scholarly journals Long-term tracking of budding yeast cells in brightfield microscopy: CellStar and the Evaluation Platform

2017 ◽  
Vol 14 (127) ◽  
pp. 20160705 ◽  
Author(s):  
Cristian Versari ◽  
Szymon Stoma ◽  
Kirill Batmanov ◽  
Artémis Llamosi ◽  
Filip Mroz ◽  
...  
Keyword(s):  
Cell Biology ◽  
High Performance ◽  
Yeast Cells ◽  
Additional Information ◽  
New Variant ◽  
Long Term Experiments ◽  
Community Effort ◽  
Set Up ◽  
Evaluation Platform

With the continuous expansion of single cell biology, the observation of the behaviour of individual cells over extended durations and with high accuracy has become a problem of central importance. Surprisingly, even for yeast cells that have relatively regular shapes, no solution has been proposed that reaches the high quality required for long-term experiments for segmentation and tracking (S&T) based on brightfield images. Here, we present CellStar , a tool chain designed to achieve good performance in long-term experiments. The key features are the use of a new variant of parametrized active rays for segmentation, a neighbourhood-preserving criterion for tracking, and the use of an iterative approach that incrementally improves S&T quality. A graphical user interface enables manual corrections of S&T errors and their use for the automated correction of other, related errors and for parameter learning. We created a benchmark dataset with manually analysed images and compared CellStar with six other tools, showing its high performance, notably in long-term tracking. As a community effort, we set up a website, the Yeast Image Toolkit, with the benchmark and the Evaluation Platform to gather this and additional information provided by others.

Crop production research in multifunctional agriculture

2003 ◽  
Vol 51 (1) ◽  
pp. 91-99 ◽  
Author(s):  
Z. Berzsenyi
Keyword(s):  
Crop Production ◽  
Field Experiments ◽  
Simulation Models ◽  
Wheat Varieties ◽  
Maize Hybrids ◽  
Long Term Experiments ◽  
Small Plot ◽  
Production Research ◽  
Set Up

The research agenda for crop science in the 21st century will depend largely on whether the present conditions regarding the global food surplus continue, or whether a food scarcity recurs. Crop production research is based chiefly on small-plot field experiments, the majority of which are either long-term experiments or experiments set up to investigate the specific agronomic responses of Martonvásár maize hybrids and wheat varieties. The sustainability of crop production is examined in long-term experiments. The agronomic responses of maize hybrids and wheat varieties are studied at various levels of biological organisation. Growth analysis facilitates the exact characterisation of agronomic responses and the grouping of response effects and types using multivariable methods. Continued experimentation coupled with crop simulation models and decision support systems are an ever more useful framework for analysing the complexity of agricultural systems.

scholarly journals Reproducibility Practice in High Performance Computing: Community Survey Results

2021 ◽  
Author(s):  
Beth Plale ◽  
Tanu Malik ◽  
Line Pouchard
Keyword(s):  
High Performance ◽  
Manuscript Submission ◽  
Educational Goals ◽  
Technical Program ◽  
Engineering Research ◽  
The Road ◽  
Community Effort ◽  
Survey Results ◽  
Long Term Impact

The integrity of science and engineering research is grounded in assumptions of rigor and transparency on the part of those engaging in such research. HPC community effort to strengthen rigor and transparency take the form of reproducibility efforts. In a recent survey of the SC conference community, we collected information about the SC Reproducibility Initiative activities. We present the survey results in this paper. Results show that the reproducibility initiative activities have contributed to higher levels of awareness on the part of SC conference technical program participants, and hint at contributing to greater scientific impact for the published papers of the SC conference series. Stringent point-of-manuscript-submission verification is problematic for reasons we point out, as are inherent difficulties of computational reproducibility in HPC. Future efforts should better decouple the community educational goals from goals that specifically strengthen a research work’s potential for long-term impact through reuse 5-10 years down the road.

Significance of the 50-year-old long-term experiments in Martonvásár in improving crop production

2010 ◽  
Vol 58 (Supplement 1) ◽  
pp. 23-34 ◽  
Author(s):  
Z. Berzsenyi
Keyword(s):  
Crop Production ◽  
Long Term Effects ◽  
Wheat Varieties ◽  
Present Generation ◽  
National Heritage ◽  
Long Term Experiments ◽  
Scientific Results ◽  
Carry Over ◽  
Set Up

Long-term experiments are indispensable for investigations on the long-term effects of various crop production methods and technologies. The long-term experiments set up in Martonvásár by Béla Győrffy are now 50 years old and can be considered as part of the national heritage. The most important of these experiments involve crop rotation vs. monoculture trials, the comparison of fertilisation systems, studies on the interactions and carry-over effects of organic and mineral fertilisers, fertiliser rate experiments and polyfactorial experiments. The long-term experiments in Martonvásár form an integral part of maize and wheat research and provide a place for testing the agronomic responses of maize hybrids and wheat varieties. Valuable scientific results are obtained from these experiments regarding the reasons for yield depression in monocultures, the yieldincreasing effect of crop rotations, the comparative benefits of organic and mineral fertilisation, the agronomic responses of genotypes, the sustainability and yield stability of crop production techniques, and the interaction between various crop production factors. These results promote the improvement of maize and wheat production and are regularly incorporated into recommendation systems. The present generation of scientists has a responsibility to maintain these experiments, so that they can continue to serve their purpose in the coming decades.

scholarly journals Reproducibility Practice in High Performance Computing: Community Survey Results

2021 ◽  
Author(s):  
Beth Plale ◽  
Tanu Malik ◽  
Line Pouchard
Keyword(s):  
High Performance ◽  
Manuscript Submission ◽  
Educational Goals ◽  
Technical Program ◽  
Engineering Research ◽  
The Road ◽  
Community Effort ◽  
Survey Results ◽  
Long Term Impact

The integrity of science and engineering research is grounded in assumptions of rigor and transparency on the part of those engaging in such research. HPC community effort to strengthen rigor and transparency take the form of reproducibility efforts. In a recent survey of the SC conference community, we collected information about the SC Reproducibility Initiative activities. We present the survey results in this paper. Results show that the reproducibility initiative activities have contributed to higher levels of awareness on the part of SC conference technical program participants, and hint at contributing to greater scientific impact for the published papers of the SC conference series. Stringent point-of-manuscript-submission verification is problematic for reasons we point out, as are inherent difficulties of computational reproducibility in HPC. Future efforts should better decouple the community educational goals from goals that specifically strengthen a research work’s potential for long-term impact through reuse 5-10 years down the road.

scholarly journals Machine learning-based automated yeast cell counting under a complicated background with ilastik and ImageJ

2021 ◽  
Author(s):  
Chenxi Li ◽  
Xiaoyu Ma ◽  
Jing Deng ◽  
Jiajia Li ◽  
Yanjie Liu ◽  
...  
Keyword(s):  
Machine Learning ◽  
Yeast Cell ◽  
Cell Biology ◽  
Low Cost ◽  
Batch Processing ◽  
Yeast Cells ◽  
Cell Counting ◽  
Industrial Fermentation ◽  
Manual Counting ◽  
Set Up

Measuring the concentration and viability of yeast cells is an important and fundamental procedure in scientific research and industrial fermentation. In consideration of the drawbacks of manual cell counting, large quantities of yeast cells require methods that provide easy, objective, and reproducible high-throughput calculations, especially for samples in complicated backgrounds. To answer this challenge, we explored and developed an easy-to-use yeast cell counting pipeline that combined the machine learning-based ilastik tool with the freeware ImageJ, as well as a conventional photomicroscope. Briefly, learning from labels provided by the user, ilastik performs segmentation and classification automatically in batch processing mode for large numbers of images and thus discriminates yeast cells from complex backgrounds. The files processed through ilastik can be recognized by ImageJ, which can set up customizable parameters based on cell size, perimeter, roundness and so on. In this work, we programmed an ImageJ macro, “Yeast Counter”, to compute the numeric results of yeast cells for automatic batch processing. Taking the yeast Cryptococccus deneoformans as an example, we observed that the customizable software algorithm for yeast counting with ilastik and ImageJ reduced inter-operator errors significantly and achieved accurate and objective results in the spotting test, while manual counting with a haemocytometer exhibited some errors between repeats and required more time. In summary, a convenient, rapid, reproducible and extremely low-cost method to count yeast cells is described here that can be applied to multiple kinds of yeasts in genetics, cell biology and industrial fermentation.

Calibration of methods for soil and diagnostic plant analysis in the Hungarian National Fertilization Long-term Trials. I. Comparison of soil P tests for agronomic purposes in the soils of long-term experiments

2011 ◽  
Vol 60 (2) ◽  
pp. 343-358
Author(s):  
Péter Csathó ◽  
Marianna Magyar ◽  
Erzsébet Osztoics ◽  
Katalin Debreczeni ◽  
Katalin Sárdi
Keyword(s):  
Plant Analysis ◽  
Soil P ◽  
Olsen P ◽  
Long Term Experiments ◽  
Soil P Tests

A szabadföldi trágyázási (tartam)kísérletek eredményeit talaj-, illetve diagnosztikai célú növényvizsgálatok segítségével tudjuk kiterjeszteni, általánosítani – figyelembe véve természetesen a kiterjesztés korlátait is. Célszerűnek láttuk ezen túl a talaj könnyen oldható tápelem-, közöttük P-tartalmát is meghatározni a hazánkban hivatalosan elfogadott AL- (ammónium-laktátos) módszer mellett az Európai Unióban és Észak-Amerikában alkalmazott P-tesztekkel is (CaCl2-, H2O-, Olsen-, Bray1-, LE-, Mehlich3- stb.) a hazai OMTK kísérletek talajmintáiban. A kísérleti helyek talajtulajdonságaiban megnyilvánuló jelentős különbségek lehetőséget adnak rá, hogy a talaj P-teszteket – és a növényi P-felvételt – jellegzetes hazai talajokon, sokszor szélsőséges talajparaméterek mellett vizsgáljuk. Az egyes P-szintek között a 28 év átlagában mintegy évi 50 kg P2O5·ha-1volt a különbség. A P0-szinten mért P-tartalmak jól jelezték az egyes kísérleti helyek talajának eltérő P-ellátottságát, illetve, közvetve, fizikai féleségében, pH és mészállapotában meglévő különbségeket. A P2-szinten – a hazai talajokra, P-igényes növényekre a hazai szabadföldi P-trágyázási tartamkísérleti adatbázisban talált összefüggésekre alapozott – új AL-P határértékek szerint csupán a bicsérdi csernozjom barna erdőtalajon nem javult a P-ellátottság legalább a „jó” szintig. Vizsgálataink megerősítették az AL-módszer függőségét a CaCO3-tartalomtól: a Mehlich3 módszerrel való összefüggésben a karbonátmentes és a karbonátos talajok csoportja erőteljesen elkülönült egymástól. Az AL-P korrekció elvégzése, azaz az AL-P értékeknek egy standard talajtulajdonság-sorra való konvertálása (KA: 36; pH(KCl): 6,8; CaCO3: 0,1%) látványosan csökkentette az AL-módszernek a talaj CaCO3-tartalmától való függőségét. Az AL-P és Olsen-P, valamint a korrigált AL-P és Olsen-P tartalmak összehasonlításában ugynakkor ugyanez az összefüggés nem volt állapítható, ami arra utal, hogy az Olsen módszer bizonyos fokig szintén pH- és mészállapot függő. Kísérleti eredményeink megerősítették a Sarkadi-féle AL-P korrekciós modell helytálló voltát. Fenti megállapításunkat ugyanakkor a növényi P-tartalmakkal való összefüggéseknek is igazolniuk kell. Szükséges tehát a talajvizsgálati eredményeknek a diagnosztikai célú növényvizsgálatokkal, valamint a terméseredményekkel való összevetése. A tartamkísérletek talajai lehetőséget nyújtanak a környezetvédelmi célú P-vizsgálatok értékelésére, a talaj P-feltöltöttsége környezeti kockázatának becslésére. Ezekkel a kérdésekkel a cikksorozat további részeiben kívánunk foglalkozni.

Efficient Co-Harvesting of Solar Energy and Low-Grade Heat by Molecular Photoswitches for High Energy Density, Long-Term Stable Solar Thermal Battery

2019 ◽  
Author(s):  
Zhao-Yang Zhang ◽  
Tao LI
Keyword(s):  
Energy Density ◽  
Solar Energy ◽  
High Performance ◽  
High Energy ◽  
Solar Thermal ◽  
High Energy Density ◽  
Low Grade ◽  
Thermal Battery ◽  
Low Grade Heat

Solar energy and ambient heat are two inexhaustible energy sources for addressing the global challenge of energy and sustainability. Solar thermal battery based on molecular switches that can store solar energy and release it as heat has recently attracted great interest, but its development is severely limited by both low energy density and short storage stability. On the other hand, the efficient recovery and upgrading of low-grade heat, especially that of the ambient heat, has been a great challenge. Here we report that solar energy and ambient heat can be simultaneously harvested and stored, which is enabled by room-temperature photochemical crystal-to-liquid transitions of small-molecule photoswitches. The two forms of energy are released together to produce high-temperature heat during the reverse photochemical phase change. This strategy, combined with molecular design, provides high energy density of 320-370 J/g and long-term storage stability (half-life of about 3 months). On this basis, we fabricate high-performance, flexible film devices of solar thermal battery, which can be readily recharged at room temperature with good cycling ability, show fast rate of heat release, and produce high-temperature heat that is >20<sup> o</sup>C higher than the ambient temperature. Our work opens up a new avenue to harvest ambient heat, and demonstrate a feasible strategy to develop high-performance solar thermal battery.

Efficient Co-Harvesting of Solar Energy and Low-Grade Heat by Molecular Photoswitches for High Energy Density, Long-Term Stable Solar Thermal Battery

2019 ◽  
Author(s):  
Zhao-Yang Zhang ◽  
Tao LI
Keyword(s):  
Energy Density ◽  
Solar Energy ◽  
High Performance ◽  
High Energy ◽  
Solar Thermal ◽  
High Energy Density ◽  
Low Grade ◽  
Thermal Battery ◽  
Low Grade Heat

Solar energy and ambient heat are two inexhaustible energy sources for addressing the global challenge of energy and sustainability. Solar thermal battery based on molecular switches that can store solar energy and release it as heat has recently attracted great interest, but its development is severely limited by both low energy density and short storage stability. On the other hand, the efficient recovery and upgrading of low-grade heat, especially that of the ambient heat, has been a great challenge. Here we report that solar energy and ambient heat can be simultaneously harvested and stored, which is enabled by room-temperature photochemical crystal-to-liquid transitions of small-molecule photoswitches. The two forms of energy are released together to produce high-temperature heat during the reverse photochemical phase change. This strategy, combined with molecular design, provides high energy density of 320-370 J/g and long-term storage stability (half-life of about 3 months). On this basis, we fabricate high-performance, flexible film devices of solar thermal battery, which can be readily recharged at room temperature with good cycling ability, show fast rate of heat release, and produce high-temperature heat that is >20<sup> o</sup>C higher than the ambient temperature. Our work opens up a new avenue to harvest ambient heat, and demonstrate a feasible strategy to develop high-performance solar thermal battery.

Use Of Tai Chi Elements To Increase Respiratory Amplitude

2019 ◽  
pp. 11-20
Author(s):  
Mihai-Alexandru Citea ◽  
Marius Neculaes
Keyword(s):  
High Performance ◽  
Tai Chi ◽  
Sports Club ◽  
Optimal Functioning ◽  
Physiological Adaptations ◽  
Competitive Activity ◽  
Abdominal Breathing ◽  
Study Participants ◽  
Different Levels

High performance sport has a major impact on the physiological adaptations of the respiratory system. The importance of the optimal functioning of this system is essential to achieve top results in high performance sport but also in maintaining a long term health status. Science journals present numerous studies that highlight the benefits of practicing Tai Chi on the general population, with effects ranging from improving cardiac function, to influencing the immune system. The purpose of this study is to identify whether by practicing Tai Chi forms a athlete can change their breathing pattern and develop their respiratory amplitude. The subjects of the study were 22 fencing practitioners, accredited at the Iași Municipal Sports Club (C.S.M. Iași), aged between 14 and 18 years, with over 3 years of competitive activity. Materials and method: The study participants were evaluated initially and at the end of 7 months of practice. The frequency was 3 sessions per week, and the duration of each session was 20-30 minutes. The evaluation consisted in measuring the circumference of the thorax at 3 different levels: subaxillary, medial thorax (T6-T7) and lower rib (diaphragmatic) in maximal inspiration and expiration. Conclusions: A constant evolution is observed in most of the exposed cases. In cases where this evolution is not visible, a change in the breathing mode can be noticed, transforming from an upper rib breathing into a thoracic or abdominal breathing. With the exception of one case, all subjects had an improvement of the value in the lower rib level.

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