Prediction of water temperature metrics using spatial modelling in the Eastern and Western Cape, South Africa

Key aspects of a river's temperature regime are described by magnitudes, timing and durations of thermal events, and frequencies of extreme exceedance events. To understand alterations to thermal regimes, it is necessary to describe thermal time series based on these statistics. Classification of sites based on their thermal metrics, and understanding of spatial patterns of these thermal statistics, provides a powerful approach for comparing study sites against reference sites. Water temperature regime dynamics should be viewed regionally, where regional divisions have an inherent underpinning by an understanding of natural thermal variability. The aim of this research was to link key water temperature metrics to readily-mapped environmental surrogates, and to produce spatial images of temperature metrics: 37 temperature metrics were derived for 12 months of sub-daily water temperatures at 90 sites in the Eastern Cape and Western Cape provinces, South Africa. These metrics were correlated with 16 environmental variables. Correlations enabled development of multiple regression models which facilitated mapping of temperature metrics over the study area. This approach has the potential to be applied at a national scale as more thermal time series are collected nationally. It is argued that the appropriateness of management decisions in rivers can be improved by including guidelines for thermal metrics at a regional scale. Such maps could facilitate incorporation of a temperature component into management guidelines for water resources

Optimisation of Bacillus thuringiensis var. israelensis (Vectobac®) applications for the blackfly control programme on the Orange River, South Africa

The Orange River, South Africa's largest river, is a critical water resource for the country. In spite of the clear economic benefits of regulating river flows through a series of impoundments, one of the significant undesirable ecological consequences of this regulation has been the regular outbreaks of the pest blackfly species Simulium chutteri and S. damnosum s.l. (Diptera: Simuliidae). The current control programme, carried out by the South African National Department of Agriculture, uses regular applications, by helicopter, of the target-specific bacterial larvicide Bacillus thuringiensis var. israelensis. While cost-benefit analyses show significant benefits to the control programme, benefits could potentially be further increased through applying smaller volumes of larvicide in an optimised manner, which incorporates upstream residual amounts of pesticide through downstream carry. Using an optimisation technique applied in the West African Onchocerciasis Control Programme, to a 136 km stretch of the Orange River which includes 31 blackfly breeding sites, we demonstrate that 28.5% less larvicide could be used to potentially achieve the same control of blackfly. This translates into potential annual savings of between R540 000 and R1 800 000. A comparison of larvicide volumes estimated using traditional vs. optimised approaches at different discharges, illustrates that the savings on optimisation decline linearly with increasing flow volumes. Larvicide applications at the lowest discharge considered (40 m3·s-1) showed the greatest benefits from optimisations, with benefits remaining but decreasing to a theoretical 30% up to median flows of 100 m3·s-1. Given that almost 70% of flows in July are less than 100 m3·s-1, we suggest that an optimised approach is appropriate for the Orange River Blackfly Control Programme, particularly for flow volumes of less than 100 m3·s-1. We recommend that trials be undertaken over two reaches of the Orange River, one using the traditional approach, and another using the optimised approach, to test the efficacy of using optimised volumes of B.t.i

Derivation of quantitative management objectives for annual instream water temperatures in the Sabie River using a biological index

Adaptive management of river systems assumes uncertainty and makes provision for system variability. Inherent within this management approach is that perceived limits of 'acceptable' system variability are regarded not only as testable hypotheses, but also as playing a central role in maintaining biodiversity. While the Kruger National Park currently functions as a flagship conservation area in South Africa, projected increases in air temperatures as a consequence of global climate change present challenges in conserving this biodiversity inside the established land boundaries. Within the rivers of the Kruger National Park, a management goal of maintaining biodiversity requires a clearer understanding of system variability. One component of this is water temperature, an important water quality parameter defining the distribution patterns of aquatic organisms. In this study, Chiloglanis anoterus Crass (1960) (Pisces: Mochokidae) was selected as a biological indicator of changes in annual water temperatures within the Sabie River in the southern Kruger National Park. Relative abundances of C. anoterus were determined using standard electro-fishing surveys. The presence or absence of C. anoterus was linked to cumulative annual heat units using a logistic regression model, and a critical annual cumulative water temperature threshold estimated. A correlative relationship between this temperature threshold and a biological index using a C. anoterus condition factor provides river ecologists with a tool to assess ecologically significant warming trends in Sabie River water temperatures. A similar approach could be applied with relative ease to other Southern African river systems. Further testing of this hypothesis is suggested, as part of the adaptive management cycle

First steps in the development of a water temperature model framework for refining the ecological Reserve in South African rivers

Ecological Reserve determination for rivers in South Africa presently does not include a water temperature component, in spite of its importance in determining species distribution patterns. To achieve this requires an understanding of how lotic thermographs from South African rivers differ from northern hemisphere rivers, to avoid mismanaging rivers based on incorrect regional assumptions. Hourly water temperatures from 20 sites in four river systems, representing a range of latitudes, altitudes and stream orders, were assessed using a range of metrics. These data were analysed using principal component analyses and multiple linear regressions to understand what variables a water temperature model for use in ecoregions within South Africa should include. While temperature data are generally lacking in low- and higher-order South African rivers, data suggest that South African rivers are warmer than northern hemisphere rivers. Water temperatures could be grouped into cool, warm and intermediate types. Based on temperature time series analyses, this paper argues that a suitable water-temperature model for use in ecological Reserve determinations should be dynamic, include flow and air temperature variables, and be adaptive through a heat exchange coefficient term. The inclusion of water temperature in the determination and management of river ecological Reserves would allow for more holistic application of the National Water Act's ecological management provisions. Water temperature guidelines added to the ecological Reserve could be integrated into heuristic aquatic monitoring programmes within priority areas identified in regional conservation plans

Effective suckling in relation to naked maternal-infant body contact in the first hour of life: an observation study

Background Best practice guidelines to promote breastfeeding suggest that (i) mothers hold their babies in naked body contact immediately after birth, (ii) babies remain undisturbed for at least one hour and (iii) breastfeeding assistance be offered during this period. Few studies have closely observed the implementation of these guidelines in practice. We sought to evaluate these practices on suckling achievement within the first hour after birth. Methods Observations of seventy-eight mother-baby dyads recorded newborn feeding behaviours, the help received by mothers and birthing room practices each minute, for sixty minutes. Results Duration of naked body contact between mothers and their newborn babies varied widely from 1 to 60 minutes, as did commencement of suckling (range = 10 to 60 minutes). Naked maternal-infant body contact immediately after birth, uninterrupted for at least thirty minutes did not predict effective suckling within the first hour of birth. Newborns were four times more likely to sustain deep rhythmical suckling when their chin made contact with their mother’s breast as they approached the nipple (OR 3.8; CI 1.03 - 14) and if their mothers had given birth previously (OR 6.7; CI 1.35 - 33). Infants who had any naso-oropharyngeal suctioning administered at birth were six times less likely to suckle effectively (OR .176; CI .04 - .9). Conclusion Effective suckling within the first hour of life was associated with a collection of practices including infants positioned so their chin can instinctively nudge the underside of their mother’s breast as they approach to grasp the nipple and attach to suckle. The best type of assistance provided in the birthing room that enables newborns to sustain an effective latch was paying attention to newborn feeding behaviours and not administering naso-oropharyngeal suction routinely

Assessing Causality in the Relationship Between Adolescents’ Risky Sexual Online Behavior and Their Perceptions of this Behavior

The main aim of this study was to investigate the causal nature of the relationship between adolescents’ risky sexual behavior on the internet and their perceptions of this behavior. Engagement in the following online behaviors was assessed: searching online for someone to talk about sex, searching online for someone to have sex, sending intimate photos or videos to someone online, and sending one’s telephone number and address to someone exclusively known online. The relationship between these behaviors and adolescents’ perceptions of peer involvement, personal invulnerability, and risks and benefits was investigated. A two-wave longitudinal study among a representative sample of 1,445 Dutch adolescents aged 12–17 was conducted (49% females). Autoregressive cross-lagged structural equation models revealed that perceived peer involvement, perceived vulnerability, and perceived risks were all significant predictors of risky sexual online behavior 6 months later. No reverse causal paths were found. When the relationships between perceptions and risky sexual online behavior were modeled simultaneously, only perceived peer involvement was a determinant of risky sexual online behavior. Findings highlight the importance of addressing peer involvement in future interventions to reduce adolescents’ risky sexual online behavior

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2–4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

Recreational and occupational field exposure to freshwater cyanobacteria – a review of anecdotal and case reports, epidemiological studies and the challenges for epidemiologic assessment

Cyanobacteria are common inhabitants of freshwater lakes and reservoirs throughout the world. Under favourable conditions, certain cyanobacteria can dominate the phytoplankton within a waterbody and form nuisance blooms. Case reports and anecdotal references dating from 1949 describe a range of illnesses associated with recreational exposure to cyanobacteria: hay fever-like symptoms, pruritic skin rashes and gastro-intestinal symptoms are most frequently reported. Some papers give convincing descriptions of allergic reactions while others describe more serious acute illnesses, with symptoms such as severe headache, pneumonia, fever, myalgia, vertigo and blistering in the mouth. A coroner in the United States found that a teenage boy died as a result of accidentally ingesting a neurotoxic cyanotoxin from a golf course pond. This death is the first recorded human fatality attributed to recreational exposure to cyanobacteria, although uncertainties surround the forensic identification of the suspected cyanotoxin in this case. We systematically reviewed the literature on recreational exposure to freshwater cyanobacteria. Epidemiological data are limited, with six studies conducted since 1990. Statistically significant increases in symptoms were reported in individuals exposed to cyanobacteria compared to unexposed counterparts in two Australian cohort studies, though minor morbidity appeared to be the main finding. The four other small studies (three from the UK, one Australian) did not report any significant association. However, the potential for serious injury or death remains, as freshwater cyanobacteria under bloom conditions are capable of producing potent toxins that cause specific and severe dysfunction to hepatic or central nervous systems. The exposure route for these toxins is oral, from ingestion of recreational water, and possibly by inhalation. A range of freshwater microbial agents may cause acute conditions that present with features that resemble illnesses attributed to contact with cyanobacteria and, conversely, acute illness resulting from exposure to cyanobacteria or cyanotoxins in recreational waters could be misdiagnosed. Accurately assessing exposure to cyanobacteria in recreational waters is difficult and unreliable at present, as specific biomarkers are unavailable. However, diagnosis of cyanobacteria-related illness should be considered for individuals presenting with acute illness following freshwater contact if a description is given of a waterbody visibly affected by planktonic mass development

Genetic mechanisms of critical illness in COVID-19.

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice

Design and construction of the MicroBooNE detector

This paper describes the design and construction of the MicroBooNE liquid argon time projection chamber and associated systems. MicroBooNE is the first phase of the Short Baseline Neutrino program, located at Fermilab, and will utilize the capabilities of liquid argon detectors to examine a rich assortment of physics topics. In this document details of design specifications, assembly procedures, and acceptance tests are reported