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Abstract In droplet-based single-cell and single-nucleus RNA-seq assays, systematic contamination of ambient RNA molecules biases the quantification of gene expression levels. Existing methods correct the contamination for all genes globally. However, there lacks specific evaluation of correction efficacy for varying contamination levels. Here, we show that DecontX and CellBender under-correct highly contaminating genes, while SoupX and scAR over-correct lowly/non-contaminating genes. Here, we develop scCDC as the first method to detect the contamination-causing genes and only correct expression levels of these genes, some of which are cell-type markers. Compared with existing decontamination methods, scCDC excels in decontaminating highly contaminating genes while avoiding over-correction of other genes.

Traditional drug development is a long and expensive process with high rates of failure. This has prompted the pharmaceutical industry to seek more efficient drug development frameworks, driving the emergence of organ-on-a-chip (OOC) based on microfluidic technologies. Unlike traditional animal experiments, OOC systems provide a more accurate simulation of human organ microenvironments and physiological responses, therefore offering a cost-effective and efficient platform for biomedical research, particularly in the development of new medicines. Additionally, OOC systems enable quick and real-time analysis, high-throughput experimentation, and automation. These advantages have shown significant promise in enhancing the drug development process. The success of an OOC system hinges on the integration of specific designs, manufacturing techniques, and biosensors to meet the need for integrated multiparameter datasets. This review focuses on the manufacturing, design, sensing systems, and applications of OOC systems, highlighting their design and sensing capabilities, as well as the technical challenges they currently face.

Background and objective Real-world evidence on persistence of interleukin-17 inhibitors (IL-17i) as a drug class among Japanese patients with psoriasis is lacking. Hence, we aimed to describe persistence rates of IL-17is among patients with psoriasis including psoriasis vulgaris (PsO), psoriatic arthritis (PsA), and generalized pustular psoriasis (GPP) or erythrodermic psoriasis (EP) in Japan. Methods We analyzed claims data from the Medical Data Vision database. Patients ≥15 years old with a psoriasis diagnosis and an IL-17i prescription between November 2016 and August 2020 were included and followed through August 2021. Persistence rates of the IL-17i class among patients with psoriasis and its subtypes (PsO, PsA, and GPP or EP), and persistence rates of ixekizumab, secukinumab, or brodalumab among patients with PsO or PsA were analyzed using Kaplan-Meier method. Analyses were conducted in the bio-naïve and bio-experienced subgroups. Results The IL-17i class had >50% persistence rates up to 36 months among patients with psoriasis and its subtypes (PsO, PsA, and GPP or EP). 36-Month persistence rates for ixekizumab, secukinumab, and brodalumab were 46.2% to 57.7% in patients with PsO and 43.0% to 48.4% in patients with PsA. Across analyses, bio-naïve patients demonstrated similar or greater persistence rates than bio-experienced patients. Conclusion IL-17is’ persistence rates over 36 months were >50% among patients with psoriasis and its subtypes (PsO, PsA, and GPP or EP) in Japan.

OBJECTIVE: The objective is to explore the correlation between carotid artery calcification score and cerebral hyperperfusion syndrome (CHS) after carotid artery stenting (CAS) in patients with carotid artery stenosis. METHODS: Consecutive patients treated for carotid artery stenosis from October 2016 to August 2021 from two centers were studied. Carotid artery calcification score was manually segmented on multi-detector row spiral computed tomography angiography scans before CAS. The associations between carotid artery calcification score and the occurrence of CHS during the in-hospital time were assessed. RESULTS: A total of 175 patients were enrolled in the study. The mean age was 72.12 ± 7.51 years. All patients were undergone CAS treatment successfully. There were 46 cases that occurred CHS (26.29%). Univariate logistic regression analyses showed that for every 1 unit (100-score) increase in carotid artery calcification score, the risk of CHS increased by 1937% (odds ratio [OR] = 20.37, 95% confidence interval [CI]: 7.54–55.03, P < 0.01). In addition, the increasing rate was significantly different between the open-cell group (OR = 261.7, P < 0.01) and the closed-cell group (OR = 11.4, P < 0.01). The area under curve of predictiong model of carotid artery calcification score to CHS was 0.84 (95% CI, 0.75–0.93). CONCLUSION: Carotid artery calcification score was an independent risk factor for CHS in patients who underwent CAS. The application of carotid artery calcification score as risk factor in clinical screening of carotid artery stenosis patients may have beneficial effects on the management of CAS.

Hepatic, biliary and pancreatic cancers are a diverse set of malignancies with poor prognoses. It is possible that common molecular mechanisms are involved in the carcinogenesis of these cancers. Here, we identified LINC01537 and seven protein‐coding genes by integrative analysis of transcriptomes of mRNAs, microRNAs and long non‐coding RNAs from cholangiocarcinoma, hepatocellular carcinoma and pancreatic adenocarcinoma cohorts in TCGA. A predictive model constructed from seven biomarkers was established to successfully predict the survival rate of patients, which was then further verified in external cohorts. Additionally, patients with high‐risk scores in our model were prone to epithelial–mesenchymal transition. Finally, activation of the biomarker PDE2A significantly attenuated migration and epithelial–mesenchymal transition in the HepG2 liver cancer cell line.

Abstract Background Medulloblastoma is the most common malignant pediatric brain tumor and group 3 subtype medulloblastoma (G3-MB) exhibits the worst prognosis. Super enhancers (SEs) are large clusters of enhancers that play important roles in cancer through transcriptional control of cell identity genes, oncogenes and tumor-dependent genes. Dissecting SE-driven transcriptional dependencies of cancer leads to identification of novel oncogenic mechanisms, therapeutic strategies and targets. Methods Integrative SE analyses of primary tissues and patient-derived tumor cell lines of G3-MB were performed to extract the conserved SE-associated gene signatures and their oncogenic potentials were evaluated by gene expression, tumor-dependency and patient prognosis analyses. SE-associated subtype-specific upregulated tumor-dependent genes, which were revealed as members of SE-driven core transcriptional regulatory network of G3-MB, were then subjected to functional validation and mechanistic investigation. SE-associated therapeutic potential was further explored by genetic or pharmaceutical targeting of SE complex components or SE-associated subtype-specific upregulated tumor-dependent genes individually or in combination, and the underlying therapeutic mechanisms were also examined. Results The identified conserved SE-associated transcripts of G3-MB tissues and cell lines were enriched of subtype-specifically upregulated tumor-dependent genes and MB patients harboring enrichment of those transcripts exhibited worse prognosis. Fourteen such conserved SE-associated G3-MB-specific upregulated tumor-dependent genes were identified to be members of SE-driven core transcriptional regulatory network of G3-MB, including three well-recognized TFs (MYC, OTX2 and CRX) and eleven newly identified downstream effector genes (ARL4D, AUTS2, BMF, IGF2BP3, KIF21B, KLHL29, LRP8, MARS1, PSMB5, SDK2 and SSBP3). An OTX2-SE-ARL4D regulatory axis was further revealed to represent a subtype-specific tumor dependency and therapeutic target of G3-MB via contributing to maintaining cell cycle progression and inhibiting neural differentiation of tumor cells. Moreover, BET inhibition with CDK7 inhibition or proteasome inhibition, two combinatory strategies of targeting SE complex components (BRD4, CDK7) or SE-associated effector gene (PSMB5), were shown to exhibit synergistic therapeutic effects against G3-MB via stronger suppression of SE-associated transcription or higher induction of ER stress, respectively. Conclusions Our study verifies the oncogenic role and therapeutic potential of SE-driven transcriptional dependencies of G3-MB, resulting in better understanding of its tumor biology and identification of novel SE-associated therapeutic strategies and targets.

Abstract Background Alopecia affects millions of individuals globally, with hair loss becoming more common among young people. Various traditional Chinese medicines (TCM) have been used clinically for treating alopecia, however, the effective compounds and underlying mechanism are less known. We sought to investigate the effect of Alpinetin (AP), a compound extracted from Fabaceae and Zingiberaceae herbs, in hair regeneration. Methods Animal model for hair regeneration was mimicked by depilation in C57BL/6J mice. The mice were then topically treated with 3 mg/ml AP, minoxidil as positive control (PC), or solvent ethanol as vehicle control (VC) on the dorsal skin. Skin color changes which reflected the hair growth stages were monitored and pictured, along with H&E staining and hair shaft length measurement. RNA-seq analysis combined with immunofluorescence staining and qPCR analysis were used for mechanism study. Meanwhile, Gli1CreERT2; R26RtdTomato and Lgr5EGFP−CreERT2; R26RtdTomato transgenic mice were used to monitor the activation and proliferation of Gli1+ and Lgr5+ HFSCs after treatment. Furthermore, the toxicity of AP was tested in keratinocytes and fibroblasts from both human and mouse skin to assess the safety. Results When compared to minoxidil-treated and vehicle-treated control mice, topical application of AP promoted anagen initiation and delayed catagen entry, resulting in a longer anagen phase and hair shaft length. Mechanistically, RNA-seq analysis combined with immunofluorescence staining of Lef1 suggested that Lgr5+ HFSCs in lower bulge were activated by AP via Wnt signaling. Other HFSCs, including K15+, Lef1+, and Gli1+ cells, were also promoted into proliferating upon AP treatment. In addition, AP inhibited cleaved caspase 3-dependent apoptosis at the late anagen stage to postpone regression of hair follicles. More importantly, AP showed no cytotoxicity in keratinocytes and fibroblasts from both human and mouse skin. Conclusion This study clarified the effect of AP in promoting hair regeneration by activating HFSCs via Wnt signaling. Our findings may contribute to the development of a new generation of pilatory that is more efficient and less cytotoxic for treating alopecia.

Abstract Background and Aim The causal relationship between Helicobacter pylori (H. pylori) infection and gastric cancer has been established. Although the magnitude of the carcinogenic effect of H. pylori is the next concern, it has not been sufficiently evaluated in Japan. Spontaneous disappearance of H. pylori infection may have provoked underestimation of the carcinogenic effect of the infection. To reduce the influence, a comparison should be carried out between subjects with and without the infection history. Cutoff values of H. pylori antibody lower than the manufacturer's recommendation are known to be more appropriate to diagnose history of H. pylori infection. The aim was to evaluate the carcinogenic effect of H. pylori. Methods A case–control study consisting of 275 gastric cancer patients and 275 age‐ and sex‐matched controls was performed. Serum H. pylori antibody was measured using the “JHM‐Cap” kit with a domestic antigen (cut value of the manufacturer's recommendation was 2.3 EV: ELISA value). Using a conditional logistic model, the odds ratios (ORs) for five cutoff values adjusted for smoking and drinking doses were calculated. Results For cutoff values of 1.25, 1.5, 1.75, 2.0, and 2.3 EV, the ORs (95% confidence intervals) were 67.7 (9.1, 502), 37.2 (8.8, 157), 21.3 (9.0, 60.2), 25.5 (9.0, 72.7), and 25.9 (9.2, 73.2), respectively. Conclusions These results suggest that the risk ratio of gastric cancer between subjects with and without history of H. pylori infection in Japan may exceed 20.

Histone H3 lysine 4 (H3K4) methyltransferase 2D (KMT2D) plays an important role in cell development in early life. However, the function of KMT2D in adult cells such as cardiomyocytes or neurons has not been reported. In this study, cardiomyocyte-specific KMT2D knockout (KMT2D-cKO) and control (KMT2D-Ctl) mice were exposed to sham or myocardial ischemia (MI) surgery. Depletion of KMT2D aggravated the ischemic area, led to the increased mortality (26.5% in KMT2D-cKO vs 12.5% in KMT2D-Ctl) of the mice, and weakened the left ventricular systolic function. RNA-seq analysis in cardiac tissues identified genes whose expression was changed by MI and KMT2D deletion. Combined with the genome-wide association study (GWAS) analysis, cardiac disease-associated genes Rasd1, Thsd7a, Ednra, and Tns1 were identified. The expression of the Rasd1 was significantly decreased by MI or the loss of KMT2D in vivo. Meanwhile, ChIP assays demonstrated that either MI or loss of KMT2D attenuated monomethylated H3K4 (H3K4me1) enrichment on the enhancer of Rasd1. By generating a KMT2D knockout (H9C2-KO) H9C2 monoclone, we verified that the expression of Rasd1 was controlled by KMT2D, and the expression of Rasd1 was decreased by serum starvation but not low-(O2) treatment in H9C2 cells. KMT2D has a protective effect on ischemic myocardium by regulating cardiac disease-associated genes including Rasd1. KMT2D is required for the H3K4me1 deposition on the enhancer of Rasd1. Our data for the first time suggest that KMT2D-mediated Rasd1 expression may play an important protective effect on adult cells during nutritional deficiency caused by ischemic injury.

Abstract Prior studies reported the association of reproductive factors with breast cancer (BC), but the evidence is inconsistent. We conducted a pooled analysis of nine cohort studies in Japan to evaluate the impact of six reproductive factors (age at menarche/age at first birth/number of births/age at menopause/use of female hormones/breastfeeding) on BC incidence. We conducted analyses according to menopausal status at the baseline or at the diagnosis. Hazard ratio (HR) and 95% confidence interval (CI) were estimated by applying Cox proportional‐hazards model in each study. These hazard ratios were integrated using a random‐effects model. Among 187,999 women (premenopausal: 61,113, postmenopausal: 126,886), we observed 873 premenopausal and 1,456 postmenopausal cases. Among premenopausal women, use of female hormones significantly increased BC incidence (HR: 1.53 [1.04–2.25]). Although P value for trend was not significant for age at first birth and number of births (P for trend: 0.15 and 0.30, respectively), women giving first birth at ages ≥36 experienced significantly higher BC incidence than at ages 21–25 years, and women who had ≥2 births experienced significantly lower BC incidence than nulliparous women. Among postmenopausal women, more births significantly decreased BC incidence (P for trend: 0.03). Although P value for trend was not significant for age at first birth and age at menopause (P for trend: 0.30 and 0.37, respectively), women giving first birth at ages 26–35 years experienced significantly higher BC incidence than at ages 21–25 years, and women with age at menopause: ≥50 years experienced significantly higher BC incidence than age at menopause: ≤44 years. BC incidence was similar according to age at menarche or breastfeeding history among both premenopausal and postmenopausal women. In conclusion, among Japanese women, use of female hormones increased BC incidence in premenopausal women, and more births decreased BC incidence in postmenopausal women.

Previous genome-wide association studies have identified risk loci for pancreatic cancer but were centered on individuals of European ancestry. Here the authors identify GP2 gene variants associated with pancreatic cancer susceptibility in populations of East Asian ancestry.

Gene regulation: linking enhancers to specific promoters Super-enhancers are regions of DNA that highly activate the expression of specific genes. Research led by H.K.L. and L.H. at the National Institutes of Health, USA, now demonstrate that a super-enhancer is much more effective when operating in synergy with its associated promoter, another gene-controlling element. They investigated super-enhancer and promoter synergy in mouse mammary gland cells. A mammary super-enhancer achieved a 5-fold activation of a gene with a common promoter, in contrast to an 80-fold activation with its own promoter together. The findings reveal that this synergy is critical for gene regulation in the mammary gland during pregnancy and lactation. They also help resolve the general issue of whether super-enhancers act independently or, as found here, can work together with a specific promoters in cell-specific genetic programs.

Hair graying is an interesting physiological alteration associated with aging and certain diseases. The occurrence is due to depigmentation of the hair caused by depletion and dysfunction of melanocyte stem cells (MeSCs). However, what causes the depletion and dysfunction of MeSCs remains unclear. MeSCs reside in the hair follicle bulge which provides the appropriate niche for the homeostasis of various stem cells within hair follicle including MeSCs. In addition to local signaling from the cells composed of hair follicle, emerging evidences have shown that nerves, adipocytes and immune cells outside of hair follicle per se also play important roles in the regulation of MeSCs. Here, we review the recent studies on different cells in the MeSCs microenvironment beyond the hair follicle per se, discuss their function in regulating hair graying and potentially novel treatments of hair graying.

Time of eating is associated with diabetes and obesity but little is known about less healthy foods and specific time of their intake over the 24 h of the day. In this study, we aimed to identify potential relationships between foods and their eating time and to see whether these associations may vary by diabetes status. The National Diet and Nutrition Survey (NDNS) including 6,802 adults (age ≥ 19 years old) collected 749,026 food recordings by a 4-day-diary. The contingency table cross-classifying 60 food groups with 7 pre-defined eating time slots (6–9 a.m., 9 a.m.–12 p.m., 12–2 p.m., 2–5 p.m., 8–10 p.m., 10 p.m.–6 a.m.) was analyzed by Correspondence Analysis (CA). CA biplots were generated for all adults and separately by diabetes status (self-reported, pre-diabetes, undiagnosed-diabetes, and non-diabetics) to visually explore the associations between food groups and time of eating across diabetes strata. For selected food groups, odds ratios (OR, 99% CI) were derived of consuming unhealthy foods at evening/night (8 p.m.–6 a.m.) vs. earlier time in the day, by logistic regression models with generalized estimating equations. The biplots suggested positive associations between evening/night and consumption of puddings, regular soft drinks, sugar confectioneries, chocolates, beers, ice cream, biscuits, and crisps for all adults in the UK. The OR (99% CIs) of consuming these foods at evening/night were, respectively, 1.43 (1.06, 1.94), 1.72 (1.44, 2.05), 1.84 (1.31, 2.59), 3.08 (2.62, 3.62), 7.26 (5.91, 8.92), 2.45 (1.84, 3.25), 1.90 (1.68, 2.16), and 1.49 (1.22, 1.82) vs. earlier time in the day adjusted for age, sex, body mass index (BMI), and social-economic levels. Stratified biplots found that sweetened beverages, sugar-confectioneries appeared more strongly associated with evening/night among undiagnosed diabetics. Foods consumed in the evening/night time tend to be highly processed, easily accessible, and rich in added sugar or saturated fat. Individuals with undiagnosed diabetes are more likely to consume unhealthy foods at night. Further longitudinal studies are required to ascertain the causal direction of the association between late-eating and diabetes status.

In order to realize the cooperative localization of multi-unmanned platforms in the GNSS-denied environment, this paper proposes a collaborative SLAM (simultaneous localization and mapping, SLAM) framework based on image feature point matching. Without GNSS, a single unmanned platform UGV and UAV (unmanned ground vehicle, UGV; unmanned aerial vehicle, UAV) equipped with vision and IMU (inertial measurement unit, IMU) sensors can exchange information through data communication to jointly build a three-dimensional visual point map, and determine the relative position of each other through visual-based position re- identification and PnP (Perspective-n-Points, PnP) methods. When any agent can receive reliable GNSS signals, GNSS positioning information will greatly improve the positioning accuracy without changing the positioning algorithm framework. In order to achieve this function, we designed a set of two-stage position estimation algorithms. In the first stage, we used the modified ORB-SLAM3 algorithm for position estimation by fusing visual and IMU information. In the second stage, we integrated GNSS positioning and cooperative positioning information using the factor graph optimization (FGO) algorithm. Our framework consists of an UGV as the central server node and three UAVs carried by the UGV, that will collaborate on space exploration missions. Finally, we simulated the influence of different visibility and lighting conditions on the framework function on the virtual simulation experiment platform built based on ROS (robot operating system, ROS) and Unity3D. The accuracy of the cooperative localization algorithm and the single platform localization algorithm was evaluated. In the two cases of GNSS-denied and GNSS-challenged, the error of co-location reduced by 15.5% and 19.7%, respectively, compared with single-platform independent positioning.

The identification of asymptomatic, non-severe presymptomatic, and severe presymptomatic coronavirus disease 2019 (COVID-19) in patients may help optimize risk-stratified clinical management and improve prognosis. This single-center case series from Wuhan Huoshenshan Hospital, China, included 2,980 patients with COVID-19 who were hospitalized between February 4, 2020 and April 10, 2020. Patients were diagnosed as asymptomatic (n = 39), presymptomatic (n = 34), and symptomatic (n = 2,907) upon admission. This study provided an overview of asymptomatic, presymptomatic, and symptomatic COVID-19 patients, including detection, demographics, clinical characteristics, and outcomes. Upon admission, there was no significant difference in clinical symptoms and CT image between asymptomatic and presymptomatic patients for diagnosis reference. The mean area under the receiver operating characteristic curve (AUC) of the differential diagnosis model to discriminate presymptomatic patients from asymptomatic patients was 0.89 (95% CI, 0.81-0.98). Importantly, the severe and non-severe presymptomatic patients can be further stratified (AUC = 0.82). In conclusion, the two-step risk-stratification model based on 10 laboratory indicators can distinguish among asymptomatic, severe presymptomatic, and non-severe presymptomatic COVID-19 patients on admission. Moreover, single-cell data analyses revealed that the CD8+T cell exhaustion correlated to the progression of COVID-19.

Background The 25-question Geriatric Locomotive Function Scale (GLFS-25) is widely used in daily clinical practice in evaluating locomotive syndrome (LS). The questionnaire contains 25 questions aiming to describe 6 aspects, including body pain, movement-related difficulty, usual care, social activities, cognitive status, and daily activities. However, its potential underlying latent factor structure of the questionnaire has not been fully examined so far. Methods Five hundred participants who were 60 years or older and were able to walk independently with or without a cane but had complaints of musculoskeletal disorders were recruited face to face at the out-patient ward of Aichi Medical University Hospital between April 2018 and June 2019. All participants completed the GLFS-25. Confirmatory factor analysis (CFA) models (single-factor model, 6-factor model as designed by the developers of the GLFS-25) were fitted and compared using Mplus 8.3 with a maximum likelihood minimization function. Modification indices, standardized expected parameter change were used, a standard strategy for scale development was followed in the search for an alternative and simpler model that could well fit the collected data. Cronbach’s α and its 95% confidence interval (CI) were also calculated. Results Mean (standard deviation) participants age was 72.6 (7.4) years old; 63.6% of them were women. Under the current criteria, 132 (26.4%) and 262 (52.4%) of the study subjects would be classified as LS stage 1 and stage 2, respectively. Overall, the Cronbach’s α (95% CI) for GLFS-25 evaluated using these data was 0.959 (0.953, 0.964). The single- and 6-factor models were rejected due to poor fit. The alternative models with either full 25 questions or a shortened GLFS-16 were found to fit the data better. These alternative models included three latent factors (body pain, movement-related difficulty, and psycho-social complication) and allowed for cross-loading and residual correlations. Discussion The findings of the CFA models provided evidence that the factor structure of the GLFS-25 might be simpler than the 6-factor model as suggested by the designers. The complex relationships between the latent factors and the observed items may also indicate that individual sub-scale use or simply combining the raw scores for evaluation is likely to be inadequate or unsatisfactory. Thus, future revisions of the scoring algorithm or questions of the GLFS-25 may be required.

Global Navigation Satellite System (GNSS) has been the most popular tool for providing positioning, navigation, and timing (PNT) information. Some methods have been developed for enhancing the GNSS performance in signal challenging environments (urban canyon, dense foliage, signal blockage, multipath, and none-line-of-sight signals). Vector Tracking Loop (VTL) was recognized as the most promising and prospective one among these technologies, since VTL realized mutual aiding between channels. However, momentary signal blockage from part of the tracking channels affected the VTL operation and the navigation solution estimation. Moreover, insufficient available satellites employed would lead to the navigation solution errors diverging quickly over time. Short-time or temporary signal blockage was common in urban areas. Aiming to improve the VTL performance during the signal outage, in this paper, the deep learning method was employed for assisting the VTL navigation solution estimation; more specifically, a Long Short-Term Memory-Recurrent Neural Network (LSTM-RNN) was employed to aid the VTL navigation filter (navigation filter was usually a Kalman filter). LSTM-RNN obtained excellent performance in time-series data processing; therefore, in this paper, the LSTM-RNN was employed to predict the navigation filter innovative sequence values during the signal outage, and then, the predicted innovative values were employed to aid the navigation filter for navigation solution estimation. The LSTM-RNN was well trained while the signal was normal, and the past innovative sequence was employed as the input of the LSTM-RNN. A simulation was designed and conducted based on an open-source Matlab GNSS software receiver; a dynamic trajectory with several temporary signal outages was designed for testing the proposed method. Compared with the conventional VTL, the LSTM-RNN-assisted VTL could keep the horizontal positioning errors within 50 meters during a signal outage. Also, conventional Support Vector Machine (SVM) and radial basis function neural network (RBF-NN) were compared with the LSTM-RNN method; LSTM-RNN-assisted VTL could maintain the positioning errors less than 20 meters during the outages, which demonstrated LSTM-RNN was superior to the SVM and RBF-NN in these applications.

Objective: The Schedule for Affective Disorders and Schizophrenia for School-Age Children-Present and Lifetime version (K-SADS-PL) is a widely used semi-structured diagnostic interview in child and adolescent psychiatry. However, given the extensive use of the K-SADS-PL in clinical practice and research and its adaptation for use in many languages and cultures, validation studies of the instrument are scarce. This study was designed to examine the inter-rater reliability, criterion validity and construct validity of the updated instrument, the K-SADS-PL for DSM-5, in Japanese outpatients totaling 95 children and adolescents. Method: We translated and adapted the updated instrument into Japanese using a standard forward-backward translation procedure. Two of nine experienced clinicians independently made diagnoses using the interview for each patient in a conjoint session. Discrepancies in diagnosis between two clinicians were resolved by consensus, and the consensus diagnosis was compared with a “best-estimate” diagnosis made by five experienced clinicians using all available data sources for patients who were blinded to the diagnosis using the K-SADS-PL for DSM-5. The “best-estimate” diagnosis of ASD was also based on the Diagnostic Interview for Social and Communication Disorders. Results: The inter-rater reliability was very good, as shown by κ ≥ 0.8 for all disorders examined: autism spectrum disorder (ASD), attention-deficit hyperactivity disorder, tic disorders, selective mutism, enuresis and encopresis. The criterion validity was good, as shown by κ ≥ 0.6 for all disorders examined, except for ASD (κ = 0.59). This study also revealed good construct validity of the instrument by confirming the expected associations with each scale from the Social Responsiveness Scale-2nd edition and the Strengths and Difficulties Questionnaire. Conclusion: These results suggest that the K-SADS-PL for DSM-5 generates valid diagnoses in child and adolescent psychiatry. Keywords: Child and adolescent psychiatry, Semi-structured interview, Reliability, Validity

CRISPR/Cas9 gene editing has been used to generate mutations in several mouse genes. Here, the authors show that targeting events using single guide RNAs cause large deletions at 17 sites in the mouse genome, suggesting that careful genotyping is needed and sequential targeting may avoid such deletions.

Abstract Background Natural killer (NK)T cells and conventional T cells share phenotypic characteristic however they differ in transcription factor requirements and functional properties. The role of histone modifying enzymes in conventional T cell development has been extensively studied, little is known about the function of enzymes regulating histone methylation in NKT cells. Results We show that conditional deletion of histone demethylases UTX and JMJD3 by CD4-Cre leads to near complete loss of liver NKT cells, while conventional T cells are less affected. Loss of NKT cells is cell intrinsic and not due to an insufficient selection environment. The absence of NKT cells in UTX/JMJD3-deficient mice protects mice from concanavalin A‐induced liver injury, a model of NKT‐mediated hepatitis. GO‐analysis of RNA-seq data indicates that cell cycle genes are downregulated in UTX/JMJD3-deleted NKT progenitors, and suggest that failed expansion may account for some of the cellular deficiency. The phenotype appears to be demethylase‐dependent, because UTY, a homolog of UTX that lacks catalytic function, is not sufficient to restore their development and removal of H3K27me3 by deletion of EZH2 partially rescues the defect. Conclusions NKT cell development and gene expression is sensitive to proper regulation of H3K27 methylation. The H3K27me3 demethylase enzymes, in particular UTX, promote NKT cell development, and are required for effective NKT function.

STAT5, a member of the family of signal transducers and activators of transcription, senses cytokines and controls the biology of cell lineages, including mammary, liver, and T cells. Here, we show that STAT5 activates lineage-specific and widely expressed genes through different mechanisms. STAT5 preferentially binds to promoter sequences of cytokine-responsive genes expressed across cell types and to putative enhancers of lineage-specific genes. While chromatin accessibility of STAT5-based enhancers was dependent on cytokine exposure, STAT5-responsive promoters of widely expressed target genes were generally constitutively accessible. While the contribution of STAT5 to enhancers is well established, its role on promoters is poorly understood. To address this, we focused on Socs2, a widely expressed cytokine-sensing gene. Upon deletion of the STAT5 response elements from the Socs2 promoter in mice, cytokine induction was abrogated, while basal activity remained intact. Our data suggest that promoter-bound STAT5 modulates cytokine responses and enhancer-bound STAT5 is mandatory for gene activation.

Genome-wide association studies (GWASs) have identified many single nucleotide polymorphisms (SNPs) that are significantly associated with pancreatic cancer susceptibility. We sought to replicate the associations of 61 GWAS-identified SNPs at 42 loci with pancreatic cancer in Japanese and to develop a risk model for the identification of individuals at high risk for pancreatic cancer development in the general Japanese population. The model was based on data including directly determined or imputed SNP genotypes for 664 pancreatic cancer case and 664 age- and sex-matched control subjects. Stepwise logistic regression uncovered five GWAS-identified SNPs at five loci that also showed significant associations in our case-control cohort. These five SNPs were included in the risk model and also applied to calculation of the polygenic risk score (PRS). The area under the curve determined with the leave-one-out cross-validation method was 0.63 (95% confidence interval, 0.60-0.66) or 0.61 (0.58-0.64) for versions of the model that did or did not include cigarette smoking and family history of pancreatic cancer in addition to the five SNPs, respectively. Individuals in the lowest and highest quintiles for the PRS had odds ratios of 0.62 (0.42-0.91) and 1.98 (1.42-2.76), respectively, for pancreatic cancer development compared with those in the middle quintile. We have thus developed a risk model for pancreatic cancer that showed moderately good discriminatory ability with regard to differentiation of pancreatic cancer patients from control individuals. Our findings suggest the potential utility of a risk model that incorporates replicated GWAS-identified SNPs and established demographic or environmental factors for the identification of individuals at increased risk for pancreatic cancer development.

The Sonic hedgehog (Shh) signaling pathway regulates developmental, homeostatic, and repair processes throughout the body. In the skin, touch domes develop in tandem with primary hair follicles and contain sensory Merkel cells. The developmental signaling requirements for touch dome specification are largely unknown. We found dermal Wnt signaling and subsequent epidermal Eda/Edar signaling promoted Merkel cell morphogenesis by inducing Shh expression in early follicles. Lineage-specific gene deletions revealed intraepithelial Shh signaling was necessary for Merkel cell specification. Additionally, a Shh signaling agonist was sufficient to rescue Merkel cell differentiation in Edar-deficient skin. Moreover, Merkel cells formed in Fgf20 mutant skin where primary hair formation was defective but Shh production was preserved. Although developmentally associated with hair follicles, fate mapping demonstrated Merkel cells primarily originated outside the hair follicle lineage. These findings suggest that touch dome development requires Wnt-dependent mesenchymal signals to establish reciprocal signaling within the developing ectoderm, including Eda signaling to primary hair placodes and ultimately Shh signaling from primary follicles to extrafollicular Merkel cell progenitors. Shh signaling often demonstrates pleiotropic effects within a structure over time. In postnatal skin, Shh is known to regulate the self-renewal, but not the differentiation, of touch dome stem cells. Our findings relate the varied effects of Shh in the touch dome to the ligand source, with locally produced Shh acting as a morphogen essential for lineage specification during development and neural Shh regulating postnatal touch dome stem cell maintenance.

Enhancers play a central role in cell-type-specific gene expression and are marked by H3K4me1/2. Active enhancers are further marked by H3K27ac. However, the methyltransferases responsible for H3K4me1/2 on enhancers remain elusive. Furthermore, how these enzymes function on enhancers to regulate cell-type-specific gene expression is unclear. In this study, we identify MLL4 (KMT2D) as a major mammalian H3K4 mono- and di-methyltransferase with partial functional redundancy with MLL3 (KMT2C). Using adipogenesis and myogenesis as model systems, we show that MLL4 exhibits cell-type- and differentiation-stage-specific genomic binding and is predominantly localized on enhancers. MLL4 co-localizes with lineage-determining transcription factors (TFs) on active enhancers during differentiation. Deletion of Mll4 markedly decreases H3K4me1/2, H3K27ac, Mediator and Polymerase II levels on enhancers and leads to severe defects in cell-type-specific gene expression and cell differentiation. Together, these findings identify MLL4 as a major mammalian H3K4 mono- and di-methyltransferase essential for enhancer activation during cell differentiation.

In order to select a better design trajectory, it needs to spend a lot of energy on parameter adjustment and calculation. Therefore, this paper establishes the intelligent optimization design model of horizontal well trajectory in with the target length and drilling string drag under rotary drilling conditions as the targets, and takes the target entry accuracy as the complex constraints. Meanwhile, multi-objective optimization algorithm and distributed calculation are used to realize the automatic optimization of the well trajectory. Under the given arithmetic conditions, compared with the original design trajectory, a horizontal well was designed with this method, the trajectory length is shortened by 92.1 m, and the maximum build-up rate is changed from 5.50° per 30 m to 4.97° per 30 m, reducing by 9.6%. Under the same BHA and boundary conditions, the drag becomes 232.42 kN, which is 6.8% lower than that before optimization. [ABSTRACT FROM AUTHOR]