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Caetano Souto-Maior, Gabriel Sylvestre, Fernando Braga Stehling Dias, M Gabriela M Gomes, Rafael Maciel-de-Freitas
Infection is a complex and dynamic process involving a population of invading microbes, the host and its responses, aimed at controlling the situation. Depending on the purpose and level of organization, infection at the organism level can be described by a process as simple as a coin toss, or as complex as a multi-factorial dynamic model; the former, for instance, may be adequate as a component of a population model, while the latter is necessary for a thorough description of the process beginning with a challenge with an infectious inoculum up to establishment or elimination of the pathogen...
March 20, 2018: PLoS Neglected Tropical Diseases
Irena Urbanovska, Magdalena Houdova Megova, Zachary Dwight, Ondrej Kalita, Magdalena Uvirova, Jarmila Simova, Lucie Tuckova, Petr Buzrla, Tomas Palecek, Marian Hajduch, Jana Dvorackova, Jiri Drabek
Mutations in IDH1/2 genes are a marker of good prognosis for glioma patients, associated with low grade gliomas and secondary glioblastomas. Immunohistochemistry and Sanger sequencing are current standards for IDH1/2 genotyping while many other methods exist. The aim of this study was to validate Competitive amplification of differentially melting amplicons (CADMA) PCR for IDH genotyping by comparison with SNaPshot assay and two immunohistochemical methods. In our study, 87 glioma patients (46 from Olomouc and 41 from Ostrava) were analyzed...
March 19, 2018: Pathology Oncology Research: POR
Caroline L Furness, Marcela B Mansur, Victoria J Weston, Luca Ermini, Frederik W van Delft, Sarah Jenkinson, Rosemary Gale, Christine J Harrison, Maria S Pombo-de-Oliveira, Marta Sanchez-Martin, Adolfo A Ferrando, Pamela Kearns, Ian Titley, Anthony M Ford, Nicola E Potter, Mel Greaves
Single-cell genetics were used to interrogate clonal complexity and the sequence of mutational events in STIL-TAL1+ T-ALL. Single-cell multicolour FISH was used to demonstrate that the earliest detectable leukaemia subclone contained the STIL-TAL1 fusion and copy number loss of 9p21.3 (CDKN2A/CDKN2B locus), with other copy number alterations including loss of PTEN occurring as secondary subclonal events. In three cases, multiplex qPCR and phylogenetic analysis were used to produce branching evolutionary trees recapitulating the snapshot history of T-ALL evolution in this leukaemia subtype, which confirmed that mutations in key T-ALL drivers, including NOTCH1 and PTEN, were subclonal and reiterative in distinct subclones...
March 20, 2018: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
Pu Wang, Gianluca Turcatel, Cosimo Arnesano, David Warburton, Scott E Fraser, Francesco Cutrale
Hyperspectral endoscopic imaging has the potential to enhance clinical diagnostics and outcome. Most commercial endoscopes utilize imaging fiber bundles to transmit the collected signal from the patient to the medical operator. These bundles consist of several fiber cores surrounded by a cladding layer creating comb structure-like artifacts, which complicate further analysis, both spatially and spectrally. Here we present an optical fiber pattern removal algorithm which we applied to hyperspectral bronchoscopic images robustly and quantitatively without the need for specific optical or electrical hardware...
February 1, 2018: Biomedical Optics Express
Kari V Vienola, Mathi Damodaran, Boy Braaf, Koenraad A Vermeer, Johannes F de Boer
Retinal motion detection with an accuracy of 0.77 arcmin corresponding to 3.7 µm on the retina is demonstrated with a novel digital micromirror device based ophthalmoscope. By generating a confocal image as a reference, eye motion could be measured from consecutively measured subsampled frames. The subsampled frames provide 7.7 millisecond snapshots of the retina without motion artifacts between the image points of the subsampled frame, distributed over the full field of view. An ophthalmoscope pattern projection speed of 130 Hz enabled a motion detection bandwidth of 65 Hz...
February 1, 2018: Biomedical Optics Express
Srilena Kundu, Soumen Majhi, Bidesh K Bera, Dibakar Ghosh, M Lakshmanan
Chimera state is defined as a mixed type of collective state in which synchronized and desynchronized subpopulations of a network of coupled oscillators coexist and the appearance of such anomalous behavior has strong connection to diverse neuronal developments. Most of the previous studies on chimera states are not extensively done in two-dimensional ensembles of coupled oscillators by taking neuronal systems with nonlinear coupling function into account while such ensembles of oscillators are more realistic from a neurobiological point of view...
February 2018: Physical Review. E
Elle Wadsworth, Colin Drummond, Paolo Deluca
The Internet has played a major role in the distribution of New Psychoactive Substances (NPS), and crypto markets are increasingly used for the anonymous sale of drugs, including NPS. This study explores the availability of individual NPS and vendors on the crypto markets and considers whether crypto markets are a reliable platform for the sale of NPS. Data was collected from 22 crypto markets that were accessed through the hidden web using the Onion Router (Tor). Data collection took place bimonthly from October 2015 to October 2016 as part of the CASSANDRA ( C omputer A ssisted S olutions for S tudying the A vailability a N d D ist R ibution of novel psycho A ctive substances) project...
March 16, 2018: Brain Sciences
Alexander B Rosenberg, Charles M Roco, Richard A Muscat, Anna Kuchina, Paul Sample, Zizhen Yao, Lucas Gray, David J Peeler, Sumit Mukherjee, Wei Chen, Suzie H Pun, Drew L Sellers, Bosiljka Tasic, Georg Seelig
To facilitate scalable profiling of single cells, we developed split-pool ligation-based transcriptome sequencing (SPLiT-seq), a single-cell RNA-seq (scRNA-seq) method that labels the cellular origin of RNA through combinatorial barcoding. SPLiT-seq is compatible with fixed cells or nuclei, allows efficient sample multiplexing and requires no customized equipment. We used SPLiT-seq to analyze 156,049 single-nucleus transcriptomes from postnatal day 2 and 11 mouse brains and spinal cords. Over 100 cell types were identified, with gene expression patterns corresponding to cellular function, regional specificity, and stage of differentiation...
March 15, 2018: Science
Paolo Calabrò, Felice Gragnano, Marco di Maio, Giuseppe Patti, Emilia Antonucci, Plinio Cirillo, Paolo Gresele, Gualtiero Palareti, Vittorio Pengo, Pasquale Pignatelli, Mauro Pennacchi, Antonino Granatelli, Stefano De Servi, Leonardo De Luca, Rossella Marcucci
The epidemiology and management of patients with acute coronary syndromes (ACSs) have evolved. We aimed to describe recent demographics and therapeutic changes in the Italian ACS population. We analyzed data from 2 multicenter consecutive Italian registries (the EYESHOT [EmploYEd antithrombotic therapies in patients with acute coronary Syndromes HOspitalised in iTalian cardiac care units] and START-ANTIPLATELET registries) enrolling patients with ACS between December 2013 and June 2016. An overall population of 3756 patients with ACS was enrolled: 2585 in the EYESHOT and 1171 in the START-ANTIPLATELET...
January 1, 2018: Angiology
Trung Hai Nguyen, David D L Minh
Implicit ligand theory enables noncovalent binding free energies to be calculated based on an exponential average of the binding potential of mean force (BPMF)-the binding free energy between a flexible ligand and rigid receptor-over a precomputed ensemble of receptor configurations. In the original formalism, receptor configurations were drawn from or reweighted to the apo ensemble. Here we show that BPMFs averaged over a holo ensemble yield binding free energies relative to the reference ligand that specifies the ensemble...
March 14, 2018: Journal of Chemical Physics
Jaepyeong Cha, Aline Broch, Scott Mudge, Kihoon Kim, Jung-Man Namgoong, Eugene Oh, Peter Kim
Accurate, real-time identification and display of critical anatomic structures, such as the nerve and vasculature structures, are critical for reducing complications and improving surgical outcomes. Human vision is frequently limited in clearly distinguishing and contrasting these structures. We present a novel imaging system, which enables noninvasive visualization of critical anatomic structures during surgical dissection. Peripheral nerves are visualized by a snapshot polarimetry that calculates the anisotropic optical properties...
March 1, 2018: Biomedical Optics Express
Zhengtao Xiao, Rongyao Huang, Xudong Xing, Yuling Chen, Haiteng Deng, Xuerui Yang
By capturing and sequencing the RNA fragments protected by translating ribosomes, ribosome profiling provides snapshots of translation at subcodon resolution. The growing needs for comprehensive annotation and characterization of the context-dependent translatomes are calling for an efficient and unbiased method to accurately recover the signal of active translation from the ribosome profiling data. Here we present our new method, RiboCode, for such purpose. Being tested with simulated and real ribosome profiling data, and validated with cell type-specific QTI-seq and mass spectrometry data, RiboCode exhibits superior efficiency, sensitivity, and accuracy for de novo annotation of the translatome, which covers various types of ORFs in the previously annotated coding and non-coding regions...
March 10, 2018: Nucleic Acids Research
Cristina Di Poto, Shisi He, Rency S Varghese, Yi Zhao, Alessia Ferrarini, Shan Su, Abdullah Karabala, Mesfin Redi, Hassen Mamo, Amol S Rangnekar, Thomas M Fishbein, Alexander H Kroemer, Mahlet G Tadesse, Rabindra Roy, Zaki A Sherif, Deepak Kumar, Habtom W Ressom
Disparities in hepatocellular carcinoma (HCC) incidence and survival have been observed between ethnic groups including African-Americans (AA) and European-Americans (EA). The evaluation of the changes in the levels of metabolites in samples stratified by race could provide a snapshot of ethnically diverse disease related pathways and identify reliable biomarkers. In this study, we considered AA and EA to investigate metabolites that may be associated with HCC in a race-specific manner. The levels of 46 metabolites in plasma samples, collected from patients recruited at MedStar Georgetown University Hospital, were analyzed by Agilent GC-qMS in selected ion monitoring (SIM) mode...
2018: PloS One
C Fraschetti, L Guarcini, C Zazza, L Mannina, S Circi, S Piccirillo, B Chiavarino, A Filippi
Conformational characterization of single α- and β-epimers of galactosamine in solution still remains an intriguing task because of their flexibility and ability to interconvert. This difficulty was circumvented by recording several "snapshots" of the epimerization process by means of fast ESI vaporization of a galactosamine·HCl sample solution at different times. Consequently, the so generated gaseous mixtures were spectroscopically investigated and the specific conformational features of both α- and β-epimers were assigned, despite the overlapping of several IR signals...
March 14, 2018: Physical Chemistry Chemical Physics: PCCP
Xiaoqing Gong, Shenghui Mei, Xindi Li, Xingang Li, Heng Zhou, Yonghong Liu, Anna Zhou, Li Yang, Zhigang Zhao, Xinghu Zhang
Thiopurines (TPRs) are effective drugs in treating neuromyelitis optica spectrum disorders (NMOSD) and other diseases. TPRs' toxicity is mainly imputed to thiopurine S-methyltransferase (TPMT) activity. In Chinese population, the most common and important variation of TPMT is TPMT*3C (rs1142345). This study aims to reveal the association between TPMT activity and genetic polymorphisms of TPMT in patients with NMOSD in China. An LC-MS/MS method was used to evaluate the TPMT activity by using 6-mercapthioprine as substrate in human erythrocyte hemolysate via 1 h incubation at 37 °C to form its methylated product 6-methylmercaptopurine (6-MMP)...
March 10, 2018: Journal of Clinical Neuroscience: Official Journal of the Neurosurgical Society of Australasia
D Zidekova, I Waczulikova, L Dolesova, L Vavrova, O Hamidova, R Lohajova Behulova, M Konecny
The average risk of breast cancer in general Slovak population of women is 4-5% and the risk of ovarian cancer is 2%. Probability of breast/ovarian cancer development is higher in individuals carrying a causative germline DNA variant in BRCA1 or BRCA2 gene responsible for hereditary breast/ovarian cancer (HBOC). Although a major proportion of inherited breast/ovarian cancers are due to the mentioned causal mutations, a number of new genes have emerged. Here we describe a rapid, multiplex and comprehensive approach for the detection of pathogenic variants in BRCA1 and BRCA2 genes which most frequently occur in Slovak HBOC population...
2018: Neoplasma
Aditi Jain, Saurabh Anand, Neer K Singh, Sandip Das
The impact of polyploidy on functional diversification of cis-regulatory elements is poorly understood. This is primarily on account of lack of well-defined structure of cis-elements and a universal regulatory code. To the best of our knowledge, this is the first report on characterization of sequence and functional diversification of paralogous and homeologous promoter elements associated with MIR164 from Brassica. The availability of whole genome sequence allowed us to identify and isolate a total of 42 homologous copies of MIR164 from diploid species-Brassica rapa (A-genome), Brassica nigra (B-genome), Brassica oleracea (C-genome), and allopolyploids-Brassica juncea (AB-genome), Brassica carinata (BC-genome) and Brassica napus (AC-genome)...
March 12, 2018: Functional & Integrative Genomics
Bo Wen, Lei Xu, Junfu Liang, Zhanming Fan, Zhonghua Sun
OBJECTIVE: The purpose of this study was to evaluate the image quality and radiation dose of computed tomography (CT) coronary angiography using a 256-row detector CT scanner in a single cardiac cycle in patients with atrial fibrillation (AF). METHODS: Seventy consecutive patients (41 men and 29 women; age range was from 37 to 84 years, mean age was 61.7 ± 10.2 years; body mass index range was from 15.08 to 36.45 kg/m, mean body mass index was 25.9 ± 3.5 kg/m) with persistent or paroxysmal AF during acquisition, who were not receiving any medications for heart rate (HR) regulation, were imaged with a 256-row detector CT scanner (Revolution CT, GE healthcare)...
March 2018: Journal of Computer Assisted Tomography
R Modi, K R Amico, A Knudson, A O Westfall, J Keruly, H M Crane, E B Quinlivan, C Golin, J Willig, A Zinski, R Moore, S Napravnik, L Bryan, M S Saag, M J Mugavero
In the first year after HIV diagnosis, patients are simultaneously processing with their diagnosis, typically with an emotional component, while also developing a routine of regular medical care visits and antiretroviral therapy (ART) adherence. Maintaining "HIV adherence" and integrating it into one's daily life is required to sustain viral load suppression (VS) over time. The HIV care continuum or "treatment cascade," an epidemiological snapshot of the national epidemic in the United States (US), indicates that a minority of persons living with HIV (PLWH) have achieved VS...
March 8, 2018: Contemporary Clinical Trials
M D Bolmers, C C van Rossem, R R Gorter, W A Bemelman, A A W van Geloven, H A Heij
PURPOSE: A laparoscopic approach for emergency appendectomy is increasingly used, in pediatric patients as well. The objective of this study is to audit the current state of diagnostic work-up, surgical techniques and its outcome in children with acute appendicitis. METHODS: A prospective consecutive observational cohort study was carried out in a 2-month study period. All patients under 18 years that were operated for suspected acute appendicitis were included...
March 9, 2018: Pediatric Surgery International
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