6-diamidino-2-phenylindole (DAPI) staining of a bacterial sample before sending it to the CytoFLEX for measurement. It is demonstrated that this method can reproducibly measure both cell density and fingerprint-like patterns of bacterial communities, generating suitable data for powerful automated data analysis and interpretation pipelines. In particular, the automated, high-resolution partitioning of clustered data into cell subsets opens up the possibility of correlation analysis to identify the operational or abiotic/biotic causes of community disturbances or state changes, which can influence the interaction potential of organisms in microbiomes or even affect the performance of individual organisms.
Development of a Visuoperceptual Measure for Fiberoptic Endoscopic Evaluation of Swallowing (V-FEES) in Adults with Oropharyngeal Dysphagia: An International Delphi Study

Visuoperceptual evaluation of fiberoptic endoscopic evaluation of swallowing (FEES) is a commonly used assessment in dysphagia or swallowing disorders. Currently, no international consensus exists regarding which visuoperceptual measures to use for the analysis of FEES recordings. Moreover, existing visuoperceptual FEES measures are limited by poor and incomplete psychometric data, identifying an urgent need for developing a visuoperceptual measure to interpret FEES recordings. Following the COSMIN group’s (COnsensus-based Standards for the selection of health Measurement INstruments) psychometric taxonomy and guidelines, this study aimed to establish the content validity of a new visuoperceptual FEES (V-FEES) measure in adults with oropharyngeal dysphagia. Using the Delphi technique, international consensus was achieved among dysphagia experts across 21 countries, resulting in a new prototype measure for V-FEES, comprising 30 items, 8 function testing items (i.e., specific tasks performed by patients while observing and rating items), and 36 unique operationalisations (i.e., defining items into measurable factors that could be measured empirically using visuoperceptual observation). This study supports good content validity for V-FEES, including participants’ feedback on the relevance, comprehensiveness, and comprehensibility of the included items. Future studies will continue the instrument development process and determine the remaining psychometric properties using both the classic test theory (CTT) and item response theory (IRT) models.