[Protective effects of total saponins from Panax japonicus against high-fat diet-induced testicular Sertoli cell junction damage in mice]

OBJECTIVE

To investigate the protective effects of total saponins from Panax japonicus (TSPJ) against high-fat dietinduced testicular Sertoli cell junction damage in mice.

METHODS

Forty male C57BL/6J mice were randomized into normal diet group, high-fat diet group, and low-dose (25 mg/kg) and high-dose (75 mg/kg) TSPJ treatment groups (n=10). The mice in the normal diet group were fed a normal diet, while the mice in the other groups were fed a high-fat diet. After TSPJ treatment via intragastric administration for 5 months, the testes and epididymis of the mice were collected for measurement of weight, testicular and epididymal indices and sperm parameters. HE staining was used for histological evaluation of the testicular tissues and measurement of seminiferous tubule diameter and seminiferous epithelium height. The expression levels of ZO-1, occludin, claudin11, N-cadherin, E-cadherin and β-catenin in Sertoli cells were detected with Western blot, and the localization and expression levels of ZO-1 and β-catenin in the testicular tissues were detected with immunofluorescence assay. The protein expressions of LC3B, p-AKT and p-mTOR in testicular Sertoli cells were detected using double immunofluorescence assay.

RESULTS

Treatment with TSPJ significantly improved high-fat diet-induced testicular dysfunction by reducing body weight (P < 0.001), increasing testicular and epididymal indices (P < 0.05), and improving sperm concentration and sperm viability (P < 0.05). TSPJ ameliorated testicular pathologies and increased seminiferous epithelium height of the mice with high-fat diet feeding (P < 0.05) without affecting the seminiferous tubule diameter. TSPJ significantly increased the expression levels of ZO-1, occludin, N-cadherin, E-cadherin and β-catenin (P < 0.05) but did not affect claudin11 expression in the testicular tissues. Immunofluorescence assay showed that TSPJ significantly increased ZO-1 and β-catenin expression in the testicular tissues (P < 0.001), downregulated LC3B expression and upregulated p-AKT and p-mTOR expressions in testicular Sertoli cells.

CONCLUSION

TSPJ alleviates high-fat diet-induced damages of testicular Sertoli cell junctions and spermatogenesis possibly by activating the AKT/mTOR signaling pathway and inhibiting autophagy of testicular Sertoli cells.

[Pediatric myofibroma/myofibromatosis of the soft tissue and bone: a clinicopathological analysis of 28 cases]

Objective: To investigate the clinicopathological features, diagnosis and differential diagnosis of pediatric myofibroma/myofibromatosis of the soft tissue and bone. Methods: All cases of pediatric myofibroma/myofibromatosis of the soft tissue and bone diagnosed between January 2011 and December 2018 were retrieved from the surgical pathology records in the Department of Pathology, Beijing Jishuitan Hospital, Beijing, China. Clinical and radiological data were collected. H&E and immunohistochemistry were used to examine histological and immunophenotypic features and to make the diagnosis and differential diagnosis. The relevant literature was also reviewed. Results: Twenty-eight cases of pediatric myofibroma/myofibromatosis of the soft tissue and bone were respectively collected. The patients' ages ranged from 2 months to 14 years, with a mean age of 7 years. There were 7 females and 21 males. There were 12 cases located in soft tissue, including the finger (n=9), upper arm (n=1) and foot (n=2). There were 14 cases located in the bone of limb, including the femur (n=8), tibia (n=4), clavicle (n=2), fibula (n=2) and radius (n=1). There were 2 cases of myofibromatosis involving multiple bones. Radiology showed lytic lesions in the bone. The proliferation of spindle-shaped myofibroblasts arranged in fascicles with indistinct eosinophilic cytoplasm and bland nuclei, with no pleomorphism and cytological atypia. The characteristic histologic structure was the biphasic nodular growth pattern with cellular and paucicellular regions. The tumors might arrange in a hemangiopericytoma-like pattern. The stroma varied between dense fibrosis and myxoid changes. The reactive new bone formation and inflammatory cell infiltration also existed. Immunohistochemical study showed that the SMA was positive. The surgical resections were performed. One of the patients had tumor recurrence as a result of 11-month follow-up. Conclusions: The pediatric myofibroma/myofibromatosis of the soft tissue and bone is a very rare benign tumor and has a good prognosis. It has a characteristic morphology and its differential diagnosis from other spindle cell tumors could be made with the immunohistochemical analysis.

Proteome Analysis of Temporomandibular Joint with Disc Displacement

Disc displacement without reduction is a common disorder of the temporomandibular joint, causing clinical symptoms and sometimes condylar degeneration. In some cases, bone regeneration is detected following disc-repositioning procedures. Until now, however, systems-wide knowledge of the protein levels for condylar outcome with disc position is still lacking. Here, we performed comprehensive expression profiling of synovial fluid from 109 patients with disc displacement without reduction using high-resolution data-independent acquisition mass spectrometry and characterized differences in 1,714 proteins. Based on magnetic resonance imaging, samples were divided into groups with versus without condylar absorption and subgroups with versus without new bone. For the proteomic analysis, 32 proteins in groups presented with statistical significance (>2-fold, P < 0.05). Pathways such as response to inorganic substances, blood coagulation, and estrogen signaling were significantly expressed in the group with bone absorption as compared with pathways such as regulation of body fluid levels, vesicle-mediated transport, and focal adhesion, which were enriched in the group without bone absorption. In subgroup analysis, 45 proteins of significant importance (>2-fold, P < 0.05) were associated with pathways including would healing, glycolysis and gluconeogenesis, and amino acid metabolism. Combined with clinical examination, molecules such as acetyl-CoA carboxylase beta (ACACB) and transforming growth factor beta 1 (TGFB1) were related to features such as visual analog scale and maximum interincisal opening (P < 0.05). In addition, 7 proteins were examined by Western blotting, including progesterone immunomodulatory binding factor 1 (PIBF1), histidine-rich glycoprotein (HRG), and protein kinase C and casein kinase substrate in neurons 2 (PACSIN2). In conclusion, this study provides the first proteome analysis of condylar absorption at disc displacement without reduction and postoperative new bone formation after disc reposition. Integrated with clinical data, this analysis provides an important insight into the proteomics of condylar modification at disc position.

Systolic blood pressure time in range and long-term clinical outcomes in patients with ischaemic cardiomyopathy

Background

The relationship between systolic blood pressure (SBP) control and long-term clinical outcomes in patients with ischaemic cardiomyopathy remains unclear. It has been previously reported that either too high or too low SBP may lead to a poorer prognosis. But current SBP control metrics may not take into account the possible effects of fluctuating SBP overtime on patients.

Purpose

This study aimed to estimate the association between time in range (TIR) of SBP and long-term clinical outcomes in patients with ischaemic cardiomyopathy.

Methods

This study was a post-hoc analysis of The Surgical Treatment of Ischaemic Heart Failure (STICH) trial, a randomized controlled trial with two hypotheses that enrolled participants with coronary artery disease and left ventricular ejection fraction ≤35%. The SBP target range of the TIR was defined as 110 to 130 mmHg and the SBP TIR was calculated by linear interpolation method. Patients were equally divided into four groups by quartiles of TIR. Multivariable-adjusted Cox proportional hazards regression models were constructed to compare the effects of different levels of TIR on a 10-year prognosis. The primary outcome was all-cause mortality. Subgroup analyses were performed according to whether patients were assigned to coronary artery bypass grafting (CABG) or medical therapy (MED), and in populations with different baseline SBP.

Results

A total of 1194 eligible patients were included according to the purpose of our study. Compared with patients in the quartile 4 group (TIR 77.87–100%), the fully adjusted hazard ratios (aHRs) and 95% confidence intervals (CIs) of all-cause mortality were 1.32 (0.98–1.78) for quartile 3 group (TIR 54.81–77.63%), 1.40 (1.03–1.90) for quartile 2 group (TIR 32.59–54.67%), and 1.53 (1.14–2.04) for quartile 1 group (TIR 0–32.56%) (P for trend = 0.005). When evaluated TIR as a continuous variable, per 1-SD decrement (29.28%) in TIR significantly increased the incidence of all-cause mortality [1.15 (1.04–1.26)]. Similarly, the decrement in TIR significantly elevated the risk of cardiovascular (CV) mortality and the risk of all-cause mortality plus CV rehospitalization. Consistent results were also observed in subgroup analyses of either CABG or MED, or different baseline SBP, indicating the robustness of our findings.

Conclusions

This study suggested that in patients with ischaemic cardiomyopathy, a higher SBP TIR was significantly associated with a decreased risk of all-cause mortality, CV mortality and the composite of all-cause mortality plus CV rehospitalization, regardless of whether the patient received CABG or MED, and the level of baseline SBP. Our findings support that TIR might be a substitutable metric of SBP control for long-term clinical outcomes in patients with ischaemic cardiomyopathy.

Funding Acknowledgement

Type of funding sources: None.

Evolution and clinical implications of right ventricular dysfunction in ischemic cardiomyopathy with or without coronary artery bypass surgery

Background

The Surgical Treatment of Ischemic Heart Failure (STICH) trial demonstrated that coronary artery bypass grafting (CABG) provides additional survival benefits to patients with ischemic cardiomyopathy. However, it remains unclear whether this benefit is affected by preoperative right ventricular (RV) function and how post-therapeutic evolution of RV function influences long-term outcomes.

Purpose

We sought to investigate the implications of baseline RV function on therapeutic decision-making in patients with ischemic cardiomyopathy, and to evaluate the prognostic implications of post-therapeutic evolution of RV function.

Methods

Patients with available baseline echocardiographic RV function assessed by experienced Echocardiography Core Laboratory physicians were included from the hypothesis 1 of the STICH trial. The primary outcome was long-term all-cause mortality.

Results

A total of 1042 patients were included, among them 757 (72.7%) had normal RV function, 143 (13.7%) mild right ventricular dysfunction (RVD), and 142 (13.6%) moderate to severe RVD. After a median follow-up of 9.8 years, patients with RVD had a higher risk of all-cause mortality compared with patients with normal RV function [mild RVD: adjusted hazard ratio (aHR) 1.32; 95% confidence interval (CI) 1.06–1.64; moderate to severe RVD: aHR, 1.74; 95% CI 1.39–2.18]. Although no significant interaction was detected between RVD degree and treatment allocation (P for interaction = 0.399), a gradually decreasing survival benefit associated with CABG was observed among patients with normal RV function (aHR: 0.79; 95% CI: 0.65–0.96), mild RVD (aHR: 0.85; 95% CI: 0.56–1.29), and moderate to severe RVD (aHR: 0.97; 95% CI: 0.67–1.43). Among 746 patients with available RV function assessed at baseline and post-therapeutic 4-month follow-up, there was a gradient of increasing risk for all-cause mortality across patients with consistent normal RV function, recovery of RVD (aHR: 1.20; 95% CI: 0.88–1.64), newly developed RVD (aHR: 1.59; 95% CI: 1.18–2.14), and consistent RVD (aHR: 2.06; 95% CI: 1.60–2.67). Independent predictors of RVD recovery included baseline left ventricular ejection fraction (per 1-percent increment, adjusted odds ratio: 1.04; 95% CI: 1.00–1.09) and mitral regurgitation ≥ grade 2 (adjusted odds ratio: 0.42; 95% CI: 0.21–0.84).

Conclusions

Baseline RVD was associated with an increased risk of long-term mortality in patients with ischemic cardiomyopathy, and adding CABG to medical therapy might provide limited survival benefits in patients with moderate to severe RVD. A gradient of increasing risk for mortality was observed across different categories of RV function evolution, which emphasizes the necessity of pre- and post-therapeutic RV assessment for prognostic evaluation.

Funding Acknowledgement

Type of funding sources: None.

Artificial Intelligence-Based Family Health Education Public Service System

Family health education is a must for every family, so that children can be taught how to protect their own health. However, in this era of artificial intelligence, many technical operations based on artificial intelligence are born, so the purpose of this study is to apply artificial intelligence technology to family health education. This paper proposes a fusion of artificial intelligence and IoT technologies. Based on the characteristics of artificial intelligence technology, it combines ZigBee technology and RFID technology in the Internet of Things technology to design an artificial intelligence-based service system. Then it designs the theme of family health education by conducting a questionnaire on students’ family education and analyzing the results of the questionnaire. And it designs database and performance analysis experiments to improve the artificial intelligence-based family health education public service system designed in this paper. Finally, a comparative experiment between the family health education public service system based on artificial intelligence and the traditional health education method will be carried out. The experimental results show that the family health education public service system based on artificial intelligence has improved by 21.74% compared with the traditional family health education method; compared with the traditional family health education method, the health education effect of the family health education public service system based on artificial intelligence has increased by 13.89%.

High precision machine learning-enabled ECG algorithm for predicting sites of idiopathic ventricular arrhythmia origin

Introduction

Radiofrequency catheter ablation (CA) is an efficient antiarrhythmic treatment with a class I indication for idiopathic ventricular arrhythmia (IVA). The accurate prediction of the origins of IVA can significantly increase the procedure success rate, reduce operation duration and decrease the risk of complications. The present work proposes an ECG analysis algorithm to estimate 21 possible origins of idiopathic ventricular arrhythmia at a clinical-grade level accuracy, which include left coronary cusp (LCC), right coronary cusp (RCC), aortomitral continuity (AMC), summit, LCC-RCC commissure, left His bundle, mitral valve (MV), left septal including left anterior fascicle (LAF), left posterior fascicle (LPF), left anterior papillary muscle (LAPM), left posterior papillary muscle (LPPM), anterior cusp (AC), left cusp (LC), right cusp (RC), RVOT septal, free wall, right His bundle, tricuspid valve (TV), and right anterior papillary muscle (RAPM).

Method

A total of 18,612 ECG recordings extracted from 545 patients who underwent successful CA to treat IVA were proportionally sampled into training, validation and testing cohorts. We designed four classification schemes responding to different hierarchical levels of the possible IVA origins. The first scheme will help the operators to figure out the origin from epicardium of left ventricular summit, right, and left ventricle. The second one can separate origins from left/right outflow tract and left/right non-out flow tract, respectively. The third one is able to predict 18 anatomical locations, and the fourth scheme can distinguish 21 possible sites. For every classification scheme, we compared 98 distinct machine learning models with optimized hyperparameter values obtained through extensive grid search and reported an optimal algorithm with the highest accuracy scores attained on the validation cohorts.

Results

In the first classification scheme used to predict right ventricular endocardium, left ventricular endocardium, and epicardium of left ventricular summit, the model achieved an accuracy of 99.79 (99.41–99.89) and a F1-score of 99.84 (99.6–99.96). For scheme 2, the proposed method reached an accuracy of 99.62 (99.09–99.78) and a F1-score of 99.42 (98.79–99.75). For scheme 3, the model achieved an accuracy of 97.78 (96.76–98.41), a F1-score of 97.74 (94.15–99.73), and an adjusted accuracy of 98.53 (98.33–99.15). For scheme 4 that can distinguish 21 origin sites, the proposed model attained an accuracy of 98.24 (97.36–98.71), a F1-score of 98.56 (97.88–99.12) and an adjusted accuracy of 98.75 (98.35–99.38).

Conclusion

The proposed machine learning model can be immediately and effortlessly deployed to electrophysiology labs allowing cardiologists to predict the exact origins of arrhythmia and provide an optimum treatment plan both before and during the CA procedure. This approach will significantly reduce the CA procedure duration and the risk of complications.

Funding Acknowledgement

Type of funding sources: Foundation. Main funding source(s): 2020 Natural Science Foundation of Zhengjiang Province Confusion matrix for classification schemes

Comparison between a novel sirolimus-eluting bioresorbable scaffold with everolimus-eluting metallic stent in patients with coronary artery disease: three-year follow-up from the neovas rct study

Background

Previous trials and meta-analyses have demonstrated that risk of adverse clinical events, especially thrombosis and target vessel myocardial infarction is increasing between 1 and 3 years after Bioresorbable Scaffolds (BRS) implantation.

Purpose

We sought to evaluate the long-term clinical outcomes of a novel NeoVas BRS in comparison with cobalt chromium everolimus-eluting stent (EES) following implantation in patients with coronary artery disease by 3-year follow-up results from the NeoVas RCT.

Methods

Overall, 560 patients with a single de novo native coronary artery lesion with reference vessel diameter 2.5–3.75 mm and lesion length ≤20 mm were randomized 1:1 to NeoVas BRS vs. cobalt-chromium everolimus-eluting stents (CoCr-EES). Optical coherence tomography (OCT) and fractional flow reserve (FFR) were both performed in a pre-specified subgroup at 3-year follow-up. Clinical outcomes from NeoVas RCT were analyzed by randomized device (intention to treat) cumulative to 3 years.

Results

Over 3 years, the overall target lesion failure (TLF) rate was 6.9% in the NeoVas group and 6.1% in the CoCr-EES group (HR 1.13, 95% CI 0.59 to 2.18; p=0.71). There was no statistically significant difference of the definite or probable stent thrombosis between the NeoVas group and the CoCr-EES group (1.1% vs. 0.7%, HR 1.51, 95% CI 0.26 to 8.73, p=0.64). In a landmark analysis of TLF, we found no difference in rate of late events from 2 to 3 years between two groups. FFR was not significantly different between the two group at 3 years (NeoVas vs. CoCr-EES, 0.89±0.07 vs. 0.90±0.05). NeoVas was largely absorbed (72.26% ± 13.21%) examined by OCT follow-up. Of 55 patients who finished 3-year absorption analysis, NeoVas was totally absorbed in 4 patients.

Conclusions

At the 3-year follow-up in the Neovas RCT trial, overall TLF rates were comparable between Neovas BRS and CoCr-EES, and adverse event rates relating to device safety were not increased with Neovas BRS compared with CoCr-EES up to 3 years after implantation.

Funding Acknowledgement

Type of funding sources: None.

[Preliminary results of surgical treatment of fibrous dysplasia of proximal femur in children]

Objective: To investigate the surgical treatment, clinical effect and revision reasons of children with proximal femoral fibrous dysplasia(FD). Methods: The clinical data of 26 children with polyostotic FD of proximal femur who underwent surgery at Department of Pediatric Orthopaedics, Beijing Jishuitan Hospital from June 2016 to June 2018 were retrospectively analyzed. There were 18 males and 8 females with a mean age of 9.2 years (range:5 to 16 years).One of them was McCune Albright syndrome. Fifteen cases were in first operation and 11 cases were in revision operation. The operation methods and results were reviewed,and the causes of revision were analyzed. Results: Among the 15 children who underwent the first operation,13 cases underwent osteotomy or fracture reduction and interlocking intramedullary nail(IMN) fixation;One case underwent valgus osteotomy and pediatric hip plate(PHP)internal fixation;One case underwent valgus osteotomy+lesion curettage+allogeneic bone graft+PHP fixation. Among the 11 children who underwent revision surgery,9 cases were treated with IMN fixation,1 case with PHP fixation,and 1 case with PHP fixation+allogeneic bone graft. The causes of revision included distal fixation failed in 6 cases,proximal fixation failed in 3 cases,plate fixation failed in 5 cases,and recurrence occurred after curettage and artificial bone graft in 2 cases. Patients were followed up for 1.4 years(range:1.0 to 3.5 years) after recent operation. The osteotomy or fracture healed well with good deformity correction. Postoperative complications included infection in 1 case and local bone partial resorption in 1 case. Conclusions: Osteotomy combined with rigid internal fixation is an effective surgical treatment for fibrous dysplasia of proximal femur in children. Internal fixation should cover the whole length of lesion. Intramedullary nail is the most common choice. Because the growth of height and the progress of the disease itself,this deformity is prone to recur in children,needing closely follow-up after operation.

Statistical Learning Methods Applicable to Genome-Wide Association Studies on Unbalanced Case-Control Disease Data

Despite the fact that imbalance between case and control groups is prevalent in genome-wide association studies (GWAS), it is often overlooked. This imbalance is getting more significant and urgent as the rapid growth of biobanks and electronic health records have enabled the collection of thousands of phenotypes from large cohorts, in particular for diseases with low prevalence. The unbalanced binary traits pose serious challenges to traditional statistical methods in terms of both genomic selection and disease prediction. For example, the well-established linear mixed models (LMM) yield inflated type I error rates in the presence of unbalanced case-control ratios. In this article, we review multiple statistical approaches that have been developed to overcome the inaccuracy caused by the unbalanced case-control ratio, with the advantages and limitations of each approach commented. In addition, we also explore the potential for applying several powerful and popular state-of-the-art machine-learning approaches, which have not been applied to the GWAS field yet. This review paves the way for better analysis and understanding of the unbalanced case-control disease data in GWAS.

Detecting PCOS susceptibility loci from genome-wide association studies via iterative trend correlation based feature screening

Background

Feature screening plays a critical role in handling ultrahigh dimensional data analyses when the number of features exponentially exceeds the number of observations. It is increasingly common in biomedical research to have case-control (binary) response and an extremely large-scale categorical features. However, the approach considering such data types is limited in extant literature. In this article, we propose a new feature screening approach based on the iterative trend correlation (ITC-SIS, for short) to detect important susceptibility loci that are associated with the polycystic ovary syndrome (PCOS) affection status by screening 731,442 SNP features that were collected from the genome-wide association studies.

Results

We prove that the trend correlation based screening approach satisfies the theoretical strong screening consistency property under a set of reasonable conditions, which provides an appealing theoretical support for its outperformance. We demonstrate that the finite sample performance of ITC-SIS is accurate and fast through various simulation designs.

Conclusion

ITC-SIS serves as a good alternative method to detect disease susceptibility loci for clinic genomic data.

Dual roles of misshapen/NIK-related kinase (MINK1) in osteoarthritis subtypes through the activation of TGFβ signaling

OBJECTIVE

To identify the role of misshapen/NIK-related kinase (MINK1) in age-related Osteoarthritis (OA) and injury-induced OA, and the effects of enhanced TGFβ signaling in these progresses.

DESIGN

The effect of MINK1 was analyzed with MINK1 knock out (Mink1-/-) mice and C57BL/6J mice. OA progress was studied in age-related OA and instability-associated OA (destabilization of the medial meniscus, DMM) models. The murine knee joint was evaluated through histological staining, Osteoarthritis Research Society International (OARSI) scores, immunohistochemistry, and μCT analysis. Primary chondrocytes were isolated from wild type and Mink1-/- mice and subjected to osteogenic induction and Western blot analysis.

RESULTS

MINK1 is highly expressed during cartilage development and in normal cartilage. Mink1-/- mice displayed markedly lower OARSI scores, aggrecan degradation neoepitope positive cells and increased Safranin O and pSMAD2 staining in aging-related OA model. However, in injury-induced OA, loss of MINK1 accelerates extracellular matrix (ECM) destruction, osteophyte formation, and subchondral bone sclerosis. Accelerated subchondral bone remodeling in Mink1-/- mice was accompanied with increased numbers of nestin-positive mesenchymal stem cells (MSCs) and osterix-positive osteoprogenitors. pSMAD2 staining was increased in the subchondral bone marrow of Mink1-/- mice and overexpression of MINK1 inhibited SMAD2 phosphorylation in vitro.

CONCLUSIONS

This study shows for the first time that activation of TGFβ/SMAD2 by MINK1 deficiency plays opposite roles in aging-related and injury-induced OA. MINK1 deficiency protects cartilage from degeneration in aging joints through increased SMAD2 activation in chondrocytes, while accelerating OA progress in injury-induced model through enhanced osteogenesis of MSCs in the subchondral bone. These findings provide insights for developing precision OA therapeutics targeting TGFβ/SMAD2 signaling.

An omnidirectional visualization model of personalized gene regulatory networks

Gene regulatory networks (GRNs) have been widely used as a fundamental tool to reveal the genomic mechanisms that underlie the individual's response to environmental and developmental cues. Standard approaches infer GRNs as holistic graphs of gene co-expression, but such graphs cannot quantify how gene-gene interactions vary among individuals and how they alter structurally across spatiotemporal gradients. Here, we develop a general framework for inferring informative, dynamic, omnidirectional, and personalized networks (idopNetworks) from routine transcriptional experiments. This framework is constructed by a system of quasi-dynamic ordinary differential equations (qdODEs) derived from the combination of ecological and evolutionary theories. We reconstruct idopNetworks using genomic data from a surgical experiment and illustrate how network structure is associated with surgical response to infrainguinal vein bypass grafting and the outcome of grafting. idopNetworks may shed light on genotype-phenotype relationships and provide valuable information for personalized medicine.

Analyzing risk factors for recurrence of developmental coxa vara after surgery

PURPOSE

To evaluate the risk factors for developmental coxa vara (DCV) recurrence following valgus osteotomy of the proximal femur.

METHODS

We retrospectively reviewed records of 32 DCV patients (46 hips) treated surgically (2005 to 2012). Recurrence-related factors, including age at initial surgery, side, sex, fixation methods, diagnosis of coxa vara, premature capital femoral physeal closure and postoperative Hilgenreiner epiphyseal (HE) angle, head-shaft (HS) angle, medial femoral offset and posterior slope angle (PSA) were analyzed.

RESULTS

At 4.7-year mean follow-up, 12 hip deformities recurred (26%). Postoperative HE angle > 41° and negative offset were statistically significant univariate and multivariate risk factors for the deformity recurrence. Increased PSA was common preoperatively, which accounted for 59% of hips. Postoperative PSA > 20° was associated with a high recurrence rate in the univariate analysis. Age was another univariate risk factor for the recurrence. Recurrence rate was 52% in the < 6.5-year age group versus 4% in the > 6.5-year age group. Other factors were not statistically significantly related to recurrence.

CONCLUSION

DCV is a 3D deformity. To prevent recurrence, HE angle should be restored to < 41° in the coronal plane. Sagittal malalignment (abnormal PSA) should be corrected concurrently, so that, the direction of surgical correction is along the true deformity plane. During valgus osteotomy, the distal fragment should be lateralized to maintain a normal mechanical axis.

LEVEL OF EVIDENCE

IV.

[Effects of physeal bar resection in treating post-traumatic distal radius partial physeal arrest]

Objective: To evaluate the effects of treatment of post-traumatic distal radius partial physeal arrest with physeal bar resection. Methods: From February 2007 to November 2017, 11 children with distal radius physeal arrest received physeal bar resection in the Department of Pediatric Orthopedics, Beijing Jishuitan Hospital. There were 2 females and 9 males. The average age of the patients was (10.1±1.8) years (range,7-13 years). All cases had previous history of distal radius trauma. The average duration from the previous fracture to the physeal bar resection operation was (22.8±3.2) months (range,22 to 41 months). Clinical and radiological evidence of distal radius physeal arrest were suggested in all patients. A CT or MRI scan was performed preoperatively to assess the size of the physeal bridge. Inclusion criteria were patients with a physeal bridge<30% of the physeal area,and with at least 2 years of growth remaining. The physeal bar resection operation was performed with the assistance of either fluoroscopy (5 cases) or intraoperative three dimensional navigation (6 cases). After resection, the void was then filled with bone wax in all cases and distal ulnar epiphysiodesis was conducted in 5 cases. The mean follow-up duration was (3.7±1.6) years (range,1-9 years). The clinical examination data and X ray were obtained during the follow up. Results: Four cases obtained fully recovery from the operation and the deformity got fully correction. The X ray showed no bone bridge recurred. The deformity did not aggravate in 1 case. The deformity aggravated and subsequent osteotomy was conducted in the left 6 cases. Three cases in the navigation group obtained fully recovery. One case in the fluoroscopy group obtained fully recovery. Conclusions: The intraoperative three dimensional navigation can precisely locate the bone bridge. The physeal bar resection is an effective technique in some post-traumatic distal radius partial physeal arrest.

Mapping morphological shape as a high-dimensional functional curve

Detecting how genes regulate biological shape has become a multidisciplinary research interest because of its wide application in many disciplines. Despite its fundamental importance, the challenges of accurately extracting information from an image, statistically modeling the high-dimensional shape and meticulously locating shape quantitative trait loci (QTL) affect the progress of this research. In this article, we propose a novel integrated framework that incorporates shape analysis, statistical curve modeling and genetic mapping to detect significant QTLs regulating variation of biological shape traits. After quantifying morphological shape via a radius centroid contour approach, each shape, as a phenotype, was characterized as a high-dimensional curve, varying as angle θ runs clockwise with the first point starting from angle zero. We then modeled the dynamic trajectories of three mean curves and variation patterns as functions of θ. Our framework led to the detection of a few significant QTLs regulating the variation of leaf shape collected from a natural population of poplar, Populus szechuanica var tibetica. This population, distributed at altitudes 2000-4500 m above sea level, is an evolutionarily important plant species. This is the first work in the quantitative genetic shape mapping area that emphasizes a sense of 'function' instead of decomposing the shape into a few discrete principal components, as the majority of shape studies do.

An adaptive threshold determination method of feature screening for genomic selection

Background

Although the dimension of the entire genome can be extremely large, only a parsimonious set of influential SNPs are correlated with a particular complex trait and are important to the prediction of the trait. Efficiently and accurately selecting these influential SNPs from millions of candidates is in high demand, but poses challenges. We propose a backward elimination iterative distance correlation (BE-IDC) procedure to select the smallest subset of SNPs that guarantees sufficient prediction accuracy, while also solving the unclear threshold issue for traditional feature screening approaches.

Results

Verified through six simulations, the adaptive threshold estimated by the BE-IDC performed uniformly better than fixed threshold methods that have been used in the current literature. We also applied BE-IDC to an Arabidopsis thaliana genome-wide data. Out of 216,130 SNPs, BE-IDC selected four influential SNPs, and confirmed the same FRIGIDA gene that was reported by two other traditional methods.

Conclusions

BE-IDC accommodates both the prediction accuracy and the computational speed that are highly demanded in the genomic selection.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-017-1617-9) contains supplementary material, which is available to authorized users.

Quantitative gene-gene and gene-environment mapping for leaf shape variation using tree-based models

Leaf shape traits have long been a focus of many disciplines, but the complex genetic and environmental interactive mechanisms regulating leaf shape variation have not yet been investigated in detail. The question of the respective roles of genes and environment and how they interact to modulate leaf shape is a thorny evolutionary problem, and sophisticated methodology is needed to address it. In this study, we investigated a framework-level approach that inputs shape image photographs and genetic and environmental data, and then outputs the relative importance ranks of all variables after integrating shape feature extraction, dimension reduction, and tree-based statistical models. The power of the proposed framework was confirmed by simulation and a Populus szechuanica var. tibetica data set. This new methodology resulted in the detection of novel shape characteristics, and also confirmed some previous findings. The quantitative modeling of a combination of polygenetic, plastic, epistatic, and gene-environment interactive effects, as investigated in this study, will improve the discernment of quantitative leaf shape characteristics, and the methods are ready to be applied to other leaf morphology data sets. Unlike the majority of approaches in the quantitative leaf shape literature, this framework-level approach is data-driven, without assuming any pre-known shape attributes, landmarks, or model structures.

A Proof of Concept Study of Function-Based Statistical Analysis of fNIRS Data: Syntax Comprehension in Children with Specific Language Impairment Compared to Typically-Developing Controls

Functional near infrared spectroscopy (fNIRS) is a neuroimaging technology that enables investigators to indirectly monitor brain activity in vivo through relative changes in the concentration of oxygenated and deoxygenated hemoglobin. One of the key features of fNIRS is its superior temporal resolution, with dense measurements over very short periods of time (100 ms increments). Unfortunately, most statistical analysis approaches in the existing literature have not fully utilized the high temporal resolution of fNIRS. For example, many analysis procedures are based on linearity assumptions that only extract partial information, thereby neglecting the overall dynamic trends in fNIRS trajectories. The main goal of this article is to assess the ability of a functional data analysis (FDA) approach for detecting significant differences in hemodynamic responses recorded by fNIRS. Children with and without SLI wore two, 3 × 5 fNIRS caps situated over the bilateral parasylvian areas as they completed a language comprehension task. FDA was used to decompose the high dimensional hemodynamic curves into the mean function and a few eigenfunctions to represent the overall trend and variation structures over time. Compared to the most popular GLM, we did not assume any parametric structure and let the data speak for itself. This analysis identified significant differences between the case and control groups in the oxygenated hemodynamic mean trends in the bilateral inferior frontal and left inferior posterior parietal brain regions. We also detected significant group differences in the deoxygenated hemodynamic mean trends in the right inferior posterior parietal cortex and left temporal parietal junction. These findings, using dramatically different approaches, experimental designs, data sets, and foci, were consistent with several other reports, confirming group differences in the importance of these two areas for syntax comprehension. The proposed FDA was consistent with the temporal characteristics of fNIRS, thus providing an alternative methodology for fNIRS analyses.

Production and genetic analysis of resynthesized Brassica napus from a B. rapa landrace from the Qinghai-Tibet Plateau and B. alboglabra

This study aimed to reveal the genetic and epigenetic variations involved in a resynthesized Brassica napus (AACC) generated from a hybridization between a B. rapa (AA) landrace and B. alboglabra (CC). Amplified fragment length polymorphism (AFLP), methylation-sensitive amplified polymorphism, and the cDNA-AFLP technique were performed to detect changes between different generations at the genome, methylation, and transcription levels. We obtained 30 lines of resynthesized B. napus with a mean 1000-seed weight of over 7.50 g. All of the lines were self-compatible, probably because both parents were self-compatible. At the genome level, the S0 generation had the lowest frequency of variations (0.18%) and the S3 generation had the highest (6.07%). The main variation pattern was the elimination of amplified restriction fragments on the CC genome from the S0 to the S4 generations. At the methylation level, we found three loci that exhibited altered methylation patterns on the parental A genome; the variance rate was 1.35%. At the transcription level, we detected 43.77% reverse mutations and 37.56% deletion mutations that mainly occurred on the A and C genomes, respectively, in the S3 generation. Our results highlight the genetic variations that occur during the diploidization of resynthesized B. napus.

Identification of candidate causal genes and their associated pathogenic mechanisms underlying teratozoospermia based on the spermatozoa transcript profiles

Teratozoospermia with unclear pathomechanism is one of the common causes for failed fertilisation. This study aimed to further explore the pathological mechanism for teratozoospermia. Spermatozoal transcript profiles generated from 13 normal fertile men and eight infertile males with a consistent severe heterogeneous teratozoospermia were used. These data were pre-processed, and differentially expressed genes were screened. Besides, gene ontology and pathway enrichment analysis were performed, and then, protein-protein interaction (PPI) network was constructed, and spermatogenesis-related genes in the PPI network were extracted. As a result, 366 up-regulated and 2158 down-regulated genes were identified. Multiple gene ontology terms and pathways including cell-cell signalling and reproduction enriched by differentially expressed genes were obtained. Moreover, four clusters including cluster 1 associated with RNA catabolic process were identified from the PPI network. In addition, genes including cyclin B1, proteasome (prosome, macropain) activator subunit 4, Rac GTPase-activating protein 1 and pituitary tumour-transforming 1 were received. In conclusion, abnormal expression of cyclin B1 and Rac GTPase-activating protein 1, still proteasome (prosome, macropain) activator subunit 4 and pituitary tumour-transforming 1 would impede cell cycle progression during sperm development and maturation, which may contribute to the occurrence and development of teratozoospermia.

Tigecycline exerts an antitumoral effect in oral squamous cell carcinoma

OBJECTIVE

To explore whether antibacterial drug tigecycline could exert an antitumoral effect in oral squamous cell carcinoma (OSCC).

MATERIALS AND METHODS

Two OSCC cell lines Tca8113 and KB were used in this study. To investigate the cytostatic effects of tigecycline in OSCC, cell growth was tested by trypan blue staining, MTT assay, and Brdu immunofluorescence staining. Then, the apoptosis proportion was measured by FITC Annexin-V and PI labeling, and cell cycle was determined by PI staining. The expression of caspase 3 (CASP3) and cell cycle regulatory protein was detected by Western blot assay. Finally, the clonogenesis and tumorigenesis capacity were analyzed by soft agar growth and xenograft model.

RESULTS

Here, we showed that tigecycline significantly inhibited cell growth and proliferation in OSCC cell lines Tca8113 and KB. It did not induce cell apoptosis but led to an increase of cells in G0/G1 phase with down-regulation of cyclin E2 (CCNE2) and cyclin-dependent kinase4 (CDK4) protein expression. We also showed that tigecycline inhibited colony formation in soft agar and reduced tumor growth in a xenograft model.

CONCLUSION

Our results suggested that tigecycline might be used as a novel candidate agent for the treatment of OSCC.

First Report of Neofusicoccum parvum Causing Panicle Blight and Leaf Spot on Vitis heyneana in China

The climbing vine, Vitis heyneana Roem. & Schult, is a member of the grape family endemic to Asia. Its fruits are used in wine production, and its roots, stems, and leaves can be used in medicinal materials. This plant is grown in Southwest China, as well as in India, Bhutan, and Nepal. Mulao Autonomous County in Guangxi Province is the only artificial cultivation area in China. During the summer of 2013, a panicle blight and leaf spot were detected on V. heyneana on four farms in Mulao Autonomous County. The symptoms were observed from the onset of florescence through fruit harvest. Brown lesions initially appeared at the base of a panicle and then extended to the whole panicle, finally causing the panicle to die and fruit to drop. When the disease developed on leaves, the symptom initially appeared as small dark brown circular spots, later enlarging into irregular spots (average diameter 6 mm) with a light brown center and dark brown rim. With severe disease, some individual leaves were affected by numerous spots, leading to premature senescence. Small sections of diseased tissue excised from 10 panicle and 10 leaf samples were plated on potato dextrose agar (PDA) and incubated at 28°C. Fungal colonies developed, initially with abundant white aerial mycelium, which turned olivaceous gray after 5 days and formed black pycnidia after 25 days. The conidia were hyaline, ellipsoidal to fusiform, externally smooth, thin-walled, and nonseptate. Thirty conidia were measured; the dimensions were 12.0 to 17.5 × 4.0 to 6.0 μm. Morphological characteristics of the isolates were similar to the descriptions of Neofusicoccum parvum (3). The isolate MPT-1 was selected as a representative for molecular identification. Genomic DNA was extracted and used for PCR to amplify the internal transcribed spacer (ITS) region and partial translation elongation factor 1-alpha (EF1-α) gene, using primers ITS1/ITS4 and EF1-728F/EF1-986R, respectively. The obtained ITS sequence (GenBank Accession No. KJ599627) and EF1-α sequence (KM921768) showed >99% homology with several GenBank sequences of N. parvum. Morphological and molecular results confirmed the isolate as N. parvum. For pathogenicity tests, detached, young healthy panicles and leaves of V. heyneana were surface-sterilized, wounded by sterile needle, and inoculated with mycelial plugs (3 mm in diameter) of four N. parvum isolates. Ten panicles and 10 leaves were used for every isolate. Control panicles and leaves were treated with sterile PDA plugs. All the samples were placed in a humid chamber (RH 90%, 28°C, 12 h of light) for 3 days. Symptoms similar to those observed in the field developed on all panicles and leaves inoculated with N. parvum isolates. N. parvum was reisolated from all inoculated, symptomatic tissues. The controls remained symptomless. N. parvum has been reported to cause trunk canker on V. vinifera (2), dieback on Cupressus funebris (3), and a leaf spot on Myristica fragrans (1). To our knowledge, this is the first report of N. parvum causing panicle blight and leaf spot on V. heyneana in China. Panicle blight caused a large number of fruits to drop and reduced the yield seriously. Some effective measures should be taken to control this disease. References: (1) V. Jayakumar et al. New Dis. Rep. 23:19, 2011. (2) J. Kaliternam et al. Plant Dis. 97:1656, 2013. (3) S. B. Li et al. Plant Dis. 94:641, 2010.

A graphical weighted power improving multiplicity correction approach for SNP selections

Controlling for the multiplicity effect is an essential part of determining statistical significance in large-scale single-locus association genome scans on Single Nucleotide Polymorphisms (SNPs). Bonferroni adjustment is a commonly used approach due to its simplicity, but is conservative and has low power for large-scale tests. The permutation test, which is a powerful and popular tool, is computationally expensive and may mislead in the presence of family structure. We propose a computationally efficient and powerful multiple testing correction approach for Linkage Disequilibrium (LD) based Quantitative Trait Loci (QTL) mapping on the basis of graphical weighted-Bonferroni methods. The proposed multiplicity adjustment method synthesizes weighted Bonferroni-based closed testing procedures into a powerful and versatile graphical approach. By tailoring different priorities for the two hypothesis tests involved in LD based QTL mapping, we are able to increase power and maintain computational efficiency and conceptual simplicity. The proposed approach enables strong control of the familywise error rate (FWER). The performance of the proposed approach as compared to the standard Bonferroni correction is illustrated by simulation and real data. We observe a consistent and moderate increase in power under all simulated circumstances, among different sample sizes, heritabilities, and number of SNPs. We also applied the proposed method to a real outbred mouse HDL cholesterol QTL mapping project where we detected the significant QTLs that were highlighted in the literature, while still ensuring strong control of the FWER.

Holm multiple correction for large-scale gene-shape association mapping

Background

Linkage Disequilibrium (LD) is a powerful approach for the identification and characterization of morphological shape, which usually involves multiple genetic markers. However, multiple testing corrections substantially reduce the power of the associated tests. In addition, the principle component analysis (PCA), used to quantify the shape variations into several principal phenotypes, further increases the number of tests. As a result, a powerful multiple testing correction for simultaneous large-scale gene-shape association tests is an essential part of determining statistical significance. Bonferroni adjustments and permutation tests are the most popular approaches to correcting for multiple tests within LD based Quantitative Trait Loci (QTL) models. However, permutations are extremely computationally expensive and may mislead in the presence of family structure. The Bonferroni correction, though simple and fast, is conservative and has low power for large-scale testing.

Results

We propose a new multiple testing approach, constructed by combining an Intersection Union Test (IUT) with the Holm correction, which strongly controls the family-wise error rate (FWER) without any additional assumptions on the joint distribution of the test statistics or dependence structure of the markers. The power improvement for the Holm correction, as compared to the standard Bonferroni correction, is examined through a simulation study. A consistent and moderate increase in power is found under the majority of simulated circumstances, including various sample sizes, Heritabilities, and numbers of markers. The power gains are further demonstrated on real leaf shape data from a natural population of poplar, Populus szechuanica var tietica, where more significant QTL associated with morphological shape are detected than under the previously applied Bonferroni adjustment.

Conclusion

The Holm correction is a valid and powerful method for assessing gene-shape association involving multiple markers, which not only controls the FWER in the strong sense but also improves statistical power.

Inhibition of farnesyl pyrophosphate synthase prevents angiotensin II-induced cardiac fibrosis in vitro

Farnesyl pyrophosphate synthase (FPPS)-catalysed isoprenoid intermediates are important for the activation of Ras homologue gene family, member A (RhoA) in angiotensin (Ang) II-induced cardiac fibrosis. This study was designed to investigate the specific role of FPPS in the development of cardiac fibrosis. We demonstrated that FPPS expression was elevated in both in-vivo and in-vitro models of Ang II-mediated cardiac fibrosis. FPPS inhibition by zolendronate and FPPS knock-down by a silencing lentivirus decreased the expression of cardiac fibrosis marker genes, including collagen I, collagen III and transforming growth factor (TGF)-β1. FPPS inhibition was reversed by geranylgeraniol (GGOH) and mimicked by RhoA knock-down with siRhoA. The antagonistic effect of GGOH on the zolendronate-mediated modulation of RhoA activation in Ang II-stimulated cardiac fibroblasts was demonstrated by a pull-down assay. Furthermore, FPPS knock-down also prevented RhoA activation by Ang II in vitro. In conclusion, FPPS and RhoA may be part of a signalling pathway that plays an important role in Ang II-induced cardiac fibrosis in vitro.

Clustering analysis of water distribution systems: identifying critical components and community impacts

Large water distribution systems (WDSs) are networks with both topological and behavioural complexity. Thereby, it is usually difficult to identify the key features of the properties of the system, and subsequently all the critical components within the system for a given purpose of design or control. One way is, however, to more explicitly visualize the network structure and interactions between components by dividing a WDS into a number of clusters (subsystems). Accordingly, this paper introduces a clustering strategy that decomposes WDSs into clusters with stronger internal connections than external connections. The detected cluster layout is very similar to the community structure of the served urban area. As WDSs may expand along with urban development in a community-by-community manner, the correspondingly formed distribution clusters may reveal some crucial configurations of WDSs. For verification, the method is applied to identify all the critical links during firefighting for the vulnerability analysis of a real-world WDS. Moreover, both the most critical pipes and clusters are addressed, given the consequences of pipe failure. Compared with the enumeration method, the method used in this study identifies the same group of the most critical components, and provides similar criticality prioritizations of them in a more computationally efficient time.

First Report of Corynespora cassiicola Causing Leaf Spot on Akebia trifoliate

Akebia species have been used for centuries in medicinal practices in a few Asian countries such as China and Japan. The dried stems of Akebia trifoliata are known as mutong in the Chinese pharmacopoeia (4) and mokutsu in Kampo, the traditional Chinese medicine developed in Japan (2). In China, the plant is grown in the provinces of Shandong, Hebei, Shanxi, Henan, Gansu, and some provinces in the south of the Yangtze River basin. During the summer of 2012, a leaf spot disease was detected on A. trifoliata grown in Nanning, Guangxi, China. The disease occurred and spread rapidly in July under conditions of high temperature and high humidity. The symptoms appeared on three sites that we inspected; disease incidences were higher than 80%. Initial symptoms consisted of small (less than 5 mm in diameter), circular, purple-brown leaf spots. Spots later enlarged and became elliptical, circular, or irregular with gray-white centers and dark brown rims. The centers were slightly concave. The spots could coalesce with each other, resulting in leaf desiccation and wilting. A fungal isolate was obtained from symptomatic leaf tissue that taken from a field (22°50'N, 108°22'E) in Nanning, Guangxi, China. Single-spore culture of the isolate was incubated on potato dextrose agar (PDA) for 7 days in the dark at 28°C. Conidiophores were straight to slightly curved, unbranched, and pale brown. Conidia (19.0 to 140.5 μm long and 7.0 to 11.0 μm wide) were formed singly or in chains, obclavate to cylindrical, straight or curved, pale brown, with a rounded apex and truncate base, and 1 to 13 pseudosepta. Morphological characteristics of the isolate were similar to the descriptions of Corynespora cassiicola (Berk. & M.A. Curtis) C.T. Wei (1). Genomic DNA of the isolate was extracted and used for PCR amplification of rDNA-ITS (internal transcribed spacer) sequence with primers ITS1 and ITS4. The PCR products were purified and sequenced. The sequence (GenBank Accession No. KC977496) was used in BLAST searches to interrogate GenBank for sequence similarity. High sequence similarity of 100% was obtained with several C. cassiicola strains. Pathogenicity of the isolate was investigated to demonstrate Koch's postulate. Young, healthy, fully expanded green leaves of A. trifoliata were surface sterilized. Fifteen leaves were inoculated with 10-μl drops of conidia suspension (10⁵ conidia per ml) and 10 leaves were inoculated with the same volume of sterile water to serve as controls. All the leaves were placed in a humid chamber for 5 days. Spots with similar symptoms to those observed in the field developed on all inoculated leaves. The pathogen was reisolated and identified as C. cassiicola. The controls remained symptomless. According to previous reports, A. trifoliata was infected by Alternaria tenuissima in China and by Colletotrichum acutatum in Japan (3). To our knowledge, this is the first report of C. cassiicola found on Akebia species worldwide. Furthermore, this new disease primarily affects plantations and reduces the quality and yield of the medicine. Some effective measures should be taken to control this disease. References: (1) M. B. Ellis and P. Holliday. CMI Description of Pathogenic Fungi and Bacteria, 303, 1971. (2) F. Kitaoka et al. J. Nat. Med. 63:374, 2009. (3) Y. Kobayshi et al. J. Gen. Plant Pathol. 70:295, 2004. (4) L. Li et al. HortScience 45:4, 2010.

Performance assessment of the single photon emission microscope: high spatial resolution SPECT imaging of small animal organs

The single photon emission microscope (SPEM) is an instrument developed to obtain high spatial resolution single photon emission computed tomography (SPECT) images of small structures inside the mouse brain. SPEM consists of two independent imaging devices, which combine a multipinhole collimator, a high-resolution, thallium-doped cesium iodide [CsI(Tl)] columnar scintillator, a demagnifying/intensifier tube, and an electron-multiplying charge-coupling device (CCD). Collimators have 300- and 450-µm diameter pinholes on tungsten slabs, in hexagonal arrays of 19 and 7 holes. Projection data are acquired in a photon-counting strategy, where CCD frames are stored at 50 frames per second, with a radius of rotation of 35 mm and magnification factor of one. The image reconstruction software tool is based on the maximum likelihood algorithm. Our aim was to evaluate the spatial resolution and sensitivity attainable with the seven-pinhole imaging device, together with the linearity for quantification on the tomographic images, and to test the instrument in obtaining tomographic images of different mouse organs. A spatial resolution better than 500 µm and a sensitivity of 21.6 counts·s^-1·MBq^-1 were reached, as well as a correlation coefficient between activity and intensity better than 0.99, when imaging ^99mTc sources. Images of the thyroid, heart, lungs, and bones of mice were registered using ^99mTc-labeled radiopharmaceuticals in times appropriate for routine preclinical experimentation of <1 h per projection data set. Detailed experimental protocols and images of the aforementioned organs are shown. We plan to extend the instrument's field of view to fix larger animals and to combine data from both detectors to reduce the acquisition time or applied activity.

Stochastic modeling of systems mapping in pharmacogenomics

As a basis of personalized medicine, pharmacogenetics and pharmacogenomics that aim to study the genetic architecture of drug response critically rely on dynamic modeling of how a drug is absorbed and transported to target tissues where the drug interacts with body molecules to produce drug effects. Systems mapping provides a general framework for integrating systems pharmacology and pharmacogenomics through robust ordinary differential equations. In this chapter, we extend systems mapping to more complex and more heterogeneous structure of drug response by implementing stochastic differential equations (SDE). We argue that SDE-implemented systems mapping provides a computational tool for pharmacogenetic or pharmacogenomic research towards personalized medicine.

Mapping shape quantitative trait loci using a radius-centroid-contour model

As the consequence of complex interactions between different parts of an organ, shape can be used as a predictor of structural-functional relationships implicated in changing environments. Despite such importance, however, it is no surprise that little is known about the genetic detail involved in shape variation, because no approach is currently available for mapping quantitative trait loci (QTLs) that control shape. Here, we address this problem by developing a statistical model that integrates the principle of shape analysis into a mixture-model-based likelihood formulated for QTL mapping. One state-of-the-art approach for shape analysis is to identify and analyze the polar coordinates of anatomical landmarks on a shape measured in terms of radii from the centroid to the contour at regular intervals. A procrustes analysis is used to align shapes to filter out position, scale and rotation effects on shape variation. To the end, the accurate and quantitative representation of a shape is produced with aligned radius-centroid-contour (RCC) curves, that is, a function of radial angle at the centroid. The high dimensionality of the RCC data, crucial for a comprehensive description of the geometric feature of a shape, is reduced by principal component (PC) analysis, and the resulting PC axes are treated as phenotypic traits, allowing specific QTLs for global and local shape variability to be mapped, respectively. The usefulness and utilization of the new model for shape mapping in practice are validated by analyzing a mapping data collected from a natural population of poplar, Populus szechuanica var tibetica, and identifying several QTLs for leaf shape in this species. The model provides a powerful tool to compute which genes determine biological shape in plants, animals and humans.