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https://www.readbyqxmd.com/read/29679878/modeling-of-intracerebral-interictal-epileptic-discharges-evidence-for-network-interactions
#1
Stephan Meesters, Pauly Ossenblok, Albert Colon, Louis Wagner, Olaf Schijns, Paul Boon, Luc Florack, Andrea Fuster
OBJECTIVE: The interictal epileptic discharges (IEDs) occurring in stereotactic EEG (SEEG) recordings are in general abundant compared to ictal discharges, but difficult to interpret due to complex underlying network interactions. A framework is developed to model these network interactions. METHODS: To identify the synchronized neuronal activity underlying the IEDs, the variation in correlation over time of the SEEG signals is related to the occurrence of IEDs using the general linear model...
April 11, 2018: Clinical Neurophysiology: Official Journal of the International Federation of Clinical Neurophysiology
https://www.readbyqxmd.com/read/29679778/recapitulating-spatiotemporal-tumor-heterogeneity-in-vitro-through-engineered-breast-cancer-microtissues
#2
Claudia Mazio, Costantino Casale, Giorgia Imparato, Francesco Urciuolo, Paolo Antonio Netti
Tumor and microenvironmental heterogeneity hinders the study of breast cancer biology and the assessment of therapeutic strategies, being associated with high variability and drug resistance. In this context, it is mandatory to develop three-dimensional breast tumor models able to reproduce this heterogeneity and the dynamic interaction occurring between tumor cells and microenvironment. Here we show a new breast cancer microtissue model (T-µTP) uniquely able to present intra-tumor morphological heterogeneity in a dynamic and responsive endogenous matrix...
April 18, 2018: Acta Biomaterialia
https://www.readbyqxmd.com/read/29679758/validation-and-bioinformatic-analysis-of-propofol-induced-differentially-expressed-micrornas-in-primary-cultured-neural-stem-cells
#3
Yan Li, Youtan Liu, Jun Fan, Quan Zhou, Xiuling Song, Zhiyong Peng, Zaisheng Qin, Tao Tao
Propofol, a widely used intravenous anesthetic, was previously considered as a neuroprotective agent. Recently, however, accumulating evidence suggests that it may cause neurotoxicity, especially in the development of neural stem cells (NSCs). The potential mechanisms contributing to propofol-induced neurotoxicity during neurogenesis, such as those involving microRNAs (miRNAs), are still unknown. In this study, a total of 27 differentially expressed miRNAs were identified in our initial screen and 6 miRNAs were validated by qRT-PCR...
April 18, 2018: Gene
https://www.readbyqxmd.com/read/29679715/molecular-phylogeny-and-comparative-morphology-indicate-that-odontostomatids-alveolata-ciliophora-form-a-distinct-class-level-taxon-related-to-armophorea
#4
Noemi M Fernandes, Vinicius F Vizzoni, Bárbara do N Borges, Carlos A G Soares, Inácio D da Silva-Neto, Thiago da S Paiva
The odontostomatids are among the least studied ciliates, possibly due to their small sizes, restriction to anaerobic environments and difficulty in culturing. Consequently, their phylogenetic affinities to other ciliate taxa are still poorly understood. In the present study, we analyzed newly obtained ribosomal gene sequences of the odontostomatids Discomorphella pedroeneasi and Saprodinium dentatum, together with sequences from the literature, including Epalxella antiquorum and a large assemblage of ciliate sequences representing the major recognized classes...
April 18, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29679704/a-separable-two-dimensional-random-field-model-of-binary-response-data-from-multi-day-behavioral-experiments
#5
Noa Malem-Shinitski, Yingzhuo Zhang, Daniel T Gray, Sara N Burke, Anne C Smith, Carol A Barnes, Demba Ba
BACKGROUND: The study of learning in populations of subjects can provide insights into the changes that occur in the brain with aging, drug intervention, and psychiatric disease. NEW METHOD: We introduce a separable two-dimensional (2D) random field (RF) model for analyzing binary response data acquired during the learning of object-reward associations across multiple days. The method can quantify the variability of performance within a day and across days, and can capture abrupt changes in learning...
April 18, 2018: Journal of Neuroscience Methods
https://www.readbyqxmd.com/read/29679694/the-introduction-of-a-rapid-response-system-in-acute-hospitals-a-pragmatic-stepped-wedge-cluster-randomised-controlled-trial
#6
Filip Haegdorens, Peter Van Bogaert, Ella Roelant, Koen De Meester, Marie Misselyn, Kristien Wouters, Koenraad G Monsieurs
AIM: Deterioration of hospitalised patients is often missed, misinterpreted, and mismanaged. Rapid Response Systems (RRSs) have been proposed to solve this problem. This study aimed to investigate the effect of an RRS on the incidence of unexpected death, cardiac arrest with cardiopulmonary resuscitation (CPR), and unplanned intensive care unit (ICU) admission. METHODS: We conducted a stepped wedge cluster randomised controlled trial including 14 Belgian acute care hospitals with two medical and two surgical wards each...
April 18, 2018: Resuscitation
https://www.readbyqxmd.com/read/29679685/identifying-and-characterizing-highly-similar-notes-in-big-clinical-note-datasets
#7
Rodney A Gabriel, Tsung-Ting Kuo, Julian McAuley, Chun-Nan Hsu
BACKGROUND: Big clinical note datasets found in electronic health records (EHR) present substantial opportunities to train accurate statistical models that identify patterns in patient diagnosis and outcomes. However, near-to-exact duplication in note texts is a common issue in many clinical note datasets. We aimed to use a scalable algorithm to de-duplicate notes and further characterize the sources of duplication. METHODS: We use an approximation algorithm to minimize pairwise comparisons consisting of three phases: 1) Minhashing with Locality Sensitive Hashing; 2) a clustering method using tree-structured disjoint sets; and 3) classification of near-duplicates (exact copies, common machine output notes, or similar notes) via pairwise comparison of notes in each cluster...
April 18, 2018: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/29679645/sequencing-of-pt5282-ctxm-p13190-kpc-and-p30860-nr-and-comparative-genomics-analysis-of-incx8-plasmids
#8
Haihong Fang, Jiao Feng, Yuanhong Xu, Ying Zhang, Zhe Zhan, Zhe Yin, Xiongbo Duan, Bo Gao, Yigang Tong, Jinglin Wang, Yanping Luo, Erhei Dai, Dongsheng Zhou
This study proposed a replicon-based scheme for typing IncX into nine separately clustering subgroups, including IncX1α, IncX1β and IncX2-8. The complete nucleotide sequences of three IncX8 plasmids, namely pT5282-CTXM and p30860-NR from Enterobacter cloacae and p13190-KPC from Klebsiella pneumoniae, were determined and compared with all the other two previously sequenced IncX8 plasmids pCAV1043-58 and pCAV1741-16. These five plasmids possessed conserved IncX8 backbones with limited genetic variations with respect to gene content and organization, and each of them carried one or three accessory modules that harbored resistance markers and metabolic gene clusters as well as transposons, insertion sequence (IS)-based transposition units and miniature inverted repeat transposable elements, indicating that the relatively small IncX8 backbones were able to integrate various foreign genetic contents...
April 18, 2018: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/29679591/the-intrauterine-device-as-emergency-contraception-how-much-do-young-women-know
#9
Suzan R Goodman, Alison M El Ayadi, Corinne H Rocca, Julia E Kohn, Courtney E Benedict, Jessica R Dieseldorff, Cynthia C Harper
BACKGROUND: Unprotected intercourse is common, especially among teens and young women. Access to intrauterine device (IUD) as emergency contraception (EC) can help interested patients more effectively prevent unintended pregnancy and can also offer ongoing contraception. This study evaluated young women's awareness of IUD as EC and interest in case of need. STUDY DESIGN: We conducted a secondary analysis of data from young women, ages 18-25years, not desiring pregnancy within 12months, and receiving contraceptive counseling within a cluster-randomized trial in 40U...
April 18, 2018: Contraception
https://www.readbyqxmd.com/read/29679573/circrna-expression-analysis-in-lung-adenocarcinoma-comparison-of-paired-fresh-frozen-and-formalin-fixed-paraffin-embedded-specimens
#10
Fan Zhang, Xing Zhao, Hongyan Dong, Jianzhen Xu
Circular RNA (circRNAs) is a novel class of endogenous non-coding RNAs which is widely involved in carcinogenesis. Archived formalin-fixed paraffin-embedded (FFPE) specimens represent valuable resources for cancer research. Currently there is a lack of systematic analysis on the feasibility of circRNAs expression analysis using FFPE samples. Here, we reported the first comparison study of circRNA expression from paired fresh frozen and FFPE specimens of lung adenocarcinoma. circRNAs expression of paired lung adenocarcinoma and adjacent normal samples, starting from either fresh frozen or FFPE materials, were analyzed via a high-throughput circRNA microarray...
April 18, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29679512/phylogenetic-analysis-of-dunaliella-chlorophyta-emphasizing-new-benthic-and-supralittoral-isolates-from-great-salt-lake
#11
William J Henley, Michael Cobbs, Lucie Novoveská, Mark A Buchheim
Dunaliella, a commercially important chlorophyte, is globally distributed in saline habitats. Morphological species have not been definitively reconciled with phylogenetic analyses. Considerable genetic diversity continues to be discovered in new isolates, especially from soil and benthic habitats. Twenty-nine new isolates from Great Salt Lake, Utah, many from benthic or supralittoral habitats, were phylogenetically analyzed using ITS1+5.8S+ITS2 in comparison to a broad sampling of available sequences. A few new isolates align in one branch of a bifurcated monophyletic D...
April 21, 2018: Journal of Phycology
https://www.readbyqxmd.com/read/29679497/ewsr1-patz1-gene-fusion-may-define-a-new-glioneuronal-tumor-entity
#12
Aurore Siegfried, Audrey Rousseau, Claude-Alain Maurage, Sarah Pericart, Yvan Nicaise, Frederic Escudie, David Grand, Alix Delrieu, Anne Gomez-Brouchet, Sophie Le Guellec, Camille Franchet, Sergio Boetto, Matthieu Vinchon, Jean-Christophe Sol, Franck-Emmanuel Roux, Valerie Rigau, Anne-Isabelle Bertozzi, David Tw Jones, Dominique Figarella-Branger, Emmanuelle Uro-Coste
We investigated the challenging diagnostic case of a ventricular cystic glioneuronal tumor with papillary features, by RNA sequencing using the Illumina TruSight RNA Fusion panel. We did not retrieve the SLC44A1-PRKCA fusion gene specific for papillary glioneuronal tumor, but an EWSR1-PATZ1 fusion transcript. RT-PCR followed by Sanger sequencing confirmed the EWSR1-PATZ1 fusion. It matched with canonic EWSR1 fusion oncogene, juxtaposing the entire N terminal transcriptional activation domain of EWSR1 gene and the C terminal DNA binding domain of a transcription factor gene, PATZ1...
April 21, 2018: Brain Pathology
https://www.readbyqxmd.com/read/29679249/lc-ms-ms-based-metabolome-analysis-of-biochemical-pathways-altered-by-food-limitation-in-larvae-of-ivory-shell-babylonia-areolata
#13
Jingqiang Fu, Minghui Shen, Yawei Shen, Wengang Lü, Miaoqin Huang, Xuan Luo, Jinjin Yu, Caihuan Ke, Weiwei You
Ivory shell, Babylonia areolata, is one of the commercially important mariculture species in China and South East Asia. Survival varies in the artificial hatching and larval rearing of B. areolata. Food deprivation may be involved in rearing mortality, and so, a better understanding of how larvae respond and adjust to starvation is needed. In this study, the metabolite profiles of newly hatched larvae with yolk (I), larvae with yolk exhaustion (II), larvae suffering 24 h starvation after yolk exhaustion (III), and larvae fed with exogenous nutrients after yolk exhaustion (IV) were analyzed by LC-MS/MS...
April 20, 2018: Marine Biotechnology
https://www.readbyqxmd.com/read/29679242/automatic-organ-segmentation-for-ct-scans-based-on-super-pixel-and-convolutional-neural-networks
#14
Xiaoming Liu, Shuxu Guo, Bingtao Yang, Shuzhi Ma, Huimao Zhang, Jing Li, Changjian Sun, Lanyi Jin, Xueyan Li, Qi Yang, Yu Fu
Accurate segmentation of specific organ from computed tomography (CT) scans is a basic and crucial task for accurate diagnosis and treatment. To avoid time-consuming manual optimization and to help physicians distinguish diseases, an automatic organ segmentation framework is presented. The framework utilized convolution neural networks (CNN) to classify pixels. To reduce the redundant inputs, the simple linear iterative clustering (SLIC) of super-pixels and the support vector machine (SVM) classifier are introduced...
April 20, 2018: Journal of Digital Imaging: the Official Journal of the Society for Computer Applications in Radiology
https://www.readbyqxmd.com/read/29679198/the-association-between-heavy-metal-soil-pollution-and-stomach-cancer-a-case-study-in-hangzhou-city-china
#15
Xufeng Fei, Zhaohan Lou, George Christakos, Zhouqiao Ren, Qingmin Liu, Xiaonan Lv
Stomach cancer (SC) is a severe health burden, with nearly half of the world's cases found in China. Noticeably, the emissions of heavy metals into the environment have increased alongside rapid urbanization and industrialization in China. However, as regards carcinogenic associations, the relationship between heavy metals and SC is yet unclear. Based on 9378 newly diagnosed SC cases in Hangzhou City from 2009 to 2012, this work is concerned with the quantitative characterization of the spatial distribution pattern of SC incidence and its geographical association with soil heavy metals by means of a novel geographical model...
April 20, 2018: Environmental Geochemistry and Health
https://www.readbyqxmd.com/read/29679119/the-role-of-iron-competition-in-the-antagonistic-action-of-the-rice-endophyte-streptomyces-sporocinereus-osish-2-against-the-pathogen-magnaporthe-oryzae
#16
Jiarui Zeng, Ting Xu, Lidan Cao, Chunyi Tong, Xuan Zhang, Dingyi Luo, Shuping Han, Pei Pang, Weibin Fu, Jindong Yan, Xuanming Liu, Yonghua Zhu
Rice blast caused by Magnaporthe oryzae severely impacts global rice yield stability. The rice endophyte Streptomyces sporocinereus OsiSh-2, with strong antagonistic activity towards M. oryzae, has been reported in our previous study. To decipher the model of the antagonistic action of OsiSh-2 towards M. oryzae, we compared the iron-capturing abilities of these two strains. The cultivation of OsiSh-2 and a M. oryzae strain under iron-rich and iron-starved conditions showed that M. oryzae depended more on iron supplementation for growth and development than did OsiSh-2...
April 20, 2018: Microbial Ecology
https://www.readbyqxmd.com/read/29679115/analyzing-chromatographic-data-using-multilevel-modeling
#17
Paweł Wiczling
It is relatively easy to collect chromatographic measurements for a large number of analytes, especially with gradient chromatographic methods coupled with mass spectrometry detection. Such data often have a hierarchical or clustered structure. For example, analytes with similar hydrophobicity and dissociation constant tend to be more alike in their retention than a randomly chosen set of analytes. Multilevel models recognize the existence of such data structures by assigning a model for each parameter, with its parameters also estimated from data...
April 21, 2018: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/29679043/identification-and-heterologous-expression-of-the-actinoallolide-biosynthetic-gene-cluster
#18
Yuki Inahashi, Taro Shiraishi, Akira Také, Atsuko Matsumoto, Yōko Takahashi, Satoshi Ōmura, Tomohisa Kuzuyama, Takuji Nakashima
Actinoallolides are anti-trypanosomal macrolides isolated from the secondary metabolites of two endophytic actinomycete strains, Actinoallomurus fulvus MK10-036 and K09-0307. A putative actinoallolide biosynthetic gene cluster was predicted from the genome sequence of the strain K09-0307. The gene cluster spans a contiguous 53 kb DNA region that comprises seven genes encoding three PKSs (aalA1, aalA2, and aalA3), cytochrome P450 (aalB), acyl-CoA dehydrogenase (aalC), crotonyl-CoA reductase (aalD), and TetR family regulator (aalR)...
April 20, 2018: Journal of Antibiotics
https://www.readbyqxmd.com/read/29679032/comparison-of-an-unsupervised-machine-learning-algorithm-and-surgeon-diagnosis-in-the-clinical-differentiation-of-metopic-craniosynostosis-and-benign-metopic-ridge
#19
Min-Jeong Cho, Rami R Hallac, Maleeh Effendi, James R Seaward, Alex A Kane
Metopic suture closure can manifest as a benign metopic ridge (BMR), a variant of normal, to "true" metopic craniosynostosis (MCS), which is associated with severe trigonocephaly. Currently, there is no gold standard for how much associated orbitofrontal dysmorphology should trigger surgical intervention. In our study, we used three-dimensional (3D) curvature analysis to separate the phenotypes along the spectrum, and to compare surgeons' thresholds for operation. Three-dimensional curvature analyses on 43 subject patients revealed that the mean curvature of mid-forehead vertical ridge was higher for patients who underwent operation than those who did not undergo operation by 1...
April 20, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29679020/comparative-genomics-provides-insights-into-the-lifestyle-and-reveals-functional-heterogeneity-of-dark-septate-endophytic-fungi
#20
Dániel G Knapp, Julianna B Németh, Kerrie Barry, Matthieu Hainaut, Bernard Henrissat, Jenifer Johnson, Alan Kuo, Joanne Hui Ping Lim, Anna Lipzen, Matt Nolan, Robin A Ohm, László Tamás, Igor V Grigoriev, Joseph W Spatafora, László G Nagy, Gábor M Kovács
Dark septate endophytes (DSE) are a form-group of root endophytic fungi with elusive functions. Here, the genomes of two common DSE of semiarid areas, Cadophora sp. and Periconia macrospinosa were sequenced and analyzed with another 32 ascomycetes of different lifestyles. Cadophora sp. (Helotiales) and P. macrospinosa (Pleosporales) have genomes of 70.46 Mb and 54.99 Mb with 22,766 and 18,750 gene models, respectively. The majority of DSE-specific protein clusters lack functional annotation with no similarity to characterized proteins, implying that they have evolved unique genetic innovations...
April 20, 2018: Scientific Reports
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