Pondicherry University

The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fields, we are lacking a clear commonly agreed definition of the term "microbiome." Moreover, a consensus on best practices in microbiome research is missing. Recently, a panel of international experts discussed the current gaps in the frame of the European-funded MicrobiomeSupport project. The meeting brought together about 40 leaders from diverse microbiome areas, while more than a hundred experts from all over the world took part in an online survey accompanying the workshop. This article excerpts the outcomes of the workshop and the corresponding online survey embedded in a short historical introduction and future outlook. We propose a definition of microbiome based on the compact, clear, and comprehensive description of the term provided by Whipps et al. in 1988, amended with a set of novel recommendations considering the latest technological developments and research findings. We clearly separate the terms microbiome and microbiota and provide a comprehensive discussion considering the composition of microbiota, the heterogeneity and dynamics of microbiomes in time and space, the stability and resilience of microbial networks, the definition of core microbiomes, and functionally relevant keystone species as well as co-evolutionary principles of microbe-host and inter-species interactions within the microbiome. These broad definitions together with the suggested unifying concepts will help to improve standardization of microbiome studies in the future, and could be the starting point for an integrated assessment of data resulting in a more rapid transfer of knowledge from basic science into practice. Furthermore, microbiome standards are important for solving new challenges associated with anthropogenic-driven changes in the field of planetary health, for which the understanding of microbiomes might play a key role. Video Abstract.

Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.

The majority of experiments in plant biology use plants grown in some kind of container or pot. We conducted a meta-analysis on 65 studies that analysed the effect of pot size on growth and underlying variables. On average, a doubling of the pot size increased biomass production by 43%. Further analysis of pot size effects on the underlying components of growth suggests that reduced growth in smaller pots is caused mainly by a reduction in photosynthesis per unit leaf area, rather than by changes in leaf morphology or biomass allocation. The appropriate pot size will logically depend on the size of the plants growing in them. Based on various lines of evidence we suggest that an appropriate pot size is one in which the plant biomass does not exceed 1gL-1. In current research practice ~65% of the experiments exceed that threshold. We suggest that researchers need to carefully consider the pot size in their experiments, as small pots may change experimental results and defy the purpose of the experiment.

Intrinsically conducting polymers (ICP) and conductive fillers incorporated conductive polymer-based composites (CPC) greatly facilitate the research in electromagnetic interference (EMI) shielding because they not only provide excellent EMI shielding but also have advantages of electromagnetic wave absorption rather than reflection. In this review, the latest developments in ICP and CPC based EMI shielding materials are highlighted. In particular, existing methods for adjusting the morphological structure, electric and magnetic properties of EMI shielding materials are discussed along with the future opportunities and challenges in developing ICP and CPC for EMI shielding applications.

Abstract Systematic assessments of species extinction risk at regular intervals are necessary for informing conservation action 1,2 . Ongoing developments in taxonomy, threatening processes and research further underscore the need for reassessment 3,4 . Here we report the findings of the second Global Amphibian Assessment, evaluating 8,011 species for the International Union for Conservation of Nature Red List of Threatened Species. We find that amphibians are the most threatened vertebrate class (40.7% of species are globally threatened). The updated Red List Index shows that the status of amphibians is deteriorating globally, particularly for salamanders and in the Neotropics. Disease and habitat loss drove 91% of status deteriorations between 1980 and 2004. Ongoing and projected climate change effects are now of increasing concern, driving 39% of status deteriorations since 2004, followed by habitat loss (37%). Although signs of species recoveries incentivize immediate conservation action, scaled-up investment is urgently needed to reverse the current trends.

Clean, renewable, and sustainable energy is required daily to improve social, economic, and environmental health, leading to economic development and productivity. The aim of the work has deliberated on the reoccurrence of renewable energies to assist in the mitigation of climate change and environmental health excellently. This work aims to determine whether renewable energy sources are viable and study how a shift from fossil fuel-based energy sources to renewable energy sources would assist in reducing climate change and its impact. State of the art in biofuels and energy generation from lignocellulosic biomasses has shown that applying advanced technologies such as biorefinery and bioreactors to the chemical transformation process is a sustained strategy. To optimally exploit biorefineries' potential, government policies must favour technological innovations in universities and in an industry that can help produce high-value fuels and products from various biomasses. This work deliberated to light the prospects allied with renewable energy sources; energy security, access to energy, social and economic progress, and climate change mitigation to reduce ecological and health impacts.

Rapid advances in DNA synthesis techniques have made it possible to engineer viruses, biochemical pathways and assemble bacterial genomes. Here, we report the synthesis of a functional 272,871-base pair designer eukaryotic chromosome, synIII, which is based on the 316,617-base pair native Saccharomyces cerevisiae chromosome III. Changes to synIII include TAG/TAA stop-codon replacements, deletion of subtelomeric regions, introns, transfer RNAs, transposons, and silent mating loci as well as insertion of loxPsym sites to enable genome scrambling. SynIII is functional in S. cerevisiae. Scrambling of the chromosome in a heterozygous diploid reveals a large increase in a-mater derivatives resulting from loss of the MATα allele on synIII. The complete design and synthesis of synIII establishes S. cerevisiae as the basis for designer eukaryotic genome biology.

The high species richness of tropical forests has long been recognized, yet there remains substantial uncertainty regarding the actual number of tropical tree species. Using a pantropical tree inventory database from closed canopy forests, consisting of 657,630 trees belonging to 11,371 species, we use a fitted value of Fisher's alpha and an approximate pantropical stem total to estimate the minimum number of tropical forest tree species to fall between ∼ 40,000 and ∼ 53,000, i.e., at the high end of previous estimates. Contrary to common assumption, the Indo-Pacific region was found to be as species-rich as the Neotropics, with both regions having a minimum of ∼ 19,000-25,000 tree species. Continental Africa is relatively depauperate with a minimum of ∼ 4,500-6,000 tree species. Very few species are shared among the African, American, and the Indo-Pacific regions. We provide a methodological framework for estimating species richness in trees that may help refine species richness estimates of tree-dependent taxa.

One of the most versatile and remunerative techniques for handling biodegradable solid wastes is composting. A large variety of such wastes of plant, animal, and synthetic origins can be gainfully composted, at scales varying from a household bin to a large industry. Compost also has an inexhaustible market as a soil conditioner and fertilizer. Apart from being a source of nitrogen, phosphorus, potassium, and other nutrients for plants, compost is also believed to suppress soil-borne diseases in plants. These virtues make composting an ideal option for processing the enormous quantities of biodegradable solid wastes that are generated in the world. In this article, a review of the state of the art of compost science is presented, encompassing the history, the mechanism, the production, the characteristics, and the effects of composting. It is hoped that this effort would stimulate further interest in composting and in the appreciation of its benefits.

Vermicomposting is a non-thermophilic, boioxidative process that involves earthworms and associated microbes. This biological organic waste decomposition process yields the biofertilizer namely the vermicompost. Vermicompost is a finely divided, peat like material with high porosity, good aeration, drainage, water holding capacity, microbial activity, excellent nutrient status and buffering capacity thereby resulting the required physiochemical characters congenial for soil fertility and plant growth. Vermicompost enhances soil biodiversity by promoting the beneficial microbes which inturn enhances plant growth directly by production of plant growth-regulating hormones and enzymes and indirectly by controlling plant pathogens, nematodes and other pests, thereby enhancing plant health and minimizing the yield loss. Due to its innate biological, biochemical and physiochemical properties, vermicompost may be used to promote sustainable agriculture and also for the safe management of agricultural, industrial, domestic and hospital wastes which may otherwise pose serious threat to life and environment.

The updated concepts on the nature of π–π interactions and their use in various fields ranging from crystal engineering to materials science to biochemistry are discussed. This is the opening paper for the Crystal Growth & Design virtual special issue on “π···π Stacking in Crystal Engineering: Fundamentals and Applications”.

3.1.2MAP estimation 3.1.3The Gaussian case with linear sensors 3.1.4Maximum likelihood estimation 3.1.5Unbiased linear MMSE estimation 3.2 Performance of estimators 3.2.1 Bias and covariance 3.2.2The error covariance of the unbiased linear MMSE estimator 3.3 Data fitting 3.3.1 Least squares fitting 3.3.2Fitting using a robust error norm 3.3.3Regression 3.4 Overview of the family of estimators 3.5 Selected bibliography 3.6 Exercises 4 State Estimation 4.1 A general framework for online estimation 4.1.1Models 4.1.2Optimal online estimation 4.2 Continuous state variables 4.2.1 Optimal online estimation in linear-Gaussian systems 4.2.2Suboptimal solutions for nonlinear systems 4.2.3Other filters for nonlinear systems 4.3 Discrete state variables 4.3.1 Hidden Markov models 4.3.2Online state estimation 4.3.3Offline state estimation 4.4 Mixed states and the particle filter 4.4.1 Importance sampling 4.4.2Resampling by selection 4.4.3The condensation algorithm 4.5 Selected bibliography 4.6 Exercises 5 Supervised Learning 5.1 Training sets 5.2 Parametric learning 5.2.1 Gaussian distribution, mean unknown vi CONTENTS 5.2.2 Gaussian distribution, covariance matrix unknown 5.2.3 Gaussian distribution, mean and covariance matrix both unknown 5.2.4 Estimation of the prior probabilities 5.2.5 Binary measurements 5.3 Nonparametric learning 5.3.1 Parzen estimation and histogramming 5.3.2Nearest neighbour classification 5.3.3Linear discriminant functions 5.3.4The support vector classifier 5.3.5The feed-forward neural network 5.4 Empirical evaluation 5.5 References 5.6 Exercises 6 Feature Extraction and Selection 6.1 Criteria for selection and extraction 6.1.1Inter/intra class distance 6.1.2Chernoff-Bhattacharyya distance 6.1.3Other criteria 6.2 Feature selection 6.2.1 Branch-and-bound 6.2.2 Suboptimal search 6.2.3 Implementation issues 6.3 Linear feature extraction 6.3.1 Feature extraction based on the Bhattacharyya distance with Gaussian distributions 6.3.2Feature extraction based on inter/intra class distance 6.4 References viii CONTENTS 9.1.3Feature extraction 9.1.4Feature selection 9.1.5Complex classifiers 9.1.6Conclusions 9.2 Time-of-flight estimation of an acoustic tone burst 9.2.1 Models of the observed waveform 9.2.2 Heuristic methods for determining the ToF 9.2.3 Curve fitting 9.2.4 Matched filtering 9.2.5 ML estimation using covariance models for the reflections 9.2.6 Optimization and evaluation 9.3 Online level estimation in an hydraulic system 9.3.1 Linearized Kalman filtering 9.3.2Extended Kalman filtering 9.3.3Particle filtering 9.3.4Discussion 9.4 References CONTENTS ix C.1.2Poisson distribution C.1.3Binomial distribution C.1.4Normal distribution C.1.5The Chi-square distribution C.2 Bivariate random variables C.3 Random vectors C.3.1 Linear operations on Gaussian random vectors C.3.2 Decorrelation C.4 Reference Appendix D Discrete-time Dynamic Systems D.1 Discrete-time dynamic systems D.2 Linear systems D.3 Linear time invariant systems D.3.1 Diagonalization of a system D.3.2 Stability D.4 References Appendix E Introduction to PRTools E.1 Motivation E.2 Essential concepts in PRTools E.3 Implementation E.4 Some details E.4

Abstract Forests are a substantial terrestrial carbon sink, but anthropogenic changes in land use and climate have considerably reduced the scale of this system 1 . Remote-sensing estimates to quantify carbon losses from global forests 2–5 are characterized by considerable uncertainty and we lack a comprehensive ground-sourced evaluation to benchmark these estimates. Here we combine several ground-sourced 6 and satellite-derived approaches 2,7,8 to evaluate the scale of the global forest carbon potential outside agricultural and urban lands. Despite regional variation, the predictions demonstrated remarkable consistency at a global scale, with only a 12% difference between the ground-sourced and satellite-derived estimates. At present, global forest carbon storage is markedly under the natural potential, with a total deficit of 226 Gt (model range = 151–363 Gt) in areas with low human footprint. Most (61%, 139 Gt C) of this potential is in areas with existing forests, in which ecosystem protection can allow forests to recover to maturity. The remaining 39% (87 Gt C) of potential lies in regions in which forests have been removed or fragmented. Although forests cannot be a substitute for emissions reductions, our results support the idea 2,3,9 that the conservation, restoration and sustainable management of diverse forests offer valuable contributions to meeting global climate and biodiversity targets.

We introduce a mechanism for generating higher-order rogue waves (HRWs) of the nonlinear Schrödinger (NLS) equation: the progressive fusion and fission of n degenerate breathers associated with a critical eigenvalue λ(0) creates an order-n HRW. By adjusting the relative phase of the breathers in the interacting area, it is possible to obtain different types of HRWs. The value λ(0) is a zero point of an eigenfunction of the Lax pair of the NLS equation and it corresponds to the limit of the period of the breather tending to infinity. By employing this mechanism we prove two conjectures regarding the total number of peaks, as well as a decomposition rule in the circular pattern of an order-n HRW.

Economic load dispatch (ELD) and economic emission dispatch (EED) have been applied to obtain optimal fuel cost and optimal emission of generating units, respectively. Combined economic emission dispatch (CEED) problem is obtained by considering both the economy and emission objectives. This biobjective CEED problem is converted into a single objective function using a price penalty factor approach. A novel modified price penalty factor is proposed to solve the CEED problem. In this paper, evolutionary computation (EC) methods such as genetic algorithm (GA), micro GA (MGA), and evolutionary programming (EP) are applied to obtain ELD solutions for three-, six-, and 13-unit systems. Investigations showed that EP was better among EC methods in solving the ELD problem. EP-based CEED problem has been tested on IEEE 14-, 30-, and 118-bus systems with and without line flow constraints. A nonlinear scaling factor is also included in EP algorithm to improve the convergence performance for the 13 units and IEEE test systems. The solutions obtained are quite encouraging and useful in the economic emission environment.

Nickel selenide (NiSe) nanoparticles uniformly supported on graphene nanosheets (G) to form NiSe-G nanohybrids were prepared by an in situ hydrothermal process. The uniform distribution of NiSe on graphene bestowed the NiSe-G nanohybrid with faster charge transport and diffusion along with abundant accessible electrochemical active sites. The synergistic effect between NiSe nanoparticles and graphene nanosheets for supercapacitor applications was systematically investigated for the first time. The freestanding NiSe-G nanohybrid electrode exhibited better electrochemical performance with a high specific capacitance of 1280 F g-1 at a current density of 1 A g-1 and a capacitance retention of 98% after 2500 cycles relative to that of NiSe nanoparticles. Furthermore, an asymmetric supercapacitor device assembled using the NiSe-G nanohybrid as the positive electrode, activated carbon as the negative electrode and an electrospun PVdF membrane containing 6 M KOH as both the separator and the electrolyte delivered a high energy density of 50.1 W h kg-1 and a power density of 816 W kg-1 at an extended operating voltage of 1.6 V. Thus, the NiSe-G nanohybrid can be used as a potential electrode material for high-performance supercapacitors.

was found to be rich with various secondary metabolites including phenolics (59.18 ± 2.91 mg gallic acid equivalents/g), flavonoids (38.50 ± 2.84 mg catechin equivalents/g), and tannins (44.28 ± 3.09 mg tannic acid equivalents/g) and determined that highly appropriate for the biosynthesis of nanoparticles. The facile phytofabrication of PF-SeNPs was confirmed by UV-visible and FTIR spectroscopic analysis. The XRD pattern and Raman spectroscopy showed that synthesized PF-SeNPs were amorphous in nature. The Zeta potential analysis confirmed that PF-SeNPs were negatively charged (-24.4 mV). The DLS analysis revealed that PF-SeNPs were in nano size and less aggregated with poly-dispersity index of less than 0.2. The SEM images depicted that PF-SeNPs were spherical in shape. The EDX analysis revealed that PF-SeNPs were constituted with Se (61.60%), C (29.96%), and O (4.41%). The HR-TEM analysis determined that PF-SeNPs were in nano size with an average diameter of 15-40 nm. The PF-SeNPs have offered fascinating bio-potential applications, such as antioxidant, antimicrobial and biocompatibility. They have also exhibited dose-dependent free radical scavenging activity, and EC50 was determined as 15.67 ± 1.41 and 18.84 ± 1.02 μg/mL for DPPH and ABTS assays, respectively. The PF-SeNPs has also shown the wide range of antimicrobial activity on foodborne pathogens, and it was found to be highly efficient on fungi followed by Gram-positive and Gram-negative bacteria. The biocompatibility of PF-SeNPs was assessed in N2a cells with much higher IC50 value (dose required to inhibit 50% of cell viability) compared to sodium selenite. Also, mitochondrial membrane potential (MMP) and caspase-3 were much less altered on treatment of PF-SeNPs related to sodium selenite. The cytotoxic studies clearly determined that PF-SeNPs was much less toxic and safer related to sodium selenite. Thus, PF-SeNPs could find suitable application as antioxidant and antimicrobial agent in food, biomedical, and pharmaceutical industry.

In this paper, we have conducted a literature review on the recent developments and publications involving the vehicle routing problem and its variants, namely vehicle routing problem with time windows (VRPTW) and the capacitated vehicle routing problem (CVRP) and also their variants. The VRP is classified as an NP-hard problem. Hence, the use of exact optimization methods may be difficult to solve these problems in acceptable CPU times, when the problem involves real-world data sets that are very large. The vehicle routing problem comes under combinatorial problem. Hence, to get solutions in determining routes which are realistic and very close to the optimal solution, we use heuristics and meta-heuristics. In this paper we discuss the various exact methods and the heuristics and meta-heuristics used to solve the VRP and its variants.

Metal-organic frameworks (MOFs) that are the wonder material of the 21st century consist of metal ions/clusters coordinated to organic ligands to form one- or more-dimensional porous structures with unprecedented chemical and structural tunability, exceptional thermal stability, ultrahigh porosity, and a large surface area, making them an ideal candidate for numerous potential applications. In this work, the recent progress in the design and synthetic approaches of MOFs and explore their potential applications in the fields of gas storage and separation, catalysis, magnetism, drug delivery, chemical/biosensing, supercapacitors, rechargeable batteries and self-powered wearable sensors based on piezoelectric and triboelectric nanogenerators are summarized. Lastly, this work identifies present challenges and outlines future opportunities in this field, which can provide valuable references.

Biofilm formation is a major concern in various sectors and cause severe problems to public health, medicine, and industry. Bacterial biofilm formation is a major persistent threat, as it increases morbidity and mortality, thereby imposing heavy economic pressure on the healthcare sector. Bacterial biofilms also strengthen biofouling, affecting shipping functions, and the offshore industries in their natural environment. Besides, they accomplish harsh roles in the corrosion of pipelines in industries. At biofilm state, bacterial pathogens are significantly resistant to external attack like antibiotics, chemicals, disinfectants, etc. Within a cell, they are insensitive to drugs and host immune responses. The development of intact biofilms is very critical for the spreading and persistence of bacterial infections in the host. Further, bacteria form biofilms on every probable substratum, and their infections have been found in plants, livestock, and humans. The advent of novel strategies for treating and preventing biofilm formation has gained a great deal of attention. To prevent the development of resistant mutants, a feasible technique that may target adhesive properties without affecting the bacterial vitality is needed. This stimulated research is a rapidly growing field for applicable control measures to prevent biofilm formation. Therefore, this review discusses the current understanding of antibiotic resistance mechanisms in bacterial biofilm and intensely emphasized the novel therapeutic strategies for combating biofilm mediated infections. The forthcoming experimental studies will focus on these recent therapeutic strategies that may lead to the development of effective biofilm inhibitors than conventional treatments.