[Organ preservation and watch-and-wait strategy in esophageal cancer: a promising future]

The traditional treatment modalities for esophageal cancer include surgery, chemotherapy, and radiotherapy, each presenting its own limitations. With advancements in endoscopic techniques and the integration of immunotherapy, the feasibility and safety of organ preservation have significantly improved, offering patients improved survival and quality of life. The selection of patients suitable for organ preservation treatment demands ongoing exploration. Those selected for this approach require rigorous monitoring, with surgical intervention as a salvation for tumor progression or metastasis, though the timing of surgery remains a topic of debate. Organ preservation and watch-and-wait strategy may provide a more conservative treatment option, aiming to maximize quality of life.

Association of LOX gene G473A polymorphism with the occurrence of allergic rhinitis and efficacy of montelukast sodium in children

Allergic rhinitis (AR) is very common in adolescents, and current treatment options are complex and unsatisfactory. The objective of this study was to analyze the association of lysyl oxidase (LOX) gene G473A polymorphism with susceptibility to AR in children. In addition, we analyzed the therapeutic effect of montelukast sodium on AR. Forty-five children with AR (research group, 8.16±2.88 years old) and 51 healthy children (control group, 8.22±3.87 years old) during the same period were selected. The LOX gene G473A polymorphism was detected with polymerase chain reaction (PCR)-restriction fragment length polymorphism method. The effect of G473A polymorphism in the occurrence of AR was assessed by logistic regression analysis. In addition, the levels of C-reactive protein (CRP), Interleukin (IL-6), and IL-8 were measured to observe the relationship between G473A polymorphism and inflammatory factors. Finally, montelukast sodium was given to children with AR to investigate the effect of G473A polymorphism on clinical outcomes. The number of G473A polymorphisms in the research group was not significantly different from the control group for GA-type (P = 0.521). However, the number of GG-type polymorphisms was less while the number of type AA was more than the control group (P = 0.044 and 0.046). Children carrying the AA gene had an approximately 4-fold increased risk of AR, while those carrying the GG gene had a decreased risk (P < 0.001). Moreover, children carrying the GG gene had lower levels of CRP, IL-6, and IL-8 and better clinical outcomes, while those carrying the AA gene had higher levels of inflammatory factors and worse outcomes (P<0.05). LOX gene G473A polymorphism is closely associated with AR pathogenesis and may have an important research value in antagonizing the therapeutic effect of montelukast sodium.

Exploration of the Stacking Ensemble Machine Learning Algorithm for Cheating Detection in Large-Scale Assessment

Cheating detection in large-scale assessment received considerable attention in the extant literature. However, none of the previous studies in this line of research investigated the stacking ensemble machine learning algorithm for cheating detection. Furthermore, no study addressed the issue of class imbalance using resampling. This study explored the application of the stacking ensemble machine learning algorithm to analyze the item response, response time, and augmented data of test-takers to detect cheating behaviors. The performance of the stacking method was compared with that of two other ensemble methods (bagging and boosting) as well as six base non-ensemble machine learning algorithms. Issues related to class imbalance and input features were addressed. The study results indicated that stacking, resampling, and feature sets including augmented summary data generally performed better than its counterparts in cheating detection. Compared with other competing machine learning algorithms investigated in this study, the meta-model from stacking using discriminant analysis based on the top two base models-Gradient Boosting and Random Forest-generally performed the best when item responses and the augmented summary statistics were used as the input features with an under-sampling ratio of 10:1 among all the study conditions.

Joint modeling of action sequences and action time in computer-based interactive tasks

Process data refers to data recorded in computer-based assessments that reflect the problem-solving processes of participants and provide greater insight into how they solve problems. Action time, namely the amount of time required to complete a state transition, is also included in such data along with actions. In this study, an action-level joint model of action sequences and action time is proposed, in which the sequential response model (SRM) is used as the measurement model for action sequences, and a new log-normal action time model is proposed as the measurement model for action time. The proposed model can be regarded as an extension of the SRM by incorporating action time within the joint-hierarchical modeling framework and as an extension of the conventional item-level joint models in process data analysis. Results of the empirical and simulation studies demonstrated that the model setup was justified, model parameters could be interpreted, parameter estimates were accurate, and taking into account participants' action time further was beneficial for obtaining a deep understanding of participants' behavioral patterns. Overall, the proposed action-level joint model provides an innovative modeling framework for analyzing process data in computer-based assessments from the latent variable modeling perspective.

Modelling multiple problem-solving strategies and strategy shift in cognitive diagnosis for growth

Problem-solving strategies, defined as actions people select intentionally to achieve desired objectives, are distinguished from skills that are implemented unintentionally. In education, strategy-oriented instructions that guide students to form problem-solving strategies are found to be more effective for low-achieving students than the skill-oriented instructions designed for enhancing their skill implementation ability. Although the existing longitudinal cognitive diagnosis models (CDMs) can model the change in students' dynamic skill mastery status over time, they are not designed to model the shift in students' problem-solving strategies. This study proposes a longitudinal CDM that considers both between-person multiple strategies and within-person strategy shift. The model, separating the strategy choice process from the skill implementation process, is intended to provide diagnostic information on strategy choice as well as skill mastery status. A simulation study is conducted to evaluate the parameter recovery of the proposed model and investigate the consequences of ignoring the presence of multiple strategies or strategy shift. Further, an empirical data analysis is conducted to illustrate the use of the proposed model to measure strategy shift, growth in skill implementation ability and skill mastery status.

4,8-dicarboxyl-8,9-iridoid-1-glycoside Promotes Neural Stem Cell Differentiation Through MeCP2

Background

Borojó (Borojoa patinoi Cuatrec) fruit has recently been shown to have a variety of health benefit, but the mechanisms have been little studied. The aim of this study was to investigate the effect of 4,8-dicarboxyl-8,9-iridoid-1-glycoside (388) on proliferation and differentiation of embryonic neural stem cells (NSCs).

Methods

NSCs were treated with 388 and stem cell differentiation was determined by western blotting and immunofluorescence staining. The role of MeCP2 in 388-mediated embryonic NSCs differentiation was examined.

Results

The results showed that in the presence of mitogen when NSCs proliferated and maintained their multipotency, treatment with 388 did not affect the viability of NSCs. Following mitogen withdrawal to initiate NSC differentiation, treatment with 388 at the doses of 10 and 50 μg/mL significantly increased neural differentiation in both cortex and spinal cord-derived culture. 388 also significantly up-regulated MeCP2 expression. The expression of the neuronal and oligodendrocytic markers was enhanced after addition of 388 in the differentiation culture. However, knockdown of MeCP2 results in inhibition of NSC differentiation, and the pro-differentiation effect of 388 was mostly abolished.

Conclusions

This study confirmed that 388 stimulates differentiation of NSCs and identifies its mechanism of action by upregulating MeCP2.

Rare variants in the outcome of social skills group training for autism

Exome sequencing has been proposed as the first-tier genetic testing in autism spectrum disorder (ASD). Here, we performed exome sequencing in autistic individuals with average to high intellectual abilities (N = 207) to identify molecular diagnoses and genetic modifiers of intervention outcomes of social skills group training (SSGT) or standard care. We prioritized variants of clinical significance (VCS), variants of uncertain significance (VUS) and generated a pilot scheme to calculate genetic scores of rare and common variants in ASD-related gene pathways. Mixed linear models were used to test the association between the carrier status of VCS/VUS or the genetic scores with intervention outcomes measured by the social responsiveness scale. Additionally, we combined behavioral and genetic features using a machine learning (ML) model to predict the individual response. We showed a rate of 4.4% and 11.3% of VCS and VUS in the cohort, respectively. Individuals with VCS or VUS had improved significantly less after standard care than non-carriers at post-intervention (β = 9.35; p = 0.036), while no such association was observed for SSGT (β = -2.50; p = 0.65). Higher rare variant genetic scores for synaptic transmission and regulation of transcription from RNA polymerase II were separately associated with less beneficial (β = 8.30, p = 0.0044) or more beneficial (β = -6.79, p = 0.014) effects after SSGT compared with standard care at follow-up, respectively. Our ML model showed the importance of rare variants for outcome prediction. Further studies are needed to understand genetic predisposition to intervention outcomes in ASD.

EV PD-L1 Contributes to Immunosuppressive CD8+ T Cells in Peripheral Blood of Pediatric Wilms Tumor

Wilms tumor (WT) is the most common renal cancer and the most prevalent abdominal cancer in children. Children with recurrent or progressive forms of WT could benefit from novel immune-targeted approaches. While the immune status of these patients, especially the immunosuppression of peripheral T cells, was rarely reported. The present study enrolled a consecutive series of 14 Chinese WT children and 14 age- and gender-matched healthy controls. We demonstrated that plasma extracellular vesicular (EV) PD-L1 levels significantly increased in WT patients than in healthy controls. EV PD-L1 significantly inhibited the activation of human CD8⁺ T cells by down-regulating the cell surface CD69 expression and the intracellular IFNγ and TNFα production in vitro. In peripheral CD8⁺ T cells of WT patients, the intracellular IFNγ and TNFα production significantly decreased than healthy controls. The level of plasma EV PD-L1 significantly correlated with the intracellular TNFα production in peripheral CD8⁺ T cells of WT patients. In conclusion, the significantly increased plasma EV PD-L1 in WT patients contributed to the immunosuppression of peripheral CD8⁺ T cells. Monitoring the level of plasma EV PD-L1 will be helpful for the selection of immune-targeted therapies for WT patients.

c-myc protects mice from ischemia stroke through elevating microRNA-200b-5p-regulated SIRT1 expression

OBJECTIVE

c-myc has been reported to attenuate ischemia stroke (IS). We initiated the research to uncover the molecular mechanism of c-myc with regard to microRNA (miR)-200b-5p/Sirtuin1 (SIRT1) axis.

METHODS

An IS mouse model was prepared by middle cerebral artery occlusion (MCAO). Measurements of c-myc, miR-200b-5p and SIRT1 levels in MCAO mice were conducted. c-myc, miR-200b-5p and SIRT1 expression levels in MCAO mice were detected. The neurological function, production of inflammatory cytokines, neuronal apoptosis, brain tissue pathology and neuronal survival of MCAO mice were observed.

RESULTS

c-myc and SIRT1 levels went downward while miR-200b-5p expression went upward in MCAO mice. Elevation of c-myc or suppression of miR-200b-5p improved neurological function, reduced inflammation and neuronal apoptosis, and attenuated brain tissue pathology and neuronal survival of MCAO mice. Enhancement of miR-200b-5p or knockdown of SIRT1 weakened c-myc-induced protection against MCAO-induced brain injury in mice.

CONCLUSION

Overall, c-myc protects mice from IS through elevating miR-200b-5p-targeted SIRT1 expression.

Founder effects facilitate the use of a genotyping-based approach to molecular diagnosis in Swedish patients with familial hypercholesterolaemia

AIM

To investigate whether genotyping could be used as a cost-effective screening step, preceding next-generation sequencing (NGS), in molecular diagnosis of familial hypercholesterolaemia (FH) in Swedish patients.

METHODS AND RESULTS

Three hundred patients of Swedish origin with clinical suspicion of heterozygous FH were analysed using a specific array genotyping panel embedding 112 FH-causing mutations in the LDLR, APOB and PCSK9 genes. The mutations had been selected from previous reports on FH patients in Scandinavia and Finland. Mutation-negative cases were further analysed by NGS. In 181 patients with probable or definite FH using the Dutch lipid clinics network (DLCN) criteria (score ≥ 6), a causative mutation was identified in 116 (64%). Of these, 94 (81%) were detected by genotyping. Ten mutations accounted for more than 50% of the positive cases, with APOB c.10580G>A being the most common. Mutations in LDLR predominated, with (c.2311+1_2312-1)(2514)del (FH Helsinki) and c.259T>G having the highest frequency. Two novel LDLR mutations were identified. In patients with DLCN score < 6, mutation detection rate was significantly higher at younger age.

CONCLUSION

A limited number of mutations explain a major fraction of FH cases in Sweden. Combination of selective genotyping and NGS facilitates the clinical challenge of cost-effective genetic screening in suspected FH. The frequency of APOB c.10580G>A was higher than previously reported in Sweden. The lack of demonstrable mutations in the LDLR, APOB and PCSK9 genes in ~1/3 of patients with probable FH strongly suggests that additional genetic mechanisms are to be found in phenotypic FH.

Variable Speed Across Dimensions of Ability in the Joint Model for Responses and Response Times

Working speed as a latent variable reflects a respondent’s efficiency to apply a specific skill, or a piece of knowledge to solve a problem. In this study, the common assumption of many response time models is relaxed in which respondents work with a constant speed across all test items. It is more likely that respondents work with different speed levels across items, in specific when these items measure different dimensions of ability in a multidimensional test. Multiple speed factors are used to model the speed process by allowing speed to vary across different domains of ability. A joint model for multidimensional abilities and multifactor speed is proposed. Real response time data are analyzed with an exploratory factor analysis as an example to uncover the complex structure of working speed. The feasibility of the proposed model is examined using simulation data. An empirical example with responses and response times is presented to illustrate the proposed model’s applicability and rationality.

High expression of LINC0163 promotes progression of papillary thyroid cancer by regulating epithelial-mesenchymal transition MITF

OBJECTIVE

The purpose of this study was to detect the expression of long non-coding ribonucleic acid 00163 (LINC00163) in human papillary thyroid cancer (PTC), and to observe the influence of downregulated LINC00163 on the proliferative and metastatic capacities of human PTC cells.

PATIENTS AND METHODS

Quantitative Reverse Transcription-Polymerase Chain Reaction (qRT-PCR) assay was applied to measure the expression level of LINC00163 in PTC tissues and para-carcinoma tissues, as well as that in normal human thyroid cells (Nthy-ori3-1) and PTC cells. After the expression of LINC00163 in PTC cells was interfered, qRT-PCR assay was performed to determine the interference efficiency, and colony formation and Cell Counting Kit-8 (CCK-8) assays were conducted to study the impacts of small interfering (si)-LINC00163 on the proliferative capacity of PTC cells. Moreover, wound healing and transwell assays were adopted to investigate the changes in the migratory and invasive abilities of PTC cells after the interference in the expression of LINC00163 in PTC cells. Finally, the changes in expressions of molecular markers in downstream signaling pathways after interference in LINC00163 expression were examined via Western blotting assay.

RESULTS

In 51 cases of PTC tissues and corresponding para-carcinoma tissues, 41 cases exhibited an up-regulated expression of LINC00163, and qRT-PCR results indicated that PTC cells also had an up-regulated expression of LINC00163 compared with normal human thyroid cells. After the expression of LINC00163 in PTC cells was interfered, the results of colony formation and CCK-8 assays manifested that the proliferative capacity of the cells declined. It was also shown in wound-healing and transwell assay results that the migratory and invasive abilities of the cells were weakened. In addition, the results of Western blotting assay revealed expression changes in the molecular markers of epithelial-mesenchymal transition (EMT).

CONCLUSIONS

The expression of LINC00163 in NSCLC tissues and cells is upregulated, and highly expressed LINC00163 can promote PTC cell proliferation and metastasis by regulating the EMT.

Enhancement of immune responses by co-administration of bacterial ghosts-mediated Neisseria gonorrhoeae DNA vaccines

AIM

Gonorrhoea remains a leading public health burden and the development of vaccine against gonorrhoea becomes more urgent. Here, a novel Neisseria gonorrhoeae DNA vaccine delivered by Salmonella enteritidis ghosts was developed and the immune responses of the vaccine candidate were evaluated.

METHODS AND RESULTS

Neisseria gonorrhoeae nspA gene was cloned into the pVAX1 vector. The constructed recombinant plasmid pVAX1-nspA was loaded into the lyophilized SE ghosts to produce SE ghosts (pVAX1-nspA). Then, the immune responses induced by SE ghosts (pVAX1-nspA) alone and co-administrated with SE ghosts (pVAX1-porB) were evaluated in mouse model. Co-administered SE ghosts (pVAX1-nspA) and SE ghosts (pVAX1-porB) could elicited significantly higher levels of specific IgG antibody responses and lymphocyte proliferative responses than the control groups. Furthermore, the group co-administered SE ghosts (pVAX1-nspA) and SE ghosts (pVAX1-porB) had the highest bactericidal antibody titres.

CONCLUSIONS

Co-administration of SE ghosts (pVAX1-nspA) and SE ghosts (pVAX1-porB) elicited significant specific humoral and cellular immune responses.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study demonstrates the potential of co-administration of SE ghosts (pVAX1-nspA) and SE ghosts (pVAX1-porB) as an attractive vaccination regimen for gonorrhoea.

The influence of common polygenic risk and gene sets on social skills group training response in autism spectrum disorder

Social skills group training (SSGT) is a frequently used behavioral intervention in autism spectrum disorder (ASD), but the effects are moderate and heterogeneous. Here, we analyzed the effect of polygenic risk score (PRS) and common variants in gene sets on the intervention outcome. Participants from the largest randomized clinical trial of SSGT in ASD to date were selected (N = 188, 99 from SSGT, 89 from standard care) to calculate association between the outcomes in the SSGT trial and PRSs for ASD, attention-deficit hyperactivity disorder (ADHD), and educational attainment. In addition, specific gene sets were selected to evaluate their role on intervention outcomes. Among all participants in the trial, higher PRS for ADHD was associated with significant improvement in the outcome measure, the parental-rated Social Responsiveness Scale. The significant association was due to better outcomes in the standard care group for individuals with higher PRS for ADHD (post-intervention: β = −4.747, P = 0.0129; follow-up: β = −5.309, P = 0.0083). However, when contrasting the SSGT and standard care group, an inferior outcome in the SSGT group was associated with higher ADHD PRS at follow-up (β = 6.67, P = 0.016). Five gene sets within the synaptic category showed a nominal association with reduced response to interventions. We provide preliminary evidence that genetic liability calculated from common variants could influence the intervention outcomes. In the future, larger cohorts should be used to investigate how genetic contribution affects individual response to ASD interventions.

Computational systematic selectivity of the Fasalog inhibitors between ROCK-I and ROCK-II kinase isoforms in Alzheimer's disease

Human Rho-associated coiled-coil forming kinase (ROCK) is a class of essential neurokinases that consists of two structurally conserved isoforms ROCK-I and ROCK-II; they have been revealed to play distinct roles in the pathogenesis of Alzheimer's disease (AD) and other neurological disorders. Selective targeting of the two kinase isoforms with small-molecule inhibitors is a great challenge due to the surprisingly high homology in kinase domain (92 %) and the full identity in kinase active site (100 %). Here, we describe a computational protocol to systematically profile the selectivity of Fasudil and its 25 analogs (termed as Fasalogs) between the two kinase isoforms. It is suggested that the substitution of Fasudil's 1,4-diazepane moiety with rigid ring such as Ripasudil and Dimehtylfasudil would render the resulting inhibitors of ROCK-II over ROCK-I (II-o-I) selectivity, while the substitution with long, flexible group such as H-89 and BDBM92607 tends to have I-o-II selectivity. Structural analysis reveals that the inhibitor affinity is not only determined by the identical active site, but also contributed from the non-identical first and second shells of the site as well as other non-conserved kinase regions, which can indirectly influence the active site and inhibitor binding through allosteric effect. A further kinase assay basically confirms the computational findings, which also exhibits a good consistence with theoretical selectivity over 10 tested samples (Rp = 0.89). In particular, the Fasalog compounds Dimehtylfasudil and H-89 are identified as II-o-I and I-o-II selective inhibitors. They can be considered as promising lead molecular entities to develop new specific ROCK isoform-selective Fasalog inhibitors.

A Sequential Higher Order Latent Structural Model for Hierarchical Attributes in Cognitive Diagnostic Assessments

The higher-order structure and attribute hierarchical structure are two popular approaches to defining the latent attribute space in cognitive diagnosis models. However, to our knowledge, it is still impossible to integrate them to accommodate the higher-order latent trait and hierarchical attributes simultaneously. To address this issue, this article proposed a sequential higher-order latent structural model (LSM) by incorporating various hierarchical structures into a higher-order latent structure. The feasibility of the proposed higher-order LSM was examined using simulated data. Results indicated that, in conjunction with the deterministic-inputs, noisy "and" gate model, the sequential higher-order LSM produced considerable improvement in person classification accuracy compared with the conventional higher-order LSM, when a certain attribute hierarchy existed. An empirical example was presented as well to illustrate the application of the proposed LSM.

Evaluation of the Genetic Association Between Adult Obesity and Neuropsychiatric Disease

Extreme obesity (EO) (BMI >50 kg/m²) is frequently associated with neuropsychiatric disease (NPD). As both EO and NPD are heritable central nervous system disorders, we assessed the prevalence of protein-truncating variants (PTVs) and copy number variants (CNVs) in genes/regions previously implicated in NPD in adults with EO (n = 149) referred for weight loss/bariatric surgery. We also assessed the prevalence of CNVs in patients referred to University College London Hospital (UCLH) with EO (n = 218) and obesity (O) (BMI 35-50 kg/m²; n = 374) and a Swedish cohort of participants from the community with predominantly O (n = 161). The prevalence of variants was compared with control subjects in the Exome Aggregation Consortium/Genome Aggregation Database. In the discovery cohort (high NPD prevalence: 77%), the cumulative PTV/CNV allele frequency (AF) was 7.7% vs. 2.6% in control subjects (odds ratio [OR] 3.1 [95% CI 2-4.1]; P < 0.0001). In the UCLH EO cohort (intermediate NPD prevalence: 47%), CNV AF (1.8% vs. 0.9% in control subjects; OR 1.95 [95% CI 0.96-3.93]; P = 0.06) was lower than the discovery cohort. CNV AF was not increased in the UCLH O cohort (0.8%). No CNVs were identified in the Swedish cohort with no NPD. These findings suggest that PTV/CNVs, in genes/regions previously associated with NPD, may contribute to NPD in patients with EO.

Joint Modeling of Compensatory Multidimensional Item Responses and Response Times

Computer-based testing (CBT) is becoming increasingly popular in assessing test-takers' latent abilities and making inferences regarding their cognitive processes. In addition to collecting item responses, an important benefit of using CBT is that response times (RTs) can also be recorded and used in subsequent analyses. To better understand the structural relations between multidimensional cognitive attributes and the working speed of test-takers, this research proposes a joint-modeling approach that integrates compensatory multidimensional latent traits and response speediness using item responses and RTs. The joint model is cast as a multilevel model in which the structural relation between working speed and accuracy are connected through their variance-covariance structures. The feasibility of this modeling approach is investigated via a Monte Carlo simulation study using a Bayesian estimation scheme. The results indicate that integrating RTs increased model parameter recovery and precision. In addition, Program of International Student Assessment (PISA) 2015 mathematics standard unit items are analyzed to further evaluate the feasibility of the approach to recover model parameters.

Mapping Background Variables With Sequential Patterns in Problem-Solving Environments: An Investigation of United States Adults' Employment Status in PIAAC

Adult assessments have evolved to keep pace with the changing nature of adult literacy and learning demands. As the importance of information and communication technologies (ICT) continues to grow, measures of ICT literacy skills, digital reading, and problem-solving in technology-rich environments (PSTRE) are increasingly important topics for exploration through computer-based assessment (CBA). This study used process data collected in log files and survey data from the Programme for the International Assessment of Adult Competencies (PIAAC), with a focus on the United States sample, to (a) identify employment-related background variables that significantly related to PSTRE skills and problem-solving behaviors, and (b) extract robust sequences of actions by subgroups categorized by significant variables. We conducted this study in two phases. First, we used regression analyses to select background variables that significantly predict the general PSTRE, literacy, and numeracy skills, as well as the response time and correctness in the example item. Second, we identified typical action sequences by different subgroups using the chi-square feature selection model to explore these sequences and differentiate the subgroups. Based on the malleable factors associated with problem-solving skills, the goal of this study is to provide information for improving competences in adult education for targeted groups.

Bayesian DINA Modeling Incorporating Within-Item Characteristic Dependency

The within-item characteristic dependency (WICD) means that dependencies exist among different types of item characteristics/parameters within an item. The potential WICD has been ignored by current modeling approaches and estimation algorithms for the deterministic inputs noisy "and" gate (DINA) model. To explicitly model WICD, this study proposed a modified Bayesian DINA modeling approach where a bivariate normal distribution was employed as a joint prior distribution for correlated item parameters. Simulation results indicated that the model parameters were well recovered and that explicitly modeling WICD improved model parameter estimation accuracy, precision, and efficiency. In addition, when potential item blocks existed, the proposed modeling approach still demonstrated good performance and high robustness. Furthermore, the fraction subtraction data were analyzed to illustrate the application and advantage of the proposed modeling approach.

[Clinical manifestations and genetics analysis of collagen type Ⅵ-related myopathy caused by variants in COL6A3 gene]

Objective: To summarize the clinical manifestations and determine the molecular etiology for two collagen type Ⅵ-related myopathy pedigrees. Methods: Two spontaneous collagen type Ⅵ-related myopathy patients were admitted to Department of Neurology, Children's Hospital, Capital Institute of Pediatrics in October 2017. Clinical data of probands and their family members were collected and their genomic DNA was obtained for genetic testing. Next generation sequencing was performed and the variants were verified by the Sanger sequencing in the family members. Results: Target region sequencing indicated that the proband of family 1 has carried a heterozygous variant of COL6A3 gene, c.6229G>C(p.Gly2077Arg), and it was de novo variant confirmed by Sanger-sequencing in the family.The patient 1, a 2-year-three-month old boy, was admitted due to motor retardation at birth. He was defined as early severe Ullrich congenital muscular dystrophy. He never achieved independent ambulation, he had onset of symptoms was found at birth, including diffuse muscle weakness, striking distal joint hyperlaxity, proximal contractures, calcaneal protrusion, kyphosis, and hip dislocation. Serum CK level was elevated slightly and EMG showed neurogenic changes. The patient 2, a 7-year-old girl with a limp for 4 years, carried one de novo variant of COL6A3 gene,c.5169_5177del (p.Glu1724_Leu1726del). This variant results in the deletion of amino acids (1724 to 1726) in α3 chain of collagen Ⅵ, which may disturb the function of this protein.She was diagnosed as Bethlem myopathy with a mild phenotype. She had delayed motor milestones and presented with walking on tiptoe, hypotonia, and ithylordosis. The contracture of proximal joints was not very obvious. Serum CK level was normal and EMG showed myogenic changes.Muscle biopsy revealed muscular dystrophy and muscle magnetic resonance imaging of patient 2 showed vastus lateral is a "sandwich" sign. Immunofluorescence staining for COL6A3 chain in the cultured skin fibroblasts from patients 2 showed decreased deposition compared with control. Conclusions: These two patients were diagnosed as spontaneous collagen type Ⅵ-related myopathy and carried different variants of COL6A3 gene. Different in pathogenetic variants could cause different genetic features and different phenotypes. Collagen type Ⅵ- related myopathy patients have various clinical manifestations. Typical phenotypes include muscular dystrophies, proximal contractures, and distal hyperlaxity. Muscle MRI shows diffuse fatty infiltration of gluteus maximus and thigh muscle. The histological staining showed the low level expression of COL6A3 chain. The seventy of phenotype was related to the genotype.

Data Mining Techniques in Analyzing Process Data: A Didactic

Due to increasing use of technology-enhanced educational assessment, data mining methods have been explored to analyse process data in log files from such assessment. However, most studies were limited to one data mining technique under one specific scenario. The current study demonstrates the usage of four frequently used supervised techniques, including Classification and Regression Trees (CART), gradient boosting, random forest, support vector machine (SVM), and two unsupervised methods, Self-organizing Map (SOM) and k-means, fitted to one assessment data. The USA sample (N = 426) from the 2012 Program for International Student Assessment (PISA) responding to problem-solving items is extracted to demonstrate the methods. After concrete feature generation and feature selection, classifier development procedures are implemented using the illustrated techniques. Results show satisfactory classification accuracy for all the techniques. Suggestions for the selection of classifiers are presented based on the research questions, the interpretability and the simplicity of the classifiers. Interpretations for the results from both supervised and unsupervised learning methods are provided.

The effects of vasoactive intestinal peptide in the rat model of experimental autoimmune neuritis and the implications for treatment of acute inflammatory demyelinating polyradiculoneuropathy or Guillain-Barré syndrome

Background

Guillain-Barré syndrome is an acute inflammatory demyelinating polyneuropathy that is characterized histologically by demyelination of peripheral nerves and nerve roots, infiltrates of T lymphocytes, and an inflammatory response that includes macrophage infiltrates. The aim of this study was to evaluate the effects of vasoactive intestinal peptide (VIP) in a rat model of experimental autoimmune neuritis (EAN).

Methods

Forty male Lewis rats were divided into a control group (N=10), an EAN group (N=10), an EAN group treated with 15 nmol of VIP (N=10), and an EAN group treated with 30 nmol of VIP (N=10). The rat model was created by subcutaneous injection of P2 polypeptide (200 µg P257-81) into the base of the tail. Intraperitoneal injection of VIP was given on day 7. Rats were weighed and functionally evaluated using an EAN score (0-10). On day 16, the rats were euthanized. The sciatic nerve was examined histologically and using immunohistochemistry with antibodies against CD8, CD68, and forkhead box p3 (Foxp3). Serum concentrations of IL-17 and interferon-α (IFN-α) were measured by ELISA on day 16 after creating the EAN model.

Results

The VIP-treated EAN groups had increased body weight and improved EAN scores compared with the untreated EAN group. CD8-positive and CD68-positive cells were significantly reduced in the EAN group treated with 30 nmol of VIP compared with 15 nmol of VIP. Foxp3-positive cells were significantly decreased in both EAN groups treated with VIP, and serum concentrations of IL-17 and IFN-α were significantly lower compared with the untreated EAN group (P<0.05).

Conclusion

In a rat model of EAN, treatment with VIP resulted in functional improvement, reduced nerve inflammation, and decreased serum levels of inflammatory cytokines.

Probabilistic-Input, Noisy Conjunctive Models for Cognitive Diagnosis

Existing cognitive diagnosis models conceptualize attribute mastery status discretely as either mastery or non-mastery. This study proposes a different conceptualization of attribute mastery as a probabilistic concept, i.e., the probability of mastering a specific attribute for a person, and developing a probabilistic-input, noisy conjunctive (PINC) model, in which the probability of mastering an attribute for a person is a parameter to be estimated from data. And a higher-order version of the PINC model is used to consider the associations among attributes. The results of simulation studies revealed a good parameter recovery for the new models using the Bayesian method. The Examination for the Certificate of Proficiency in English (ECPE) data set was analyzed to illustrate the implications and applications of the proposed models. The results indicated that PINC models had better model-data fit, smaller item parameter estimates, and more refined estimates of attribute mastery.

Using the Stan Program for Bayesian Item Response Theory

Stan is a new Bayesian statistical software program that implements the powerful and efficient Hamiltonian Monte Carlo (HMC) algorithm. To date there is not a source that systematically provides Stan code for various item response theory (IRT) models. This article provides Stan code for three representative IRT models, including the three-parameter logistic IRT model, the graded response model, and the nominal response model. We demonstrate how IRT model comparison can be conducted with Stan and how the provided Stan code for simple IRT models can be easily extended to their multidimensional and multilevel cases.

Cognitive diagnosis modelling incorporating item response times

To provide more refined diagnostic feedback with collateral information in item response times (RTs), this study proposed joint modelling of attributes and response speed using item responses and RTs simultaneously for cognitive diagnosis. For illustration, an extended deterministic input, noisy 'and' gate (DINA) model was proposed for joint modelling of responses and RTs. Model parameter estimation was explored using the Bayesian Markov chain Monte Carlo (MCMC) method. The PISA 2012 computer-based mathematics data were analysed first. These real data estimates were treated as true values in a subsequent simulation study. A follow-up simulation study with ideal testing conditions was conducted as well to further evaluate model parameter recovery. The results indicated that model parameters could be well recovered using the MCMC approach. Further, incorporating RTs into the DINA model would improve attribute and profile correct classification rates and result in more accurate and precise estimation of the model parameters.

Rare Copy Number Variants in Array-Based Comparative Genomic Hybridization in Early-Onset Skeletal Fragility

Early-onset osteoporosis is characterized by low bone mineral density (BMD) and fractures since childhood or young adulthood. Several monogenic forms have been identified but the contributing genes remain inadequately characterized. In search for novel variants and novel candidate loci, we screened a cohort of 70 young subjects with mild to severe skeletal fragility for rare copy-number variants (CNVs). Our study cohort included 15 subjects with primary osteoporosis before age 30 years and 55 subjects with a pathological fracture history and low or normal BMD before age 16 years. A custom-made high-resolution comparative genomic hybridization array with enriched probe density in >1,150 genes important for bone metabolism and ciliary function was used to search for CNVs. We identified altogether 14 rare CNVs. Seven intronic aberrations were classified as likely benign. Five CNVs of unknown clinical significance affected coding regions of genes not previously associated with skeletal fragility (ETV1-DGKB, AGBL2, ATM, RPS6KL1-PGF, and SCN4A). Finally, two CNVs were pathogenic and likely pathogenic, respectively: a 4 kb deletion involving exons 1-4 of COL1A2 (NM_000089.3) and a 12.5 kb duplication of exon 3 in PLS3 (NM_005032.6). Although both genes have been linked to monogenic forms of osteoporosis, COL1A2 deletions are rare and PLS3 duplications have not been described previously. Both CNVs were identified in subjects with significant osteoporosis and segregated with osteoporosis within the families. Our study expands the number of pathogenic CNVs in monogenic skeletal fragility and shows the validity of targeted CNV screening to potentially pinpoint novel candidate loci in early-onset osteoporosis.

CELSR2 is a candidate susceptibility gene in idiopathic scoliosis

A Swedish pedigree with an autosomal dominant inheritance of idiopathic scoliosis was initially studied by genetic linkage analysis, prioritising genomic regions for further analysis. This revealed a locus on chromosome 1 with a putative risk haplotype shared by all affected individuals. Two affected individuals were subsequently exome-sequenced, identifying a rare, non-synonymous variant in the CELSR2 gene. This variant is rs141489111, a c.G6859A change in exon 21 (NM_001408), leading to a predicted p.V2287I (NP_001399.1) change. This variant was found in all affected members of the pedigree, but showed reduced penetrance. Analysis of tagging variants in CELSR1-3 in a set of 1739 Swedish-Danish scoliosis cases and 1812 controls revealed significant association (p = 0.0001) to rs2281894, a common synonymous variant in CELSR2. This association was not replicated in case-control cohorts from Japan and the US. No association was found to variants in CELSR1 or CELSR3. Our findings suggest a rare variant in CELSR2 as causative for idiopathic scoliosis in a family with dominant segregation and further highlight common variation in CELSR2 in general susceptibility to idiopathic scoliosis in the Swedish-Danish population. Both variants are located in the highly conserved GAIN protein domain, which is necessary for the auto-proteolysis of CELSR2, suggesting its functional importance.

PLS3 Deletions Lead to Severe Spinal Osteoporosis and Disturbed Bone Matrix Mineralization

Mutations in the PLS3 gene, encoding Plastin 3, were described in 2013 as a cause for X-linked primary bone fragility in children. The specific role of PLS3 in bone metabolism remains inadequately understood. Here we describe for the first time PLS3 deletions as the underlying cause for childhood-onset primary osteoporosis in 3 boys from 2 families. We carried out thorough clinical, radiological, and bone tissue analyses to explore the consequences of these deletions and to further elucidate the role of PLS3 in bone homeostasis. In family 1, the 2 affected brothers had a deletion of exons 4-16 (NM_005032) in PLS3, inherited from their healthy mother. In family 2, the index patient had a deletion involving the entire PLS3 gene (exons 1-16), inherited from his mother who had osteoporosis. The 3 patients presented in early childhood with severe spinal compression fractures involving all vertebral bodies. The 2 brothers in family 1 also displayed subtle dysmorphic facial features and both had developed a myopathic gait. Extensive analyses of a transiliac bone biopsy from 1 patient showed a prominent increase in osteoid volume, osteoid thickness, and in mineralizing lag time. Results from quantitative backscattered electron imaging and Raman microspectroscopy showed a significant hypomineralization of the bone. Together our results indicate that PLS3 deletions lead to severe childhood-onset osteoporosis resulting from defective bone matrix mineralization, suggesting a specific role for PLS3 in the mineralization process. © 2017 American Society for Bone and Mineral Research.

PLS3 sequencing in childhood-onset primary osteoporosis identifies two novel disease-causing variants

Altogether 95 children with primary bone fragility were screened for variants in PLS3, the gene underlying X-linked osteoporosis. Two children with multiple peripheral and spinal fractures and low BMD had novel disease-causing PLS3 variants. Children with milder phenotypes had no pathogenic variants. PLS3 screening is indicated in childhood-onset primary osteoporosis.

INTRODUCTION

The study aimed to determine the role of pathogenic PLS3 variants in children's bone fragility and to elucidate the associated phenotypic features.

METHODS

Two cohorts of children with bone fragility were screened for variants in PLS3, the gene underlying X-linked osteoporosis. Cohort I comprised 31 patients with childhood-onset primary osteoporosis of unknown etiology. Cohort II comprised 64 children who had sustained multiple fractures but were otherwise healthy. Clinical and radiological data were reviewed. Peripheral blood DNA was Sanger sequenced for coding exons and flanking intronic regions of PLS3.

RESULTS

In two patients of cohort I, where other common genetic causes had been excluded, we identified two novel disease-causing PLS3 variants. Patient 1 was a male with bilateral femoral fractures at 10 years, low BMD (Z-score -4.1; 18 years), and multiple vertebral compression fractures. He had a novel nonsense variant in PLS3. Patient 2 was a girl with multiple long bone and vertebral fractures and low BMD (Z-score -6.6 at 6 years). She had a de novo missense variant in PLS3; whole exome sequencing and array-CGH identified no other genetic causes. Iliac crest bone biopsies confirmed low-turnover osteoporosis in both patients. In cohort II, no pathogenic PLS3 variants were identified in any of the subjects.

CONCLUSIONS

Two novel disease-causing variants in PLS3 were identified in a boy and a girl with multiple peripheral and spinal fractures and very low BMD while no pathogenic variants were identified in children with less severe skeletal fragility. PLS3 screening is warranted in male and female patients with childhood-onset primary osteoporosis.

Sequence analysis of pooled bacterial samples enables identification of strain variation in group A streptococcus

Knowledge of the genomic variation among different strains of a pathogenic microbial species can help in selecting optimal candidates for diagnostic assays and vaccine development. Pooled sequencing (Pool-seq) is a cost effective approach for population level genetic studies that require large numbers of samples such as various strains of a microbe. To test the use of Pool-seq in identifying variation, we pooled DNA of 100 Streptococcus pyogenes strains of different emm types in two pools, each containing 50 strains. We used four variant calling tools (Freebayes, UnifiedGenotyper, SNVer, and SAMtools) and one emm1 strain, SF370, as a reference genome. In total 63719 SNPs and 164 INDELs were identified in the two pools concordantly by at least two of the tools. Majority of the variants (93.4%) from six individually sequenced strains used in the pools could be identified from the two pools and 72.3% and 97.4% of the variants in the pools could be mined from the analysis of the 44 complete Str. pyogenes genomes and 3407 sequence runs deposited in the European Nucleotide Archive respectively. We conclude that DNA sequencing of pooled samples of large numbers of bacterial strains is a robust, rapid and cost-efficient way to discover sequence variation.

Whole-Exome Sequencing Suggests LAMB3 as a Susceptibility Gene for Morbid Obesity

Identification of rare sequencing variants with a larger functional impact has the potential to highlight new pathways contributing to obesity. Using whole-exome sequencing followed by genotyping, we have identified a low-frequency coding variant rs2076349 (V527M) in the laminin subunit β3 (LAMB3) gene showing strong association with morbid obesity and thereby risk of type 2 diabetes. We exome-sequenced 200 morbidly obese subjects and 100 control subjects with pooled DNA samples. After several filtering steps, we retained 439 obesity-enriched low-frequency coding variants. Associations between genetic variants and obesity were validated sequentially in two case-control cohorts. In the final analysis of 1,911 morbidly obese and 1,274 control subjects, rs2076349 showed strong association with obesity (P = 9.67 × 10(-5); odds ratio 1.84). This variant was also associated with BMI and fasting serum leptin. Moreover, LAMB3 expression in adipose tissue was positively correlated with BMI and adipose morphology (few but large fat cells). LAMB3 knockdown by small interfering RNA in human adipocytes cultured in vitro inhibited adipogenesis. In conclusion, we identified a previously not reported low-frequency coding variant that was associated with morbid obesity in the LAMB3 gene. This gene may be involved in the development of excess body fat.

Different Approaches to Covariate Inclusion in the Mixture Rasch Model

The present study investigates different approaches to adding covariates and the impact in fitting mixture item response theory models. Mixture item response theory models serve as an important methodology for tackling several psychometric issues in test development, including the detection of latent differential item functioning. A Monte Carlo simulation study is conducted in which data generated according to a two-class mixture Rasch model with both dichotomous and continuous covariates are fitted to several mixture Rasch models with misspecified covariates to examine the effects of covariate inclusion on model parameter estimation. In addition, both complete response data and incomplete response data with different types of missingness are considered in the present study in order to simulate practical assessment settings. Parameter estimation is carried out within a Bayesian framework vis-à-vis Markov chain Monte Carlo algorithms.

Flow cytometric analyses of the viability, surface marker expression and function of lymphocytes from children following cryopreservation

Flow cytometric analysis is important for the investigation and clinical preparation of lymphocytes from children. However, the strict requirement of cell freshness and inter‑assay variability limits the application of this methodology for pediatric investigations. Therefore, it is necessary to identify a reliable cryopreservative method capable of maintaining high cell viability and proper cell function in lymphocytes from children. In the present study, eight commonly‑used cell cyropreservative methods were used, and their effects on cell viability, surface marker expression and cell function were examined. In addition, how these methods affect the distribution of T‑cell receptor Vβ subfamilies were also determined. The results of the present study provided valuable experimental evidence, based on which the optimal method for the cryopreservation of lymphocytes from children in pediatric investigations and clinical applications can be selected.

A fully automated microfluidic micellar electrokinetic chromatography analyzer for organic compound detection

An integrated microfluidic chemical analyzer utilizing micellar electrokinetic chromatography (MEKC) is developed using a pneumatically actuated Lifting-Gate microvalve array and a capillary zone electrophoresis (CZE) chip. Each of the necessary liquid handling processes such as metering, mixing, transferring, and washing steps are performed autonomously by the microvalve array. In addition, a method is presented for automated washing of the high resistance CZE channel for device reuse and periodic automated in situ analyses. To demonstrate the functionality of this MEKC platform, amino acids and thiols are labeled and efficiently separated via a fully automated program. Reproducibility of the automated programs for sample labeling and periodic in situ MEKC analysis was tested and found to be equivalent to conventional sample processing techniques for capillary electrophoresis analysis. This platform enables simple, portable, and automated chemical compound analysis which can be used in challenging environments.

Investigation of rare and low-frequency variants using high-throughput sequencing with pooled DNA samples

High-throughput sequencing using pooled DNA samples can facilitate genome-wide studies on rare and low-frequency variants in a large population. Some major questions concerning the pooling sequencing strategy are whether rare and low-frequency variants can be detected reliably, and whether estimated minor allele frequencies (MAFs) can represent the actual values obtained from individually genotyped samples. In this study, we evaluated MAF estimates using three variant detection tools with two sets of pooled whole exome sequencing (WES) and one set of pooled whole genome sequencing (WGS) data. Both GATK and Freebayes displayed high sensitivity, specificity and accuracy when detecting rare or low-frequency variants. For the WGS study, 56% of the low-frequency variants in Illumina array have identical MAFs and 26% have one allele difference between sequencing and individual genotyping data. The MAF estimates from WGS correlated well (r = 0.94) with those from Illumina arrays. The MAFs from the pooled WES data also showed high concordance (r = 0.88) with those from the individual genotyping data. In conclusion, the MAFs estimated from pooled DNA sequencing data reflect the MAFs in individually genotyped samples well. The pooling strategy can thus be a rapid and cost-effective approach for the initial screening in large-scale association studies.