Portability of genomic predictions trained on sparse factorial designs across two maize silage breeding cycles

KEY MESSAGE

We validated the efficiency of genomic predictions calibrated on sparse factorial training sets to predict the next generation of hybrids and tested different strategies for updating predictions along generations. Genomic selection offers new prospects for revisiting hybrid breeding schemes by replacing extensive phenotyping of individuals with genomic predictions. Finding the ideal design for training genomic prediction models is still an open question. Previous studies have shown promising predictive abilities using sparse factorial instead of tester-based training sets to predict single-cross hybrids from the same generation. This study aims to further investigate the use of factorials and their optimization to predict line general combining abilities (GCAs) and hybrid values across breeding cycles. It relies on two breeding cycles of a maize reciprocal genomic selection scheme involving multiparental connected reciprocal populations from flint and dent complementary heterotic groups selected for silage performances. Selection based on genomic predictions trained on a factorial design resulted in a significant genetic gain for dry matter yield in the new generation. Results confirmed the efficiency of sparse factorial training sets to predict candidate line GCAs and hybrid values across breeding cycles. Compared to a previous study based on the first generation, the advantage of factorial over tester training sets appeared lower across generations. Updating factorial training sets by adding single-cross hybrids between selected lines from the previous generation or a random subset of hybrids from the new generation both improved predictive abilities. The CDmean criterion helped determine the set of single-crosses to phenotype to update the training set efficiently. Our results validated the efficiency of sparse factorial designs for calibrating hybrid genomic prediction experimentally and showed the benefit of updating it along generations.

Genomic prediction of hybrid performance: comparison of the efficiency of factorial and tester designs used as training sets in a multiparental connected reciprocal design for maize silage

Calibrating a genomic selection model on a sparse factorial design rather than on tester designs is advantageous for some traits, and equivalent for others. In maize breeding, the selection of the candidate inbred lines is based on topcross evaluations using a limited number of testers. Then, a subset of single-crosses between these selected lines is evaluated to identify the best hybrid combinations. Genomic selection enables the prediction of all possible single-crosses between candidate lines but raises the question of defining the best training set design. Previous simulation results have shown the potential of using a sparse factorial design instead of tester designs as the training set. To validate this result, a 363 hybrid factorial design was obtained by crossing 90 dent and flint inbred lines from six segregating families. Two tester designs were also obtained by crossing the same inbred lines to two testers of the opposite group. These designs were evaluated for silage in eight environments and used to predict independent performances of a 951 hybrid factorial design. At a same number of hybrids and lines, the factorial design was as efficient as the tester designs, and, for some traits, outperformed them. All available designs were used as both training and validation set to evaluate their efficiency. When the objective was to predict single-crosses between untested lines, we showed an advantage of increasing the number of lines involved in the training set, by (1) allocating each of them to a different tester for the tester design, or (2) reducing the number of hybrids per line for the factorial design. Our results confirm the potential of sparse factorial designs for genomic hybrid breeding.

SAT0272 THE VALUE OF CLINICAL AND LABORATORY FEATURES TO PREDICT EXTENT OF LARGE VESSEL VASCULITIS ON PET CT

Background:

Giant cell arteritis (GCA) is an idiopathic vasculitis affecting large and medium-sized vessels. The pattern of arterial involvement is heterogeneous with two overlapping categories recognised: classical cranial GCA and extra-cranial GCA (or large vessel vasculitis – LVV) that predominantly affects the aorta and its proximal branches. Although LVV is present in around 80% of patients with cranial GCA, and around one third will develop large vessel complications, there are no guidelines for which patients should be screened for it (1). We sought to investigate whether clinical and laboratory features were a useful guide to the severity of LVV on FDG PET-CT.

Objectives:

To retrospectively analyse whether baseline patient characteristics are able to predict the extent of large vessel vasculitis on PET-CT.

Methods:

Clinical data for 65 patients referred for a PET-CT scan by Rheumatology at the Freeman Hospital, Newcastle between January 2015 and May 2018 were retrospectively analysed. The most recent full blood count and inflammatory markers prior to the scan were used. Scans were reviewed by a consultant radiologist and trainee. The arterial network was split in to ten potentially involved territories (aortic arch, thoracic aorta, abdominal aorta, iliac vessels, axillary, brachiocephalic, subclavian, carotid, vertebral and femoral arteries. Both the value of highest standardised uptake value (SUV max) and the territory affected was recorded for each positive scan.

Results:

In the period analysed 65 PET-CT scans were requested, mostly (77%) as baseline investigations for symptoms with LVV in the differential diagnosis. Of these 22 (34%) were positive for LVV and in that group the majority of patients (64%) were female. In those with a negative scan, 47.5% were on concurrent steroid treatment compared to 9% with a positive scan. Regression analysis suggested that the number of systemic features (weight loss, pyrexia, polymyalgia) was weakly correlated with the number of affected territories (p=0.04). In contrast there was no correlation between laboratory tests ((CRP (p=0.91), ESR (p=0.46), Hb (p=0.44), platelets (p=0.74)) and the number of territories affected. The aortic arch (47%) was most commonly the territory with the highest degree of FDG uptake (SUV max) followed by the abdominal aorta (21%) and thoracic (10%) and femoral arteries (10%). There was no correlation between SUV max and laboratory tests ((CRP (p=0.55), ESR (p=0.89), Hb (p=0.82), platelets (p=0.17)) or the number of systemic features (p=0.7). There was no significant difference in the number of territories affected between those on steroid treatment at the time of the scan and steroid-naïve patients, albeit the number of positive scans in those on steroid treatment was low (n=5).

Conclusion:

These results suggest that clinical and laboratory features are a poor guide to predicting the maximal severity and extent of disease on FDG PET-CT.

References:

[1]Koster MJ, Matteson EL, Warrington KJ. Large-vessel giant cell arteritis: diagnosis, monitoring and management. Rheumatology (Oxford). 2018;57(suppl_2):ii32-ii42.

Disclosure of Interests:

None declared

Multi-scale laboratory routine in the efficacy assessment of conservative products for natural stones

The evaluation of conservative treatments' efficacy on natural building stones are usually based on standard recommendation routines finalized to evaluate compatibility and harmfulness of products in turn of the substrate. However, the visualization and the quantification of products inside pore structure of natural stones is not immediate through standard tests, so that imaging and advanced techniques are recently proposed in material conservation field to improve knowledge on penetration depth, modification of pore-air interface at different scale and monitor dynamic absorption processes. Moreover, natural stones are usually characterized by complex structure, which changes due to conservative treatments have to be inspected at different scale (from micrometer to nanometer). In this prospective, the assessment of laboratory practices able to integrate multiscale methods and give back a complete overview on interaction between new conservative formulates and natural stones is of high interest. In this paper, we propose a methodological routine for efficacy assessment of conservative products, incorporating classical and innovative nondestructive techniques. Validation of the workflow has been verified on a high porous natural stone treated with new hybrid formulates appropriately customized for conservation issues. •The study intends to add new insights on problems related to consolidation of high porous carbonate stone, application methods in consolidating natural stones and methods to evaluate efficacy of new products.•A multi-scale laboratory investigation procedure is proposed by integrating standard and innovative nondestructive methods. Merits and limits of each applied method are discussed during validation.•The possibility to incorporate standard routines and/or substitute destructive testing with non-destructive ones seem to be a valid alternative to evaluate efficiency and monitor behavior of stones treated with consolidating products.

Multi-scale laboratory routine in the efficacy assessment of conservative products for natural stones

The evaluation of conservative treatments' efficacy on natural building stones are usually based on standard recommendation routines finalized to evaluate compatibility and harmfulness of products in turn of the substrate. However, the visualization and the quantification of products inside pore structure of natural stones is not immediate through standard tests, so that imaging and advanced techniques are recently proposed in material conservation field to improve knowledge on penetration depth, modification of pore-air interface at different scale and monitor dynamic absorption processes. Moreover, natural stones are usually characterized by complex structure, which changes due to conservative treatments have to be inspected at different scale (from micrometer to nanometer). In this prospective, the assessment of laboratory practices able to integrate multiscale methods and give back a complete overview on interaction between new conservative formulates and natural stones is of high interest. In this paper, we propose a methodological routine for efficacy assessment of conservative products, incorporating classical and innovative nondestructive techniques. Validation of the workflow has been verified on a high porous natural stone treated with new hybrid formulates appropriately customized for conservation issues. •The study intends to add new insights on problems related to consolidation of high porous carbonate stone, application methods in consolidating natural stones and methods to evaluate efficacy of new products.•A multi-scale laboratory investigation procedure is proposed by integrating standard and innovative nondestructive methods. Merits and limits of each applied method are discussed during validation.•The possibility to incorporate standard routines and/or substitute destructive testing with non-destructive ones seem to be a valid alternative to evaluate efficiency and monitor behavior of stones treated with consolidating products.

Analyzing two different data processing strategies for monitoring concrete structures using ultrasonic pulse velocity

RESUMENO crescente aumento dos sintomas de deterioração precoce em estruturas de concreto serve de argumento para o desenvolvimento e validação de técnicas de monitoramento do estado de conservação das mesmas. Além disto, fornecerem dados para estimar a vida útil das estruturas. A utilização de Ensaios Não Destrutivos permite a prevenção e o controle da deterioração de estruturas de concreto, sem danificar o material. O ensaio de Velocidade de Propagação do Pulso Ultrassônico (VPU) é uma forma bastante eficaz para realizar o controle de qualidade. Utilizando os resultados do ensaio de VPU é possível verificar a uniformidade de concreto, acompanhar sua deterioração, detectar falhas e vazios internos e, por meio de uma comparação com as amostras de referência, até mesmo estimar a resistência à compressão. Os resultados obtidos neste trabalho indicam que através do mapeamento superficial consegue-se analisar e visualizar os resultados dos ensaios de VPU.Palabras Clave: concreto; ultrassom; mapeamento superficial; análise estatística.ABSTRACTThe increasing number of early deterioration symptoms found in relatively new concrete structures provides a strong argument for the development and validation of techniques to monitor the condition state of concrete elements and provide data to estimate the potential service life. The use of NDT monitoring techniques is an important way to prevent and control the deterioration of concrete structures without damaging the material. Ultrasonic Pulse Velocity (UPV) measurements seem to be a quite effective way to perform quality control, since this reliable and flexible test method allows an in-depth analysis of the material’s condition. Using UPV data it is possible to check the concrete uniformity, accompany the deterioration, detect internal flaws and voids and, by means of a comparison with reference specimens, even estimate the compressive strength. The results indicate that surface mapping seems to be a better way to analyze and visualize UPV results.Keywords: concrete; ultrasonic methods; surface mapping; statistical analysis.

Modification of thrombomodulin plasma levels in refractory myeloma patients during treatment with thalidomide and dexamethasone

Deep venous thrombosis (DVT) has been variably reported in multiple myeloma patients during treatment with thalidomide alone or in combination with chemotherapy or dexamethasone. With the aim of investigating this complication, we performed, on a cohort of 13 relapsed refractory MM patients treated with low-dose thalidomide (100 mg/day) and dexamethasone (20 mg p.o./day for 4 days every 2 weeks), a serial evaluation of different laboratory parameters implicated in DVT. No significant abnormalities in all genetic, serologic, or plasmatic parameters studied were registered, apart from thrombomodulin which showed significant variations between baseline and 1st-month values and 1st- and 3rd-month values. In conclusion, the evidence of significant variations of thrombomodulin values in the 1st month of therapy, which is considered to involve the highest risk of thrombosis, might support a role for thrombomodulin in this complex mechanism.

Urinary proteins in multiple myeloma: correlation with clinical parameters and diagnostic implications

Renal failure is one of the worst complications occurring in multiple myeloma (MM) patients. It does not affect survival if reverted by a prompt chemotherapy before the damage becomes irreversible; therefore, the early diagnosis of renal dysfunction is crucial. High and low molecular weight urinary proteins have proved to be helpful in diagnosing initial renal damage since they are more sensitive than urea and creatinine serum levels or creatinine clearance. We studied the renal function of 111 MM patients through serum creatinine, urea, urinary IgG, alpha(1)-microglobulin (alpha(1)-M), and albumin (Alb). Two successive controls were made in a subset of 30 patients, categorized in three groups (improved, stable, worsened) according to the behavior of tumor burden markers (bone marrow plasmacytosis, monoclonal component, and beta(2)-microglobulin). In every group, we evaluated the behavior of urinary proteins. Renal dysfunction evaluated with serum parameters was present in 19 patients (17%), while if studied with urinary proteins was revealed in 71 patients (64.5%). Urinary proteins statistically correlated with each other. They correlated with creatinine, IgG, and alpha(1)-M also with urea. By contrast, they showed a variable correlation with clinical parameters: alpha(1)-M correlated with bone marrow plasmacytosis (BMPC) ( p=0.02) and beta(2)-M ( p=0.000001), IgG with all three disease parameters (MC p=0.0005, BMPC p=0.009, beta(2)-M p=0.007), and Alb only with beta(2)-M ( p=0.0004). In the subset of 30 patients followed with two successive controls, urinary proteins showed a parallel behavior with the indices of tumor burden. In conclusion, IgG, alpha(1)-microglobulin, and albumin are reliable and sensitive to precociously reveal renal damage, and we recommend their routine use for the definition and monitoring of renal function in multiple myeloma patients, mainly those in early stage, to better identify initial signs of progression.

Biochemical markers of bone disease in asymptomatic early stage multiple myeloma. A study on their role in identifying high risk patients

BACKGROUND AND OBJECTIVES

Skeletal involvement is typical of multiple myeloma (MM) and its occurrence increases with the progression of the disease. We performed a study to evaluate the clinical importance of osteocalcin (bone gla-protein, BGP) and bone alkaline phosphatase (b-AP) as indices of osteoblastic activity, and deoxypyridoline (DPD) as a marker of bone resorption.

DESIGN AND METHODS

Fifty-two MM patients, 39 patients with monoclonal gammopathy of undetermined significance (MGUS), and 30 normal controls entered the study. Of the 52 MM patients, 10 showed lytic lesions at standard X-rays and 42 did not; 21 were untreated and 31 had been treated with chemotherapy (combined with bisphophonates in 15). Of these last, 12 had progressive disease and 19 were in plateau phase.

RESULTS

DPD levels were higher in MM patients than in patients with MGUS or healthy controls (p = 0.0001 and p = 0.0008, respectively). No statistical differences were seen between patients with MGUS and healthy controls. BGP serum levels were significantly lower in MM patients than in MGUS patients (p = 0.001) or healthy controls (p = 0.001). b-AP was significantly higher in MGUS patients than in MM patients (p = 0.04). Biochemical parameters were analyzed in a continuous fashion and after dichotomization into low and high values with respect to normal ones. Abnormal high values of DPD showed statistically significant correlations with presence of osteolysis (p = 0.008), advanced stage (p = 0.03) and abnormal beta2-microglobulin (beta2M) values (p = 0.03), while DPD as a continuous variable correlated significantly only with the presence of osteolysis (p = 0.02). In contrast, neither BGP nor b-AP showed statistical correlations with the presence of lytic lesions, or with other clinical or laboratory parameters. In 15 patients followed with serial controls, modifications of DPD levels reflected bone disease status well. Of the 42 patients without radiologic evidence of skeletal lesions, 15 had abnormal DPD values. Spinal magnetic resonance imaging (MRI) showed initial lytic lesions in 10 of them.

INTERPRETATION AND CONCLUSIONS

Biochemical markers of bone metabolism are useful in evaluating and monitoring skeletal involvement in MM patients. They may help clinicians to identify: 1) from among patients without radiologic evidence of lytic lesions, those who deserve more accurate radiologic examinations (namely MRI); 2) from among asymptomatic patients, and in association with spinal MRI, those patients at higher risk of progression who might benefit from early treatment.

Missense mutation in exon 11 (Codon 378) of the presenilin-1 gene in a French family with early-onset Alzheimer's disease and transmission study by mismatch enhanced allele specific amplification. Mutations in brief no. 141. Online. besancon@rockefeller1.univ.lyon1.fr

Mutations in the presenilin-1 (PS1) gene account for the majority of familial early-onset Alzheimer's disease (EOAD) cases. We screened the coding part of the PS1 gene for the present of mutations in a French family with EOAD, using single strand conformation polymorphism (SSCP) analysis. Patients in the pedigree showed a missense mutation in exon 11 of the PS1 gene involving a transition of G to A, altering glycine to glutamate at codon 378. The cosegregation of the mutation with EOAD in the family was studied by allele specific amplification, enhanced by the introduction of a mismatch at the penultimate position near the 3' primer end. The mutation has not been described before and is located within the third large cytoplasmic loop and may lead to the appearance of a short additional a-helix.

A reconciliation of continuous and tidal ventilation gas exchange models

Continuous-ventilation mathematical gas exchange models are widely used since their analytical equations are amenable to physiological interpretation. They describe qualitatively the respiratory system's response to changing physiological conditions, but do not calculate accurate values for respiratory parameters when experimental tidal ventilation expired gas data are inserted into their analytical expressions. A simple mathematical expression is presented to reconcile continuous and tidal ventilation gas exchange models. Tidal ventilation experimental data can then be inserted into conventional continuous ventilation equations to produce more accurate measures of lung volume. This hypothesis is tested with controlled experimental tidal ventilation tracer gas data obtained from both wash-out and forced inspired sinusoid experiments, using a mechanical lung model with known volume; tidal volume, VT; and series 'airway' dead space VD. We show that the subtraction of 1/2 (VT + VD) from the lung volume calculated from the continuous ventilation theory can produce lung volume measurements which agree with the true lung volume to within +/-5%, for physiological lung volume values, for both wash-out and forced sinusoid techniques.

Evaluation of automatic antimicrobial susceptibility testing with the MS-2 system

We present the results of sensitivity of 191 Gram-negative bacteria towards the following antibiotics: aminoglycosides (amikacin, gentamicin, tobramycin, netilmicin), cephalosporines (moxalactam, cefotaxime, ceftazidime) and piperacilline obtained by agar diffusion method (Kirby-Bauer) versus automatic system MS 2 Abbott. Essential accord expressed in percentage is for amikacin 96%, for gentamicin 93%, for moxalactam 91%, for tobramycin 95%, for cefotaxime 92%, for piperacilline 89%, for netilmicin 90%, for ceftazidime 92. Full accord gives more discrepant results especially for cephalosporins. For aminoglycosides no significative differences were observed between the two methods. For cephalosporins the incidence of discordance was a little more high. A better sensitivity was obtained by Kirby-Bauer method versus automatic system, which can be considered a therapeutical tool as it furnishes rapidly (4 hours) MIC values, useful to establish antibiotic doses.