Evolution and Impact of High Content Imaging

Abstract/outline: The field of high content imaging has steadily evolved and expanded substantially across many industry and academic research institutions since it was first described in the early 1990′s. High content imaging refers to the automated acquisition and analysis of microscopic images from a variety of biological sample types. Integration of high content imaging microscopes with multiwell plate handling robotics enables high content imaging to be performed at scale and support medium- to high-throughput screening of pharmacological, genetic and diverse environmental perturbations upon complex biological systems ranging from 2D cell cultures to 3D tissue organoids to small model organisms. In this perspective article the authors provide a collective view on the following key discussion points relevant to the evolution of high content imaging:• Evolution and impact of high content imaging: An academic perspective• Evolution and impact of high content imaging: An industry perspective• Evolution of high content image analysis• Evolution of high content data analysis pipelines towards multiparametric and phenotypic profiling applications• The role of data integration and multiomics• The role and evolution of image data repositories and sharing standards• Future perspective of high content imaging hardware and softwar

Components of Antineutrino Emission in Nuclear Reactor

New ${\bar{\nu}_e},e$ scattering experiments aimed for sensitive searches of the ${\nu}_e$ magnetic moment and projects to explore small mixing angle oscillations at reactors call for a better understanding of the reactor antineutrino spectrum. Here we consider six components, which contribute to the total ${\bar{\nu}_e}$ spectrum generated in nuclear reactor. They are: beta decay of the fission fragments of $^{235}$U, $^{239}$Pu, $^{238}$U and $^{241}$Pu, decay of beta-emitters produced as a result of neutron capture in $^{238}$U and also due to neutron capture in accumulated fission fragments which perturbs the spectrum. For antineutrino energies less than 3.5 MeV we tabulate evolution of ${\bar{\nu}_e}$ spectra corresponding to each of the four fissile isotopes vs fuel irradiation time and their decay after the irradiation is stopped and also estimate relevant uncertainties. Small corrections to the ILL spectra are considered.Comment: LaTex 8 pages, 2 ps figure

Impact of Space Weather on Climate and Habitability of Terrestrial Type Exoplanets

The current progress in the detection of terrestrial type exoplanets has opened a new avenue in the characterization of exoplanetary atmospheres and in the search for biosignatures of life with the upcoming ground-based and space missions. To specify the conditions favorable for the origin, development and sustainment of life as we know it in other worlds, we need to understand the nature of astrospheric, atmospheric and surface environments of exoplanets in habitable zones around G-K-M dwarfs including our young Sun. Global environment is formed by propagated disturbances from the planet-hosting stars in the form of stellar flares, coronal mass ejections, energetic particles, and winds collectively known as astrospheric space weather. Its characterization will help in understanding how an exoplanetary ecosystem interacts with its host star, as well as in the specification of the physical, chemical and biochemical conditions that can create favorable and/or detrimental conditions for planetary climate and habitability along with evolution of planetary internal dynamics over geological timescales. A key linkage of (astro) physical, chemical, and geological processes can only be understood in the framework of interdisciplinary studies with the incorporation of progress in heliophysics, astrophysics, planetary and Earth sciences. The assessment of the impacts of host stars on the climate and habitability of terrestrial (exo)planets will significantly expand the current definition of the habitable zone to the biogenic zone and provide new observational strategies for searching for signatures of life. The major goal of this paper is to describe and discuss the current status and recent progress in this interdisciplinary field and to provide a new roadmap for the future development of the emerging field of exoplanetary science and astrobiology.Comment: 206 pages, 24 figures, 1 table; Review paper. International Journal of Astrobiology (2019

Engaging Hashima: Memory Work, Site-Based Affects, and the Possibilities of Interruption

How is memory embodied, narrated, interrupted, and reworked? Here, we take a postphenomenological approach to memory work that is attentive to how site-based affects prompt and ossify, but also transmogrify, memory of place. With reference to an intensely traumatized, but also domesticated and entropied, environment—the island of Hashima, off the coast from Nagasaki City in Japan—we demonstrate the relevance and explanatory reach of culturally specific accounts of memory, time, and place; how an attentiveness to cultural context in the making of meaning helps mark out the epistemological violences that accrue around sites such as Hashima as objects of analysis in and of themselves; and the affective capacities of the materialities and forces that compose such sites, which can present a welter of surfaces and interiorities that are sensuously “felt” as memory

Introduction: microbes, networks, knowledge—disease ecology and emerging infectious diseases in time of COVID-19

This is an introduction to the topical collection Microbes, Networks, Knowledge: Disease Ecology in the twentieth Century, based on a workshop held at Queen Mary, University London on July 6–7 2016. More than twenty years ago, historian of science and medicine Andrew Mendelsohn asked, “Where did the modern, ecological understanding of epidemic disease come from?” Moving beyond Mendelsohn’s answer, this collection of new essays considers the global history of disease ecology in the past century and shows how epidemics and pandemics have made “microbes complex”

Transmission electron microscopy for characterization of acrosomal damage after Percoll gradient centrifugation of cryopreserved bovine spermatozoa

The objective of this study was to characterize acrosomal ultrastructure following discontinuous Percoll gradient centrifugation of cryopreserved bovine sperm. Semen was collected from six bulls of different breeds and three ejaculates per bull were evaluated. Frozen semen samples were thawed and the acrosomal region of sperm cells was evaluated by transmission electron microscopy (TEM) before (n = 18) and after (n = 18) Percoll centrifugation. The evaluation of 20 sperm heads from each of the 36 samples analyzed ensured that a large number of cells were investigated. The data were subjected to analysis of variance at a level of significance of 5%. Percoll centrifugation reduced the percentage of sperm exhibiting normal acrosomes (from 61.77 to 30.24%), reduced the percentage of sperm presenting atypical acrosome reactions (from 28.38 to 4.84%) and increased the percentage of sperm exhibiting damage in the acrosome (from 6.14 to 64.26%). The percentage of sperm with typical acrosome reactions was not significantly different before (3.70%) and after (0.67%) centrifugation. TEM distinguished four different types of acrosomal status and enabled ultrastructural characterization of acrosomal injuries. The percentage of sperm exhibiting normal acrosomes decreased and damage in the acrosome was the most frequent acrosomal injury with the Percoll gradient centrifugation protocol utilized

RAIphy: Phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles

Background: Computational analysis of metagenomes requires the taxonomical assignment of the genome contigs assembled from DNA reads of environmental samples. Because of the diverse nature of microbiomes, the length of the assemblies obtained can vary between a few hundred bp to a few hundred Kbp. Current taxonomic classification algorithms provide accurate classification for long contigs or for short fragments from organisms that have close relatives with annotated genomes. These are significant limitations for metagenome analysis because of the complexity of microbiomes and the paucity of existing annotated genomes. Results: We propose a robust taxonomic classification method, RAIphy, that uses a novel sequence similarity metric with iterative refinement of taxonomic models and functions effectively without these limitations. We have tested RAIphy with synthetic metagenomics data ranging between 100 bp to 50 Kbp. Within a sequence read range of 100 bp-1000 bp, the sensitivity of RAIphy ranges between 38%-81% outperforming the currently popular composition-based methods for reads in this range. Comparison with computationally more intensive sequence similarity methods shows that RAIphy performs competitively while being significantly faster. The sensitivityspecificity characteristics for relatively longer contigs were compared with the PhyloPythia and TACOA algorithms. RAIphy performs better than these algorithms at varying clade-levels. For an acid mine drainage (AMD) metagenome, RAIphy was able to taxonomically bin the sequence read set more accurately than the currently available methods, Phymm and MEGAN, and more accurately in two out of three tests than the much more computationally intensive method, PhymmBL. Conclusions: With the introduction of the relative abundance index metric and an iterative classification method, we propose a taxonomic classification algorithm that performs competitively for a large range of DNA contig lengths assembled from metagenome data. Because of its speed, simplicity, and accuracy RAIphy can be successfully used in the binning process for a broad range of metagenomic data obtained from environmental samples

Bacteriological and physico-chemical assessment of wastewater in different region of Tunisia: impact on human health

<p>Abstract</p> <p>Background</p> <p>In many parts of the world, health problems and diseases have often been caused by discharging untreated or inadequately treated wastewater. In this study, we aimed to control physico-chemical parameters in wastewater samples. Also, microbiological analyses were done to reveal <it>Salmonella </it>strains and each <it>Escherichia coli </it>(<it>E.coli</it>) pathotype.</p> <p>Findings</p> <p>Sixty wastewater samples were collected from fifteen different regions of Tunisia. All physico-chemical parameters (pH, residual free chlorine, total suspended solids, biological oxygen demand, and chemical oxygen demand) were evaluated.</p> <p>For microbiological analyses, samples were filtered to concentrate bacteria. DNA was extracted by boiling and subjected to polymerase chain reaction (PCR) using different pairs of primers.</p> <p>The mean pH values recorded for the sampling point were above the WHO pH tolerance limit. The total suspended solids (TSS) concentrations varied between 240 mg/L and 733 mg/L in entrance points and between 13 mg/L and 76 mg/L in exit points. In entrance points, the studied wastewater has an average COD concentration that varied between 795 mg/mL to 1420 mg/mL. Whereas, BOD concentration of the wastewater ranged between 270 mg/L to 610 mg/L. In exit points, COD concentration varied between 59 mg/L and 141 mg/L, whereas BOD concentration ranged from 15 mg/L to 87 mg/L.</p> <p>The bacteriological control of wastewaters showed that, in entrance points, <it>Escherichia coli </it>(<it>E.coli</it>) was detected at the rate of 76.6%. Three <it>E.coli </it>pathotypes were found: ETEC (53.3%), EAEC (16.6%) and EIEC (6.6%).</p> <p>Concerning the ETEC isolated strains, 8 of 16 (50%) have only the heat-labile toxin gene, 5 of 16 (31.2%) present only the heat-stable toxin gene and 3 of 16 (18.7%) of strains possess both heat-labile toxin gene and heat-stable toxin gene. In exist point, the same pathotypes were found but all detected ETEC strains present only the "est" gene.</p> <p>Concerning <it>Salmonella </it>isolated strains; percentages of 66.6% and 20% were found in entrance and exit points respectively.</p> <p>Conclusions</p> <p>Wastewaters contain a large amount of pathogenic bacteria that present a real impact on human health. Assessment wastewater treatment stations have to consider in account enterobacterial pathogens as potential pathogens that should be correctly controlled.</p