The Mesozoic Era experienced several instances of abrupt environmental change that are associated with instabilities in the climate, reorganizations of the global carbon cycle, and elevated ...extinction rates. Often during these perturbations, oxygen-deficient conditions developed in the oceans resulting in the widespread deposition of organic-rich sediments — these events are referred to as Oceanic Anoxic Events or OAEs. Such events have been linked to massive injections of greenhouse gases into the ocean–atmosphere system by transient episodes of voluminous volcanism and the destabilization of methane clathrates within marine environments. Nevertheless, uncertainty surrounds the specific environmental drivers and feedbacks that occurred during the OAEs that caused perturbations in the carbon cycle; this is particularly true of the Early Jurassic Toarcian OAE (∼183.1 Ma). Here, we present biostratigraphically constrained carbon isotope data from western North America (Alberta and British Columbia, Canada) to better assess the global extent of the carbon cycle perturbations. We identify the large negative carbon isotope excursion associated with the OAE along with high-frequency oscillations and steps within the onset of this excursion. We propose that these high-frequency carbon isotope excursions reflect changes to the global carbon cycle and also that they are related to the production and release of greenhouse gases from terrestrial environments on astronomical timescales. Furthermore, increased terrestrial methanogenesis should be considered an important climatic feedback during Ocean Anoxic Events and other similar events in Earth history after the proliferation of land plants.
•Analyzed δ13Corg values from two North American sites across the Toarcian Oceanic Anoxic Event.•Highest-resolution study of Toarcian carbon isotope excursions from outside of Europe.•Documented small-scale carbon isotope excursions during onset of Toarcian carbon isotope excursion.•Small-scale carbon isotope excursions during Toarcian were global phenomena.•Increased terrestrial methanogenesis implicated in global warming and carbon isotope excursions.
In Australia, a land subject to high annual variation in grain yields, farmers find it challenging to adjust crop production inputs to yield prospects. Scientists have responded to this problem by ...developing Decision Support Systems, yet the scientists' enthusiasm for developing these tools has not been reciprocated by farm managers or their advisers, who mostly continue to avoid their use. Preceding papers in this series described the FARMSCAPE intervention: a new paradigm for decision support that had significant effects on farmers and their advisers. These effects were achieved in large measure because of the intensive effort which scientists invested in engaging with their clients. However, such intensive effort is time consuming and economically unsustainable and there remained a need for a more cost-effective tool. In this paper, we report on the evolution, structure, and performance of Yield Prophet®: an internet service designed to move on from the FARMSCAPE model to a less intensive, yet high quality, service to reduce farmer uncertainty about yield prospects and the potential effects of alternative management practices on crop production and income. Compared with conventional Decision Support Systems, Yield Prophet offers flexibility in problem definition and allows farmers to more realistically specify the problems in their fields. Yield Prophet also uniquely provides a means for virtual monitoring of the progress of a crop throughout the season. This is particularly important for in-season decision support and for frequent reviewing, in real time, of the consequences of past decisions and past events on likely future outcomes. The Yield Prophet approach to decision support is consistent with two important, but often ignored, lessons from decision science: that managers make their decisions by satisficing rather than optimising and that managers' fluid approach to decision making requires ongoing monitoring of the consequences of past decisions.
Thymine kinase 2 (TK2) is a mitochondrial matrix protein encoded in nuclear DNA and phosphorylates the pyrimidine nucleosides: thymidine and deoxycytidine. Autosomal recessive
mutations cause a ...spectrum of disease from infantile onset to adult onset manifesting primarily as myopathy.
To perform a retrospective natural history study of a large cohort of patients with TK2 deficiency.
The study was conducted by 42 investigators across 31 academic medical centres.
We identified 92 patients with genetically confirmed diagnoses of TK2 deficiency: 67 from literature review and 25 unreported cases. Based on clinical and molecular genetics findings, we recognised three phenotypes with divergent survival: (1) infantile-onset myopathy (42.4%) with severe mitochondrial DNA (mtDNA) depletion, frequent neurological involvement and rapid progression to early mortality (median post-onset survival (POS) 1.00, CI 0.58 to 2.33 years); (2) childhood-onset myopathy (40.2%) with mtDNA depletion, moderate-to-severe progression of generalised weakness and median POS at least 13 years; and (3) late-onset myopathy (17.4%) with mild limb weakness at onset and slow progression to respiratory insufficiency with median POS of 23 years. Ophthalmoparesis and facial weakness are frequent in adults. Muscle biopsies show multiple mtDNA deletions often with mtDNA depletion.
In TK2 deficiency, age at onset, rate of weakness progression and POS are important variables that define three clinical subtypes. Nervous system involvement often complicates the clinical course of the infantile-onset form while extraocular muscle and facial involvement are characteristic of the late-onset form. Our observations provide essential information for planning future clinical trials in this disorder.
FARMSCAPE (Farmers', Advisers', Researchers', Monitoring, Simulation, Communication And Performance Evaluation) is a program of participatory research with the farming community of northeast ...Australia. It initially involved research to explore whether farmers and their advisers could gain benefit from tools such as soil characterisation and sampling, climate forecasts and, in particular, simulation modelling. Its current focus is facilitating the implementation of commercial delivery systems for these same tools in order to meet industry demand for their access. This paper presents the story of what was done over the past decade, it provides performance indicators of impact, it reflects on what was learnt over this period and it outlines where this research is likely to head in the future.
Over the past 10 years, the FARMSCAPE team employed a Participatory Action Research approach to explore whether farmers could value simulation as a decision support tool for managing their farming system and if so, could it be delivered cost-effectively. Through farmer group engagement, on-farm trials, soil characterisation, monitoring of crops, soils and climate, and sessions to apply the APSIM systems simulator, FARMSCAPE represented a research program on decision support intervention. Initial scepticism by farmers and commercial consultants about the value of APSIM was addressed by testing its performance both against measured data from on-farm trials and against farmers' experiences with past commercial crops. Once this credibility check was passed, simulation sessions usually evolved into participants interactively inquiring of the model the consequence of alternative management options. These ‘What if’ questions using APSIM were contextualised using local climate and soil data and the farmer's actual or proposed management rules.
The active participation of farmers and their advisers, and working in the context of their own farming operations, were the key ingredients in the design, implementation and interpretation of the FARMSCAPE approach to decision support. The attraction of the APSIM systems simulator to farmers contemplating change was that it allowed them to explore their own system in a manner equivalent to learning from experience. To achieve this, APSIM had to be credible and flexible. While direct engagement of farmers initially enabled only a limited number of beneficiaries, this approach generated a commercial market for timely and high quality interactions based on soil monitoring and simulation amongst a significant sector of the farming community. Current efforts are therefore focused on the training, support and accreditation of commercial agronomists in the application of the FARMSCAPE approach and tools.
The FARMSCAPE approach to decision support has come to represent an approach to guiding science-based engagement with farm decision making which is being tested nationally and internationally.
•APSIM was evaluated using an Asian dataset covering 12 countries, numerous soils, crops, and practices.•Assessment was from both crop and soil simulation perspectives, including sequence ...effects.•The model performed well in simulating the diversity of cropping systems to which it was applied.•Input parameter estimation challenges, some indicating possible model deficiencies, were noted.•Desirable future APSIM improvements were identified.
Resource shortages, driven by climatic, institutional and social changes in many regions of Asia, combined with growing imperatives to increase food production whilst ensuring environmental sustainability, are driving research into modified agricultural practices. Well-tested cropping systems models that capture interactions between soil water and nutrient dynamics, crop growth, climate and farmer management can assist in the evaluation of such new agricultural practices. One such cropping systems model is the Agricultural Production Systems Simulator (APSIM). We evaluated APSIM’s ability to simulate the performance of cropping systems in Asia from several perspectives: crop phenology, production, water use, soil dynamics (water and organic carbon) and crop CO2 response, as well as its ability to simulate cropping sequences without reset of soil variables. The evaluation was conducted over a diverse range of environments (12 countries, numerous soils), crops and management practices throughout the region. APSIM’s performance was statistically assessed against assembled replicated experimental datasets. Once properly parameterised, the model performed well in simulating the diversity of cropping systems to which it was applied with RMSEs generally less than observed experimental standard deviations (indicating robust model performance), and with particular strength in simulation of multi-crop sequences. Input parameter estimation challenges were encountered, and although ‘work-arounds’ were developed and described, in some cases these actually represent model deficiencies which need to be addressed. Desirable future improvements have been identified to better position APSIM as a useful tool for Asian cropping systems research into the future. These include aspects related to harsh environments (high temperatures, diffuse light conditions, salinity, and submergence), conservation agriculture, greenhouse gas emissions, as well as aspects more specific to Southern Asia and low input systems (such as deficiencies in soil micro-nutrients).
Achieving export growth in rice production from variable rainfed lowland rice ecosystems is at risk if depending on conventional breeding or genetic development alone. Sustained, long-term production ...requires building adaption capacity of smallholder farmers to better manage the challenges of seasonal climate variability and future climate change. Better understanding of the risks and constraints that farmers face in managing their current cropping system helps develop strategies for improving rice production in Cambodia. System models are now considered valuable assessment tools for evaluating cropping systems performance worldwide but require validation at the local level. This paper presents an evaluation of the APSIM-Oryza model for 15 Cambodian rice varieties under recommended practice. Data from a field experiment in 2011, conducted in a non-limiting water and nutrient environment, are used to calibrate varietal-specific coefficients and model input parameters. An independent dataset is then used to validate the model performance for a ‘real-world’ situation using on-farm data for six rice varieties planted in 54 farmer fields on 32 farms in two villages of Southeastern Cambodia. From this analysis, the APSIM-Oryza model is shown to be an acceptable tool for exploring the mismatch between current on-farm yields and potential production through yield gap analysis and the exploration of cropping system options for smallholder farmers to increase production, adapt to seasonal climate variability and be prepared for potential climate changes.
•Modern rice varieties, increased mechanisation and improved agronomy increase cropping options, yield and income under variable seasonal conditions.•Basing land preparation and crop establishment on ...field water depth enables selection of the most appropriate crop response option.•Direct seeding reduces labour demand and provides opportunities for off-farm investment opportunities.•Responses to seasonal conditions in near real-time allows optimal management of cropping challenges and a flexibility in thinking in meeting the challenges of climate change.
With high levels of seasonal climatic variability impacting on the consistency of rice production in Cambodian rainfed, lowland systems, there is a need to identify strategies that improve farmer food security and better meet national domestic and export demands. While there is a substantial gap between actual and potential rice yield, little research has been undertaken in Cambodia to improve rainfed rice agronomy or the efficiency of use of natural resources which, in a climate constrained environment can hold the key to better productivity and food security.
On-station and on-farm research, in combination with farming systems simulation and social research provide the capacity to evaluate cropping options through the lens of climate variability. The testing of technologies and strategies, including the use of modern, short and medium duration varieties, opportunistic timing of crop establishment, mechanisation, supplementary irrigation and improved agronomic practice has shown that there is potential to mitigate the effects of variable climate on farm productivity and household income. However, this requires an increased level of farmer/systems flexibility to allow for near to real-time changes in cropping response to observed seasonal conditions. These factors differentiate this research and provide the opportunities to improve the individuals’ livelihood and in meeting national rice production targets.
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•Model response to elevated temperature and CO2 correlates well with known physiological responses for rice.•‘Response’ farming more appropriate than rigid traditional practice under ...current climate variability and future climate change.•Distribution and timing of rainfall substantially influencing current rainfed rice systems.•Future demand for irrigation infrastructure to mitigate climate variability to increase over current levels.
Rice production is the major source of food security in Cambodia where 85% of the total arable land is cultivated to rice with traditional transplanted medium and later maturity varieties accounting for>70% of the plantings during the monsoon period. Climate change poses risks and opportunities to the sustained productivity of rice based farming systems in Cambodia. The objective of this study is to evaluate adaptation strategies that support the replacement of traditional low input systems with a ‘response’ farming approach for better temporal utilisation of available labour, land and water resources. Options include replacing a traditional transplanted crop with short duration varieties, more efficient crop establishment methods and better agronomic and fertiliser management that responds to timing, intensity and longevity of the monsoon and has potential to mitigate effects of current and future climate variability. To achieve this, we apply the APSIM farming systems model to evaluate how adaptation options for smallholder farmers can increase or maintain overall productivity within present day climate variability and future climates, using downscaled GCM baseline and 2030 climate scenarios. To extend beyond the 2030 climate change scenarios, we also assess production risk from an increase in ambient air temperature of 1.4–4.3°C, atmospheric CO2 concentration of 545–885ppm and variation in rainfall, for rainfed and irrigated systems to 2090. Modelled scenarios indicate a yield response to elevated CO2 of 17.5% at a concentration of 680ppm for current temperature and rainfall and are consistent with established physiological effects of CO2 on crop yields. In response to temperature, yields decreased by 4% per degree increase from an average annual baseline temperature of 28°C. Adaptation strategies involving deployment of short duration rice varieties, in conjunction with direct seeding and better N management, indicate comparable and improved production can be achieved to 2030 under likely future climate projections. However, beyond 2030, the distribution and timing of rainfall has a significant influence on rainfed lowland rice in Cambodia. In this case a more transformational approach involving widespread provision of irrigation water will be required to offset climate change impacts.
The utility of genetic testing in sporadic focal segmental glomerulosclerosis (FSGS) is unclear. We sought to determine the frequency of podocyte-related gene mutations in a heterogeneous population ...of adults and children with biopsy-proven FSGS.
The prevalence of pathogenic mutations in five genes (NPHS2, TRPC6, ACTN4, INF2 and PLCE1) and of APOL1 risk alleles (G1 and G2) was ascertained in children and adults diagnosed between 1984 and 2011 with FSGS by renal biopsy. Clinical data were extracted from medical records.
A total of 65 patients (28 children, 37 adults) with sporadic FSGS were identified (34 females, 31 males), with a mean age of 25 ± 16 years (range from 3 to 62 years). The majority of patients were African American (39 African American, 21 White and 2 Hispanic). We identified biallelic pathogenic NPHS2 mutations in 2 of 28 (7.1%) children, both of whom were of non-Hispanic Caucasian background. A homozygous NPHS2 p.R138Q/p.R138Q mutation was detected in a 5-year-old Caucasian female. Two compound heterozygous NPHS2 mutations p.R138Q/p.R229Q were identified in a 7-year-old Caucasian male patient. One novel, potentially pathogenic non-synonymous variant in INF2 was identified in an African American patient. The proportion of African Americans with two APOL1 risk alleles was 69.2%.
This study delineates a role for genetic testing for NPHS2 in children with biopsy-proven sporadic FSGS. Further studies which specify clinical and pathological details of patients will help further define whether there are specific populations that warrant systematic testing of other podocyte-related genes in sporadic FSGS.
The long-term benefits of retaining or planting trees on farms to rehabilitate land and protect the soil from erosion or salinity problems has to be traded off against the impact of tree competition ...on commercial crops, especially in the medium to low rainfall regions of Australia. The incentive to plant trees would increase if tree competition could be offset by economic returns gained from farm forestry products and by the beneficial impacts of tree windbreaks on crop yields and resource sustainability. The Agricultural Production Systems Simulator (APSIM) has a well-established capability to simulate cropping systems and this paper reports on progress in applying APSIM to agroforestry systems in order to quantify the potential benefits and risks of planting trees as windbreaks to cropping land in Australia. A simple case study indicating one possible model configuration is used to demonstrate this emergent capability for simulating tree and crop productivity and their interactions. The simulated agroforestry system consisted of the growth of a belt of trees (
Eucalyptus
argophloia) positioned as a windbreak on the edge of a field where a crop of winter chickpea (
Cicer arietinum L.) is grown over a 30-year period. The example simulations quantify the yield and economic returns of annual chickpea crops in addition to the discounted economic return from timber production after 30 years of tree growth. This example demonstrates how APSIM can be used to quantify the economic tradeoffs in planting trees as windbreaks on a commercial farm in a low rainfall region of Australia.
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