Analysis of Legacy and Novel Neutral Per- and Polyfluoroalkyl Substances in Soils from an Industrial Manufacturing Facility.

Per- and polyfluoroalkyl substances (PFASs) have been detected in an array of environmental media due to their ubiquitous use in industrial and consumer products as well as potential release from fluorochemical manufacturing facilities. During their manufacture, many fluorotelomer (FT) facilities rely on neutral intermediates in polymer production including the FT-alcohols (FTOHs). These PFAS are known to transform to the terminal acids (perfluoro carboxylic acids; PFCAs) at rates that vary with environmental conditions. In the current study on soils from a FT facility, we employed gas chromatography coupled with conventional- and high-resolution mass spectrometry (GC-MS and GC-HRMS) to investigate the profile of these precursor compounds, the intermediary secondary alcohols (sFTOHs), FT-acrylates (FTAcr), and FT-acetates (FTAce) in soils around the former FT-production facility. Of these precursors, the general trend in detection intensity was [FTOHs] > [sFTOHs] > [FTAcrs], while for the FTOHs, homologue intensities generally were [12:2 FTOH] > [14:2 FTOH] > [16:2 FTOH] > [10:2 FTOH] > [18:2 FTOH] > [20:2 FTOH] > [8:2 FTOH] ∼ [6:2 FTOH]. The corresponding terminal acids were also detected in all soil samples and positively correlated with the precursor concentrations. GC-HRMS confirmed the presence of industrial manufacturing byproducts such as FT-ethers and FT-esters and aided in the tentative identification of previously unreported dimers and other compounds. The application of GC-HRMS to the measurement and identification of precursor PFAS is in its infancy, but the methodologies described here will help refine its use in tentatively identifying these compounds in the environment.

Impact of Hurricanes, Tropical Storms, and Coastal Extratropical Storms on Indoor Air VOC Concentrations.

Understanding vapor intrusion (VI) temporal variability is key for the design of sampling strategies intended to assess reasonable maximum exposure of indoor air concentrations of volatile organic compounds (VOCs) as well as risk evaluation and mitigation planning. VI temporal variability has previously been shown to be dependent on the complex interactions of multiple independent variables-meteorological, hydrogeological, and human behavioral. Several meteorological variables, including barometric pressure, wind speed, and rainfall, are linked during tropical and extratropical storm events. High-frequency meteorological and indoor VOC data from a series of seven tropical storms and four extratropical storms were collected at a single industrial building with multiple heating, ventilation, and air conditioning (HVAC) zones. The storms and sampling zones showed a variety of effects on trichloroethylene (TCE) concentrations in indoor air. In one zone (supply room), increases in TCE concentrations often, but not always, closely coincided with decreasing barometric pressure, sustained wind speeds over 32 km/h (20 mph), and differential pressures indicating subslab to indoor flow. A second zone, in a restroom, did not show a consistent pattern of temporal correlation between meteorological factors and indoor air concentrations. While peak indoor air concentrations may be associated with the passage of cyclonic storms at some sampling locations, this does not appear to be generalizable to all sampling locations. The observed increase in indoor air concentration potentially attributable to these storms is typically less than an order of magnitude and the duration ranges from a day to a week.

Aboriginal mitogenomes reveal 50,000 years of regionalism in Australia.

Aboriginal Australians represent one of the longest continuous cultural complexes known. Archaeological evidence indicates that Australia and New Guinea were initially settled approximately 50 thousand years ago (ka); however, little is known about the processes underlying the enormous linguistic and phenotypic diversity within Australia. Here we report 111 mitochondrial genomes (mitogenomes) from historical Aboriginal Australian hair samples, whose origins enable us to reconstruct Australian phylogeographic history before European settlement. Marked geographic patterns and deep splits across the major mitochondrial haplogroups imply that the settlement of Australia comprised a single, rapid migration along the east and west coasts that reached southern Australia by 49-45 ka. After continent-wide colonization, strong regional patterns developed and these have survived despite substantial climatic and cultural change during the late Pleistocene and Holocene epochs. Remarkably, we find evidence for the continuous presence of populations in discrete geographic areas dating back to around 50 ka, in agreement with the notable Aboriginal Australian cultural attachment to their country.

Seamount coral reefs are egg case nurseries for deep-sea skates.

Egg case nurseries of the boreal skate (Amblyraja hyperborea) and Richardson's skate (Bathyraja richardsoni) were defined and mapped on a bathyal seascape (c. 500-1900 m depths) south of Tasmania, Australia, using 99 towed-camera transects (157 linear km; N = 50,858 images). In total, 738 skate egg cases were observed (present in 240 images, absent in 50,618); among 113 egg cases examined to identify parent species, 70% were A. hyperborea, 10% B. richardsoni and 20% unidentified Bathyraja species. "Recently laid" egg cases were differentiated from "aged" ones by classifying their colour and condition. The great majority (98%) of egg cases were observed in c. 1100-1400 m depths on seamounts (15 of 36 surveyed), not seamount bases or adjacent continental slope. Egg cases were associated with reefs formed by accumulated skeletal matrix of the stony coral Solenosmilia variabilis, with >90% egg cases (including most of those recently laid) observed on living S. variabilis that characterises a "coral zone" in c. 950-1350 m depths. Water in the coral zone is warmer (+0.66 to 2.37°C) than at the deep distributional limits of adult A. hyperborea and B. richardsoni (2000 and 3000 m, respectively), potentially providing for accelerated embryonic development. Co-occurrence with living coral infers an energetically favourable local-scale hydrodynamic environment for egg cases, particularly on seamount peaks, where increased water flow over egg cases would avert smothering by suspended sediment, and compensate for lower oxygen concentration compared to deeper depths occupied by adult skates. Criteria identifying egg case nurseries are strongly met for A. hyperborea at Seamount Z110 (468 egg cases of varied ages, maximum density of 5.47 m-2 ) and to a lesser extent on five others (Seamounts K1, Z16, Hill U, Z5 and Hill V). An abundance (density) criterion for defining nurseries needs to be flexible because it is a spatially scale-dependent measure that differs between surveys according to the tools and design employed. Off Australia, coral reef egg case nursery habitat is restricted to a narrow depth range in temperate latitudes where it is scarce and impacted by historical bottom trawl fishing in many locations. There has been effective conservation of nursery habitat, however, because four of the six nursery sites identified here and extensive coral reef areas are protected within marine parks.

HIV incidence in US first-time blood donors and transfusion risk with a 12-month deferral for men who have sex with men.

In 2015, the US Food and Drug Administration published revised guidance that recommended a change in blood donor deferral of men who have sex with men (MSM) from an indefinite to a 12-month deferral since the donor last had sex with a man. We assessed whether HIV incidence in first-time blood donors or associated transfusion risk increased. Donations in 4 major blood collection organizations were monitored for 15 months before and 2 years after implementation of the 12-month MSM deferral policy. HIV-positive donations were classified as recently acquired or long-term using a recent infection testing algorithm and incidence in both periods estimated. Residual transfusion transmission risk was estimated by multiplying incidence by the length of the infectious window period. The latter was estimated using a model based on infectious dose and the sensitivity of nucleic acid testing. Factors associated with incident infection in each period were assessed using Poisson regression. Overall HIV incidence in first-time donors before implementation of the 12-month MSM deferral was estimated at 2.62 cases per 100 000 person-years (105 PY) (95% credible interval [CI], 1.53-3.93 cases/105 PY), and after implementation at 2.85 cases/105 PY (95% CI, 1.96-3.93 cases/105 PY), with no statistically significant change. In male first-time donors, the incidence difference was 0.93 cases/105 PY (95% CI, -1.74-3.58 cases/105 PY). The residual risk of HIV transfusion transmission through components sourced from first-time donors was estimated at 0.32 transmissions per million (106) packed red blood cell transfusions (95% CI, 0.29-0.65 transmissions/106 transfusions) before and 0.35 transmissions/106 transfusions (95% CI, 0.31-0.65 transmissions/106 transfusions) after implementation. The difference was not statistically significant. Factors associated with incident infection were the same in each period. We observed no increase in HIV incidence or HIV transfusion transmission risk after implementation of a 12-month MSM deferral policy.

HIV antiretroviral therapy and prevention use in US blood donors: a new blood safety concern.

Antiretroviral therapy (ART) to treat and pre-exposure prophylaxis (PrEP) to prevent HIV infection are effective tools to help end the HIV epidemic. However, their use could affect HIV transfusion-transmission risk. Three different ART/PrEP prevalence analyses in blood donors were conducted. First, blood samples from HIV-positive and a comparison group of infection-nonreactive donors were tested under blind using liquid chromatography-tandem mass spectrometry for ART. Second, blood donor samples from infection-nonreactive, 18- to 45-year-old, male, first-time blood donors in 6 US locations were tested for emtricitabine and tenofovir. Third, in men who have sex with men (MSM) participating in the 2017 Centers for Disease Control and Prevention National HIV Behavioral Surveillance (NHBS) from 5 US cities, self-reported PrEP use proximate to donation was assessed. In blind testing, no ART was detected in 300 infection-nonreactive donor samples, but in 299 HIV confirmed-infected donor samples, 46 (15.4%; 95% confidence interval [CI], 11.5% to 20.0%) had evidence of ART. Of the 1494 samples tested from first-time male donors, 9 (0.6%; 95% CI, 0.03% to 1.1%) had tenofovir and emtricitabine. In the NHBS MSM survey, 27 of 591 respondents (4.8%; 95% CI, 3.2% to 6.9%) reported donating blood in 2016 or 2017 and PrEP use within the same time frame as blood donation. Persons who are HIV positive and taking ART and persons taking PrEP to prevent HIV infection are donating blood. Both situations could lead to increased risk of HIV transfusion transmission if blood screening assays are unable to detect HIV in donations from infected donors.

Detection of allergic transfusion-related adverse events from electronic medical records.

BACKGROUND: Transfusion-related adverse events can be unrecognized and unreported. As part of the US Food and Drug Administration's Center for Biologics Evaluation and Research Biologics Effectiveness and Safety initiative, we explored whether machine learning methods, such as natural language processing (NLP), can identify and report transfusion allergic reactions (ARs) from electronic health records (EHRs). STUDY DESIGN AND METHODS: In a 4-year period, all 146 reported transfusion ARs were pulled from a database of 86,764 transfusions in an academic health system, along with a random sample of 605 transfusions without reported ARs. Structured and unstructured EHR data were retrieved, including demographics, new symptoms, medications, and lab results. In unstructured data, evidence from clinicians' notes, test results, and prescriptions fields identified transfusion ARs, which were used to extract NLP features. Clinician reviews of selected validation cases assessed and confirmed model performance. RESULTS: Clinician reviews of selected validation cases yielded a sensitivity of 67.9% and a specificity of 97.5% at a threshold of 0.9, with a positive predictive value (PPV) of 84%, estimated to 4.5% when extrapolated to match transfusion AR incidence in the full transfusion dataset. A higher threshold achieved sensitivity of 43% with specificity/PPV of 100% in our validation set. Essential features predicting ARs were recognized transfusion reactions, administration of antihistamines or glucocorticoids, and skin symptoms (e.g., hives and itching). Removal of NLP features decreased model performance. DISCUSSION: NLP algorithms can identify transfusion reactions from the EHR with a reasonable level of precision for subsequent clinician review and confirmation.

HIV, HCV, and HBV incidence and residual risk in US blood donors before and after implementation of the 12-month deferral policy for men who have sex with men.

BACKGROUND: In December 2015, the men who have sex with men (MSM) deferral was reduced to 12 months in the United States. We compared human immunodeficiency virus (HIV), hepatitis C virus (HCV), and hepatitis B virus (HBV) incidence and residual risk before and after this policy change using data from >50% of the US blood supply. STUDY DESIGN AND METHODS: Three estimation intervals from the Transfusion-Transmissible Infections Monitoring System were compared: 15-months pre- and two consecutive, nonoverlapping 15-month post-MSM deferral implementation. Repeat, first-time, and weighted all-donor incidences were estimated. Residual risk was calculated for all incidence estimates using the incidence/window-period method. RESULTS: HIV repeat donor incidence was 1.57 per 100 000 person-years (phtpy) in the second 15-month post change and not significantly different from pre-MSM incidence of 2.19 phtpy. Similar values were seen for HCV (1.49 phtpy vs 1.46 phtpy) and HBV (1.14 phtpy vs 0.97 phtpy). In some cases, higher estimated incidence, but without significant change from pre-MSM to the second post change period occurred for males and first-time donors (eg, first-time donors, second post change period: 6.12 phtpy HIV, 6.41 phtpy HCV and 5.34 phtpy HBV). Estimated per donation residual risk was 1:1.6 million for HIV, 1:2.0 million for HCV and 1:1.0 million for HBV based on weighted incidence for all donors. CONCLUSIONS: Repeat, first-time, and overall donor incidence did not vary significantly comparing pre-MSM to either of the post-MSM estimation intervals. Residual risk estimates vary by study, but all yield residual risks in the United States of ≤1 per million, and thus far have not shown increasing risk with the 12-month MSM policy change.

When did Homo sapiens first reach Southeast Asia and Sahul?

Anatomically modern humans (Homo sapiens, AMH) began spreading across Eurasia from Africa and adjacent Southwest Asia about 50,000-55,000 years ago (ca 50-55 ka). Some have argued that human genetic, fossil, and archaeological data indicate one or more prior dispersals, possibly as early as 120 ka. A recently reported age estimate of 65 ka for Madjedbebe, an archaeological site in northern Sahul (Pleistocene Australia-New Guinea), if correct, offers what might be the strongest support yet presented for a pre-55-ka African AMH exodus. We review evidence for AMH arrival on an arc spanning South China through Sahul and then evaluate data from Madjedbebe. We find that an age estimate of >50 ka for this site is unlikely to be valid. While AMH may have moved far beyond Africa well before 50-55 ka, data from the region of interest offered in support of this idea are not compelling.

Elephants in the Room, Part 1: Protons in Redox Reactions.

Many oxidation and reduction reactions involve transfer of both electrons and protons. It is shown how this arises and how the energetics may be understood.

Chemical Education.

The transfer of electrons and protons is compared. Electron transfer over long distances is possible through a series of relays. The range of proton transfer is an order of magnitude less than for electrons but it may be directed along hydrogen bonds.

Prevalence of human immunodeficiency virus, hepatitis B virus, and hepatitis C virus in United States blood donations, 2015 to 2019: The Transfusion-Transmissible Infections Monitoring System (TTIMS).

BACKGROUND: The Transfusion-Transmissible Infections Monitoring System (TTIMS) combines data from four US blood collection organizations including approximately 60% of all donations to monitor demographic and temporal trends in infectious disease markers and policy impacts. STUDY DESIGN AND METHODS: Human immunodeficiency virus (HIV), hepatitis B virus (HBV), and hepatitis C virus (HCV) consensus-positive definitions combined serology and nucleic acid testing results. These along with donor and donation characteristics were assembled into a single data set. Overall donation prevalence and demographic subsets were compared pre- and post-implementation of the 2015 change in men who have sex with men (MSM) deferral policy, among other prevalence comparisons. RESULTS: From October 2015 to September 2019, there were 712 HIV-, 1735 HBV-, and 5217 HCV-positive samples identified from approximately 27.5 million donations (>9.4 million donors). Prevalences per 100 000 donations were 2.6 (HIV), 6.3 (HBV), and 19.0 (HCV), and the highest for all three agents were in donations from first-time male donors. Two slight but significant increases in HIV prevalence were observed, both for comparisons of Year 1 (pre-MSM policy change) versus Year 4 (post-MSM policy change) for first-time males and first-time females; in contrast, similar comparisons demonstrated decreases in HCV prevalence (all donors and general trends for males and females). Except for HIV, prevalence increased with age; for all agents, prevalence was markedly higher in the south. CONCLUSIONS: No major trends were observed over 4 years covering the MSM policy change from indefinite to a 12-month deferral, but ongoing monitoring is warranted. Demographic trends are consistent with those observed in other donor studies and community trends.

Recently acquired infection among HIV-seropositive donors in the US from 2010-2018.

BACKGROUND: Monitoring of transfusion-transmissible infections in the blood supply is essential for blood safety, as the donor population is not static, and changes in policy, donor behavior, or other factors could increase the risk of recipient infection. We assessed patterns of recently acquired HIV infection in US blood donors, including before and after the implementation of the 12-month deferral for men who have sex with men (MSM). STUDY DESIGN AND METHODS: A large convenience sample of donations from donors testing HIV-1 nucleic acid testing (NAT) and serology-reactive were further tested with the Sedia HIV-1 Limiting Antigen enzyme immunoassay. Samples were analyzed across available demographic and donation data to provide an assessment of recently acquired HIV infection in US blood donors from 2010 to 2018. RESULTS: Overall, 317 of 1154 (27.5%; 95% confidence interval, 24.9%-30.1%) donations from HIV NAT and serology-reactive donors had recently acquired HIV infection. There was no evidence of change in the percentages of recent HIV infection by year over the study period, either in all donors or in male donors, including after the MSM policy change. In multivariable logistic regression analysis, donors aged 24 years or younger were over 2.7 times more likely and repeat donors 2.2 times more likely to have recently acquired HIV infection compared to donors aged 55 years or older and first-time donors, respectively. CONCLUSION: Patterns of recently acquired HIV infection varied by demographics but not over time. These findings suggest no impact of the MSM policy change on recently acquired HIV infection in US blood donors.

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data.

In many disciplines, data are highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such databases depends on the discipline of data science and on the humble bricks and mortar that make integration possible; identifiers are a core component of this integration infrastructure. Drawing on our experience and on work by other groups, we outline 10 lessons we have learned about the identifier qualities and best practices that facilitate large-scale data integration. Specifically, we propose actions that identifier practitioners (database providers) should take in the design, provision and reuse of identifiers. We also outline the important considerations for those referencing identifiers in various circumstances, including by authors and data generators. While the importance and relevance of each lesson will vary by context, there is a need for increased awareness about how to avoid and manage common identifier problems, especially those related to persistence and web-accessibility/resolvability. We focus strongly on web-based identifiers in the life sciences; however, the principles are broadly relevant to other disciplines.

Baseline characterization of aerobic hydrocarbon degrading microbial communities in deep-sea sediments of the Great Australian Bight, Australia.

Exploratory drilling for deep-sea oil and gas resources is planned for the Great Australian Bight (GAB). There is scant knowledge of the region's benthic ecosystems and no baseline information of the region's indigenous oil degrading bacteria. To address this knowledge gap, we used next generation sequencing (NGS) of three marker genes (alkB, c23o and pmoA) to detect and characterize the microbial communities capable of aerobic hydrocarbon degradation. Unique, highly novel microbial communities capable of degrading hydrocarbons occur in surface sediments at depths between 200 and 2800 m. Clustering at 97% demonstrated differences in community structure with depth, changing most markedly between 400 and 1000 m depth on the continental slope, and identified putative functional 'ecotypes' related to depth. Observed differences in community structure showed strong correlations with temperature, other physicochemical properties of the overlying water column and are further modulated by differences in sediment grain size. This study provides important baseline data on hydrocarbon degrading microbial communities prior to the start of petroleum resource extraction. Our data will inform future ecological monitoring of the GAB deep-sea ecosystem.

PartsGenie: an integrated tool for optimizing and sharing synthetic biology parts.

Motivation: Synthetic biology is typified by developing novel genetic constructs from the assembly of reusable synthetic DNA parts, which contain one or more features such as promoters, ribosome binding sites, coding sequences and terminators. PartsGenie is introduced to facilitate the computational design of such synthetic biology parts, bridging the gap between optimization tools for the design of novel parts, the representation of such parts in community-developed data standards such as Synthetic Biology Open Language, and their sharing in journal-recommended data repositories. Consisting of a drag-and-drop web interface, a number of DNA optimization algorithms, and an interface to the well-used data repository JBEI ICE, PartsGenie facilitates the design, optimization and dissemination of reusable synthetic biology parts through an integrated application. Availability and implementation: PartsGenie is freely available at https://parts.synbiochem.co.uk.

FAIRDOMHub: a repository and collaboration environment for sharing systems biology research.

The FAIRDOMHub is a repository for publishing FAIR (Findable, Accessible, Interoperable and Reusable) Data, Operating procedures and Models (https://fairdomhub.org/) for the Systems Biology community. It is a web-accessible repository for storing and sharing systems biology research assets. It enables researchers to organize, share and publish data, models and protocols, interlink them in the context of the systems biology investigations that produced them, and to interrogate them via API interfaces. By using the FAIRDOMHub, researchers can achieve more effective exchange with geographically distributed collaborators during projects, ensure results are sustained and preserved and generate reproducible publications that adhere to the FAIR guiding principles of data stewardship.

Activity modification in heat: critical assessment of guidelines across athletic, occupational, and military settings in the USA.

Exertional heat illness (EHI) risk is a serious concern among athletes, laborers, and warfighters. US Governing organizations have established various activity modification guidelines (AMGs) and other risk mitigation plans to help ensure the health and safety of their workers. The extent of metabolic heat production and heat gain that ensue from their work are the core reasons for EHI in the aforementioned population. Therefore, the major focus of AMGs in all settings is to modulate the work intensity and duration with additional modification in adjustable extrinsic risk factors (e.g., clothing, equipment) and intrinsic risk factors (e.g., heat acclimatization, fitness, hydration status). Future studies should continue to integrate more physiological (e.g., valid body fluid balance, internal body temperature) and biometeorological factors (e.g., cumulative heat stress) to the existing heat risk assessment models to reduce the assumptions and limitations in them. Future interagency collaboration to advance heat mitigation plans among physically active population is desired to maximize the existing resources and data to facilitate advancement in AMGs for environmental heat.

The Gestation and Growth of the Periodic Table.

The development of ideas of chemical periodicity from Lavoisier to Mendeleyev's first periodic table of 1869 is surveyed. Although his first periodic table contained a number of errors and weaknesses, his remarkable predictions of the properties of several then unknown elements, together with his capacity to adapt the table to new discoveries, slowly led to its general acceptance. The theory of atomic structure slowly developed to a point where it could rationalise the structure of the table which had, however, been established solely on the basis of experimental observations. Chemistry has played the central role, up to and including the final modification of Seaborg to introduce the actinides - although this had been foreseen by Alfred Werner! Finally we discuss the many physical forms in which the table has been presented.

Calsequestrin interacts directly with the cardiac ryanodine receptor luminal domain.

Cardiac muscle contraction requires sarcoplasmic reticulum (SR) Ca2+ release mediated by the quaternary complex comprising the ryanodine receptor 2 (RyR2), calsequestrin 2 (CSQ2), junctin (encoded by ASPH) and triadin. Here, we demonstrate that a direct interaction exists between RyR2 and CSQ2. Topologically, CSQ2 binding occurs at the first luminal loop of RyR2. Co-expression of RyR2 and CSQ2 in a human cell line devoid of the other quaternary complex proteins results in altered Ca2+-release dynamics compared to cells expressing RyR2 only. These findings provide a new perspective for understanding the SR luminal Ca2+ sensor and its involvement in cardiac physiology and disease.