scholarly journals SynapsEM: computer-assisted synapse morphometry

2020 ◽  
Author(s):  
Shigeki Watanabe ◽  
M Wayne Davis ◽  
Grant F Kusick ◽  
Janet Iwasa ◽  
Erik M Jorgensen
Keyword(s):  
Absolute Number ◽  
Structural Features ◽  
Comprehensive Analysis ◽  
Computer Assisted ◽  
Matlab Program ◽  
Synaptic Structure ◽  
Synaptic Ultrastructure ◽  
Daunting Task ◽  
Dense Projections ◽  
Synaptic Parameters

AbstractThe structural features of a synapse, in part, determine its output. Synapses are extremely small and tightly packed with vesicles and other organelles. Visualizing synaptic structure requires imaging by electron microscopy, and the features in micrographs must be quantified using morphometry. Three parameters are typically assessed from each specimen: 1) the sizes of individual vesicles and organelles, 2) the absolute number and densities of organelles, and 3) distances between organelles and key features at synapses such as active zone membranes and dense projections. For data to be valid, the analysis must be repeated from hundreds or thousands of images from several biological replicates, a daunting task. Here we report a custom computer program to analyze these features: SynapsEM. In short, we developed macros for ImageJ/Fiji to record x,y-coordinates of segmented structures; the coordinates are then exported as text files. Independent investigators can reload the images and text files to confirm or re-evaluate the segmentation using ImageJ. The Matlab program calculates and reports key synaptic parameters from the coordinates. Since the values are calculated, rather than measured from each micrograph, other parameters can be extracted in Matlab by additional scripting. Thus, this program can accelerate morphometry of synapses and promote a more comprehensive analysis of synaptic ultrastructure.

scholarly journals SynapsEM: Computer-Assisted Synapse Morphometry

2020 ◽  
Vol 12 ◽  
Author(s):  
Shigeki Watanabe ◽  
M. Wayne Davis ◽  
Grant F. Kusick ◽  
Janet Iwasa ◽  
Erik M. Jorgensen
Keyword(s):  
Active Zone ◽  
Absolute Number ◽  
Structural Features ◽  
Computer Assisted ◽  
Matlab Program ◽  
Synaptic Structure ◽  
Synaptic Ultrastructure ◽  
Daunting Task ◽  
Dense Projections ◽  
Synaptic Parameters

The structural features of a synapse help determine its function. Synapses are extremely small and tightly packed with vesicles and other organelles. Visualizing synaptic structure requires imaging by electron microscopy, and the features in micrographs must be quantified, a process called morphometry. Three parameters are typically assessed from each specimen: (1) the sizes of individual vesicles and organelles; (2) the absolute number and densities of organelles; and (3) distances between organelles and key features at synapses, such as active zone membranes and dense projections. For data to be meaningful, the analysis must be repeated from hundreds to thousands of images from several biological replicates, a daunting task. Here we report a custom computer program to analyze key structural features of synapses: SynapsEM. In short, we developed ImageJ/Fiji macros to record x,y-coordinates of segmented structures. The coordinates are then exported as text files. Independent investigators can reload the images and text files to reexamine the segmentation using ImageJ. The Matlab program then calculates and reports key synaptic parameters from the coordinates. Since the values are calculated from coordinates, rather than measured from each micrograph, other parameters such as locations of docked vesicles relative to the center of an active zone can be extracted in Matlab by additional scripting. Thus, this program can accelerate the morphometry of synapses and promote a more comprehensive analysis of synaptic ultrastructure.

The Issue of Sustainability in Third World Food Production (The Distinguishedl Lecture)

1992 ◽  
Vol 31 (4I) ◽  
pp. 511-534
Author(s):  
Winfried Von Urff
Keyword(s):  
Developing Countries ◽  
Population Growth ◽  
Food Production ◽  
Third World ◽  
Total Population ◽  
Absolute Number ◽  
Comprehensive Analysis ◽  
World Food ◽  
The Absolute ◽  
The Difference

In spite of the fact that food production in developing countries doubled over the last 25 years undernutrition is still widely spread. At the beginning of the eighties, according to FAO, 335 to 494 million people in developing countries suffered from serious undernutrition the difference being due to different concepts to determine undernutrition on which scientist were unable to find a consensus.) Unfortunately there is no recent comprehensive analysis of the food situation comparable to those of previous World Food Surveys but it can be taken for sure that the absolute number of undernourished has increased. According to unofficial FAO sources a figure of 870 million was estimated for 1990 (22 percent of the total population in developing countries) using the same concept that led to the figure of 494 million in 1979-81 (23 percent of the total population in developing countries) which means that most probably the number of undernourished increased at a rate slightly less than population growth.

Mimicry between neurokinin-1 and fibronectin may explain the transport and stability of increased substance P immunoreactivity in patients with bone marrow fibrosis

Blood ◽  
2001 ◽  
Vol 97 (10) ◽  
pp. 3025-3031 ◽  
Author(s):  
Pranela Rameshwar ◽  
Deval D. Joshi ◽  
Prem Yadav ◽  
Jing Qian ◽  
Pedro Gascon ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Substance P ◽  
Mononuclear Cells ◽  
Cdna Probe ◽  
Structural Features ◽  
Cdna Libraries ◽  
Future Research ◽  
Computer Assisted ◽  
Partial Clone ◽  
Neurokinin 1

Abstract Bone marrow (BM) fibrosis may occur in myeloproliferative diseases, lymphoma, myelodysplastic syndrome, myeloma, and infectious diseases. In this study, the role of substance P (SP), a peptide with pleiotropic functions, was examined. Some of its functions—angiogenesis, fibroblast proliferation, and stimulation of BM progenitors—are amenable to inducing BM fibrosis. Indeed, a significant increase was found in SP-immunoreactivity (SP-IR) in the sera of patients with BM fibrosis (n = 44) compared with the sera of patients with hematologic disorders and no histologic evidence of fibrosis (n = 46) (140 ±12 vs 18 ±3; P < .01). Immunoprecipitation of sera SP indicated that this peptide exists in the form of a complex with other molecule(s). It was, therefore, hypothesized that SP might be complexed with NK-1, its natural receptor, or with a molecule homologous to NK-1. To address this, 3 cDNA libraries were screened that were constructed from pooled BM stroma or mononuclear cells with an NK-1 cDNA probe. A partial clone (clone 1) was retrieved that was 97% homologous to the ED-A region of fibronectin (FN). Furthermore, sequence analyses indicated that clone 1 shared significant homology with exon 5 of NK-1. Immunoprecipitation and Western blot analysis indicated co-migration of SP and FN in 27 of 31 patients with BM fibrosis. Computer-assisted molecular modeling suggested that similar secondary structural features between FN and NK-1 and the relative electrostatic charge might explain a complex formed between FN (negative) and SP (positive). This study suggests that SP may be implicated in the pathophysiology of myelofibrosis, though its role would have to be substantiated in future research.

scholarly journals A phylogenetic view and functional annotation of the animal β1,3-glycosyltransferases of the GT31 CAZy family

Glycobiology ◽  
2020 ◽  
Author(s):  
Daniel Petit ◽  
Roxana Elin Teppa ◽  
Anne Harduin-Lepers
Keyword(s):  
Gene Structure ◽  
Functional Annotation ◽  
Common Ancestor ◽  
Structural Features ◽  
Comprehensive Analysis ◽  
Evolutionary Relationships ◽  
Last Common Ancestor ◽  
Carbohydrate Active Enzymes ◽  
Lower Vertebrates ◽  
Shed Light

Abstract The formation of β1,3-linkages on animal glycoconjugates is catalyzed by a subset of β1,3-glycosyltransferases grouped in the Carbohydrate-Active enZYmes family glycosyltransferase-31 (GT31). This family represents an extremely diverse set of β1,3-N-acetylglucosaminyltransferases [B3GNTs and Fringe β1,3-N-acetylglucosaminyltransferases], β1,3-N-acetylgalactosaminyltransferases (B3GALNTs), β1,3-galactosyltransferases [B3GALTs and core 1 β1,3-galactosyltransferases (C1GALTs)], β1,3-glucosyltransferase (B3GLCT) and β1,3-glucuronyl acid transferases (B3GLCATs or CHs). The mammalian enzymes were particularly well studied and shown to use a large variety of sugar donors and acceptor substrates leading to the formation of β1,3-linkages in various glycosylation pathways. In contrast, there are only a few studies related to other metazoan and lower vertebrates GT31 enzymes and the evolutionary relationships of these divergent sequences remain obscure. In this study, we used bioinformatics approaches to identify more than 920 of putative GT31 sequences in Metazoa, Fungi and Choanoflagellata revealing their deep ancestry. Sequence-based analysis shed light on conserved motifs and structural features that are signatures of all the GT31. We leverage pieces of evidence from gene structure, phylogenetic and sequence-based analyses to identify two major subgroups of GT31 named Fringe-related and B3GALT-related and demonstrate the existence of 10 orthologue groups in the Urmetazoa, the hypothetical last common ancestor of all animals. Finally, synteny and paralogy analysis unveiled the existence of 30 subfamilies in vertebrates, among which 5 are new and were named C1GALT2, C1GALT3, B3GALT8, B3GNT10 and B3GNT11. Altogether, these various approaches enabled us to propose the first comprehensive analysis of the metazoan GT31 disentangling their evolutionary relationships.

scholarly journals Bony Resection Outliers: Insights from 10,144 Clinical Cases using A Contemporary Computer-Assisted Total Knee Arthroplasty System

10.29007/bwjk ◽  
2019 ◽  
Author(s):  
Yifei Dai ◽  
Charlotte Bolch ◽  
Siyuan Gao ◽  
Amaury Jung ◽  
Cyril Hamad
Keyword(s):  
Total Knee Arthroplasty ◽  
Surgical Resection ◽  
Knee Arthroplasty ◽  
Accurate Solution ◽  
Comprehensive Analysis ◽  
Computer Assisted ◽  
Application Software ◽  
Technology Learning ◽  
Total Knee ◽  
Geographic Regions

This study accessed the alignment outliers of intraoperatively measured bony resection during total knee arthroplasty on 10,144 cases performed using a modern CAOS system. The impacts from geographic regions, surgeon’s adoption of the technology (learning or proficient phases), and historical progression of the CAOS application (software versions) were evaluated. The comprehensive analysis demonstrated that the CAOS system is a robust and accurate solution to assist the surgeons to achieve his/her surgical resection goals across its application history.

scholarly journals DISCA: high-throughput cryo-ET structural pattern mining by deep unsupervised clustering

2021 ◽  
Author(s):  
Xiangrui Zeng ◽  
Anson Kahng ◽  
Liang Xue ◽  
Julia Mahamid ◽  
Yi-Wei Chang ◽  
...  
Keyword(s):  
High Throughput ◽  
Pattern Mining ◽  
Electron Tomography ◽  
Structural Features ◽  
Computer Assisted ◽  
Label Free ◽  
Structural Pattern ◽  
Cryo Electron Tomography ◽  
Homogeneous Structures

Cryo-electron tomography directly visualizes heterogeneous macromolecular structures in complex cellular environments, but existing computer-assisted sorting approaches are low-throughput or inherently limited due to their dependency on available templates and manual labels. We introduce a high-throughput template-and-label-free deep learning approach that automatically discovers subsets of homogeneous structures by learning and modeling 3D structural features and their distributions. Diverse structures emerging from sorted subsets enable systematic unbiased recognition of macromolecular complexes in situ.

scholarly journals Structural Analysis of Enhanced Performance Organic Light Emitting Diodes (OLEDs)

2020 ◽  
Vol 8 (9) ◽  
pp. 80-83
Keyword(s):  
High Efficiency ◽  
Structural Features ◽  
Comprehensive Analysis ◽  
Organic Light Emitting Diodes ◽  
Organic Leds ◽  
Light Sources ◽  
Light Emitting ◽  
Organic Light ◽  
Depth Analysis ◽  
Pi Bonds

We present a detailed study on structure of Organic LEDs (OLEDs) that promise flexibility and enhanced performance. Ordinary LEDs fail when it comes to need of ultra-smart size, thin, flexible smart screens and high efficiency light sources. With electroluminescent layer made of organic compounds, OLEDs promise all such features. We did a comprehensive analysis to find what structural features distinguish OLEDs from semiconductor LEDs. We found that it is the special six layered structure with organic emissive layer and delocalized charges due to weak pi bonds that enable OLEDs to perform better. We dis-cuss a few limitations related to production and life of these LEDs and suggest possible solutions to overcome these challenges. A rigorous, in-depth analysis of this structure is imperative to further comprehend the working of this device in order to make future devices cheaper and more efficient

scholarly journals ANALYSIS OF TUBERCULOSIS/HIV CO-INFECTION TRENDS IN UKRAINE IN 2008-2017

2019 ◽  
Vol 72 (5) ◽  
pp. 903-907
Author(s):  
Tetiana V. Stepanova ◽  
Olga P. Nedospasova ◽  
Mykhailo V. Golubchykov
Keyword(s):  
Epidemiological Study ◽  
Clinical Characteristics ◽  
Healthcare Delivery ◽  
Absolute Number ◽  
Comprehensive Analysis ◽  
Active Tuberculosis ◽  
Southern Region ◽  
Urban Residents ◽  
Newly Diagnosed ◽  
Health Statistics

Introduction: According to WHO estimates for the European Region in 2017, Ukraine had the highest proportion of active tuberculosis cases co-infected with HIV – 21.6%, with an average of 12% in the Region, and the absolute number of tuberculosis/HIV co-infection cases in Ukraine was estimated at the level of 8,000. The aim: carry out a comprehensive analysis of the epidemical situation regarding tuberculosis/HIV co-infection in Ukraine according to selected epidemiological and clinical characteristics. Materials and methods: The retrospective epidemiological study was based on the data from national reporting forms “Annual Active TB Report”, which was being collected by the Center for Health Statistics of the Ministry of Health of Ukraine for period 2008-2017. Review: The incidence of newly diagnosed active tuberculosis associated with HIV in Ukraine increased by 89,4% – from 6,1 per 100,000 population in 2008 to 11,6 per 100,000 population in 2017, against the backdrop of a gradual decrease in the incidence of active tuberculosis by 36.5% over the same period. The rates of comorbidity TB/HIV increased by 2.8 times from 7.9% to 20.3%. The highest rates of incidence tuberculosis/HIV co-infection are observed in person aged 25-44, males, urban residents, and in the southern region of Ukraine. Conclusions: The revealed tendency to increase the rate of the incidence and comorbidity of tuberculosis/HIV causes necessitates reviewing the organizational approaches to healthcare delivery for tuberculosis/HIV co-infection patients.

scholarly journals Structural and mineragenetic features of the Getkan area

2020 ◽  
Vol 192 ◽  
pp. 03015
Author(s):  
Yury Manilov
Keyword(s):  
Geophysical Methods ◽  
Structural Features ◽  
Comprehensive Analysis ◽  
Physical Characteristics ◽  
New Approaches ◽  
Different Types ◽  
Petrophysical Data ◽  
Different Characteristics ◽  
Physical Principles

Deep structural features of tectonic and mineragenetic zones of the region have been established based on the comprehensive analysis of geological, gravity, magnetic, and petrophysical data. Geophysical methods that are based on different physical principles have been shown to reflect different characteristics of lithosphere. Considering structural features and physical characteristics of mineragenetic objects, the obtained data allow genesis of endogenous mineralization of different types were identified and new approaches to the forecasting process was developed.

scholarly journals Determinants of sperm quality and fertility in domestic species

Reproduction ◽  
2007 ◽  
Vol 134 (1) ◽  
pp. 3-17 ◽  
Author(s):  
A M Petrunkina ◽  
D Waberski ◽  
A R Günzel-Apel ◽  
E Töpfer-Petersen
Keyword(s):  
Flow Cytometry ◽  
Sperm Quality ◽  
Absolute Number ◽  
Fertilization Success ◽  
Cell Counting ◽  
Computer Assisted ◽  
Timely Manner ◽  
Domestic Species ◽  
Image Area

Fertilization success cannot be attributed solely to the absolute number of vital, motile, morphologically normal spermatozoa inseminated into the female but more especially to their functional competence. A range ofin vitrotests has therefore been developed to monitor crucial aspects of sperm function: their ability to adapt to changing osmotic conditions, to bind to the oviductal epithelium, and to undergo capacitation in an appropriate and timely manner. The tests employ flow cytometry in conjunction with fluorescent techniques, electronic cell counting, and computer-assisted image area analysis. The highly quantitative analysis provided by electronic sizing and flow cytometry enables assessment of representative cell numbers in a very short time with high reproducibility. More importantly, it allows the detection of physiological heterogeneity within an ejaculate in terms of the development of cell subpopulations and enables the kinetic analysis of changes in living cell suspensions. The tests offer a promising strategy for evaluating fertility in domestic animals. The capability for volume regulation ensures that sperm recover from the tonic shocks experienced at ejaculation and during cryopreservation. Assessment of capacitationin vitroprovides valuable information on both the sperm’s ability to respond to fertilizing conditions and the sequence and rates of ongoing capacitation/destabilization processes. The monitoring of response to capacitating conditions in kinetic terms allows the sensitive and adequate detection of sperm populations expressing fertilization attributes and their ability to respond to external stimuli in a timely manner. However, subfertility is likely to be associated with a suboptimal response (i.e. too high or too low) rather than a minimal response.

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