The importance of benthic-pelagic coupling for marine ecosystem functioning in a changing world.

Benthic-pelagic coupling is manifested as the exchange of energy, mass, or nutrients between benthic and pelagic habitats. It plays a prominent role in aquatic ecosystems, and it is crucial to functions from nutrient cycling to energy transfer in food webs. Coastal and estuarine ecosystem structure and function are strongly affected by anthropogenic pressures; however, there are large gaps in our understanding of the responses of inorganic nutrient and organic matter fluxes between benthic habitats and the water column. We illustrate the varied nature of physical and biological benthic-pelagic coupling processes and their potential sensitivity to three anthropogenic pressures - climate change, nutrient loading, and fishing - using the Baltic Sea as a case study and summarize current knowledge on the exchange of inorganic nutrients and organic material between habitats. Traditionally measured benthic-pelagic coupling processes (e.g., nutrient exchange and sedimentation of organic material) are to some extent quantifiable, but the magnitude and variability of biological processes are rarely assessed, preventing quantitative comparisons. Changing oxygen conditions will continue to have widespread effects on the processes that govern inorganic and organic matter exchange among habitats while climate change and nutrient load reductions may have large effects on organic matter sedimentation. Many biological processes (predation, bioturbation) are expected to be sensitive to anthropogenic drivers, but the outcomes for ecosystem function are largely unknown. We emphasize how improved empirical and experimental understanding of benthic-pelagic coupling processes and their variability are necessary to inform models that can quantify the feedbacks among processes and ecosystem responses to a changing world.

Quality assurance in proton beam therapy using a plastic scintillator and a commercially available digital camera.

PURPOSE: In this article, we evaluate a plastic scintillation detector system for quality assurance in proton therapy using a BC-408 plastic scintillator, a commercial camera, and a computer. METHODS: The basic characteristics of the system were assessed in a series of proton irradiations. The reproducibility and response to changes of dose, dose-rate, and proton energy were determined. Photographs of the scintillation light distributions were acquired, and compared with Geant4 Monte Carlo simulations and with depth-dose curves measured with an ionization chamber. A quenching effect was observed at the Bragg peak of the 60 MeV proton beam where less light was produced than expected. We developed an approach using Birks equation to correct for this quenching. We simulated the linear energy transfer (LET) as a function of depth in Geant4 and found Birks constant by comparing the calculated LET and measured scintillation light distribution. We then used the derived value of Birks constant to correct the measured scintillation light distribution for quenching using Geant4. RESULTS: The corrected light output from the scintillator increased linearly with dose. The system is stable and offers short-term reproducibility to within 0.80%. No dose rate dependency was observed in this work. CONCLUSIONS: This approach offers an effective way to correct for quenching, and could provide a method for rapid, convenient, routine quality assurance for clinical proton beams. Furthermore, the system has the advantage of providing 2D visualization of individual radiation fields, with potential application for quality assurance of complex, time-varying fields.

Investigating neuropsychological and reward-related deficits in a chronic corticosterone-induced model of depression.

Chronic stress is a known risk factor for the development of major depression (MDD) and is commonly used to induce a depression-like phenotype in rodents. Similar phenotypic effects are also observed in rodents when treated chronically with the stress hormone corticosterone. In this study, we investigated the neuropsychological consequences of chronic corticosterone treatment in male rats using two translational rodent assays of affective bias, the judgement bias task (JBT) and affective bias test (ABT). We also used the reward learning assay (RLA) and sucrose preference test (SPT) to quantify reward-related behaviours. Negative biases in decision-making were observed in the chronic corticosterone-treated group but only when the treatment was given shortly before each behavioural session. The same dose of corticosterone, when given daily after completion of the behavioural session had no effects. Chronic corticosterone treatment did not potentiate negative affective biases in the ABT induced by either an acute pharmacological or stress manipulation but both reward learning and reward sensitivity were blunted. Analysis of the brain tissue from animals receiving chronic corticosterone found reduced hippocampal neurogenesis consistent with previous studies suggesting corticosterone-induced neurotrophic deficits. Taken together, these data suggest chronic corticosterone treatment induces neuropsychological effects related to changes in reward learning, memory and negative biases in decision making, but these decision-making biases depend on whether rewarding outcomes were experienced during the acute effects of the drug. These findings suggest an important interaction between psychological and biological factors resulting in negative biases in decision-making in this model.

Reasons for non-attendance in youth mental health clinics: Insights from mobile messaging communications.

AIM: Non-attendance at appointments in youth mental health services is a common problem which contributes to reduced service effectiveness and unmet needs. Reasons cited by young people for non-attendance are poorly understood. Information derived from short-message-service (SMS) conversations about appointments between patients and clinicians can uncover new insights about the circumstances leading to 'did not attend' events. METHODS: Text messages between young people and clinicians were examined in a retrospective audit of medical records in two youth mental health services in Perth, Australia. Frequently non-attending young people aged 16-24 (n = 40) engaged in 302 SMS message chains about appointments. Mixed methods included quantitative data and qualitative thematic analysis of textual data. RESULTS: Medical reasons (32/190, 16.8%) and forgetfulness (20/190, 10.5%) were the most frequent reasons for non-attendance. Major issues included non-avoidable events while others were potentially preventable and could be addressed by the service. CONCLUSIONS: The analysis of mobile communications in clinical practice can be used for service evaluation and to reveal barriers that impede attendance to ongoing care.

Homelessness youth and mental health service utilization: A long-term follow-up study.

BACKGROUND: There is currently an incomplete picture of the long-term impact of homelessness on youth with mental health issues. There are also questions regarding homelessness as a predictor of mental health re-admissions. AIMS: To examine the mental health service presentation profile of young people affected by homelessness and mental health issues. METHODS: A retrospective analysis was conducted of the medical records of homeless (n = 29) and non-homeless (n = 32) youth who attended the YouthLink specialist mental health service in 2010. We tracked their pattern of mental health service admissions at five time points during a total period of 10 years, including 2 years prior to, and up to 8 years following the YouthLink presentation. A regression analysis was used to examine factors hypothesized to contribute to mental health re-admissions. RESULTS: Homeless youth had significantly more frequent presentations to inpatient and outpatient mental health services, and emergency departments for mental health reasons. They were 11 times more likely to be re-admitted to a mental health inpatient ward than non-homeless youth. Prior hospital admission was an independent predictor, increasing by a factor of 2.2 for every inpatient admission. CONCLUSION: The impact of homelessness on mental health issues is enduring, and is a long-term predictor of hospital re-admission.

Enhancing Resilience in Canadian Military Families and Communities: A Qualitative Analysis of the Reaching In Reaching Out and Bounce Back and Thrive! Resiliency Skills Training Programs.

Introduction: A new vision of resilience and well-being for Canadian military service members (SMs), Veterans and their families has been championed by the Canadian Armed Forces (CAF) and Veterans Affairs Canada (VAC). Operationalizing this vision, which aims to support those who serve/have served and their families as they navigate life during and post-service, requires the support of service providers (SPs). Training SPs to deliver complementary resilience-training programs Reaching In… Reaching Out (RIRO; for adults working with parents of young children) and Bounce Back and Thrive! (BBT; for parents of children aged 0-8 years of age) may support this vision. Objective: To assess the appropriateness of RIRO/BBT trainer training for SPs, and RIRO and BBT resilience-training for military populations and families. Methods: This qualitative descriptive study involved the delivery of RIRO/BBT trainer training to SPs (n = 20), followed by focus groups (n = 6) with SPs and organisational leaders (n = 4). Focus groups were recorded, and data were transcribed and thematically-analysed. Results: Several themes emerged: (1) RIRO/BBT trainer training enabled SPs to model resilience and deliver the resilience-training programs, (2) training was appropriate and adaptable for the CAF and SMs/CMFs, and (3) training could support the development of resilient communities. Discussion: RIRO/BBT trainer training and RIRO and BBT resilience-training programs use a holistic, integrated, experiential, and community approach to resilience-building and align with CAF and VAC initiatives. Once contextualised, such programs could support resilience-building in the military context.

Resilient Parents Resilient Communities: A Pilot Study Trialing the Bounce Back and Thrive! Resilience-Training Program With Military Families.

INTRODUCTION: The resilience of Canadian military families (CMFs) - the main support of the Canadian Armed Forces service members (SMs) - is imperative. The Canadian Armed Forces aims to ensure that SMs and their families are resilient and SMs ready to respond when called upon for combat, peacekeeping or pandemic/disaster-response. Family concerns, however, can realistically distract SMs from the mission, potentially compromising themselves, their unit and the mission. Resilience-training programs such as Bounce Back and Thrive! (BBT) can help families manage the realities of military life. OBJECTIVE: This pilot study aimed to evaluate suitability of BBT implementation by Military Family Resource Centers (MFRCs), including whether BBT: (1) fosters resilience-building among parents, (2) facilitates CMF resilience-building, (3) can be contextualized for CMFs, and (4) supports MFRCs in cultivating a culture of resilience. METHODS: An exploratory qualitative design was used. BBT was offered to parents face-to-face. Participants completed focus groups after the first 6 sessions, final 4 sessions, and one-year post-intervention. Data was thematically analyzed. RESULTS: Nine military parents participated. Four major themes resulted: (1) military parent resilience-building, (2) CMF resilience-building, (3) BBT program feedback and contextualization, and (4) MFRCs as community resilience hubs. DISCUSSION: BBT enabled parents to gain a new perspective on resilience, engage in dialogue and intentionally role model resilience skills. Military-specific BBT contextualization and online-delivery formats would increase suitability and access for CMFs. Access to resilience programs delivered through MFRCs would support CMFs. Further research is warranted.

Identification of EMS-induced mutations in Drosophila melanogaster by whole-genome sequencing.

Next-generation methods for rapid whole-genome sequencing enable the identification of single-base-pair mutations in Drosophila by comparing a chromosome bearing a new mutation to the unmutagenized sequence. To validate this approach, we sought to identify the molecular lesion responsible for a recessive EMS-induced mutation affecting egg shell morphology by using Illumina next-generation sequencing. After obtaining sufficient sequence from larvae that were homozygous for either wild-type or mutant chromosomes, we obtained high-quality reads for base pairs composing approximately 70% of the third chromosome of both DNA samples. We verified 103 single-base-pair changes between the two chromosomes. Nine changes were nonsynonymous mutations and two were nonsense mutations. One nonsense mutation was in a gene, encore, whose mutations produce an egg shell phenotype also observed in progeny of homozygous mutant mothers. Complementation analysis revealed that the chromosome carried a new functional allele of encore, demonstrating that one round of next-generation sequencing can identify the causative lesion for a phenotype of interest. This new method of whole-genome sequencing represents great promise for mutant mapping in flies, potentially replacing conventional methods.

Limited evidence for common interannual trends in Baltic Sea summer phytoplankton biomass.

The Baltic Sea summer phytoplankton community plays an important role in biogeochemical cycling and in the transfer of energy through the food web via zooplankton. We aimed to improve the understanding of the degree to which large-scale versus local environmental dynamics regulate phytoplankton dynamics by analyzing time series at the Baltic Sea scale. We used dynamic factor analysis to study if there are common patterns of interannual variation that are shared ("common trends") among summer phytoplankton total and class-level biomass time series observed across Baltic Sea latitudinal gradients in salinity and temperature. We evaluated alternative hypotheses regarding common trends among summer phytoplankton biomass: Baltic Sea-wide common trends; common trends by geography (latitude and basin); common trends differing among functional groups (phytoplankton classes); or common trends driven by both geography and functional group. Our results indicated little support for a common trend in total summer phytoplankton biomass. At a finer resolution, classes had common trends that were most closely associated with the cryptophyte and cyanobacteria time series with patterns that differed between northern and southern sampling stations. These common trends were also very sensitive to two anomalous years (1990, 2008) of cryptophyte biomass. The Baltic Sea Index, a regional climate index, was correlated with two common class trends that shifted in mean state around the mid-1990s. The limited coherence in phytoplankton biomass variation over time despite known, large-scale, ecosystem shifts suggests that stochastic dynamics at local scales limits the ability to observe common trends at the scale of monitoring data collection.

Technical Note: Simulation of dose buildup in proton pencil beams.

PURPOSE: The purpose of this study is to characterize the magnitude and depth of dose buildup in pencil beam scanning proton therapy. METHODS: We simulate the integrated depth-dose curve of realistic proton pencil beams in a water phantom using the Geant4 Monte Carlo toolkit. We independently characterize the electronic and protonic components of dose buildup as a function of proton beam energy from 40 to 400 MeV, both with and without an air gap. RESULTS: At clinical energies, electronic buildup over a distance of about 1 mm leads to a dose reduction at depth of the basal layer (0.07 mm) by up to 6% compared to if no buildup effect were present. Protonic buildup reduces the dose to the basal layer by up to 16% and has effects at depths of up to 150 mm. Secondary particles with a mass number A > 1 do not contribute to dose buildup. An air gap of 1 m has no significant effect on protonic buildup but reduces electronic buildup below 1%. CONCLUSIONS: Protonic and electronic dose buildup are relevant for accurate dosimetry in proton therapy although a realistic air gap reduces the electronic buildup to levels where it can be safely neglected. We recommend including electrons and secondary protons in Monte Carlo-based treatment planning systems down to a predicted range of 10-20 µ m in order to accurately model the dose at depths of the basal layer, no matter the size of the air gap between nozzle and patient.

A novel method to remove the background from x-ray diffraction signal.

The first step that is required to extract the correct information from a two-dimensional (2D) diffraction signature is to remove the background accurately. However, direct background subtraction inevitably overcorrects the signal as it does not take into account the attenuation by the sample. Other traditional background removal methods, such as the rolling ball technique, can separate sharp diffraction peaks of crystalline materials from their background. These methods are unsuitable for biological tissue, which is amorphous and does not have sharp diffraction peaks. This technical note proposes a novel method that combines peak fitting and experimental results to estimate the background for 2D XRD signals.

Improved X-ray computed tomography reconstruction of the largest fragment of the Antikythera Mechanism, an ancient Greek astronomical calculator.

The Antikythera Mechanism is an extraordinarily complex ancient Greek astronomical calculating device whose mode of operation is now relatively well understood particularly since imaging studies in 2005 revealed gears and inscriptions which were previously illegible. Unfortunately, the highest resolution X-ray computed tomography image of the largest fragment had some errors which meant that the reconstructed images were not as clear as had been expected. Here, the original X-ray data have been reanalysed and reconstructed. The new X-ray computed tomography images have improved contrast and resolution, leading to better clarity and legibility. The improvement in image quality is characterised and some examples of writing on the Mechanism which can now be read with increased confidence are given.

Providing culturally informed mental health services to Aboriginal youth: The YouthLink model in Western Australia.

AIM: Aboriginal young people are more likely to experience mental health issues and to access mental health services than other young Australians, yet there are few culturally informed mental health programs and services available. This study describes and documents the effectiveness of the culturally sensitive model within YouthLink, a state-wide mental health service program in Western Australia for young people aged 13 to 24 years of age. METHODS: A mixed-method design including a descriptive approach reporting on the YouthLink framework and an empirical research design where 40 Aboriginal clients completed client feedback monitoring measures between 2014 and 2016. RESULTS: The YouthLink culturally informed conceptual framework adheres to best practice principles relevant to work with Indigenous people, family and communities. Aboriginal young people indicated improvement across the treatment period as shown by within-group differences between the first and last session scores on feedback measures. Therapeutic alliance (together with lower baseline acuity and female gender) also contributed significantly to positive treatment outcomes. CONCLUSIONS: Through a strong role of Aboriginal practitioners, relationships with Aboriginal communities, and greater service flexibility that embraces cultural meaning and knowledge, YouthLink has sought to enhance its response to the needs of Aboriginal youth.

Biotic control of stream fluxes: spawning salmon drive nutrient and matter export.

Organisms can control movements of nutrients and matter by physically modifying habitat. We examined how an ecosystem engineer, sockeye salmon (Oncorhynchus nerka), influences seasonal fluxes of sediments, nitrogen (N), and phosphorus (P) in streams of southwestern Alaska. The purpose of this study was to investigate whether salmon act as net importers or net exporters of matter and nutrients from streams and how these roles change as a function of salmon population density. We measured discharge and concentrations of suspended sediments and total N and P every 7-14 days for up to four summers in 10 streams spanning a gradient in salmon densities. We statistically allocated whole-season fluxes to salmon activities, such as excretion and bioturbation, and to export by hydrologic discharge. In addition, we used counts of spawning salmon to estimate nutrient and matter imports by salmon to streams. Large seasonal pulses of suspended sediments, P, and N were associated with salmon spawning activities, often increasing export an order of magnitude higher than during pre-salmon levels. Years and streams with more salmon had significantly higher levels of export of sediments and nutrients. In addition, years with higher precipitation had higher background export of P and N. Salmon exported an average of the equivalent of 189%, 60%, and 55% of total matter, P, and N that salmon imported in their bodies. The relative magnitude of export varied; salmon exported more than their bodies imported in 80%, 20%, and 16% across all streams and years for sediments, P, and N, respectively. A bioassay experiment indicated that the P exported by salmon is directly available for use by primary producers in the downstream lake. These results demonstrate that salmon not only move nutrients upstream on large spatial scales via their migration from the ocean and subsequent death, but also redistribute matter and nutrients on finer spatial scales through their spawning activities.

High-throughput engineering of the mouse genome coupled with high-resolution expression analysis.

One of the most effective approaches for determining gene function involves engineering mice with mutations or deletions in endogenous genes of interest. Historically, this approach has been limited by the difficulty and time required to generate such mice. We describe the development of a high-throughput and largely automated process, termed VelociGene, that uses targeting vectors based on bacterial artificial chromosomes (BACs). VelociGene permits genetic alteration with nucleotide precision, is not limited by the size of desired deletions, does not depend on isogenicity or on positive-negative selection, and can precisely replace the gene of interest with a reporter that allows for high-resolution localization of target-gene expression. We describe custom genetic alterations for hundreds of genes, corresponding to about 0.5-1.0% of the entire genome. We also provide dozens of informative expression patterns involving cells in the nervous system, immune system, vasculature, skeleton, fat and other tissues.

Development of a method to quantify gene expression levels for glycosylation pathway genes in chinese hamster ovary cell cultures.

Changes in protein glycosylation owing to changes in environmental conditions are not well understood. To better understand these relationships, methods to quantify controlling factors are needed. Because enzymes are translated from genes, the ability to quantify gene expression levels for glycosylation-related enzymes would be advantageous. We developed quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) assays to monitor gene expression in Chinese hamster ovary (CHO) cells for five terminal glycosylation genes. The five enzymes were sialidase, a putative alpha2,3-sialyltransferase, beta1,4-galactosyltransferase, cytosine monophosphate-sialic acid transporter, and uracil diphosphate-galactosyl transporter. Four of these CHO cell genes were publicly available from GenBank; however, the alpha2,3-sialyltransferase gene for Cricetulus griseus (CHO cell species) was not available and, therefore, was sequenced as a part of this work. The qRT-PCR primers and probes (based on the TaqMan chemistry) were designed and validated for these five genes. The gene expression profiles were obtained for CHO cells producing the recombinant interleukin-4/13 cytokine trap molecule in batch reactors.

Performance of salmon fishery portfolios across western North America.

Quantifying the variability in the delivery of ecosystem services across the landscape can be used to set appropriate management targets, evaluate resilience and target conservation efforts. Ecosystem functions and services may exhibit portfolio-type dynamics, whereby diversity within lower levels promotes stability at more aggregated levels. Portfolio theory provides a framework to characterize the relative performance among ecosystems and the processes that drive differences in performance. We assessed Pacific salmon Oncorhynchus spp. portfolio performance across their native latitudinal range focusing on the reliability of salmon returns as a metric with which to assess the function of salmon ecosystems and their services to humans. We used the Sharpe ratio (e.g. the size of the total salmon return to the portfolio relative to its variability (risk)) to evaluate the performance of Chinook and sockeye salmon portfolios across the west coast of North America. We evaluated the effects on portfolio performance from the variance of and covariance among salmon returns within each portfolio, and the association between portfolio performance and watershed attributes. We found a positive latitudinal trend in the risk-adjusted performance of Chinook and sockeye salmon portfolios that also correlated negatively with anthropogenic impact on watersheds (e.g. dams and land-use change). High-latitude Chinook salmon portfolios were on average 2·5 times more reliable, and their portfolio risk was mainly due to low variance in the individual assets. Sockeye salmon portfolios were also more reliable at higher latitudes, but sources of risk varied among the highest performing portfolios. Synthesis and applications. Portfolio theory provides a straightforward method for characterizing the resilience of salmon ecosystems and their services. Natural variability in portfolio performance among undeveloped watersheds provides a benchmark for restoration efforts. Locally and regionally, assessing the sources of portfolio risk can guide actions to maintain existing resilience (protect habitat and disturbance regimes that maintain response diversity; employ harvest strategies sensitive to different portfolio components) or improve restoration activities. Improving our understanding of portfolio reliability may allow for management of natural resources that is robust to ongoing environmental change. Portfolio theory provides a straightforward method for characterizing the resilience of salmon ecosystems and their services. Natural variability in portfolio performance among undeveloped watersheds provides a benchmark for restoration efforts. Locally and regionally, assessing the sources of portfolio risk can guide actions to maintain existing resilience (protect habitat and disturbance regimes that maintain response diversity; employ harvest strategies sensitive to different portfolio components) or improve restoration activities. Improving our understanding of portfolio reliability may allow for management of natural resources that is robust to ongoing environmental change.