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https://www.readbyqxmd.com/read/29679848/a-deep-boltzmann-machine-driven-level-set-method-for-heart-motion-tracking-using-cine-mri-images
#1
Jian Wu, Thomas R Mazur, Su Ruan, Chunfeng Lian, Nalini Daniel, Hilary Lashmett, Laura Ochoa, Imran Zoberi, Mark A Anastasio, H Michael Gach, Sasa Mutic, Maria Thomas, Hua Li
Heart motion tracking for radiation therapy treatment planning can result in effective motion management strategies to minimize radiation-induced cardiotoxicity. However, automatic heart motion tracking is challenging due to factors that include the complex spatial relationship between the heart and its neighboring structures, dynamic changes in heart shape, and limited image contrast, resolution, and volume coverage. In this study, we developed and evaluated a deep generative shape model-driven level set method to address these challenges...
April 6, 2018: Medical Image Analysis
https://www.readbyqxmd.com/read/29679371/fitting-the-epigenome-into-the-picture-methylation-classification-for-paediatric-brain-tumours
#2
EDITORIAL
J A Cotter, A R Judkins
Meaningful classification of paediatric brain tumours has been a topic of revived discussion in the current era of molecular analysis. In recent years, we have seen the practice of diagnostic neuropathology not only incorporate routine biomarker interpretation (e.g. INI1/SMARCB1 and BRAF V600E immunohistochemistry), but also extend its reach into the molecular pathology laboratory. Next-generation sequencing, fusion analysis, and copy number profiling are now commonly-employed diagnostic tools, particularly in histologically challenging or clinically difficult cases...
April 20, 2018: Neuropathology and Applied Neurobiology
https://www.readbyqxmd.com/read/29678961/-capn1-mutations-broadening-the-hereditary-spastic-paraplegia-spinocerebellar-ataxia-phenotype
#3
Jeffrey Lambe, Bernadette Monaghan, Tudor Munteanu, Janice Redmond
Increasing availability of next-generation sequencing technologies has revealed several limitations of diagnosis-driven traditional clinicogenetic disease classifications, particularly among patients with an atypical or mixed phenotype. Hereditary spastic paraplegia (HSP) and spinocerebellar ataxia (SCA) are two such disease entities with an often overlapping presentation, in which next generation exome sequencing has played a key role in identification of genes causing disease along a continuum of ataxia and spasticity...
April 20, 2018: Practical Neurology
https://www.readbyqxmd.com/read/29678912/characterizing-the-ecology-of-vibrio-in-the-neuse-river-estuary-north-carolina-using-heat-shock-protein-60-hsp60-next-generation-amplicon-sequencing
#4
Kelsey J Jesser, Rachel T Noble
Of marine eubacteria, the genus Vibrio is intriguing because member species are relevant to both marine ecology and human health. Many have touted the relationships of Vibrio to environmental factors, especially temperature and salinity, to predict total Vibrio abundance, but these studies lacked the taxonomic resolution to identify relationships among species and key drivers of Vibrio dynamics. In order to improve NGS surveys of Vibrio, we have conducted both 16S small subunit ribosomal RNA (rRNA) and heat shock protein 60 ( hsp60 ) amplicon sequencing of water samples collected at two well-studied locations in the Neuse River Estuary, NC...
April 20, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29677560/effective-discovery-of-rare-variants-by-pooled-target-capture-sequencing-a-comparative-analysis-with-individually-indexed-target-capture-sequencing
#5
Seungjin Ryu, Jeehae Han, Trina M Norden-Krichmar, Nicholas J Schork, Yousin Suh
Identification of all genetic variants associated with complex traits is one of the most important goals in modern human genetics. Genome-wide association studies (GWAS) have been successfully applied to identify common variants, which thus far explain only small portion of heritability. Interests in rare variants have been increasingly growing as an answer for this missing heritability. While next-generation sequencing allows detection of rare variants, its cost is still prohibitively high to sequence a large number of human DNA samples required for rare variant association studies...
March 30, 2018: Mutation Research
https://www.readbyqxmd.com/read/29675967/shrub-range-expansion-alters-diversity-and-distribution-of-soil-fungal-communities-across-an-alpine-elevation-gradient
#6
Courtney G Collins, Jason E Stajich, Sören E Weber, Nuttapon Pombubpa, Jeffrey M Diez
Global climate and land use change are altering plant and soil microbial communities worldwide, particularly in arctic and alpine biomes where warming is accelerated. The widespread expansion of woody shrubs into historically herbaceous alpine plant zones is likely to interact with climate to affect soil microbial community structure and function, however our understanding of alpine soil ecology remains limited. This study aimed to 1) determine whether the diversity and community composition of soil fungi vary across elevation gradients and to 2) assess the impact of woody shrub expansion on these patterns...
April 19, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29675645/fine-mapping-and-identification-of-a-novel-locus-qgl12-2-control-grain-length-in-wild-rice-oryza-rufipogon-griff
#7
Lan Qi, Yingbin Ding, Xiaoming Zheng, Rui Xu, Lizhen Zhang, Yanyan Wang, Xiaoning Wang, Lifang Zhang, Yunlian Cheng, Weihua Qiao, Qingwen Yang
A wild rice QTL qGL12.2 for grain length was fine mapped to an 82-kb interval in chromosome 12 containing six candidate genes and none was reported previously. Grain length is an important trait for yield and commercial value in rice. Wild rice seeds have a very slender shape and have many desirable genes that have been lost in cultivated rice during domestication. In this study, we identified a quantitative trait locus, qGL12.2, which controls grain length in wild rice. First, a wild rice chromosome segment substitution line, CSSL41, was selected that has longer glume and grains than does the Oryza sativa indica cultivar, 9311...
April 19, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29674926/a-taxonomic-study-of-quercus-langbianensis-complex-based-on-morphology-and-dna-barcodes-of-classic-and-next-generation-sequences
#8
Hoang Thi Binh, Nguyen Van Ngoc, Shuichiro Tagane, Hironori Toyama, Keiko Mase, Chika Mitsuyuki, Joeri Sergej Strijk, Yoshihisa Suyama, Tetsukazu Yahara
The taxonomy of Quercus langbianensis and its relatives in Vietnam and Cambodia have been revised based on evidence obtained from field observations, morphological comparison of herbarium specimens and molecular analyses using both classic and next generation DNA markers. Based on Bayesian inference using rbc L, mat K and ITS regions and Neighbour-joining tree using genome-wide sequences amplified with multiplexed inter-simple sequence repeat (ISSR) primers (MIG-seq), the authors recognised ten species in the complex in Vietnam and Cambodia, three of which are newly described in this paper: Q...
2018: PhytoKeys
https://www.readbyqxmd.com/read/29674707/targeted-genomic-landscape-of-metastases-compared-to-primary-tumours-in-clear-cell-metastatic-renal-cell-carcinoma
#9
Guillermo de Velasco, Stephanie A Wankowicz, Russell Madison, Siraj M Ali, Craig Norton, Audrey Duquette, Jeffrey S Ross, Dominick Bossé, Aly-Khan A Lalani, Vincent A Miller, Philip J Stephens, Lauren Young, A Ari Hakimi, Sabina Signoretti, Sumanta K Pal, Toni K Choueiri
BACKGROUND: The genomic landscape of primary clear cell renal cell carcinoma (ccRCC) has been well described. However, little is known about cohort genomic alterations (GA) landscape in ccRCC metastases, or how it compares to primary tumours in aggregate. The genomic landscape of metastases may have biological, clinical, and therapeutic implications. METHODS: We collected targeted next-generation sequencing mutation calls from two independent cohorts and described the metastases GA landscape and descriptively compared it to the GA landscape in primary tumours...
April 20, 2018: British Journal of Cancer
https://www.readbyqxmd.com/read/29674641/the-impact-of-storage-buffer-dna-extraction-method-and-polymerase-on-microbial-analysis
#10
Luisa K Hallmaier-Wacker, Simone Lueert, Christian Roos, Sascha Knauf
Next-generation sequencing approaches used to characterize microbial communities are subject to technical caveats that can lead to major distortion of acquired data. Determining the optimal sample handling protocol is essential to minimize the bias for different sample types. Using a mock community composed of 22 bacterial strains of even concentration, we studied a combination of handling conditions to determine the optimal conditions for swab material. Examining a combination of effects simulates the reality of handling environmental samples and may thus provide a better foundation for the standardization of protocols...
April 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29674443/recent-advances-in-the-treatment-of-peripheral-t-cell-lymphoma
#11
REVIEW
Kamel Laribi, Mustapha Alani, Catherine Truong, Alix Baugier de Materre
Peripheral T-cell lymphoma (PTCL) is a heterogeneous group of clinically aggressive diseases associated with poor outcome. Despite progress in the last several years, resulting in a deeper understanding of the natural history and biology of PTCL based on molecular profiling and next-generation sequencing, there is a need for improvement in efficacy of chemotherapeutic regimens for newly diagnosed patients. Treatment in the front-line setting is most often cyclophosphamide, doxorubicin, vincristine, and prednisone (CHOP) or CHOP-like regimens, which are associated with a high failure rate and frequent relapses...
April 19, 2018: Oncologist
https://www.readbyqxmd.com/read/29674394/acetyl-coa-promotes-glioblastoma-cell-adhesion-and-migration-through-ca-2-nfat-signaling
#12
Joyce V Lee, Corbett T Berry, Karla Kim, Payel Sen, Taehyong Kim, Alessandro Carrer, Sophie Trefely, Steven Zhao, Sully Fernandez, Lauren E Barney, Alyssa D Schwartz, Shelly R Peyton, Nathaniel W Snyder, Shelley L Berger, Bruce D Freedman, Kathryn E Wellen
The metabolite acetyl-coenzyme A (acetyl-CoA) is the required acetyl donor for lysine acetylation and thereby links metabolism, signaling, and epigenetics. Nutrient availability alters acetyl-CoA levels in cancer cells, correlating with changes in global histone acetylation and gene expression. However, the specific molecular mechanisms through which acetyl-CoA production impacts gene expression and its functional roles in promoting malignant phenotypes are poorly understood. Here, using histone H3 Lys27 acetylation (H3K27ac) ChIP-seq (chromatin immunoprecipitation [ChIP] coupled with next-generation sequencing) with normalization to an exogenous reference genome (ChIP-Rx), we found that changes in acetyl-CoA abundance trigger site-specific regulation of H3K27ac, correlating with gene expression as opposed to uniformly modulating this mark at all genes...
April 19, 2018: Genes & Development
https://www.readbyqxmd.com/read/29674095/effects-of-tri%C3%AF-uralin-on-the-soil-microbial-community-and-functional-groups-involved-in-nitrogen-cycling
#13
Pengqiang Du, Xiaohu Wu, Jun Xu, Fengshou Dong, Xingang Liu, Yongquan Zheng
Large amounts of trifluralin are applied each year for weed control; however, its effects on soil microbial communities and functions are unknown. Two agricultural soils, one silty loam and one silty clay were spiked with TFL (0, 0.84, 8.4, and 84 mg kg-1 ) and studied the effects using a laboratory microcosm approach. The half-lives were 44.19-61.83 d in all cases. Bacterial abundance increased 1.12-5.56 times by TFL, but the diversity decreased. From the next-generation sequencing results, TFL altered the bacterial community structure, which initially diverged from the control community structure, then recovered, and then diverged again...
April 10, 2018: Journal of Hazardous Materials
https://www.readbyqxmd.com/read/29673993/dynamics-of-bacterial-composition-and-the-fate-of-antibiotic-resistance-genes-and-mobile-genetic-elements-during-the-co-composting-with-gentamicin-fermentation-residue-and-lovastatin-fermentation-residue
#14
Yuanwang Liu, Yao Feng, Dengmiao Cheng, Jianming Xue, Steven Wakelin, Zhaojun Li
Dynamics in bacterial community composition, along with 13 antibiotic resistance genes (ARGs) and eight mobile genetic elements (MGEs), were assessed during co-composting with gentamicin and lovastatin fermentation residue (GFR and LFR, respectively). Using next generation sequencing, the key bacterial taxa associated with the different stages of composting were identified. Most importantly, Bacillus, belonging to Phylum Firmicutes, was associated with enhanced degradation of gentamicin, decomposition of organic matter (OM) and dissolved organic carbon (DOC), and also extension of the thermophilic phase of the composting cycle...
April 5, 2018: Bioresource Technology
https://www.readbyqxmd.com/read/29673906/interest-of-next-generation-sequencing-in-bcg-treated-high-risk-bladder-cancer
#15
C Jungels, N Martinez Chanza, S Albisinni, M Mercier, N d'Haene, S Rorive, T Roumeguère
OBJECTIVES: There are only few predictive factors for response of non-musculo-invasive bladder cancer (NMIBC) to Bacillus Calmette-Guérin (BCG) therapy. Our study analyzed the results of the sequencing of new generation (NGS) targeted on 50 genes of oncological interest obtained on bladder resection parts in high-risk NMIBC patients treated with BCG, to describe this population from a molecular point of view and try to correlate these results in patients who present or not recurrence after BCG...
April 16, 2018: Progrès en Urologie
https://www.readbyqxmd.com/read/29673712/update-on-systemic-prostate-cancer-therapies-management-of-metastatic-castration-resistant-prostate-cancer-in-the-era-of-precision-oncology
#16
REVIEW
Philipp Nuhn, Johann S De Bono, Karim Fizazi, Stephen J Freedland, Maurizio Grilli, Philip W Kantoff, Guru Sonpavde, Cora N Sternberg, Srinivasan Yegnasubramanian, Emmanuel S Antonarakis
CONTEXT: Introduction of novel agents for the management of advanced prostate cancer provides a range of treatment options with notable benefits for men with metastatic castration-resistant prostate cancer (mCRPC). At the same time, understanding of optimal patient selection, effective sequential use, and development of resistance patterns remains incomplete. OBJECTIVE: To review current systemic therapies and recent advances in drug development for mCRPC and strategies to aid in patient selection and optimal sequencing...
April 16, 2018: European Urology
https://www.readbyqxmd.com/read/29673582/in-silico-prediction-of-the-pathogenic-effect-of-a-novel-variant-of-bckdha-leading-to-classical-maple-syrup-urine-disease-identified-using-clinical-exome-sequencing
#17
Cynthia Fernández-Lainez, Carmen Aláez-Verson, Isabel Ibarra-González, Sergio Enríquez-Flores, Karol Carrillo-Sanchez, Leonardo Flores-Lagunes, Sara Guillén-López, Leticia Belmont-Martínez, Marcela Vela-Amieva
Maple syrup urine disease (MSUD) is a metabolic disorder caused by mutations in three of the branched-chain α-keto acid dehydrogenase complex (BCKDC) genes. Classical MSUD symptom can be observed immediately after birth and include ketoacidosis, irritability, lethargy, and coma, which can lead to death or irreversible neurodevelopmental delay in survivors. The molecular diagnosis of MSUD can be time-consuming and difficult to establish using conventional Sanger sequencing because it could be due to pathogenic variants of any of the BCKDC genes...
April 16, 2018: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/29673316/a-study-on-fast-calling-variants-from-next-generation-sequencing-data-using-decision-tree
#18
Zhentang Li, Yi Wang, Fei Wang
BACKGROUND: The rapid development of next-generation sequencing (NGS) technology has continuously been refreshing the throughput of sequencing data. However, due to the lack of a smart tool that is both fast and accurate, the analysis task for NGS data, especially those with low-coverage, remains challenging. RESULTS: We proposed a decision-tree based variant calling algorithm. Experiments on a set of real data indicate that our algorithm achieves high accuracy and sensitivity for SNVs and indels and shows good adaptability on low-coverage data...
April 19, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29673048/emerging-diagnostic-tests-for-vitreoretinal-lymphoma
#19
REVIEW
Abby C Dawson, Keryn A Williams, Binoy Appukuttan, Justine R Smith
Vitreoretinal lymphoma, which most commonly is diffuse large B cell non-Hodgkin in type, is a rare cancer with high morbidity and high mortality. Making a tissue diagnosis of vitreoretinal lymphoma is a major challenge for clinicians due to biological and technical factors. Yet, the delay in start of treatment may have vision- and life- threatening consequences, and there is considerable interest in the application of molecular assays to improve the accuracy of the diagnostic process: detection of a clonal immunoglobulin heavy chain rearrangements in lymphoma cells by polymerase chain reaction; measurement of vitreous or aqueous interleukin-10 protein levels in ocular fluids; and identification of mutations in the myeloid differentiation primary response gene 88 in tumour cells...
April 19, 2018: Clinical & Experimental Ophthalmology
https://www.readbyqxmd.com/read/29672931/x-linked-ichthyosis-clinical-and-molecular-findings-in-35-italian-patients
#20
Andrea Diociaiuti, Adriano Angioni, Elisa Pisaneschi, Viola Alesi, Giovanna Zambruno, Antonio Novelli, May El Hachem
Recessive X-linked ichthyosis (XLI), the second most common ichthyosis, is caused by mutations in the STS gene encoding the steroid sulfatase enzyme. A complete deletion of the STS gene is found in 85-90% of cases. Rarely, larger deletions involving contiguous genes are detected in syndromic patients. We report the clinical and molecular genetic findings in a series of 35 consecutive Italian male patients. All patients underwent molecular testing by MLPA or aCGH, followed, in case of negative results, by next generation sequencing analysis...
April 19, 2018: Experimental Dermatology
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