scholarly journals An Inexpensive Way to Record and Quantify Bacterial Swarming

2019 ◽  
Author(s):  
Weijie Chen ◽  
Jay X. Tang ◽  
Sridhar Mani
Keyword(s):  
Collective Motion ◽  
Biological Process ◽  
Time Lapse ◽  
Extensive Study ◽  
Controlled Environment ◽  
Rapid Spread ◽  
Bacterial Swarming ◽  
Semi Solid ◽  
Over Time ◽  
Time Lapse Photography

Abstract Bacterial swarming refers to a rapid spread, with coordinated motion, of flagellated bacteria on a semi-solid surface1. There has been extensive study on this particular mode of motility among microbiologists and biophysicists because of its interesting biological and physical properties (e.g. enhanced antibiotic resistance2, turbulent collective motion3). The existing equipment for recording swarm expansion rate can easily go beyond tens of thousands dollars4, yet the conditions are not accurately controlled, resulting in large variations across the assays. Here, we report a reliable protocol to perform reproducible bacterial swarming assays and an inexpensive way to record and quantify the swarming activity by time-lapse photography. This novel protocol consists of three main parts: 1) building a “homemade”, environment-controlled photographing incubator; 2) performing bacterial swarming assay; 3) taking serial photos over time and calculating the swarming rate. The homemade incubator is economical, easy to operate, and has wide applications. In fact, this system can be applied for any slow evolving biological process that needs to be monitored by camera under a controlled environment.

Embryonic stages: morphology, timing, and variance in the toad Bombina orientalis

1978 ◽  
Vol 56 (7) ◽  
pp. 1540-1545 ◽  
Author(s):  
Paul Sussman ◽  
T. W. Betz
Keyword(s):  
Embryonic Development ◽  
Rana Pipiens ◽  
Time Lapse ◽  
Time Data ◽  
Bombina Orientalis ◽  
Stage Of Development ◽  
Curve Fit ◽  
Stage Change ◽  
Over Time ◽  
Time Lapse Photography

A Staged series (n = 25–476} with time data for Bombina orientalis embryonic development is presented. Stages for Bombina and Rana pipiens seem identical except that approximately 50% of opercular closures are symmetrical in Bombina. Counting numbers of embryos at a stage at regular intervals allowed mathematical interpolation of the average time of stage change. A single systematic curve fit the average time per stage of embryonic development, while the increase with time in variance per stage of development was primarily linear. It is possible that the increasing complexity of morphological interstage changes causes increases in the interstage interval and variance per stage over time. The reported method of arriving al a staged series for a previously undocumented species seems more efficient than time-lapse photography. The unusually easy maintenance and dependability or Bombina, contrasting with some amphibians, suggest its use where others have been less practical.

scholarly journals Visual4DTracker: a tool to interact with 3D + t image stacks

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ermanno Cordelli ◽  
Paolo Soda ◽  
Giulio Iannello
Keyword(s):  
Synthetic Data ◽  
Time Lapse ◽  
Temporal Data ◽  
Image Stack ◽  
Biological Phenomena ◽  
Insulin Granules ◽  
Matlab Package ◽  
User Friendly ◽  
Drosophila Cells ◽  
Over Time

Abstract Background Biological phenomena usually evolves over time and recent advances in high-throughput microscopy have made possible to collect multiple 3D images over time, generating $$3D+t$$ 3 D + t (or 4D) datasets. To extract useful information there is the need to extract spatial and temporal data on the particles that are in the images, but particle tracking and feature extraction need some kind of assistance. Results This manuscript introduces our new freely downloadable toolbox, the Visual4DTracker. It is a MATLAB package implementing several useful functionalities to navigate, analyse and proof-read the track of each particle detected in any $$3D+t$$ 3 D + t stack. Furthermore, it allows users to proof-read and to evaluate the traces with respect to a given gold standard. The Visual4DTracker toolbox permits the users to visualize and save all the generated results through a user-friendly graphical user interface. This tool has been successfully used in three applicative examples. The first processes synthetic data to show all the software functionalities. The second shows how to process a 4D image stack showing the time-lapse growth of Drosophila cells in an embryo. The third example presents the quantitative analysis of insulin granules in living beta-cells, showing that such particles have two main dynamics that coexist inside the cells. Conclusions Visual4DTracker is a software package for MATLAB to visualize, handle and manually track $$3D+t$$ 3 D + t stacks of microscopy images containing objects such cells, granules, etc.. With its unique set of functions, it remarkably permits the user to analyze and proof-read 4D data in a friendly 3D fashion. The tool is freely available at https://drive.google.com/drive/folders/19AEn0TqP-2B8Z10kOavEAopTUxsKUV73?usp=sharing

Automated Text Simplification

2021 ◽  
Vol 54 (2) ◽  
pp. 1-36
Author(s):  
Suha S. Al-Thanyyan ◽  
Aqil M. Azmi
Keyword(s):  
Reading Comprehension ◽  
Information Content ◽  
Evaluation Methods ◽  
Extensive Study ◽  
Low Literacy ◽  
Essential Tool ◽  
Text Simplification ◽  
Over Time ◽  
Original Information ◽  
Research Studies

Text simplification (TS) reduces the complexity of the text to improve its readability and understandability, while possibly retaining its original information content. Over time, TS has become an essential tool in helping those with low literacy levels, non-native learners, and those struggling with various types of reading comprehension problems. In addition, it is used in a preprocessing stage to enhance other NLP tasks. This survey presents an extensive study of current research studies in the field of TS, as well as covering resources, corpora, and evaluation methods that have been used in those studies.

scholarly journals Module to Support Real-Time Microscopic Imaging of Living Organisms on Ground-Based Microgravity Analogs

2021 ◽  
Vol 11 (7) ◽  
pp. 3122
Author(s):  
Srujana Neelam ◽  
Audrey Lee ◽  
Michael A. Lane ◽  
Ceasar Udave ◽  
Howard G. Levine ◽  
...  
Keyword(s):  
Real Time ◽  
High Speed ◽  
Simulated Microgravity ◽  
Image Acquisition ◽  
Time Lapse ◽  
Moving Frames ◽  
Cell Functions ◽  
Microgravity Simulation ◽  
Division Cell ◽  
Over Time

Since opportunities for spaceflight experiments are scarce, ground-based microgravity simulation devices (MSDs) offer accessible and economical alternatives for gravitational biology studies. Among the MSDs, the random positioning machine (RPM) provides simulated microgravity conditions on the ground by randomizing rotating biological samples in two axes to distribute the Earth’s gravity vector in all directions over time. Real-time microscopy and image acquisition during microgravity simulation are of particular interest to enable the study of how basic cell functions, such as division, migration, and proliferation, progress under altered gravity conditions. However, these capabilities have been difficult to implement due to the constantly moving frames of the RPM as well as mechanical noise. Therefore, we developed an image acquisition module that can be mounted on an RPM to capture live images over time while the specimen is in the simulated microgravity (SMG) environment. This module integrates a digital microscope with a magnification range of 20× to 700×, a high-speed data transmission adaptor for the wireless streaming of time-lapse images, and a backlight illuminator to view the sample under brightfield and darkfield modes. With this module, we successfully demonstrated the real-time imaging of human cells cultured on an RPM in brightfield, lasting up to 80 h, and also visualized them in green fluorescent channel. This module was successful in monitoring cell morphology and in quantifying the rate of cell division, cell migration, and wound healing in SMG. It can be easily modified to study the response of other biological specimens to SMG.

scholarly journals Rapid Spread of the SARS-CoV-2 Variant of Concern 202012/01 in Southern Italy (December 2020–March 2021)

2021 ◽  
Vol 18 (9) ◽  
pp. 4766
Author(s):  
Daniela Loconsole ◽  
Francesca Centrone ◽  
Caterina Morcavallo ◽  
Silvia Campanella ◽  
Anna Sallustio ◽  
...  
Keyword(s):  
Clinical Characteristics ◽  
Large Scale ◽  
Southern Italy ◽  
Whole Genome ◽  
Third Wave ◽  
Gene Target ◽  
The Third ◽  
Rapid Spread ◽  
Pharmaceutical Interventions ◽  
Over Time

Epidemiological and virological studies have revealed that SARS-CoV-2 variants of concern (VOCs) are emerging globally, including in Europe. The aim of this study was to evaluate the spread of B.1.1.7-lineage SARS-CoV-2 in southern Italy from December 2020–March 2021 through the detection of the S gene target failure (SGTF), which could be considered a robust proxy of VOC B.1.1.7. SGTF was assessed on 3075 samples from week 52/2020 to week 10/2021. A subset of positive samples identified in the Apulia region during the study period was subjected to whole-genome sequencing (WGS). A descriptive and statistical analysis of the demographic and clinical characteristics of cases according to SGTF status was performed. Overall, 20.2% of samples showed SGTF; 155 strains were confirmed as VOC 202012/01 by WGS. The proportion of SGTF-positive samples rapidly increased over time, reaching 69.2% in week 10/2021. SGTF-positive cases were more likely to be symptomatic and to result in hospitalization (p < 0.0001). Despite the implementation of large-scale non-pharmaceutical interventions (NPIs), such as the closure of schools and local lockdowns, a rapid spread of VOC 202012/01 was observed in southern Italy. Strengthened NPIs and rapid vaccine deployment, first among priority groups and then among the general population, are crucial both to contain the spread of VOC 202012/01 and to flatten the curve of the third wave.

The Mechanism of Cell-division

1953 ◽  
Vol s3-94 (28) ◽  
pp. 369-379
Author(s):  
M. M. SWANN
Keyword(s):  
Carbon Monoxide ◽  
Cell Division ◽  
Sea Urchin ◽  
White Light ◽  
Time Lapse ◽  
Psammechinus Miliaris ◽  
Energy Store ◽  
Time Lapse Photography

1. Developing eggs of the sea-urchin Psammechinus miliaris were subjected to carbon monoxide inhibition, which was controlled by changing from green to white light. The behaviour of the eggs was recorded by time-lapse photography. 2. If inhibition is applied before the eggs enter mitosis, their first cleavage is delayed by a time which is roughly equal to the period of the inhibition. 3. If the inhibition is applied when the cells have already entered mitosis, they complete mitosis and cleave with little or no delay, but their second cleavage is delayed by a time which is roughly equal to the period of the inhibition. 4. It is suggested that the necessary energy for the second mitosis and cleavage is being stored up during the first mitosis and cleavage, and that this energy store operates like a reservoir which is continually being filled but siphons out when it is full. Once the energy has siphoned out, it carries mitosis and cleavage through, even though the reservoir is not filling up because of carbon monoxide inhibition.

scholarly journals Molecular epidemiological analysis of HIV-1 variants circulating in Russia in 1987—2015

2017 ◽  
Vol 89 (11) ◽  
pp. 44-49 ◽  
Author(s):  
I A Lapovok ◽  
A E Lopatukhin ◽  
D E Kireev ◽  
E V Kazennova ◽  
A V Lebedev ◽  
...  
Keyword(s):  
Hiv Infection ◽  
Drug Users ◽  
Extensive Study ◽  
Nucleotide Sequences ◽  
Epidemiological Analysis ◽  
On Line ◽  
Diagnosis Date ◽  
Hiv 1 ◽  
Virus Subtype ◽  
Over Time

Aim. To simultaneously analyze HIV-1 samples from all Russian regions to characterize the epidemiology of HIV infection in the country as a whole. Subjects and methods. The most extensive study was conducted to examine nucleotide sequences of the pol gene of HIV-1 samples isolated from HIV-positive persons in different regions of Russia, with the diagnosis date being fixed during 1987—2015. The nucleotide sequences of the HIV-1 genome were analyzed using computer programs and on-line applications to identify a virus subtype and new recombinant forms. Results. The nucleotide sequences of the pol gene were analyzed in 1697 HIV-1 samples and the findings were that the genetic variant subtype A1 (IDU-A) was dominant throughout the entire territory of Russia (in more than 80% of all infection cases). Other virus variants circulating in Russia were analyzed; the phenomenon of the higher distribution of the recombinant form CRF63/02A in Siberia, which had been previously described in the literature, was also confirmed. Four new recombinant forms generated by the virus subtype A1 (IDU-A) and B and two AG recombinant forms were found. There was a larger genetic distance between the viruses of IDU-A variant circulating among the injecting drug users and those infected through heterosexual contact, as well as a change in the viruses of subtype G that caused the outbreak in the south of the country over time in 1988—1989. Conclusion. The findings demonstrate continuous HIV-1 genetic variability and recombination over time in Russia, as well as increased genetic diversity with higher HIV infection rates in the population.

scholarly journals The Scenario of a Pandemic Spread of the Coronavirus SARS-CoV-2 is Based on a Statistical Fallacy

2020 ◽  
Author(s):  
Christof Kuhbandner
Keyword(s):  
Apparent Increase ◽  
Rapid Spread ◽  
Almost All ◽  
Over Time ◽  
Coronavirus Infections

In view of the rapidly increasing numbers of reported new coronavirus infections, many speak of an upcoming pandemic. However, since the number of conducted coronavirus tests has rapidly increased over time as well, the apparent increase in infections may actually reflect increased testing, rather than a rapid spread of the coronavirus. To examine this issue, data from Austria, Belgium, France, Germany, Italy, and USA were analyzed. In all countries, the rapid increase in reported new infections was largely attributable to the rapid increase in conducted tests. Statistically controlling for the increased amount of testing revealed that the increases in reported infections dramatically overestimate the true increases in every country. According to the estimated true courses of new infections, the increases were initially much smaller, and the courses of new infections have already flattened or are even decreasing since the beginning of calendar week 13 (March 23) in almost all countries. The courses of reported new infections and deaths started to increase almost simultaneously in every country, which further confirms that the increases in reported new infections reflect effects of increased testing. These results indicate that the scenario of a coronavirus pandemic is based on a statistical fallacy.<br>

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