Triangle Singularity as the Origin of the a_{1}(1420).

The COMPASS Collaboration experiment recently discovered a new isovector resonancelike signal with axial-vector quantum numbers, the a_{1}(1420), decaying to f_{0}(980)π. With a mass too close to and a width smaller than the axial-vector ground state a_{1}(1260), it was immediately interpreted as a new light exotic meson, similar to the X, Y, Z states in the hidden-charm sector. We show that a resonancelike signal fully matching the experimental data is produced by the decay of the a_{1}(1260) resonance into K^{*}(→Kπ)K[over ¯] and subsequent rescattering through a triangle singularity into the coupled f_{0}(980)π channel. The amplitude for this process is calculated using a new approach based on dispersion relations. The triangle-singularity model is fitted to the partial-wave data of the COMPASS experiment. Despite having fewer parameters, this fit shows a slightly better quality than the one using a resonance hypothesis and thus eliminates the need for an additional resonance in order to describe the data. We thereby demonstrate for the first time in the light-meson sector that a resonancelike structure in the experimental data can be described by rescattering through a triangle singularity, providing evidence for a genuine three-body effect.

Assessment of Allergen-Responsive Regulatory T Cells in Experimental Asthma Induced in Different Mouse Strains.

BACKGROUND: Regulatory T cells (Tregs) are important in regulating responses to innocuous antigens, such as allergens, by controlling the Th2 response, a mechanism that appears to be compromised in atopic asthmatic individuals. Different isogenic mouse strains also have distinct immunological responses and susceptibility to the experimental protocols used to develop lung allergic inflammation. In this work, we investigated the differences in the frequency of Treg cell subtypes among A/J, BALB/c, and C57BL/6, under normal conditions and following induction of allergic asthma with ovalbumin (OVA). METHODS: Subcutaneous sensitization followed by 4 consecutive intranasal OVA challenges induced asthma characteristic changes such as airway hyperreactivity, inflammation, and production of Th2 cytokines (IL-4, IL-13, IL-5, and IL-33) in the lungs of only A/J and BALB/c but not C57BL/6 strain and evaluated by invasive whole-body plethysmography, flow cytometry, and ELISA, respectively. RESULTS: A/J strain naturally showed a higher frequency of CD4+IL-10+ T cells in the lungs of naïve mice compared to the other strains, accompanied by higher frequencies of CD4+IL-4+ T cells. C57BL/6 mice did not develop lung inflammation and presented higher frequency of CD4+CD25+Foxp3+ Treg cells in the bronchoalveolar lavage fluid (BALF) after the allergen challenge. In in vitro settings, allergen-specific stimulation of mediastinal LN (mLN) cells from OVA-challenged animals induced higher frequency of CD4+IL-10+ Treg cells from A/J strain and CD4+CD25+Foxp3+ from C57BL/6. CONCLUSIONS: The observed differences in the frequencies of Treg cell subtypes associated with the susceptibility of the animals to experimental asthma suggest that CD4+CD25+Foxp3+ and IL-10-producing CD4+ Treg cells may play different roles in asthma control. Similar to asthmatic individuals, the lack of an efficient regulatory response and susceptibility to the development of experimental asthma in A/J mice further suggests that this strain could be preferably chosen in experimental models of allergic asthma.

Haplosporosomes, sporoplasmosomes and their putative taxonomic relationships in rhizarians and myxozoans.

This paper reviews current knowledge of the structure, genesis, cytochemistry and putative functions of the haplosporosomes of haplosporidians (Urosporidium, Haplosporidium, Bonamia, Minchinia) and paramyxids (Paramyxa, Paramyxoides, Marteilia, Marteilioides, Paramarteilia), and the sporoplasmosomes of myxozoans (Myxozoa - Malacosporea, Myxosporea). In all 3 groups, these bodies occur in plasmodial trophic stages, disappear at the onset of sporogony, and reappear in the spore. Some haplosporidian haplosporosomes lack the internal membrane regarded as characteristic of these bodies and that phylum. Haplosporidian haplosporogenesis is through the Golgi (spherulosome in the spore), either to form haplosporosomes at the trans-Golgi network, or for the Golgi to produce formative bodies from which membranous vesicles bud, thus acquiring the external membrane. The former method also forms sporoplasmosomes in malacosporeans, while the latter is the common method of haplosporogenesis in paramyxids. Sporoplasmogenesis in myxosporeans is largely unknown. The haplosporosomes of Haplosporidium nelsoni and sporoplasmosomes of malacosporeans are similar in arraying themselves beneath the plasmodial plasma membrane with their internal membranes pointing to the exterior, possibly to secrete their contents to lyse host cells or repel haemocytes. It is concluded that these bodies are probably multifunctional within and between groups, their internal membranes separating different functional compartments, and their origin may be from common ancestors in the Neoproterozoic.

Molecular data infers the involvement of a marine aurantiactinomyxon in the life cycle of the myxosporean parasite Paramyxidium giardi (Cnidaria, Myxozoa).

An aurantiactinomyxon type is described from the marine naidid Tubificoides pseudogaster (Dahl, 1960), collected from the lower estuary of a Northern Portuguese River. This type constitutes the first of its collective group to be reported from Portugal, and only the fourth described from a marine oligochaete worldwide. Extensive morphological comparisons of new aurantiactinomyxon isolates to all known types without available molecular data are proposed to be unnecessary, given the artificiality of the usage of morphological criteria for actinosporean differentiation and the apparent strict host specificity of the group. Recognition of naidid oligochaetes as the hosts of choice for marine types of aurantiactinomyxon and other collective groups, suggests that the family Naididae played a preponderant role in the myxosporean colonization of estuarine communities. Molecular analyses of the type in study further infer its involvement in the life cycle of Paramyxidium giardi (Cépède, 1906) Freeman and Kristmundsson, 2018, a species that infects the kidney of European eel Anguilla anguilla (Linnaeus, 1758) and that has been reported globally, including from Portuguese waters. The low intraspecific difference registered in relation to Icelandic isolates of P. giardi (0.6%) is hypothesized to result from the emergence of genotypically different subspecies due to geographic isolation.

Phylogeny and comprehensive revision of mugiliform-infecting myxobolids (Myxozoa, Myxobolidae), with the morphological and molecular redescription of the cryptic species Myxobolus exiguus.

Mullets inhabit a wide range of habitats from tropical to temperate regions and play a critical role in their ecosystems. This commercially important fish group constitutes a significant source of food in several geographic regions, and the production of some species for consumption is an increasing trend. About 64 myxosporean species have been reported in mullets, some of which are cryptic, as is the case of Myxobolus exiguus, and M. muelleri. This paper provides, for the first time, a detailed and critical revision of the data available for myxobolids reported in mullets, determining the species that have bona fide mugiliform fish hosts, in accordance with the original species descriptions, the available molecular data and the currently accepted taxonomic and phylogenetic criteria. Phylogenetic analyses using Bayesian inference and maximum-likelihood methodologies suggest that the evolutionary history of myxobolids with bona fide mugiliform fish hosts reflects that of its vertebrate hosts, while reinforcing known evolutionary factors and old systematic issues of the clade of myxobolids. A comprehensive morphological, ultrastructural and molecular redescription is also provided for the cryptic species M. exiguus, from infections in the visceral peritoneum of the thinlip-grey mullet Chelon ramada in the River Minho, Portugal.

Demonstration of Single-Barium-Ion Sensitivity for Neutrinoless Double-Beta Decay Using Single-Molecule Fluorescence Imaging.

A new method to tag the barium daughter in the double-beta decay of ^{136}Xe is reported. Using the technique of single molecule fluorescent imaging (SMFI), individual barium dication (Ba^{++}) resolution at a transparent scanning surface is demonstrated. A single-step photobleach confirms the single ion interpretation. Individual ions are localized with superresolution (∼2 nm), and detected with a statistical significance of 12.9σ over backgrounds. This lays the foundation for a new and potentially background-free neutrinoless double-beta decay technology, based on SMFI coupled to high pressure xenon gas time projection chambers.

First Measurement of Transverse-Spin-Dependent Azimuthal Asymmetries in the Drell-Yan Process.

The first measurement of transverse-spin-dependent azimuthal asymmetries in the pion-induced Drell-Yan (DY) process is reported. We use the CERN SPS 190 GeV/c π^{-} beam and a transversely polarized ammonia target. Three azimuthal asymmetries giving access to different transverse-momentum-dependent (TMD) parton distribution functions (PDFs) are extracted using dimuon events with invariant mass between 4.3 GeV/c^{2} and 8.5 GeV/c^{2}. Within the experimental uncertainties, the observed sign of the Sivers asymmetry is found to be consistent with the fundamental prediction of quantum chromodynamics (QCD) that the Sivers TMD PDFs extracted from DY have a sign opposite to the one extracted from semi-inclusive deep-inelastic scattering (SIDIS) data. We present two other asymmetries originating from the pion Boer-Mulders TMD PDFs convoluted with either the nucleon transversity or pretzelosity TMD PDFs. A recent COMPASS SIDIS measurement was obtained at a hard scale comparable to that of these DY results. This opens the way for possible tests of fundamental QCD universality predictions.

Assessing the expected response to genomic selection of individuals and families in Eucalyptus breeding with an additive-dominant model.

We report a genomic selection (GS) study of growth and wood quality traits in an outbred F2 hybrid Eucalyptus population (n=768) using high-density single-nucleotide polymorphism (SNP) genotyping. Going beyond previous reports in forest trees, models were developed for different selection targets, namely, families, individuals within families and individuals across the entire population using a genomic model including dominance. To provide a more breeder-intelligible assessment of the performance of GS we calculated the expected response as the percentage gain over the population average expected genetic value (EGV) for different proportions of genomically selected individuals, using a rigorous cross-validation (CV) scheme that removed relatedness between training and validation sets. Predictive abilities (PAs) were 0.40-0.57 for individual selection and 0.56-0.75 for family selection. PAs under an additive+dominance model improved predictions by 5 to 14% for growth depending on the selection target, but no improvement was seen for wood traits. The good performance of GS with no relatedness in CV suggested that our average SNP density (~25 kb) captured some short-range linkage disequilibrium. Truncation GS successfully selected individuals with an average EGV significantly higher than the population average. Response to GS on a per year basis was ~100% more efficient than by phenotypic selection and more so with higher selection intensities. These results contribute further experimental data supporting the positive prospects of GS in forest trees. Because generation times are long, traits are complex and costs of DNA genotyping are plummeting, genomic prediction has good perspectives of adoption in tree breeding practice.

Life cycle inference and phylogeny of Ortholinea labracis n. sp. (Myxosporea: Ortholineidae), a parasite of the European seabass Dicentrarchus labrax (Teleostei: Moronidae), in a Portuguese fish farm.

Ortholinea labracis n. sp. is described and its life cycle is inferred from a Southern Portuguese fish farm, with basis on microscopic and molecular procedures. This myxosporean parasite infects the urinary bladder of the European seabass Dicentrarchus labrax and the intestinal epithelium of a marine oligochaete of the genus Tectidrilus. Myxospores subspherical in valvular view and ellipsoidal in sutural view measuring 7.6 ± 0.3 (6.8-8.7) µm in length, 7.2 ± 0.2 (6.7-7.7) µm in width and 6.5 ± 0.4 (5.8-7.7) µm in thickness. Two polar capsules, 3.0 ± 0.2 (2.6-3.4) µm long and 2.4 ± 0.1 (2.0-2.9) µm wide, located at the same level, but with divergent orientation and opening to opposite sides of the suture line. Sequencing of the SSU rRNA gene revealed a similarity of 100% between the analysed myxospores and triactinomyxon actinospores. The phylogenetic setting of O. labracis n. sp. shows subgrouping in correlation with tissue tropism, but identifies this parasite as another exception to the main division of Myxosporea into the main freshwater and marine lineages.

Regularized quantile regression applied to genome-enabled prediction of quantitative traits.

Genomic selection (GS) is a variant of marker-assisted selection, in which genetic markers covering the whole genome predict individual genetic merits for breeding. GS increases the accuracy of breeding values (BV) prediction. Although a variety of statistical models have been proposed to estimate BV in GS, few methodologies have examined statistical challenges based on non-normal phenotypic distributions, e.g., skewed distributions. Traditional GS models estimate changes in the phenotype distribution mean, i.e., the function is defined for the expected value of trait-conditional on markers, E(Y|X). We proposed an approach based on regularized quantile regression (RQR) for GS to improve the estimation of marker effects and the consequent genomic estimated BV (GEBV). The RQR model is based on conditional quantiles, Qτ(Y|X), enabling models that fit all portions of a trait probability distribution. This allows RQR to choose one quantile function that "best" represents the relationship between the dependent and independent variables. Data were simulated for 1000 individuals. The genome included 1500 markers; most had a small effect and only a few markers with a sizable effect were simulated. We evaluated three scenarios according to symmetrical, positively, and negatively skewed distributions. Analyses were performed using Bayesian LASSO (BLASSO) and RQR considering three quantiles (0.25, 0.50, and 0.75). The use of RQR to estimate GEBV was efficient; the RQR method achieved better results than BLASSO, at least for one quantile model fit for all evaluated scenarios. The gains in relation to BLASSO were 86.28 and 55.70% for positively and negatively skewed distributions, respectively.

Early syphilis treatment in HIV-infected patients: single dose vs. three doses of benzathine penicillin G.

BACKGROUND: Current treatment guidelines for early stages of syphilis are the same regardless of HIV serostatus. There is still controversy about the best treatment for syphilis in HIV patients and the current recommendations are based on limited data. OBJECTIVE: The primary goal of this study was to compare the serological response rates to a single dose vs. three weekly doses of benzathine penicillin G (BPG) in HIV-infected patients with early syphilis and to assess the adequacy of current recommendations. METHODS: Clinical and laboratory data of HIV patients with early syphilis treated in Sexually Transmitted Disease Clinic between January 2000 and December 2014 were recorded. A good serological response was defined as a ≥4-fold decline in Venereal Disease Research Laboratory (VDRL) titre within 12 months after treatment. Serological failure was defined as a lack of at least fourfold decrease in VDRL titres within 12 months after treatment. RESULTS: After applying inclusion and exclusion criteria, 60 patients were enrolled in the study. Seventeen (28.3%) patients were treated with a single dose of BPG, while in 43 (71.7%) patients, three weekly doses were used. Fifty eight (96.7%) had a good serological response at 12 months and seroconversion was confirmed in 29 (48.3%) patients. There was no statistically significant difference between the two treatment groups regarding serological response, seroconversion rate and the time needed to obtain a good serological response. Furthermore, treatment response was not affected by the number of CD4 cells. CONCLUSIONS: The results of our study support the current international treatment guidelines, recommending early syphilis treatment with a single dose of BPG in HIV patients.

Genomic prediction for additive and dominance effects of censored traits in pigs.

Age at the time of slaughter is a commonly used trait in animal breeding programs. Since studying this trait involves incomplete observations (censoring), analysis can be performed using survival models or modified linear models, for example, by sampling censored data from truncated normal distributions. For genomic selection, the greatest genetic gains can be achieved by including non-additive genetic effects like dominance. Thus, censored traits with effects on both survival models have not yet been studied under a genomic selection approach. We aimed to predict genomic values using the Cox model with dominance effects and compare these results with the linear model with and without censoring. Linear models were fitted via the maximum likelihood method. For censored data, sampling through the truncated normal distribution was used, and the model was called the truncated normal linear via Gibbs sampling (TNL). We used an F2 pig population; the response variable was time (days) from birth to slaughter. Data were previously adjusted for fixed effects of sex and contemporary group. The model predictive ability was calculated based on correlation of predicted genomic values with adjusted phenotypic values. The results showed that both with and without censoring, there was high agreement between Cox and linear models in selection of individuals and markers. Despite including the dominance effect, there was no increase in predictive ability. This study showed, for the first time, the possibility of performing genomic prediction of traits with censored records while using the Cox survival model with additive and dominance effects.

Using artificial neural networks to select upright cowpea (Vigna unguiculata) genotypes with high productivity and phenotypic stability.

Cowpea (Vigna unguiculata) is grown in three Brazilian regions: the Midwest, North, and Northeast, and is consumed by people on low incomes. It is important to investigate the genotype x environment (GE) interaction to provide accurate recommendations for farmers. The aim of this study was to identify cowpea genotypes with high adaptability and phenotypic stability for growing in the Brazilian Cerrado, and to compare the use of artificial neural networks with the Eberhart and Russell (1966) method. Six trials with upright cowpea genotypes were conducted in 2005 and 2006 in the States of Mato Grosso do Sul and Mato Grosso. The data were subjected to adaptability and stability analysis by the Eberhart and Russell (1966) method and artificial neural networks. The genotypes MNC99-537F-4 and EVX91-2E-2 provided grain yields above the overall environment means, and exhibited high stability according to both methods. Genotype IT93K-93-10 was the most suitable for unfavorable environments. There was a high correlation between the results of both methods in terms of classifying the genotypes by their adaptability and stability. Therefore, this new approach would be effective in quantifying the GE interaction in upright cowpea breeding programs.

New accuracy estimators for genomic selection with application in a cassava (Manihot esculenta) breeding program.

Genomic selection is the main force driving applied breeding programs and accuracy is the main measure for evaluating its efficiency. The traditional estimator (TE) of experimental accuracy is not fully adequate. This study proposes and evaluates the performance and efficiency of two new accuracy estimators, called regularized estimator (RE) and hybrid estimator (HE), which were applied to a practical cassava breeding program and also to simulated data. The simulation study considered two individual narrow sense heritability levels and two genetic architectures for traits. TE, RE, and HE were compared under four validation procedures: without validation (WV), independent validation, ten-fold validation through jacknife allowing different markers, and with the same markers selected in each cycle. RE presented accuracies closer to the parametric ones and less biased and more precise ones than TE. HE proved to be very effective in the WV procedure. The estimators were applied to five traits evaluated in a cassava experiment, including 358 clones genotyped for 390 SNPs. Accuracies ranged from 0.67 to 1.12 with TE and from 0.22 to 0.51 with RE. These results indicated that TE overestimated the accuracy and led to one accuracy estimate (1.12) higher than one, which is outside of the parameter space. Use of RE turned the accuracy into the parameter space. Cassava breeding programs can be more realistically implemented using the new estimators proposed in this study, providing less risky practical inferences.

Genome wide selection in Citrus breeding.

Genome wide selection (GWS) is essential for the genetic improvement of perennial species such as Citrus because of its ability to increase gain per unit time and to enable the efficient selection of characteristics with low heritability. This study assessed GWS efficiency in a population of Citrus and compared it with selection based on phenotypic data. A total of 180 individual trees from a cross between Pera sweet orange (Citrus sinensis Osbeck) and Murcott tangor (Citrus sinensis Osbeck x Citrus reticulata Blanco) were evaluated for 10 characteristics related to fruit quality. The hybrids were genotyped using 5287 DArT_seqTM (diversity arrays technology) molecular markers and their effects on phenotypes were predicted using the random regression - best linear unbiased predictor (rr-BLUP) method. The predictive ability, prediction bias, and accuracy of GWS were estimated to verify its effectiveness for phenotype prediction. The proportion of genetic variance explained by the markers was also computed. The heritability of the traits, as determined by markers, was 16-28%. The predictive ability of these markers ranged from 0.53 to 0.64, and the regression coefficients between predicted and observed phenotypes were close to unity. Over 35% of the genetic variance was accounted for by the markers. Accuracy estimates with GWS were lower than those obtained by phenotypic analysis; however, GWS was superior in terms of genetic gain per unit time. Thus, GWS may be useful for Citrus breeding as it can predict phenotypes early and accurately, and reduce the length of the selection cycle. This study demonstrates the feasibility of genomic selection in Citrus.

Factor analysis applied to genome prediction for high-dimensional phenotypes in pigs.

The aim of the present study was to propose and evaluate the use of factor analysis (FA) in obtaining latent variables (factors) that represent a set of pig traits simultaneously, for use in genome-wide selection (GWS) studies. We used crosses between outbred F2 populations of Brazilian Piau X commercial pigs. Data were obtained on 345 F2 pigs, genotyped for 237 SNPs, with 41 traits. FA allowed us to obtain four biologically interpretable factors: "weight", "fat", "loin", and "performance". These factors were used as dependent variables in multiple regression models of genomic selection (Bayes A, Bayes B, RR-BLUP, and Bayesian LASSO). The use of FA is presented as an interesting alternative to select individuals for multiple variables simultaneously in GWS studies; accuracy measurements of the factors were similar to those obtained when the original traits were considered individually. The similarities between the top 10% of individuals selected by the factor, and those selected by the individual traits, were also satisfactory. Moreover, the estimated markers effects for the traits were similar to those found for the relevant factor.

Observation of a New Narrow Axial-Vector Meson a1(1420).

The COMPASS Collaboration at CERN has measured diffractive dissociation of 190 GeV/c pions into the π(-)π(-)π(+) final state using a stationary hydrogen target. A partial-wave analysis (PWA) was performed in bins of 3π mass and four-momentum transfer using the isobar model and the so far largest PWA model consisting of 88 waves. A narrow peak is observed in the f0(980)π channel with spin, parity and C-parity quantum numbers J(PC)=1(++). We present a resonance-model study of a subset of the spin-density matrix selecting 3π states with J(PC)=2(++) and 4(++) decaying into ρ(770)π and with J(PC)=1(++) decaying into f0(980)π. We identify a new a1 meson with mass (1414(-13)(+15)) MeV/c2 and width (153(-23)(+8)) MeV/c2. Within the final states investigated in our analysis, we observe the new a1(1420) decaying only into f0(980)π, suggesting its exotic nature.

Comparison of dimensionality reduction methods to predict genomic breeding values for carcass traits in pigs.

A significant contribution of molecular genetics is the direct use of DNA information to identify genetically superior individuals. With this approach, genome-wide selection (GWS) can be used for this purpose. GWS consists of analyzing a large number of single nucleotide polymorphism markers widely distributed in the genome; however, because the number of markers is much larger than the number of genotyped individuals, and such markers are highly correlated, special statistical methods are widely required. Among these methods, independent component regression, principal component regression, partial least squares, and partial principal components stand out. Thus, the aim of this study was to propose an application of the methods of dimensionality reduction to GWS of carcass traits in an F2 (Piau x commercial line) pig population. The results show similarities between the principal and the independent component methods and provided the most accurate genomic breeding estimates for most carcass traits in pigs.

Genomic selection for slaughter age in pigs using the Cox frailty model.

The aim of this study was to compare genomic selection methodologies using a linear mixed model and the Cox survival model. We used data from an F2 population of pigs, in which the response variable was the time in days from birth to the culling of the animal and the covariates were 238 markers [237 single nucleotide polymorphism (SNP) plus the halothane gene]. The data were corrected for fixed effects, and the accuracy of the method was determined based on the correlation of the ranks of predicted genomic breeding values (GBVs) in both models with the corrected phenotypic values. The analysis was repeated with a subset of SNP markers with largest absolute effects. The results were in agreement with the GBV prediction and the estimation of marker effects for both models for uncensored data and for normality. However, when considering censored data, the Cox model with a normal random effect (S1) was more appropriate. Since there was no agreement between the linear mixed model and the imputed data (L2) for the prediction of genomic values and the estimation of marker effects, the model S1 was considered superior as it took into account the latent variable and the censored data. Marker selection increased correlations between the ranks of predicted GBVs by the linear and Cox frailty models and the corrected phenotypic values, and 120 markers were required to increase the predictive ability for the characteristic analyzed.

Estimating additive and dominance variances for complex traits in pigs combining genomic and pedigree information.

Knowledge of dominance effects should improve ge-netic evaluations, provide the accurate selection of purebred animals, and enable better breeding strategies, including the exploitation of het-erosis in crossbreeds. In this study, we combined genomic and pedi-gree data to study the relative importance of additive and dominance genetic variation in growth and carcass traits in an F2 pig population. Two GBLUP models were used, a model without a polygenic effect (ADM) and a model with a polygenic effect (ADMP). Additive effects played a greater role in the control of growth and carcass traits than did dominance effects. However, dominance effects were important for all traits, particularly in backfat thickness. The narrow-sense and broad-sense heritability estimates for growth (0.06 to 0.42, and 0.10 to 0.51, respectively) and carcass traits (0.07 to 0.37, and 0.10 to 0.76, respec-tively) exhibited a wide variation. The inclusion of a polygenic effect in the ADMP model changed the broad-sense heritability estimates only for birth weight and weight at 21 days of age.