Miracle-dz/UniFAR-FTUs huggingface dataset:
Avian MHC Evolution in the Era of Genomics: Phase 1.0

Birds are a wonderfully diverse and accessible clade with an exceptional range of ecologies and behaviors, making the study of the avian major histocompatibility complex (MHC) of great interest. In the last 20 years, particularly with the advent of high-throughput sequencing, the avian MHC has been explored in great depth in several dimensions: its ability to explain ecological patterns in nature, such as mating preferences; its correlation with parasite resistance; and its structural evolution across the avian tree of life. Here, we review the latest pulse of avian MHC studies spurred by high-throughput sequencing. Despite high-throughput approaches to MHC studies, substantial areas remain in need of improvement with regard to our understanding of MHC structure, diversity, and evolution. Recent studies of the avian MHC have nonetheless revealed intriguing connections between MHC structure and life history traits, and highlight the advantages of long-term ecological studies for understanding the patterns of MHC variation in the wild. Given the exceptional diversity of birds, their accessibility, and the ease of sequencing their genomes, studies of avian MHC promise to improve our understanding of the many dimensions and consequences of MHC variation in nature. However, significant improvements in assembling complete MHC regions with long-read sequencing will be required for truly transformative studies.
Linkage-linkage disequilibrium dissection of the epigenetic quantitative trait loci (epiQTLs) underlying growth and wood properties in Populus.

Increasing evidence indicates that DNA methylation is heritable and serves as an essential marker contributing to phenotypic variation. We used linkage-linkage disequilibrium mapping to decipher the epigenetic architecture underlying nine growth and wood property traits in a linkage population (550 F1 progeny) and a natural population (435 unrelated individuals) of Populus using methylation-sensitive amplification polymorphism (MSAP)-based analysis and further unveiled the interactions between genetic and epigenetic variants in the causative genes using expression quantitative trait methylation (eQTM) and nucleotide (eQTN) mapping strategies. We mapped 163 epigenetic quantitative trait loci (epiQTLs; LOD ≥ 3.0), explaining 1.7-44.5% of phenotypic variations, to a high-resolution epigenetic map with 19 linkage groups, which was supported by the significant MSAP associations (P < 0.001) in the two populations. We determined 23 causal genes involved in growth regulation and wood formation, whose markers were located in epiQTLs and associated with the same traits in both populations. Further eQTN and eQTM mapping showed that causal genetic and epigenetic variants within the 23 candidate genes may interact more in trans in gene expression and phenotype. Our study provides strategies for investigating epigenetic architecture and the interaction between genetic and epigenetic variants modulating complex traits in forest trees.
Predicting postoperative fatigue in surgically treated lung cancer patients in Norway: a longitudinal 5-month follow-up study

Objectives Despite the negative influence of fatigue on quality of life in patients who undergo lung cancer surgery, little is known about the possible predictors of postoperative fatigue. The aim of this study was to examine demographic and clinical characteristics that might predict postoperative fatigue 5 months after lung cancer surgery. Design A prospective longitudinal follow-up study comprising preoperative and postoperative questionnaires, including Lee Fatigue Scale, and sociodemographic and clinical data. Setting Three university hospitals in Norway (eg, Oslo University Hospital, St. Olav University Hospital and Haukeland University Hospital). Participants In total, 196 surgically treated patients who answered the questionnaires both preoperatively and at 5-month follow-up with valid fatigue scores. Results Bivariate analyses showed that preoperative fatigue was associated with comorbidities and the symptoms of shortness of breath, cough, depression, anxiety, sleep disturbance and pain. Only cough was directly associated with preoperative fatigue in a regression model. Comorbidities and the symptoms of shortness of breath, cough, depression and sleep disturbance were associated with postoperative fatigue in the bivariate analyses, but only shortness of breath was associated with postoperative fatigue in the regression model. We did not find any significant correlations between fatigue and any treatment variable. Conclusion Clinicians should pay special attention to lung symptoms and be aware that these may lead to long-term postoperative fatigue. Further research should examine whether interventions reducing lung symptoms, such as shortness of breath and coughing, may prevent development of fatigue in patients undergoing lung cancer surgery.
Optical Coherence Tomography Angiography Findings in Active and Inactive Ocular Behçet Disease

ABSTRACT Purpose To study macular microvascular changes in ocular Behçet disease (OBD) using optical coherence tomography angiography (OCTA). Methods Quantitative and qualitative analyses of OCTA were performed on 23 OBD patients with active or inactive uveitis and compared with healthy controls. Results Deep capillary plexus (DCP) is the most frequently involved in OBD (p < 0.001). Its vessel density (VD) is reduced compared with controls in both active (p < 0.007) and inactive uveitis (p = 0.03). In inactive uveitis, VD is inversely related to the number of uveitis relapses (superficial capillary plexus: r = –0.694, p = 0.004; DCP: r = –0.541, p = 0.037) and it is significantly reduced in patients with a uveitis-free period ≥5 years compared with healthy controls (p < 0.038). Conclusions Macular VD is reduced in Behçet patients with active and inactive uveitis, especially in DCP. In inactive uveitis, VD is inversely related to the number of ocular relapses and cannot be restored during time.
Characteristic of Stimulus Frequency Otoacoustic Emissions: Detection Rate, Musical Training Influence, and Gain Function

Stimulus frequency otoacoustic emission (SFOAE) is an active acoustic signal emitted by the inner ear providing salient information about cochlear function and dysfunction. To provide a basis for laboratory investigation and clinical use, we investigated the characteristics of SFOAEs, including detection rate, musical training influence, and gain function. Sixty-five normal hearing subjects (15 musicians and 50 non-musicians, aged 16–45 years) were tested and analyzed at the probe level of 30 and 50 dB sound pressure levels (SPL) in the center frequency of 1 and 4 kHz in the study. The results indicate that (1) the detection rates of SFOAE are sensitive to the gender, (2) musicians reveal enhanced hearing capacity and SFOAE amplitudes compared with non-musicians, and (3) probe frequency has a significant effect on the compression threshold of SFOAE. Our findings highlight the importance of SFOAE in the clinical hearing screening and diagnosis and emphasize the use of musical training for the rehabilitation enhancement of the auditory periphery and hearing threshold.
Targeting EZH2 Enhances Antigen Presentation, Antitumor Immunity, and Circumvents Anti–PD-1 Resistance in Head and Neck Cancer

Purpose: Anti–programmed death-1 (PD-1) receptor–based therapeutics improve survival in patients with recurrent head and neck squamous cell carcinoma (HNSCC), but many do not benefit due to a low response rate. Herein, we identified EZH2 as a therapeutic target that enhanced tumor cell antigen presentation and subsequently sensitized resistant tumors to anti–PD-1 therapy. Experimental Design: EZH2 regulation of antigen presentation was defined using EZH2 inhibitors (GSK126 and EPZ6438) in human and mouse HNSCC cell lines. Mechanistic dissection of EZH2 in regulation of antigen presentation was investigated using flow cytometry, qRT-PCR, ELISA, and chromatin-immunoprecipitation assays. EZH2-deficient cell lines were generated using CRISPR-CAS9. GSK126 and anti–PD‐1–blocking antibody were used in testing combinatorial therapy in vivo. Results: EZH2 expression was negatively correlated with antigen-processing machinery pathway components in HNSCC data sets in The Cancer Genome Atlas. EZH2 inhibition resulted in significant upregulation of MHC class I expression in human and mouse human papillomavirus–negative HNSCC lines in vitro and in mouse models in vivo. Enhanced antigen presentation on the tumor cells by EZH2 inhibitors or CRISPR–mediated EZH2 deficiency increased antigen-specific CD8+ T-cell proliferation, IFNγ production, and tumor cell cytotoxicity. Mechanistically, EZH2 inhibition reduced the histone H3K27me3 modification on the β-2-microglobulin promoter. Finally, in an anti–PD-1–resistant model of HNSCC, tumor growth was suppressed with combination therapy. Conclusions: Our results demonstrated that targeting EZH2 enhanced antigen presentation and was able to circumvent anti–PD-1 resistance. Thus, combining EZH2 targeting with anti–PD-1 may increase therapeutic susceptibility in HNSCC.
Protocolled practice nurse-led care for children with asthma in primary care: protocol for a cluster randomised trial

Introduction In children with asthma, daily symptoms and exacerbations have a significant impact on the quality of life of both children and parents. More effective use of asthma medication and, consequently, better asthma control is advocated, since both overtreatment and undertreatment are reported in primary care. Trials in adults suggest that asthma control is better when patients receive a regular medical review. Therefore, protocolled care by the general practitioner may also lead to better asthma control in children. However, such protocolled care by the general practitioner may be time consuming and less feasible. Therefore, this study aims to determine whether protocolled practice nurse-led asthma care for children in primary care provides more effective asthma control than usual care. Methods and analysis The study will be a cluster-randomised open-label trial with an 18-month follow-up. Practice nurses will be the units of randomisation and children with asthma the units of analysis. It is planned to include 180 children aged 6–12 years. Primary outcome will be average asthma control during the 18-month follow-up measured by the Childhood Asthma Control Test (C-ACT). Secondary outcomes include C-ACT scores at t=3, t=6, t=12 and t=18 months; the frequency and severity of exacerbations; cost-effectiveness; quality of life; satisfaction with delivered care; forced expiratory volume in 1 s and forced expiratory flow at 75% and the association of high symptoms scores at baseline and baseline characteristics. Besides, we will conduct identical measurements in a non-randomised sample of children. Ethics and dissemination This will be the first trial to evaluate the effectiveness of protocolled practice nurse-led care for children with asthma in primary care. The results may lead to improvements in asthma care for children and can be directly implemented in revisions of asthma guidelines. The study protocol was approved by the Medical Research Ethics Committee of the Erasmus Medical Centre in Rotterdam. Trial registration NTR6847.
TNF-Mediated Compensatory Immunity to Mycobacterium avium in the Absence of Macrophage Activation by IFN-γ

Key Points Mice can control Mycobacterium avium infections independently of MΦ activation by IFN-γ. TNF compensates for the lack of MΦ activation by IFN-γ. Granulomas form without MΦ activation by IFN-γ. Granuloma formation is a hallmark of several infectious diseases, including those caused by Mycobacterium sp. These structures are composed of accumulations of inflammatory cells, and it has been shown that cytokines such as IFN-γ and TNF-α are required for granuloma assembly during M. avium infections in mice. Macrophages (MΦs) insensitive to IFN-γ (MIIG) mice have MΦs, monocytes, and dendritic cells that are unresponsive to IFN-γ. We observed that although IFN-γ−/− mice present an exacerbated infection, the same is not true for MIIG animals, where the same levels of protection as the wild-type animals were observed in the liver and partial protection in the spleen. Unlike IFN-γ−/− mice, MIIG mice still develop well-defined granulomas, suggesting that IFN-γ–mediated MΦ activation is not required for granuloma assembly. This work also shows that MIIG animals exhibit increased cell recruitment with higher CD4+ T cells numbers as well as increased IFN-γ and TNF-α expression, suggesting that TNF-α may have a role in protection and may compensate the lack of MΦ response to IFN-γ in the MIIG model. TNF-α–deficient MIIG mice (MIIG.TNF-α−/−) exhibited increased bacterial burdens when compared with MIIG mice. These results suggest that in the absence of IFN-γ signaling in MΦs, TNF-α has a protective role against M. avium.
Silk Fibroin as a Functional Biomaterial for Drug and Gene Delivery

Silk is a natural polymer with unique physicochemical and mechanical properties which makes it a desirable biomaterial for biomedical and pharmaceutical applications. Silk fibroin (SF) has been widely used for preparation of drug delivery systems due to its biocompatibility, controllable degradability and tunable drug release properties. SF-based drug delivery systems can encapsulate and stabilize various small molecule drugs as well as large biological drugs such as proteins and DNA to enhance their shelf lives and control the release to enhance their circulation time in the blood and thus the duration of action. Understanding the properties of SF and the potential ways of manipulating its structure to modify its physicochemical and mechanical properties allows for preparation of modulated drug delivery systems with desirable efficacies. This review will discuss the properties of SF material and summarize the recent advances of SF-based drug and gene delivery systems. Furthermore, conjugation of the SF to other biomolecules or polymers for tissue-specific drug delivery will also be discussed.
An international survey of perceptions of the 2014 FIFA World Cup: National levels of corruption as a context for perceptions of institutional corruption

We conducted a survey about the 2014 FIFA World Cup that measured attitudes about FIFA, players, and officials in 18 languages with 4600 respondents from 29 countries. Sixty percent of respondents perceived FIFA officials as being dishonest, and people from countries with less institutional corruption and stronger rule of law perceived FIFA officials as being more corrupt and less competent running the tournament than people from countries with more corruption and weaker rule of law. In contrast, respondents evaluated players as skilled and honest and match officials as competent and honest. We discuss the implications of our findings for perceptions of corruption in general.
Real-Time Monitoring of Suicide Risk among Adolescents: Potential Barriers, Possible Solutions, and Future Directions

Recent advances in real-time monitoring technology make this an exciting time to study risk for suicidal thoughts and behaviors among youth. Although there is good reason to be excited about these methods, there is also reason for caution in adopting them without first understanding their limitations. In this article, we present several broad future directions for using real-time monitoring among youth at risk for suicide focused around three broad themes: novel research questions, novel analytic methods, and novel methodological approaches. We also highlight potential technical, logistical, and ethical challenges with these methodologies, as well as possible solutions to these challenges.
PERFORMANCE ANALYSIS OF A DIESEL ENGINE WITHIN A MULTI-DIMENSIONAL FRAMEWORK

In this study, large-bore diesel engine combustion was modeled using development combustion model Extended Coherent Flame Models 3 Zones (ECFM-3Z). During this work, the study was made about an engine configuration with compression, spray injection, combustion and emission of the diesel engine. Prediction of incylinder combustion phenomenon, effects of turbulence levels, flow structures and emission modeling have an importance in designing efficient engines. Effects of in-cylinder flow structures, fuel injection and design parameters were investigated for the engine performance and emission results. The results agree broadly with experimental and computational studies. As a result, it is aimed to find out the flow structure, spray, combustion and emission characteristics of the large-bore diesel engine. In a precombustion chamber structure, it is seen that controlled combustion starts and then high-pressure gas mixture uniformly spreads into the main combustion chamber.
Genome-Wide Association Study for Reproductive Traits in a Duroc Pig Population

Simple Summary Reproductive traits are economically important in the pig industry, and it is critical to explore their underlying genetic architecture. Hence, four reproductive traits, including litter size at birth (LSB), litter weight at birth (LWB), litter size at weaning (LSW), and litter weight at weaning (LWW), were examined. Through a genome-wide association study in a Duroc pig herd, several candidate single-nucleotide polymorphisms (SNPs) and genes were found potentially associated with the traits of interest. These findings help to understand the genetic basis of porcine reproductive traits and could be applied in pig breeding programs. Abstract In the pig industry, reproductive traits constantly influence the production efficiency. To identify markers and candidate genes underlying porcine reproductive traits, a genome-wide association study (GWAS) was performed in a Duroc pig population. In total, 1067 pigs were genotyped using single-nucleotide polymorphism (SNP) chips, and four reproductive traits, including litter size at birth (LSB), litter weight at birth (LWB), litter size at weaning (LSW), and litter weight at weaning (LWW), were examined. The results showed that 20 potential SNPs reached the level of suggestive significance and were associated with these traits of interest. Several important candidate genes, including TXN2, KCNA1, ENSSSCG00000003546, ZDHHC18, MAP2K6, BICC1, FAM135B, EPHB2, SEMA4D, ST3GAL1, KCTD3, FAM110A, TMEM132D, TBX3, and FAM110A, were identified and might compose the underlying genetic architecture of porcine reproductive traits. These findings help to understand the genetic basis of porcine reproductive traits and provide important information for molecular breeding in pigs.
Chemical Structure–Antioxidant Activity Relationship of Water–Based Enzymatic Polymerized Rutin and Its Wound Healing Potential

The flavonoid rutin (RU) is a known antioxidant substance of plant origin. Its potential application in pharmaceutical and cosmetic fields is, however, limited, due to its low water solubility. This limitation can be overcome by polymerization of the phenolic RU into polyrutin (PR). In this work, an enzymatic polymerization of RU was performed in water, without the addition of organic solvents. Further, the chemical structure of PR was investigated using 1H NMR, and FTIR spectroscopy. Size-exclusion chromatography (SEC) was used to determine the molecular weight of PR, while its acid/base character was studied by potentiometric charge titrations. Additionally, this work investigated the antioxidant and free radical scavenging potential of PR with respect to its chemical structure, based on its ability to (i) scavenge non biological stable free radicals (ABTS), (ii) scavenge biologically important oxidants, such as O2•, NO•, and OH•, and (iii) chelate Fe2+. The influence of PR on fibroblast and HaCaT cell viability was evaluated to confirm the applicability of water soluble PR for wound healing application.
Deep Learning on Point Clouds and Its Application: A Survey

Point cloud is a widely used 3D data form, which can be produced by depth sensors, such as Light Detection and Ranging (LIDAR) and RGB-D cameras. Being unordered and irregular, many researchers focused on the feature engineering of the point cloud. Being able to learn complex hierarchical structures, deep learning has achieved great success with images from cameras. Recently, many researchers have adapted it into the applications of the point cloud. In this paper, the recent existing point cloud feature learning methods are classified as point-based and tree-based. The former directly takes the raw point cloud as the input for deep learning. The latter first employs a k-dimensional tree (Kd-tree) structure to represent the point cloud with a regular representation and then feeds these representations into deep learning models. Their advantages and disadvantages are analyzed. The applications related to point cloud feature learning, including 3D object classification, semantic segmentation, and 3D object detection, are introduced, and the datasets and evaluation metrics are also collected. Finally, the future research trend is predicted.
Exploring the microbiota of upper respiratory tract during the development of pneumonia in a mouse model

The alteration of the microbial community in the upper respiratory tract (URT) can contribute to the colonization and invasion of respiratory pathogens. However, there are no studies regarding whether the characteristics of the URT microbiota can be affected by infections in lower respiratory tract (LRT). To elucidate the microbial profiles of the URT during pneumonia, the oral, nasal, and lung microbiota was evaluated at the early phase in a murine pneumonia model by direct intratracheal inoculation of Klebsiella pneumoniae. The meta 16S rRNA sequencing of bronchoalveolar lavage fluid after K. pneumoniae inoculation presented alterations in the beta diversity of the microbes, but not in the alpha diversity. At this point, a significant increase in microbial alpha diversity was observed in the oral cavity, but not in the nasal cavity. The significant increase was observed in the family Carnobacteriaceae and family Enterococcaceae. These results suggest that characterizing the microbial community of the respiratory tract may not just involve a simple downstream relationship from the URT to the LRT. The health status of the LRT may influence the oral microbiota. Thus, evaluation of the oral microbiota may contribute towards monitoring lung health; the oral microbiota may act as a diagnostic marker of pneumonia.