Applications of Machine Learning in Chemical and Biological Oceanography.

Machine learning (ML) refers to computer algorithms that predict a meaningful output or categorize complex systems based on a large amount of data. ML is applied in various areas including natural science, engineering, space exploration, and even gaming development. This review focuses on the use of machine learning in the field of chemical and biological oceanography. In the prediction of global fixed nitrogen levels, partial carbon dioxide pressure, and other chemical properties, the application of ML is a promising tool. Machine learning is also utilized in the field of biological oceanography to detect planktonic forms from various images (i.e., microscopy, FlowCAM, and video recorders), spectrometers, and other signal processing techniques. Moreover, ML successfully classified the mammals using their acoustics, detecting endangered mammalian and fish species in a specific environment. Most importantly, using environmental data, the ML proved to be an effective method for predicting hypoxic conditions and harmful algal bloom events, an essential measurement in terms of environmental monitoring. Furthermore, machine learning was used to construct a number of databases for various species that will be useful to other researchers, and the creation of new algorithms will help the marine research community better comprehend the chemistry and biology of the ocean.

Meta-analysis cum machine learning approaches address the structure and biogeochemical potential of marine copepod associated bacteriobiomes.

Copepods are the dominant members of the zooplankton community and the most abundant form of life. It is imperative to obtain insights into the copepod-associated bacteriobiomes (CAB) in order to identify specific bacterial taxa associated within a copepod, and to understand how they vary between different copepods. Analysing the potential genes within the CAB may reveal their intrinsic role in biogeochemical cycles. For this, machine-learning models and PICRUSt2 analysis were deployed to analyse 16S rDNA gene sequences (approximately 16 million reads) of CAB belonging to five different copepod genera viz., Acartia spp., Calanus spp., Centropages sp., Pleuromamma spp., and Temora spp.. Overall, we predict 50 sub-OTUs (s-OTUs) (gradient boosting classifiers) to be important in five copepod genera. Among these, 15 s-OTUs were predicted to be important in Calanus spp. and 20 s-OTUs as important in Pleuromamma spp.. Four bacterial s-OTUs Acinetobacter johnsonii, Phaeobacter, Vibrio shilonii and Piscirickettsiaceae were identified as important s-OTUs in Calanus spp., and the s-OTUs Marinobacter, Alteromonas, Desulfovibrio, Limnobacter, Sphingomonas, Methyloversatilis, Enhydrobacter and Coriobacteriaceae were predicted as important s-OTUs in Pleuromamma spp., for the first time. Our meta-analysis revealed that the CAB of Pleuromamma spp. had a high proportion of potential genes responsible for methanogenesis and nitrogen fixation, whereas the CAB of Temora spp. had a high proportion of potential genes involved in assimilatory sulphate reduction, and cyanocobalamin synthesis. The CAB of Pleuromamma spp. and Temora spp. have potential genes accountable for iron transport.

In Silico Study on Tumor-Size-Dependent Thermal Profiles inside an Anthropomorphic Female Breast Phantom Subjected to Multi-Dipole Antenna Array.

Electromagnetic hyperthermia as a potent adjuvant for conventional cancer therapies can be considered valuable in modern oncology, as its task is to thermally destroy cancer cells exposed to high-frequency electromagnetic fields. Hyperthermia treatment planning based on computer in silico simulations has the potential to improve the localized heating of breast tissues through the use of the phased-array dipole applicators. Herein, we intended to improve our understanding of temperature estimation in an anatomically accurate female breast phantom embedded with a tumor, particularly when it is exposed to an eight-element dipole antenna matrix surrounding the breast tissues. The Maxwell equations coupled with the modified Pennes' bioheat equation was solved in the modelled breast tissues using the finite-difference time-domain (FDTD) engine. The microwave (MW) applicators around the object were modelled with shortened half-wavelength dipole antennas operating at the same 1 GHz frequency, but with different input power and phases for the dipole sources. The total input power of an eight-dipole antenna matrix was set at 8 W so that the temperature in the breast tumor did not exceed 42 °C. Finding the optimal setting for each dipole antenna from the matrix was our primary objective. Such a procedure should form the basis of any successful hyperthermia treatment planning. We applied the algorithm of multi for multi-objective optimization for the power and phases for the dipole sources in terms of maximizing the specific absorption rate (SAR) parameter inside the breast tumor while minimizing this parameter in the healthy tissues. Electro-thermal simulations were performed for tumors of different radii to confirm the reliable operation of the given optimization procedure. In the next step, thermal profiles for tumors of various sizes were calculated for the optimal parameters of dipole sources. The computed results showed that larger tumors heated better than smaller tumors; however, the procedure worked well regardless of the tumor size. This verifies the effectiveness of the applied optimization method, regardless of the various stages of breast tumor development.

Bioconversion of chitin and concomitant production of chitinase and N-acetylglucosamine by novel Achromobacter xylosoxidans isolated from shrimp waste disposal area.

Marine pollution is a significant issue in recent decades, with the increase in industries and their waste harming the environment and ecosystems. Notably, the rise in shellfish industries contributes to tons of shellfish waste composed of up to 58% chitin. Chitin, the second most ample polymer next to cellulose, is insoluble and resistant to degradation. It requires chemical-based treatment or enzymatic hydrolysis to cleave the chitin polymers. The chemical-based treatment can lead to environmental pollution, so to solve this problem, enzymatic hydrolysis is the best option. Moreover, the resulting biopolymer by-products can be used to boost the fish immune system and also as drug delivery agents. Many marine microbial strains have chitinase producing ability. Nevertheless, we still lack an economical and highly stable chitinase enzyme for use in the industrial sector. So we isolate a novel marine bacterial strain Achromobacter xylosoxidans from the shrimp waste disposal site using chitin minimal medium. Placket-Burman and central composite design statistical models for culture condition optimisation predicted a 464.2 U/ml of chitinase production. The culture conditions were optimised for maximum chitinase production recording up to 467 U/ml. This chitinase from the A. xylosoxidans was 100% active at an optimum temperature of 45 °C (withstand up to 55 °C) and pH 8 with 80% stability. The HPLC analysis of chitinase degraded shellfish waste reveals a major amino acid profile composition-arginine, lysine, aspartic acid, alanine, threonine and low levels of isoleucine and methionine. These chitinase degraded products and by-products can be used as supplements in the aquaculture industry.

Metagenomic 16S rDNA amplicon data of microbial diversity and its predicted metabolic functions in the Southern Ocean (Antarctic).

Antarctica holds about 70% of all the freshwater on the planet in the form of ice. The seawater, it chills, affect the currents and temperature everywhere. Global warming risks the melting of the icecaps as it has already increased the ocean temperature by 1 °C to the West Antarctic peninsula since 1955. A better understanding of the microbial community in this extreme environment of utmost importance is of interest to the scientific community. Herein, we document our metagenomics analysis of the microbial diversity and abundance in the Southern Ocean [Lat 55″ 33' 396 S; Lon 55″ 31' 448 E] using Next Generation Sequencing (NGS), QIIME 1.9.1, Silvangs and a naïve Bayesian classifier. Such metagenomics data hold the potential to aid predictive analysis, which is critical to our understanding of the dynamics of the microbial communities and their role in the Southern Ocean at present and in the future.

Numerical Model for Magnetic Fluid Hyperthermia in a Realistic Breast Phantom: Calorimetric Calibration and Treatment Planning.

This paper aims to apply a proposed, based on calorimetric measurements, a reliable numerical model for magnetic fluid hyperthermia (MFH) treatment planning of breast cancer. Furthermore, we perform a comparative analysis of magnetic nanoparticles (MNPs) and tumour tissue interactions by means of the magnetic-field-dependent Néel and Brownian relaxation times. The analysis was based on an anatomically correct breast model (developed in-house) and a modified linear response theory, which was applied to investigate the heat dissipation from the magnetic nanoparticles dispersed in the breast tumour. The calculations of the single-domain magnetic power losses were conducted for a case where the magnetic field value and the applied frequency were known, but also for the different concentrations of the MNPs in the tumour. Two scenarios were considered: The MNPs mobilised and immobilised in the tumour. In parallel, the eddy currents effect, together with the related temperature distributions, were considered in order to analyse safety issues. By changing the MNP concentration in the tumour, the corresponding temperature distributions were calculated. The eddy current effect, together with the related temperature distribution, were considered in order to analyse safety issues. Varying the MNP concentration in the tumour, the corresponding temperature distribution was calculated. Moreover, the cumulative equivalent minutes at 43   ℃ were analysed. In the anatomically correct breast phantoms, the tissue location can lead to "hot spots" due to the eddy current effect and subsequently to the high gradients of the temperature. That is why the analysis of safety issues related to the overheating side effect should be taken into consideration during the treatment planning of magnetic fluid hyperthermia. The phenomenon of heat dissipation from MNPs is very sophisticated and depends on their concentration, the distribution and the relaxation mechanism in the tumour, together with magnetic field strength and frequency. Furthermore, we inferred that the phenomenon of heat dissipation from MNPs equally depends on MNP-tissue interactions, and it can lead to 30% differences in the power assessment. Nevertheless, the aforementioned factors should be considered in parallel using anatomical, volume-dependent models to enhance the efficiency of in vivo treatment.

Metagenomic data of vertical distribution and abundance of bacterial diversity in the hypersaline sediments of Mad Boon-mangrove ecosystem, Bay of Bengal.

Bacterial diversity studies in hypersaline soil often yield novel organisms and contribute to our understanding of this extreme environment. Soil from Mad Boon is previously uncharacterized, with dense mangrove forest in one side and hypersaline soil in another side of backwater located in Southeast coast of Tamil Nadu, India. We surveyed to characterize the structure and diversity of the bacterial community. Samples were collected in a partially vegetated upland, exposed backwater sedimentation and water-logged location. In this study, we investigate the bacterial community structure using pyrosequence analysis of the V5- V9 gene region. After quality checks a total of 3919, 7298 and 7399 reads were obtained. About 42 phyla were observed, among them Proteobacteria were dominant phylum followed by Acidobacteria, Firmicutes and Chloroflexi. Classes including Deltaproteobacteria and Gammaproteobacteriawere observed. All sequences generated in this study were submitted to NCBI SRA under the accession numbers SRR627695, SRR63011 and SRR631012.

An in vivo coil setup for AC magnetic field-mediated magnetic nanoparticle heating experiments.

In vitro and in vivo evaluation of magnetic nanoparticles in relation to magnetic fluid hyperthermia (MFH) treatment is an on-going quest. This current paper demonstrates the design, fabrication, and evaluation of an in vivo coil setup for real-time, whole body thermal imaging. Numerical calculations estimating the flux densities, and in silico analysis suggest that the proposed in vivo coil setup could be used for real-time thermal imaging during MFH experiments (within the limitations due to issues of penetration depth). Such in silico evaluations provide insights into the design of suitable AMF applicators for AC magnetic field-mediated in vivo MNP heating as demonstrated in this study.

A.Eye Drive: Gaze-based semi-autonomous wheelchair interface.

Existing wheelchair control interfaces, such as sip & puff or screen based gaze-controlled cursors, are challenging for the severely disabled to navigate safely and independently as users continuously need to interact with an interface during navigation. This puts a significant cognitive load on users and prevents them from interacting with the environment in other forms during navigation. We have combined eyetracking/gaze-contingent intention decoding with computer vision context-aware algorithms and autonomous navigation drawn from self-driving vehicles to allow paralysed users to drive by eye, simply by decoding natural gaze about where the user wants to go: A.Eye Drive. Our "Zero UI" driving platform allows users to look and interact visually with at an object or destination of interest in their visual scene, and the wheelchair autonomously takes the user to the intended destination, while continuously updating the computed path for static and dynamic obstacles. This intention decoding technology empowers the end-user by promising more independence through their own agency.

Oscillating Magnet Array-Based Nanomagnetic Gene Transfection: A Valuable Tool for Molecular Neurobiology Studies.

To develop treatments for neurodegenerative disorders, it is critical to understand the biology and function of neurons in both normal and diseased states. Molecular studies of neurons involve the delivery of small biomolecules into cultured neurons via transfection to study genetic variants. However, as cultured primary neurons are sensitive to temperature change, stress, and shifts in pH, these factors make biomolecule delivery difficult, particularly non-viral delivery. Herein we used oscillating nanomagnetic gene transfection to successfully transfect SH-SY5Y cells as well as primary hippocampal and cortical neurons on different days in vitro. This novel technique has been used to effectively deliver genetic material into various cell types, resulting in high transfection efficiency and viability. From these observations and other related studies, we suggest that oscillating nanomagnetic gene transfection is an effective method for gene delivery into hard-to-transfect neuronal cell types.

A Pilot Study Into the Use of FDG-mNP as an Alternative Approach in Neuroblastoma Cell Hyperthermia.

Herein, we present a pilot study concerning the use of fluorodeoxy glucose conjugated magnetite nanoparticles (FDG-mNP) as a potential agent in magnetic nanoparticle mediated neuroblastoma cancer cell hyperthermia. This approach makes use of the 'Warburg effect', utilizing the fact that cancer cells have a higher metabolic rate than normal cells. FDG-mNP were synthesized, then applied to the SH-SY5Y neuroblastoma cancer cell line and exposed to an ac magnetic field. 3D Calorimetry was performed on the FDG-mNP compound. Simulations were performed using SEMCAD X software using Thelonious, (an anatomically correct male child model) in order to understand more about the end requirements with respect to cancer cell destruction. We investigated FDG-mNP mediated neuroblastoma cytotoxicity in conjunction with ac magnetic field exposure. Results are presented for 3D FDG-mNP SAR mnp (10.86 ± 0.99 W/g of particles) using a therapeutic dose of 0.83 mg/ mL. Human model simulations suggest that 43 W/kg SAR Theo would be required to obtain 42 °C within the centre of a liver tumor (Tumor size, bounding box x = 64, y = 61, z = 65 [mm]), and that the temperature distribution is inhomogeneous within the tumor. Our study suggests that this approach could potentially be used to increase the temperature within cells that would result in cancer cell death due to hyperthermia. Further development of this research will also involve using whole tumors removed from living organisms in conjunction with magnetic resonance imaging and positron emission tomography.

A coil system for real-time magnetic fluid hyperthermia microscopy studies.

PURPOSE: We describe the design and application of a new apparatus for applying Radiofrequency (RF) electromagnetic fields to cells in culture on a microscope stage. This new design enables real-time studies of the actuation of magnetic nanoparticles bound to membrane receptors or internalised within cells together with the study of magnetic fluid hyperthermia (MFH)-associated effects. MATERIALS AND METHODS: RF coils were fabricated and electromagnetic simulations were performed along with compatibility evaluations and calorimetric experiments using this apparatus at discreet frequencies between 100 kHz and 1 MHz. Cell killing via MFH was investigated in a neuroblastoma tumour cell line. RESULTS: Simulations and evaluations showed that the field intensity and homogeneity experienced by the cells within the chamber is best with a planar coil configuration. The incubation chamber was suitable for cell culture and the design was compatible with mountings on different makes of microscopes as it mimics a standard 96/24/6 tissue-culture well plate. Successful calorimetric and MFH cytotoxicity proof-of-principle experiments were performed and are presented. CONCLUSIONS: We conclude from these experiments that alternating magnetic field (AMF)-mediated activation and magnetic fluid hyperthermia (MFH) research will benefit from this RF coil that fits inside an incubation chamber, mounted onto a microscope. This new design could be used to assist real-time MFH studies in vitro.

Enhanced nanomagnetic gene transfection of human prenatal cardiac progenitor cells and adult cardiomyocytes.

Magnetic nanoparticle-based gene transfection has been shown to be an effective, non-viral technique for delivery of both plasmid DNA and siRNA into cells in culture. It has several advantages over other non-viral delivery techniques, such as short transfection times and high cell viability. These advantages have been demonstrated in a number of primary cells and cell lines. Here we report that oscillating magnet array-based nanomagnetic transfection significantly improves transfection efficiency in both human prenatal cardiac progenitor cells and adult cardiomyocytes when compared to static magnetofection, cationic lipid reagents and electroporation, while maintaining high cell viability. In addition, transfection of adult cardiomyocytes was improved further by seeding the cells onto Collagen I-coated plates, with transfection efficiencies of up to 49% compared to 24% with lipid reagents and 19% with electroporation. These results demonstrate that oscillating nanomagnetic transfection far outperforms other non-viral transfection techniques in these important cells.