Implications of crop model ensemble size and composition for estimates of adaptation effects and agreement of recommendations

Climate change is expected to severely affect cropping systems and food production in many parts of the world unless local adaptation can ameliorate these impacts. Ensembles of crop simulation models can be useful tools for assessing if proposed adaptation options are capable of achieving target yields, whilst also quantifying the share of uncertainty in the simulated crop impact resulting from the crop models themselves. Although some studies have analysed the influence of ensemble size on model outcomes, the effect of ensemble composition has not yet been properly appraised. Moreover, results and derived recommendations typically rely on averaged ensemble simulation results without accounting sufficiently for the spread of model outcomes. Therefore, we developed an Ensemble Outcome Agreement (EOA) index, which analyses the effect of changes in composition and size of a multi-model ensemble (MME) to evaluate the level of agreement between MME outcomes with respect to a given hypothesis (e.g. that adaptation measures result in positive crop responses). We analysed the recommendations of a previous study performed with an ensemble of 17 crop models and testing 54 adaptation options for rainfed winter wheat (Triticum aestivum L.) at Lleida (NE Spain) under perturbed conditions of temperature, precipitation and atmospheric CO2 concentration. Our results confirmed that most adaptations recommended in the previous study have a positive effect. However, we also showed that some options did not remain recommendable in specific conditions if different ensembles were considered. Using EOA, we were able to identify the adaptation options for which there is high confidence in their effectiveness at enhancing yields, even under severe climate perturbations. These include substituting spring wheat for winter wheat combined with earlier sowing dates and standard or longer duration cultivars, or introducing supplementary irrigation, the latter increasing EOA values in all cases. There is low confidence in recovering yields to baseline levels, although this target could be attained for some adaptation options under moderate climate perturbations. Recommendations derived from such robust results may provide crucial information for stakeholders seeking to implement adaptation measures.

Use of crop simulation modelling to aid ideotype design of future cereal cultivars

A major challenge of the 21st century is to achieve food supply security under a changing climate and roughly a doubling in food demand by 2050 compared to present, the majority of which needs to be met by the cereals wheat, rice, maize, and barley. Future harvests are expected to be especially threatened through increased frequency and severity of extreme events, such as heat waves and drought, that pose particular challenges to plant breeders and crop scientists. Process-based crop models developed for simulating interactions between genotype, environment, and management are widely applied to assess impacts of environmental change on crop yield potentials, phenology, water use, etc. During the last decades, crop simulation has become important for supporting plant breeding, in particular in designing ideotypes, i.e. 'model plants', for different crops and cultivation environments. In this review we (i) examine the main limitations of crop simulation modelling for supporting ideotype breeding, (ii) describe developments in cultivar traits in response to climate variations, and (iii) present examples of how crop simulation has supported evaluation and design of cereal cultivars for future conditions. An early success story for rice demonstrates the potential of crop simulation modelling for ideotype breeding. Combining conventional crop simulation with new breeding methods and genetic modelling holds promise to accelerate delivery of future cereal cultivars for different environments. Robustness of model-aided ideotype design can further be enhanced through continued improvements of simulation models to better capture effects of extremes and the use of multi-model ensembles.

Proteomic identification of allergenic seed proteins, napin and cruciferin, from cold-pressed rapeseed oils

In Finland and France atopic children commonly react to seeds of oilseed rape and turnip rape in skin prick tests (SPT) and open food challenges. These seeds are not as such in dietary use and therefore the routes of sensitization are unknown. Possible allergens were extracted from commercial cold-pressed and refined rapeseed oils and identified by gel-based tandem nanoflow liquid chromatography mass spectrometry (LC-MS/MS). Napin (a 2S albumin), earlier identified as a major allergen in the seeds of oilseed rape and turnip rape, and cruciferin (an 11S globulin), a new potential seed allergen, were detected in cold-pressed oils, but not in refined oils. Pooled sera from five children sensitized or allergic to oilseed rape and turnip rape seeds reacted to these proteins from cold-pressed oil preparations and individual sera from five children reacted to these proteins extracted from the seeds when examined with IgE immunoblotting. Hence cold-pressed rapeseed oil might be one possible route of sensitization for these allergens.

Changes in time of sowing, flowering and maturity of cereals in Europe under climate change

The phenological development of cereal crops from emergence through flowering to maturity is largely controlled by temperature, but also affected by day length and potential physiological stresses. Responses may vary between species and varieties. Climate change will affect the timing of cereal crop development, but exact changes will also depend on changes in varieties as affected by plant breeding and variety choices. This study aimed to assess changes in timing of major phenological stages of cereal crops in Northern and Central Europe under climate change. Records on dates of sowing, flowering, and maturity of wheat, oats and maize were collected from field experiments conducted during the period 1985-2009. Data for spring wheat and spring oats covered latitudes from 46 to 64°N, winter wheat from 46 to 61°N, and maize from 47 to 58°N. The number of observations (site-year-variety combinations) varied with phenological phase, but exceeded 2190, 227, 2076 and 1506 for winter wheat, spring wheat, spring oats and maize, respectively. The data were used to fit simple crop development models, assuming that the duration of the period until flowering depends on temperature and day length for wheat and oats, and on temperature for maize, and that the duration of the period from flowering to maturity in all species depends on temperature only. Species-specific base temperatures were used. Sowing date of spring cereals was estimated using a threshold temperature for the mean air temperature during 10 days prior to sowing. The mean estimated temperature thresholds for sowing were 6.1, 7.1 and 10.1°C for oats, wheat and maize, respectively. For spring oats and wheat the temperature threshold increased with latitude. The effective temperature sums required for both flowering and maturity increased with increasing mean annual temperature of the location, indicating that varieties are well adapted to given conditions. The responses of wheat and oats were largest for the period from flowering to maturity. Changes in timing of cereal phenology by 2040 were assessed for two climate model projections according to the observed dependencies on temperature and day length. The results showed advancements of sowing date of spring cereals by 1-3 weeks depending on climate model and region within Europe. The changes were largest in Northern Europe. Timing of flowering and maturity were projected to advance by 1-3 weeks. The changes were largest for grain maize and smallest for winter wheat, and they were generally largest in the western and northern part of the domain. There were considerable differences in predicted timing of sowing, flowering and maturity between the two climate model projections applied.

The association of antibodies to cardiolipin,β2‐glycoprotein I, prothrombin, and oxidized low‐density lipoprotein with thrombosis in 292 patients with familial and sporadic systemic lupus erythematosus

OBJECTIVE

To determine the prevalence of antibodies to phospholipid-binding plasma proteins (aPL) and to oxidized low-density lipoprotein (OX-LDL), and to study the association of these antibodies with thrombosis and coronary heart disease (CHD) in patients with systemic lupus erythematosus (SLE).

METHODS

Clinical data and sera from 89 Finnish patients with familial and 203 with sporadic SLE were available for the study. Enzyme-linked immunosorbent assays (ELISA) were used for antibody determination.

RESULTS

The occurrence of thrombosis in our SLE patients was 13.7% (40/292) and of clinically diagnosed CHD was 1.4% (4/292). All antibody assays, except IgM-aCL, were significantly associated with thrombosis. IgG-aCL alone or in combination with anti beta 2-GPI or with anti OX-LDL were reasonably sensitive (38%, 48%, and 58%, respectively) and specific (87%, 80% and 72%, respectively) for a history of thrombosis. A high risk of arterial thrombosis (TIA or stroke) was associated with positivity of IgG-aCL, anti beta 2-GPI, and anti-prothrombin. Venous thrombosis was significantly associated with all other assays except IgM-aCL and anti-prothrombin. No test correlated with CHD, but the number of affected patients was small. There were three multiplex SLE families with two patients having a history of thrombosis: no consistent pattern of aPL or anti OX-LDL was found in these patients.

CONCLUSION

IgG-aCL alone or in combination with anti beta 2-GPI or anti OX-LDL are sensitive and specific tests for detecting SLE patients at increased risk of thrombosis. The aetiopathogenesis of thrombosis in familial SLE appears to be multifactorial.

Systematically missing confounders in individual participant data meta-analysis of observational cohort studies

One difficulty in performing meta-analyses of observational cohort studies is that the availability of confounders may vary between cohorts, so that some cohorts provide fully adjusted analyses while others only provide partially adjusted analyses. Commonly, analyses of the association between an exposure and disease either are restricted to cohorts with full confounder information, or use all cohorts but do not fully adjust for confounding. We propose using a bivariate random-effects meta-analysis model to use information from all available cohorts while still adjusting for all the potential confounders. Our method uses both the fully adjusted and the partially adjusted estimated effects in the cohorts with full confounder information, together with an estimate of their within-cohort correlation. The method is applied to estimate the association between fibrinogen level and coronary heart disease incidence using data from 154 012 participants in 31 cohorts.† Copyright © 2009 John Wiley & Sons, Ltd.

C-reactive protein in population samples

The significance of C-reactive protein (CRP) was studied in three different sets of specimens. Raised levels (greater than 10 mg/l) were detected in 2.0% of 380 healthy blood donors from whom two blood specimens, taken at an interval of half a year, were tested. Except for two cases, only one of the two specimens was positive. Raised levels were found three times as frequently (in 6.6%) in a random middle-aged population sample consisting of 531 subjects. More than 40% of the raised levels could be connected to acute respiratory infections, and about 20% to smoking. Five of the 35 subjects (14%) in the population sample with elevated CRP had rheumatoid arthritis. The third set of sera comprised pre-illness specimens from 22 subjects who developed rheumatoid arthritis a few months to five years later. Although it had previously been proved that the majority of these sera contained rheumatoid factors, the CRP concentration was increased in one specimen only.

Hev b 6.01 and Hev b 5 induce pro-inflammatory cytokines and chemokines from peripheral blood mononuclear cells in latex allergy

BACKGROUND

Hev b 6.01 (prohevein) and Hev b 5 [acidic natural rubber latex (NRL) protein] are major IgE-binding allergens in NRL allergy.

OBJECTIVE

To examine allergen-specific cytokine and chemokine responses in NRL-allergic patients.

METHODS

Fourteen NRL-allergic patients and 10 healthy controls participated in the study. Hev b 6.01 and Hev b 5 were purified under non-denaturating conditions by chromatographic methods. Specific IgE antibodies were measured by ELISA and proliferation of peripheral blood mononuclear cells (PBMC) by (3)H-thymidine incorporation assay. Allergen-specific induction of cytokine and chemokine mRNA in PBMC was measured by real-time PCR and protein levels by ELISA. Surface expression of chemokine receptors was analysed by flow cytometry.

RESULTS

Twelve (86%) NRL-allergic patients had positive skin prick test reactions and IgE antibodies against Hev b 6.01, but less than 30% responded to Hev b 5. Cell proliferation against Hev b 6.01, but not against Hev b 5, was significantly increased. Both allergens elicited significantly higher expression of pro-inflammatory and T-helper type 2 cytokines (TNF, IL-12p40, IL-13) and chemokines (CCL3, CCL4, CCL20) in the NRL-allergic patients than in controls. Interestingly, mRNA expression of the regulatory cytokine TGF-beta1 was reduced, whereas IL-10 expression was enhanced after allergen stimulations in patients with NRL allergy. Finally, the NRL-allergic patients showed increased CCR4 expression on CD3(+)CD8(-) T cells and decreased CXCR3 expression on CD3(+)CD8(+) T cells.

CONCLUSION

Allergen-specific induction of cytokines and chemokines in PBMC and chemokine receptor expression on circulating T cells may contribute to the pathogenesis of NRL allergy.

Latex allergy: low prevalence of immunoglobulin E to highly purified proteins Hev b 2 and Hev b 13

BACKGROUND

Hevea brasiliensis (Hev b) 2 and Hev b 13 have recently been identified as major latex allergens by detecting specific IgE antibodies in >50% of sera from Hev b latex-allergic individuals.

OBJECTIVE

We assessed the prevalence rates for sensitization to extensively purified latex allergens in patients from three diverse geographical areas.

METHODS

Native Hev b 2, Hev b 5, Hev b 6.01 and Hev b 13 were purified by non-denaturating chromatography and were used in ELISAs to assess sera from 215 latex-allergic patients and 172 atopic non-sensitized controls from Finland, Spain and the United States to detect allergen-specific IgE antibodies.

RESULTS

Unexpectedly, even highly purified Hev b 13 contained epitope(s) to which Hev b 6-specific human IgE antibodies bound effectively. Further purification, however, reduced the prevalence of IgE antibody reactivity to low levels: 15%, 5% and 11% for Hev b 2, and 18%, 30% and 27% for Hev b 13 among latex-allergic Finnish, Spanish and American patients, respectively. Interestingly, Finnish patients had a lower prevalence of Hev b 5-specific IgE antibody (28%) as compared with Spanish (49%) and American (71%) patients. The prevalence of Hev b 6.01-specific IgE reactivity was uniformly >50% in all three populations.

CONCLUSION

Neither Hev b 2 nor Hev b 13 appear to be major latex allergens when evaluated in serological assays using highly purified allergens. The reason(s) for the observed differences in published sensitization rates in various geographic regions requires further study. The purity of the allergen preparations has a marked impact on the accuracy of latex-specific IgE antibody detection in epidemiological studies and in the serological diagnosis of latex allergy.

Latex allergy: the sum quantity of four major allergens shows the allergenic potential of medical gloves

BACKGROUND

Assessment of allergenic potential of medical devices made of natural rubber latex (NRL) requires the measurement of concentrations of specific allergenic proteins or polypeptides eluting from rubber.

METHODS

Four NRL allergens (Hev b 1, 3, 5, and 6.02) were quantified in all medical glove brands marketed in Finland in 1999, 2001, and 2003 (n = 208) by a capture enzyme immunoassay. The results were compared with those obtained from previous nationwide market surveys, using a skin prick test-validated human IgE-based ELISA-inhibition method.

RESULTS

A high overall correlation (r = 0.87, 95% CI 0.83-0.90) emerged between the sum values of the four allergens(microg/g glove) and IgE-ELISA inhibition (allergen units, AU/ml, 1 : 5 diluted glove extract). The sum of four allergens when set at 0.15 microg/g discriminated 'low allergenic' (<10 AU/ml) from 'moderate- to high-allergenic' (>/=10 AU/ml) gloves at a sensitivity of 0.93 (95% CI 0.85-0.98) and specificity of 0.90 (95% CI 0.83-0.94). When the sum was below the detection limit (0.03 microg/g) all gloves belonged to the previously defined low-allergen category.

CONCLUSIONS

By comparing the sum concentration of four selected NRL allergens with results obtained in human IgE-ELISA inhibition, it was possible set a cut-off level (0.15 microg/g) below which virtually all gloves contain low or insignificant amounts of allergens, and can be considered as low allergenic. At different cut-off-points, one could calculate the likelihood of a given glove to belong to the previously defined low, moderate or high allergen categories.

Turnip rape and oilseed rape are new potential food allergens in children with atopic dermatitis

BACKGROUND

When skin prick testing (SPT) young children with atopic dermatitis (AD) for suspected food allergy, we frequently found positive reactions with turnip rape (Brassica rapa) and oilseed rape (Brassica napus). We performed food challenge to examine whether these children react clinically to turnip rape.

METHODS

A total of 1887 children were screened with SPTs for sensitization to turnip rape and oilseed rape. Twenty-eight children with clearly positive SPT (> or =5 mm) were first subjected to labial challenge with turnip rape seeds followed, if negative, by open oral challenge for up to 7 days. Twenty-five children with AD but negative SPT to turnip rape and oilseed rape served as controls.

RESULTS

Two-hundred and six (10.9%) children had positive SPT to turnip rape and/or oilseed rape. Twenty-five (89%) of 28 children showed a positive challenge reaction to turnip rape. Seventeen reacted with labial whealing, and eight in oral challenge with facial urticaria, flare-up of AD or abdominal symptoms. All 25 control children remained negative in the labial challenge.

CONCLUSIONS

Turnip rape and oilseed rape seem to be new important food allergens in young children with AD. The modes of exposure to these allergens and the possible routes of sensitization remain to be established.

Plasma fibrinogen level and the risk of major cardiovascular diseases and nonvascular mortality: an individual participant meta-analysis

CONTEXT

Plasma fibrinogen levels may be associated with the risk of coronary heart disease (CHD) and stroke.

OBJECTIVE

To assess the relationships of fibrinogen levels with risk of major vascular and with risk of nonvascular outcomes based on individual participant data.

DATA SOURCES

Relevant studies were identified by computer-assisted searches, hand searches of reference lists, and personal communication with relevant investigators.

STUDY SELECTION

All identified prospective studies were included with information available on baseline fibrinogen levels and details of subsequent major vascular morbidity and/or cause-specific mortality during at least 1 year of follow-up. Studies were excluded if they recruited participants on the basis of having had a previous history of cardiovascular disease; participants with known preexisting CHD or stroke were excluded.

DATA EXTRACTION

Individual records were provided on each of 154,211 participants in 31 prospective studies. During 1.38 million person-years of follow-up, there were 6944 first nonfatal myocardial infarctions or stroke events and 13,210 deaths. Cause-specific mortality was generally available. Analyses involved proportional hazards modeling with adjustment for confounding by known cardiovascular risk factors and for regression dilution bias.

DATA SYNTHESIS

Within each age group considered (40-59, 60-69, and > or =70 years), there was an approximately log-linear association with usual fibrinogen level for the risk of any CHD, any stroke, other vascular (eg, non-CHD, nonstroke) mortality, and nonvascular mortality. There was no evidence of a threshold within the range of usual fibrinogen level studied at any age. The age- and sex- adjusted hazard ratio per 1-g/L increase in usual fibrinogen level for CHD was 2.42 (95% confidence interval [CI], 2.24-2.60); stroke, 2.06 (95% CI, 1.83-2.33); other vascular mortality, 2.76 (95% CI, 2.28-3.35); and nonvascular mortality, 2.03 (95% CI, 1.90-2.18). The hazard ratios for CHD and stroke were reduced to about 1.8 after further adjustment for measured values of several established vascular risk factors. In a subset of 7011 participants with available C-reactive protein values, the findings for CHD were essentially unchanged following additional adjustment for C-reactive protein. The associations of fibrinogen level with CHD or stroke did not differ substantially according to sex, smoking, blood pressure, blood lipid levels, or several features of study design.

CONCLUSIONS

In this large individual participant meta-analysis, moderately strong associations were found between usual plasma fibrinogen level and the risks of CHD, stroke, other vascular mortality, and nonvascular mortality in a wide range of circumstances in healthy middle-aged adults. Assessment of any causal relevance of elevated fibrinogen levels to disease requires additional research.

Immune activation in the small intestine in patients with rheumatoid arthritis

OBJECTIVES

To determine whether inflammation in the gut associated immune system is activated in rheumatoid arthritis (RA). The expression of chemokine receptor- (CCR4, CCR5) and cytokine- (interleukin (IL)2, IL10, interferon gamma (IFNgamma), tumour necrosis factor alpha (TNFalpha), and transforming growth factor beta (TGFbeta)) specific mRNA in intestinal biopsy samples from patients with RA was examined.

METHODS

Duodenal biopsy samples from 13 patients with RA and 15 control subjects were studied. The mRNA expression of CCR4, CCR5, IL2, IL10, IFNgamma, TNFalpha, and TGFbeta in intestinal biopsy samples was demonstrated by real time quantitative reverse transcriptase-polymerase chain reaction.

RESULTS

The mRNA expression of CCR4, CCR5, and IL10 in intestinal biopsy samples was increased in patients with RA in comparison with control subjects (p = 0.001, p = 0.046, p = 0.019). No difference in the expression levels of IL2, IFNgamma, TNFalpha, or TGFbeta was seen between patients with RA and controls.

CONCLUSIONS

The increased intestinal mRNA expression of IL10, CCR5, and CCR4 suggests that gut associated immune cells are activated in patients with RA.

Cytokine and chemokine receptor profile of peripheral blood mononuclear cells during treatment with infliximab in patients with active rheumatoid arthritis

OBJECTIVES

To analyse immunological changes during treatment with a monoclonal anti-tumour necrosis factor alpha (TNFalpha) antibody, infliximab, in patients with rheumatoid arthritis (RA).

METHODS

25 patients with RA and 5 patients with other arthritides were studied during the first 6 weeks of treatment with infliximab. At the start of treatment and after 2 and 6 weeks, spontaneous expression of CCR3 and CCR5 on peripheral blood T cells and monocytes was studied by flow cytometry. The secretion and mRNA expression of interferon gamma (IFNgamma), interleukin (IL)4, IL5, and TNFalpha from phytohaemagglutinin (PHA) stimulated peripheral blood mononuclear cells was measured with an ELISA and RT-PCR. Plasma levels of C reactive protein, serum amyloid protein A, rheumatoid factor, and antibodies to filaggrin and citrullinated cyclic peptide were measured with an ELISA.

RESULTS

The number of CD4 T cells and CD14 monocytes expressing CCR3 (p = 0.013, p = 0.009, respectively) and CD8 T cells expressing CCR5 (p = 0.040) as well as PHA stimulated secretion of IL4 and IFNgamma (p<0.05) increased during treatment in patients with RA. 15 (60%) patients with RA achieved clinical response (at least ACR20) during the first 2 weeks. The number of T cells expressing CCR3 and CCR5 was higher before treatment in non-responders than in responders (p<0.05). The number of T cells increased in responders.

CONCLUSION

Increase in secretion of Th1 and Th2 cytokines together with induced expression of chemokine receptors on T cells and monocytes suggest restoration of peripheral cell mediated immunity and blockade of the accumulation of inflammatory cells in joints as response to treatment.

Peptidylarginine deiminase, the arginine to citrulline converting enzyme, is frequently recognized by sera of patients with rheumatoid arthritis, systemic lupus erythematosus and primary Sjögren syndrome

OBJECTIVE

Antibodies to citrulline-containing epitopes of filaggrin are highly specific for rheumatoid arthritis (RA). We studied whether the enzyme peptidylarginine deiminase (PAD), responsible for the post-translational modification of peptide-bound arginine residues to citrulline, constitutes an antigen for patients with RA.

METHODS

IgG antibodies to PAD were measured by enzyme-linked immunosorbent assay (ELISA) in sera from patients with RA, systemic lupus erythematosus (SLE), primary Sjögren syndrome (pSS), multiple sclerosis (MS) and healthy controls.

RESULTS

Compared to healthy controls, raised levels of IgG antibodies to PAD were found in 50 of 57 recent-onset RA patients (88%) and in 40 (70%) of the same 57 patients 3 years later (p<0.0001 for both comparisons). Eleven of 51 (22%) patients with RA of long duration, 19/43 (44%) patients with SLE and 16/19 (84%) patients with pSS, but none of 20 patients with MS, had elevated anti-PAD levels.

CONCLUSION

The arginine-citrulline converting enzyme PAD was recognized as a new antigen against which patients with inflammatory rheumatic diseases frequently show IgG class antibodies.