Automatic plankton quantification using deep features

The study of marine plankton data is vital to monitor the health of the world’s oceans. In recent decades, automatic plankton recognition systems have proved useful to address the vast amount of data collected by specially engineered in situ digital imaging systems. At the beginning, these systems were developed and put into operation using traditional automatic classification techniques, which were fed with handdesigned local image descriptors (such as Fourier features), obtaining quite successful results. In the past few years, there have been many advances in the computer vision community with the rebirth of neural networks. In this paper, we leverage how descriptors computed using Convolutional Neural Networks (CNNs) trained with out-of-domain data are useful to replace hand-designed descriptors in the task of estimating the prevalence of each plankton class in a water sample. To achieve this goal, we have designed a broad set of experiments that show how effective these deep features are when working in combination with state-of-the-art quantification algorithms

Diversity of Synechococcus at the Martha\u27s Vineyard Coastal Observatory: Insights from Culture Isolations, Clone Libraries, and Flow Cytometry

The cyanobacterium Synechococcus is a ubiquitous, important phytoplankter across the world’s oceans. A high degree of genetic diversity exists within the marine group, which likely contributes to its global success. Over 20 clades with different distribution patterns have been identified. However, we do not fully understand the environmental factors that control clade distributions. These factors are likely to change seasonally, especially in dynamic coastal systems. To investigate how coastal Synechococcus assemblages change temporally, we assessed the diversity of Synechococcus at the Martha’s Vineyard Coastal Observatory (MVCO) over three annual cycles with culture-dependent and independent approaches. We further investigated the abundance of both phycoerythrin (PE)-containing and phycocyanin (PC)-only Synechococcus with a flow cytometric setup that distinguishes PC-only Synechococcus from picoeukaryotes. We found that the Synechococcus assemblage at MVCO is diverse (13 different clades identified), but dominated by clade I representatives. Many clades were only isolated during late summer and fall, suggesting more favorable conditions for isolation at this time. PC-only strains from four different clades were isolated, but these cells were only detected by flow cytometry in a few samples over the time series, suggesting they are rare at this site. Within clade I, we identified four distinct subclades. The relative abundances of each subclade varied over the seasonal cycle, and the high Synechococcus cell concentration at MVCO may be maintained by the diversity found within this clade. This study highlights the need to understand how temporal aspects of the environment affect Synechococcus community structure and cell abundance

Mesoscale variability in intact and ghost colonies of Phaeocystis antarctica in the Ross Sea : distribution and abundance

© The Author(s), 2016. This is the author's version of the work and is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Journal of Marine Systems 166 (2017): 97-107, doi:10.1016/j.jmarsys.2016.05.007.Phaeocystis, a genus with a cosmopolitan distribution and a polymorphic life cycle, was observed during summer in the Ross Sea, Antarctica, where large blooms of this haptophyte regularly occur. The mesoscale vertical and horizontal distributions of colonies of P. antarctica were assessed using a towed Video Plankton Recorder (VPR). The mean size of colonies was 1.20 mm, and mean abundances within the three VPR surveys were 4.86, 1.96, and 11.5 mL-1. In addition to the typical spherical, transparent colonies, the VPR quantified an optically dissimilar form of colony that had a distinctive translucent appearance. It also measured the abundance of collapsed colonies, similar to those observed previously from cultures and mesocosms, which we called “ghost colonies”. The translucent colonial form had a different distribution than the more common colonial form, and at times was more abundant. Relative to intact colonies, the ghost colonies occurred less frequently, with mean abundances in the three surveys being 0.01, 0.08, and 0.0004 mL-1. Ghost colonies generally were found below the euphotic zone, where they often were in greater abundance than intact colonies. However, the relationship of ghost colonies to intact P. antarctica colonies was not direct or consistent, suggesting that the formation of ghost colonies from living colonies and their appearance within the water column were not tightly coupled. Given their relative scarcity and low carbon content, it is unlikely that ghost colonies contribute substantially to vertical flux; however, it is possible that we did not sample periods of major flux events, and as a result minimized the importance of ghost colonies to vertical flux. They do, however, represent a poorly documented feature of polar haptophyte life cycles.This research was supported by grants from the National Science Foundation (ANT-0944254 and ANT-0944165). HMS and EEP acknowledge support of the Gordon and Betty Moore Foundation (Grant #2649) for image informatics development.2018-06-0

All-cause and cause-specific mortality among people with regular or problematic cocaine use:A systematic review and meta-analysis

Aims: To estimate pooled all-cause and cause-specific mortality risk for people with regular or problematic cocaine use.Methods: Systematic review and meta-analysis of prospective or retrospective cohort studies or clinical trials (n ≥30) of people with regular or problematic cocaine use with data on all-cause or cause-specific mortality. Of 2808 papers, 28 were eligible and reported on 21 cohorts, with a total 170 019 individuals. Cohorts identified based on acute care for drug poisoning or other severe health presentation were excluded. Title/abstract screening was conducted by one reviewer; a second reviewer independently checked 10% of excluded studies. Two reviewers conducted full-text screening. Data were extracted by one reviewer and checked by a second. A customized review-specific study reporting quality/risk of bias tool was used. Data on crude mortality rates (CMR) and standardized mortality ratios were extracted for both all-cause and cause-specific mortality. Standardized mortality ratios were imputed where not provided by the author using extracted data and information from the Global Burden of Disease Study 2017. Data were pooled using a random-effects model.Results: The pooled all-cause crude mortality rate was 1.24 per 100 person-years [95% confidence interval (CI) = 0.86, 1.78; n = 16 cohorts], but with considerable heterogeneity (I2 = 98.8%). The pooled all-cause standardized mortality ratio (SMR) was 6.13 (95% CI = 4.15, 9.05; n = 16 cohorts). Suicide (SMR = 6.26, 95% CI = 2.84, 13.80), accidental injury (SMR = 6.36, 95% CI = 4.18, 9.68), homicide (SMR = 9.38, 95% CI 3.45-25.48) and AIDS-related mortality (SMR = 23.12, 95% CI = 11.30, 47.31) were all elevated compared with age and sex peers in the general population.Conclusions: There are elevated rates of mortality among people with regular or problematic cocaine use for traumatic deaths and deaths attributable to infectious disease

Long-term biological effects of petroleum residues on fiddler crabs in salt marshes

Author Posting. © The Author(s), 2007. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Marine Pollution Bulletin 54 (2007): 955-962, doi:10.1016/j.marpolbul.2007.02.015.In September 1969,the Florida barge spilled 700,000 L of No. 2 fuel oil into the salt marsh sediments of Wild Harbor (Buzzards Bay, MA). Today the aboveground environment appears unaffected, but a substantial amount of moderately degraded petroleum still remains 8 to 20 cm below the surface. The salt marsh fiddler crabs, Uca pugnax, which burrow into the sediments at depths of 5 to 25 cm, are chronically exposed to the spilled oil. Behavioral studies conducted with U. pugnax from Wild Harbor and a control site, Great Sippewissett marsh, found that crabs exposed to the oil avoided burrowing into oiled layers, suffered delayed escape responses, lowered feeding rates, and lower densities. The oil residues are therefore biologically active and affect U. pugnax populations. Our results add new knowledge about long-term consequences of spilled oil, a dimension that should be included when assessing oil-impacted areas and developing management plans designed to restore, rehabilitate, or replace impacted areas.This work was funded by a grant from the Woods Hole Oceanographic Institution Sea Grant Program, under grants from the National Oceanic and Atmospheric Administration, U.S. Department of Commerce, under Grant No. NA16RG2273, project no. R/P-73. Additional support was provided by funding from the NSF funded Research Experience for Undergraduates program, award 0453292, an Office of Naval Research Young Investigator Award (N00014-04-01-0029) to C. Reddy, and an USEPA Science to Achieve Results Graduate Fellowship (FP91661801) to E. Peacock

Neonatal iron deficiency causes abnormal phosphate metabolism by elevating FGF23 in normal and ADHR mice.

Fibroblast growth factor 23 (FGF23) gain of function mutations can lead to autosomal dominant hypophosphatemic rickets (ADHR) disease onset at birth, or delayed onset following puberty or pregnancy. We previously demonstrated that the combination of iron deficiency and a knock-in R176Q FGF23 mutation in mature mice induced FGF23 expression and hypophosphatemia that paralleled the late-onset ADHR phenotype. Because anemia in pregnancy and in premature infants is common, the goal of this study was to test whether iron deficiency alters phosphate handling in neonatal life. Wild-type (WT) and ADHR female breeder mice were provided control or iron-deficient diets during pregnancy and nursing. Iron-deficient breeders were also made iron replete. Iron-deficient WT and ADHR pups were hypophosphatemic, with ADHR pups having significantly lower serum phosphate (p 50 fold; p < 0.01). WT and ADHR pups receiving low iron had elevated intact serum FGF23; ADHR mice were affected to a greater degree (p < 0.01). Iron-deficient mice also showed increased Cyp24a1 and reduced Cyp27b1, and low serum 1,25-dihydroxyvitamin D (1,25D). Iron repletion normalized most abnormalities. Because iron deficiency can induce tissue hypoxia, oxygen deprivation was tested as a regulator of FGF23, and was shown to stimulate FGF23 mRNA in vitro and serum C-terminal FGF23 in normal rats in vivo. These studies demonstrate that FGF23 is modulated by iron status in young WT and ADHR mice and that hypoxia independently controls FGF23 expression in situations of normal iron. Therefore, disturbed iron and oxygen metabolism in neonatal life may have important effects on skeletal function and structure through FGF23 activity on phosphate regulation

A regional, early spring bloom of Phaeocystis pouchetii on the New England continental shelf

Author Posting. © American Geophysical Union, 2021. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Oceans 126(2), (2021): e2020JC016856, https://doi.org/10.1029/2020JC016856.The genus Phaeocystis is distributed globally and has considerable ecological, biogeochemical, and societal impacts. Understanding its distribution, growth and ecological impacts has been limited by lack of extensive observations on appropriate scales. In 2018, we investigated the biological dynamics of the New England continental shelf and encountered a substantial bloom of Phaeocystis pouchetii. Based on satellite imagery during January through April, the bloom extended over broad expanses of the shelf; furthermore, our observations demonstrated that it reached high biomass levels, with maximum chlorophyll concentrations exceeding 16 µg L−1 and particulate organic carbon levels > 95 µmol L−1. Initially, the bloom was largely confined to waters with temperatures <6°C, which in turn were mostly restricted to shallow areas near the coast. As the bloom progressed, it appeared to sink into the bottom boundary layer; however, enough light and nutrients were available for growth. The bloom was highly productive (net community production integrated through the mixed layer from stations within the bloom averaged 1.16 g C m−2 d−1) and reduced nutrient concentrations considerably. Long‐term coastal observations suggest that Phaeocystis blooms occur sporadically in spring on Nantucket Shoals and presumably expand onto the continental shelf. Based on the distribution of Phaeocystis during our study, we suggest that it can have a significant impact on the overall productivity and ecology of the New England shelf during the winter/spring transition.This project was supported by the US National Science Foundation (Grants 1657855, 1657803, and 1657489). NES‐LTER contributions were supported by grants to HMS from NSF (Grant 1655686) and the Simons Foundation (Grant 561126). VPR operations were supported by the Dalio Explore Fund.2021-07-1

Quality of Life and Socioeconomic Indicators Associated with Survival of Myeloid Leukemias in Canada

Understanding how patient‐reported quality of life (QoL) and socioeconomic status (SES) relate to survival of acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS) may improve prognostic information sharing. This study explores associations among QoL, SES, and survival through administration of the Euro‐QoL 5‐Dimension, 3‐level and Functional Assessment of Cancer Therapy‐Leukemia and financial impact questionnaires to 138 adult participants with newly diagnosed AML or MDS in a longitudinal, pan‐Canadian study. Cox regression and lasso variable selection models were used to explore associations among QoL, SES, and established predictors of survival. Secondary outcomes were changes in QoL, performance of the QoL instruments, and lost income. We found that higher QoL and SES were positively associated with survival. The Lasso model selected the visual analog scale of the EQ‐5D‐3L as the most important predictor among all other variables (P&nbsp;=&nbsp;.03; 92% selection). Patients with AML report improved QoL after treatment, despite higher mean out‐of‐pocket expenditures compared with MDS (up to $599 CDN/month for AML vs$239 for MDS;&nbsp;P&nbsp;=&nbsp;.05), greater loss of productivity‐related income (reaching id="mce_marker"786/month for AML vs $709 for MDS;&nbsp;P&nbsp;&lt;&nbsp;.05), and greater caregiver effects (65%&nbsp;vs 35% caregiver productivity losses for AML vs MDS;&nbsp;P&nbsp;&lt;&nbsp;.05). Our results suggest that including patient‐reported QoL and socioeconomic indicators can improve the accuracy of survival models

Antibodies in healthcare personnel following severe acute respiratory syndrome coronavirus virus 2 (SARS-CoV-2) infection

In a prospective cohort of healthcare personnel (HCP), we measured severe acute respiratory syndrome coronavirus virus 2 (SARS-CoV-2) nucleocapsid IgG antibodies after SARS-CoV-2 infection. Among 79 HCP, 68 (86%) were seropositive 14-28 days after their positive PCR test, and 54 (77%) of 70 were seropositive at the 70-180-day follow-up. Many seropositive HCP (95%) experienced an antibody decline by the second visit