Fall Detection System Based on Point Cloud Enhancement Model for 24 GHz FMCW Radar

Automatic fall detection plays a significant role in monitoring the health of senior citizens. In particular, millimeter-wave radar sensors are relevant for human pose recognition in an indoor environment due to their advantages of privacy protection, low hardware cost, and wide range of working conditions. However, low-quality point clouds from 4D radar diminish the reliability of fall detection. To improve the detection accuracy, conventional methods utilize more costly hardware. In this study, we propose a model that can provide high-quality three-dimensional point cloud images of the human body at a low cost. To improve the accuracy and effectiveness of fall detection, a system that extracts distribution features through small radar antenna arrays is developed. The proposed system achieved 99.1% and 98.9% accuracy on test datasets pertaining to new subjects and new environments, respectively.

Generative Adversarial Network-Enhanced Ultra-Low-Dose [18F]-PI-2620 τ PET/MRI in Aging and Neurodegenerative Populations

BACKGROUND AND PURPOSE

With the utility of hybrid τ PET/MR imaging in the screening, diagnosis, and follow-up of individuals with neurodegenerative diseases, we investigated whether deep learning techniques can be used in enhancing ultra-low-dose [18F]-PI-2620 τ PET/MR images to produce diagnostic-quality images.

MATERIALS AND METHODS

Forty-four healthy aging participants and patients with neurodegenerative diseases were recruited for this study, and [18F]-PI-2620 τ PET/MR data were simultaneously acquired. A generative adversarial network was trained to enhance ultra-low-dose τ images, which were reconstructed from a random sampling of 1/20 (approximately 5% of original count level) of the original full-dose data. MR images were also used as additional input channels. Region-based analyses as well as a reader study were conducted to assess the image quality of the enhanced images compared with their full-dose counterparts.

RESULTS

The enhanced ultra-low-dose τ images showed apparent noise reduction compared with the ultra-low-dose images. The regional standard uptake value ratios showed that while, in general, there is an underestimation for both image types, especially in regions with higher uptake, when focusing on the healthy-but-amyloid-positive population (with relatively lower τ uptake), this bias was reduced in the enhanced ultra-low-dose images. The radiotracer uptake patterns in the enhanced images were read accurately compared with their full-dose counterparts.

CONCLUSIONS

The clinical readings of deep learning-enhanced ultra-low-dose τ PET images were consistent with those performed with full-dose imaging, suggesting the possibility of reducing the dose and enabling more frequent examinations for dementia monitoring.

[Study on efficacy, recurrence rate and related risk factors between ablation index and contact force guided radiofrequency ablation of paroxysmal atrial fibrillation in elderly patients]

Objective: To compare the efficacy, safety and recurrence rate between ablation index (AI) and contact force (CF) guided radiofrequency ablation of paroxysmal atrial fibrillation in elderly patients. Methods: Elderly patients (age ≥60 years) with paroxysmal atrial fibrillation who received radiofrequency ablation for the first time at Department of Cardiology, Beijing Friendship Hospital from April 2018 to April 2019 were enrolled. Patients were divided into 2 groups: AI-group (n=40) and CF group (n=37) depending on their ablation methods. Follow-up was performed until 1 year post the procedure, and efficacy related indexes like first-pass pulmonary vein isolation (PVI) rate, ablation duration, operation duration and major complications were compared between 2 groups. The recurrence rates between 2 groups and related risk factors after radiofrequency ablation were analyzed. Results: A total of 77 patients [mean age (68.5±6.4) years, 40 were male] were enrolled at last. In AI guided patients, frequency of first-pass PVI rate was higher [52.5%(21 cases) vs 29.7%(3 cases), P=0.011] with a shorter ablation duration [(24.5±1.7) min vs (33.7±2.2) min, P<0.001] and operation duration [(136.6±6.1) min vs (139.7±7.4) min, P=0.048] compared with CF guided group. At 1 year follow-up, AI group showed an amendatory recurrence rate in Kaplan-Meier analysis (22.5% vs 40.5%,log-rank P=0.048). Multivariate Cox regression analysis showed that CF guided ablation (HR=3.272,95%CI:1.319-8.114,P=0.011), enlarged anteroposterior diameter of the left atrium (HR=4.233,95%CI:1.511-11.862,P=0.006) and complicated with coronary heart disease (HR=4.829,95%CI:1.399-16.666,P=0.013) were independent risk factors for recurrence of atrial fibrillation in elderly patients. Conclusions: Compared with CF guided ablation, radiofrequency ablation of paroxysmal atrial fibrillation in elderly patients guided by AI showed a higher first-pass PVI rate, shorter procedure duration of both ablation time and total operation time, meanwhile a lower recurrence rate. Further analysis revealed that different ablation alternation (AI or CF), enlarged anteroposterior diameter of left atrium, and complicated with coronary heart disease are independent risk factors for recurrence after radiofrequency ablation of atrial fibrillation in elderly patients.

[Correlation analysis between lactic, procalcitonin and disease severity in patients with imported malaria from Africa]

Objective: To explore the clinical characteristics, the correlation between lactate, procalcitonin and disease severity of imported malaria from Africa. Methods: The clinical data of 186 patients with imported malaria were collected from January 1, 2018 to April 30, 2021 in the Guangzhou Eighth People's Hospital, Guangzhou Medical University. The general conditions, clinical symptoms, laboratory tests, treatment, and prognosis of the patients were analyzed retrospectively. Receiver operating characteristic (ROC) curves were drawn to evaluate the value of relevant indicators in predicting severe malaria. Results: A total of 186 patients were divided into severe cases (n=48) and non-severe cases (n=138) in this study, of which the mean age was (38.3±10.3) years, 169(90.9%) cases were male, 17(9.1%) cases were female. The main infection species was Plasmodium falciparum, in a total of 166 cases (89.2%). The severe cases were all falciparum malarias. Compared with the non-severe group, the lactic, procalcitonin, white blood cell count and neutrophil count of the severe group were all increased, the differences were all statistically significant (all P<0.01); the percentage of monocytes, red blood cell count, hemoglobin, hematocrit and platelet count were all decreased, the difference were all statistically significant (all P<0.01). The areas under the ROC curves (AUC)(95%CI) of lactate, procalcitonin, red blood cell count, hemoglobin, hematocrit and platelet count for predicting severe malaria was 0.753(0.663-0.844), 0.755(0.670-0.841), 0.782(0.700-0.864), 0.738(0.652-0.823), 0.760(0.676-0.844), 0.778(0.699-0.857), respectively (all P<0.01). When the Youden indexes were at their maximum, the best cut-off value of lactic was 2.29 mmol/L, with sensitivity in predicting of severe malaria was 56.3%, and the specificity was 93.5%; the best cut-off value of procalcitonin was 2.12 μg/L, with sensitivity in predicting of severe malaria was 77.1%, and the specificity was 68.1%. The fatality rate of severe malaria was 4.2% (2/48). Conclusions: Anemia and thrombocytopenia are common indicators for predicting the severity of malaria. Lactic and procalcitonin also have higher predictive value for severe malaria, which could help to identify severe malaria as early as possible, improve the cure rate and reduce the risk of death.

MRI biomarker of muscle composition is associated with severity of pelvic organ prolapse

BACKGROUND

The pathophysiology of pelvic organ prolapse is largely unknown. We hypothesized that reduced muscle mass on magnetic resonance defecography (MRD) is associated with increased pelvic floor laxity. The aim of this study was to compare the psoas and puborectalis muscle mass composition and cross-sectional area among patients with or without pelvic laxity.

METHODS

An observational retrospective study was conducted on women > age 18 years old who had undergone MRD for pelvic floor complaints from January 2020 to December 2020 at Stanford Pelvic Health Center. Pelvic floor laxity, pelvic organ descent, and rectal prolapse were characterized by standard measurements on MRD and compared to the psoas (L4 level) and puborectalis muscle index (cross-sectional area adjusted by height) and relative fat fraction, quantified by utilizing a 2-point Dixon technique. Regression analysis was used to quantify the association between muscle characteristics and pelvic organ measurements.

RESULTS

The psoas fat fraction was significantly elevated in patients with abnormally increased resting and strain H and M lines (p < 0.05) and increased with rising grades of Oxford rectal prolapse (p = 0.0001), uterovaginal descent (p = 0.001) and bladder descent (p = 0.0005). In multivariate regression analysis, adjusted for age and body mass index, the psoas fat fraction (not muscle index) was an independent risk factor for abnormal strain H and M line; odds ratio (95% confidence interval) of 17.8 (2-155.4) and 18.5 (1.3-258.3) respectively, and rising Oxford grade of rectal prolapse 153.9 (4.4-5383) and bladder descent 12.4 (1.5-106). Puborectalis fat fraction was increased by rising grades of Oxford rectal prolapse (p = 0.0002).

CONCLUSIONS

Severity of pelvic organ prolapse appears to be associated with increasing psoas muscle fat fraction, a biomarker for reduced skeletal muscle mass. Future prospective research is needed to determine if sarcopenia may predict postsurgical outcomes after pelvic organ prolapse repair.

Effects of adolescent substance use disorders on central cholinergic function

Adolescence is a transitional period between childhood and adulthood, in which the individual undergoes significant cognitive, behavioral, physical, emotional, and social developmental changes. During this period, adolescents engage in experimentation and risky behaviors such as licit and illicit drug use. Adolescents' high vulnerability to abuse drugs and natural reinforcers leads to greater risk for developing substance use disorders (SUDs) during adulthood. Accumulating evidence indicates that the use and abuse of licit and illicit drugs during adolescence and emerging adulthood can disrupt the cholinergic system and its processes. This review will focus on the effects of peri-adolescent nicotine and/or alcohol use, or exposure, on the cholinergic system during adulthood from preclinical and clinical studies. This review further explores potential cholinergic agents and pharmacological manipulations to counteract peri-adolescent nicotine and/or alcohol abuse.

PADI4, negatively regulated by miR-335-5p, participates in regulating the proliferation, migration, invasion and radiosensitivity of nasopharyngeal carcinoma cells

Peptidyl arginine deiminase 4 (PADI4), an enzyme that converts arginine residues to citrulline residues in the presence of calcium ions, affects the biochemical activities of proteins. The biological function of PADI4 as well as its mechanism in nasopharyngeal carcinoma (NPC) necessitates further investigation. PADI4 expression in NPC tissues and cells was detected using Western blot. qRT-PCR was used to determine the expression of miR-335-5p and PADI4 mRNA in NPC tissues and cells. BrdU assay and CCK-8 assay were employed to detect cell proliferation. Cell migration and invasion were evaluated using Transwell assay. NPC cells were exposed to different doses of radiation in vitro, and then colony formation assays were used to detect colony survival. The target relationship between miR-335-5p and PADI4 was verified using Western blot, qRT-PCR, and dual-luciferase reporter gene assays. Compared with normal mucosal epithelial tissues and cell lines, the expression level of PADI4 in NPC tissues and cells was significantly up-regulated. PADI4 overexpression promoted the proliferation, migration, and invasion of NPC cells. Under radiation, NPC cell survival was significantly promoted by the up-regulation of PADI4. Conversely, knock-down of PADI4 suppressed the above-mentioned malignant phenotypes. MiR-335-5p could bind with the 3' UTR of PADI4 mRNA, and suppressed the expression of PADI4. PADI4 down-regulated the expression of p21 and activated the mTOR signaling pathway. PADI4, which is negatively regulated by miR-335-5p, promotes the proliferation, migration, invasion and radioresistance of NPC cells by regulating the p21 and mTOR signaling pathways.

Long noncoding RNA LINC01296 is associated with poor prognosis in ESCC and promotes ESCC cell proliferation, migration and invasion

OBJECTIVE

Recent studies have reported that long intergenic non-protein-coding RNA 1296 (LINC01296) regulates the tumorigenesis and the progression of several tumors, but the role of LINC01296 in esophageal squamous cell carcinoma (ESCC) remains unclear. The purpose of this study was to examine the expression, function, and clinical significance of LINC01296 in ESCC.

PATIENTS AND METHODS

Expression of LINC01296 was analyzed in 221 ESCC tissues and three ESCC cell lines by Real-time quantitative RT-PCR. The correlation between LINC01296 levels and other clinical features, disease-free survival (DFS), and overall survival (OS) was analyzed statistically. The function of LINC01296 on cell proliferation, migration, and invasion was confirmed in vitro through MTT assay and transwell assay.

RESULTS

We found that LINC01296 was upregulated in ESCC cell lines and cancerous tissues, as compared with normal esophagus cells and adjacent normal tissue samples. High LINC01296 expression was significantly correlated with differentiation grade (p=0.000), lymph nodes metastasis (p=0.002), distant metastasis (p=0.002), and TNM stage (p = 0.015). Moreover, ESCC patients with high LINC01296 expression experienced shorter OS and DFS (p=0.0009 and p=0.0005, respectively). In addition, univariate and multivariate analysis showed that LINC01296 expression was an independent predictor for both OS and DFS in ESCC. Functionally, the results of in vitro assay indicated that down-regulation of LINC01296 significantly suppressed ESCC cells proliferation, migration, and invasion, suggesting that LINC01296 contributed to tumorigenesis of ESCC.

CONCLUSIONS

Our findings indicate that LINC01296 exerts a role in promoting the development of human ESCC. Up-regulation of LINC01296 could be considered as a predictor for diagnosis and prognosis of ESCC patients.

Reduced SPOCK1 expression inhibits non-small cell lung cancer cell proliferation and migration through Wnt/β-catenin signaling

OBJECTIVE

Accumulating evidence suggests that SPARC/osteonectin, cwcv, and kazal-like domain proteoglycan 1 (SPOCK1) contributes to the initiation and progression of human cancers. However, little is known about the function mechanisms of SPOCK1 in non-small cell lung cancer (NSCLC). The aim of this study was to investigate the molecular mechanism of SPOCK1 in NSCLC.

PATIENTS AND METHODS

The expression levels of SPOCK1 in NSCLC tissues and cell lines were analyzed by qRT-PCR and Western blotting. The proliferative activity of NSCLC cells was determined by MTT and colony formation assays. The transwell assay was used to examine the cell migration and invasive ability. To study the impact of SPOCK1 on Wnt/β‑catenin signaling, we further performed Western blotting for related proteins in this pathway.

RESULTS

We observed that the expression of SPOCK1 at both protein and mRNA levels was also increased in human NSCLC tissues and cell lines. Functionally, down-regulation of SPOCK1 in NSCLC cells markedly suppressed cell proliferation, colony formation, migration and invasion in vitro. Mechanistically, we found that indicated the activation of Wnt/β-catenin pathway was suppressed by SPOCK1 silencing.

CONCLUSIONS

The expression of SPOCK1 served as a tumor promoter, possibly through the Wnt/β-catenin signaling pathway in NSCLC. Targeting SPOCK1 could be a potential therapeutic strategy in NSCLC.

Mutant Dentin Sialophosphoprotein Causes Dentinogenesis Imperfecta

Dentin sialophosphoprotein (DSPP) is an extracellular matrix protein highly expressed by odontoblasts in teeth. DSPP mutations in humans may cause dentinogenesis imperfecta (DGI), an autosomal dominant dentin disorder. We recently generated a mouse model (named "Dspp^P19L/+ mice") that expressed a mutant DSPP in which the proline residue at position 19 was replaced by a leucine residue. We found that the Dspp^P19L/+ and Dspp^P19L/P19L mice at a younger age displayed a tooth phenotype resembling human DGI type III characterized by enlarged dental pulp chambers, while the teeth of older Dspp^P19L/+ and Dspp^P19L/P19L mice had smaller dental pulp chambers mimicking DGI type II. The teeth of Dspp^P19L/+ and Dspp^P19L/P19L mice had a narrower pulp chamber roof predentin layer, thinner pulp chamber roof dentin, and thicker pulp chamber floor dentin. In addition, these mice also had increased enamel attrition, accompanied by excessive deposition of peritubular dentin. Immunohistochemistry, in situ hybridization, and real-time polymerase chain reaction analyses showed that the odontoblasts in both Dspp^P19L/+ and Dspp^P19L/P19L mice had reduced DSPP expression, compared to the wild-type mice. We also observed that the levels of DSPP expression were much higher in the roof-forming odontoblasts than in the floor-forming odontoblasts in the wild-type mice and mutant mice. Moreover, immunohistochemistry showed that while the immunostaining signals of dentin sialoprotein (N-terminal fragment of DSPP) were decreased in the dentin matrix, they were remarkably increased in the odontoblasts of the Dspp^P19L/+ and Dspp^P19L/P19L mice. Consistently, our in vitro studies showed that the secretion of the mutant DSPP was impaired and accumulated within endoplasmic reticulum. These findings suggest that the dental phenotypes of the mutant mice were associated with the intracellular retention of the mutant DSPP in the odontoblasts of the DSPP-mutant mice.

Bactericidal efficacy of hydrogen peroxide on Cutibacterium acnes

Objectives

The purpose of this study was to examine the bactericidal efficacy of hydrogen peroxide (H₂O₂) on Cutibacterium acnes (C. acnes). We hypothesize that H₂O₂ reduces the bacterial burden of C. acnes.

Methods

The effect of H₂O₂ was assessed by testing bactericidal effect, time course analysis, growth inhibition, and minimum bactericidal concentration. To assess the bactericidal effect, bacteria were treated for 30 minutes with 0%, 1%, 3%, 4%, 6%, 8%, or 10% H₂O₂ in saline or water and compared with 3% topical H₂O₂ solution. For time course analysis, bacteria were treated with water or saline (controls), 3% H₂O₂ in water, 3% H₂O₂ in saline, or 3% topical solution for 5, 10, 15, 20, and 30 minutes. Results were analyzed with a two-way analysis of variance (ANOVA) (p < 0.05).

Results

Minimum inhibitory concentration of H₂O₂ after 30 minutes is 1% for H₂O₂ prepared in saline and water. The 3% topical solution was as effective when compared with the 1% H₂O₂ prepared in saline or water. The controls of both saline and water showed no reduction of bacteria. After five minutes of exposure, all mixtures of H₂O₂ reduced the percentage of live bacteria, with the topical solution being most effective (p < 0.0001). Maximum growth inhibition was achieved with topical 3% H₂O₂.

Conclusion

The inexpensive and commercially available topical solution of 3% H₂O₂ demonstrated superior bactericidal effect as observed in the minimum bactericidal inhibitory concentration, time course, and colony-forming unit (CFU) inhibition assays. These results support the use of topical 3% H₂O₂ for five minutes before surgical skin preparation prior to shoulder surgery to achieve eradication of C. acnes for the skin.Cite this article: P. Hernandez, B. Sager, A. Fa, T. Liang, C. Lozano, M. Khazzam. Bactericidal efficacy of hydrogen peroxide on Cutibacterium acnes. Bone Joint Res 2019;8:3-10. DOI: 10.1302/2046-3758.81.BJR-2018-0145.R1.

MicroRNA-433 inhibits migration and invasion of ovarian cancer cells via targeting Notch1

We aimed to determine the effects of miR-433 on the malignant behaviors of ovarian cancer cells, as well as to elucidate the possible mechanisms of ovarian cancer development. A total of 9 ovarian cancer tissues and 9 matched normal ovary tissues were obtained, and the expression levels of miR-433 and Notch1 were then determined by real-time PCR. Human ovarian cancer cell lines SKOV3 and OVCAR3 were transfected with miR-433 mimics, negative miR-control and Notch1 siRNA. The expression of Notch1 protein in transfected cells was determined by western blot. In addition, the proliferation, migration and invasion of SKOV3 and OVCAR3 cells in vitro were then evaluated using Cell Counting Kit 8, wound healing assay and Transwell invasion assay, respectively. Besides, bioinformatics methods and luciferace reporter assay were performed to confirm whether Notch1 was a direct target of miR-433. The expression of miR-433 was markedly down-regulated while Notch1 expression was significantly up-regulated in ovarian cancer tissues compared with matched normal ovary tissues. Overexpression of miR-433 significantly inhibited the migration and invasion of ovarian cancer cells, but had not significant effects on cell proliferation. In addition, Notch1 was a direct target of miR-433. Besides, down-regulation of Notch1 inhibited the invasion of ovarian cancer cells. Our findings indicate that miR-433 may inhibit cell migration and invasion in the development of ovarian cancer via down-regulation of Notch1. Notch1 may serve as a potential target in cancer therapy.

Macleaya cordata extracts suppressed the increase of a part of antibiotic resistance genes in fecal microorganism of weaned pigs

This study was designed to evaluate the effects of Macleaya cordata extracts (Chinese herbal medicine extracts) and antibiotics combination with chlortetracycline (CTC) on the antibiotic resistance genes in fecal microorganism. Compared with the group without antibiotics, the relative abundances of all six tetracycline resistance genes were increased after 75 mg kg−1 CTC supplementation. Interestingly, M. cordata extracts in feed suppressed the increase of a part of tetracycline resistance genes in fecal microorganism of weaned pigs.

Screening of parathyroid gland by high frequency ultrasound and the relationship between recurrent urinary calculi and primary hyperparathyroidism

OBJECTIVE

To understand the value of high frequency ultrasound in the clinical screening of parathyroid gland, and to summarize the intrinsic relationship between primary hyperparathyroidism and recurrent urinary calculi.

PATIENTS AND METHODS

98 cases of urinary calculi were randomly selected, and the patients were admitted to our hospital from March 2014 to August 2017. A total of 100 healthy subjects were selected as group B in the same period. High frequency color Doppler ultrasonography scan recorded the results.

RESULTS

Among the subjects in group A, 67 (68.37%) showed parathyroid gland, 14 cases (14.29%) had tumor mass in the parathyroid system, 40 cases more than those in group B (40.00%) and 2 cases (2.00%), (p <0.05). There were 10 cases (10.20%) of primary hyperparathyroidism in group A and no cases of primary hyperparathyroidism in group B (p < 0.05). The occurrence of primary hyperparathyroidism was 26.92% (7/26) in the number of cases, with 3 and more cases of urinary calculi, which was higher than that in the first recurrent cases (3/72), (p<0.005).

CONCLUSIONS

One of the key causes of recurrent episodes of urinary calculi is primary hyperparathyroidism, which can be applied to high frequency ultrasonography to develop professional screening of parathyroid gland in cases of urinary calculi.

Application of Reduced-FOV Diffusion-Weighted Imaging in Evaluation of Normal Pituitary Glands and Pituitary Macroadenomas

BACKGROUND AND PURPOSE

FOV optimized and constrained undistorted single-shot imaging provides relatively high-resolution images with few artifacts. This study evaluated the image quality and value of FOV optimized and constrained undistorted single-shot DWI in the evaluation of normal pituitary glands and pituitary macroadenomas.

MATERIALS AND METHODS

Subjects with normal pituitary glands and patients with pituitary macroadenomas underwent FOV optimized and constrained undistorted single-shot and EPI DWI. Two neuroradiologists graded the image quality based on visualization of the pituitary stalk, pituitary gland, and pituitary macroadenoma. Intra- and interobserver agreements were assessed by κ statistics. Image quality and ADCs were compared between the 2 methods by the paired Wilcoxon signed rank test and t test. Differences in ADC between normal pituitary glands and macroadenomas were analyzed by the independent-samples t test.

RESULTS

Twenty-eight subjects with normal pituitary glands and 16 patients with macroadenomas were enrolled. Intra- and interobserver agreements for image-quality assessment were moderate to substantial. Relative to EPI DWI, FOV optimized and constrained undistorted single-shot DWI exhibited obviously better image quality both in normal pituitary glands and macroadenomas. There was no significant difference in ADCs of macroadenomas between the 2 methods. Macroadenomas with soft consistency (0.75 ± 0.14 × 10^-3 mm²/s) had significantly lower mean ADC than normal pituitary glands (1.18 ± 0.19 × 10^-3 mm²/s; P < .001).

CONCLUSIONS

FOV optimized and constrained undistorted single-shot DWI helps acquire high-resolution images of normal pituitary glands and pituitary macroadenomas with relatively few susceptibility artifacts in a clinically feasible scan time. This sequence might be helpful for evaluating the consistency of pituitary macroadenomas.

Baicalin inhibits Escherichia coli isolates in bovine mastitic milk and reduces antimicrobial resistance

In this study, we aimed to evaluate the inhibitory effect of baicalin on Escherichia coli in vitro and the effects of baicalin treatment on antimicrobial resistance of the E. coli isolates. Through isolation, purification, and identification, a total of 56 E. coli strains were isolated from 341 mastitic milk samples. The study of inhibition effect of baicalin on the E. coli strains in vitro was focused on permeability and morphology of the isolates using an alkaline phosphatase kit and scanning electron microscopy. Furthermore, the resistance spectrum of the isolates to the common antimicrobial agents was tested at sub-minimum inhibitory concentrations of baicalin by the agar dilution method. Extended-spectrum β-lactamase and plasmid-mediated quinolone resistance genes were amplified by PCR before and after incubation with baicalin. The results revealed that baicalin has certain inhibitory effects on the isolates in vitro. The alkaline phosphatase enzyme activity was significantly increased from 1.246 to 2.377 U/100 mL, and the surface of E. coli was concave and shriveled. Analysis of the resistance spectrum and PCR amplification showed that, after administration with baicalin, the sensitivity of most strains to the selected antimicrobial agents was enhanced. Strikingly, the drug-resistant genes from 71.43% (40/56) of these isolates were found to have drug-resistant genes to different extents. Altogether, the current study confirmed both the inhibitory effect on Escherichia coli in vitro and the reduction of antimicrobial resistance by baicalin. This is the first comprehensive study to report on baicalin, a traditional Chinese medicine that acts on E. coli isolated from the mastitic milk samples.

MAPK pathway regulated the cardiomyocyte apoptosis in mice with post-infarction heart failure

BACKGROUND

To explore the role of the MAPK signaling pathway in the cardiomyocyte apoptosis of mice with post-infarction heart failure (HF).

METHODS

Mice were divided into sham and myocardial infarction (MI) groups. Before surgery, the MI group was divided into SB203580 and PBS subgroups. A post-infarction HF model was established by ligating the left anterior descending coronary artery. Ventricular dilatation and cardiac function were observed by small animal echocardiography. The growth of primary cardiomyocytes was observed under an inverted phase contrast microscope. The mRNA and protein expressions of endoplasmic reticulum stress (ERS) markers, GRP78 and CHOP, were detected by qRT-PCR and immunofluorescence assay, respectively.

RESULTS

The MI group had enlarged left ventricle and decreased cardiac function. GRP78 and CHOP protein expressions in myocardial tissues, especially those of SB203580 subgroup, significantly increased (p < 0.05). The expressions of p-JNK and cleaved caspase 12 proteins, especially those of SB203580 subgroup, were significantly up-regulated. Cardiomyocytes of MI group were significantly more prone to apoptosis (p < 0.05), with SB203580 subgroup being more obvious.

CONCLUSION

MI was accompanied by ERS, probably involving the MAPK signaling pathway. SB203580, a specific inhibitor of this pathway, can relieve cardiomyocyte apoptosis and protect the myocardium by suppressing such stress (Tab. 3, Fig. 7, Ref. 20).

Increasing expression of miR-5100 in non-small-cell lung cancer and correlation with prognosis

OBJECTIVE

A previous study indicated that miR-5100 served as a tumor oncogene in lung cancer. However, whether miR-5100 may serve as a novel prognostic marker in non-small cell lung cancer (NSCLC), has not been investigated. The aim of this study was to investigate miR-5100 expression and its clinical significance in NSCLC patients.

PATIENTS AND METHODS

Expression of miR-5100 was detected in NSCLC tissues and matched normal lung tissues by quantitative Real-time polymerase chain reaction. The correlation between miR-5100 expression and clinical features were statistically analyzed. Survival rate was analyzed by log-rank test, and survival curves were plotted according to Kaplan-Meier. The correlation between miR-5100 expression and prognosis of NSCLC patients was further evaluated by univariate and multivariate analysis.

RESULTS

As revealed by qRT-PCR analysis, the relative level of miR-5100 expression in NSCLC tissues was significantly upregulated, compared with that in corresponding noncancerous tissues (p < 0.01). Additionally, high miR-5100 expression was statistically associated with higher clinical stage (p < 0.001), N classification (p = 0.003) and M classification (p = 0.027), but lower differentiated degree (p < 0.001). Furthermore, the results of Kaplan-Meier suggested that NSCLC patients with higher miR-5100 expression had significantly poorer overall survival (p < 0.0001) and progression-free survival (p < 0.0001). Multivariate survival analysis verified that miR-5100 expression level was an independent predictor of both overall survival and progression-free survival for NSCLC patients.

CONCLUSIONS

Our data suggested that up-regulation of miR-5100 was correlated with NSCLC progression, which provided a potential prognostic biomarker and therapeutic target.

Charge optimized many body (COMB) potentials for Pt and Au

Interatomic potentials for Pt and Au are developed within the third generation charge optimized many-body (COMB3) formalism. The potentials are capable of reproducing phase order, lattice constants, and elastic constants of Pt and Au systems as experimentally measured or calculated by density functional theory. We also fit defect formation energies, surface energies and stacking fault energies for Pt and Au metals. The resulting potentials are used to map a 2D contour of the gamma surface and simulate the tensile test of 16-grain polycrystalline Pt and Au structures at 300 K. The stress-strain behaviour is investigated and the primary slip systems {1 1 1}〈1 [Formula: see text] 0〉 are identified. In addition, we perform high temperature (1800 K for Au and 2300 K for Pt) molecular dynamics simulations of 30 nm Pt and Au truncated octahedron nanoparticles and examine morphological changes of each particle. We further calculate the activation energy barrier for surface diffusion during simulations of several nanoseconds and report energies of [Formula: see text] eV for Pt and [Formula: see text] eV for Au. This initial parameterization and application of the Pt and Au potentials demonstrates a starting point for the extension of these potentials to multicomponent systems within the COMB3 framework.

Genetic differences in oestrous signs and oestrogen metabolism-related genes between Chinese Mi and European Landrace-Large White pigs

Oestrous signs affect timely mating and reproductive efficiency in swine breeding herds. To study the genetic difference of oestrous signs between Chinese and European pigs, 100 Landrace-Large White (LLW) cross gilts and 50 Chinese Mi gilts were assessed for oestrous signs and the concentrations of serum estradiol-17β and progesterone were determined. The genotype of 39 single nucleotide polymorphisms (SNPs) in 11 oestrogen metabolism and function-related genes was determined by Sequenom iPLEX platform. Compared with LLW gilts, Mi gilts had longer time of standing reflex (p < .001), higher scores of vulva reddening (p = .001) and greater serum estradiol-17β concentration (p < .01). Gilts with greater serum estradiol-17β concentrations also had greater (p < .05) scores for oestrous signs. Genetic polymorphisms of nine genes in oestrogen metabolism pathways had significant differences (p < .05) between LLW and Mi gilts. There were three and six haploblocks of SNPs in LLW and Mi, respectively. Compared with LLW, the distribution of haplotypes was more centralized in Mi pigs. Genetic polymorphisms of oestrogen metabolism-related genes have considerable differences between Chinese Mi and European LLW pigs. Because of the important roles of oestrogen during the oestrus, some genes of oestrogen metabolism pathway could be considered as candidate genes for oestrous signs.

RADIATION DOSE MEASUREMENTS FOR HIGH-INTENSITY LASER INTERACTIONS WITH SOLID TARGETS AT SLAC

A systematic study of photon and neutron radiation doses generated in high-intensity laser-solid interactions is underway at SLAC National Accelerator Laboratory. These laser-solid experiments are being performed using a 25 TW (up to 1 J in 40 fs) femtosecond pulsed Ti:sapphire laser at the Linac Coherent Light Source's (LCLS) Matter in Extreme Conditions (MEC) facility. Radiation measurements were performed with passive and active detectors deployed at various locations inside and outside the target chamber. Results from radiation dose measurements for laser-solid experiments at SLAC MEC in 2014 with peak intensity between 10¹⁸ and 7.1 × 10¹⁹ W cm^-2 are presented.

Long non-coding RNA HNF1A-AS1 up-regulation in non-small cell lung cancer correlates to poor survival

OBJECTIVE

Accumulating studies have focused on the role of the newly identified lncRNAs in the tumor. We aimed to investigate the clinical correlation between long non-coding RNA HNF1A-AS (HNF1A-AS1) expression and non-small cell lung cancer (NSCLC).

PATIENTS AND METHODS

Real-time polymerase chain reaction (PCR) was employed to detect HNF1A-AS expression in NSCLC tissues and corresponding adjacent tissues. The c2-test was used to compare the clinicopathological characteristics between different groups. Survival analysis was performed using the Kaplan-Meier method. The univariate and multivariate analyses were performed to investigate the prognostic significance of HNF1A-AS for NSCLC.

RESULTS

The level of HNF1A-AS was higher in tumor tissues than that in normal tissues (p < 0.01). In addition, HNF1A-AS level was significantly associated with TNM stage (p = 0.002) and Lymph node metastasis (p = 0.005). Kaplan-Meier analysis indicated that a high level of HNF1A-AS expression predicted unfavorable overall survival (p < 0.001). The univariate and multivariate analysis identified HNF1A-AS as an independent poor prognostic factor for overall survival in NSCLC patients (p < 0.05).

CONCLUSIONS

These results demonstrated that overexpression of HNF1A-AS might act a poor prognosis indicator in patients with NSCLC.

Detection of myasthenia gravis using electrooculography signals

Myasthenia gravis (MG) is an autoimmune neuromuscular disorder resulting from skeletal muscle weakness and fatigue. An early common symptom is fatigable weakness of the extrinsic ocular muscles; if symptoms remain confined to the ocular muscles after a few years, this is classified as ocular myasthenia gravis (OMG). Diagnosis of MG when there are mild, isolated ocular symptoms can be difficult, and currently available diagnostic techniques are insensitive, non-specific or technically cumbersome. In addition, there are no accurate biomarkers to follow severity of ocular dysfunction in MG over time. Single-fiber electromyography (SFEMG) and repetitive nerve stimulation (RNS) offers a way of detecting and measuring ocular muscle dysfunction in MG, however, challenges of these methods include a poor signal to noise ratio in quantifying eye muscle weakness especially in mild cases. This paper presents one of the attempts to use the electric potentials from the eyes or electrooculography (EOG) signals but obtained from three different forms of sleep testing to differentiate MG patients from age- and gender-matched controls. We analyzed 8 MG patients and 8 control patients and demonstrated a difference in the average eye movements detected between the groups. A classification accuracy as high as 68.8% was achieved using a linear discriminant analysis based classifier.

Human genome meeting 2016 : Houston, TX, USA. 28 February - 2 March 2016

O1 The metabolomics approach to autism: identification of biomarkers for early detection of autism spectrum disorder A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, T. Wood, F. Luo, R. Stevenson O2 Phenome-wide association study for smoking- and drinking-associated genes in 26,394 American women with African, Asian, European, and Hispanic descents R. Polimanti, J. Gelernter O3 Effects of prenatal environment, genotype and DNA methylation on birth weight and subsequent postnatal outcomes: findings from GUSTO, an Asian birth cohort X. Lin, I. Y. Lim, Y. Wu, A. L. Teh, L. Chen, I. M. Aris, S. E. Soh, M. T. Tint, J. L. MacIsaac, F. Yap, K. Kwek, S. M. Saw, M. S. Kobor, M. J. Meaney, K. M. Godfrey, Y. S. Chong, J. D. Holbrook, Y. S. Lee, P. D. Gluckman, N. Karnani, GUSTO study group O4 High-throughput identification of specific qt interval modulating enhancers at the SCN5A locus A. Kapoor, D. Lee, A. Chakravarti O5 Identification of extracellular matrix components inducing cancer cell migration in the supernatant of cultivated mesenchymal stem cells C. Maercker, F. Graf, M. Boutros O6 Single cell allele specific expression (ASE) IN T21 and common trisomies: a novel approach to understand DOWN syndrome and other aneuploidies G. Stamoulis, F. Santoni, P. Makrythanasis, A. Letourneau, M. Guipponi, N. Panousis, M. Garieri, P. Ribaux, E. Falconnet, C. Borel, S. E. Antonarakis O7 Role of microRNA in LCL to IPSC reprogramming S. Kumar, J. Curran, J. Blangero O8 Multiple enhancer variants disrupt gene regulatory network in Hirschsprung disease S. Chatterjee, A. Kapoor, J. Akiyama, D. Auer, C. Berrios, L. Pennacchio, A. Chakravarti O9 Metabolomic profiling for the diagnosis of neurometabolic disorders T. R. Donti, G. Cappuccio, M. Miller, P. Atwal, A. Kennedy, A. Cardon, C. Bacino, L. Emrick, J. Hertecant, F. Baumer, B. Porter, M. Bainbridge, P. Bonnen, B. Graham, R. Sutton, Q. Sun, S. Elsea O10 A novel causal methylation network approach to Alzheimer’s disease Z. Hu, P. Wang, Y. Zhu, J. Zhao, M. Xiong, David A Bennett O11 A microRNA signature identifies subtypes of triple-negative breast cancer and reveals MIR-342-3P as regulator of a lactate metabolic pathway A. Hidalgo-Miranda, S. Romero-Cordoba, S. Rodriguez-Cuevas, R. Rebollar-Vega, E. Tagliabue, M. Iorio, E. D’Ippolito, S. Baroni O12 Transcriptome analysis identifies genes, enhancer RNAs and repetitive elements that are recurrently deregulated across multiple cancer types B. Kaczkowski, Y. Tanaka, H. Kawaji, A. Sandelin, R. Andersson, M. Itoh, T. Lassmann, the FANTOM5 consortium, Y. Hayashizaki, P. Carninci, A. R. R. Forrest O13 Elevated mutation and widespread loss of constraint at regulatory and architectural binding sites across 11 tumour types C. A. Semple O14 Exome sequencing provides evidence of pathogenicity for genes implicated in colorectal cancer E. A. Rosenthal, B. Shirts, L. Amendola, C. Gallego, M. Horike-Pyne, A. Burt, P. Robertson, P. Beyers, C. Nefcy, D. Veenstra, F. Hisama, R. Bennett, M. Dorschner, D. Nickerson, J. Smith, K. Patterson, D. Crosslin, R. Nassir, N. Zubair, T. Harrison, U. Peters, G. Jarvik, NHLBI GO Exome Sequencing Project O15 The tandem duplicator phenotype as a distinct genomic configuration in cancer F. Menghi, K. Inaki, X. Woo, P. Kumar, K. Grzeda, A. Malhotra, H. Kim, D. Ucar, P. Shreckengast, K. Karuturi, J. Keck, J. Chuang, E. T. Liu O16 Modeling genetic interactions associated with molecular subtypes of breast cancer B. Ji, A. Tyler, G. Ananda, G. Carter O17 Recurrent somatic mutation in the MYC associated factor X in brain tumors H. Nikbakht, M. Montagne, M. Zeinieh, A. Harutyunyan, M. Mcconechy, N. Jabado, P. Lavigne, J. Majewski O18 Predictive biomarkers to metastatic pancreatic cancer treatment J. B. Goldstein, M. Overman, G. Varadhachary, R. Shroff, R. Wolff, M. Javle, A. Futreal, D. Fogelman O19 DDIT4 gene expression as a prognostic marker in several malignant tumors L. Bravo, W. Fajardo, H. Gomez, C. Castaneda, C. Rolfo, J. A. Pinto O20 Spatial organization of the genome and genomic alterations in human cancers K. C. Akdemir, L. Chin, A. Futreal, ICGC PCAWG Structural Alterations Group O21 Landscape of targeted therapies in solid tumors S. Patterson, C. Statz, S. Mockus O22 Genomic analysis reveals novel drivers and progression pathways in skin basal cell carcinoma S. N. Nikolaev, X. I. Bonilla, L. Parmentier, B. King, F. Bezrukov, G. Kaya, V. Zoete, V. Seplyarskiy, H. Sharpe, T. McKee, A. Letourneau, P. Ribaux, K. Popadin, N. Basset-Seguin, R. Ben Chaabene, F. Santoni, M. Andrianova, M. Guipponi, M. Garieri, C. Verdan, K. Grosdemange, O. Sumara, M. Eilers, I. Aifantis, O. Michielin, F. de Sauvage, S. Antonarakis O23 Identification of differential biomarkers of hepatocellular carcinoma and cholangiocarcinoma via transcriptome microarray meta-analysis S. Likhitrattanapisal O24 Clinical validity and actionability of multigene tests for hereditary cancers in a large multi-center study S. Lincoln, A. Kurian, A. Desmond, S. Yang, Y. Kobayashi, J. Ford, L. Ellisen O25 Correlation with tumor ploidy status is essential for correct determination of genome-wide copy number changes by SNP array T. L. Peters, K. R. Alvarez, E. F. Hollingsworth, D. H. Lopez-Terrada O26 Nanochannel based next-generation mapping for interrogation of clinically relevant structural variation A. Hastie, Z. Dzakula, A. W. Pang, E. T. Lam, T. Anantharaman, M. Saghbini, H. Cao, BioNano Genomics O27 Mutation spectrum in a pulmonary arterial hypertension (PAH) cohort and identification of associated truncating mutations in TBX4 C. Gonzaga-Jauregui, L. Ma, A. King, E. Berman Rosenzweig, U. Krishnan, J. G. Reid, J. D. Overton, F. Dewey, W. K. Chung O28 NORTH CAROLINA macular dystrophy (MCDR1): mutations found affecting PRDM13 K. Small, A. DeLuca, F. Cremers, R. A. Lewis, V. Puech, B. Bakall, R. Silva-Garcia, K. Rohrschneider, M. Leys, F. S. Shaya, E. Stone O29 PhenoDB and genematcher, solving unsolved whole exome sequencing data N. L. Sobreira, F. Schiettecatte, H. Ling, E. Pugh, D. Witmer, K. Hetrick, P. Zhang, K. Doheny, D. Valle, A. Hamosh O30 Baylor-Johns Hopkins Center for Mendelian genomics: a four year review S. N. Jhangiani, Z. Coban Akdemir, M. N. Bainbridge, W. Charng, W. Wiszniewski, T. Gambin, E. Karaca, Y. Bayram, M. K. Eldomery, J. Posey, H. Doddapaneni, J. Hu, V. R. Sutton, D. M. Muzny, E. A. Boerwinkle, D. Valle, J. R. Lupski, R. A. Gibbs O31 Using read overlap assembly to accurately identify structural genetic differences in an ashkenazi jewish trio S. Shekar, W. Salerno, A. English, A. Mangubat, J. Bruestle O32 Legal interoperability: a sine qua non for international data sharing A. Thorogood, B. M. Knoppers, Global Alliance for Genomics and Health - Regulatory and Ethics Working Group O33 High throughput screening platform of competent sineups: that can enhance translation activities of therapeutic target H. Takahashi, K. R. Nitta, A. Kozhuharova, A. M. Suzuki, H. Sharma, D. Cotella, C. Santoro, S. Zucchelli, S. Gustincich, P. Carninci O34 The undiagnosed diseases network international (UDNI): clinical and laboratory research to meet patient needs J. J. Mulvihill, G. Baynam, W. Gahl, S. C. Groft, K. Kosaki, P. Lasko, B. Melegh, D. Taruscio O36 Performance of computational algorithms in pathogenicity predictions for activating variants in oncogenes versus loss of function mutations in tumor suppressor genes R. Ghosh, S. Plon O37 Identification and electronic health record incorporation of clinically actionable pharmacogenomic variants using prospective targeted sequencing S. Scherer, X. Qin, R. Sanghvi, K. Walker, T. Chiang, D. Muzny, L. Wang, J. Black, E. Boerwinkle, R. Weinshilboum, R. Gibbs O38 Melanoma reprogramming state correlates with response to CTLA-4 blockade in metastatic melanoma T. Karpinets, T. Calderone, K. Wani, X. Yu, C. Creasy, C. Haymaker, M. Forget, V. Nanda, J. Roszik, J. Wargo, L. Haydu, X. Song, A. Lazar, J. Gershenwald, M. Davies, C. Bernatchez, J. Zhang, A. Futreal, S. Woodman O39 Data-driven refinement of complex disease classification from integration of heterogeneous functional genomics data in GeneWeaver E. J. Chesler, T. Reynolds, J. A. Bubier, C. Phillips, M. A. Langston, E. J. Baker O40 A general statistic framework for genome-based disease risk prediction M. Xiong, L. Ma, N. Lin, C. Amos O41 Integrative large-scale causal network analysis of imaging and genomic data and its application in schizophrenia studies N. Lin, P. Wang, Y. Zhu, J. Zhao, V. Calhoun, M. Xiong O42 Big data and NGS data analysis: the cloud to the rescue O. Dobretsberger, M. Egger, F. Leimgruber O43 Cpipe: a convergent clinical exome pipeline specialised for targeted sequencing S. Sadedin, A. Oshlack, Melbourne Genomics Health Alliance O44 A Bayesian classification of biomedical images using feature extraction from deep neural networks implemented on lung cancer data V. A. A. Antonio, N. Ono, Clark Kendrick C. Go O45 MAV-SEQ: an interactive platform for the Management, Analysis, and Visualization of sequence data Z. Ahmed, M. Bolisetty, S. Zeeshan, E. Anguiano, D. Ucar O47 Allele specific enhancer in EPAS1 intronic regions may contribute to high altitude adaptation of Tibetans C. Zeng, J. Shao O48 Nanochannel based next-generation mapping for structural variation detection and comparison in trios and populations H. Cao, A. Hastie, A. W. Pang, E. T. Lam, T. Liang, K. Pham, M. Saghbini, Z. Dzakula O49 Archaic introgression in indigenous populations of Malaysia revealed by whole genome sequencing Y. Chee-Wei, L. Dongsheng, W. Lai-Ping, D. Lian, R. O. Twee Hee, Y. Yunus, F. Aghakhanian, S. S. Mokhtar, C. V. Lok-Yung, J. Bhak, M. Phipps, X. Shuhua, T. Yik-Ying, V. Kumar, H. Boon-Peng O50 Breast and ovarian cancer prevention: is it time for population-based mutation screening of high risk genes? I. Campbell, M.-A. Young, P. James, Lifepool O53 Comprehensive coverage from low DNA input using novel NGS library preparation methods for WGS and WGBS C. Schumacher, S. Sandhu, T. Harkins, V. Makarov O54 Methods for large scale construction of robust PCR-free libraries for sequencing on Illumina HiSeqX platform H. DoddapaneniR. Glenn, Z. Momin, B. Dilrukshi, H. Chao, Q. Meng, B. Gudenkauf, R. Kshitij, J. Jayaseelan, C. Nessner, S. Lee, K. Blankenberg, L. Lewis, J. Hu, Y. Han, H. Dinh, S. Jireh, K. Walker, E. Boerwinkle, D. Muzny, R. Gibbs O55 Rapid capture methods for clinical sequencing J. Hu, K. Walker, C. Buhay, X. Liu, Q. Wang, R. Sanghvi, H. Doddapaneni, Y. Ding, N. Veeraraghavan, Y. Yang, E. Boerwinkle, A. L. Beaudet, C. M. Eng, D. M. Muzny, R. A. Gibbs O56 A diploid personal human genome model for better genomes from diverse sequence data K. C. C. Worley, Y. Liu, D. S. T. Hughes, S. C. Murali, R. A. Harris, A. C. English, X. Qin, O. A. Hampton, P. Larsen, C. Beck, Y. Han, M. Wang, H. Doddapaneni, C. L. Kovar, W. J. Salerno, A. Yoder, S. Richards, J. Rogers, J. R. Lupski, D. M. Muzny, R. A. Gibbs O57 Development of PacBio long range capture for detection of pathogenic structural variants Q. Meng, M. Bainbridge, M. Wang, H. Doddapaneni, Y. Han, D. Muzny, R. Gibbs O58 Rhesus macaques exhibit more non-synonymous variation but greater impact of purifying selection than humans R. A. Harris, M. Raveenedran, C. Xue, M. Dahdouli, L. Cox, G. Fan, B. Ferguson, J. Hovarth, Z. Johnson, S. Kanthaswamy, M. Kubisch, M. Platt, D. Smith, E. Vallender, R. Wiseman, X. Liu, J. Below, D. Muzny, R. Gibbs, F. Yu, J. Rogers O59 Assessing RNA structure disruption induced by single-nucleotide variation J. Lin, Y. Zhang, Z. Ouyang P1 A meta-analysis of genome-wide association studies of mitochondrial dna copy number A. Moore, Z. Wang, J. Hofmann, M. Purdue, R. Stolzenberg-Solomon, S. Weinstein, D. Albanes, C.-S. Liu, W.-L. Cheng, T.-T. Lin, Q. Lan, N. Rothman, S. Berndt P2 Missense polymorphic genetic combinations underlying down syndrome susceptibility E. S. Chen P4 The evaluation of alteration of ELAM-1 expression in the endometriosis patients H. Bahrami, A. Khoshzaban, S. Heidari Keshal P5 Obesity and the incidence of apolipoprotein E polymorphisms in an assorted population from Saudi Arabia population K. K. R. Alharbi P6 Genome-associated personalized antithrombotical therapy for patients with high risk of thrombosis and bleeding M. Zhalbinova, A. Akilzhanova, S. Rakhimova, M. Bekbosynova, S. Myrzakhmetova P7 Frequency of Xmn1 polymorphism among sickle cell carrier cases in UAE population M. Matar P8 Differentiating inflammatory bowel diseases by using genomic data: dimension of the problem and network organization N. Mili, R. Molinari, Y. Ma, S. Guerrier P9 Vulnerability of genetic variants to the risk of autism among Saudi children N. Elhawary, M. Tayeb, N. Bogari, N. Qotb P10 Chromatin profiles from ex vivo purified dopaminergic neurons establish a promising model to support studies of neurological function and dysfunction S. A. McClymont, P. W. Hook, L. A. Goff, A. McCallion P11 Utilization of a sensitized chemical mutagenesis screen to identify genetic modifiers of retinal dysplasia in homozygous Nr2e3^rd7 mice Y. Kong, J. R. Charette, W. L. Hicks, J. K. Naggert, L. Zhao, P. M. Nishina P12 Ion torrent next generation sequencing of recessive polycystic kidney disease in Saudi patients B. M. Edrees, M. Athar, F. A. Al-Allaf, M. M. Taher, W. Khan, A. Bouazzaoui, N. A. Harbi, R. Safar, H. Al-Edressi, A. Anazi, N. Altayeb, M. A. Ahmed, K. Alansary, Z. Abduljaleel P13 Digital expression profiling of Purkinje neurons and dendrites in different subcellular compartments A. Kratz, P. Beguin, S. Poulain, M. Kaneko, C. Takahiko, A. Matsunaga, S. Kato, A. M. Suzuki, N. Bertin, T. Lassmann, R. Vigot, P. Carninci, C. Plessy, T. Launey P14 The evolution of imperfection and imperfection of evolution: the functional and functionless fractions of the human genome D. Graur P16 Species-independent identification of known and novel recurrent genomic entities in multiple cancer patients J. Friis-Nielsen, J. M. Izarzugaza, S. Brunak P18 Discovery of active gene modules which are densely conserved across multiple cancer types reveal their prognostic power and mutually exclusive mutation patterns B. S. Soibam P19 Whole exome sequencing of dysplastic leukoplakia tissue indicates sequential accumulation of somatic mutations from oral precancer to cancer D. Das, N. Biswas, S. Das, S. Sarkar, A. Maitra, C. Panda, P. Majumder P21 Epigenetic mechanisms of carcinogensis by hereditary breast cancer genes J. J. Gruber, N. Jaeger, M. Snyder P22 RNA direct: a novel RNA enrichment strategy applied to transcripts associated with solid tumors K. Patel, S. Bowman, T. Davis, D. Kraushaar, A. Emerman, S. Russello, N. Henig, C. Hendrickson P23 RNA sequencing identifies gene mutations for neuroblastoma K. Zhang P24 Participation of SFRP1 in the modulation of TMPRSS2-ERG fusion gene in prostate cancer cell lines M. Rodriguez-Dorantes, C. D. Cruz-Hernandez, C. D. P. Garcia-Tobilla, S. Solorzano-Rosales P25 Targeted Methylation Sequencing of Prostate Cancer N. Jäger, J. Chen, R. Haile, M. Hitchins, J. D. Brooks, M. Snyder P26 Mutant TPMT alleles in children with acute lymphoblastic leukemia from México City and Yucatán, Mexico S. Jiménez-Morales, M. Ramírez, J. Nuñez, V. Bekker, Y. Leal, E. Jiménez, A. Medina, A. Hidalgo, J. Mejía P28 Genetic modifiers of Alström syndrome J. Naggert, G. B. Collin, K. DeMauro, R. Hanusek, P. M. Nishina P31 Association of genomic variants with the occurrence of angiotensin-converting-enzyme inhibitor (ACEI)-induced coughing among Filipinos E. M. Cutiongco De La Paz, R. Sy, J. Nevado, P. Reganit, L. Santos, J. D. Magno, F. E. Punzalan , D. Ona , E. Llanes, R. L. Santos-Cortes , R. Tiongco, J. Aherrera, L. Abrahan, P. Pagauitan-Alan; Philippine Cardiogenomics Study Group P32 The use of “humanized” mouse models to validate disease association of a de novo GARS variant and to test a novel gene therapy strategy for Charcot-Marie-Tooth disease type 2D K. H. Morelli, J. S. Domire, N. Pyne, S. Harper, R. Burgess P34 Molecular regulation of chondrogenic human induced pluripotent stem cells M. A. Gari, A. Dallol, H. Alsehli, A. Gari, M. Gari, A. Abuzenadah P35 Molecular profiling of hematologic malignancies: implementation of a variant assessment algorithm for next generation sequencing data analysis and clinical reporting M. Thomas, M. Sukhai, S. Garg, M. Misyura, T. Zhang, A. Schuh, T. Stockley, S. Kamel-Reid P36 Accessing genomic evidence for clinical variants at NCBI S. Sherry, C. Xiao, D. Slotta, K. Rodarmer, M. Feolo, M. Kimelman, G. Godynskiy, C. O’Sullivan, E. Yaschenko P37 NGS-SWIFT: a cloud-based variant analysis framework using control-accessed sequencing data from DBGAP/SRA C. Xiao, E. Yaschenko, S. Sherry P38 Computational assessment of drug induced hepatotoxicity through gene expression profiling C. Rangel-Escareño, H. Rueda-Zarate P40 Flowr: robust and efficient pipelines using a simple language-agnostic approach;ultraseq; fast modular pipeline for somatic variation calling using flowr S. Seth, S. Amin, X. Song, X. Mao, H. Sun, R. G. Verhaak, A. Futreal, J. Zhang P41 Applying “Big data” technologies to the rapid analysis of heterogenous large cohort data S. J. Whiite, T. Chiang, A. English, J. Farek, Z. Kahn, W. Salerno, N. Veeraraghavan, E. Boerwinkle, R. Gibbs P42 FANTOM5 web resource for the large-scale genome-wide transcription start site activity profiles of wide-range of mammalian cells T. Kasukawa, M. Lizio, J. Harshbarger, S. Hisashi, J. Severin, A. Imad, S. Sahin, T. C. Freeman, K. Baillie, A. Sandelin, P. Carninci, A. R. R. Forrest, H. Kawaji, The FANTOM Consortium P43 Rapid and scalable typing of structural variants for disease cohorts W. Salerno, A. English, S. N. Shekar, A. Mangubat, J. Bruestle, E. Boerwinkle, R. A. Gibbs P44 Polymorphism of glutathione S-transferases and sulphotransferases genes in an Arab population A. H. Salem, M. Ali, A. Ibrahim, M. Ibrahim P46 Genetic divergence of CYP3A5*3 pharmacogenomic marker for native and admixed Mexican populations J. C. Fernandez-Lopez, V. Bonifaz-Peña, C. Rangel-Escareño, A. Hidalgo-Miranda, A. V. Contreras P47 Whole exome sequence meta-analysis of 13 white blood cell, red blood cell, and platelet traits L. Polfus, CHARGE and NHLBI Exome Sequence Project Working Groups P48 Association of adipoq gene with type 2 diabetes and related phenotypes in african american men and women: The jackson heart study S. Davis, R. Xu, S. Gebeab, P Riestra, A Gaye, R. Khan, J. Wilson, A. Bidulescu P49 Common variants in casr gene are associated with serum calcium levels in koreans S. H. Jung, N. Vinayagamoorthy, S. H. Yim, Y. J. Chung P50 Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with multiple exponential functions Y. Zhou, S. Xu P51 A Bayesian framework for generalized linear mixed models in genome-wide association studies X. Wang, V. Philip, G. Carter P52 Targeted sequencing approach for the identification of the genetic causes of hereditary hearing impairment A. A. Abuzenadah, M. Gari, R. Turki, A. Dallol P53 Identification of enhancer sequences by ATAC-seq open chromatin profiling A. Uyar, A. Kaygun, S. Zaman, E. Marquez, J. George, D. Ucar P54 Direct enrichment for the rapid preparation of targeted NGS libraries C. L. Hendrickson, A. Emerman, D. Kraushaar, S. Bowman, N. Henig, T. Davis, S. Russello, K. Patel P56 Performance of the Agilent D5000 and High Sensitivity D5000 ScreenTape assays for the Agilent 4200 Tapestation System R. Nitsche, L. Prieto-Lafuente P57 ClinVar: a multi-source archive for variant interpretation M. Landrum, J. Lee, W. Rubinstein, D. Maglott P59 Association of functional variants and protein physical interactions of human MUTY homolog linked with familial adenomatous polyposis and colorectal cancer syndrome Z. Abduljaleel, W. Khan, F. A. Al-Allaf, M. Athar , M. M. Taher, N. Shahzad P60 Modification of the microbiom constitution in the gut using chicken IgY antibodies resulted in a reduction of acute graft-versus-host disease after experimental bone marrow transplantation A. Bouazzaoui, E. Huber, A. Dan, F. A. Al-Allaf, W. Herr, G. Sprotte, J. Köstler, A. Hiergeist, A. Gessner, R. Andreesen, E. Holler P61 Compound heterozygous mutation in the LDLR gene in Saudi patients suffering severe hypercholesterolemia F. Al-Allaf, A. Alashwal, Z. Abduljaleel, M. Taher, A. Bouazzaoui, H. Abalkhail, A. Al-Allaf, R. Bamardadh, M. Athar

Sn-doped Bi1.1Sb0.9Te2S bulk crystal topological insulator with excellent properties

A long-standing issue in topological insulator research has been to find a bulk single crystal material that provides a high-quality platform for characterizing topological surface states without interference from bulk electronic states. This material would ideally be a bulk insulator, have a surface state Dirac point energy well isolated from the bulk valence and conduction bands, display quantum oscillations from the surface state electrons and be growable as large, high-quality bulk single crystals. Here we show that this material obstacle is overcome by bulk crystals of lightly Sn-doped Bi_1.1Sb_0.9Te₂S grown by the vertical Bridgman method. We characterize Sn-BSTS via angle-resolved photoemission spectroscopy, scanning tunnelling microscopy, transport studies, X-ray diffraction and Raman scattering. We present this material as a high-quality topological insulator that can be reliably grown as bulk single crystals and thus studied by many researchers interested in topological surface states.

An ideal topological insulator possesses an insulating bulk and a unique conducting surface however such behaviour is typically inhibited by bulk conduction due to defects. Here, the authors show that Sn-doped Bi_1.1Sb_0.9Te₂S grown by the vertical Bridgman technique might overcome this hurdle.

A Genetic Animal Model of Alcoholism for Screening Medications to Treat Addiction

The purpose of this review is to present up-to-date pharmacological, genetic, and behavioral findings from the alcohol-preferring P rat and summarize similar past work. Behaviorally, the focus will be on how the P rat meets criteria put forth for a valid animal model of alcoholism with a highlight on its use as an animal model of polysubstance abuse, including alcohol, nicotine, and psychostimulants. Pharmacologically and genetically, the focus will be on the neurotransmitter and neuropeptide systems that have received the most attention: cholinergic, dopaminergic, GABAergic, glutamatergic, serotonergic, noradrenergic, corticotrophin releasing hormone, opioid, and neuropeptide Y. Herein, we sought to place the P rat's behavioral and neurochemical phenotypes, and to some extent its genotype, in the context of the clinical literature. After reviewing the findings thus far, this chapter discusses future directions for expanding the use of this genetic animal model of alcoholism to identify molecular targets for treating drug addiction in general.

STAT3 selectively interacts with Smad3 to antagonize TGF-β signalling

Smad and STAT proteins are critical signal transducers and transcription factors in controlling cell growth and tumorigenesis. Here we report that the STAT3 signaling pathway attenuates TGF-β-induced responses through a direct Smad3-STAT3 interplay. Activated STAT3 blunts TGF-β-mediated signaling. Depletion of STAT3 promotes TGF-β-mediated transcriptional and physiological responses, including cell cycle arrest, apoptosis and epithelial-to-mesenchymal transition. STAT3 directly interacts with Smad3 in vivo and in vitro, resulting in attenuation of the Smad3-Smad4 complex formation and suppression of DNA-binding ability of Smad3. The N-terminal region of DNA-binding domain of STAT3 is responsible for the STAT3-Smad3 interaction and also indispensable for STAT3-mediated inhibition of TGF-β signaling. Thus, our finding illustrates a direct crosstalk between the STAT3 and Smad3 signaling pathways that may contribute to tumor development and inflammation.

In vivo Toll-like receptor 5 (TLR5) imaging with radiolabeled anti-TLR5 monoclonal antibody in rapamycin-treated mouse allogeneic skin transplantation model

BACKGROUND

In organ transplantation, increasing evidence, both in experimental and human studies, indicates that Toll-like receptor (TLR) activation is involved in the innate immune recognition of allograft. TLR5, the only protein recognition receptor of TLRs, is indicated potentially to be the immune regulation target. This study was designed to determine whether TLR5 could be a biomarker for in vivo allograft visualization, after immunosuppressant rapamycin treatment, using radiolabeled sodium iodide ((131) I)-anti-TLR5 monoclonal antibody (mAb).

METHODS

BALB/c mice were transplanted with C57BL/6 skin, with/without rapamycin treatment (the rapamycin-treated group and the phosphate buffered saline [PBS]-rejection group, respectively). In vivo dynamic whole-body phosphor-autoradiography and ex vivo biodistribution studies were conducted after (131) I-anti-TLR5 mAb injection.

RESULTS

Dynamic phosphor-autoradiography imaging showed clear graft localization from 12 h onward. At 72 h after injection, graft uptake quantified from images was higher for the rapamycin-treated group (26,448 ± 904 digital light units [DLU]/mm(2) ), compared with the PBS-treated allo-rejection group (9176 ± 576 DLU/mm(2) ). Treatment with anti-TLR5 mAb inhibited graft uptake. Organ biodistribution study reflected the same tendency, and (131) I-anti-TLR5 mAb uptake reached a maximum of 12.05 ± 1.86 %ID/g (percent injected dose per gram) at 1 h, and graft-to-native skin ratio reached 8.10 ± 0.10 %ID/g at 72 h after injection in rapamycin-treated grafts.

CONCLUSION

Radiolabeled anti-TLR5 mAb showed higher uptake in allo-treated grafts compared with allo-rejection grafts, which was proved by non-invasive dynamic phosphor-autoradiography imaging, and invasive ex vivo biodistribution. Radiolabeled anti-TLR5 mAb is a new tracer for non-invasive in vivo imaging of TLR5 in rapamycin-treated allograft.

High pitch, low voltage dual source CT pulmonary angiography: assessment of image quality and diagnostic acceptability with hybrid iterative reconstruction

Increased use of CT Pulmonary angiography in suspected pulmonary embolism (PE) has driven research to minimize radiation dose while maintaining image quality and diagnostic accuracy. Following institutional review board approval, we performed a retrospective comparison study in patients with suspected PE. Patients were scanned using an ultra high pitch dual source technique (pitch = 2.6) using 120 kV (SVCTPA) (n = 54) or 100 kV (RV-CTPA) (n = 52). SV-CTPA images were reconstructed using filtered back projection (SV-wFBP) and RV-CTPA images were reconstructed using both FBP (RV-wFBP) and Iterative Reconstruction (RV-IR). Comparison of radiation dose, diagnostic ability, subjective image noise, quality, and sharpness, diagnostic agreement, signal to noise (SNR) and contrast to noise ratios (CNR) were performed. Mean effective dose was 2.56 ± 0.19 mSv for the RV protocol compared to 5.36 ± 0.60 mSv for the SV. The RV-CTPA protocol resulted in a mean DLP reduction of 52 % and mean CTDI reduction of 51 %. Pulmonary artery SNR and CNR were significantly higher on RV-IR images than SV-wFBP (p = 0.007, p = 0.003). Mean subjective image noise, quality and sharpness scores did not differ significantly between the SV-wFBP and RVIR images (p > 0.05). Subjective quality scores were significantly better for the RV-IR group compared to the RV-wFBP group (p < 0.001). Agreement between readers for presence or absence of pulmonary emboli on RV-IR images was almost perfect (κ = 0.891, p < 0.001). Iterative reconstruction complements ultra high pitch dual source CTPA examinations acquired using a reduced voltage resulting in higher mean pulmonary artery SNR and CNR when compared to both RV-wFBP and SV-CTPA.

A charge optimized many-body potential for titanium nitride (TiN)

This work presents a new empirical, variable charge potential for TiN systems in the charge-optimized many-body potential framework. The potential parameters were determined by fitting them to experimental data for the enthalpy of formation, lattice parameters, and elastic constants of rocksalt structured TiN. The potential does a good job of describing the fundamental physical properties (defect formation and surface energies) of TiN relative to the predictions of first-principles calculations. This potential is used in classical molecular dynamics simulations to examine the interface of fcc-Ti(0 0 1)/TiN(0 0 1) and to characterize the adsorption of oxygen atoms and molecules on the TiN(0 0 1) surface. The results indicate that the potential is well suited to model TiN thin films and to explore the chemistry associated with their oxidation.

Superconducting properties and electronic structure of NaBi

Resistivity, dc magnetization, and heat capacity measurements are reported for superconducting NaBi. T(c), the electronic contribution to the specific heat γ, the ΔC(p)/γT(c) ratio, and the Debye temperature are found to be 2.15 K, 3.4 mJ mol(-1) K(-2), 0.78, and 140 K respectively. The calculated electron-phonon coupling constant (λ(ep) = 0.62) implies that NaBi is a moderately coupled superconductor. The upper critical field and coherence length are found to be 250 Oe and 115 nm, respectively. Electronic structure calculations show NaBi to be a good metal, in agreement with the experiments; the p(x) and p(y) orbitals of Bi dominate the electronic states at the Fermi Energy.

A review of various techniques of mouse liver transplantation

OBJECTIVES

Liver transplantation in a mouse model is a valuable tool for studying transplantation immunobiology and clinic-relevant issues. However, the successful establishment is highly technical and demanding, impeding its widespread use. Herein, the aims of this study were to review and analyze the various techniques of liver transplantation in mice to circumvent pitfalls and minimize the incidence of complications.

MATERIALS AND METHODS

A search of PubMed was made by using the key words "mouse liver transplantation" for articles published between January 1973 and July 2012. Of the 473 publications identified, 14 were shown to be closely associated with mouse liver transplantation and 4 articles discussed specific microsurgical techniques. Through reviewing these articles, a series of potential factors were collected and analyzed in combination with other murine transplantation models, which might influence successfully establishing a mouse model for liver transplantation.

RESULTS

A mouse liver transplantation model is feasible and practical for experimental studies. Mouse strain, type of anesthesia, type of perfusion and storage solution, and reconstruction of bile duct are relevant factors but not determinants for a successful transplantation. Cold and warm ischemia time should be less than 4.0 hours and 20 minutes, respectively.

CONCLUSIONS

The cuff preparation, reconstruction of the hepatic artery, and length of the anhepatic phase play critical roles in successfully establishing a liver transplantation model in mice.