scholarly journals Thermography methods to assess stomatal behaviour in a dynamic environment

2020 ◽  
Vol 71 (7) ◽  
pp. 2329-2338 ◽  
Author(s):  
Silvere Vialet-Chabrand ◽  
Tracy Lawson
Keyword(s):  
Water Status ◽  
Dynamic Environment ◽  
Relevant Information ◽  
Ease Of Use ◽  
Gas Exchange Parameters ◽  
Stress Indices ◽  
Biologically Relevant ◽  
Stomatal Behaviour ◽  
Leaf Transpiration ◽  
Evaporative Flux

Abstract Although thermography allows rapid, non-invasive measurements of large numbers of plants, it has not been used extensively due to the difficulty in deriving biologically relevant information such as leaf transpiration (E) and stomatal conductance (gsw) from thermograms. Methods normalizing leaf temperature using temperatures from reference materials (e.g. with and without evaporative flux) to generate stress indices are generally preferred due to their ease of use to assess plant water status. Here, a simplified method to solve dynamic energy balance equations is presented, which enables the calculation of ‘wet’ and ‘dry’ leaf temperatures in order to derive stress indices, whilst providing accurate estimates of E and gsw. Comparing stress indices and gas exchange parameters highlights the limitation of stress indices in a dynamic environment and how this problem can be overcome using artificial leaf references with known conductance. Additionally, applying the equations for each pixel of a thermogram to derive the rapidity of stomatal response over the leaf lamina in wheat revealed the spatial heterogeneity of stomatal behaviour. Rapidity of stomatal movements is an important determinant of water use efficiency, and our results showed ‘patchy’ responses that were linked to both the spatial and temporal response of gsw.

scholarly journals NoRCE: non-coding RNA sets cis enrichment tool

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gulden Olgun ◽  
Afshan Nabi ◽  
Oznur Tastan
Keyword(s):  
Expression Patterns ◽  
Target Prediction ◽  
Enrichment Analysis ◽  
Fruit Fly ◽  
Relevant Information ◽  
R Package ◽  
Data Repository ◽  
Biologically Relevant ◽  
Gene Sets ◽  
Data Files

Abstract Background While some non-coding RNAs (ncRNAs) are assigned critical regulatory roles, most remain functionally uncharacterized. This presents a challenge whenever an interesting set of ncRNAs needs to be analyzed in a functional context. Transcripts located close-by on the genome are often regulated together. This genomic proximity on the sequence can hint at a functional association. Results We present a tool, NoRCE, that performs cis enrichment analysis for a given set of ncRNAs. Enrichment is carried out using the functional annotations of the coding genes located proximal to the input ncRNAs. Other biologically relevant information such as topologically associating domain (TAD) boundaries, co-expression patterns, and miRNA target prediction information can be incorporated to conduct a richer enrichment analysis. To this end, NoRCE includes several relevant datasets as part of its data repository, including cell-line specific TAD boundaries, functional gene sets, and expression data for coding & ncRNAs specific to cancer. Additionally, the users can utilize custom data files in their investigation. Enrichment results can be retrieved in a tabular format or visualized in several different ways. NoRCE is currently available for the following species: human, mouse, rat, zebrafish, fruit fly, worm, and yeast. Conclusions NoRCE is a platform-independent, user-friendly, comprehensive R package that can be used to gain insight into the functional importance of a list of ncRNAs of any type. The tool offers flexibility to conduct the users’ preferred set of analyses by designing their own pipeline of analysis. NoRCE is available in Bioconductor and https://github.com/guldenolgun/NoRCE.

scholarly journals Noise matters: elephants show risk-avoidance behaviour in response to human-generated seismic cues

2021 ◽  
Vol 288 (1953) ◽  
pp. 20210774
Author(s):  
Beth Mortimer ◽  
James A. Walker ◽  
David S. Lolchuragi ◽  
Michael Reinwald ◽  
David Daballen
Keyword(s):  
Seismic Noise ◽  
Information Transfer ◽  
Conservation Management ◽  
Sensory Ecology ◽  
Loxodonta Africana ◽  
Relevant Information ◽  
African Elephants ◽  
Risk Avoidance ◽  
Biologically Relevant ◽  
Seismic Vibrations

African elephants ( Loxodonta africana ) use many sensory modes to gather information about their environment, including the detection of seismic, or ground-based, vibrations. Seismic information is known to include elephant-generated signals, but also potentially encompasses biotic cues that are commonly referred to as ‘noise’. To investigate seismic information transfer in elephants beyond communication, here we tested the hypothesis that wild elephants detect and discriminate between seismic vibrations that differ in their noise types, whether elephant- or human-generated. We played three types of seismic vibrations to elephants: seismic recordings of elephants (elephant-generated), white noise (human-generated) and a combined track (elephant- and human-generated). We found evidence of both detection of seismic noise and discrimination between the two treatments containing human-generated noise. In particular, we found evidence of retreat behaviour, where seismic tracks with human-generated noise caused elephants to move further away from the trial location. We conclude that seismic noise are cues that contain biologically relevant information for elephants that they can associate with risk. This expands our understanding of how elephants use seismic information, with implications for elephant sensory ecology and conservation management.

State-of-the-Art Information Retrieval Tools for Biological Resources

2018 ◽  
pp. 77-96
Author(s):  
Shashi Bhushan Lal ◽  
Anu Sharma ◽  
Krishna Kumar Chaturvedi ◽  
Mohammad Samir Farooqi ◽  
Sanjeev Kumar ◽  
...  
Keyword(s):  
Information Retrieval ◽  
Statistical Analysis ◽  
Relevant Information ◽  
Ease Of Use ◽  
Video Data ◽  
Biological Databases ◽  
Biological Resources ◽  
Sequencing Technologies ◽  
Scientific Experiments ◽  
Insight Into

With the advancements in sequencing technologies, there is an exponential growth in the availability of the biological databases. Biological databases consist of information and knowledge collected from scientific experiments, published literature and statistical analysis of text, numerical, image and video data. These databases are widely spread across the globe and are being maintained by many organizations. A number of tools have been developed to retrieve the information from these databases. Most of these tools are available on web but are scattered. So, finding a relevant information is a very difficult, and tedious task for the researchers. Moreover, many of these databases use disparate storage formats but are linked to each other. So, an important issue concerning present biological resources is their availability and integration at single platform. This chapter provides an insight into existing biological resources with an aim to provide consolidated information at one place for ease of use and access by researchers, academicians and students.

Exploring Dimensions of the Media Dream

2016 ◽  
pp. 1-39 ◽  
Author(s):  
Rollin McCraty ◽  
Stephen Brock Schafer
Keyword(s):  
Heart Rate ◽  
Heart Rate Variability ◽  
Electromagnetic Coupling ◽  
Relevant Information ◽  
Living Systems ◽  
Biologically Relevant ◽  
Dream Analysis ◽  
Psychological Analysis ◽  
Dramatic Structure ◽  
The Media

The earth's magnetic fields are carriers of biologically relevant information that connects all living systems. The electromagnetic coupling of the human brain, cardiovascular and nervous systems, and geomagnetic frequencies supports the hypothesis that the mediated reality of electromagnetic bandwidths can be correlated with bio-energetic and geomagnetic frequencies. Understood as bio-energetic functions (Thinking, Feeling, Sensing, & Intuiting), the media-sphere becomes measurable according to principles of coherency (measured as heart-rate variability, HRV) and principles of Jungian dream analysis (compensation and dramatic structure). It has been demonstrated that the rhythmic patterns in beat-to-beat heart rate variability reflect emotional functions, permeate every bodily cell, and play a central role in the generation and transmission of system-wide information via the electromagnetic field. So, the “media dream” becomes susceptible to psychological analysis leading to a better understanding of unconscious cognitive archetypal patterns of contextual collectives.

scholarly journals Co-expression networks for plant biology: why and how

2019 ◽  
Vol 51 (10) ◽  
pp. 981-988 ◽  
Author(s):  
Xiaolan Rao ◽  
Richard A Dixon
Keyword(s):  
Gene Expression ◽  
Network Analysis ◽  
Expression Analysis ◽  
Expression Profiling ◽  
Recent Literature ◽  
Genomic Data ◽  
Relevant Information ◽  
Plant Biology ◽  
Biologically Relevant

Abstract Co-expression network analysis is one of the most powerful approaches for interpretation of large transcriptomic datasets. It enables characterization of modules of co-expressed genes that may share biological functional linkages. Such networks provide an initial way to explore functional associations from gene expression profiling and can be applied to various aspects of plant biology. This review presents the applications of co-expression network analysis in plant biology and addresses optimized strategies from the recent literature for performing co-expression analysis on plant biological systems. Additionally, we describe the combined interpretation of co-expression analysis with other genomic data to enhance the generation of biologically relevant information.

Probing the response of Deinococcus radiodurans exposed to simulated space conditions

2019 ◽  
Vol 19 (3) ◽  
pp. 203-209
Author(s):  
Gabriel Guarany de Araujo ◽  
Fabio Rodrigues ◽  
Douglas Galante
Keyword(s):  
Vacuum Ultraviolet ◽  
Deinococcus Radiodurans ◽  
Traditional Approach ◽  
High Vacuum ◽  
Relevant Information ◽  
Molecular Probes ◽  
Ultra High Vacuum ◽  
Planetary Protection ◽  
Biologically Relevant ◽  
Space Conditions

AbstractThe extremotolerant bacterium Deinococcus radiodurans is used as a model to explore the limits of life on Earth and beyond. In experiments performed in an ultra-high vacuum chamber with a vacuum ultraviolet (VUV) synchrotron beamline, this microorganism was exposed to conditions present on an extraterrestrial environment unprotected by an atmosphere, such as outside a spacecraft or on an asteroid, relevant in the context of planetary protection and panspermia hypothesis. Different methods were used to obtain the biologically relevant information from this investigation. Counting of colony forming units, the traditional approach for viability assessment, is limited to measuring the survival of the cells. For a more in-depth study of damage mechanisms at subcellular levels, specific molecular probes (propidium iodide and dihydrorhodamine 123) were applied and whole populations could be analysed, cell by cell, by flow cytometry. VUV radiation caused a substantial loss of viability, though only a fraction of the cells presented membrane damages even at the largest tested fluences. Additionally, intracellular oxidative stress was also detected upon exposure. These results point to significant VUV inactivating effects extending beyond the cells' outermost structures, in contrast to a more superficial role that could be expected due to the highly interacting nature of this radiation range. Nevertheless, it was observed that microscopic-level shading sufficed to allow the persistence of a small surviving subpopulation for the longer expositions. This study contributes to unveiling the response of biological systems under space conditions, assessing not just cell viability but also the mechanisms that lead to inactivation.

Embryonic tissues are viscoelastic materials

2000 ◽  
Vol 78 (3) ◽  
pp. 243-251 ◽  
Author(s):  
D A Beysens ◽  
G Forgacs ◽  
J A Glazier
Keyword(s):  
Surface Tension ◽  
Metastatic Potential ◽  
Relevant Information ◽  
Specific Cell ◽  
Biologically Relevant ◽  
Embryonic Tissues ◽  
Differential Adhesion ◽  
Equilibrium Configurations ◽  
Experimental Findings ◽  
Differential Adhesion Hypothesis

Early embryonic development is characterized by spectacular morphogenetic processes such as sorting or spreading of tissues. Analogy between viscoelastic fluids and certain properties of embryonic tissues turned out to be useful in interpreting some aspects of these morphogenetic phenomena. In accordance with the differential adhesion hypothesis, the values of tissue-specific surface tensions have been shown to be consistent with the equilibrium configurations such tissues reach in the course of sorting and spreading. A method to measure tissue surface tension and viscoelastic properties is described. Notions like the Laplace's equation relating surface tension to radii of curvature, or the Kelvin model of viscoelasticity are used to analyze the results of these measurements. The fluid analogy is extended to time-dependent phenomena, in particular, to the analysis of cellular pattern evolution in the course of spreading. On the basis of recent experimental findings, we demonstrate that the kinetics of spreading and nucleation in binary fluids can be analyzed using the same formalism. We illustrate how our results can be used to obtain biologically relevant information on the strength of binding between specific cell adhesion molecules under near physiological conditions. We also suggest a diagnostic application of our method to monitor the metastatic potential of tumors. PACS No.: 03.65Ge

scholarly journals Development of a DSS and Online Tools to Support Sleep Disorder Consultations using Design Science.

2016 ◽  
Vol 20 ◽  
Author(s):  
Jacqueline Blake ◽  
Don Kerr ◽  
John Gammack
Keyword(s):  
Medical Decision Making ◽  
Design Science ◽  
Dynamic Environment ◽  
Relevant Information ◽  
Medical Decision ◽  
Primary Users ◽  
Online Tools ◽  
Medical Diagnostic ◽  
Technical Evaluation ◽  
Usage Context

Medical decision making takes place in a complex and dynamic environment, involving various individual and organisational stakeholders. In such contexts supportive information systems are required to be designed for practical efficacy, emphasising transparency, usability, and usefulness to their primary users. At the same time, they need to demonstrate improved efficiency and diagnostic accuracy.  In addition, they also need to provide effective communication of relevant information. This paper describes the use of design science to develop and evaluate a DSS incorporated into online tools to support sleep physician’s diagnosis of sleep disorders.  The design science approach offers guidance for developing this solution, that ensure the artefacts fit into their usage context, and that development and evaluation principles that generalise to similar problem domains are identified. How this project fits in the design science guidelines is specified, thus demonstrating how this philosophy and methodology advances theory particularly relevant to other similar medical diagnostic domains.  The usability and technical evaluation of the set of tools indicated provide clear practical benefits at patient, physician and organisational levels.

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