Gene ontology functional annotation datasets for the ITAG3.2 and ITAG4.0 tomato (Solanum lycopersicum) genome annotations.

Functional annotation based on Gene Ontology has provided a structured and comprehensive system to access the current knowledge about the function of genes. For model plants such as Arabidopsis thaliana, there is a constant updating and restructuring of the functional annotation that increases the reliability of the analyses that use it. For tomato (Solanum lycopersicum), a crop widely used as a model plant for the study of fleshy fruits, there is no functional annotation, at least not freely accessible, even though its genome has long been sequenced and annotated. In this work, we generated, using a simplified version of the maize GAMER pipeline, a tomato Gene Ontology functional annotation with 72.42% (ITAG3.2) and 74.2% (ITAG4.0) of protein-coding genes with at least one GO term association. With this dataset, we share a reliable and easy-to-use tool with the tomato community.

Exploring protective factors in a high-risk subsample: the pivotal role of paternal support in preventing depression in a cohort of young adults.

BACKGROUND: Major depressive disorder (MDD) is a global concern due to its widespread prevalence and morbidity. Identifying protective factors in high-risk individuals, including those with a familial predisposition, maltreatment history, and socio-economic vulnerabilities, is crucial. METHODS: We assessed a high-risk subsample within a young adult population cohort (n = 791; mean age = 31.94 [SD = 2.18]) across three waves. Using multiple regression models to analyse higher education, feeling supported, spirituality, psychotherapy access, higher socioeconomic status, involvement in activities, cohabitation, and family unity in Waves 1 and 2, and their association with MDD resilience at Wave 3. RESULTS: In the high-risk group, MDD incidence was 13.7% (n=24). Paternal support had a protective effect on MDD incidence (OR = 0.366; 95% CI [0.137 to 0.955], p = 0.040) and suicidal attempt risk (OR = 0.380; 95% CI [0.150 to 0.956], p = 0.038). Higher resilience scores were also protective (OR = 0.975; 95% CI [0.953 to 0.997], p = 0.030), correlating with reduced BDI (r = 0.0484; B = -0.2202; 95% CI [-0.3572 to -0.0738]; p = 0.003) and MADRS scores (r = 0.0485; B = -0.2204; 95% CI [-0.3574 to -0.0741]; p = 0.003). CONCLUSIONS: Our paper emphasizes reorienting the MDD approach, focusing on positive prevention strategies. It highlights fathers' crucial role in family-based interventions and promoting resilience in high-risk populations.

Novel Pseudomonas Species Prevent the Growth of the Phytopathogenic Fungus Aspergillus flavus.

In response to the escalating demand for sustainable agricultural methodologies, the utilization of microbial volatile organic compounds (VOCs) as antagonists against phytopathogens has emerged as a viable eco-friendly alternative. Microbial volatiles exhibit rapid diffusion rates, facilitating prompt chemical interactions. Moreover, microorganisms possess the capacity to emit volatiles constitutively, as well as in response to biological interactions and environmental stimuli. In addition to volatile compounds, these bacteria demonstrate the ability to produce soluble metabolites with antifungal properties, such as APE Vf, pyoverdin, and fragin. In this study, we identified two Pseudomonas strains (BJa3 and MCal1) capable of inhibiting the in vitro mycelial growth of the phytopathogenic fungus Aspergillus flavus, which serves as the causal agent of diseases in sugarcane and maize. Utilizing GC/MS analysis, we detected 47 distinct VOCs which were produced by these bacterial strains. Notably, certain volatile compounds, including 1-heptoxydecane and tridecan-2-one, emerged as primary candidates for inhibiting fungal growth. These compounds belong to essential chemical classes previously documented for their antifungal activity, while others represent novel molecules. Furthermore, examination via confocal microscopy unveiled significant morphological alterations, particularly in the cell wall, of mycelia exposed to VOCs emitted by both Pseudomonas species. These findings underscore the potential of the identified BJa3 and MCal1 Pseudomonas strains as promising agents for fungal biocontrol in agricultural crops.

Molecular detection of Bartonella spp. in bat-associated macronyssid mites (Acari: Macronyssidae) from Southern and Southeastern Brazil.

Despite the worldwide occurrence and high genetic diversity of Bartonella spp. in bats, few studies investigate their occurrence in bat-associated mites. To date, 26 species of Macronyssidae mite species have been reported from Brazil, and 15 of which were found parasitizing bats. The present study aimed to investigate the presence of Bartonella DNA in bat-associated macronyssid mites from Brazil. For this purpose, 393 macronyssid specimens were selected by convenience from the tissue bank of the Acari Collection of the Instituto Butantan (IBSP). These mites were collected from 14 different bat species in three different Brazilian States (Minas Gerais, Paraná, and Rio de Janeiro). Out of 165 mites positive in the PCR for the endogenous 18S rRNA gene, only eight were positive in the qPCR for Bartonella spp. based on the nuoG gene, and we were able to obtain two sequences base in this same gene, and one sequence based on the 16S rRNA gene. The phylogenetic inference based on the nuoG gene grouped the obtained sequences with Bartonella genotypes previously detected in bats and associated bat flies, while the phylogeny based on the 16S rRNA grouped the obtained sequence in the same clade of Bartonella genotypes previously detected in Dermanyssus gallinae. These findings suggest that macronyssid mites might be associated with the maintenance of bartonellae among bats.

A MaxEnt Model of Citrus Black Fly Aleurocanthus woglumi Ashby (Hemiptera: Aleyrodidae) under Different Climate Change Scenarios.

The citrus blackfly (CBF), Aleurocanthus woglumi Ashby, is an exotic pest native to Southeast Asia that has spread rapidly to the world's main centers of citrus production, having been recently introduced to Brazil. In this study, a maximum entropy niche model (MaxEnt) was used to predict the potential worldwide distribution of CBF under current and future climate change scenarios for 2030 and 2050. These future scenarios came from the Coupled Model Intercomparison Project Phase 6 (CMIP6), SSP1-2.6, and SSP5-8.5. The MaxEnt model predicted the potential distribution of CBF with area under receiver operator curve (AUC) values of 0.953 and 0.930 in the initial and final models, respectively. The average temperature of the coldest quarter months, precipitation of the rainiest month, isothermality, and precipitation of the driest month were the strongest predictors of CBF distribution, with contributions of 36.7%, 14.7%, 13.2%, and 10.2%, respectively. The model based on the current time conditions predicted that suitable areas for the potential occurrence of CBF, including countries such as Brazil, China, the European Union, the USA, Egypt, Turkey, and Morocco, are located in tropical and subtropical regions. Models from SSP1-2.6 (2030 and 2050) and SSP5-8.5 (2030) predicted that suitable habitats for CBF are increasing dramatically worldwide under future climate change scenarios, particularly in areas located in the southern US, southern Europe, North Africa, South China, and part of Australia. On the other hand, the SSP5-8.5 model of 2050 indicated a great retraction of the areas suitable for CBF located in the tropical region, with an emphasis on countries such as Brazil, Colombia, Venezuela, and India. In general, the CMIP6 models predicted greater risks of invasion and dissemination of CBF until 2030 and 2050 in the southern regions of the USA, European Union, and China, which are some of the world's largest orange producers. Knowledge of the current situation and future propagation paths of the pest serve as tools to improve the strategic government policies employed in CBF's regulation, commercialization, inspection, combat, and phytosanitary management.

The Nucleocapsid Protein of SARS-CoV-2, Combined with ODN-39M, Is a Potential Component for an Intranasal Bivalent Vaccine with Broader Functionality.

Despite the rapid development of vaccines against COVID-19, they have important limitations, such as safety issues, the scope of their efficacy, and the induction of mucosal immunity. The present study proposes a potential component for a new generation of vaccines. The recombinant nucleocapsid (N) protein from the SARS-CoV-2 Delta variant was combined with the ODN-39M, a synthetic 39 mer unmethylated cytosine-phosphate-guanine oligodeoxynucleotide (CpG ODN), used as an adjuvant. The evaluation of its immunogenicity in Balb/C mice revealed that only administration by intranasal route induced a systemic cross-reactive, cell-mediated immunity (CMI). In turn, this combination was able to induce anti-N IgA in the lungs, which, along with the specific IgG in sera and CMI in the spleen, was cross-reactive against the nucleocapsid protein of SARS-CoV-1. Furthermore, the nasal administration of the N + ODN-39M preparation, combined with RBD Delta protein, enhanced the local and systemic immune response against RBD, with a neutralizing capacity. Results make the N + ODN-39M preparation a suitable component for a future intranasal vaccine with broader functionality against Sarbecoviruses.

Eutrichophilus cordiceps Mjöberg, 1910 (Ischnocera: Trichodectidae) in Spiny Tree Porcupines (Coendou villosus): New locality records and the first molecular evidence of association with Bartonella sp.

The chewing louse genus Eutrichophilus Mjöberg has 19 species only associated with porcupines (Rodentia: Erethizontidae). Of these species, E. cercolabes, E. cordiceps, E. emersoni, E. minor, E. moojeni, and E. paraguayensis have been recorded in Brazil. In the present study, we report E. cordiceps for the first time in the São Paulo State (Bauru Municipality) and for the second time in the Santa Catarina State (Lages Municipality), providing scanning electron images and light microscopy for the eggs, as well as the first molecular data (18S rRNA) for the genus. Additionally, Bartonella sp. was detected for the first time in this chewing lice species.

Economic Injury Levels and Economic Thresholds for Leucoptera coffeella as a Function of Insecticide Application Technology in Organic and Conventional Coffee (Coffea arabica), Farms.

Leucoptera coffeella (Lepidoptera: Lyonetiidae) is one of the main pests in coffee crops. The economic injury level (EIL) is the lowest density of the pest at which economic damages match the costs of control measures. The economic threshold (ET) is the density of the pest at which control measures must be taken so that this population does not reach the EIL. These are the main indices used for pest control decision-making. Control of L. coffeella is carried out by manual, tractor, airplane or drone applications. This work aimed to determine EILs and ETs for L. coffeella as a function of insecticide application technology in conventional and organic Coffea arabica crops. Data were collected over five years in commercial C. arabica crops on seven 100 ha central pivots. The cost of control in organic crops was 16.98% higher than conventional. The decreasing order of control cost was manual > drone > airplane > tractor application. Coffee plants were tolerant to low densities (up to 15% mined leaves) of the pest that caused losses of up to 6.56%. At high pest densities (54.20% mined leaves), losses were high (85.62%). In organic and conventional crops and with the use of different insecticide application technologies, EIL and ET were similar. The EIL and ET were 14% and 11% of mined leaves, respectively. Therefore, these indices can be incorporated in integrated pest management programs in C. arabica crops. The indices determined as a function of insecticide application technology in organic and conventional coffee are important as they serve producers with different technological levels. Additionally, EILs and ETs can contribute to more sustainable production, as control methods will only be employed when the pest density reaches these indices.

Advancing Efficiency Sustainability in Poultry Farms through Data Envelopment Analysis in a Brazilian Production System.

The production efficiency factor is widely used to measure the zootechnical performance of a batch of broilers. The unit cost of production brings new elements to improve efficiency evaluation and financial sustainability for this activity in agriculture. This research aims to evaluate the production efficiency level of the crop to maximize the return on investment. This study uses Data Envelopment Analysis (DEA) with the computational processing of the SIAD software (Integrated Decision Support System). The variables selected were poultry housing, age at slaughter, feed consumed, mortality, and unit cost. The chosen output variable was the total available weight. The analysis spans 31 decision-making units (DMUs) composed of integrated producers, unveiling a frontier of efficiency delineated by the most exemplary DMUs. Notably, only two DMUs, specifically DMU 4 and DMU 23, approached the threshold of maximum relative efficiency. This research illuminates the critical role of unit cost in enhancing the assessment of production efficiency and financial sustainability within the agriculture environment. By setting benchmarks for efficient management and operational protocols, our findings serve as a cornerstone for improving practices among less efficient DMUs, contributing significantly to the literature on agricultural efficiency and offering actionable insights for the poultry farming sector.

The genus Perissopalla Brennan and White, 1960 (Trombidiformes: Trombiculidae) in Brazil: Redescriptions, new localities, and host records with the first molecular data for the genus.

The genus Perissopalla Brennan and White (Trombidiformes: Trombiculidae) is currently represented by ten species with three from Brazil: Perissopalla barticonycteris Brennan, Perissopalla ipeani Brennan, and Perissopalla tanycera Brennan. In the present study, these three species are redescribed and illustrated based on the types and additional non-type specimens. New host and locality records for P. ipeani and P. tanycera are included. Additionally, a partial sequence for the 18S rRNA gene for P. ipeani was provided.

Micro-Addition of Silver to Copper: One Small Step in Composition, a Change for a Giant Leap in Biocidal Activity.

The use of copper as an antimicrobial agent has a long history and has gained renewed interest in the context of the COVID-19 pandemic. In this study, the authors investigated the antimicrobial properties of an alloy composed of copper with a small percentage of silver (Cu-0.03% wt.Ag). The alloy was tested against various pathogens, including Escherichia coli, Staphylococcus aureus, Candida albicans, Pseudomonas aeruginosa, and the H1N1 virus, using contact exposure tests. Results showed that the alloy was capable of inactivating these pathogens in two hours or less, indicating its strong antimicrobial activity. Electrochemical measurements were also performed, revealing that the small addition of silver to copper promoted a higher resistance to corrosion and shifted the formation of copper ions to higher potentials. This shift led to a slow but continuous release of Cu2+ ions, which have high biocidal activity. These findings show that the addition of small amounts of silver to copper can enhance its biocidal properties and improve its effectiveness as an antimicrobial material.

Radical prostatectomy cancer grade and percentage of Gleason pattern 4 estimated by global vs individual tumor grading correlate differently with the risk of biochemical recurrence in Grade Group 2 and 3 cancers.

OBJECTIVES: There are 2 grading approaches to radical prostatectomy (RP) in multifocal cancer: Grade Group (GG) and percentage of Gleason pattern 4 (GP4%). We investigated whether RP GG and GP4% generated by global vs individual tumor grading correlate differently with biochemical recurrence. METHODS: We reviewed 531 RP specimens with GG2 or GG3 cancer. Each tumor was scored separately with assessment of tumor volume and GP4%. Global grade and GP4% were assigned by combining Gleason pattern 3 and 4 volumes for all tumors. Correlation of GG and GP4% generated by 2 methods with biochemical recurrence was assessed by Cox proportional hazard regression and receiver operating characteristic curves, with optimism adjustment using a bootstrap analysis. RESULTS: Median age was 63 (range, 42-79) years. Median prostate-specific antigen was 6.3 (range, 0.3-62.9) ng/mL. In total, the highest-grade tumor in 371 (36.9%) men was GG2 and in 160 (30.1%) men was GG3. Global grading was downgraded from GG3 to GG2 in 37 of 121 (30.6%) specimens with multifocal disease, and 145 of 404 (35.9%) specimens had GP4% decreased by at least 10%. Ninety-eight men experienced biochemical recurrence within a median of 13 (range, 3-119) months. Men without biochemical recurrence were followed up for a median of 47 (range, 12-205) months. Grade Group, GP4%, and margin status correlated with the risk of biochemical recurrence using highest-grade tumor and global grading, but the degrees of these correlations varied and were statistically significantly different between the 2 grading approaches. CONCLUSIONS: Grade Group, GP4%, and margin status derived by global vs individual tumor grading predict postoperative biochemical recurrence statistically significantly differently. This difference has important implications if results derived from cohorts graded using different methods are compared.

Factors associated with suicide risk in young women with premenstrual dysphoric disorder: A population-based study.

PURPOSE: Women with premenstrual dysphoric disorder (PMDD) are more likely to report suicide ideation and behavior when compared to women without PMDD. However, there is a lack of studies investigating the risk factors for suicide risk in women with PMDD. Thus, the aim of this study is to assess the factors associated with suicide risk in young women with PMDD. METHODS: This is a cross-sectional study including 128 young women with PMDD who were recruited from the community. PMDD and suicide risk were assessed by trained psychologists using the Mini International Neuropsychiatric Interview (MINI-PLUS). Suicide risk evaluation includes six questions that assess suicidal intention, planning and previous attempts. Subjects who answer yes to any of the six questions are classified as having current suicide risk. RESULTS: The prevalence of current suicide risk in women with PMDD was 28.1%. The factors associated with suicide risk in this population were: presenting current panic disorder (OR: 18.71 [95% CI: 1.02 - 343.27], p=0.048), a non-white skin color (OR: 4.18 [CI 95%: 1.28 - 13.61], p=0.018), greater severity of depressive symptoms (OR: 1.22 [95% CI: 1.12 - 1.32], < 0.001), and history of childhood trauma (OR: 1.04 [95% CI: 1.01 - 1.08], 0.010). CONCLUSION: Our findings indicate that there are key sociodemographic and clinical factors associated with suicide risk in young women with PMDD, enabling clinicians to identify at-risk individuals who could benefit from further screening and interventions.

Influence of malocclusion on sleep bruxism and orofacial pain: data from a study in school children.

OBJECTIVES: This cross-sectional school-based study explored the influence of malocclusion on temporomandibular disorders (TMD) pain complaints, and whether this association would be mediated by sleep bruxism in a representative sample of 7- to 8-year-old children. METHODS: Path analysis estimated direct, indirect, and total effects of occlusal features on sleep bruxism and TMD pain in 7- to 8-year-old children. Occlusal features were assessed with Dental Aesthetic Index (DAI), orofacial pain complaints using the TMD pain screener, possible sleep bruxism based on self-reports, and probable sleep bruxism based on self-reports combined with clinical findings. Structural equation modeling analyzed data with confounding factors. RESULTS: From 580 participants, possible sleep bruxism was observed in 136 children (31.5%), probable sleep bruxism in 30 children (6.7%), and TMD pain complaints in 78 children (13.8%). Malocclusion had no direct effect on either possible sleep bruxism [standardized coefficient (SC) 0.000; p = 0.992], or TMD pain complaints (SC - 0.01; p = 0.740). When probable sleep bruxism was set as the mediator of interest, malocclusion did not directly affect probable sleep bruxism (SC 0.01; p = 0.766), nor TMD pain complaints (SC - 0.02; p = 0.515). A direct effect of probable sleep bruxism on TMD pain complaints was observed with an SC of 0.60 (p < 0.001). However, in neither case, malocclusion indirectly affected TMD pain complaints via bruxism. CONCLUSION: Malocclusion in 7- to 8-year-old children did not directly influence possible or probable sleep bruxism or TMD pain complaints. Instead, probable sleep bruxism was strongly associated with TMD pain complaints. CLINICAL SIGNIFICANCE: The impact of occlusal features on TMD pain complaints and bruxism has been a long-standing controversy in dentistry. However, the scientific literature linking this association may be inconsistent, mainly due to biased sample selection methods with inadequate consideration of confounders. Further research should try to identify additional risk factors for TMD pain in addition to probable sleep bruxism in children.

All-fiber broadband spectral acousto-optic modulation of a tubular-lattice hollow-core optical fiber.

We demonstrate a broadband acousto-optic notch filter based on a tubular-lattice hollow-core fiber for the first time to our knowledge. The guided optical modes are modulated by acoustically induced dynamic long-period gratings along the fiber. The device is fabricated employing a short interaction length (7.7 cm) and low drive voltages (10 V). Modulated spectral bands with 20 nm half-width and maximum depths greater than 60% are achieved. The resonant notch wavelength is tuned from 743 to 1355 nm (612 nm span) by changing the frequency of the electrical signal. The results indicate a broader tuning range compared to previous studies using standard and hollow-core fibers. It further reveals unique properties for reconfigurable spectral filters and fiber lasers, pointing to the fast switching and highly efficient modulation of all-fiber photonic devices.

Co-infestation caused by Goniodes pavonis (L., 1758) (Ischnocera: Goniodidae) and Goniocotes rectangulatus Nitzsch [In Giebel], 1866 on white Indian peafowl, Pavo cristatus L., 1758 (Galliformes: Phasianidaede) in Brazil.

The genus Goniodes Nitzsch and Goniocotes Burmeister (Ischnocera: Goniogodidae) are distributed worldwide, and exclusively parasitizing avian hosts of the Galliformes. In Brazil, there are only four species recorded: Goniodes dissimilis Denny, Goniodes gigas (Taschenberg), Goniodes pavonis (L.), and Goniocotes gallinae (DeGeer). In the present study, we are reporting the co-parasitism of G. pavonis and G. rectangulatus Nitzsch [In Giebel] on specimens of the white Pavo cristatus, popularly known as 'white Indian peafowl' for the first time. Furthermore, a new Brazilian locality for G. pavonis species has been reported, as well as the first time that G. rectangulatus is reported to Brazil. Additionally, we provide the first molecular information for G. pavonis.

Interrelationships among skeletal age, growth status and motor performances in female athletes 10-15 years.

BACKGROUND: Motor performances of youth are related to growth and maturity status, among other factors. AIM: To estimate the contribution of skeletal maturity status per se to the motor performances of female athletes aged 10-15 years and the mediation effects of growth status on the relationships. SUBJECTS AND METHODS: Skeletal age (TW3 RUS SA), body size, proportions, estimated fat-free mass (FFM), motor performances, training history and participation motivation were assessed in 80 non-skeletally mature female participants in several sports. Hierarchical and regression-based statistical mediation analyses were used. RESULTS: SA per se explained a maximum of 1.8% and 5.8% of the variance in motor performances of athletes aged 10-12 and 13-15 years, respectively, over and above that explained by covariates. Body size, proportions, and hours per week of training and participation motivation explained, respectively, a maximum of 40.7%, 18.8%, and 22.6% of the variance in performances. Mediation analysis indicated specific indirect effects of SA through stature and body mass, alone or in conjunction with FFM on performances. CONCLUSION: SA per se accounted for small and non-significant amounts of variance in several motor performances of female youth athletes; rather, SA influenced performances indirectly through effects on stature, body mass and estimated FFM.

SARS-CoV-2 papain-like protease activates nociceptors to drive sneeze and pain.

SARS-CoV-2, the virus responsible for COVID-19, triggers symptoms such as sneezing, aches and pain.1 These symptoms are mediated by a subset of sensory neurons, known as nociceptors, that detect noxious stimuli, densely innervate the airway epithelium, and interact with airway resident epithelial and immune cells.2-6 However, the mechanisms by which viral infection activates these neurons to trigger pain and airway reflexes are unknown. Here, we show that the coronavirus papain-like protease (PLpro) directly activates airway-innervating trigeminal and vagal nociceptors in mice and human iPSC-derived nociceptors. PLpro elicits sneezing and acute pain in mice and triggers the release of neuropeptide calcitonin gene-related peptide (CGRP) from airway afferents. We find that PLpro-induced sneeze and pain requires the host TRPA1 ion channel that has been previously demonstrated to mediate pain, cough, and airway inflammation.7-9 Our findings are the first demonstration of a viral product that directly activates sensory neurons to trigger pain and airway reflexes and highlight a new role for PLpro and nociceptors in COVID-19.

Technical note: RP Atlas-an unprecedented proposal for a Brazilian population dental development chart based on the London atlas.

Age estimation methods through developmental atlases are simplified by image comparison using radiographs. Atlas-based methods have been utilized to create population-specific charts addressing population diversity. To tackle the absence of a dedicated atlas for the Brazilian population, the objective of the present study was to create a new atlas for dental development in Brazil based on the London Atlas chart. The new atlas (RP Atlas) is based on the median of tooth development, eruption, and resorption in individuals aged 5 to 23. The sample (567 individuals) was divided between females (n = 290) and males (n = 277). The RP Atlas was handcrafted, scanned, colored, and clustered in two atlases divided by sex. The development of a specific atlas for the Brazilian population has the potential to enhance the accuracy of age estimation in forensic scenarios, notably in a mixed country like Brazil. Further research is needed to assess the suitability of the newly developed atlas for the Brazilian population.