scholarly journals Methods for On-Orbit Germination of Arabidopsis thaliana for Proteomic Analysis

2020 ◽  
Vol 4 (2) ◽  
pp. 20-27
Author(s):  
Sarahann Hutchinson ◽  
Proma Basu ◽  
Sarah E. Wyatt ◽  
Darron R. Luesse
Keyword(s):  
Proteomic Analysis ◽  
Large Scale ◽  
Space Station ◽  
Petri Dish ◽  
Biological Research ◽  
Original Research ◽  
Temperature Growth ◽  
Proteomic Approach ◽  
Crowding Stress ◽  
The Impact

AbstractLarge-scale omics approaches make excellent choices for research aboard the International Space Station (ISS) because they provide large amounts of data that can be continually mined even after the original research has been completed. A proteomic approach can provide information about which proteins are produced, degraded, or post-translationally modified, potentially shedding light on cellular strategies that cannot be discerned from transcriptomic data. To collect sufficient tissue from a Biological Research In Canisters (BRIC)-grown experiment on the ISS for proteomic analysis, several modifications were made to existing protocols. Approximately 800–1000 seeds were housed in each Petri Dish Fixation Units (PDFU). These were germinated up to 120 h after planting by transferring the BRIC from cold stasis to room temperature. Growth continued for only 72 h after germination to allow sufficient tissue for extraction, and to minimize the impact of ethylene and crowding stress. Seedlings were then exposed to RNAlater®. Results indicate that RNAlater® - treated Arabidopsis seedlings yield an equal amount of protein to those flash-frozen in liquid nitrogen.

scholarly journals Active Learning Strategies for Phenotypic Profiling of High-Content Screens

2014 ◽  
Vol 19 (5) ◽  
pp. 685-695 ◽  
Author(s):  
Kevin Smith ◽  
Peter Horvath
Keyword(s):  
Active Learning ◽  
Learning Strategies ◽  
Large Scale ◽  
Classification Performance ◽  
New Drugs ◽  
Supervised Machine Learning ◽  
Biological Research ◽  
Time Investment ◽  
Active Learning Strategies ◽  
The Impact

High-content screening is a powerful method to discover new drugs and carry out basic biological research. Increasingly, high-content screens have come to rely on supervised machine learning (SML) to perform automatic phenotypic classification as an essential step of the analysis. However, this comes at a cost, namely, the labeled examples required to train the predictive model. Classification performance increases with the number of labeled examples, and because labeling examples demands time from an expert, the training process represents a significant time investment. Active learning strategies attempt to overcome this bottleneck by presenting the most relevant examples to the annotator, thereby achieving high accuracy while minimizing the cost of obtaining labeled data. In this article, we investigate the impact of active learning on single-cell–based phenotype recognition, using data from three large-scale RNA interference high-content screens representing diverse phenotypic profiling problems. We consider several combinations of active learning strategies and popular SML methods. Our results show that active learning significantly reduces the time cost and can be used to reveal the same phenotypic targets identified using SML. We also identify combinations of active learning strategies and SML methods which perform better than others on the phenotypic profiling problems we studied.

scholarly journals Design and Validation of a Device for Mitigating Fluid Microgravity Effects in Biological Research in Canister Spaceflight Hardware

2021 ◽  
Vol 2 ◽  
Author(s):  
Wayne L. Nicholson ◽  
Patricia Fajardo-Cavazos ◽  
Caleb Turner ◽  
Taylor M. Currie ◽  
Geoffrey Gregory ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Space Station ◽  
Petri Dish ◽  
Microgravity Environment ◽  
Direct Result ◽  
Ground Control ◽  
Biological Research ◽  
Transcriptomic Response ◽  
Liquid Cultures ◽  
Control Samples

The major factor influencing the behavior of microbes growing in liquids in space is microgravity. We recently measured the transcriptomic response of the Gram-positive bacterium Bacillus subtilis to the microgravity environment inside the International Space Station (ISS) in spaceflight hardware called Biological Research in Canisters-Petri Dish Fixation Units (BRIC-PDFUs). In two separate experiments in the ISS, dubbed BRIC-21 and BRIC-23, we grew multiple replicates of the same B. subtilis strain in the same hardware, growth medium, and temperature with matching ground control samples (npj Micrograv. 5:1.2019, doi: 10.1038/s41526-018-0061-0). In both experiments we observed similar responses of the transcriptome to spaceflight. However, we also noted that the liquid cultures assumed a different configuration in microgravity (a toroidal shape) compared with the ground control samples (a flat disc shape), leading us to question whether the transcriptome differences we observed were a direct result of microgravity, or a secondary result of the different liquid geometries of the samples affecting, for example, oxygen availability. To mitigate the influence of microgravity on liquid geometry in BRIC canisters, we have designed an insert to replace the standard 60-mm Petri dish in BRIC-PDFU or BRIC-LED sample compartments. In this design, liquid cultures are expected to assume a more disk-like configuration regardless of gravity or its absence. We have: (i) constructed a prototype device by 3D printing; (ii) evaluated different starting materials, treatments, and coatings for their wettability (i.e., hydrophilicity) using contact angle measurements; (iii) confirmed that the device performs as designed by drop-tower testing and; (iv) performed material biocompatibility studies using liquid cultures of Bacillus subtilis and Staphylococcus aureus bacteria. Future microgravity testing of the device in the ISS is planned.

scholarly journals Encroaching genomics: adapting large-scale science to small academic laboratories

2000 ◽  
Vol 2 (3) ◽  
pp. 85-92
Author(s):  
MARGRET B. EINARSON ◽  
ERICA A. GOLEMIS
Keyword(s):  
Large Scale ◽  
Biological Research ◽  
Public Attention ◽  
Protein Protein Interaction ◽  
Genome Wide ◽  
Genomic Consortium ◽  
The Face ◽  
Multiple Species ◽  
The Impact

Einarson, Margret B., and Erica A. Golemis. Encroaching genomics: adapting large-scale science to small academic laboratories. Physiol Genomics 2: 85–92, 2000.—The process of conducting biological research is undergoing a profound metamorphosis due to the technological innovations and torrent of information resulting from the execution of multiple species genome projects. The further tasks of mapping polymorphisms and characterizing genome-wide protein-protein interaction (the characterization of the proteome) will continue to garner resources, talent, and public attention. Although some elements of these whole genome size projects can only be addressed by large research groups, consortia, or industry, the impact of these projects has already begun to transform the process of research in many small laboratories. Although the impact of this transformation is generally positive, laboratories engaged in types of research destined to be dominated by the efforts of a genomic consortium may be negatively impacted if they cannot rapidly adjust strategies in the face of new large-scale competition. The focus of this report is to outline a series of strategies that have been productively utilized by a number of small academic laboratories that have attempted to integrate such genomic resources into research plans with the goal of developing novel physiological insights.

scholarly journals Urban Planning by Experiment: Practices, Outcomes, and Impacts

2021 ◽  
Vol 6 (1) ◽  
pp. 156-160
Author(s):  
Christian Scholl ◽  
Joop De Kraker
Keyword(s):  
Urban Planning ◽  
Learning Outcomes ◽  
Large Scale ◽  
Single Case ◽  
Original Research ◽  
Illustrative Case ◽  
Large Scale Integration ◽  
Scale Integration ◽  
The Impact ◽  
Planning Approaches

The impact of urban experimentation on urban planning approaches is so far insufficiently assessed and discussed. This thematic issue sets out to investigate the possibilities and limitations of ‘urban planning by experiment,’ defined as an approach that uses experimentation to innovate and improve urban planning instruments, approaches, and outcomes. It brings together eight contributions presenting original research on urban experimentation and its relation to urban planning. All contributions are empirically grounded in (illustrative) case studies, mostly from European cities. Here, we summarize and discuss the major findings across the eight contributions with respect to three key themes: the practices of urban experimentation, its outcomes, and its impacts on urban planning. We conclude that the practices of urban experimentation described in the contributions generated a wide variety of substantive and learning outcomes, which, according to the authors, represent worthwhile additions or alternatives to the current repertoire of approaches and instruments of urban planning. However, except for a single case, large-scale integration of experimentation in established approaches to urban planning was not observed, let alone a complete transformation of urban planning practices. An area for further research concerns the relation between the way urban experiments are organized and conducted, and their impact on urban planning.

Impact of COVID-19 on Nuclear Medicine in Germany, Austria and Switzerland: An International Survey in April 2020

2020 ◽  
Vol 59 (04) ◽  
pp. 294-299 ◽  
Author(s):  
Lutz S. Freudenberg ◽  
Ulf Dittmer ◽  
Ken Herrmann
Keyword(s):  
Nuclear Medicine ◽  
Health Systems ◽  
Personal Protective Equipment ◽  
Large Scale ◽  
Diagnostic Procedures ◽  
Protective Equipment ◽  
Current Crisis ◽  
Web Based ◽  
Public Versus Private ◽  
The Impact

Abstract Introduction Preparations of health systems to accommodate large number of severely ill COVID-19 patients in March/April 2020 has a significant impact on nuclear medicine departments. Materials and Methods A web-based questionnaire was designed to differentiate the impact of the pandemic on inpatient and outpatient nuclear medicine operations and on public versus private health systems, respectively. Questions were addressing the following issues: impact on nuclear medicine diagnostics and therapy, use of recommendations, personal protective equipment, and organizational adaptations. The survey was available for 6 days and closed on April 20, 2020. Results 113 complete responses were recorded. Nearly all participants (97 %) report a decline of nuclear medicine diagnostic procedures. The mean reduction in the last three weeks for PET/CT, scintigraphies of bone, myocardium, lung thyroid, sentinel lymph-node are –14.4 %, –47.2 %, –47.5 %, –40.7 %, –58.4 %, and –25.2 % respectively. Furthermore, 76 % of the participants report a reduction in therapies especially for benign thyroid disease (-41.8 %) and radiosynoviorthesis (–53.8 %) while tumor therapies remained mainly stable. 48 % of the participants report a shortage of personal protective equipment. Conclusions Nuclear medicine services are notably reduced 3 weeks after the SARS-CoV-2 pandemic reached Germany, Austria and Switzerland on a large scale. We must be aware that the current crisis will also have a significant economic impact on the healthcare system. As the survey cannot adapt to daily dynamic changes in priorities, it serves as a first snapshot requiring follow-up studies and comparisons with other countries and regions.

HOME VISITS DURING THE FIRST MONTH OF DELIVERY FOR RECENTLY DELIVERED WOMEN IN UTTAR PRADESH, INDIA

2020 ◽  
Vol 6 (5) ◽  
pp. 1183-1189
Author(s):  
Dr. Tridibesh Tripathy ◽  
Dr. Umakant Prusty ◽  
Dr. Chintamani Nayak ◽  
Dr. Rakesh Dwivedi ◽  
Dr. Mohini Gautam
Keyword(s):  
Large Scale ◽  
National Level ◽  
Uttar Pradesh ◽  
Life Time ◽  
Structured Interview ◽  
The Other ◽  
Registration System ◽  
Action Group ◽  
Current Article ◽  
The Impact

The current article of Uttar Pradesh (UP) is about the ASHAs who are the daughters-in-law of a family that resides in the same community that they serve as the grassroots health worker since 2005 when the NRHM was introduced in the Empowered Action Group (EAG) states. UP is one such Empowered Action Group (EAG) state. The current study explores the actual responses of Recently Delivered Women (RDW) on their visits during the first month of their recent delivery. From the catchment area of each of the 250 ASHAs, two RDWs were selected who had a child in the age group of 3 to 6 months during the survey. The response profiles of the RDWs on the post- delivery first month visits are dwelled upon to evolve a picture representing the entire state of UP. The relevance of the study assumes significance as detailed data on the modalities of postnatal visits are available but not exclusively for the first month period of their recent delivery. The details of the post-delivery first month period related visits are not available even in large scale surveys like National Family Health Survey 4 done in 2015-16. The current study gives an insight in to these visits with a five-point approach i.e. type of personnel doing the visit, frequency of the visits, visits done in a particular week from among those four weeks separately for the three visits separately. The current study is basically regarding the summary of this Penta approach for the post- delivery one-month period.     The first month period after each delivery deals with 70% of the time of the postnatal period & the entire neonatal period. Therefore, it does impact the Maternal Mortality Rate & Ratio (MMR) & the Neonatal Mortality Rates (NMR) in India and especially in UP through the unsafe Maternal & Neonatal practices in the first month period after delivery. The current MM Rate of UP is 20.1 & MM Ratio is 216 whereas the MM ratio is 122 in India (SRS, 2019). The Sample Registration System (SRS) report also mentions that the Life Time Risk (LTR) of a woman in pregnancy is 0.7% which is the highest in the nation (SRS, 2019). This means it is very risky to give birth in UP in comparison to other regions in the country (SRS, 2019). This risk is at the peak in the first month period after each delivery. Similarly, the current NMR in India is 23 per 1000 livebirths (UNIGME,2018). As NMR data is not available separately for states, the national level data also hold good for the states and that’s how for the state of UP as well. These mortalities are the impact indicators and such indicators can be reduced through long drawn processes that includes effective and timely visits to RDWs especially in the first month period after delivery. This would help in making their post-natal & neonatal stage safe. This is the area of post-delivery first month visit profile detailing that the current article helps in popping out in relation to the recent delivery of the respondents.   A total of four districts of Uttar Pradesh were selected purposively for the study and the data collection was conducted in the villages of the respective districts with the help of a pre-tested structured interview schedule with both close-ended and open-ended questions.  The current article deals with five close ended questions with options, two for the type of personnel & frequency while the other three are for each of the three visits in the first month after the recent delivery of respondents. In addition, in-depth interviews were also conducted amongst the RDWs and a total 500 respondents had participated in the study.   Among the districts related to this article, the results showed that ASHA was the type of personnel who did the majority of visits in all the four districts. On the other hand, 25-40% of RDWs in all the 4 districts replied that they did not receive any visit within the first month of their recent delivery. Regarding frequency, most of the RDWs in all the 4 districts received 1-2 times visits by ASHAs.   Regarding the first visit, it was found that the ASHAs of Barabanki and Gonda visited less percentage of RDWs in the first week after delivery. Similarly, the second visit revealed that about 1.2% RDWs in Banda district could not recall about the visit. Further on the second visit, the RDWs responded that most of them in 3 districts except Gonda district did receive the second postnatal visit in 7-15 days after their recent delivery. Less than half of RDWs in Barabanki district & just more than half of RDWs in Gonda district received the third visit in 15-21 days period after delivery. For the same period, the majority of RDWs in the rest two districts responded that they had been entertained through a home visit.

Utopias of One

2019 ◽  
Author(s):  
Joshua Kotin
Keyword(s):  
United States ◽  
Soviet Union ◽  
World War I ◽  
Large Scale ◽  
Jim Crow ◽  
Personal Autonomy ◽  
The United States ◽  
Soviet Period ◽  
Original Research ◽  
The Soviet Union

This book is a new account of utopian writing. It examines how eight writers—Henry David Thoreau, W. E. B. Du Bois, Osip and Nadezhda Mandel'shtam, Anna Akhmatova, Wallace Stevens, Ezra Pound, and J. H. Prynne—construct utopias of one within and against modernity's two large-scale attempts to harmonize individual and collective interests: liberalism and communism. The book begins in the United States between the buildup to the Civil War and the end of Jim Crow; continues in the Soviet Union between Stalinism and the late Soviet period; and concludes in England and the United States between World War I and the end of the Cold War. In this way it captures how writers from disparate geopolitical contexts resist state and normative power to construct perfect worlds—for themselves alone. The book contributes to debates about literature and politics, presenting innovative arguments about aesthetic difficulty, personal autonomy, and complicity and dissent. It models a new approach to transnational and comparative scholarship, combining original research in English and Russian to illuminate more than a century and a half of literary and political history.

The Impact of Quantitative Easing on Emerging Markets – Literature Review

e-Finanse ◽  
2018 ◽  
Vol 14 (4) ◽  
pp. 67-76
Author(s):  
Piotr Bartkiewicz
Keyword(s):  
Emerging Markets ◽  
Large Scale ◽  
Empirical Literature ◽  
Quantitative Easing ◽  
Methodological Choices ◽  
The Subject ◽  
Methodological Approaches ◽  
The Impact ◽  
Sufficient Precision

AbstractThe article presents the results of the review of the empirical literature regarding the impact of quantitative easing (QE) on emerging markets (EMs). The subject is of interest to policymakers and researchers due to the increasingly larger role of EMs in the world economy and the large-scale capital flows occurring after 2009. The review is conducted in a systematic manner and takes into consideration different methodological choices, samples and measurement issues. The paper puts the summarized results in the context of transmission channels identified in the literature. There are few distinct methodological approaches present in the literature. While there is a consensus regarding the direction of the impact of QE on EMs, its size and durability have not yet been assessed with sufficient precision. In addition, there are clear gaps in the empirical findings, not least related to relative underrepresentation of the CEE region (in particular, Poland).

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