Deep learning-based fully automatic screening of carotid artery plaques in computed tomography angiography: a multicenter study

AIM

To develop and validate a deep learning (DL) algorithm for the automated detection and classification of carotid artery plaques (CAPs) on computed tomography angiography (CTA) images.

MATERIALS AND METHODS

This retrospective study enrolled 400 patients (300 in the Center Ⅰ and 100 in Ⅱ). Three radiologists co-labeled CAPs, and their revised calcification status (noncalcified, mixed, and calcified) was regarded as ground truth. Center Ⅰ patients were randomly divided into training and internal validation datasets, while Center Ⅱ patients served as the external validation dataset. Carotid artery regions were segmented using a modified 3D-UNet network, followed by CAPs detection and classification using a ResUNet-based architecture in a two-step DL system. The DL model's detection and classification performance were evaluated on the validation dataset using precision-recall curve, free-response receiver operating characteristic (fROC) curve, Cohen's kappa, and ROC curve analysis.

RESULTS

The DL model had achieved 83.4% sensitivity at 3.0 false positives (FPs)/CTA scan in internal validation and 78.9% in external validation. F1-scores were 0.764 and 0.769 at the optimal threshold, and area under fROC curves were 0.756 and 0.738, respectively, indicating good overall accuracy for CAP detection. The DL model also showed good performance for the ternary classification of CAPs, with Cohen's kappa achieved 0.728 and 0.703 in both validation datasets.

CONCLUSION

This study demonstrated the feasibility of using a fully automated DL-based algorithm for the detection and ternary classification of CAPs, which could be helpful for the workloads of radiologists.

TSPAN8+ myofibroblastic cancer-associated fibroblasts promote chemoresistance in patients with breast cancer

Cancer-associated fibroblasts (CAFs) are abundant stromal cells in the tumor microenvironment that promote cancer progression and relapse. However, the heterogeneity and regulatory roles of CAFs underlying chemoresistance remain largely unclear. Here, we performed a single-cell analysis using high-dimensional flow cytometry analysis and identified a distinct senescence-like tetraspanin-8 (TSPAN8)+ myofibroblastic CAF (myCAF) subset, which is correlated with therapeutic resistance and poor survival in multiple cohorts of patients with breast cancer (BC). TSPAN8+ myCAFs potentiate the stemness of the surrounding BC cells through secretion of senescence-associated secretory phenotype (SASP)-related factors IL-6 and IL-8 to counteract chemotherapy. NAD-dependent protein deacetylase sirtuin 6 (SIRT6) reduction was responsible for the senescence-like phenotype and tumor-promoting role of TSPAN8+ myCAFs. Mechanistically, TSPAN8 promoted the phosphorylation of ubiquitin E3 ligase retinoblastoma binding protein 6 (RBBP6) at Ser772 by recruiting MAPK11, thereby inducing SIRT6 protein destruction. In turn, SIRT6 down-regulation up-regulated GLS1 and PYCR1, which caused TSPAN8+ myCAFs to secrete aspartate and proline, and therefore proved a nutritional niche to support BC outgrowth. By demonstrating that TSPAN8+SIRT6low myCAFs were tightly associated with unfavorable disease outcomes, we proposed that the combined regimen of anti-TSPAN8 antibody and SIRT6 activator MDL-800 is a promising approach to overcome chemoresistance. These findings highlight that senescence contributes to CAF heterogeneity and chemoresistance and suggest that targeting TSPAN8+ myCAFs is a promising approach to circumvent chemoresistance.

Identifying critical genes and pathways of doxorubicin-induced cardiomyopathy via bioinformatics analysis

OBJECTIVE

The pathogenesis of doxorubicin (DOX) induced cardiomyopathy (DCM) is still uncertain. We aimed to identify the critical genes and pathways involved in DCM based on bioinformatics analysis.

MATERIALS AND METHODS

The GSE59672 and GSE23598 mice heart tissue microarray data were obtained from Gene Expression Omnibus (GEO) database. The "limma" package of R software was used to screen the differently expressed genes (DEGs). GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses were performed on DEGs by using "clusterProfiler" package in R software. The PPI (Protein - Protein Interaction) network of DEGs constructed by STRING online database and thereby the top 15 hub genes selected by cytoHubba in Cytoscape software. The hub genes interaction was performed by GeneMANIA online database. The "Corrplot" R package was employed to assess hub genes correlation.

RESULTS

Finally, a total of 492 and 501 DEGs were screened in GSE59672 and GSE23598 datasets, respectively. GO analyses revealed that DEGs were mainly involved in the regulation of extracellular matrix organization, metabolic process, regulation of collagen-containing extracellular matrix. KEGG pathway analyses indicated that DEGs were mainly involved in protein digestion and absorption, ECM-receptor interaction, phagosome, and p53 signaling pathway. Finally, the 8 hub genes were identified, including Col1a1, Col3a1, Col1a2, Col6a1, Ptprc, Tyrobp, Itgb2, and Ctss.

CONCLUSIONS

The present study identified a series of key genes, including Col1a1, Col3a1, Col1a2, Col6a1, Ptprc, Tyrobp, Itgb2, and Ctss. In addition, important pathways were also discovered. The results of this study may provide a novel molecular mechanism and potential therapeutic targets for DCM.

CPT1A mediates chemoresistance in human hypopharyngeal squamous cell carcinoma via ATG16L1-dependent cellular autophagy

Hypopharyngeal squamous cell carcinoma (HSCC) is a highly aggressive malignancy that constitutes approximately 95% of all hypopharyngeal carcinomas, and it carries a poor prognosis. The primary factor influencing the efficacy of anti-cancer drugs for this type of carcinoma is chemoresistance. Carnitine palmitoyltransferase 1A (CPT1A) has been associated with tumor progression in various cancers, including breast, gastric, lung, and prostate cancer. The inhibition or depletion of CPT1A can lead to apoptosis, curbing cancer cell proliferation and chemoresistance. However, the role of CPT1A in HSCC is not yet fully understood. In this study, we discovered that CPT1A is highly expressed in HSCC and is associated with an advanced T-stage and a poor 5-year survival rate among patients. Furthermore, the overexpression of CPT1A contributes to HSCC chemoresistance. Mechanistically, CPT1A can interact with the autophagy-related protein ATG16L1 and stimulate the succinylation of ATG16L1, which in turn drives autophagosome formation and autophagy. We also found that treatment with 3-methyladenine (3-MA) can reduce cisplatin resistance in HSCC cells that overexpress CPT1A. Our findings also showed that a CPT1A inhibitor significantly enhances cisplatin sensitivity both in vitro and in vivo. This study is the first to suggest that CPT1A has a regulatory role in autophagy and is linked to poor prognosis in HSCC patients. It presents novel insights into the roles of CPT1A in tumorigenesis and proposes that CPT1A could be a potential therapeutic target for HSCC treatment.

Lactylation of METTL16 promotes cuproptosis via m6A-modification on FDX1 mRNA in gastric cancer

Cuproptosis, caused by excessively high copper concentrations, is urgently exploited as a potential cancer therapeutic. However, the mechanisms underlying the initiation, propagation, and ultimate execution of cuproptosis in tumors remain unknown. Here, we show that copper content is significantly elevated in gastric cancer (GC), especially in malignant tumors. Screening reveals that METTL16, an atypical methyltransferase, is a critical mediator of cuproptosis through the m6A modification on FDX1 mRNA. Furthermore, copper stress promotes METTL16 lactylation at site K229 followed by cuproptosis. The process of METTL16 lactylation is inhibited by SIRT2. Elevated METTL16 lactylation significantly improves the therapeutic efficacy of the copper ionophore- elesclomol. Combining elesclomol with AGK2, a SIRT2-specific inhibitor, induce cuproptosis in gastric tumors in vitro and in vivo. These results reveal the significance of non-histone protein METTL16 lactylation on cuproptosis in tumors. Given the high copper and lactate concentrations in GC, cuproptosis induction becomes a promising therapeutic strategy for GC.

Development and validation of a multiphase CT radiomics nomogram for the preoperative prediction of lymphovascular invasion in patients with gastric cancer

AIM

To develop a nomogram to predict lymphovascular invasion (LVI) in gastric cancer by integrating multiphase computed tomography (CT) radiomics and clinical risk factors.

MATERIALS AND METHODS

One hundred and seventy-two gastric cancer patients (121 training and 51 validation) with preoperative contrast-enhanced CT images and clinicopathological data were collected retrospectively. The clinical risk factors were selected by univariate and multivariate regression analysis. Radiomic features were extracted and selected from the arterial phase (AP), venous phase (VP), and delayed phase (DP) CT images of each patient. Clinical risk factors, radiomic features, and integration of both were used to develop the clinical model, radiomic models, and nomogram, respectively.

RESULTS

Radiomic features from AP (n=6), VP (n=6), DP (n=7) CT images and three selected clinical risk factors were used for model development. The nomogram showed better performance than the AP, VP, DP, and clinical models in the training and validation datasets, providing areas under the curves (AUCs) of 0.890 (95% CI: 0.820-0.940) and 0.885 (95% CI:0.765-0.957), respectively. All models indicated good calibration, and decision curve analysis proved that the net benefit of the nomogram was superior to that of the clinical and radiomic models throughout the vast majority of the threshold probabilities.

CONCLUSIONS

The nomogram integrating multiphase CT radiomics and clinical risk factors showed favourable performance in predicting LVI of gastric cancer, which may benefit clinical practice.

TBMaLT, a flexible toolkit for combining tight-binding and machine learning

Tight-binding approaches, especially the Density Functional Tight-Binding (DFTB) and the extended tight-binding schemes, allow for efficient quantum mechanical simulations of large systems and long-time scales. They are derived from ab initio density functional theory using pragmatic approximations and some empirical terms, ensuring a fine balance between speed and accuracy. Their accuracy can be improved by tuning the empirical parameters using machine learning techniques, especially when information about the local environment of the atoms is incorporated. As the significant quantum mechanical contributions are still provided by the tight-binding models, and only short-ranged corrections are fitted, the learning procedure is typically shorter and more transferable as it were with predicting the quantum mechanical properties directly with machine learning without an underlying physically motivated model. As a further advantage, derived quantum mechanical quantities can be calculated based on the tight-binding model without the need for additional learning. We have developed the open-source framework-Tight-Binding Machine Learning Toolkit-which allows the easy implementation of such combined approaches. The toolkit currently contains layers for the DFTB method and an interface to the GFN1-xTB Hamiltonian, but due to its modular structure and its well-defined interfaces, additional atom-based schemes can be implemented easily. We are discussing the general structure of the framework, some essential implementation details, and several proof-of-concept applications demonstrating the perspectives of the combined methods and the functionality of the toolkit.

Experimental evaluation and structure-activity relationship analysis of bridged-ring terpenoid derivatives as novel Blattella germanica repellent

Cockroaches are urban pests that are very difficult to control. Using repellents is a green, safe and effective strategy for their control. In order to find novel cockroach repellents, the repellent activity of 45 bridged-ring terpenoid derivatives synthesized from β-pinene against Blattella germanica was tested. The relationship between the molecular structure of these bridged-ring terpenoid derivatives and their repellent activity against Blattella germanica was also analysed. The results show that some of the bridged-ring terpenoid derivatives exhibit good repellent activity against Blattella germanica, and six compounds (RR = 60.44-87.32%) show higher repellent activity against Blattella germanica than DEET (RR = 54.77%), making them promising for development as new cockroach repellents. Quantitative structure-activity relationship (QSAR) analysis revealed that the HOMO-1 energy, Kier and Hall index (order 2), Balaban index, and relative positive charged surface area of bridged-ring terpenoid derivatives have effects on repellent activity against Blattella germanica. The present study may provide a theoretical basis for the high-value use of β-pinene and can be helpful to the development of novel repellents against Blattella germanica.

Few-cycle Yb laser source at 20 kHz using multidimensional solitary states in hollow-core fibers

We demonstrate ultrashort pulse compression from 300 fs down to 17 fs at a repetition rate of 20 kHz and 160-µJ output pulse energy (3.2 W of average power) using multidimensional solitary states (MDSS) in a 1-meter hollow-core fiber (HCF) filled with N₂O. Under static pressure, thermal limitations at this repetition rate annihilate the MDSS with suppression of spectral broadening. The results obtained in differential pressure configuration mitigate thermal effects and significantly increase the range of repetition rate over which MDSS can be used to compress sub-picosecond laser pulses.

COVID 19 pandemic: Impact of changes experienced on social workers' professional quality of life in Singapore

COVID-19 has impacted all spheres of life massively. Among the emerging studies on the psychosocial impact of the pandemic, few studies look specifically at how social workers are impacted. To understand this gap, this study surveyed 337 social workers. The findings showed that changes experienced in the workplace were enormous and caused secondary traumatic stress while engendering compassion satisfaction among social workers, but the presence of social support moderated to keep the secondary traumatic stress at bay. Resilience mediated association between social and workplace support and compassion fatigue. Social support seemed to have the largest effect on reducing stress through resilience. Workplace support also helped mitigate burnout. In conclusion, continued social and workplace support will be key to supporting social workers during a pandemic.

The transcription factor KLF14 regulates macrophage glycolysis and immune function by inhibiting HK2 in sepsis

Sepsis is a heterogeneous syndrome induced by a dysregulated host response to infection. Glycolysis plays a role in maintaining the immune function of macrophages, which is crucial for severely septic patients. However, how the pathways that link glycolysis and macrophages are regulated is still largely unknown. Here, we provide evidence to support the function of KLF14, a novel Krüppel-like transcription factor, in the regulation of glycolysis and the immune function of macrophages during sepsis. KLF14 deletion led to significantly increased mortality in lethal models of murine endotoxemia and sepsis. Mechanistically, KLF14 decreased glycolysis and the secretion of inflammatory cytokines by macrophages by inhibiting the transcription of HK2. In addition, we confirmed that the expression of KLF14 was upregulated in septic patients. Furthermore, pharmacological activation of KLF14 conferred protection against sepsis in mice. These findings uncover a key role of KLF14 in modulating the inflammatory signaling pathway and shed light on the development of KLF14-targeted therapeutics for sepsis.

EGFR signaling promotes nuclear translocation of plasma membrane protein TSPAN8 to enhance tumor progression via STAT3-mediated transcription

TSPAN family of proteins are generally considered to assemble as multimeric complexes on the plasma membrane. Our previous work uncovered that TSPAN8 can translocate into the nucleus as a membrane-free form, a process that requires TSPAN8 palmitoylation and association with cholesterol to promote its extraction from the plasma membrane and subsequent binding with 14-3-3θ and importin-β. However, what upstream signal(s) regulate(s) the nuclear translocation of TSPAN8, the potential function of TSPAN8 in the nucleus, and the underlying molecular mechanisms all remain unclear. Here, we demonstrate that, epidermal growth factor receptor (EGFR) signaling induces TSPAN8 nuclear translocation by activating the kinase AKT, which in turn directly phosphorylates TSPAN8 at Ser129, an event essential for its binding with 14-3-3θ and importin ß1. In the nucleus, phosphorylated TSPAN8 interacts with STAT3 to enhance its chromatin occupancy and therefore regulates transcription of downstream cancer-promoting genes, such as MYC, BCL2, MMP9, etc. The EGFR-AKT-TSPAN8-STAT3 axis was found to be hyperactivated in multiple human cancers, and associated with aggressive phenotype and dismal prognosis. We further developed a humanized monoclonal antibody hT8^Ab4 that specifically recognizes the large extracellular loop of TSPAN8 (TSPAN8-LEL), thus being able to block the extraction of TSPAN8 from the plasma membrane and consequently its nuclear localization. Importantly, both in vitro and in vivo studies demonstrated an antitumor effect of hT8^Ab4. Collectively, we discovered an unconventional function of TSPAN8 and dissected the underlying molecular mechanisms, which not only showcase a new layer of biological complexity of traditional membrane proteins, but also shed light on TSPAN8 as a novel therapeutic target for refractory cancers.

Low-dose three-dimensional CT angiography for the evaluation of posterolateral protrusion of the vertebral artery over the posterior arch of the atlas: a quantitative anatomical comparison study of the rotational and neutral positions

AIM

To investigate the changes in relevant anatomical parameters of posterolateral protrusion of the vertebral artery (VA) between head-neck rotational and neutral positions using low-dose three-dimensional computed tomography angiography (3D-CTA).

MATERIALS AND METHODS

Low-dose 3D-CTA images obtained for various craniocervical diseases in 36 non-dominant VA side patients with neutral, left and right head-neck rotational positions were evaluated. The relevant parameters from superior and inferior views, including external diameter (ED), internal diameter (ID), transverse diameter (TD), heights and diameters of posterolateral protrusion of the VA over the posterior arch of the atlas in the neutral and rotational positions, were recorded and compared.

RESULTS

There was no significant differences in the rotational angle (left/right: 31.23 ± 6.60/29.94 ± 6.09°, p>0.05). There were no significant differences in heights and diameters of bilateral VA between rotational and neutral positions (all p>0.05). The contralateral ID, ED, and TD of the rotational positions were significantly shorter than those of the neutral position (all p<0.05), while there were no significant differences in the three ipsilateral diameters (all p>0.05).

CONCLUSIONS

Posterolateral protrusion of the VA is not uncommon in the population, and surgeons should be aware of its presence, especially the increased possibility of injury to the VA caused by head-neck rotation, during the operation; thus, preoperative evaluation by low-dose 3D-CTA should be considered.

Nanoscale zero-valent iron particles supported on sludge-based biochar for the removal of chromium (VI) from aqueous system

Biochar (BC) obtained by the co-pyrolysis of municipal sewage sludge (MSS) and sunflower seed shells (SSS) was utilized to support nanoscale zero-valent iron particles (nZVI) for the synthesis of a composite material (nZVI-BC) for Cr(VI) removal from aqueous systems. A series of characterization methods confirmed successful immobilization of nZVI on the surface of biochar with no aggregation. Batch experiments showed that the initial pH, initial Cr(VI) concentration, and nZVI-BC dose all significantly affected the Cr(VI) removal using nZVI-BC. The kinetics for Cr(VI) removal via nZVI-BC could be better explained by the pseudo-second-order (PSO) adsorption model. Adsorption isotherms analysis demonstrated the superior Cr(VI) removal capability of nZVI-BC in comparison to bare nZVI and BC. nZVI-BC can be reused after the regeneration process by applying 0.1 M H₂SO₄ and 0.1 M NaBH₄ solutions. The reaction mechanism for Cr(VI) removal might involve its chemical reduction on the nZVI-BC surface. Overall, environmentally friendly nZVI-BC was highly efficient in Cr(VI) removal from aqueous systems.

A high stem to leaf ratio reduced rainfall use efficiency under altered rainfall patterns in a semi-arid grassland in northeast China

Rainfall use efficiency (RUE) is crucial for understanding the changes in grassland productivity due to variations in future rainfall patterns. Recently, numerous studies have been conducted on the relationship between RUE and the amount of rainfall, but there has been little research on the influence of rainfall distribution and the interactive effect of rainfall amounts and distribution on RUE. Here, a simulated rainfall experiment was conducted to evaluate the impacts of rainfall amount (average rainfall amount (R0), 334 mm; decreased (R-) and increased (R+) rainfall amounts, 233 mm and 434 mm, respectively) and dry intervals (comprising 6-day, 9-day, 12-day, 15-day, 18-day and 21-day intervals between rainfall) on productivity and RUE in Leymus chinensis (Trin.) Tzvel., a dominant grass of the Eastern Eurasian Steppe. Our results showed that (1) for biomass production and RUE, moderate extension of dry intervals was conducive to enhancing total biomass production and RUE. The peak values of total biomass and RUE appeared during the 15-day interval for R-, and the 18-day interval for R0 and R+. (2) For biomass allocation, extension of dry intervals decreased the stem to leaf ratio (S/L) and the root to shoot ratio (R/S). (3) Further, the S/L ratio was significantly negatively correlated with RUE. These results suggest that variations in rainfall patterns can alter the RUE by changing the S/L ratio, and finally influence biomass production in L. chinensis. These findings have important implications for understanding and predicting the effect of future climate change on productivity in semi-arid grassland.

SOX9 is a critical regulator of TSPAN8-mediated metastasis in pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) is the deadliest cancer mainly owing to its proclivity to early metastasis and the lack of effective targeted therapeutic drugs. Hence, understanding the molecular mechanisms underlying early invasion and metastasis by PDAC is imperative for improving patient outcomes. The present study identified that upregulation of TSPAN8 expression in PDAC facilitates metastasis in vivo and in vitro. We found SOX9 as a key transcriptional regulator of TSPAN8 expression in response to EGF stimulation. SOX9 modulation was sufficient to positively regulate endogenous expression of TSPAN8, with concomitant in vitro phenotypic changes such as loss of cell-matrix adherence and increased invasion. Moreover, increased SOX9 and TSPAN8 levels were shown to correlate in human pancreatic cancer specimens and downregulated in vitro by EGFR tyrosine kinase inhibitors. High expression of SOX9 and TSPAN8 has been associated with tumor stage, poor prognosis and poor patient survival in PDAC. In conclusion, this study highlights the importance of the EGF-SOX9-TSPAN8 signaling cascade in the control of PDAC invasion and implies that TSPAN8 may be a promising novel therapeutic target for the treatment of PDAC.

The loss of SHMT2 mediates 5-fluorouracil chemoresistance in colorectal cancer by upregulating autophagy

5-Fluorouracil (5-FU)-based chemotherapy is the first-line treatment for colorectal cancer (CRC) but is hampered by chemoresistance. Despite its impact on patient survival, the mechanism underlying chemoresistance against 5-FU remains poorly understood. Here, we identified serine hydroxymethyltransferase-2 (SHMT2) as a critical regulator of 5-FU chemoresistance in CRC. SHMT2 inhibits autophagy by binding cytosolic p53 instead of metabolism. SHMT2 prevents cytosolic p53 degradation by inhibiting the binding of p53 and HDM2. Under 5-FU treatment, SHMT2 depletion promotes autophagy and inhibits apoptosis. Autophagy inhibitors decrease low SHMT2-induced 5-FU resistance in vitro and in vivo. Finally, the lethality of 5-FU treatment to CRC cells was enhanced by treatment with the autophagy inhibitor chloroquine in patient-derived and CRC cell xenograft models. Taken together, our findings indicate that autophagy induced by low SHMT2 levels mediates 5-FU resistance in CRC. These results reveal the SHMT2-p53 interaction as a novel therapeutic target and provide a potential opportunity to reduce chemoresistance.

70 mJ nonlinear compression and scaling route for an Yb amplifier using large-core hollow fibers

In this Letter, we investigate the energy-scaling rules of hollow-core fiber (HCF)-based nonlinear pulse propagation and compression merged with high-energy Yb-laser technology, in a regime where the effects such as plasma disturbance, optical damages, and setup size become important limiting parameters. As a demonstration, 70 mJ 230 fs pulses from a high-energy Yb laser amplifier were compressed down to 40 mJ 25 fs by using a 2.8-m-long stretched HCF with a core diameter of 1 mm, resulting in a record peak power of 1.3 TW. This work presents a critical advance of a high-energy pulse (hundreds of mJ level) nonlinear interactions platform based on high energy sub-ps Yb technology with considerable applications, including driving intense THz, X-ray pulses, Wakefield acceleration, parametric wave mixing and ultraviolet generation, and tunable long-wavelength generation via enhanced Raman scattering.

The deacetylation-phosphorylation regulation of SIRT2-SMC1A axis as a mechanism of antimitotic catastrophe in early tumorigenesis

Improper distribution of chromosomes during mitosis can contribute to malignant transformation. Higher eukaryotes have evolved a mitotic catastrophe mechanism for eliminating mitosis-incompetent cells; however, the signaling cascade and its epigenetic regulation are poorly understood. Our analyses of human cancerous tissue revealed that the NAD-dependent deacetylase SIRT2 is up-regulated in early-stage carcinomas of various organs. Mass spectrometry analysis revealed that SIRT2 interacts with and deacetylates the structural maintenance of chromosomes protein 1 (SMC1A), which then promotes SMC1A phosphorylation to properly drive mitosis. We have further demonstrated that inhibition of SIRT2 activity or continuously increasing SMC1A-K579 acetylation causes abnormal chromosome segregation, which, in turn, induces mitotic catastrophe in cancer cells and enhances their vulnerability to chemotherapeutic agents. These findings suggest that regulation of the SIRT2-SMC1A axis through deacetylation-phosphorylation permits escape from mitotic catastrophe, thus allowing early precursor lesions to overcome oncogenic stress.

The probiotic Lactobacillus casei Shirota attenuates symptoms of vestibular migraine: a randomised placebo-controlled double-blind clinical trial

Vestibular migraine (VM) has emerged as one of the major vestibular syndromes. Although probiotics have exhibited beneficial effects on migraine headache, its effect on VM is not clear. This trial aimed to investigate the treatment efficacy of the probiotic Lactobacillus casei Shirota (LcS) on symptoms of VM. 247 VM patients were enrolled, of which 204 eligible patients receiving either LcS or placebo on a daily basis completed the 4 month study. They were re-visited at 2 and 4 months after study initiation to assess treatment outcomes. The primary endpoints were vestibular symptoms, evaluated by the number of vertiginous attacks during the past week, the Vertigo Severity Score (VSS), and Dizziness Handicap Inventory (DHI) scores. The secondary endpoints were anxiety and depressive symptoms, evaluated using Beck Anxiety Inventory (BAI) and Beck Depression Inventory (BDI) scores. Efficacy of LcS over placebo was not obvious at 2 month follow-up. At 4 month follow-up, while both LcS and placebo groups of VM patients displayed alleviated symptoms, the extents of the improvements were significantly better in LcS group than those of placebo group, with regard to vestibular symptoms using DHI and VSS, as well as anxiety and depressive symptoms using BAI and BDI. Although placebo effect cannot be ignored in intervention for VM patients, the probiotic LcS still exhibits considerable efficacy against VM symptoms over a 4 month study period, supporting further clinical study of a larger and more diverse cohort.

High energy redshifted and enhanced spectral broadening by molecular alignment

We demonstrate an efficient approach for enhancing the spectral broadening of long laser pulses and for efficient frequency redshifting by exploiting the intrinsic temporal properties of molecular alignment inside a gas-filled hollow-core fiber (HCF). We find that laser-induced alignment with durations comparable to the characteristic rotational time scale TRotAlign enhances the efficiency of redshifted spectral broadening compared to noble gases. The applicability of this approach to Yb lasers with (few hundred femtoseconds) long pulse duration is illustrated, for which efficient broadening based on conventional Kerr nonlinearity is challenging to achieve. Furthermore, this approach proposes a practical solution for high energy broadband long-wavelength light sources, and it is attractive for many strong field applications.

Activated CD4+ T cells-derived exosomal miR-142-3p boosts post-ischemic ventricular remodeling by activating myofibroblast

Cardiac fibrosis is a primary phenotype of cardiac remodeling that contributes to cardiac dysfunction and heart failure. The expansion and activation of CD4⁺ T cells in the heart has been identified to facilitate pathological cardiac remodeling and dysfunction; however, the underlying mechanisms remained not well clarified. Herein, we found that exosomes derived from activated CD4⁺ T cells (CD4-activated Exos) evoked pro-fibrotic effects of cardiac fibroblasts, and their delivery into the heart aggravated cardiac fibrosis and dysfunction post-infarction. Mechanistically, miR-142-3p that was enriched in CD4-activated Exos recapitulated the pro-fibrotic effects of CD4-activated Exos in cardiac fibroblasts, and vice versa. Furthermore, miR-142-3p directly targeted and inhibited the expression of Adenomatous Polyposis Coli (APC), a negative WNT signaling pathway regulator, contributing to the activation of WNT signaling pathway and cardiac fibroblast activation. Thus, CD4-activated Exos promote post-ischemic cardiac fibrosis through exosomal miR-142-3p-WNT signaling cascade-mediated activation of myofibroblasts. Targeting miR-142-3p in CD4-activated Exos may hold promise for treating cardiac remodeling post-MI.

Identification of factors associated with minimal erythema dose variations in a large-scale population study of 22 146 subjects

Background

Minimal erythema dose (MED) has substantial inter‐ and intraindividual variations, reflecting the influence of very diverse factors. However, related studies showed little consistency probably because of their limited sample size.

Objective

To identify the factors associated with MED variations in a large‐scale population study.

Methods

The MED test was performed by following the international standard procedure on 22 146 subjects. The results were analysed in adjusted multivariable linear and logistic regression models.

Results

This large‐scale study revealed that lower MED was consistently associated with lighter skin [β‐coefficient = −0.33, 95% confidence interval (CI) −0.36 to 0.30, P = 6.41 × 10⁻⁸⁴]. Females had significantly higher MED than male (β = 0.91, 0.32–1.50, P = 2.93 × 10⁻³). Stratified analyses showed that MED was not associated with age [female: odds ratio (OR) = 0.99, 0.98–1.01; male: OR = 0.99, 0.97–1.00]. MED was lower in summer than in other seasons (spring: OR = 1.08, 1.06–1.11; autumn: OR = 1.11, 1.08–1.13; winter: OR = 1.20, 1.18–1.22). Furthermore, MED was associated with air temperature (β = −0.36, −0.49 to 0.23, P = 4.81 × 10⁻⁸) and air pressure (β = −0.64, −0.82 to 0.46, P = 8.01 × 10⁻¹²) in summer only while not in other seasons.

Conclusions

This study provides unprecedented evidence that MED is associated with skin colour, sex, season and meteorological factors, but not with age.

The accuracy of bone mineral density measurement using dual-energy spectral CT and quantitative CT: a comparative phantom study

AIM

To compare bone mineral density (BMD) measurement accuracy by dual-energy spectral computed tomography (CT) and quantitative CT (QCT) using an anthropomorphic European spine phantom (ESP).

MATERIALS AND METHODS

An ESP containing three hydroxyapatite inserts with densities of 50, 100, and 200 mg/cm³ was scanned 10 times each using spectral CT and QCT protocols. Their BMD values were measured using hydroxyapatite-based spectral CT material decomposition images and QCT images and compared with the true values in ESP.

RESULTS

Both protocols had good repeatability in BMD measurement with low coefficient-of-variance (spectral CT: <2.31%; QCT: <1.17%). There were biases in BMD measurement for the 50, 100, and 200 mg/cm³ hydroxyapatite insert with relative errors of 2.34% (48.83±1.13 mg/cm³), 2% (98±1.25 mg/cm³) and 5.96% (188.09±2.11 mg/cm³), in spectral CT, and 11% (55.5±0.65 mg/cm³), 9.85% (109.85±0.42 mg/cm³) and 4.04% (208.07±0.54 mg/cm³) in QCT, respectively.

CONCLUSION

BMD can be accurately measured using either QCT or spectral CT, and spectral CT has smaller bias than QCT.

Evaluation of a molecular point-of-care testing for viral and atypical pathogens on intravenous antibiotic duration in hospitalized adults with lower respiratory tract infection: a randomized clinical trial

Objectives

The primary objective was to evaluate whether a molecular point-of-care test (POCT) for viral and atypical pathogens added to routine real-time PCR could reduce duration of intravenous antibiotics in hospitalized patients with lower respiratory tract infection (LRTI) compared with routine real-time PCR.

Methods

In this single-centre, open-label, randomized controlled study, we enrolled hospitalized adults diagnosed with LRTI. Patients were randomized to an intervention group (POCT FilmArray Panel for 20 viruses, atypical pathogens and bacteria plus routine real-time PCR) or a control group (routine real-time PCR for ten pathogens). The primary outcome was duration of intravenous antibiotics during hospitalization. The secondary outcomes included length of stay, cost of hospitalization and de-escalation within 72 hours and between 72 hours and 7 days. Intention-to-treat analysis was used.

Results

Between October 2017 and July 2018, we enrolled 800 eligible patients (398 in the intervention group and 402 in the control group). Duration of intravenous antibiotics in the intervention group was shorter than in the control (7.0 days (interquartile range (IQR) 5.0–9.0) versus 8.0 days (IQR 6.0–11.0); p <0.001). Length of hospital stay in the intervention group was significantly shorter (8.0 days (IQR 7.0–11.0) versus 9.0 days (IQR 7.0–12.0; p <0.001) and the cost of hospitalization in the intervention group was significantly lower ($1804.7 (IQR 1298.4–2633.8) versus $2042.5 (IQR 1427.4–2926.2); p 0.002) than control group. More patients in the intervention group achieved de-escalation within 72 hours (7.9%, 29/367 versus 3.2%, 12/377; p 0.005) and between 72 hours and 7 days (29.7%, 109/367 versus 22.0%, 83/377; p 0.024).

Conclusions

Use of molecular POCT testing for respiratory viruses and atypical pathogens might help to reduce intravenous antibiotic use in hospitalized LRTI patients.

Clinical Trial Registration

clinicaltrials.gov Identifier: NCT03391076.

Deep Learning-Based Automatic Segmentation of Lumbosacral Nerves on CT for Spinal Intervention: A Translational Study

BACKGROUND AND PURPOSE

3D reconstruction of a targeted area ("safe" triangle and Kambin triangle) may benefit the viability assessment of transforaminal epidural steroid injection, especially at the L5/S1 level. However, manual segmentation of lumbosacral nerves for 3D reconstruction is time-consuming. The aim of this study was to investigate the feasibility of deep learning-based segmentation of lumbosacral nerves on CT and the reconstruction of the safe triangle and Kambin triangle.

MATERIALS AND METHODS

A total of 50 cases of spinal CT were manually labeled for lumbosacral nerves and bones using Slicer 4.8. The ratio of training/validation/testing was 32:8:10. A 3D U-Net was adopted to build the model SPINECT for automatic segmentations of lumbosacral structures. The Dice score, pixel accuracy, and Intersection over Union were computed to assess the segmentation performance of SPINECT. The areas of Kambin and safe triangles were measured to validate the 3D reconstruction.

RESULTS

The results revealed successful segmentation of lumbosacral bone and nerve on CT. The average pixel accuracy for bone was 0.940, and for nerve, 0.918. The average Intersection over Union for bone was 0.897 and for nerve, 0.827. The Dice score for bone was 0.945, and for nerve, it was 0.905. There were no significant differences in the quantified Kambin triangle or safe triangle between manually segmented images and automatically segmented images (P > .05).

CONCLUSIONS

Deep learning-based automatic segmentation of lumbosacral structures (nerves and bone) on routine CT is feasible, and SPINECT-based 3D reconstruction of safe and Kambin triangles is also validated.

Radiotherapy improves the survival of patients with metastatic esophageal squamous cell carcinoma: a propensity score matched analysis of Surveillance, Epidemiology, and End Results database

The survival advantage of radiotherapy (RT) for patients with metastatic esophagus cancer has not been adequately evaluated. This study aims to find out the role of RT for metastatic esophagus cancer and to find the different effect for RT to esophageal adenocarcinoma (EAC) and esophageal squamous cell carcinoma (ESCC). This study included 5,970 metastatic esophagus cancer patients from the Surveillance, Epidemiology, and End Results (SEER) database, registered from January 2004 to December 2013. Propensity score (PS) analysis with 1:1 nearest neighbor matching method was used to ensure well-balanced characteristics of all comparison groups by histological types. The Kaplan-Meier and Cox proportional hazardous models were used to evaluate the overall survival (OS), cancer-specific survival (CSS), and corresponding 95% confidence interval (CI). Generally speaking, EAC did not get survival benefit from RT (median OS for RT group vs. no-RT group-8.0, 7.6-8.4 vs. 9.0, 8.5-9.5, P = 0.073), whereas RT for metastatic ESCC did significantly improve OS (median OS for RT group vs. no-RT group-8.0, 7.4-8.6 vs. 7.0, 6.4-7.6, P = 0.044). Therefore, compared with adenocarcinoma, ESCC could get more survival benefit from RT.

External Quality Assessment for Rubella Virus RNA Detection Using Armored RNA in China

BACKGROUND

Although tremendous efforts have been made to reduce rubella incidence, there are still 300 new cases of congenital rubella syndrome daily; thus, rubella infections remain one of the leading causes of preventable congenital birth defects. An effective surveillance system, which could be achieved and maintained by using an external quality assessment program, is critical for prevention and control of this disease.

METHODS

Armored RNAs, which are noninfectious and RNase-resistant, were used for encapsulation of the E1 gene of rubella virus and for preparation of a 10-specimen panel for external quality assessment. Thirty-two laboratories across mainland China that used nucleic acid tests for rubella virus RNA detection were included in the external quality assessment program organized by the National Center for Clinical Laboratories of China.

RESULTS

Different kinds of commercial kits were used by the laboratories for nucleic acid extraction and TaqMan real-time reverse-transcription PCR for rubella virus RNA detection; 99.2% sensitivity and 100% specificity were achieved in this external quality assessment program.

CONCLUSIONS

Most of the participating laboratories obtained accurate results for rubella nucleic acid tests, thereby achieving the quality required for regional rubella and congenital rubella syndrome elimination.

Radiation reduction of minimally invasive transforaminal lumbar interbody fusion with localisation system in overweight patients: practical technique

AIMS

Minimally invasive transforaminal lumbar interbody fusion (MITLIF) has been well validated in overweight and obese patients who are consequently subject to a higher radiation exposure. This prospective multicentre study aimed to investigate the efficacy of a novel lumbar localisation system for MITLIF in overweight patients.

PATIENTS AND METHODS

The initial study group consisted of 175 patients. After excluding 49 patients for various reasons, 126 patients were divided into two groups. Those in Group A were treated using the localisation system while those in Group B were treated by conventional means. The primary outcomes were the effective radiation dosage to the surgeon and the exposure time.

RESULTS

There were 62 patients in Group A and 64 in Group B. The mean effective dosage was 0.0217 mSv (standard deviation (sd) 0.0079) in Group A and 0.0383 mSv (sd 0.0104) in Group B (p < 0.001). The mean fluoroscopy exposure time was 26.42 seconds (sd 5.91) in Group A and 40.67 seconds (sd 8.18) in Group B (p < 0.001). The operating time was 175.56 minutes (sd 32.23) and 206.08 minutes (sd 30.15) (p < 0.001), respectively. The mean pre-operative localisation time was 4.73 minutes (sd 0.84) in Group A and 7.03 minutes (sd 1.51) in Group B (p < 0.001). The mean screw placement time was 47.37 minutes (sd 10.43) in Group A and 67.86 minutes (sd 14.15) in Group B (p < 0.001). The pedicle screw violation rate was 0.35% (one out of 283) in Group A and 2.79% (eight out of 287) in Group B (p = 0.020).

CONCLUSION

The study shows that the localisation system can effectively reduce radiation exposure, exposure time, operating time, pre-operative localisation time, and screw placement time in overweight patients undergoing MITLIF. Cite this article: Bone Joint J 2017;99-B:944-50.

SIRT1 Functions as a Negative Regulator of Eukaryotic Poly(A)RNA Transport

Most eukaryotic mRNAs are polyadenylated in the nucleus, and the poly(A)-tail is required for efficient mRNA export and translation. However, mechanisms governing mRNA transport remain unclear. Here, we report that the nicotinamide adenine dinucleotide (NAD)-dependent deacetylase SIRT1 acts as an energy sensor and negatively regulates poly(A)RNA transport via deacetylating a poly(A)-binding protein, PABP1. Upon energy starvation, SIRT1 interacts with and deacetylates PABP1 and deactivates its poly(A)RNA binding, leading to nuclear accumulation of PABP1 and poly(A)RNA and thus facilitating eukaryotic cells to attenuate protein synthesis and energy consumption to adapt to energy stress. Moreover, AMPK-directed SIRT1 phosphorylation is required for energy starvation-induced PABP1-SIRT1 association, PABP1 deacetylation, and poly(A)RNA nuclear retention. In addition, the SIRT1-PABP1 association is not specific to energy starvation but represents a common stress response. These observations provide insights into dynamic modulation of eukaryotic mRNA transport and translation, suggesting that the poly(A)-tail also provides a basis for eukaryotes to effectively shut down mature mRNA transport and thereby tailor protein synthesis to maintain energy homeostasis under stress conditions.

Quantitative structure-activity relationship study of amide mosquito repellents

A quantitative structure-activity relationship (QSAR) study on 43 amide repellents was carried out by the heuristic method in order to reveal the correlations between molecular parameters of these amides and their repellency against Aedes aegypti. Sketches and optimizations of molecular structures were achieved by the Gaussian software package. Generation and screening of molecular parameters were accomplished using CODESSA 2.7.10 software. The leave-one-out method was applied for the model validation. The results showed that a four-descriptor QSAR model with r² of 0.897 was obtained. The average r² values of the training set and test set of the QSAR model were 0.901 and 0.863, respectively, which suggested that the stability and predictability of the model were confirmed. Analysis of the implications of the descriptors that constitute the QSAR model indicated that all the descriptors were related to the charge distribution over the molecule and affect the dipole moment of the repellents.

X-SEA-F-SPIDER characterization of over octave spanning pulses in the infrared range

We show a practical implementation of a pulse characterization method for sub-cycle pulse measurements in the infrared spectral range based on spectral shearing interferometry. We employ spatially-encoded arrangement filter-based spectral phase interferometry for direct electric field reconstruction with external ancila pulses (X-SEA-F-SPIDER). We show merits and limitations of the setup and an in-depth comparison to another widely used temporal characterization technique - Second-Harmonic Generation Frequency Resolved Optical Gating (SHG-FROG). The X-SEA-F-SPIDER implementation presented in this paper allows measurement of sub-cycle pulses with over one octave wide spectrum spanning the 900-2400 nm range without adding any extra dispersion due to the pulse characterization apparatus.

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

Loss of KLF14 triggers centrosome amplification and tumorigenesis

Centrosome amplification is frequent in cancer, but the underlying mechanisms remain unclear. Here we report that disruption of the Kruppel-like factor 14 (KLF14) gene in mice causes centrosome amplification, aneuploidy and spontaneous tumorigenesis. Molecularly, KLF14 functions as a transcriptional repressor of Plk4, a polo-like kinase whose overexpression induces centrosome overduplication. Transient knockdown of KLF14 is sufficient to induce Plk4-directed centrosome amplification. Clinically, KLF14 transcription is significantly downregulated, whereas Plk4 transcription is upregulated in multiple types of cancers, and there exists an inverse correlation between KLF14 and Plk4 protein expression in human breast and colon cancers. Moreover, KLF14 depletion promotes AOM/DSS-induced colon tumorigenesis. Our findings reveal that KLF14 reduction serves as a mechanism leading to centrosome amplification and tumorigenesis. On the other hand, forced expression of KLF14 leads to mitotic catastrophe. Collectively, our findings identify KLF14 as a tumour suppressor and highlight its potential as biomarker and therapeutic target for cancer.

Association of proinflammatory cytokines and chemotherapy-associated cognitive impairment in breast cancer patients: a multi-centered, prospective, cohort study

BACKGROUND

Existing evidence suggests that proinflammatory cytokines play an intermediary role in postchemotherapy cognitive impairment. This is one of the largest multicentered, cohort studies conducted in Singapore to evaluate the prevalence and proinflammatory biomarkers associated with cognitive impairment in breast cancer patients.

PATIENTS AND METHODS

Chemotherapy-receiving breast cancer patients (stages I-III) were recruited. Proinflammatory plasma cytokines concentrations [interleukin (IL)-1β, IL-2, IL-4, IL-6, IL-8, IL-10, granulocyte-macrophage colony-stimulating factor, interferon-γ and tumor necrosis factor-α] were evaluated at 3 time points (before chemotherapy, 6 and 12 weeks after chemotherapy initiation). The FACT-Cog (version 3) was utilized to evaluate patients' self-perceived cognitive disturbances and a computerized neuropsychological assessment (Headminder) was administered to evaluate patients' memory, attention, response speed and processing speed. Changes of cognition throughout chemotherapy treatment were compared against the baseline. Linear mixed-effects models were applied to test the relationships of clinical variables and cytokine concentrations on self-perceived cognitive disturbances and each objective cognitive domain.

RESULTS

Ninety-nine patients were included (age 50.5 ± 8.4 years; 81.8% Chinese; mean duration of education = 10.8 ± 3.3 years). Higher plasma IL-1β was associated with poorer response speed performance (estimate: -0.78; 95% confidence interval (CI) -1.34 to -0.03; P = 0.023), and a higher concentration of IL-4 was associated with better response speed performance (P = 0.022). Higher concentrations of IL-1β and IL-6 were associated with more severe self-perceived cognitive disturbances (P = 0.018 and 0.001, respectively). Patients with higher concentrations of IL-4 also reported less severe cognitive disturbances (P = 0.022).

CONCLUSIONS

While elevated concentrations of IL-6 and IL-1β were observed in patients with poorer response speed performance and perceived cognitive disturbances, IL-4 may be protective against chemotherapy-associated cognitive impairment. This study is important because cytokines would potentially be mechanistic mediators of chemotherapy-associated cognitive changes.

Improvement of the facial evenness of leave-on skincare products by a modified application method in Chinese women

OBJECTIVE

To understand the habits of Chinese women applying leave-on skincare products (LOSCP) and to improve female facial evenness of anti-ageing cosmetics through modifying facial skincare smear ways.

METHODS

A questionnaire on the method of applying LOSCP was distributed to 60 women with habit of using LOSCP. Their facial images before and after applying LOSCP were taken, and their positioning and grey value were used to analyse the effects of different applying methods on the uniformity of facial LOSCP.

RESULTS

LOSCP including anti-ageing cosmetics have been widely used among Chinese women for a long time. However, some women do not concern how to properly apply LOSCP. In our survey, the main focal points of the face are forehead, malar region, cheek, mouth corners and chin when they looking into the mirror, and mouth corners and inner canthus are often overlooked when applying cosmetic products. The image analysis found that after applying the LOSCP, the greyscale of the forehead, glabella, malar region, upper lip region and jaw changed significantly whereas that of canthus, mouth corners and lateral cheek region was not significantly different. Applying an improved smear method (11-point method)could significantly increase the grey values of various facial areas.

CONCLUSION

The way of Chinese women applying LOSCP may result in facial unevenness of skin products. By improving facial skincare smear method, one can make the products even in all facial areas, thereby ensuring the efficacy of anti-ageing cosmetics. Thus, further improvement and education regarding skincare is required.

The REGγ proteasome regulates hepatic lipid metabolism through inhibition of autophagy

The ubiquitin-proteasome and autophagy-lysosome systems are major proteolytic pathways, whereas function of the Ub-independent proteasome pathway is yet to be clarified. Here, we investigated roles of the Ub-independent REGγ-proteasome proteolytic system in regulating metabolism. We demonstrate that mice deficient for the proteasome activator REGγ exhibit dramatic autophagy induction and are protected against high-fat diet (HFD)-induced liver steatosis through autophagy. Molecularly, prevention of steatosis in the absence of REGγ entails elevated SirT1, a deacetylase regulating autophagy and metabolism. REGγ physically binds to SirT1, promotes its Ub-independent degradation, and inhibits its activity to deacetylate autophagy-related proteins, thereby inhibiting autophagy under normal conditions. Moreover, REGγ and SirT1 dissociate from each other through a phosphorylation-dependent mechanism under energy-deprived conditions, unleashing SirT1 to stimulate autophagy. These observations provide a function of the REGγ proteasome in autophagy and hepatosteatosis, underscoring mechanistically a crosstalk between the proteasome and autophagy degradation system in the regulation of lipid homeostasis.