Highly Scalable Algorithms for Robust String Barcoding

String barcoding is a recently introduced technique for genomic-based identification of microorganisms. In this paper we describe the engineering of highly scalable algorithms for robust string barcoding. Our methods enable distinguisher selection based on whole genomic sequences of hundreds of microorganisms of up to bacterial size on a well-equipped workstation, and can be easily parallelized to further extend the applicability range to thousands of bacterial size genomes. Experimental results on both randomly generated and NCBI genomic data show that whole-genome based selection results in a number of distinguishers nearly matching the information theoretic lower bounds for the problem

A Technical Review of Lawn Mower Technology

This paper summarizes and reviews different technological developments for making efficient and cost effective lawn mowers. Such lawn mower may be powered by solar energy, conventional electric and internal combustion engine. For each type of energy source mentioned above, we discuss the mechanisms followed for lawn mower device, the design of the model and results obtained in various literatures. Sometimes two such energy sources may be used in combination, like solar powered robotic lawn mower.Keywords: lawn mower, solar energy, sensor, motor, battery, exhaus

RADON: Repairable Atomic Data Object in Networks

Erasure codes offer an efficient way to decrease storage and communication costs while implementing atomic memory service in asynchronous distributed storage systems. In this paper, we provide erasure-code-based algorithms having the additional ability to perform background repair of crashed nodes. A repair operation of a node in the crashed state is triggered externally, and is carried out by the concerned node via message exchanges with other active nodes in the system. Upon completion of repair, the node re-enters active state, and resumes participation in ongoing and future read, write, and repair operations. To guarantee liveness and atomicity simultaneously, existing works assume either the presence of nodes with stable storage, or presence of nodes that never crash during the execution. We demand neither of these; instead we consider a natural, yet practical network stability condition N1 that only restricts the number of nodes in the crashed/repair state during broadcast of any message. We present an erasure-code based algorithm RADON_{C} that is always live, and guarantees atomicity as long as condition N1 holds. In situations when the number of concurrent writes is limited, RADON_{C} has significantly improved storage and communication cost over a replication-based algorithm RADON_{R}, which also works under N1. We further show how a slightly stronger network stability condition N2 can be used to construct algorithms that never violate atomicity. The guarantee of atomicity comes at the expense of having an additional phase during the read and write operations

Scale interactions near the foothills of Himalayas during CAIPEEX

Scale interactions associated with small scale (<100 km) dynamics might play a crucial role in the distribution of aerosol in the Himalayan foothills region. Turbulence measurements from a horizontal flight path during Cloud Aerosol Interaction and Precipitation Enhancement EXperiment (CAIPEEX) are used to illustrate the scale interactions in the vertically sheared flow below the high-level subtropical westerly jet, which is important in the transport of pollution. Data analysis reveals the three dimensional property of large eddies that scale 10-12 km near the slopes, which could bring pollution from the valley to the Tibetan Plateau through a circulation adhering to the slopes. This circulation has a subsidence region away from the slopes and may also contribute to the buildup of pollution in elevated layers over the Plains. The vertical velocity and temperature spectra from research flight data showed clear indications of (-5/3) slope in the mesoscale range. The isotropic behavior of the velocity spectra was noticed for cloud-free traverses, while this behavior is distorted for cloudy conditions with the enhancement of energy at smaller scales as well as with low frequency gravity wave generation. A high-resolution cloud allowing model simulation over the flight path is used to examine the representation of these dynamical interactions in the numerical model. Based on the analysis of observational data and model inferences, a conceptual understanding of the flow in the region close to the foot hills and its role in the distribution of aerosol and cloud condensation nuclei is presented

Rapid and simple DNA extraction protocol from goat rumen digesta for metagenomic analysis

Abstract: In contrast to the traditional culturing techniques and microscopy that have led to the identification and characterization of only about 15-20 % of the rumen microbes till date, nucleic acid-based molecular approaches are rapid, reproducible, and allow both the qualitative and quantitative assessment of microbial diversity. The aim of this study was to develop a simple, rapid and effective extraction protocol for the recovery of high-molecular-weight and cloneable metagenomic DNA (mDNA) from goat rumen contents. An efficient method was devised to isolate highmolecular-weight mDNA (&gt;23kb) that was pure and cloneable after isolation in a relatively short period (3.5 h). This is the first report wherein purification of isolated mDNA could be passed. The purity and cloneability of mDNA was found to be possible with the successful restriction digestion, 16S rDNA PCR amplification of the isolated mDNA and mDNA library construction.The screening of 1600 clones from the metagenomic library revealed one clone with adistinct hydrolytic activity on carboxymethyl cellulose (CMC) agar suggesting its endoglucanase activity. Agarose gel electrophoresis showed aDNA insert of ~1.5kb size on digestion with BamH1. The metagenomic clones offer a prodigious non-conventional means to explore the genetically untapped resources from nature

The effect of physical activity on white matter integrity in aging and prodromal to mild Alzheimer’s disease with vascular comorbidity

Data availability statement; The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.Supplementary material: The Supplementary material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fnagi.2023.1096798/full#supplementary-materialCopyright © 2023 Konwar, Manca, De Marco, Soininen and Venneri. Background: Physical activity is a modifiable lifestyle factor that has been previously associated with reduced vascular burden and reduced risk of dementia. Objectives: This study tested whether physical activity (i.e., being inactive vs. active) contributed to preservation of white matter microstructure in healthy aging controls and patients in prodromal to mild Alzheimer’s disease with low/high vascular burden. Materials: A total of 213 participants were recruited from memory clinics. They were classified as being either physically active (n = 113) or inactive (n = 100) based on the Cardiovascular Risk Factors, Aging and Dementia (CAIDE) questionnaire. Diffusion-weighted images were acquired for all participants and pre-processed based on a standard protocol. Methods: A factorial design using voxel-wise tract-based spatial statistics (TBSS) was adopted, with 5,000 permutations and threshold-free cluster enhancement (TFCE), to identify significant clusters for fractional anisotropy (FA), axial diffusivity (AxD), mean diffusivity (MD), and radial diffusivity (RD). Results: Clusters of higher FA and lower AxD, MD, and RD values were found for physically active compared with inactive participants that were widespread covering mainly association and projection tracts but also some commissural tracts. A three-way Group × Physical Activity × Vascular Burden interaction effect was found for FA mostly in a variety of projection tracts with a right predominance, and some commissural and association tracts. Post hoc analyses revealed higher FA in patients with high vascular burden who were physically active compared with those patients with high vascular burden who were inactive mainly in projection and association/limbic tracts with a right predominance. Additionally, higher FA was observed in physically active patients with high vascular burden as compared with physically inactive controls with high vascular burden, mainly in bilateral projection fibers and cerebellar regions. Conclusion: Voxel-wise TBSS analysis revealed better preservation of white matter microstructure that was prominent in the high-risk group such as the patients with high vascular burden, specifically those who were physically active. The beneficial effects of physical activity on white matter microstructure were not observed in the controls.This study was supported by the European Union Seventh Framework Programme (FP7/2007e2013) (grant agreement no. 601055, VPH-DARE@IT) to AV and HS

Pathway-centric analysis of microbial metabolic potential and expression along nutrient and energy gradients in the western Atlantic Ocean

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Cavaco, M. A., Bhatia, M. P., Hawley, A. K., Torres-Beltran, M., Johnson, W. M., Longnecker, K., Konwar, K., Kujawinski, E. B., & Hallam, S. J. Pathway-centric analysis of microbial metabolic potential and expression along nutrient and energy gradients in the western Atlantic Ocean. Frontiers in Marine Science, 9, (2022): 867310, https://doi.org/10.3389/fmars.2022.867310.Microbial communities play integral roles in driving nutrient and energy transformations in the ocean, collectively contributing to fundamental biogeochemical cycles. Although it is well known that these communities are stratified within the water column, there remains limited knowledge of how metabolic pathways are distributed and expressed. Here, we investigate pathway distribution and expression patterns from surface (5 m) to deep dark ocean (4000 m) at three stations along a 2765 km transect in the western South Atlantic Ocean. This study is based on new data, consisting of 43 samples for 16S rRNA gene sequencing, 20 samples for metagenomics and 19 samples for metatranscriptomics. Consistent with previous observations, we observed vertical zonation of microbial community structure largely partitioned between light and dark ocean waters. The metabolic pathways inferred from genomic sequence information and gene expression stratified with depth. For example, expression of photosynthetic pathways increased in sunlit waters. Conversely, expression of pathways related to carbon conversion processes, particularly those involving recalcitrant and organic carbon degradation pathways (i.e., oxidation of formaldehyde) increased in dark ocean waters. We also observed correlations between indicator taxa for specific depths with the selective expression of metabolic pathways. For example, SAR202, prevalent in deep waters, was strongly correlated with expression of the methanol oxidation pathway. From a biogeographic perspective, microbial communities along the transect encoded similar metabolic potential with some latitudinal stratification in gene expression. For example, at a station influenced by input from the Amazon River, expression of pathways related to oxidative stress was increased. Finally, when pairing distinct correlations between specific particulate metabolites (e.g., DMSP, AMP and MTA) and both the taxonomic microbial community and metatranscriptomic pathways across depth and space, we were able to observe how changes in the marine metabolite pool may be influenced by microbial function and vice versa. Taken together, these results indicate that marine microbial communities encode a core repertoire of widely distributed metabolic pathways that are differentially regulated along nutrient and energy gradients. Such pathway distribution patterns are consistent with robustness in microbial food webs and indicate a high degree of functional redundancy.This work was funded by the NSF Division of Ocean Sciences (Grant no. OCE-1154320 to EK and KL) and a small (“Microbial controls on marine organic carbon cycling”) and large (“Marine microbial communities from the Southern Atlantic Ocean transect to study dissolved organic matter and carbon cycling”) community sequencing grants from the Joint Genome Institute (US Department of Energy, Walnut Creek, CA) to SH and MB. MB was supported by an NSERC post-doctoral fellowship and a CIFAR Global Scholars fellowship. MC was supported by a Campus Alberta Innovates Program (CAIP) chair to MB