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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Shimaa S. El-Malah; Kashif Rasool; Khadeeja Abdul Jabbar; Muhammad Umar Sohail; +2 Authors

    Severe environmental conditions can have a diverse impact on marine microorganisms, including bacteria. This can have an inevitable impact on the biofouling of membrane-based desalination plants. In this work, we have utilized indicator bacteria such as total coliform, fecal coliform, and Pseudomonas aeruginosa, as well as 16S rRNA sequencing, to investigate the impact of environmental conditions and spatial variations on the diversity of bacterial communities in the coastal waters and sediments from selected sites in Qatar. The concentration levels of indicator bacteria were affected by increasing temperatures and pH, and by decreasing salinity of seawater samples. Diversity indices and the molecular phylogeny demonstrated that Proteobacteria, Bacteroidetes, and Cyanobacteria were the dominant phyla in all locations. The most abundant operational taxonomic units (OTUs) at the family level were from Flavobacteriaceae (27.07%, 4.31%) and Rhodobacteraceae (22.51%, 9.86%) in seawater and sediment, respectively. Alphaproteobacteria (33.87%, 16.82%), Flavobacteria (30.68%, 5.84%), and Gammaproteobacteria (20.35%, 12.45%) were abundant at the species level in both seawater and sediment, while Clostridia (13.72%) was abundant in sediment only. The results suggest that sediment can act as a reservoir for indicator bacteria, with higher diversity and lower abundance compared to seawater.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Microorganismsarrow_drop_down
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    Microorganisms
    Article . 2023 . Peer-reviewed
    License: CC BY
    Data sources: Crossref
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    Microorganisms
    Article . 2023
    Data sources: DOAJ
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Microorganismsarrow_drop_down
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      Microorganisms
      Article . 2023 . Peer-reviewed
      License: CC BY
      Data sources: Crossref
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      Microorganisms
      Article . 2023
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: M. M. P. B. Fuentes; A. J. B. Santos; A. Abreu‐Grobois; R. Briseño‐Dueñas; +70 Authors

    Sea turtles are vulnerable to climate change since their reproductive output is influenced by incubating temperatures, with warmer temperatures causing lower hatching success and increased feminization of embryos. Their ability to cope with projected increases in ambient temperatures will depend on their capacity to adapt to shifts in climatic regimes. Here, we assessed the extent to which phenological shifts could mitigate impacts from increases in ambient temperatures (from 1.5 to 3°C in air temperatures and from 1.4 to 2.3°C in sea surface temperatures by 2100 at our sites) on four species of sea turtles, under a “middle of the road” scenario (SSP2-4.5). Sand temperatures at sea turtle nesting sites are projected to increase from 0.58 to 4.17°C by 2100 and expected shifts in nesting of 26–43 days earlier will not be sufficient to maintain current incubation temperatures at 7 (29%) of our sites, hatching success rates at 10 (42%) of our sites, with current trends in hatchling sex ratio being able to be maintained at half of the sites. We also calculated the phenological shifts that would be required (both backward for an earlier shift in nesting and forward for a later shift) to keep up with present-day incubation temperatures, hatching success rates, and sex ratios. The required shifts backward in nesting for incubation temperatures ranged from −20 to −191 days, whereas the required shifts forward ranged from +54 to +180 days. However, for half of the sites, no matter the shift the median incubation temperature will always be warmer than the 75th percentile of current ranges. Given that phenological shifts will not be able to ameliorate predicted changes in temperature, hatching success and sex ratio at most sites, turtles may need to use other adaptive responses and/or there is the need to enhance sea turtle resilience to climate warming. © 2023 The Authors. Global Change Biology published by John Wiley & Sons Ltd.

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    Global Change Biology; Pamukkale GCRIS Database
    Article . 2023 . Peer-reviewed
    License: CC BY
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    Repositório do ISPA
    Article . 2023
    License: CC BY
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      Global Change Biology; Pamukkale GCRIS Database
      Article . 2023 . Peer-reviewed
      License: CC BY
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      Repositório do ISPA
      Article . 2023
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Al-Sulaiti, Maetha M.; Soubra, Lama; Ramadan, Gouda A.; Ahmed, Abdullah Qasem Saif; +1 Authors

    This study investigates the mercury (Hg) levels distribution in fish and fish products and their relationships with fish types, weights, protein, and lipid contents in Qatar. Principal component analysis (PCA) was employed to analyze the influence of lipids and protein content on Hg accumulation in the fish tissues. Additionally, the impact of Hg concentration and fish consumption on the estimated weekly intake (EWI). The PCA results showed that Hg contamination levels are primarily affected by protein-lipid content in predatory species. The results showed that high lipid content reflected lower Hg levels and that high Hg levels in fish with high lipid content indicated a polluted environment. The finding of the PCA of EWI, consumption, and Mercury concentration indicate that EWI is highly correlated to Mercury concentration except in the case of low Mercury concentration. 2023 Elsevier Ltd This publication was made possible by Qatar University grant # [QUST-1-CAS-2022-312]. The findings achieved herein are solely the responsibility of the author[s]. Special thanks to the Central Food Laboratories, Public Health Department, Qatar. Scopus

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    Food Chemistry
    Article . 2023 . Peer-reviewed
    License: Elsevier TDM
    Data sources: Crossref
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Qatar University Ins...arrow_drop_down
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      Food Chemistry
      Article . 2023 . Peer-reviewed
      License: Elsevier TDM
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: O. Bruyère; R. Le Gendre; M. Chauveau; B. Bourgeois; +8 Authors

    Abstract. Between 2018 and 2022, four pearl farming Tuamotu atolls of French Polynesia were monitored with autonomous oceanographic instruments to measure the hydrodynamics of atoll lagoons and the ocean–lagoon water exchanges. These surveys were conducted within the framework of the ANR-funded MANA (Management of Atolls) project and its extensions to additional sites. The overarching goal was to improve knowledge on the processes influencing the spat collection of the pearl oyster Pinctada margaritifera, the oyster species used to produce black pearls. These data sets are also critical for the calibration and validation of 3D high spatial resolution hydrodynamic models used to study oyster larval dispersal within lagoons. The observational strategies focused on the characterization of ocean–lagoon exchanges through passes and hoa (i.e., shallow reef flats), lagoon circulation, incident waves breaking on the forereef, water elevation inside the lagoon as well as spatial temperature variability. Chronologically, the investigated atolls were first Raroia Atoll with 9 months of measurements between May 2018 and March 2019 during which the MALIS1 and MALIS2 cruises on-board the R/V ALIS took place. It was followed by a 4 month deployment in Takapoto Atoll (November 2021 to March 2022). In late April 2022, Apataki Atoll was instrumented until end of July, followed by Takaroa measurements between July and October 2022. Apataki (Leg2) and Takaroa Atoll were conjointly instrumented during the MALIS 3 oceanographic cruise. Altogether, those multi-atoll data bring a worldwide unique oceanographic atoll data set that is useful for addressing local pearl farming questions but potentially beneficial for other fundamental and applied investigations. Each data set was post-processed, quality controlled and converted into NetCDF format. Files are available in open source into dedicated repositories in the SEANOE marine data platform. Links (DOI) of individual data sets are provided in Table 2.

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    Earth System Science Data (ESSD)
    Other literature type . 2023
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    https://doi.org/10.5194/essd-2...
    Preprint . 2023 . Peer-reviewed
    License: CC BY
    Data sources: Crossref
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    Earth System Science Data (ESSD)
    Article . 2023 . Peer-reviewed
    License: CC BY
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    Earth System Science Data
    Article . 2023
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      Earth System Science Data (ESSD)
      Other literature type . 2023
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      https://doi.org/10.5194/essd-2...
      Preprint . 2023 . Peer-reviewed
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      Earth System Science Data (ESSD)
      Article . 2023 . Peer-reviewed
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      Earth System Science Data
      Article . 2023
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    Authors: Ahmed S. A. Ibrahim; Radwan Al-Farawati;

    The importance of selenium in the marine environment is highlighted by its bilateral behavior as a nutrient and toxic element. The cathodic stripping voltammetry validated method was used to determine the selenium concentration. The concentration of total dissolved selenium (TDSe) in Al-Arbaeen and Sharm Obhur lagoons along the eastern Red Sea coastal waters was determined. The total selenium concentration in seven fish species’ muscles was determined. TDSe in the surface water of Al-Arbaeen and Sharm Obhur lagoons showed a maximum concentration of 18.56 and 8.38 nM, respectively. TDSe in the surface water of Al-Arbaeen revealed high concentrations near the wastewater discharging pipes in the lagoon. The linear regression between the TDSe and salinity reflected that the discharged water is the source of selenium with a significant negative correlation of (R2 = 0.80, p 2 = 0.78, p Herklotsichthys punctatus and Herklotsichthys revealed high concentrations of 3.99 and 2.40 µg/g, respectively, which exceeded the permissible levels of the WHO, FAO, and ASTDR.

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    Water
    Other literature type . Article . 2023 . Peer-reviewed
    License: CC BY
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    Water
    Article . 2023
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      Water
      Other literature type . Article . 2023 . Peer-reviewed
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      Article . 2023
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    Authors: Zhiyi Jiang; Chris M. Brierley; Jürgen Bader; Pascale Braconnot; +14 Authors

    AbstractThe Atlantic Meridional Overturning Circulation (AMOC) is a key feature of the North Atlantic with global ocean impacts. The AMOC's response to past changes in forcings during the Holocene provides important context for the coming centuries. Here, we investigate AMOC trends using an emerging set of transient simulations using multiple global climate models for the past 6,000 years. Although some models show changes, no consistent trend in overall AMOC strength during the mid‐to‐late Holocene emerges from the ensemble. We interpret this result to suggest no overall change in AMOC, which fits with our assessment of available proxy reconstructions. The decadal variability of the AMOC does not change in ensemble during the mid‐ and late‐Holocene. There are interesting AMOC changes seen in the early Holocene, but their nature depends a lot on which inputs are used to drive the experiment.

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    UCL Discovery
    Article . 2023
    Data sources: UCL Discovery
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    MPG.PuRe
    Article . 2023
    License: CC BY
    Data sources: MPG.PuRe
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    MPG.PuRe
    Article . 2023
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      UCL Discovery
      Article . 2023
      Data sources: UCL Discovery
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      MPG.PuRe
      Article . 2023
      License: CC BY
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    Authors: Maria Siddiqua; Samir Brahim Belhaouari; Naeem Akhter; Aneela Zameer; +1 Authors

    Various vision-based tasks suffer from inaccurate navigation and poor performance due to inevitable problems, such as adverse weather conditions like haze, fog, rain, snow, and clouds affecting ground and aerial navigation, as well as underwater images being degraded with blue-green tones and mud affecting marine navigation. Existing techniques in the literature typically focus on restoring specific degradations using separate models, leading to computational inefficiency. To address this, an all-in-one Multidomain Attention-based Conditional Generative Adversarial Network (MACGAN) is proposed to improve scene visibility for optimal ground, aerial, and marine navigation, using the same set of parameters across all domains. The MACGAN is a lightweight network with four encoder and decoder blocks and multiple attention blocks in between, which enhances the image restoration process by focusing on the most important features. To evaluate the effectiveness of MACGAN, extensive qualitative and quantitative comparisons are conducted with state-of-the-art image-to-image translation models, all-in-one adverse weather removal models, and single-effect removal models. The results highlight the superior performance of MACGAN in terms of scene visibility improvement and restoration quality. Additionally, MACGAN is tested on real-world unseen image domains, including smog, dust, fog, rain, snow, and lightning, further validating its generalizability and robustness. Furthermore, an ablation study is conducted to analyze the contributions of the discriminator and attention blocks within the MACGAN architecture. The results confirm that both components play significant roles in the effectiveness of MACGAN, with the discriminator ensuring adversarial training and the attention blocks effectively capturing and enhancing important image features.

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    IEEE Access
    Article . 2023 . Peer-reviewed
    License: CC BY
    Data sources: Crossref
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    IEEE Access
    Article . 2023
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      IEEE Access
      Article . 2023 . Peer-reviewed
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      IEEE Access
      Article . 2023
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    Authors: Cecilia Cisar; Nicholas Keener; Mathew Ruffalo; Benedict Paten;

    AbstractIn recent years, high-throughput spatial transcriptomics has emerged as a powerful tool for investigating the spatial distribution of mRNA expression and the effects it may have on cellular function. There is a lack of standardized tools for analyzing spatial transcriptomics data, leading many groups to write their own in-house tools that are often poorly documented and not generalizable to other datasets. Currently, the only publicly available tools for extracting annotated transcript locations from raw multiplexed fluorescentin situhybridization (FISH) images are starfish, which is lacking in key areas, and MERlin, which is restricted to only MERFISH data. To address this, we have expanded and improved the starfish library and used those tools to create PIPEFISH, a semi-automated and generalizable pipeline that performs transcript annotation for FISH-based spatial transcriptomics. PIPEFISH has options for image processing, decoding, and cell segmentation, and calculates quality control metrics on the output to allow the user to assess the pipeline’s performance on their data. We used this pipeline to annotate transcript locations from three real datasets from three different common types of FISH image-based experiments: MERFISH, seqFISH, and targetedin situsequencing (ISS), and verified that the results were high quality using the internal quality metrics of the pipeline and also a comparison to a orthogonal method of measuring RNA expression in a similar tissue sample. We have made PIPEFISH publicly available through Github for anyone interested in analyzing data from FISH-based spatial transcriptomic assays.

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    Cell Genomics
    Article . 2023 . Peer-reviewed
    License: CC BY
    Data sources: Crossref
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    Cell Genomics
    Article . 2023
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      Cell Genomics
      Article . 2023 . Peer-reviewed
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      Cell Genomics
      Article . 2023
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    Authors: Preecha Prempree; Donal Bisanzio; Prayuth Sudathip; Jerdsuda Kanjanasuwan; +7 Authors

    AbstractBackgroundThailand has made substantial progress toward malaria elimination, with 46 of the country’s 77 provinces declared malaria free as part of the subnational verification program. Nonetheless, these areas remain vulnerable to the reintroduction of malaria parasites and the reestablishment of indigenous transmission. As such, prevention of reestablishment (POR) planning is of increasing concern to ensure timely response to increasing cases. A thorough understanding of both risk of parasite importation and receptivity for transmission is essential for successful POR planning.MethodsRoutine geolocated case- and foci-level epidemiological and case-level demographic data were extracted from Thailand’s national malaria information system for all active foci from October 2012 to September 2020. A spatial analysis examined environmental and climate factors associated with remaining active foci. A logistic regression model collated surveillance data with remote sensing data to investigate associations with the probability of having reported an indigenous case within the previous year.ResultsActive foci are highly concentrated along international borders, particularly Thailand’s western border with Myanmar. Although there is heterogeneity in the habitats surrounding active foci, land covered by tropical forest and plantation was significantly higher for active foci than other foci. The regression results showed that tropical forest, plantations, forest disturbance, distance from international borders, historical foci classification, percentage of males, and percentage of short-term residents were associated with high probability to report indigenous cases.ConclusionThese results confirm that Thailand’s emphasis on border areas and forest-going populations is well placed. The results suggest that environmental factors alone are not driving malaria transmission in Thailand; rather, other factors, including demographics and behaviors, may also be contributors. However, these factors are syndemic, so human activities in areas covered by tropical forests and plantations may result in malaria importation and potentially, local transmission, in foci that previously had been cleared. These factors should be addressed in POR planning.

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    Authors: Sonia K M Gueroun; Stefano Piraino; Ons KÉfi-Daly Yahia; Mohamed Néjib Daly Yahia;

    Abstract Jellyfish (Cnidaria and Ctenophora) are an essential component of marine ecosystems and represent a potential effect, positive or negative, for several economic activities. Jellyfish blooms and non-indigenous species (NIS) introduction can shift ecological community structure and energy transfer. Despite their importance in ecosystem function and services, knowledge of jellyfish fauna diversity and phenology are largely lacking for the southern Mediterranean Sea. Here, we present an overview of the current state of jellyfish biodiversity in Tunisia. Based on a comprehensive literature survey, historical records and unpublished data, 66 jellyfish species, including 11 non-indigenous species, have been recorded in Tunisia between 1994 and 2020. Additionally, based on field surveys and a citizen science sighting program between 2004 and 2020, we present data on the spatial distribution of 13 conspicuous jellyfish taxa and the phenology of the eight most frequently detected species (Aurelia solida, Cotylorhiza tuberculata, Pelagia noctiluca, Phyllorhiza punctata, Rhizostoma pulmo, Rhopilema nomadica, Olindias muelleri and Velella velella) in Tunisian two ecoregions, the Western Mediterranean and the Tunisian Plateau. The 17 year survey showed a shift in R. pulmo, A. solida and P. noctiluca phenology. Additionally, citizen science revealed an increase in the spatial range of P. punctata (NIS) and the distinct phenologies of populations in the two ecoregions.

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    Journal of Plankton Research
    Article . 2022 . Peer-reviewed
    License: OUP Standard Publication Reuse
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      Journal of Plankton Research
      Article . 2022 . Peer-reviewed
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Shimaa S. El-Malah; Kashif Rasool; Khadeeja Abdul Jabbar; Muhammad Umar Sohail; +2 Authors

    Severe environmental conditions can have a diverse impact on marine microorganisms, including bacteria. This can have an inevitable impact on the biofouling of membrane-based desalination plants. In this work, we have utilized indicator bacteria such as total coliform, fecal coliform, and Pseudomonas aeruginosa, as well as 16S rRNA sequencing, to investigate the impact of environmental conditions and spatial variations on the diversity of bacterial communities in the coastal waters and sediments from selected sites in Qatar. The concentration levels of indicator bacteria were affected by increasing temperatures and pH, and by decreasing salinity of seawater samples. Diversity indices and the molecular phylogeny demonstrated that Proteobacteria, Bacteroidetes, and Cyanobacteria were the dominant phyla in all locations. The most abundant operational taxonomic units (OTUs) at the family level were from Flavobacteriaceae (27.07%, 4.31%) and Rhodobacteraceae (22.51%, 9.86%) in seawater and sediment, respectively. Alphaproteobacteria (33.87%, 16.82%), Flavobacteria (30.68%, 5.84%), and Gammaproteobacteria (20.35%, 12.45%) were abundant at the species level in both seawater and sediment, while Clostridia (13.72%) was abundant in sediment only. The results suggest that sediment can act as a reservoir for indicator bacteria, with higher diversity and lower abundance compared to seawater.

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    Microorganisms
    Article . 2023 . Peer-reviewed
    License: CC BY
    Data sources: Crossref
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    Microorganisms
    Article . 2023
    Data sources: DOAJ
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      Microorganisms
      Article . 2023 . Peer-reviewed
      License: CC BY
      Data sources: Crossref
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      Microorganisms
      Article . 2023
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    Authors: M. M. P. B. Fuentes; A. J. B. Santos; A. Abreu‐Grobois; R. Briseño‐Dueñas; +70 Authors

    Sea turtles are vulnerable to climate change since their reproductive output is influenced by incubating temperatures, with warmer temperatures causing lower hatching success and increased feminization of embryos. Their ability to cope with projected increases in ambient temperatures will depend on their capacity to adapt to shifts in climatic regimes. Here, we assessed the extent to which phenological shifts could mitigate impacts from increases in ambient temperatures (from 1.5 to 3°C in air temperatures and from 1.4 to 2.3°C in sea surface temperatures by 2100 at our sites) on four species of sea turtles, under a “middle of the road” scenario (SSP2-4.5). Sand temperatures at sea turtle nesting sites are projected to increase from 0.58 to 4.17°C by 2100 and expected shifts in nesting of 26–43 days earlier will not be sufficient to maintain current incubation temperatures at 7 (29%) of our sites, hatching success rates at 10 (42%) of our sites, with current trends in hatchling sex ratio being able to be maintained at half of the sites. We also calculated the phenological shifts that would be required (both backward for an earlier shift in nesting and forward for a later shift) to keep up with present-day incubation temperatures, hatching success rates, and sex ratios. The required shifts backward in nesting for incubation temperatures ranged from −20 to −191 days, whereas the required shifts forward ranged from +54 to +180 days. However, for half of the sites, no matter the shift the median incubation temperature will always be warmer than the 75th percentile of current ranges. Given that phenological shifts will not be able to ameliorate predicted changes in temperature, hatching success and sex ratio at most sites, turtles may need to use other adaptive responses and/or there is the need to enhance sea turtle resilience to climate warming. © 2023 The Authors. Global Change Biology published by John Wiley & Sons Ltd.

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    Global Change Biology; Pamukkale GCRIS Database
    Article . 2023 . Peer-reviewed
    License: CC BY
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    Repositório do ISPA
    Article . 2023
    License: CC BY
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      Global Change Biology; Pamukkale GCRIS Database
      Article . 2023 . Peer-reviewed
      License: CC BY
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      Repositório do ISPA
      Article . 2023
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    Authors: Al-Sulaiti, Maetha M.; Soubra, Lama; Ramadan, Gouda A.; Ahmed, Abdullah Qasem Saif; +1 Authors

    This study investigates the mercury (Hg) levels distribution in fish and fish products and their relationships with fish types, weights, protein, and lipid contents in Qatar. Principal component analysis (PCA) was employed to analyze the influence of lipids and protein content on Hg accumulation in the fish tissues. Additionally, the impact of Hg concentration and fish consumption on the estimated weekly intake (EWI). The PCA results showed that Hg contamination levels are primarily affected by protein-lipid content in predatory species. The results showed that high lipid content reflected lower Hg levels and that high Hg levels in fish with high lipid content indicated a polluted environment. The finding of the PCA of EWI, consumption, and Mercury concentration indicate that EWI is highly correlated to Mercury concentration except in the case of low Mercury concentration. 2023 Elsevier Ltd This publication was made possible by Qatar University grant # [QUST-1-CAS-2022-312]. The findings achieved herein are solely the responsibility of the author[s]. Special thanks to the Central Food Laboratories, Public Health Department, Qatar. Scopus

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    Food Chemistry
    Article . 2023 . Peer-reviewed
    License: Elsevier TDM
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      Food Chemistry
      Article . 2023 . Peer-reviewed
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    Authors: O. Bruyère; R. Le Gendre; M. Chauveau; B. Bourgeois; +8 Authors

    Abstract. Between 2018 and 2022, four pearl farming Tuamotu atolls of French Polynesia were monitored with autonomous oceanographic instruments to measure the hydrodynamics of atoll lagoons and the ocean–lagoon water exchanges. These surveys were conducted within the framework of the ANR-funded MANA (Management of Atolls) project and its extensions to additional sites. The overarching goal was to improve knowledge on the processes influencing the spat collection of the pearl oyster Pinctada margaritifera, the oyster species used to produce black pearls. These data sets are also critical for the calibration and validation of 3D high spatial resolution hydrodynamic models used to study oyster larval dispersal within lagoons. The observational strategies focused on the characterization of ocean–lagoon exchanges through passes and hoa (i.e., shallow reef flats), lagoon circulation, incident waves breaking on the forereef, water elevation inside the lagoon as well as spatial temperature variability. Chronologically, the investigated atolls were first Raroia Atoll with 9 months of measurements between May 2018 and March 2019 during which the MALIS1 and MALIS2 cruises on-board the R/V ALIS took place. It was followed by a 4 month deployment in Takapoto Atoll (November 2021 to March 2022). In late April 2022, Apataki Atoll was instrumented until end of July, followed by Takaroa measurements between July and October 2022. Apataki (Leg2) and Takaroa Atoll were conjointly instrumented during the MALIS 3 oceanographic cruise. Altogether, those multi-atoll data bring a worldwide unique oceanographic atoll data set that is useful for addressing local pearl farming questions but potentially beneficial for other fundamental and applied investigations. Each data set was post-processed, quality controlled and converted into NetCDF format. Files are available in open source into dedicated repositories in the SEANOE marine data platform. Links (DOI) of individual data sets are provided in Table 2.

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    Earth System Science Data (ESSD)
    Other literature type . 2023
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    https://doi.org/10.5194/essd-2...
    Preprint . 2023 . Peer-reviewed
    License: CC BY
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    Earth System Science Data (ESSD)
    Article . 2023 . Peer-reviewed
    License: CC BY
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    Earth System Science Data
    Article . 2023
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      Earth System Science Data (ESSD)
      Other literature type . 2023
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      https://doi.org/10.5194/essd-2...
      Preprint . 2023 . Peer-reviewed
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      Earth System Science Data (ESSD)
      Article . 2023 . Peer-reviewed
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      Earth System Science Data
      Article . 2023
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    Authors: Ahmed S. A. Ibrahim; Radwan Al-Farawati;

    The importance of selenium in the marine environment is highlighted by its bilateral behavior as a nutrient and toxic element. The cathodic stripping voltammetry validated method was used to determine the selenium concentration. The concentration of total dissolved selenium (TDSe) in Al-Arbaeen and Sharm Obhur lagoons along the eastern Red Sea coastal waters was determined. The total selenium concentration in seven fish species’ muscles was determined. TDSe in the surface water of Al-Arbaeen and Sharm Obhur lagoons showed a maximum concentration of 18.56 and 8.38 nM, respectively. TDSe in the surface water of Al-Arbaeen revealed high concentrations near the wastewater discharging pipes in the lagoon. The linear regression between the TDSe and salinity reflected that the discharged water is the source of selenium with a significant negative correlation of (R2 = 0.80, p 2 = 0.78, p Herklotsichthys punctatus and Herklotsichthys revealed high concentrations of 3.99 and 2.40 µg/g, respectively, which exceeded the permissible levels of the WHO, FAO, and ASTDR.

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    Water
    Other literature type . Article . 2023 . Peer-reviewed
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    Water
    Article . 2023
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      Water
      Other literature type . Article . 2023 . Peer-reviewed
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      Water
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    Authors: Zhiyi Jiang; Chris M. Brierley; Jürgen Bader; Pascale Braconnot; +14 Authors

    AbstractThe Atlantic Meridional Overturning Circulation (AMOC) is a key feature of the North Atlantic with global ocean impacts. The AMOC's response to past changes in forcings during the Holocene provides important context for the coming centuries. Here, we investigate AMOC trends using an emerging set of transient simulations using multiple global climate models for the past 6,000 years. Although some models show changes, no consistent trend in overall AMOC strength during the mid‐to‐late Holocene emerges from the ensemble. We interpret this result to suggest no overall change in AMOC, which fits with our assessment of available proxy reconstructions. The decadal variability of the AMOC does not change in ensemble during the mid‐ and late‐Holocene. There are interesting AMOC changes seen in the early Holocene, but their nature depends a lot on which inputs are used to drive the experiment.

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    UCL Discovery
    Article . 2023
    Data sources: UCL Discovery
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    MPG.PuRe
    Article . 2023
    License: CC BY
    Data sources: MPG.PuRe
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    MPG.PuRe
    Article . 2023
    Data sources: MPG.PuRe
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    Access Routes
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      UCL Discovery
      Article . 2023
      Data sources: UCL Discovery
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      MPG.PuRe
      Article . 2023
      License: CC BY
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      MPG.PuRe
      Article . 2023
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    Authors: Maria Siddiqua; Samir Brahim Belhaouari; Naeem Akhter; Aneela Zameer; +1 Authors

    Various vision-based tasks suffer from inaccurate navigation and poor performance due to inevitable problems, such as adverse weather conditions like haze, fog, rain, snow, and clouds affecting ground and aerial navigation, as well as underwater images being degraded with blue-green tones and mud affecting marine navigation. Existing techniques in the literature typically focus on restoring specific degradations using separate models, leading to computational inefficiency. To address this, an all-in-one Multidomain Attention-based Conditional Generative Adversarial Network (MACGAN) is proposed to improve scene visibility for optimal ground, aerial, and marine navigation, using the same set of parameters across all domains. The MACGAN is a lightweight network with four encoder and decoder blocks and multiple attention blocks in between, which enhances the image restoration process by focusing on the most important features. To evaluate the effectiveness of MACGAN, extensive qualitative and quantitative comparisons are conducted with state-of-the-art image-to-image translation models, all-in-one adverse weather removal models, and single-effect removal models. The results highlight the superior performance of MACGAN in terms of scene visibility improvement and restoration quality. Additionally, MACGAN is tested on real-world unseen image domains, including smog, dust, fog, rain, snow, and lightning, further validating its generalizability and robustness. Furthermore, an ablation study is conducted to analyze the contributions of the discriminator and attention blocks within the MACGAN architecture. The results confirm that both components play significant roles in the effectiveness of MACGAN, with the discriminator ensuring adversarial training and the attention blocks effectively capturing and enhancing important image features.

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    IEEE Access
    Article . 2023 . Peer-reviewed
    License: CC BY
    Data sources: Crossref
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    IEEE Access
    Article . 2023
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      IEEE Access
      Article . 2023 . Peer-reviewed
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      IEEE Access
      Article . 2023
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    Authors: Cecilia Cisar; Nicholas Keener; Mathew Ruffalo; Benedict Paten;

    AbstractIn recent years, high-throughput spatial transcriptomics has emerged as a powerful tool for investigating the spatial distribution of mRNA expression and the effects it may have on cellular function. There is a lack of standardized tools for analyzing spatial transcriptomics data, leading many groups to write their own in-house tools that are often poorly documented and not generalizable to other datasets. Currently, the only publicly available tools for extracting annotated transcript locations from raw multiplexed fluorescentin situhybridization (FISH) images are starfish, which is lacking in key areas, and MERlin, which is restricted to only MERFISH data. To address this, we have expanded and improved the starfish library and used those tools to create PIPEFISH, a semi-automated and generalizable pipeline that performs transcript annotation for FISH-based spatial transcriptomics. PIPEFISH has options for image processing, decoding, and cell segmentation, and calculates quality control metrics on the output to allow the user to assess the pipeline’s performance on their data. We used this pipeline to annotate transcript locations from three real datasets from three different common types of FISH image-based experiments: MERFISH, seqFISH, and targetedin situsequencing (ISS), and verified that the results were high quality using the internal quality metrics of the pipeline and also a comparison to a orthogonal method of measuring RNA expression in a similar tissue sample. We have made PIPEFISH publicly available through Github for anyone interested in analyzing data from FISH-based spatial transcriptomic assays.

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    Cell Genomics
    Article . 2023 . Peer-reviewed
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    Cell Genomics
    Article . 2023
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      Cell Genomics
      Article . 2023 . Peer-reviewed
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      Cell Genomics
      Article . 2023
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    Authors: Preecha Prempree; Donal Bisanzio; Prayuth Sudathip; Jerdsuda Kanjanasuwan; +7 Authors

    AbstractBackgroundThailand has made substantial progress toward malaria elimination, with 46 of the country’s 77 provinces declared malaria free as part of the subnational verification program. Nonetheless, these areas remain vulnerable to the reintroduction of malaria parasites and the reestablishment of indigenous transmission. As such, prevention of reestablishment (POR) planning is of increasing concern to ensure timely response to increasing cases. A thorough understanding of both risk of parasite importation and receptivity for transmission is essential for successful POR planning.MethodsRoutine geolocated case- and foci-level epidemiological and case-level demographic data were extracted from Thailand’s national malaria information system for all active foci from October 2012 to September 2020. A spatial analysis examined environmental and climate factors associated with remaining active foci. A logistic regression model collated surveillance data with remote sensing data to investigate associations with the probability of having reported an indigenous case within the previous year.ResultsActive foci are highly concentrated along international borders, particularly Thailand’s western border with Myanmar. Although there is heterogeneity in the habitats surrounding active foci, land covered by tropical forest and plantation was significantly higher for active foci than other foci. The regression results showed that tropical forest, plantations, forest disturbance, distance from international borders, historical foci classification, percentage of males, and percentage of short-term residents were associated with high probability to report indigenous cases.ConclusionThese results confirm that Thailand’s emphasis on border areas and forest-going populations is well placed. The results suggest that environmental factors alone are not driving malaria transmission in Thailand; rather, other factors, including demographics and behaviors, may also be contributors. However, these factors are syndemic, so human activities in areas covered by tropical forests and plantations may result in malaria importation and potentially, local transmission, in foci that previously had been cleared. These factors should be addressed in POR planning.

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    Authors: Sonia K M Gueroun; Stefano Piraino; Ons KÉfi-Daly Yahia; Mohamed Néjib Daly Yahia;

    Abstract Jellyfish (Cnidaria and Ctenophora) are an essential component of marine ecosystems and represent a potential effect, positive or negative, for several economic activities. Jellyfish blooms and non-indigenous species (NIS) introduction can shift ecological community structure and energy transfer. Despite their importance in ecosystem function and services, knowledge of jellyfish fauna diversity and phenology are largely lacking for the southern Mediterranean Sea. Here, we present an overview of the current state of jellyfish biodiversity in Tunisia. Based on a comprehensive literature survey, historical records and unpublished data, 66 jellyfish species, including 11 non-indigenous species, have been recorded in Tunisia between 1994 and 2020. Additionally, based on field surveys and a citizen science sighting program between 2004 and 2020, we present data on the spatial distribution of 13 conspicuous jellyfish taxa and the phenology of the eight most frequently detected species (Aurelia solida, Cotylorhiza tuberculata, Pelagia noctiluca, Phyllorhiza punctata, Rhizostoma pulmo, Rhopilema nomadica, Olindias muelleri and Velella velella) in Tunisian two ecoregions, the Western Mediterranean and the Tunisian Plateau. The 17 year survey showed a shift in R. pulmo, A. solida and P. noctiluca phenology. Additionally, citizen science revealed an increase in the spatial range of P. punctata (NIS) and the distinct phenologies of populations in the two ecoregions.

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    Journal of Plankton Research
    Article . 2022 . Peer-reviewed
    License: OUP Standard Publication Reuse
    Data sources: Crossref
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      Journal of Plankton Research
      Article . 2022 . Peer-reviewed
      License: OUP Standard Publication Reuse
      Data sources: Crossref
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