Gradient Boosted Decision Trees (GBDT’s) are a powerful tool for classification and regression tasks in Big Data. Researchers should be familiar with the strengths and weaknesses of current ...implementations of GBDT’s in order to use them effectively and make successful contributions. CatBoost is a member of the family of GBDT machine learning ensemble techniques. Since its debut in late 2018, researchers have successfully used CatBoost for machine learning studies involving Big Data. We take this opportunity to review recent research on CatBoost as it relates to Big Data, and learn best practices from studies that cast CatBoost in a positive light, as well as studies where CatBoost does not outshine other techniques, since we can learn lessons from both types of scenarios. Furthermore, as a Decision Tree based algorithm, CatBoost is well-suited to machine learning tasks involving categorical, heterogeneous data. Recent work across multiple disciplines illustrates CatBoost’s effectiveness and shortcomings in classification and regression tasks. Another important issue we expose in literature on CatBoost is its sensitivity to hyper-parameters and the importance of hyper-parameter tuning. One contribution we make is to take an interdisciplinary approach to cover studies related to CatBoost in a single work. This provides researchers an in-depth understanding to help clarify proper application of CatBoost in solving problems. To the best of our knowledge, this is the first survey that studies all works related to CatBoost in a single publication.
This survey investigates current techniques for representing qualitative data for use as input to neural networks. Techniques for using qualitative data in neural networks are well known. However, ...researchers continue to discover new variations or entirely new methods for working with categorical data in neural networks. Our primary contribution is to cover these representation techniques in a single work. Practitioners working with big data often have a need to encode categorical values in their datasets in order to leverage machine learning algorithms. Moreover, the size of data sets we consider as big data may cause one to reject some encoding techniques as impractical, due to their running time complexity. Neural networks take vectors of real numbers as inputs. One must use a technique to map qualitative values to numerical values before using them as input to a neural network. These techniques are known as embeddings, encodings, representations, or distributed representations. Another contribution this work makes is to provide references for the source code of various techniques, where we are able to verify the authenticity of the source code. We cover recent research in several domains where researchers use categorical data in neural networks. Some of these domains are natural language processing, fraud detection, and clinical document automation. This study provides a starting point for research in determining which techniques for preparing qualitative data for use with neural networks are best. It is our intention that the reader should use these implementations as a starting point to design experiments to evaluate various techniques for working with qualitative data in neural networks. The third contribution we make in this work is a new perspective on techniques for using categorical data in neural networks. We organize techniques for using categorical data in neural networks into three categories. We find three distinct patterns in techniques that identify a technique as determined, algorithmic, or automated. The fourth contribution we make is to identify several opportunities for future research. The form of the data that one uses as an input to a neural network is crucial for using neural networks effectively. This work is a tool for researchers to find the most effective technique for working with categorical data in neural networks, in big data settings. To the best of our knowledge this is the first in-depth look at techniques for working with categorical data in neural networks.
A full understanding of NO metabolism and signalling requires the consideration of threshold levels, compartmentalization, and how the redox state of cells influences redox couples.
Abstract
Nitric ...oxide (NO) and other reactive nitrogen species (RNS) are immensely important signalling molecules in plants, being involved in a range of physiological responses. However, the exact way in which NO fits into signal transduction pathways is not always easy to understand. Here, some of the issues that should be considered are discussed. This includes how NO may interact directly with other reactive signals, such as reactive oxygen and sulfur species, how NO metabolism is almost certainly compartmentalized, that threshold levels of RNS may need to be reached to have effects, and how the intracellular redox environment may impact on NO signalling. Until better tools are available to understand how NO is generated in cells, where it accumulates, and to what levels it reaches, it will be hard to get a full understanding of NO signalling. The interaction of RNS metabolism with the intracellular redox environment needs further investigation. A changing redox poise will impact on whether RNS species can thrive in or around cells. Such mechanisms will determine whether specific RNS can indeed control the responses needed by a cell.
Signaling through the Primary Cilium Wheway, Gabrielle; Nazlamova, Liliya; Hancock, John T
Frontiers in cell and developmental biology,
02/2018, Letnik:
6
Journal Article
Recenzirano
Odprti dostop
The presence of single, non-motile "primary" cilia on the surface of epithelial cells has been well described since the 1960s. However, for decades these organelles were believed to be vestigial, ...with no remaining function, having lost their motility. It wasn't until 2003, with the discovery that proteins responsible for transport along the primary cilium are essential for hedgehog signaling in mice, that the fundamental importance of primary cilia in signal transduction was realized. Little more than a decade later, it is now clear that the vast majority of signaling pathways in vertebrates function through the primary cilium. This has led to the adoption of the term "the cells's antenna" as a description for the primary cilium. Primary cilia are particularly important during development, playing fundamental roles in embryonic patterning and organogenesis, with a suite of inherited developmental disorders known as the "ciliopathies" resulting from mutations in genes encoding cilia proteins. This review summarizes our current understanding of the role of these fascinating organelles in a wide range of signaling pathways.
Signaling in cells involving reactive compounds is well established. Reactive oxygen species (ROS) and nitric oxide (NO) are known to be extremely influential in the control of a range of ...physiological responses in many organisms, from animals to plants. Often, their generation is triggered in reaction to stress, and it is common for ROS and NO metabolism to interact to give a coordinated response. Recently, hydrogen sulfide (H2S) has also been found to be an important signaling molecule, being shown to be involved in vascular tone in animals. Of relevance to respiration, in plants, H2S has been shown to affect stomatal apertures and the transpiration stream, while, in animals, H2S has been shown to be a source of electrons for ATP synthesis in mitochondria. However, in signaling, H2S does not work in isolation, and it is likely that it will interact with both ROS and NO. This may occur at a variety of levels, from influencing the generation of such molecules, interacting directly, or competing for control of downstream signaling events. A full understanding of the impact of this toxic molecule in the control of cells requires all these factors to be taken into account.
Biofilms are multicellular communities of bacteria that can adhere to virtually any surface. Bacterial biofilms are clinically relevant, as they are responsible for up to two-thirds of hospital ...acquired infections and contribute to chronic infections. Troublingly, the bacteria within a biofilm are adaptively resistant to antibiotic treatment and it can take up to 1000 times more antibiotic to kill cells within a biofilm when compared to planktonic bacterial cells. Identifying and optimizing compounds that specifically target bacteria growing in biofilms is required to address this growing concern and the reported antibiofilm activity of natural and synthetic host defence peptides has garnered significant interest. However, a standardized assay to assess the activity of antibiofilm agents has not been established. In the present work, we describe two simple assays that can assess the inhibitory and eradication capacities of peptides towards biofilms that are formed by both Gram-positive and negative bacteria. These assays are suitable for high-throughput workflows in 96-well microplates and they use crystal violet staining to quantify adhered biofilm biomass as well as tetrazolium chloride dye to evaluate the metabolic activity of the biofilms. The effect of media composition on the readouts of these biofilm detection methods was assessed against two strains of
(PAO1 and PA14), as well as a methicillin resistant strain of
Our results demonstrate that media composition dramatically alters the staining patterns that were obtained with these dye-based methods, highlighting the importance of establishing appropriate biofilm growth conditions for each bacterial species to be evaluated. Confocal microscopy imaging of
biofilms grown in flow cells revealed that this is likely due to altered biofilm architecture under specific growth conditions. The antibiofilm activity of several antibiotics and synthetic peptides were then evaluated under both inhibition and eradication conditions to illustrate the type of data that can be obtained using this experimental setup.
Future climate change will present many plants with environmental challenges, including extreme temperatures and drought. Hydrogen sulfide (H2S) has emerged as an important signal transmitting ...molecule in plants, especially important in many stress responses and it is known to regulate numerous physiological and developmental processes. Being recently suggested as a signaling molecule, research exploring the regulatory functions is continuously progressing regarding the role of H2S in plant science, agriculture and horticulture. Biosynthesis of H2S occurs in different cellular compartments from where it can freely translocate via membranes to where needed or be excluded where not required. H2S interacts with related signaling molecules which together mediate stress tolerance against a plethora of harsh conditions. The H2S induced tolerance against stresses occurs via regulation of antioxidants activities, endogenous levels of GSH, osmoregulator accumulation, cell signaling proteins, and stress-related gene expression. Overall this efficiently eliminates excessive reactive oxygen species (ROS) and maintains the intracellular redox balance. The current review summarizes the recent progress on H2S or H2S donor-mediated abiotic stress tolerance with special reference to climate change and horticulture crops, pre- and post-harvest. Elucidating the role of H2S in cell signaling pathways may open new horizons towards understanding how exogenous treatments with H2S in horticulture plants may aid in the tolerance to stress, especially as environmental conditions change, and can secure better crop yields and avoid post-harvest losses.
•Hydrogen sulfide (H2S) is an endogenous molecule having vital roles in cell signaling pathways.•Climate change may cause many environmental stresses, including drought, temperature, heavy metals and salt stress, whilst H2S may mediate responses.•H2S regulates enzyme activities and gene expressions for the alteration in the cellular activities.•In horticulture, H2S also mitigates oxidative stress during post-harvest.•H2S is mooted as a focus for future agricultural treatments for better food security, especially during future climate changes.
Nitric oxide (NO) and other reactive nitrogen species (RNS) are key signalling molecules in plants, but they do not work in isolation. NO is produced in cells, often increased in response to stress ...conditions, but many other reactive compounds used in signalling are generated and accumulate spatially and temporally together. This includes the reactive oxygen species (ROS), such as hydrogen peroxide (H2O2), and hydrogen sulfide (H2S). Here, the interactions with such other reactive molecules is briefly reviewed. Furthermore, along with ROS and H2S, NO will potentially contribute to the overall intracellular redox of the cell. However, RNS will exist in redox couples and therefore the influence of the cellular redox on such couples will be explored. In discussions of the aberrations in intracellular redox it is usually oxidation, so-called oxidative stress, which is discussed. Here, we consider the notion of reductive stress and how this may influence the signalling which may be mediated by NO. By getting a more holistic view of NO biology, the influence on cell activity of NO and other RNS can be more fully understood, and may lead to the elucidation of methods for NO-based manipulation of plant physiology, leading to better stress responses and improved crops in the future.
Regulating the regulator Gupta, Kapuganti Jagadis; Kolbert, Zsuzsanna; Durner, Jorg ...
The New phytologist,
September 2020, Letnik:
227, Številka:
5
Journal Article
Recenzirano
Odprti dostop
Nitric oxide (NO) is perfectly suited for the role of a redox signalling molecule. Akey route for NO bioactivity occurs via protein S-nitrosation, and involves the addition of a NO moiety to a ...protein cysteine (Cys) thiol (–SH) to form an S-nitrosothiol (SNO). This process is thought to underpin a myriad of cellular processes in plants that are linked to development, environmental responses and immune function. Here we collate emerging evidence showing that NO bioactivity regulates a growing number of diverse post-translational modifications including SUMOylation, phosphorylation, persulfidation and acetylation. We provide examples of how NO orchestrates these processes to mediate plant adaptation to a variety of cellular cues.
During the early periods of evolution, as well as in niche environments today, organisms have had to learn to tolerate the presence of many reactive compounds, such as reactive oxygen species, nitric ...oxide, and hydrogen sulfide. It is now known that such compounds are instrumental in the signaling processes in plant cells. There are enzymes which can make them, while downstream of their signaling pathways are coming to light. These include the production of cGMP, the activation of MAP kinases and transcription factors, and the modification of thiol groups on many proteins. However, organisms have also had to tolerate other reactive compounds such as ammonia, methane, and hydrogen gas, and these too are being found to have profound effects on signaling in cells. Before a holistic view of how such signaling works, the full effects and interactions of all such reactive compounds needs to be embraced. A full understanding will be beneficial to both agriculture and future therapeutic strategies.
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