Phenotype-Genotype analysis of caucasian patients with high risk of osteoarthritis

Background: Osteoarthritis (OA) is a common cause of disability and pain around the world. Epidemiologic studies of family history have revealed evidence of genetic influence on OA. Although many efforts have been devoted to exploring genetic biomarkers, the mechanism behind this complex disease remains unclear. The identified genetic risk variants only explain a small proportion of the disease phenotype. Traditional genome-wide association study (GWAS) focuses on radiographic evidence of OA and excludes sex chromosome information in the analysis. However, gender differences in OA are multifactorial, with a higher frequency in women, indicating that the chromosome X plays an essential role in OA pathology. Furthermore, the prevalence of comorbidities among patients with OA is high, indicating multiple diseases share a similar genetic susceptibility to OA. Methods: In this study, we performed GWAS of OA and OA-associated key comorbidities on 3366 OA patient data obtained from the Osteoarthritis Initiative (OAI). We performed Mendelian randomization to identify the possible causal relationship between OA and OA-related clinical features. Results: One significant OA-associated locus rs2305570 was identified through sex-specific genome-wide association. By calculating the LD score, we found OA is positively correlated with heart disease and stroke. A strong genetic correlation was observed between knee OA and inflammatory disease, including eczema, multiple sclerosis, and Crohn's disease. Our study also found that knee alignment is one of the major risk factors in OA development, and we surprisingly found knee pain is not a causative factor of OA, although it was the most common symptom of OA. Conclusion: We investigated several significant positive/negative genetic correlations between OA and common chronic diseases, suggesting substantial genetic overlaps between OA and these traits. The sex-specific association analysis supports the critical role of chromosome X in OA development in females.

Enabling ultra-low-voltage switching in BaTiO3

Single crystals of BaTiO₃ exhibit small switching fields and energies, but thin-film performance is considerably worse, thus precluding their use in next-generation devices. Here, we demonstrate high-quality BaTiO₃ thin films with nearly bulk-like properties. Thickness scaling provides access to the coercive voltages (<100 mV) and fields (<10 kV cm^-1) required for future applications and results in a switching energy of <2 J cm^-3 (corresponding to <2 aJ per bit in a 10 × 10 × 10 nm³ device). While reduction in film thickness reduces coercive voltage, it does so at the expense of remanent polarization. Depolarization fields impact polar state stability in thicker films but fortunately suppress the coercive field, thus driving a deviation from Janovec-Kay-Dunn scaling and enabling a constant coercive field for films <150 nm in thickness. Switching studies reveal fast speeds (switching times of ~2 ns for 25-nm-thick films with 5-µm-diameter capacitors) and a pathway to subnanosecond switching. Finally, integration of BaTiO₃ thin films onto silicon substrates is shown. We also discuss what remains to be demonstrated to enable the use of these materials for next-generation devices.

[Study on mechanisms of Th17/Treg imbalance in patients with cystic echinococcosis based on miRNA expression profiles]

OBJECTIVE

To investigate the serum microRNA (miRNA) expression and examine the impact of miRNA expression profiles on T helper type 17 (Th17)/regulatory T cells (Treg) imbalance among patients with cystic echinococcosis, so as to provide insights into the illustration of the mechanisms underlying chronic Echinococcus granulosus infections, and long-term pathogenesis.

METHODS

Total RNA was extracted from the sera of cystic echinococcosis patients and healthy controls, and subjected to high-throughput sequencing with the Illumina sequencing platform. Known miRNAs were annotated and new miRNAs were predicted using the miRBase database and the miRDeep2 tool, and differentially expressed miRNAs were identified. The target genes of differentially expressed miRNAs were predicted using the software miRanda and TargetScan, and the intersection was selected for Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Among the differentially expressed miRNAs with the 20 highest fold changes, miRNAs that targeted genes relating to key transcription factors RORC and FOXP3 that determine the production of Th17 and Treg cells or their important regulatory pathways (PI3K-Akt and mTOR pathways) were matched.

RESULTS

A total of 53 differentially expressed miRNAs were screened in sera of cystic echinococcosis patients and healthy controls, including 47 up-regulated miRNAs and 6 down-regulated miRNAs. GO enrichment analysis showed that these differentially expressed miRNA were involved DNA transcription and translation, cell components, cell morphology, neurodevelopment and metabolic decomposition, and KEGG pathway analysis showed that the differentially expressed miRNA were mainly involved in MAPK, PI3K-Akt and mTOR signaling pathways. Among the differentially expressed miRNAs with the 20 highest fold changes, there were 3 miRNAs that had a potential for target regulation of RORC, and 15 miRNAs that had a potential to target the PI3K-Akt and mTOR signaling pathways.

CONCLUSIONS

Significant changes are found in serum miRNA expression profiles among patients with E. granulosus infections, and differentially expressed miRNAs may lead to Th17/Treg imbalance through targeting the key transcription factors of Th17/Treg or PI3K-Akt and mTOR pathways, which facilitates the long-term parasitism of E. granulosus in hosts and causes a chronic disease.

Morphological and transcriptional evaluation of multiple facial cutaneous hyperpigmented spots

Background

Morphological characteristics of major facial hyperpigmented spots have been well documented. However, detailed alterations of respective transcriptional profile for each spot and in-depth comparisons across multiple spot types have not been reported.

Objectives

To comprehensively assess and compare multiple facial hyperpigmented spot types at the morphological and molecular levels by utilising transcriptional expression profiling with correlation to quantified histological features.

Methods

Multiple types of facial spot biopsies were collected from Chinese women and compared to additional biopsies taken from adjacent healthy skin. The types of spots included Solar Lentigos with both elongated dermal-epidermal junction (DEJ) (SL[E]) and flat DEJ (SL[F]), Seborrhoeic Keratosis (SK), Melasma, Freckles, Post-inflammatory hyperpigmentation of resolving acne (PIH[A]) and other stimuli (PIH[O]). Combined histomorphometry, immunohistology, and transcriptome analysis for suprabasal-epidermis, basal-epidermis, and dermal compartments dissected by Laser Capture Microdissection (LCM) were conducted and compared across different spot types.

Results

Each spot type was confirmed to have the unique histological pathology already documented elsewhere. Most of the spot types except Melasma and PIH (A) revealed similar melanocyte density to adjacent skin. All spots exhibited increased melanin synthesis, melanosome transportation, as well as enhanced melanocyte dendricity, however, each spot revealed a distinct transcriptome regulation pattern in pigmentation pathways. Upregulation of pigmentation genes was also observed in the dermis of SL(F), SL(E), SK and PIH(O), associated with significant modulation of DEJ related genes in basal-epidermis and/or dermal compartments, suggesting potential melanocyte infiltration into the dermis due to impaired DEJ quality. Beyond upregulated pigmentation, for most spots, gene expression in the suprabasal-epidermis regulating keratinisation was significantly upregulated in conjunction with thickened stratum corneum. Furthermore, downregulation of tight junction related genes represented by claudin-1 was observed in majority of spot types, suggesting compromised barrier function could be a similarity across spots. Additionally, Cyclin-Dependent Kinase Inhibitor 2A (CDKN2A) was upregulated in all types of spots, indicating involvement of cell senescence as a common theme.

Conclusion

This comprehensive and comparative study based on the histological and transcriptional analysis of three skin compartments provided unique insights into specific causations as well as differences and similarities across multiple hyperpigmented spot types.

[Development of a Ranking Tool for Scientificity, Transparency and Applicability of Clinical Practice Guidelines]

Objective: To address the limitations of existing methods and tools for evaluating clinical practice guidelines, we aimed to develop a comprehensive instrument focusing on the three main dimensions of guideline development: scientificity, transparency, applicability. We will use it to rank the guidelines according to the scores. We abbreviated it as STAR, and its reliability, validity and usability were also tested. Methods: A multidisciplinary expert working group was set up, including methodologists, statisticians, journal editors, medical professionals, and others. Scoping review, Delphi methods and hierarchical analysis were used to determine the final checklist of STAR. Results: The new instrument contained 11 domains and 39 items. Intrinsic reliability of each domain was indicated by Cronbach's α coefficient, with a average value of 0.646. The Cohen's kappa coefficients for methodological evaluators and clinical evaluators were 0.783 and 0.618. The overall content validity index was 0.905. The R2 for the criterion validity analysis was 0.76. The average score for usability of the items was 4.6, and the mean time spent to evaluate each guideline was 20 minutes. Conclusion: The instrument has good reliability, validity and evaluating efficiency, and can be used for evaluating and ranking guidelines more comprehensively.

Yeast culture (Saccharomyces cerevisiae) and its active metabolites affect the cecal microbiome of broilers

Yeast cultures (YCs) are defined as promising feed additives that maintain the health of birds and improve growth performance by modulating gut microbiota. YCs contain effective metabolites such as glycine, fructose, inositol, galactose, and sucrose. This study investigated the effects of YCs and their effective metabolites on carcass traits and cecal microflora in broilers. A total of 280 one-day-old mixed-sex Arbor Acres broilers were randomly allocated to seven groups. The basal diet (control DZ) was supplemented with various proportions of glycine, fructose, inositol, galactose, and sucrose (Groups A, B, and C), 24-hour grown Saccharomyces cerevisiae cultures (Group D) (YC), and a commercial yeast culture product (SZ) at concentrations of 0.1% and 1% (Groups E and F). Bodyweight of broilers was correlated positively with proportions of Proteobacteria in Group C and Lactobacillus and Roseburia in Group B (P <0.05). Broilers fed diets supplemented with YC or its active metabolites had the highest proportions of bacteria involved in nucleotide metabolism, and amino acid and carbohydrate metabolism. These results suggested that the dietary addition of YC could alter the proliferation of beneficial bacteria in broilers.

[Mapping Regulatory Elements within 5' and 3' UTRs of SIGLEC15 with a Use of Reporter System]

Siglec-15 is an immune suppressor with broad upregulation on various cancer types and has emerged as a potential target for cancer immunotherapy. However, it remains unclear how SIGLEC15 expression is controlled in normal or cancer cells. In this work, we utilized reporter assays to evaluate the impact of the 5' UTR and the 3' UTR of SIGLEC15 mRNA on gene expression. We found that the 3' UTR dramatically reduced reporter protein production, whereas the 5' UTR showed modest inhibitory effect. Quantification of steady-state mRNA revealed the good coupling of protein amount and mRNA abundance that was associated with the 3' UTR. In contrast, the 5' UTR had little effect on mRNA abundance compared with the empty control. By measuring mRNA half-life, we showed that the 3' UTR markedly promoted mRNA degradation. Testing shortened 3' UTR fragments demonstrated five out of the six having notable inhibitory effect, with the one spanning 993-1317 had the most robust activity. More interestingly, the 993-1317 region contains a predicted 43-nt stem-loop structure that showed apparent inhibitory activity in four cell lines tested. These results suggested that the 3' UTR inhibited reporter gene expression by accelerating mRNA decay possibly via multiple cis-regulatory elements, but the 5' UTR repressed gene expression by inhibiting translation. Thus, our findings provided a clue to the molecular mechanism underlying the regulation of SIGLEC15 expression.

Making copper, silver and gold fullerene cages breathe

We show that optical properties change when the fullerene structures of Au₃₂, Cu₃₂and Ag₃₂inflate and deflate. We first observe significant differences in the extinction spectra employing a classical approach based on the Green's dyadic method. By means of real-time time-dependent density functional theory. We continue to calculate the optical spectrum (OP) via aδ-kick simulation, comparing results with the ground-state energetic property the HOMO-LUMO (HL) gap. Red-shift of the OP is expected as the fullerenes inflate, with only ±10% change in the size. As the fullerene breathes, a 0.8 eV shift in the first peak position could be observed in the gold nanoparticle. Ag has a smoother behaviour than both Au and Cu. We have also found changes in the optical spectra can not be directly interpreted as a result of changes in the HL gap.

Exerimental method and preliminary studies of the passive containment water film evaporation mass transfer

For larger containments and higher operation parameters, characteristics of the outside cooling of the PCCS are very important for the analysis on the containment integrity. A preliminary analysis was made and a four-step experimental method was used to numerically analyze the falling water film evaporation for the advanced passive containment. Then, the water flow stability along the outside wall of the containment was studied. The results fit well with those correlations without airflow when the air velocity is less than 5.0 m/s. However, when the air velocity is larger than 5.0 m/s, the influence of the air velocity on the water film will appear and the mean water film thickness will be thicker. Based on the prototype operation parameters, experimental studies were carried and the results were compared with the Dittus-Boelter correlation within the operation ranges. A modification factor was proposed for the conservative application of this correlation for nuclear safety analysis.

CCPE: cell cycle pseudotime estimation for single cell RNA-seq data

Pseudotime analysis from scRNA-seq data enables to characterize the continuous progression of various biological processes, such as the cell cycle. Cell cycle plays an important role in cell fate decisions and differentiation and is often regarded as a confounder in scRNA-seq data analysis when analyzing the role of other factors. Therefore, accurate prediction of cell cycle pseudotime and identification of cell cycle stages are important steps for characterizing the development-related biological processes. Here, we develop CCPE, a novel cell cycle pseudotime estimation method to characterize cell cycle timing and identify cell cycle phases from scRNA-seq data. CCPE uses a discriminative helix to characterize the circular process of the cell cycle and estimates each cell's pseudotime along the cell cycle. We evaluated the performance of CCPE based on a variety of simulated and real scRNA-seq datasets. Our results indicate that CCPE is an effective method for cell cycle estimation and competitive in various applications compared with other existing methods. CCPE successfully identified cell cycle marker genes and is robust to dropout events in scRNA-seq data. Accurate prediction of the cell cycle using CCPE can also effectively facilitate the removal of cell cycle effects across cell types or conditions.

The combination of sucrose dilaurate and sucrose laurate suppresses HMGB1: an enhancer of melanocyte dendricity and melanosome transfer to keratinocytes

BACKGROUND

Hyperpigmented spots are common issues in all ethnicities, involving multiple intrinsic and extrinsic factors such as UVB exposure, hormone balance, inflammatory status and ageing.

OBJECTIVES

To determine (i) melanocyte dendricity in multiple facial spot types, (ii) impact of High Mobility Group Box 1 (HMGB1), and the combination of sucrose dilaurate and sucrose laurate (SDL) on melanogenesis and melanocyte dendricity, and (iii) SDL effect on facial spots in a human use test.

METHODS

Facial spot and adjacent non-spot skin biopsies were collected from Chinese women (age 20-70). Histological assessment of melanocyte dendricity was performed for 3 spot types (solar lentigo, melasma and postinflammatory hyperpigmentation) by immunofluorescent staining for c-kit/MITF. Keratinocyte, melanocyte and melanocyte-keratinocyte co-culture models were used to assess HMGB1 release by UVB radiation, the effects of HMGB1 and SDL on melanin production, melanocyte dendricity and melanosome transfer. The effect of an SDL-containing moisturizer on appearance of facial hyperpigmented spots was assessed against a vehicle control in an 8-week human use test.

RESULTS

Melanocytes in spot areas are more dendritic than melanocytes in adjacent non-spot skin across three investigated spot types. In cell culture models, a moderate UVB-radiation exposure caused release of HMGB1 from keratinocytes. HMGB1 did not alter melanin production in melanocytes, but enhanced melanocyte dendricity and melanosome transfer. SDL reduced HMGB1 release from keratinocytes, inhibited melanin production, reversibly suppressed melanocyte dendricity and reduced melanosome transfer. In the human use test, SDL-containing moisturizer reduced appearance of spots versus vehicle.

CONCLUSION

Increased melanocyte dendricity was observed in multiple types of facial spots. Addition of HMGB1 protein increased melanocyte dendricity and melanosome transfer in cell cultures, implicating potential involvement in spot formation. SDL suppressed melanin production, melanocyte dendricity and melanosome transfer in vitro and reduced appearance of spots in the use test, suggesting SDL is an effective solution to address hyperpigmented spot concerns.

Distinguish bipolar and major depressive disorder in adolescents based on multimodal neuroimaging: Results from the Adolescent Brain Cognitive Development study®

Background

Major depressive disorder and bipolar disorder in adolescents are prevalent and are associated with cognitive impairment, executive dysfunction, and increased mortality. Early intervention in the initial stages of major depressive disorder and bipolar disorder can significantly improve personal health.

Methods

We collected 309 samples from the Adolescent Brain Cognitive Development study, including 116 adolescents with bipolar disorder, 64 adolescents with major depressive disorder, and 129 healthy adolescents, and employed a support vector machine to develop classification models for identification. We developed a multimodal model, which combined functional connectivity of resting-state functional magnetic resonance imaging and four anatomical measures of structural magnetic resonance imaging (cortical thickness, area, volume, and sulcal depth). We measured the performances of both multimodal and single modality classifiers.

Results

The multimodal classifiers showed outstanding performance compared with all five single modalities, and they are 100% for major depressive disorder versus healthy controls, 100% for bipolar disorder versus healthy control, 98.5% (95% CI: 95.4–100%) for major depressive disorder versus bipolar disorder, 100% for major depressive disorder versus depressed bipolar disorder and the leave-one-site-out analysis results are 77.4%, 63.3%, 79.4%, and 81.7%, separately.

Conclusions

The study shows that multimodal classifiers show high classification performances. Moreover, cuneus may be a potential biomarker to differentiate major depressive disorder, bipolar disorder, and healthy adolescents. Overall, this study can form multimodal diagnostic prediction workflows for clinically feasible to make more precise diagnose at the early stage and potentially reduce loss of personal pain and public society.

The Notch receptor-ligand Delta is involved in the immune response of Penaeus vannamei

In the Notch signaling pathway in vertebrates and invertebrates, the ligand Delta plays crucial roles in cell proliferation, differentiation, and immunity. Although the Notch signaling pathway has recently been implicated in the immune defense of Penaeus vannamei, the association of Delta with this immune response remains unclear. Here, we cloned and characterized the Delta homolog in P. vannamei (designated as PvDelta). PvDelta has a 2493 bp open reading frame (ORF) encoding a putative protein of 830 amino acids. Bioinformatics analysis revealed that PvDelta contains an N-terminal signal peptide, a conserved Notch ligand (MNNL) domain, a Delta/Serrate/Lag-2 segment, 9 epidermal growth factors segments, a transmembrane domain, and shares high homology with other Delta family members. Transcripts of PvDelta were detected in all shrimp tissues tested and were induced by Vibrio parahaemolyticus, white spot syndrome virus (WSSV), and lipopolysaccharide (LPS), indicating its involvement in shrimp immune response. Moreover, after PvDelta knockdown followed by LPS stimulation, the expression of Notch signaling pathway genes (i.e., PvNotch, PvCSL, and PvHey) was downregulated. Finally, shrimp depleted of PvDelta showed a lower survival rate in response to V. parahaemolyticus challenge. In sum, our data reveal that PvDelta is involved in the innate immunity of shrimp by positively modulating the Notch signaling pathway.

Review: What have we learned about the effects of heat stress on the pig industry?

Pig production faces seasonal fluctuations. The low farrowing rate of sows mated in summer, increased carcass fatness of progeny born to the sows mated in summer, and slower growth rate of finisher pigs in summer are three economically important impacts identified in the pig industry. The purpose of this review is to examine advances over the past decade in understanding the mechanisms underlying the three impacts associated with summer conditions, particularly heat stress (HS), and to provide possible amelioration strategies. For impact 1, summer mating results in low farrowing rates mainly caused by the high frequency of early pregnancy disruptions. The contributions of semen DNA damage, poor oocyte quality, local progesterone concentrations, and suboptimal embryonic oestrogen secretion are discussed, as these all may contribute to HS-mediated effects around conception. Despite this, it is still unclear what the underlying mechanisms might be and thus, there is currently a lack of commercially viable solutions. For impact 2, there have been recent advances in the understanding of gestational HS on both the sow and foetus, with gestational HS implicated in decreased foetal muscle fibre number, a greater proportion of lighter piglets, and increased carcass fatness at slaughter. So far, no effective strategies have been developed to mitigate the impacts associated with gestational HS on foetuses. For impact 3, the slowed growth rate of pigs during summer is one reason for the reduced carcass weights in summer. Studies have shown that the reduction in growth rates may be due to more than reductions in feed intake alone, and the impaired intestinal barrier function and inflammatory response may also play a role. In addition, it is consistently reported that HS attenuates fat mobilisation which can potentially exacerbate carcass fatness when carcass weight is increased. Novel feed additives have exhibited the potential to reduce the impacts of HS on intestinal barrier function in grower pigs. Collectively, based on these three impacts, the economic loss associated with HS can be estimated. A review of these impacts is warranted to better align the future research directions with the needs of the pig industry. Ultimately, a better understanding of the underlying mechanisms and continuous investments in developing commercially viable strategies to combat HS will benefit the pig industry.