A Regional, Early Spring Bloom of Phaeocystis pouchetii on the New England Continental Shelf

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 \u3e 95 μmol L−1. Initially, the bloom was largely confined to waters with temperatures \u3c6°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

Finding Data Compatibility Bugs with JSON Subschema Checking

JSON is a data format used pervasively in web APIs, cloud computing, NoSQL databases, and increasingly also machine learning. To ensure that JSON data is compatible with an application, one can define a JSON schema and use a validator to check data against the schema. However, because validation can happen only once concrete data occurs during an execution, it may detect data compatibility bugs too late or not at all. Examples include evolving the schema for a web API, which may unexpectedly break client applications, or accidentally running a machine learning pipeline on incorrect data. This paper presents a novel way of detecting a class of data compatibility bugs via JSON subschema checking. Subschema checks find bugs before concrete JSON data is available and across all possible data specified by a schema. For example, one can check if evolving a schema would break API clients or if two components of a machine learning pipeline have incompatible expectations about data. Deciding whether one JSON schema is a subschema of another is non-trivial because the JSON Schema specification language is rich. Our key insight to address this challenge is to first reduce the richness of schemas by canonicalizing and simplifying them, and to then reason about the subschema question on simpler schema fragments using type-specific checkers. We apply our subschema checker to thousands of real-world schemas from different domains. In all experiments, the approach is correct whenever it gives an answer (100% precision and correctness), which is the case for most schema pairs (93.5% recall), clearly outperforming the state-of-the-art tool. Moreover, the approach reveals 43 previously unknown bugs in popular software, most of which have already been fixed, showing that JSON subschema checking helps finding data compatibility bugs early

Diatom hotspots driven by western boundary current instability

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 Geophysical Research Letters 48(11), (2021): e2020GL091943, https://doi.org/10.1029/2020GL091943.Climatic changes have decreased the stability of the Gulf Stream (GS), increasing the frequency at which its meanders interact with the Mid-Atlantic Bight (MAB) continental shelf and slope region. These intrusions are thought to suppress biological productivity by transporting low-nutrient water to the otherwise productive shelf edge region. Here we present evidence of widespread, anomalously intense subsurface diatom hotspots in the MAB slope sea that likely resulted from a GS intrusion in July 2019. The hotspots (at ∼50 m) were associated with water mass properties characteristic of GS water (∼100 m); it is probable that the hotspots resulted from the upwelling of GS water during its transport into the slope sea, likely by a GS meander directly intruding onto the continental slope east of where the hotspots were observed. Further work is required to unravel how increasingly frequent direct GS intrusions could influence MAB marine ecosystems.This research was supported by the National Science Foundation (OCE-1657803 and OCE-1657855) and the Dalio Explorer Fund. H. Oliver was supported by a WHOI Postdoctoral Scholar award

Diatom Hotspots Driven by Western Boundary Current Instability

Abstract Climatic changes have decreased the stability of the Gulf Stream (GS), increasing the frequency at which its meanders interact with the Mid-Atlantic Bight (MAB) continental shelf and slope region. These intrusions are thought to suppress biological productivity by transporting low-nutrient water to the otherwise productive shelf edge region. Here we present evidence of widespread, anomalously intense subsurface diatom hotspots in the MAB slope sea that likely resulted from a GS intrusion in July 2019. The hotspots (at ∼50 m) were associated with water mass properties characteristic of GS water (∼100 m); it is probable that the hotspots resulted from the upwelling of GS water during its transport into the slope sea, likely by a GS meander directly intruding onto the continental slope east of where the hotspots were observed. Further work is required to unravel how increasingly frequent direct GS intrusions could influence MAB marine ecosystems

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

Infection Risk in the First Year After ABO-incompatible Kidney Transplantation: A Nationwide Prospective Cohort Study.

BACKGROUND ABO-incompatible (ABOi) kidney transplantation (KT) expands the kidney donor pool and may help to overcome organ shortage. Nonetheless, concerns about infectious complications associated with ABOi-KT have been raised. METHODS In a nationwide cohort (Swiss Transplant Cohort Study), we compared the risk for infectious complications among ABOi and ABO-compatible (ABOc) renal transplant recipients. Infections needed to fulfill rigorous, prespecified criteria to be classified as clinically relevant. Unadjusted and adjusted competing risk regression models were used to compare the time to the first clinically relevant infection among ABOi-KT and ABOc-KT recipients. Inverse probability weighted generalized mixed-effects Poisson regression was used to estimate incidence rate ratios for infection. RESULTS We included 757 living-donor KT recipients (639 ABOc; 118 ABOi) and identified 717 infection episodes. The spectrum of causative pathogens and the anatomical sites affected by infections were similar between ABOi-KT and ABOc-KT recipients. There was no significant difference in time to first posttransplant infection between ABOi-KT and ABOc-KT recipients (subhazard ratio, 1.24; 95% confidence interval [CI], 0.93-1.66; P = 0.142). At 1 y, the crude infection rate was 1.11 (95% CI, 0.93-1.33) episodes per patient-year for ABOi patients and 0.94 (95% CI, 0.86-1.01) for ABOc-KT recipients. Inverse probability weighted infection rates were similar between groups (adjusted incidence rate ratio, 1.12; 95% CI, 0.83-1.52; P = 0.461). CONCLUSIONS The burden of infections during the first year posttransplant was high but not relevantly different in ABOi-KT and ABOc-KT recipients. Our results highlight that concerns regarding infectious complications should not affect the implementation of ABOi-KT programs

Trajectories of humoral and cellular immunity and responses to a third dose of mRNA vaccines against SARS-CoV-2 in patients with a history of anti-CD20 therapy.

BACKGROUND The majority of patients with B-cell-depleting therapies show compromised vaccination-induced immune responses. Herein, we report on the trajectories of anti-SARS-CoV-2 immune responses in patients of the RituxiVac study compared with healthy volunteers and investigate the immunogenicity of a third vaccination in previously humoral non-responding patients. METHODS We investigated the humoral and cell-mediated immune response after SARS-CoV-2 messanger RNA vaccination in patients with a history with anti-CD20 therapies. Coprimary outcomes were antispike and SARS-CoV-2-stimulated interferon-γ concentrations in vaccine responders 4.3 months (median; IQR: 3.6-4.8 months) after first evaluation, and humoral and cell-mediated immunity (CMI) after a third vaccine dose in previous humoral non-responders. Immunity decay rates were compared using analysis of covariance in linear regression. RESULTS 5.6 months (IQR: 5.1-6.7) after the second vaccination, we detected antispike IgG in 88% (29/33) and CMI in 44% (14/32) of patients with a humoral response after two-dose vaccination compared with 92% (24/26) healthy volunteers with antispike IgG and 69% (11/16) with CMI 6.8 months after the second vaccination (IQR: 6.0-7.1). Decay rates of antibody concentrations were comparable between patients and controls (p=0.70). In two-dose non-responders, a third SARS-CoV-2 vaccine elicited humoral responses in 19% (6/32) and CMI in 32% (10/31) participants. CONCLUSION This study reveals comparable immunity decay rates between patients with anti-CD20 treatments and healthy volunteers, but inefficient humoral or CMI after a third SARS-CoV-2 vaccine in most two-dose humoral non-responders calling for individually tailored vaccination strategies in this population.Trial registration numberNCT04877496; ClinicalTrials.gov number

The Evolutionary Pathway to Obligate Scavenging in Gyps Vultures

The evolutionary pathway to obligate scavenging in Gyps vultures remains unclear. We propose that communal roosting plays a central role in setting up the information transfer network critical for obligate scavengers in ephemeral environments and that the formation of a flotilla-like foraging group is a likely strategy for foraging Gyps vultures. Using a spatial, individual-based, optimisation model we find that the communal roost is critical for establishing the information network that enables information transfer owing to the spatial-concentration of foragers close to the roost. There is also strong selection pressure for grouping behaviour owing to the importance of maintaining network integrity and hence information transfer during foraging. We present a simple mechanism for grouping, common in many animal species, which has the added implication that it negates the requirement for roost-centric information transfer. The formation of a flotilla-like foraging group also improves foraging efficiency through the reduction of overlapping search paths. Finally, we highlight the importance of consideration of information transfer mechanisms in order to maximise the success of vulture reintroduction programmes

Physical and Biological Processes at the Middle Atlantic Bight Shelf-Break Front

The Middle Atlantic Bight (MAB) is a highly productive ecosystem, supporting several economically important commercial fisheries. Chlorophyll enhancement at the MAB shelf-break front has been observed only intermittently, despite numerous studies that suggest persistent upwelling at the front. High resolution cross-frontal transect crossings were collected from three two-week cruises in April 2018, May 2019, and July 2019. Chapter 2 focused on applying a novel method of classifying planktonic images taken by a Video Plankton Recorder to enable processing of the large volumes of data collected with the instrument. Chapter 3 investigated cross-frontal trends by temporally averaging in both Eulerian and frontally-aligned coordinates. For April 2018, transient chlorophyll enhancement was seen at the front in individual transects and within the frontally-aligned mean transect, but not within the Eulerian mean transect. The Eulerian mean for May 2019 showed chlorophyll enhancement as a result of frontal eddies, which were further explored in chapter 4. No frontal enhancement was observed in July 2019. The frontal eddies observed in May 2019 were simulated using an idealized model, which showed that upwelling occurred within both of the frontal eddies, despite having opposite rotational directions. This result was consistent with nutrient enhancement observed within the centers of both eddies. Biological enhancement within each eddy was observed, which may have been a result of advection from source waters and/or a local response to upwelled nutrients. The influence of frontal variability and frontal eddies on nutrients and plankton at the front argues for the necessity for 3-D models to fully explain frontal behavior and its effects on biological responses.Ph.D