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Developmental abnormalities in otoliths can impact growth and survival in teleost fishes. Here, we quantified the frequency and severity of developmental anomalies in otoliths of delta smelt (Hypomesus transpacificus), a critically endangered estuarine fish that is endemic to the San Francisco Estuary. Left-right asymmetry and anomalous crystalline polymorphs (i.e., vaterite) were quantified and compared between wild and cultured populations using digital image analysis. Visual estimates of vaterite were validated using X-ray diffraction, Raman spectroscopy, laser ablation ICPMS, and electron probe microanalysis. Results indicated that cultured delta smelt were 80 times more likely to contain a vateritic otolith and 18 times more likely to contain relatively large (≥ 15%) amounts of vaterite. Similarly, cultured fish exhibited 30% greater asymmetry than wild fish. These results indicate that cultured delta smelt exhibit a significantly higher frequency of vestibular abnormalities which are known to reduce fitness and survival. Such hatchery effects on otolith development could have important implications for captive culture practices and the supplementation of wild fish populations with cultured individuals.

Numerous links have been reported between immune response and DNA damage repair pathways in both plants and animals but the precise nature of the relationship between these fundamental processes is not entirely clear. Here, we report that XAP5 CIRCADIAN TIMEKEEPER (XCT), a protein highly conserved across eukaryotes, acts as a negative regulator of immunity in Arabidopsis thaliana and plays a positive role in responses to DNA damaging radiation. We find xct mutants have enhanced resistance to infection by a virulent bacterial pathogen, Pseudomonas syringae pv. tomato DC3000, and are hyper-responsive to the defense-activating hormone salicylic acid (SA) when compared to wild-type. Unlike most mutants with constitutive effector-triggered immunity (ETI), xct plants do not have increased levels of SA and retain enhanced immunity at elevated temperatures. Genetic analysis indicates XCT acts independently of NONEXPRESSOR OF PATHOGENESIS RELATED GENES1 (NPR1), which encodes a known SA receptor. Since DNA damage has been reported to potentiate immune responses, we next investigated the DNA damage response in our mutants. We found xct seedlings to be hypersensitive to UV-C and γ radiation and deficient in phosphorylation of the histone variant H2A.X, one of the earliest known responses to DNA damage. These data demonstrate that loss of XCT causes a defect in an early step of the DNA damage response pathway. Together, our data suggest that alterations in DNA damage response pathways may underlie the enhanced immunity seen in xct mutants.

Objective: The present study evaluated an intervention designed to introduce University students as potential users of Johannesburg's cycle lanes. Participants: A total of 393 undergraduate and postgraduate students from the University of Johannesburg took part. Methods: Following cycling and safety training, participants undertook a 1.2 km supervised cycle ride between University of Johannesburg campuses using loaned bicycles. The evaluation of the intervention drew on quantitative and qualitative data collected using participant questionnaires; and fieldworkers' photographic and reflective accounts. Results: Perceived cycling competency improved following the intervention, though similar proportions of participants became more "and" less interested in bicycle ownership (7-8%). The physical effort entailed; and flaws in the design and maintenance of cycle lanes (that affected utility and safety) were the strongest themes emerging from the qualitative analyses. Conclusions: The supervised cycle rides improved perceived cycling competency, but also enabled participants to reappraise the potential benefits and desirability of bicycle ownership.

The quantitative assessment of eye tracking data quality is critical for ensuring accuracy and precision of gaze position measurements. However, researchers often report the eye tracker's optimal manufacturer's specifications rather than empirical data about the accuracy and precision of the eye tracking data being presented. Indeed, a recent report indicates that less than half of eye tracking researchers surveyed take the eye tracker's accuracy into account when determining areas of interest for analysis, an oversight that could impact the validity of reported results and conclusions. Accordingly, we designed a calibration verification protocol to augment independent quality assessment of eye tracking data and examined whether accuracy and precision varied between three age groups of participants. We also examined the degree to which our externally quantified quality assurance metrics aligned with those reported by the manufacturer. We collected data in standard laboratory conditions to demonstrate our method, to illustrate how data quality can vary with participant age, and to give a simple example of the degree to which data quality can differ from manufacturer reported values. In the sample data we collected, accuracy for adults was within the range advertised by the manufacturer, but for school-aged children, accuracy and precision measures were outside this range. Data from toddlers were less accurate and less precise than data from adults. Based on an "a priori" inclusion criterion, we determined that we could exclude approximately 20% of toddler participants for poor calibration quality quantified using our calibration assessment protocol. We recommend implementing and reporting quality assessment protocols for any eye tracking tasks with participants of any age or developmental ability. We conclude with general observations about our data, recommendations for what factors to consider when establishing data inclusion criteria, and suggestions for stimulus design that can help accommodate variability in calibration. The methods outlined here may be particularly useful for developmental psychologists who use eye tracking as a tool, but who are not experts in eye tracking "per se." The calibration verification stimuli and data processing scripts that we developed, along with step-by-step instructions, are freely available for other researchers.

Temporality-driven covariate classification had limited impact on: the specification of directed acyclic graphs (DAGs) by 85 novice analysts (medical undergraduates); or the risk of bias in DAG-informed multivariable models designed to generate causal inference from observational data. Only 71 students (83.5%) managed to complete the "Temporality-driven Covariate Classification" task, and fewer still completed the "DAG Specification" task (77.6%) or both tasks in succession (68.2%). Most students who completed the first task misclassified at least one covariate (84.5%), and misclassification rates were even higher among students who specified a DAG (92.4%). Nonetheless, across the 512 and 517 covariates considered by each of these tasks, "confounders" were far less likely to be misclassified (11/252, 4.4% and 8/261, 3.1%) than "mediators" (70/123, 56.9% and 56/115, 48.7%) or "competing exposures" (93/137, 67.9% and 86/138, 62.3%), respectively. Since estimates of total causal effects are biased in multivariable models that: fail to adjust for "confounders"; or adjust for "mediators" (or "consequences of the outcome") misclassified as "confounders" or "competing exposures," a substantial proportion of any models informed by the present study's DAGs would have generated biased estimates of total causal effects (50/66, 76.8%); and this would have only been slightly lower for models informed by temporality-driven covariate classification alone (47/71, 66.2%). Supplementary materials for this article are available online.

Objective: The present study examined potential barriers to cycle-based transport amongst undergraduate students, to inform the design of future cycling promotion interventions at the University of Johannesburg (UJ). Participants: A total of 606 first, second and third year UJ undergraduates took part. Methods: Sociodemographic and economic determinants of bicycle/car ownership, cycling competency and behavior were evaluated using data derived from a 9-item questionnaire, before and after adjustment for measured confounders. Results: While 70% of respondents knew how to cycle, only 26% owned/had access to a bicycle, and only 18% had last cycled for transport. Bicycle ownership and competency were far commoner amongst male and older participants, and those whose parents had the means to own a car. Conclusions: Interventions to promote cycle-based transport must address the many (predominantly female) students who: have limited cycling competency; do not own/have access to a bicycle; or have little/no experience of cycling for transport.

The Samail ophiolite in Oman is undergoing modern hydration and carbonation of peridotite and may host a deep subsurface biosphere. Previous investigations of hyperalkaline fluids in Oman have focused on fluids released at surface seeps, which quickly lose their reducing character and precipitate carbonates upon contact with the O2/CO2-rich atmosphere. In this work, geochemical analysis of rocks and fluids from the subsurface provides new insights into the operative reactions in serpentinizing aquifers. Serpentinite rock and hyperalkaline fluids (pH > 10), which exhibit millimolar concentrations of Ca2+, H2 and CH4, as well as variable sulfate and nitrate, were accessed from wells situated in mantle peridotite near Ibra and studied to investigate their aqueous geochemistry, gas concentrations, isotopic signatures, mineralogy, Fe speciation and microbial community composition.The bulk mineralogy of drill cuttings is dominated by olivine, pyroxene, brucite, serpentine and magnetite. At depth, Fe-bearing brucite is commonly intermixed with serpentine, whereas near the surface, olivine and brucite are lost and increased magnetite and serpentine is detected. Micro-Raman spectroscopy reveals at least two distinct generations of serpentine present in drill cuttings recovered from several depths from two wells. Fe K-edge X-ray absorption near-edge spectroscopy (XANES) analysis of the lizardite shows a strong tetrahedral Fe coordination, suggesting a mixture of both Fe(II) and Fe(III) in the serpentine. Magnetite veins are also closely associated with this second generation serpentine, and 2-10 μm magnetite grains overprint all minerals in the drill cuttings. Thus we propose that the dissolved H2 that accumulates in the subsurface hyperalkaline fluids was evolved through low temperature oxidation and hydration of relict olivine, as well as destabilization of pre-existing brucite present in the partially serpentinized dunites and harzburgites. In particular, we hypothesize that Fe-bearing brucite is currently reacting with dissolved silica in the aquifer fluids to generate late-stage magnetite, additional serpentine and dissolved H2. Dissolved CH4 in the fluids exhibits the most isotopically heavy carbon in CH4 reported in the literature thus far. The CH4 may have formed through abiotic reduction of dissolved CO2 or through biogenic pathways under extreme carbon limitation. The methane isotopic composition may have also been modified by significant methane oxidation. 16S rRNA sequencing of DNA recovered from filtered hyperalkaline well fluids reveals an abundance of Meiothermus, Thermodesulfovibrionaceae (sulfate-reducers) and Clostridia (fermenters). The fluids also contain candidate phyla OP1 and OD1, as well as Methanobacterium (methanogen) and Methylococcus sp. (methanotroph). The composition of these microbial communities suggests that low-temperature hydrogen and methane generation, coupled with the presence of electron acceptors such as nitrate and sulfate, sustains subsurface microbial life within the Oman ophiolite.

This study examined pathways to retirement and the role of circumstances at work and at home (including the introduction of financially-enhanced early retirement schemes) on retirement-related decision-making. In-depth qualitative interviews were conducted within 2 years of retirement with 59 British civil servants participating in the Whitehall II Study. Focusing on the experiences of 33 interviewees who spontaneously discussed "early retire-ment" we identified three pathways to retirement (non-applicants, successful applicants, and unsuccessful applicants for early retirement) each influenced by a range of complementary positive and negative factors at work and at home. The early retirement schemes influenced the balance between these factors in three ways: by encouraging participants to reflect on (and reconsider) existing retirement plans; by offering financial incentives to retire early; and because they were part of the ongoing process of restructuring and downsizing within the Civil Service which was accompanied by a perceived deterioration in conditions at work. (Contains 2 tables and 1 figure.)

Background: Contact precautions are a widely accepted strategy to reduce in-hospital transmission of meticillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE). However, these practices may have unintended deleterious effects on patients.Aim: To evaluate the effect of a modification in hospital-wide contact precaution practices on emergency department (ED) admission times.Methods: During the study period, the hospital changed its contact precaution policy from requiring contact precautions for all patients with a history of MRSA or VRE to only those who presented with clinical conditions likely to contaminate the environment with pathogens. An interrupted time series analysis of ED admission times for adults for one year preceding and one year following this change was performed at a two-campus hospital. The main outcome was admission time, defined as time from decision to admit to arrival in an inpatient bed, for patients with MRSA or VRE compared with all other patients. The in-hospital MRSA and VRE acquisition rates were evaluated over the same period and have been published previously.Findings: At one campus, admission time decreased immediately by 161min for MRSA patients (P=0.008) and 135min for VRE patients (P=0.003), and both continued to decrease over the duration of the study. There was no significant change in admission time at the second campus.Conclusions: Modifying contact precaution requirements for MRSA and VRE may be associated with improved ED admission time without significantly altering in-hospital MRSA and VRE acquisition. [ABSTRACT FROM AUTHOR]

Background and objectives: The human immune system is an ever-changing composition of innumerable cells and proteins, continually ready to respond to pathogens or insults. The cost of maintaining this state of immunological readiness is rarely considered. In this paper we aim to discern a cost to non-acute immune function by investigating how low levels of C-reactive protein (CRP) relate to other energetic demands and resources in adolescent Gambian girls. Methodology: Data from a longitudinal study of 66 adolescent girls was used to test hypotheses around investment in immune function. Non-acute (under 2 mg/L) CRP was used as an index of immune function. Predictor variables include linear height velocity, adiposity, leptin, and measures of energy balance. Results: Non-acute log CRP was positively associated with adiposity (β = 0.16, P < 0.001, R2 = 0.17) and levels of the adipokine leptin (β = 1.17, P = 0.006, R2 = 0.09). CRP was also negatively associated with increased investment in growth, as measured by height velocity (β = −0.58, P < 0.001, R2 = 0.13) and lean mass deposition β = −0.42, P = 0.005, R2 = 0.08). Relationships between adiposity and growth explained some, but not all, of this association. We do not find that CRP was related to energy balance. Conclusions and implications: These data support a hypothesis that investment in non-acute immune function is facultative, and sensitive to energetic resources and demands. We also find support for an adaptive association between the immune system and adipose tissue.