Category Archives: ORIGINAL ARTICLE

Antixenosis and antibiosis mechanisms of resistance to Asian rice gall midge, Orseolia oryzae (Wood‐Mason) in rice land races

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Antixenosis and antibiosis mechanisms of resistance to Asian rice gall midge, Orseolia oryzae (Wood-Mason) in rice land races

Rice gall midge resistance was governed by antixenosis and antibiosis mechanisms working in tandem. Antixenosis tests showed susceptible genotypes were preferred for egg laying and had faster adult emergence with a higher sex ratio. Resistant genotypes had higher levels of phenols, wax, flavonoids, and free amino acids, while susceptible ones had more sugars and protein. This study informs breeding for gall midge-resistant rice varieties.


Abstract

Asian rice gall midge is one of the important pests of rice, which attacks the crop from nursery to the end of the tillering stage. Managing this pest through plant resistance is the most viable and economical. Two hundred-two rice genotypes were phenotyped against Asian rice gall midge, Orseolia oryzae (Wood-Mason) and the mechanism of resistance in terms of antixenosis and antibiosis was studied. Antixenosis mechanism for adult settlement and egg laying indicated that the susceptible genotypes were preferred more than the resistant genotypes in a free choice test. First instar maggots were found and did not continue their growth on resistant genotypes further. However, in susceptible genotypes, they molted successfully and emerged as adults. No choice tests revealed that the emergence of adults in susceptible genotypes took less time than in resistant genotypes. Higher adult sex ratio was found in susceptible genotypes. Estimation of biochemical components in rice shoot apices of selected genotypes revealed that higher levels of total phenols, wax content, total flavonoids and total free amino acids were present in the resistant genotypes. Still, the number of total sugars, reducing sugars and total protein contents were significantly higher in the susceptible genotypes. Hence, the resistance mechanism in rice gall midge was displayed as a combination of antixenosis and antibiosis mechanism. The output of the study would be helpful in breeding for rice varieties resistant to Asian rice gall midge.

Randomized phase I/II study of vascular endothelial growth factor receptor peptide vaccines for patients with hepatocellular carcinoma

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Abstract

Aim

We evaluated the safety and efficacy of vascular endothelial growth factor receptor (VEGFR)-targeted peptide vaccines for the immunization of patients with unresectable hepatocellular carcinoma (HCC) who had responded to transarterial chemoembolization.

Methods

Twenty-two patients were randomized 1:1 to receive VEGFR-targeted peptides or placebo. The primary end-point was the safety assessment of the immunization. The secondary end-points were evaluation of immunological responses and clinical outcomes.

Results

No severe adverse events were induced by the study agents. Among the 12 patients in the vaccine group, a VEGFR1-specific cytotoxic T lymphocyte (CTL) response was induced in eight (66.7%) patients and a VEGFR2-specific CTL response was induced in 10 (83.3%). The median progression-free survival (PFS) and overall survival (OS) rates were 4.8 and 52.0 months, respectively, in the vaccine group, and 2.7 and 21.8 months, respectively, in the placebo group. No statistically significant differences were found between the two groups (PFS p = 0.925, OS p = 0.190). When divided into two groups according to immunoreactivity, the median PFS of patients with and without a strong immune response to VEGFR1 were 7.4 and 2.7 months, and that to VEGFR2 were 10.6 and 2.7 months, respectively; there were significant differences according to the immune response.

Conclusions

Immunotherapy with peptide vaccines targeting VEGFR1 and VEGFR2 was well tolerated with no serious adverse events. It also effectively induced peptide-specific CTLs in patients with unresectable HCC.

Metabolic dysfunction‐associated steatotic liver disease criteria may underestimate the number of lean female nonalcoholic fatty liver disease patients with significant liver fibrosis

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Abstract

Aim

It remains unclear whether the newly defined concept of metabolic dysfunction-associated steatotic liver disease (MASLD) appropriately includes patients with nonalcoholic fatty liver disease with significant liver fibrosis.

Methods

A total of 4112 patients in whom nonalcoholic fatty liver disease was diagnosed by ultrasonography during medical checkups were enrolled. We defined a fibrosis-4 index ≥1.3 in patients aged <65 years and ≥2.0 in patients aged ≥65 years as significant liver fibrosis.

Results

The numbers of patients with a low, intermediate, and high probability of advanced fibrosis based on the fibrosis-4 index were 3360 (81.7%), 668 (16.2%), and 84 (2.0%). There were 3828 (93.1%) and 284 (6.9%) patients diagnosed with MASLD and non-MASLD. The non-MASLD group, compared with the MASLD group, was significantly younger (44 vs. 55 years) and had a higher percentage of women (62.3% vs. 27.7%). Significant fibrosis, defined based on the fibrosis-4 index, was present in 18.5% of the MASLD group and 15.5% of the non-MASLD group. In a multivariable analysis, female sex (OR 6.170, 95% CI 3.180–12.000; p < 0.001) was independently associated with non-MASLD in patients with a significant fibrosis. Among non-MASLD patients with a significant fibrosis (n = 44), body mass index was significantly lower in females than in males (p < 0.001). In a multivariable analysis of patients aged <65 years, female sex (OR, 7.700; 95% CI, 3.750–15.800; p < 0.001) remained independently associated with non-MASLD in patients with a significant fibrosis.

Conclusions

MASLD may inappropriately exclude patients with significant fibrosis, especially lean females with nonalcoholic fatty liver disease.

Lethality of pesticides on immature and adult stages of Ceratitis capitata (Diptera: Tephritidae)

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Lethality of pesticides on immature and adult stages of Ceratitis capitata (Diptera: Tephritidae)

This manuscript provides information Using sub-doses of the insecticides to simulate the degradation of the active ingredients at levels below the 100% concentration. We showed that Deltamethrin (pyrethroid) showed little efficiency for the control of C. capitata when compared to Malathion (organophosphate) and Spinetoram (spinosyn). The article also provides information on the effect of these pesticides on different life stages of the insect (egg, larva, pupa, and adults).


Abstract

The species Ceratitis capitata (Weidemann, 1824), known as Mediterranean fruit fly, is an important pest for fruit trees worldwide. The control of this pest is carried out mainly by the chemical method, using organophosphorus, pyrethroid, and spinosyn pesticides. The lethality of doses of malathion, deltamethrin, and spinetoram on immature and adult stages of C. capitata was evaluated under laboratory conditions. The egg, larval, pupal, and adult stages were exposed to doses of pesticides through contact and ingestion. The doses were obtained by decreasing the recommended doses (malathion: 200 mL L−1, deltamethrin: 50 mL L−1, and spinetoram: 120 g ha−1) with intervals of 20%, this being the minimum dose used. The variables evaluated were: viability of eggs and pupae and mortality of larvae and adults. Application of spinetoram and malathion through contact caused high mortality of adults, with LD90 at the sub-doses of 43.74% (52.48 g c.p. ha−1) and 68.81% (137.62 mL c.p. 100 L−1), respectively. The mortality of adults by ingestion of deltamethrin and malathion allowed us to estimate only the LD50. Only the pesticide deltamethrin presented LD50 for the egg stage. The larval and pupal stages the effect of the pesticides on larvae treated through contact resulted in 52% mortality with spinetoram and 62% with malathion. The mortality of larvae and pupae treated through ingestion was below 20% for the three pesticides. Sub-doses of spinetoram (43.74%; 52.48 g c.p. ha−1) and malathion (68.81%; 137.62 mL c.p. 100 L−1) can be used since they present a 90% efficiency on C. capitata adult when applied by contact under laboratory conditions.

The impact of the COVID‐19 pandemic on hepatocellular carcinoma diagnosis and treatment in Japan: A multicenter collaborative observational study

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The impact of the COVID-19 pandemic on hepatocellular carcinoma diagnosis and treatment in Japan: A multicenter collaborative observational study

The number of hepatocellular carcinoma-related general medical practices decreased during the first state of emergency. However, there were no major significant delays leading to hepatocellular carcinoma stage progression for patients newly diagnosed with hepatocellular carcinoma due to the coronavirus disease 2019 pandemic.


Abstract

Aim

Coronavirus disease 2019 emerged in December 2019 and spread worldwide. This study aimed to clarify the impact of the coronavirus disease 2019 pandemic on the diagnosis and treatment of hepatocellular carcinoma (HCC) in Japan.

Methods

First, we collected the monthly numbers of HCC-related general medical practices from January 2019 to December 2021 at liver disease-specific medical institutions in Japan. Next, we collected individual clinical information from patients with newly diagnosed HCC during this period.

Results

There was a decrease in the number of HCC-related medical practices, including referrals, enhanced abdominal ultrasonography and radiofrequency ablation, in Japan's first state of emergency (SOE; April–May 2020) compared with 2019. Fewer patients were diagnosed with new HCC during the first SOE than before or after it. There was no difference in tumor diameter, number of tumors or Barcelona Clinic Liver Cancer stage between patients diagnosed before the first SOE and those diagnosed during or after the first SOE. The median waiting times for treatment of patients diagnosed during and after the first SOE were 31 and 37 days, which were significantly shorter and not longer than that of patients diagnosed before the first SOE (36 days), respectively.

Conclusion

The number of HCC-related general medical practices decreased during the first SOE. However, the coronavirus disease 2019 pandemic did not lead to HCC progression by diagnostic delays or cause HCC treatment delays in Japan.

Cost‐effectiveness analysis of adult living‐donor liver transplantation in Japan

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Cost-effectiveness analysis of adult living-donor liver transplantation in Japan

We performed a cost-effectiveness analysis of living-donor liver transplantation (LDLT) compared to conservative management (CM) for adult patients using the Japanese nationwide database of the Diagnostic Procedure Combination research group. LDLT compared with CM for patients with Child–Pugh class C was cost-effective, with an incremental cost-effectiveness ratio (ICER) of 2.08 million JPY/QALY (20,708 USD/QALY), whereas LDLT versus CM for patients with Child–Pugh class B was not cost-effective, with an ICER of 5.24 million JPY/QALY (52,153 USD/QALY).


Abstract

Aim

Living-donor liver transplantation (LDLT) is a highly effective life-saving procedure; however, it requires substantial medical resources, and the cost-effectiveness of LDLT versus conservative management (CM) for adult patients with end-stage liver disease (ESLD) remains unclear in Japan.

Methods

We performed a cost-effectiveness analysis using the Diagnostic Procedure Combination (DPC) data from the nationwide database of the DPC research group. We selected adult patients (18 years or older) who were admitted or discharged between 2010 and 2021 with a diagnosis of ESLD with Child–Pugh class C or B. A decision tree and Markov model were constructed, and all event probabilities were computed in 3-month cycles over a 10-year period. The willingness-to-pay per quality-adjusted life-year (QALY) was set at 5 million Japanese yen (JPY) (49,801 US dollars [USD]) from the perspective of the public health-care payer.

Results

After propensity score matching, we identified 1297 and 111,849 patients in the LDLT and CM groups, respectively. The incremental cost-effectiveness ratio for LDLT versus CM for Child–Pugh classes C and B was 2.08 million JPY/QALY (20,708 USD/QALY) and 5.24 million JPY/QALY (52,153 USD/QALY), respectively. The cost-effectiveness acceptability curves showed the probabilities of being below the willingness-to-pay of 49,801 USD/QALY as 95.4% in class C and 48.5% in class B. Tornado diagrams revealed all variables in class C were below 49,801 USD/QALY while their ranges included or exceeded 49,801 USD/QALY in class B.

Conclusions

Living-donor liver transplantation for adult patients with Child–Pugh class C was cost-effective compared with CM, whereas LDLT versus CM for class B patients was not cost-effective in Japan.

Alternative SNP weighting for multi‐step and single‐step genomic BLUP in the presence of causative variants

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Abstract

The accuracy of genetic selection in dairy can be increased by the adoption of new technologies, such as the inclusion of sequence data. In simulation studies, assigning different weights to causative single-nucleotide polymorphism (SNP) markers led to better predictions depending on the genomic prediction method used. However, it is still not clear how the weights should be calculated. Our objective was to evaluate the accuracy of a multi-step method (GBLUP) and single-step GBLUP with simulated data using regular SNP, causatives variants (QTN) and the combination of both. Additionally, we compared the accuracies of all previous scenarios using alternatives for SNP weighting. The data were simulated assuming a single trait with a heritability of 0.3. The effective population size (Ne) was approximately 200. The pedigree contained 440,000 animals, and approximately 16,800 individuals were genotyped. A total of 49,974 SNP markers were evenly placed throughout the genome, and 100, 1000 and 2000 causative QTN were simulated. Both GBLUP and ssGBLUP were used in this study. We evaluated quadratic and nonlinear SNP weights in addition to the unweighted G. The inclusion of QTN to panels led to significant accuracy gains. Nonlinear A was demonstrated to be superior to quadratic weighting and unweighted approaches; however, results from Nonlinear A were dependent on the equation parameters. The unweighted approach was more suitable for less polygenic scenarios. Finally, SNP weighting might help elucidate trait architecture features based on changes in the accuracy of genomic prediction.

Population genomic structures and signatures of selection define the genetic uniqueness of several fancy and meat rabbit breeds

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Abstract

Following the recent domestication process of the European rabbit (Oryctolagus cuniculus), many different breeds and lines, distinguished primarily by exterior traits such as coat colour, fur structure and body size and shape, have been constituted. In this study, we genotyped, with a high-density single-nucleotide polymorphism panel, a total of 645 rabbits from 10 fancy breeds (Belgian Hare, Champagne d'Argent, Checkered Giant, Coloured Dwarf, Dwarf Lop, Ermine, Giant Grey, Giant White, Rex and Rhinelander) and three meat breeds (Italian White, Italian Spotted and Italian Silver). ADMIXTURE analysis indicated that breeds with similar phenotypic traits (e.g. coat colour and body size) shared common ancestries. Signatures of selection using two haplotype-based approaches (iHS and XP-EHH), combined with the results obtained with other methods previously reported that we applied to the same breeds, we identified a total of 5079 independent genomic regions with some signatures of selection, covering about 1777 Mb of the rabbit genome. These regions consistently encompassed many genes involved in pigmentation processes (ASIP, EDNRA, EDNRB, KIT, KITLG, MITF, OCA2, TYR and TYRP1), coat structure (LIPH) and body size, including two major genes (LCORL and HMGA2) among many others. This study revealed novel genomic regions under signatures of selection and further demonstrated that population structures and signatures of selection, left into the genome of these rabbit breeds, may contribute to understanding the genetic events that led to their constitution and the complex genetic mechanisms determining the broad phenotypic variability present in these untapped rabbit genetic resources.

Genetic parameter estimation for pork production and litter performance traits of Landrace, Large White, and Duroc pigs in Japan

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Abstract

We estimated genetic parameters for two pork production and six litter performance traits of Landrace, Large White, and Duroc pigs reared in Japan. Pork production traits were average daily gain from birth to end of performance testing and backfat thickness at end of testing (46,042 records for Landrace, 40,467 records for Large White, and 42,920 records for Duroc). Litter performance traits were number born alive, litter size at weaning (LSW), number of piglets dead during suckling (ND), survival rate of piglets during suckling (SV), total piglet weight at weaning (TWW), and average piglet weight at weaning (AWW) (27,410, 26,716, and 12,430 records for Landrace, Large White, and Duroc, respectively). ND was calculated as the difference between LSW and litter size at start of suckling (LSS). SV was calculated as LSW/LSS. AWW was calculated as TWW/LSW. Pedigree data for Landrace, Large White, and Duroc breeds contained 50,193, 44,077, and 45,336 pigs, respectively. Trait heritability was estimated via single-trait analysis and genetic correlation between two traits was estimated via two-trait analysis. When considering the linear covariate of LSS in the statistical model for LSW and TWW, for all breeds, the heritability was estimated to be 0.4–0.5 for pork production traits and below 0.2 for litter performance traits. Estimated genetic correlation between average daily gain and backfat thickness was small, ranging from 0.057 to 0.112, and those between pork production traits and litter performance traits were negligible to moderate, ranging from −0.493 to 0.487. A wide range of genetic correlation values among the litter performance traits was estimated, while that between LSW and ND could not be obtained. The results of genetic parameter estimation were affected by whether the linear covariate of LSS was included in the statistical model for LSW and TWW or not. This finding implies the necessity of carefully interpreting the results according to the choice of statistical model. Our results could give fundamental information on simultaneously improving productivity and female reproductivity for pigs.

Impact of multi‐output and stacking methods on feed efficiency prediction from genotype using machine learning algorithms

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Abstract

Feeding represents the largest economic cost in meat production; therefore, selection to improve traits related to feed efficiency is a goal in most livestock breeding programs. Residual feed intake (RFI), that is, the difference between the actual and the expected feed intake based on animal's requirements, has been used as the selection criteria to improve feed efficiency since it was proposed by Kotch in 1963. In growing pigs, it is computed as the residual of the multiple regression model of daily feed intake (DFI), on average daily gain (ADG), backfat thickness (BFT), and metabolic body weight (MW). Recently, prediction using single-output machine learning algorithms and information from SNPs as predictor variables have been proposed for genomic selection in growing pigs, but like in other species, the prediction quality achieved for RFI has been generally poor. However, it has been suggested that it could be improved through multi-output or stacking methods. For this purpose, four strategies were implemented to predict RFI. Two of them correspond to the computation of RFI in an indirect way using the predicted values of its components obtained from (i) individual (multiple single-output strategy) or (ii) simultaneous predictions (multi-output strategy). The other two correspond to the direct prediction of RFI using (iii) the individual predictions of its components as predictor variables jointly with the genotype (stacking strategy), or (iv) using only the genotypes as predictors of RFI (single-output strategy). The single-output strategy was considered the benchmark. This research aimed to test the former three hypotheses using data recorded from 5828 growing pigs and 45,610 SNPs. For all the strategies two different learning methods were fitted: random forest (RF) and support vector regression (SVR). A nested cross-validation (CV) with an outer 10-folds CV and an inner threefold CV for hyperparameter tuning was implemented to test all strategies. This scheme was repeated using as predictor variables different subsets with an increasing number (from 200 to 3000) of the most informative SNPs identified with RF. Results showed that the highest prediction performance was achieved with 1000 SNPs, although the stability of feature selection was poor (0.13 points out of 1). For all SNP subsets, the benchmark showed the best prediction performance. Using the RF as a learner and the 1000 most informative SNPs as predictors, the mean (SD) of the 10 values obtained in the test sets were: 0.23 (0.04) for the Spearman correlation, 0.83 (0.04) for the zero–one loss, and 0.33 (0.03) for the rank distance loss. We conclude that the information on predicted components of RFI (DFI, ADG, MW, and BFT) does not contribute to improve the quality of the prediction of this trait in relation to the one obtained with the single-output strategy.