scholarly journals Nessys: a novel method for accurate nuclear segmentation in 3D

2018 ◽  
Author(s):  
Guillaume Blin ◽  
Daina Sadurska ◽  
Rosa Portero Migueles ◽  
Naiming Chen ◽  
Julia Alice Watson ◽  
...  
Keyword(s):  
Three Dimensions ◽  
Live Cells ◽  
Computer Memory ◽  
Adult Tissue ◽  
Manual Curation ◽  
Trained Classifier ◽  
History Of ◽  
Novel Method ◽  
User Friendly ◽  
Nuclear Segmentation

Methods for measuring the properties of individual cells within their native 3D environment will enable a deeper understanding of embryonic development, tissue regeneration, and tumorigenesis. However current methods for segmenting nuclei in 3D tissues are not designed for situations where nuclei are densely packed, non-spherical, heterogeneous in shape, size, or texture, all of which are true of many embryonic and adult tissue types as well as in many cases for cells differentiating in culture. Here we overcome this bottleneck by devising a novel method based on labelling the nuclear envelope (NE) and automatically distinguishing individual nuclei using a tree structured ridge tracing method followed by shape ranking according to a trained classifier. The method is fast and makes it possible to process images that are larger than computer memory. We consistently obtain accurate segmentation rates of >90% even for challenging images such as mid-gestation embryos or 3D cultures. We provide a 3D editor and inspector for the manual curation of the segmentation results as well as a program to assess the accuracy of the segmentation. We have also generated a live reporter of the NE that can be used to track live cells in three dimensions over time. We use this to monitor the history of cell interactions and occurrences of neighbour exchange within cultures of pluripotent cells during differentiation. We provide these tools in an open-access user-friendly format.

scholarly journals Interrogating the Egypto-Sudanic Arabic Connection

Languages ◽  
2021 ◽  
Vol 6 (3) ◽  
pp. 123
Author(s):  
Thomas A. Leddy-Cecere
Keyword(s):  
The Novel ◽  
Present Contribution ◽  
Phonological Processes ◽  
Verbal Inflection ◽  
Segmental Phonology ◽  
Language Data ◽  
History Of ◽  
Novel Method ◽  
Dialect Classification ◽  
Arabic Speaking

The Arabic dialectology literature repeatedly asserts the existence of a macro-level classificatory relationship binding the Arabic speech varieties of the combined Egypto-Sudanic area. This proposal, though oft-encountered, has not previously been formulated in reference to extensive linguistic criteria, but is instead framed primarily on the nonlinguistic premise of historical demographic and genealogical relationships joining the Arabic-speaking communities of the region. The present contribution provides a linguistically based evaluation of this proposed dialectal grouping, to assess whether the postulated dialectal unity is meaningfully borne out by available language data. Isoglosses from the domains of segmental phonology, phonological processes, pronominal morphology, verbal inflection, and syntax are analyzed across six dialects representing Arabic speech in the region. These are shown to offer minimal support for a unified Egypto-Sudanic dialect classification, but instead to indicate a significant north–south differentiation within the sample—a finding further qualified via application of the novel method of Historical Glottometry developed by François and Kalyan. The investigation concludes with reflection on the implications of these results on the understandings of the correspondence between linguistic and human genealogical relationships in the history of Arabic and in dialectological practice more broadly.

scholarly journals Poly(catecholamine) Coating and Biofunctionalization of CsPbBr3 Microcrystals

2021 ◽  
Author(s):  
Sangyeon Cho ◽  
Seok-Hyun Yun
Keyword(s):  
Lipid Bilayers ◽  
Environmental Stability ◽  
Live Cells ◽  
Functional Coatings ◽  
Common Strategy ◽  
Novel Method ◽  
Halide Perovskites ◽  
The Stability ◽  
New Applications

<p>Lead halide perovskites (LHP) microcrystals are promising materials for various optoelectronic applications. Surface coating on particles is a common strategy to improve their functionality and environmental stability, but LHP is not amenable to most coating chemistries because of its intrinsic weakness against polar solvents. Here, we describe a novel method of synthesizing LHP microcrystals in a super-saturated polar solvent using sonochemistry and applying various functional coatings on individual microcrystals <i>in situ</i>. We synthesize cesium lead bromine perovskite (CsPbBr<sub>3</sub>) microparticles capped with organic poly-norepinephrine (pNE) layers. The catechol group of pNE coordinates to bromine-deficient lead atoms, forming a defect-passivating and diffusion-blocking shell. The pNE layer enhances the stability of CsPbBr<sub>3</sub> in water by 2,000-folds, enabling bright luminescence and lasing from single microcrystals in water. Furthermore, the pNE shell permits biofunctionalization with proteins, small molecules, and lipid bilayers. Luminescence from CsPbBr<sub>3</sub> microcrystals is sustained in water over 1 hour and observed in live cells. The functionalization method may enable new applications of LHP particles in water-rich environments.<b></b></p>

Implementation of Business Intelligence in Product Services a Banking (Case Study: PT Bank Sumsel Babel Baturaja Branch)

2017 ◽  
Vol 9 (2) ◽  
Author(s):  
Sekar Sari Wiradarma ◽  
Ken Dhita Tania ◽  
Dinna Yunika Hardiyanti
Keyword(s):  
Decision Making ◽  
Business Intelligence ◽  
Quality Information ◽  
Product Data ◽  
Product Service ◽  
History Of ◽  
Adaptive Nature ◽  
User Friendly ◽  
Intelligence Application

AbstractBusiness Intelligence (BI) is a collection of theories, methodologies, processes, architectures, and technologies that convert raw data into quality information for business purposes. BI can handle a large amount of information that can help in identifying problems and developing new opportunities. In designing and implementing Business Intelligence (BI) concept for monitoring banking product service using reference business intelligence roadmap approach. Business intelligence roadmap is one example of BI development that can be emulated because of its agile and adaptive nature and is intended to support the development of BI. By utilizing Business Intelligence application on transaction history of banking product data, it is hoped able to produce information that can support in giving recommendation and decision making appropriately. The data and information generated also become more accessible and easier to understand (user friendly).Keywords: business intelligence, business intelligence roadmap, OLAP, banking products

How Do We Think the Present? From Ontology of Contemporary Reality to Ontology without Being1

2016 ◽  
Author(s):  
Gabriel Rockhill
Keyword(s):  
Michel Foucault ◽  
Social Practice ◽  
Three Dimensions ◽  
Apparent Contradiction ◽  
New Era ◽  
Late Work ◽  
Critical Attitude ◽  
Time Space ◽  
History Of ◽  
Contemporary Reality

The opening chapter explores a philosophic question that reflexively sheds light on the orientation of the book as a whole: how can we write the history of the present? Against the backdrop of the more specific question of how to understand the present state of philosophy, it turns to the late work of Michel Foucault and his unique account of the ontology of actuality or of contemporary reality (ontologie de l’actualité). It carefully reconstitutes his concern with providing a historico-philosophical justification of his own project, which he situates in a trajectory that begins with the emergence of the ontology of actuality in the later Kant. It assesses the contemporary relevancy of his critique of historical periodization and his redefinition of modernity in terms of a critical attitude. Given the apparent contradiction between his rejection of periodic history and his identification of a new era of historical thought, the chapter goes on to suggest that an alternative logic of history—founded on the three dimensions of time, space and social practice—would allow us to completely reformulate the way in which we think the present.

Graph Applications in Chemoinformatics and Structural Bioinformatics

2011 ◽  
pp. 386-420
Author(s):  
Eleanor Joyce Gardiner
Keyword(s):  
Graph Theory ◽  
Molecular Graph ◽  
Structural Bioinformatics ◽  
Three Dimensions ◽  
Chemical Graph ◽  
Labeled Graph ◽  
3D Space ◽  
Chemical Graph Theory ◽  
Computer Representation ◽  
History Of

The focus of this chapter will be the uses of graph theory in chemoinformatics and in structural bioinformatics. There is a long history of chemical graph theory dating back to the 1860’s and Kekule’s structural theory. It is natural to regard the atoms of a molecule as nodes and the bonds as edges (2D representations) of a labeled graph (a molecular graph). This chapter will concentrate on the algorithms developed to exploit the computer representation of such graphs and their extensions in both two and three dimensions (where an edge represents the distance in 3D space between a pair of atoms), together with the algorithms developed to exploit them. The algorithms will generally be summarized rather than detailed. The methods were later extended to larger macromolecules (such as proteins); these will be covered in less detail.

scholarly journals T26. VISUO-TACTILE TRANSFER AND AUDIO-VISUAL INTEGRATION IMPAIRMENT AS A NEW VULNERABILITY MARKER IN CHILDREN-AT-RISK OF SCHIZOPHRENIA, BIPOLAR DISORDER OR RECURRENT DEPRESSIVE DISORDER

2020 ◽  
Vol 46 (Supplement_1) ◽  
pp. S241-S241
Author(s):  
Martin Roy ◽  
Elsa Gilbert ◽  
Michel Maziade ◽  
Pierre Marquet
Keyword(s):  
At Risk ◽  
Bipolar Disorder ◽  
Sensory Modality ◽  
Multisensory Perception ◽  
Children At Risk ◽  
Self Development ◽  
History Of ◽  
Sensory Defect ◽  
Almost All ◽  
User Friendly

Abstract Background Major psychiatric disorders (MPD) such as schizophrenia, bipolar disorder and recurrent major depression have shared neurodevelopmental vulnerability due to early neuronal and sensory defect as revealed by sensory and cognitive endophenotypes observed in our cohorts (e.g. Gagné et al., Schizophr. Res., 2019). There is considerable evidence that a harmonious self-development - known to be disrupted in MPDs - requires a synchronized multisensory perception and an adequate integration of sensory afferences (e.g. tactile, visual, auditory and proprio / interoception) with cognition. Early impairment in intermodal transfer (IMT) and multisensory integration (MSI) may jeopardize a stable and unified self’s and world’s representation and then would undermine self-development and represent a risk factor for MPD. IMT is the capability to transfer a percept coming exclusively from a sensory modality (e.g. tactile) to another modality (e.g. visual). MSI is the ability to integrate sensory inputs from different modalities (e.g. visual and auditory) to have a better information processing. This study shows that impairment in IMT/MSI may be a vulnerability marker in children genetically at-risk. Methods Sample: Forty-four offspring (21 girls) of patients suffering from a MPD and thus genetically at-risk for MPD (GatR) aged from 9–15 years old (mean age = 12.06) were recruited from the cohort study INTERCEPT through the HoPE program of the CIUSSS de la Capitale-Nationale. Twenty-five controls (19 girls) with no family history of MPD and no DSM-V disorder aged from 9–15 years old (mean age = 12.87) were recruited using advertisements or control bank. IMT Task: Each condition has 12 trials and the shapes are hidden from sight during palpation. MSI Task: - Simple reaction time (RT) task comprising 80 trials with unimodal stimuli (Auditory OR Visual) and 40 trials with AV (Auditory and Visual simultaneously) multimodal stimuli presented randomly. Results IMT task: When compared to controls, GatR were impaired in the three conditions (T-T: 9.77 vs. 10.32, T-V: 9.89 vs. 9.96, V-T: 9,11 vs. 9.92) with significant impairments both for T-T (t(60.53) = 2.18, p = 0.017) and V-T (t (57.28) = 2.33, p = 0.012) conditions. MSI task: GatR showed a deficit in MSI for almost all RT ranges (except for a peak at 185 ms), while control participants showed MSI facilitation for ranges from 150 to 200 ms. Discussion Developmentally genetically high-risk children would show significant impairments both in IMT and MSI that might enter into the group of indicators of brain dysfunctions, or risk endophenotypes, that both children at risk and adult patients carry (Paccalet et al., Schizophr. Res., 2016; Maziade, New Eng J Medicine, 2017). In addition, the two tasks would be valid and sensitive to the early sensory alterations in self-development. Finally, the battery is brief, user-friendly and playful for children.

The use of echo density to quantify pulmonary right-to-left shunt in transthoracic contrast echocardiography

2020 ◽  
Author(s):  
Steven Kroon ◽  
Mitch C J Van Thor ◽  
Veerle M M Vorselaars ◽  
Anna E Hosman ◽  
Martin J Swaans ◽  
...  
Keyword(s):  
Contrast Echocardiography ◽  
Chest Ct ◽  
Independent Study ◽  
Ct Scans ◽  
Strongly Correlated ◽  
History Of ◽  
Study Population ◽  
Novel Method ◽  
Grading Scale ◽  
Transthoracic Contrast Echocardiography

Abstract Aims Transthoracic contrast echocardiography (TTCE) is the recommended screening tool to detect pulmonary right-to-left shunt (RLS) caused by pulmonary arteriovenous malformations (PAVMs). We assessed a novel method to quantify the RLS using the change in echo density (ED) following contrast injection. Methods and results An analysis of 437 consecutive patients [58% female, 47 years, interquartile range (IQR) 33–60] who underwent TTCE for the detection of a pulmonary RLS. Using ImageJ (National Institutes of Health), the change in ED was measured for each patient. This method was strongly correlated (Spearman’s ρ = 0.89; P &lt; 0.0001) with our standard method based on a four-point grading scale (no, mild, moderate, and severe RLS). In patients without a history of embolotherapy (n = 334), a PAVM was detected with chest computed tomography (CT) in 66 and embolotherapy was judged possible in 35 of these patients. The median increase in ED was higher in the latter: +20.1% (IQR 12.3–34.0) compared to non-treatable PAVM +0.2% (IQR −0.2 to 1.1). The specificity to detect treatable PAVMs increased from 87% to 90% when using the novel method without affecting the sensitivity (of 100%). Using the optimal cut-off value of +4.5% increase in ED, 8/74 (11%) needed chest CT-scans—individuals with a moderate or severe RLS—were no longer required without missing any treatable PAVM. Conclusions The use of ED quantification for pulmonary RLS is promising; resulting in a substantial decrease in the number of chest CT scans needed. However, this method and the threshold should be validated in an independent study population.

scholarly journals WALTZ-DB 2.0: an updated database containing structural information of experimentally determined amyloid-forming peptides

2019 ◽  
Vol 48 (D1) ◽  
pp. D389-D393 ◽  
Author(s):  
Nikolaos Louros ◽  
Katerina Konstantoulea ◽  
Matthias De Vleeschouwer ◽  
Meine Ramakers ◽  
Joost Schymkowitz ◽  
...  
Keyword(s):  
Open Access ◽  
Amyloid Fibrils ◽  
Amyloid Fibril ◽  
Structural Information ◽  
3D Models ◽  
Accurate Prediction ◽  
Binding Assays ◽  
Manual Curation ◽  
Open Access Database ◽  
User Friendly

Abstract Transition of soluble proteins into insoluble amyloid fibrils is driven by self-propagating short sequence stretches. However, accurate prediction of aggregation determinants remains challenging. Here, we describe WALTZ-DB 2.0, an updated and significantly expanded open-access database providing information on experimentally determined amyloid-forming hexapeptide sequences (http://waltzdb.switchlab.org/). We have updated WALTZ-DB 2.0 with new entries, including: (i) experimental validation of an in-house developed dataset of 229 hexapeptides, using electron microscopy and Thioflavin-T binding assays; (ii) manual curation of 98 amyloid-forming peptides isolated from literature. Furthermore, the content has been expanded by adding novel structural information for peptide entries, including sequences of the previous version. Using a computational methodology developed in the Switch lab, we have generated 3D-models of the putative amyloid fibril cores of WALTZ-DB 2.0 entries. Structural models, coupled with information on the energetic contributions and fibril core stabilities, can be accessed through individual peptide entries. Customized filtering options for subset selections and new modelling graphical features were added to upgrade online accessibility, providing a user-friendly interface for browsing, downloading and updating. WALTZ-DB 2.0 remains the largest open-access repository for amyloid fibril formation determinants and will continue to enhance the development of new approaches focused on accurate prediction of aggregation prone sequences.

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