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https://www.readbyqxmd.com/read/28334115/faster-a-user-friendly-tool-for-ultrafast-and-robust-cell-segmentation-in-large-scale-microscopy
#1
Oliver Hilsenbeck, Michael Schwarzfischer, Dirk Loeffler, Sotiris Dimopoulos, Simon Hastreiter, Carsten Marr, Fabian J Theis, Timm Schroeder
Motivation: Quantitative large-scale cell microscopy is widely used in biological and medical research. Such experiments produce huge amounts of image data and thus require automated analysis. However, automated detection of cell outlines (cell segmentation) is typically challenging due to, e.g., high cell densities, cell-to-cell variability and low signal-to-noise ratios. Results: Here, we evaluate accuracy and speed of various state-of-the-art approaches for cell segmentation in light microscopy images using challenging real and synthetic image data...
February 22, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28333621/reconstructing-evolving-tree-structures-in-time-lapse-sequences-by-enforcing-time-consistency
#2
Przemyslaw Glowacki, Miguel Amavel Pinheiro, Agata Mosinska, Engin Turetken, Daniel Lebrecht, Anthony Holtmaat, Raphael Sznitman, Jan Kybic, Pascal Fua
We propose a novel approach to reconstructing curvilinear tree structures evolving over time, such as road networks in 2D aerial images or neural structures in 3D microscopy stacks acquired in vivo. To enforce temporal consistency, we simultaneously process all images in a sequence, as opposed to reconstructing structures of interest in each image independently. We formulate the problem as a Quadratic Mixed Integer Program and demonstrate the additional robustness that comes from using all available visual clues at once, instead of working frame by frame...
March 10, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28333328/the-time-course-of-diagnostic-delay-in-inflammatory-bowel-disease-over-the-last-sixty-years-an-italian-multicentre-study
#3
Laura Cantoro, Antonio Di Sabatino, Claudio Papi, Giovanna Margagnoni, Sandro Ardizzone, Paolo Giuffrida, Diana Giannarelli, Alessandro Massari, Rita Monterubbianesi, Marco Vincenzo Lenti, Gino Roberto Corazza, Anna Kohn
Background and Aims: Inflammatory bowel disease (IBD) patients are still under-diagnosed or diagnosed with serious delay. We examined whether diagnostic delay (DD) in IBD has changed over the last 60 years, and explored the risk factors of longer DD. Methods: 3392 IBD patients recorded in the registry of four IBD Italian centres were divided according to the year of diagnosis into a historical cohort (HC: 1955-1984) and modern cohort (MC: 1985-2014). DD, i.e. time lapse between onset of symptoms indicative of IBD and definitive diagnosis, was divided into four sub-periods (0-6, 7-12, 13-24, >24 months) which were correlated with age and disease location/behaviour at diagnosis...
March 17, 2017: Journal of Crohn's & Colitis
https://www.readbyqxmd.com/read/28325928/a-microplate-reader-based-system-for-visualizing-transcriptional-activity-during-in-vivo-microbial-interactions-in-space-and-time
#4
Rosanna C Hennessy, Peter Stougaard, Stefan Olsson
Here, we report the development of a microplate reader-based system for visualizing gene expression dynamics in living bacterial cells in response to a fungus in space and real-time. A bacterium expressing the red fluorescent protein mCherry fused to the promoter region of a regulator gene nunF indicating activation of an antifungal secondary metabolite gene cluster was used as a reporter system. Time-lapse image recordings of the reporter red signal and a green signal from fluorescent metabolites combined with microbial growth measurements showed that nunF-regulated gene transcription is switched on when the bacterium enters the deceleration growth phase and upon physical encounter with fungal hyphae...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28324613/analysis-of-protein-kinetics-using-fluorescence-recovery-after-photobleaching-frap
#5
Nickolaos Nikiforos Giakoumakis, Maria Anna Rapsomaniki, Zoi Lygerou
Fluorescence recovery after photobleaching (FRAP) is a cutting-edge live-cell functional imaging technique that enables the exploration of protein dynamics in individual cells and thus permits the elucidation of protein mobility, function, and interactions at a single-cell level. During a typical FRAP experiment, fluorescent molecules in a defined region of interest within the cell are bleached by a short and powerful laser pulse, while the recovery of the fluorescence in the region is monitored over time by time-lapse microscopy...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28322328/5d-imaging-via-light-sheet-microscopy-reveals-cell-dynamics-during-the-eye-antenna-disc-primordium-formation-in-drosophila
#6
Yu Shan Huang, Hui Yu Ku, Yun Chi Tsai, Chin Hao Chang, Sih Hua Pao, Y Henry Sun, Arthur Chiou
5D images of engrailed (en) and eye gone (eyg) gene expressions during the course of the eye-antenna disc primordium (EADP) formation of Drosophila embryos from embryonic stages 13 through 16 were recorded via light sheet microscopy and analyzed to reveal the cell dynamics involved in the development of the EADP. Detailed analysis of the time-lapsed images revealed the process of EADP formation and its invagination trajectory, which involved an inversion of the EADP anterior-posterior axis relative to the body...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28319017/preliminary-investigation-of-the-prevalence-and-implantation-potential-of-abnormal-embryonic-phenotypes-assessed-using-time-lapse-imaging
#7
Amy Barrie, Roy Homburg, Garry McDowell, Jeremy Brown, Charles Kingsland, Stephen Troup
This retrospective, single site observational study aimed to delineate five abnormal embryonic developmental phenotypes, assessing their prevalence, development potential and suitability for inclusion in embryo selection models for IVF. In total, 15,819 embryos from 4559 treatment cycles cultured in EmbryoScope® incubators between January 2014 and January 2016 were included. Time-lapse images were assessed retrospectively for five abnormal embryo phenotypes: direct cleavage, reverse cleavage, absent cleavage, chaotic cleavage and cell lysis...
March 1, 2017: Reproductive Biomedicine Online
https://www.readbyqxmd.com/read/28316864/in-vitro-quantification-of-the-radiopacity-of-onyx-during-embolization
#8
Yuan Yuan Jiang, Ye-Eun Jo, Jung Min Woo, Ok Kyun Lim, Changmo Hwang, Jun Young Maeng, Jieun Kim, Namkug Kim, Deok Hee Lee
PURPOSE: Onyx has been successfully applied in the treatment of various neurovascular lesions. However, some experience is required to get accustomed to its unpredictable fluoroscopic visibility during injection. This in vitro study aimed to evaluate the characteristics of radiopacity change in a simulated embolization procedure. MATERIALS AND METHODS: Using a bench-top Onyx injection experiment simulating a typical brain arteriovenous malformation embolization, nine cycles of casting modes (continuous injection) and plugging modes (injection with intermittent pauses) were performed...
March 2017: Neurointervention
https://www.readbyqxmd.com/read/28303523/initiation-switching-and-cessation-of-psoriasis-treatments-among-patients-with-moderate-to-severe-psoriasis-in-the-united-states
#9
April W Armstrong, J Will Koning, Simon Rowse, Huaming Tan, Carla Mamolo, Mandeep Kaur
BACKGROUND: Psoriasis patients frequently switch among multiple therapies while managing their psoriasis. Determining treatment transitions is fundamental to understanding how patients access and use treatments. OBJECTIVE: We aimed to identify patterns of treatment transitions of US patients with moderate to severe psoriasis over 5 years. METHODS: This was a retrospective, longitudinal cohort study in which US patients aged ≥18 years who had at least one psoriasis claim (International Classification of Diseases, Ninth Revision [ICD-9] diagnosis) were continuously enrolled in a health plan between October 2007 and September 2012...
March 16, 2017: Clinical Drug Investigation
https://www.readbyqxmd.com/read/28302911/real-time-insights-into-regulated-exocytosis
#10
REVIEW
Duy T Tran, Kelly G Ten Hagen
Real-time imaging of regulated exocytosis in secreting organs can provide unprecedented temporal and spatial detail. Here, we highlight recent advances in 3D time-lapse imaging in Drosophila salivary glands at single-granule resolution. Using fluorescently labeled proteins expressed in the fly, it is now possible to image the dynamics of vesicle biogenesis and the cytoskeletal factors involved in secretion. 3D imaging over time allows one to visualize and define the temporal sequence of events, including clearance of cortical actin, fusion pore formation, mixing of the vesicular and plasma membranes and recruitment of components of the cytoskeleton...
March 16, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28300704/the-further-exploration-of-hidden-blood-loss-in-posterior-lumbar-fusion-surgery
#11
Derong Xu, Zhinan Ren, Xin Chen, Qianyu Zhuang, Shangyi Hui, Lin Sheng, Shugang Li
PURPOSE: Hidden blood loss (HBL) plays an important role in lumbar fusion surgery.However, there was huge computation error when calculating hidden loss in previous studiesbecause they regarded the volume of drainage as postoperative blood loss.Weshould not ignore the fact that the composition of drainage varies from person to person and also with time-lapse after operation.The purpose of this study was to demonstrate a more accurate HBL calculation formula by comparing it with previous formula and to address the importance of HBL in patients undergoing posterior lumbar fusion surgeries...
March 11, 2017: Orthopaedics & Traumatology, Surgery & Research: OTSR
https://www.readbyqxmd.com/read/28299700/dynamic-antibiotic-susceptibility-test-via-a-3d-microfluidic-culture-device
#12
Zining Hou, Yu An, Zhigang Wu
This study presents a novel microfluidic approach to the investigation of bacterial susceptibility against antibiotics gradient concentration in a quantitative way. A linear concentration gradient of antibiotics in a microfluidic chamber is used with time-lapse photography. This approach provides high-resolution information in real time. Traditional tests for this type of study involve Clinical and Laboratory Standard Institute (CLSI) recommended test and Etest. All of these tests need different trials to present different concentrations...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28299568/time-lapse-effect-of-ancient-plant-coal-biochar-on-some-soil-agrochemical-parameters-and-soil-characteristics
#13
Tamás Kocsis, Borbála Biró, Ákos Ulmer, Mónika Szántó, Zsolt Kotroczó
Biochar is a solid material obtained from reductive, oxygen-free processes, i.e. the thermo-chemical conversion of biomass in oxygen-limited environment. The obtained products have high carbon sequestration potential and strong nutrient-water absorption capacities because of the enlarged carbon surfaces. It is not yet clear how carbon stimulates agrochemical parameters in soil and how those characteristics are developing as time goes on a long-term basis. Samples of ancient (25, 35, 80 years old) plant coal-affected soils were collected in a temperate deciduous forest site located in the south part of the Bükk Mountains (in North Eastern Hungary)...
March 15, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28298846/menkes-disease-and-response-to-copper-histidine-an-indian-case-series
#14
Sangeetha Yoganathan, Sniya Valsa Sudhakar, Gautham Arunachal, Maya Thomas, Annadurai Subramanian, Renu George, Sumita Danda
BACKGROUND: Menkes disease (MD) is an X-linked recessive neurodegenerative disorder caused by mutations in ATP7A gene. Depending on the residual ATP7A activity, manifestation may be classical MD, occipital horn syndrome, or distal motor neuropathy. Neurological sparing is expected in female carriers. However, on rare occasions, females may manifest with classical clinical phenotype due to skewed X-chromosome inactivation, X-autosome translocation, and XO genotype. Here, we describe a small series of probands with MD and their response to copper histidine therapy...
January 2017: Annals of Indian Academy of Neurology
https://www.readbyqxmd.com/read/28298491/cyk-4-regulates-rac-but-not-rho-during-cytokinesis
#15
Yelena Zhuravlev, Sophia M Hirsch, Shawn N Jordan, Julien Dumont, Mimi Shirasu-Hiza, Julie C Canman
Cytokinesis is driven by constriction of an actomyosin contractile ring that is controlled by Rho family small GTPases. Rho, activated by the Guanine-nucleotide Exchange Factor (GEF) ECT-2, is upstream of both myosin-II activation and diaphanous formin-mediated filamentous actin (f-actin) assembly, which drive ring constriction. The role for Rac and its regulators is more controversial but, based on the finding that Rac inactivation can rescue cytokinesis failure when the GTPase Activating Protein (GAP) CYK-4 is disrupted, Rac activity was proposed to be inhibitory to contractile ring constriction and thus specifically inactivated by CYK-4 at the division plane...
March 15, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28298264/ecological-momentary-assessment-in-behavioral-research-addressing-technological-and-human-participant-challenges
#16
Lora E Burke, Saul Shiffman, Edvin Music, Mindi A Styn, Andrea Kriska, Asim Smailagic, Daniel Siewiorek, Linda J Ewing, Eileen Chasens, Brian French, Juliet Mancino, Dara Mendez, Patrick Strollo, Stephen L Rathbun
BACKGROUND: Ecological momentary assessment (EMA) assesses individuals' current experiences, behaviors, and moods as they occur in real time and in their natural environment. EMA studies, particularly those of longer duration, are complex and require an infrastructure to support the data flow and monitoring of EMA completion. OBJECTIVE: Our objective is to provide a practical guide to developing and implementing an EMA study, with a focus on the methods and logistics of conducting such a study...
March 15, 2017: Journal of Medical Internet Research
https://www.readbyqxmd.com/read/28296247/comprehensive-proteome-analysis-of-human-skeletal-muscle-in-cachexia-and-sarcopenia-a-pilot-study
#17
H Alexander Ebhardt, Simone Degen, Valentina Tadini, Alain Schilb, Neil Johns, Carolyn A Greig, Kenneth C H Fearon, Ruedi Aebersold, Carsten Jacobi
BACKGROUND: Cancer cachexia (cancer-induced muscle wasting) is found in a subgroup of cancer patients leaving the patients with a poor prognosis for survival due to a lower tolerance of the chemotherapeutic drug. The cause of the muscle wasting in these patients is not fully understood, and no predictive biomarker exists to identify these patients early on. Skeletal muscle loss is an inevitable consequence of advancing age. As cancer frequently occurs in old age, identifying and differentiating the molecular mechanisms mediating muscle wasting in cancer cachexia vs...
March 15, 2017: Journal of Cachexia, Sarcopenia and Muscle
https://www.readbyqxmd.com/read/28295391/electrophysiological-correlates-of-adaptive-control-and-attentional-engagement-in-patients-with-first-episode-schizophrenia-and-healthy-young-adults
#18
Megan A Boudewyn, Cameron S Carter
The goal of this study was to investigate the neural dynamics of error processing and post-error adjustments in cognitive control and attention to a cognitive task in schizophrenia. We adopted a time-frequency approach in order to examine activity in the theta and alpha frequency bands as indices of cognitive control and attentional engagement. The results showed that error processing was characterized by increases in theta-band activity, accompanied by decreases in alpha-band activity, in both healthy control participants and participants with schizophrenia...
March 15, 2017: Psychophysiology
https://www.readbyqxmd.com/read/28295267/pyoderma-gangrenosum-clinical-characteristics-associated-diseases-and-responses-to-treatment-in-a-retrospective-cohort-study-of-31-patients
#19
Aldana S Vacas, Ana C Torre, María L Bollea-Garlatti, Fernando Warley, Ricardo L Galimberti
OBJECTIVE: The aim of this study was to describe the clinical characteristics of patients with pyoderma gangrenosum (PG) and to evaluate the association between these characteristics, the treatment followed, and the patient responses, relapses, and mortality rates. MATERIAL AND METHODS: This retrospective cohort study identified adults diagnosed with pyoderma gangrenosum over the duration of 10 years. RESULTS: Thirty-one patients were evaluated; 58% were women and 55% were older than 65 years, 87% presented with the ulcerative type, and 77% showed lower limb compromise...
April 2017: International Journal of Dermatology
https://www.readbyqxmd.com/read/28295054/microfluidic-device-enabled-quantitative-time-lapse-microscopic-photography-for-phenotyping-vegetative-and-reproductive-phases-in-fusarium-virguliforme-which-is-pathogenic-to-soybean
#20
Jill Marshall, Xuan Qiao, Jordan Baumbach, Jingyu Xie, Liang Dong, Madan K Bhattacharyya
Time-lapse microscopic-photography allows in-depth phenotyping of microorganisms. Here we report development of such a system using a microfluidic device, generated from polydimethylsiloxane and glass slide, placed on a motorized stage of a microscope for conducting time-lapse microphotography of multiple observations in 20 channels simultaneously. We have demonstrated the utility of the device in studying growth, germination and sporulation in Fusarium virguliforme that causes sudden death syndrome in soybean...
March 15, 2017: Scientific Reports
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