Nectriaceae species associated to root rot of nursery and young Eucalyptus smithii trees in Uruguay with Ilyonectria charruensis as novel species.

Forestry constitutes an important agronomical activity in Uruguay, involving the cultivation of exotic trees mainly for cellulose pulp production with Eucalyptus species. Over the last decade, E. smithii emerged as a species of interest for cellulose pulping. However, its rapid expansion has coincided with high mortality rates among young trees ranging from 5 to 85%, especially during the first and second summer after plantation. Disease surveys conducted on nine E. smithii commercial fields and three nurseries in southern and eastern Uruguay, yielded a collection of 25 isolates from E. smithii root rot belonging to the Nectriaceae family. In this study, we aimed to identify and characterize these isolates employing phenotypical and molecular studies and to assess their pathogenicity on E. smithii seedlings. Based on morphological features, the Nectriaceae isolates were subdivided into two groups, one resembling Calonectria (n=15) and another Cylindrocarpon-like (n=10). DNA sequences of the partial histone H3 (his3), actine, calmodulin, RNA polymerase II second largest subunit, translation elongation factor 1-alpha (tef1) and ß-tubulin (tub2) genes were amplified for Calonectria, as well as partial his3, tef1, tub2 and internal-transcribed spacer and intervening 5.8S (ITS) for the Cylindrocarpon-like group. Based on phylogenetic analysis and phenotypical features three species were identified and characterized; Calonectria pauciramosa (n=15), Dactylonectria novozelandica (n=2), and a novel taxon which we describe here as Ilyonectria charruensis sp. nov. (n=8). The pathogenicity trials revealed that isolates from the three species significantly reduced both shoot and root dry weights of inoculated E. smithii seedlings compared to control plants.

First report of Neofusicoccum nonquaesitum causing branch dieback of English walnut (Juglans regia) in Maule region, Chile.

English walnut (Juglans regia) cultivation has been expanding in recent years in Chile, with a surface of 9,000 ha planted in the Maule Region (35° 26' S, 71° 40' W), central Chile. In a field survey conducted between August (2022) and January (2023) in three localities of the Maule Region, several declined trees were observed. English walnuts exhibited small chlorotic leaves, cankers, dead twigs, and dieback of branches, with an incidence of 10 to 35% of trees affected per orchard. Internally, diseased branches exhibit brown to dark brown wood cankers. Symptomatic branches (n = 30) were collected and surface disinfected with 96% ethanol, and flamed. Pieces of wood (approximately 5 mm) were placed on potato dextrose agar (PDA), supplemented with 0.005% tetracycline, 0.01% streptomycin, and 0.1% Igepal CO-630 (Díaz et al. 2018), and incubated at 22°C for 5 days in darkness. Four isolates (VLC-1-6-20, VLC-1-10-20, VLC-1-12-20, and VLC-1-15-20) exhibited moderate growth rates (16.4 mm/day), developing a white hue to olivaceous black colonies after 7 days at 22°C on PDA. Chlamydospores were absent. Black pycnidia were formed individually or in clusters. The isolates produced aseptate, hyaline, and fusiform, with base truncate conidia measuring 24.8 ± 1.6 x 6.8 ± 0.63 µm (l/w = 3.1; n = 50). The four isolates characterized were amplified using of the internal transcribed spacer (ITS1/ITS4), a portion of beta-tubulin (Bt2a/Bt2b), and part of the translation elongation factor 1- α (EF1-728/EF1-968) genes (Phillips et al. 2013). Blast analyses showed 100, 99 and 100 % identity with ex-type isolate PD-484 of Neofusicoccum nonquaesitum for ITS (deposited as GenBank accession no. PP697845 to PP697848), Bt (PP789576 to PP789579) and EF1 (PP830824 to PP830827) regions, respectively. Combined phylogenetic analysis using MEGA 7 software and the maximum likelihood test clustered the four isolates with ex-type of N. nonquaesitum. Pathogenicity was performed using two isolates (VLC-1-6-20 and VLC-1-10-20), which were inoculated in healthy tree walnuts cv. Chandler (8 years old), using 40 µl of mycelial suspension (105 fragments of mycelium/ml) on rounded wounds in the middle of each attached young branch (n=30 branches) (Twizeyimana et al. 2013). Sterile distilled water was used as a control treatment. Pathogenicity tests were repeated twice. After 6 months, necrotic streaks with mean lengths of 13 mm and 28 mm were observed in the middle of wounded young branches. No necrotic lesions were observed in the control treatments. Reisolation of N. nonquaesitum was positive (100%) only from inoculated branches and molecularly identified (EF1-a), fulfilling Koch's postulates. Previously, N. nonquaesitum has been reported causing dieback on English walnut in California (Chen et al. 2014). To our knowledge, this is the first report of N. nonquaesitum causing canker and branch dieback of English walnut in central Chile. Previously, Diplodia mutila, Dothiorella sarmentorum, and N. austral have been associated with walnut dieback in Chile (Díaz et al. 2018; Iqbal et al. 2023; Barcos et al. 2023). In conclusion, it is imperative to implement epidemiological studies to avoid the spread and severity of branch dieback of walnuts in the Maule region, central Chile.

Gut microbiota, allergic rhinitis, vasomotor rhinitis, Mendelian randomization, causal association.

OBJECTIVE: Continuous research on the structure and function of intestinal microecology has confirmed the association between gut microbiota and the occurrence, development, and outcome of allergic diseases. Here, we explored the genetic causality between gut microbiota and rhinitis. METHODS: We conducted a two-sample Mendelian Randomization (MR) study to investigate the genetic causal relationship between gut microbiota and allergic rhinitis and vasomotor rhinitis. Genetic variations in the human gut microbiota were obtained from the summary statistics of the MiBioGen study. Genome-wide summary statistics of rhinitis were obtained from the FinnGen consortium. The causal effect between gut microbiota and rhinitis was assessed using the inverse variance weighted, MR-Egger regression, and weighted median methods. In addition, sensitivity analyses were conducted using different methods, including maximum likelihood, simple mode, and weighted model methods. RESULTS: The IVW approach revealed a causal association of the genus Ruminococcus gauvreauii group with an increased risk of allergic rhinitis (IVW Odds Ratio [OR = 1.26] [1.04, 1.53], p-value = 0.01645). In addition, the genus Fusicatenibacter (IVW OR = 1.20 [1.02, 1.41], p-value = 0.02868) was causally associated with an increased risk of vasomotor rhinitis. CONCLUSION: Gut microbiota belonging to different genera exert different effects on allergic rhinitis and vasomotor rhinitis, including reducing the risk of rhinitis, and increasing the risk of rhinitis. New insights into the mechanisms of underlying gut microbiota-associated rhinitis are provided. LEVEL OF EVIDENCE: Level 5.

Association between Helicobacter pylori antibodies and otolaryngological diseases.

OBJECTIVE: Observational studies have shown that Helicobacter pylori is related to some otolaryngological diseases. However, it is unclear if H. pylori infection causally affects these diseases. To elucidate H. pylori role in 12 common otolaryngological diseases, we conducted two-sample Mendelian randomization analysis. METHODS: Single-nucleotide polymorphisms associated with 7 H. pylori antibodies (IgG, CagA, Catalase, GroEL, OMP, UREA and Vac A) served as instrumental variables. We primarily employed random-effects inverse variance weighting for causal estimation, supplemented by MR Egger, weighted median, simple mode, and weighted mode. Sensitivity analyses, including heterogeneity, pleiotropy, and leave-one-out tests, validated robustness. RESULTS: MR analysis using inverse variance weighting (random effects) revealed genetically predicted H. pylori CagA antibodies correlated with increased risk of nonsuppurative otitis media (OR = 1.0778, 95% CI 1.0114-1.1487, p-value = 0.021). No causal relationship was observed between H. pylori antibodies and other common otolaryngological diseases. Sensitivity analyses found no pleiotropy or heterogeneity, affirming result reliability. CONCLUSION: This study suggests that the levels of H. pylori CagA antibodies may contribute to the development of nonsuppurative otitis media. Further studies are needed in the future to elucidate the specific mechanism of H. pylori in this disease. LEVEL OF EVIDENCE: Level III.

The Role of Inflammation and Psycho-Behavioral Factors as Mediators Between Acculturation and Time to Incident Dementia Among Older Mexican Americans.

Background: The mechanisms through which acculturation influences the onset of cognitive impairment and dementia are not well understood, especially among older Hispanics. Objective: To investigate whether inflammation and psycho-behavioral factors mediate the relationship between acculturation and incident dementia among older Mexican Americans. Methods: We analyzed the Sacramento Area Latino Study on Aging (1998-2007, SALSA), a longitudinal study (N = 1,194) with 10 years of follow-up, and used g-computation for mediation analysis with pooled logistic regression to evaluate whether acculturation (assessed by the Revised Acculturation Rating Scale for Mexican Americans [ARSMA-II]) affected dementia or cognitive impairment but not dementia (CIND) through inflammation (i.e., interleukin 6 [IL-6], tumor necrosis factor-α (TNF-α), high-sensitivity C-reactive protein [hs-CRP]), smoking, alcohol consumption, and depressive symptoms. The potential mediators were assessed at baseline. Results: The 10-year average adjusted risk ratio (aRR) for the effect of high U.S. acculturation and dementia/CIND was 0.66, 95% CI (0.36, 1.30). The indirect effects were: IL-6 (aRR = 0.98, 95% CI (0.88, 1.05)); TNF-α (aRR:0.99, 95% CI (0.93, 1.05)); hs-CRP: (aRR = 1.21, 95% CI (0.84, 1.95)); current smoking: aRR = 0.97, 95% CI (0.84, 1.16); daily/weekly alcohol consumption (aRR = 1.00, 95% CI (0.96, 1.05)); and depressive symptom score (aRR = 1.03, 95% CI (0.95, 1.26)). Hs-CRP yielded a proportion mediated of -26%, suggesting that hs-CRP could suppress the potential effect of high U.S. acculturation. The other factors explored resulted in little to no mediation. Conclusions: The effect of acculturation on time to incident dementia/CIND varied over time. Our study suggests that inflammation could suppress the effect between high U.S. acculturation and dementia risk.

First report of Gnomoniopsis castaneae associated with branch dieback on chestnut tree (Castanea sativa) in Southern Chile.

European chestnut (Castanea sativa Mill.) currently reaches 1,470 ha, distributed from the Maule region to the Los Rios region in Chile. Almost 3000 tons of fruit have been exported in the last three years. A survey was carried out in January 2023 in an eight-year-old orchard located in Vilcún (38°34'46.22"S 72° 9'58.61"O), Araucanía Region. Chestnut trees with branch die back and reduced growth and vigor were detected. The incidence in the orchard was 3% (6 out of 200 trees) estimated by visual observation. Cross and longitudinal sections of the woody trunk of two trees were collected and examined, and an internal dark-brown discoloration to partial necrosis lesion was observed. To identify the causal agent, small pieces of wood from the edge of the symptomatic area were surface sterilized with 70% ethanol, rinsed twice with sterile distilled water, blotted on dry sterile filter paper, plated on potato dextrose agar (PDA) and incubated at 22°C. Fungal colonies were consistently isolated, and after 5 days, pure cultures were obtained by transferring mycelium to new PDA plates, preliminarily identified as Gnomoniopsis sp. (Visentin et al. 2012, Shuttleworth 2012). All cultures exhibited characteristics consistent with the description of G. castaneae (Syn. G. smithogilvyi), such as concentric development of greyish-brown mycelium, abundant stroma, hyaline conidia of 7.2 ±0.54 (6.1-8.1) X 2.3 ±0.26 (1.5-2.9) µm (n= 30), mainly biguttulate and fusoid. Total DNA was extracted, rDNA amplified using ITS1/ITS4 primers (White et al. 1990), and the fragment was Sanger sequenced and the sequence was deposited in GenBank (OR665735). BLAST analysis revealed a 99% identity to G. castaneae (MH384925). In addition, the DNA of the isolate was evaluated in a species-specific multiplex PCR (Silva-Campos et al. 2022), and the amplicons were electrophoretically separated, giving a similar band profile to G. smithogilvyi RGM 2903 and RGM 2904 strain from Chilean Collection of Microbial Genetic Resources. Pathogenicity of G. castaneae isolate (CV-11) was tested on ten replicates of 3-year-old C. sativa plants. Two wounds were made on the same season growing shoot and two on the previous season shoot. Longitudinal wounds (5 mm long, 4 mm wide and 2 mm depth) were made using a scalpel without removing the outer bark to inoculate the plants. Each wound was inoculated with a 5-mm mycelium plug, covered with the outer bark, and wrapped with Parafilm. Plugs of PDA were placed onto the wounds of two plants as control. The plants were kept in a growth chamber (22 ±1 0C and 90± 5% RH). All plants showed dark brown cankers measuring 20 to 40 mm long two weeks after inoculation. Also, most plants inoculated in the same season shoot presented wilted and chlorotic foliage. Mature conidiomata with cirri developed in most of the cankers. No symptoms were observed in the control. Fungal colonies of G. castaneae were reisolated on PDA from all inoculated chestnut plants and were not recovered from the controls. Recently, G. smithogilvyi has been identified as the causal agent of brown rot on chestnut nuts in Chile (Cisterna Oyarce et al. 2022); however, in several countries, it has also been associated as the causal agent of cankers in branch and stem of chestnut, as well as an endophyte in different hardwood species. Future studies on the incidence of this pathogen and its impact on chestnut yield should be carried out in the producing regions because it represents an emerging threat to Chilean chestnut production.

Comparing causal random forest and linear regression to estimate the independent association of organisational factors with ICU efficiency.

PURPOSE: Parametric regression models have been the main statistical method for identifying average treatment effects. Causal machine learning models showed promising results in estimating heterogeneous treatment effects in causal inference. Here we aimed to compare the application of causal random forest (CRF) and linear regression modelling (LRM) to estimate the effects of organisational factors on ICU efficiency. METHODS: A retrospective analysis of 277,459 patients admitted to 128 Brazilian and Uruguayan ICUs over three years. ICU efficiency was assessed using the average standardised efficiency ratio (ASER), measured as the average of the standardised mortality ratio (SMR) and the standardised resource use (SRU) according to the SAPS-3 score. Using a causal inference framework, we estimated and compared the conditional average treatment effect (CATE) of seven common structural and organisational factors on ICU efficiency using LRM with interaction terms and CRF. RESULTS: The hospital mortality was 14 %; median ICU and hospital lengths of stay were 2 and 7 days, respectively. Overall median SMR was 0.97 [IQR: 0.76,1.21], median SRU was 1.06 [IQR: 0.79,1.30] and median ASER was 0.99 [IQR: 0.82,1.21]. Both CRF and LRM showed that the average number of nurses per ten beds was independently associated with ICU efficiency (CATE [95 %CI]: -0.13 [-0.24, -0.01] and -0.09 [-0.17,-0.01], respectively). Finally, CRF identified some specific ICUs with a significant CATE in exposures that did not present a significant average effect. CONCLUSION: In general, both methods were comparable to identify organisational factors significantly associated with CATE on ICU efficiency. CRF however identified specific ICUs with significant effects, even when the average effect was nonsignificant. This can assist healthcare managers in further in-dept evaluation of process interventions to improve ICU efficiency.

First Report of Beet Western Yellows Virus Infecting Vasconcellea x heilbornii (Caricaceae) in Ecuador.

Vasconcellea x heilbornii, known as babaco, is a hybrid native to Ecuador grown in small orchards in sub-tropical highland regions. Over the last decade, several viruses have been identified in babaco using high-throughput sequencing (HTS) (Cornejo-Franco et al. 2020, (Reyes-Proaño et al. 2023). In 2021, total RNA from a babaco plant showing distinctive leaf yellowing was extracted using the PureLink RNA Mini Kit (Thermo Fischer Scientific, USA) and subjected to HTS on an Illumina NovaSeq6000 system as 150 paired-end reads (Macrogen Inc., South Korea). Library construction was done using the TruSeq Stranded Total RNA Sample kit with Plant Ribo-Zero, as described (Villamor et al. 2022). Reads were processed using BBDuk and de novo assembled using SPAdes 3.15. both implemented in Geneious 2022. Contig analysis was done by BLASTx using the NCBI viral sequence database (as of November 2022). HTS generated 54 million reads, of which 12% assembled into contigs corresponding to genomes of previously reported babaco viruses including babaco virus Q (BabVQ), babaco nucleorhabdovirus 1 (BabRV1) and babaco ilarvirus 1 (BabIV1). Interestingly, 144 reads (0.0003%) assembled into seven contigs ranging from 100 to 480 nucleotides (nt) in length. These contigs showed homology, with 97% amino acid (aa) identity (100% query coverage), to regions of the RNA-dependent-RNA-polymerase (RdRp) of beet western yellows virus (BWYV, Acc. No. NC_004756), a member of the Polerovirus genus. To confirm the occurrence of BWYV in babaco, double-stranded RNA (dsRNA) was extracted from 15 g of leaf tissue from the original sample as described (Dodds et al. 1984) and used as template for reverse-transcription (RT)-PCR using overlapping primers designed to span all short contigs. RT-PCR amplified fragments were cloned into a pGEM®T-easy vector (Promega, USA) and sequenced by the Sanger method (Macrogen Inc., South Korea). The sequences were assembled into a single 2.7 kbp BWYV genome fragment comprising the complete protein 1 (P1) and partial RdRp gene (GenBank Acc. No. PP480670). Sequence alignments between the partially sequenced genome of the babaco isolate and its corresponding fragment from the closest BWYV isolate (NC_004756) revealed 94% and 97% identities at the nt and aa levels, respectively. To assess the prevalence of BWYV in babaco, 30 leaf samples showing yellowing symptoms from Pichincha (n=15) and Azuay (n=15) provinces were tested by RT-PCR using total RNA. Total RNA extraction and reverse transcription were done using the methodology described by Halgren et al. (2007). For RT-PCR, the primer set BWYV_Bab_F: 5'-CAGTGTCCTCCAAGTGCAACAT-3' / BWYV_Bab_R: 5'GGTTCCTTCCCAGTTTGGTGGT-3', which amplifies a 235 nt-long P1 region, was used. Three RT-PCR products from each positive sample were purified using the GeneJET PCR clean-up kit (Thermo Scientific, USA) and sequenced. BWYV was confirmed in 9 out of 15 samples (60%) from Pichincha, and in 10 out of 15 samples (64%) from Azuay. Samples were also tested for additional babaco viruses as described (Reyes-Proaño et al. 2023). All BWYV-infected plants turned out positive for papaya ringspot virus (PRSV), babaco mosaic virus (BabMV), BabVQ, and BabIV1. Hence, the impact of BWYV infection on babaco plants in single and mixed infections warrants further investigation. To the best of our knowledge, this is the first report of BWYV in a crop in Ecuador, and the first time it has been found in a Caricaceae species.

Comparative Effectiveness of Switching to Bictegravir From Dolutegravir-, Efavirenz-, or Raltegravir-Based Antiretroviral Therapy Among Individuals With HIV Who are Virologically Suppressed.

Background: We aimed to determine the effectiveness of switching to bictegravir in maintaining an undetectable viral load (<50 copies/mL) among people with HIV (PWH) as compared with continuing dolutegravir-, efavirenz-, or raltegravir-based antiretroviral therapy using nationwide observational data from Mexico. Methods: We emulated 3 target trials comparing switching to bictegravir vs continuing with dolutegravir, efavirenz, or raltegravir. Eligibility criteria were PWH aged ≥16 years with a viral load <50 copies/mL and at least 3 months of current antiretroviral therapy (dolutegravir, efavirenz, or raltegravir) between July 2019 and September 2021. Weekly target trials were emulated during the study period, and individuals were included in every emulation if they continued to be eligible. The main outcome was the probability of an undetectable viral load at 3 months, which was estimated via an adjusted logistic regression model. Estimated probabilities were compared via differences, and 95% CIs were calculated via bootstrap. Outcomes were also ascertained at 12 months, and sensitivity analyses were performed to test our analytic choices. Results: We analyzed data from 3 028 619 PWH (63 581 unique individuals). The probability of an undetectable viral load at 3 months was 2.9% (95% CI, 1.9%-3.8%), 1.3% (95% CI, .9%-1.6%), and 1.2% (95% CI, .8%-1.7%) higher when switching to bictegravir vs continuing with dolutegravir, efavirenz, and raltegravir, respectively. Similar results were observed at 12 months and in other sensitivity analyses. Conclusions: Our findings suggest that switching to bictegravir could be more effective in maintaining viral suppression than continuing with dolutegravir, efavirenz, or raltegravir.

Causal inference and GWAS: Rubin, Pearl, and Mendelian randomization.

Although Genome Wide Analysis (GWAS) have been widely used to understand the genetic architecture of complex quantitative traits, interpreting their results in terms of the biological processes that determine those traits has been difficult or even lacking, because of the variability in responses to the tests of hypotheses within a trait, species, and breed or cross, and the lack of follow-up studies. It is then essential employing appropriate statistical tests that point out to the causal genes responsible of the relevant fraction of the genetic variability observed. We briefly review the main theoretical aspects of the two schools of causal inference (Rubin's Causal Model, RCM, and Pearl's causal inference, PCI). RCM approachs the hypothesis testing from a randomization perspective by considering a wider space of the observation, i.e. the "potential outcomes", rather than the narrower space that results from defining "treatment" effects after observing the data. Next, we discuss the assumptions involved to meet the requirements of randomization for RCM with observational data (non-designed experiments) with special emphasis on the Stable Unit Treatment Analysis (SUTVA). Due to the presence of "confounders" (i.e. systematic fixed effects, environmental permanent effects, interaction among genes, etc.), causal average treatment effects are viewed through the familiar lens of normal linear (or mixed) models. To overcome the difficulties of association analyses, a tests of causal effects is introduced using independent predicted residual breeding values from animal models of genetic evaluation that avoids the effects of population structure and confounder effects. An independent section discusses the issue of whether the additive effects defined at the "gene" level by R. A. Fisher and popularized in D. S. Falconer's textbook of quantitative genetics can be termed causal from either RCM or PCI.

First report of basal rot of yellow dragon fruit (Selenicereus megalanthus) caused by Fusarium oxysporum in Peru.

Cultivation of yellow dragon fruit (Selenicereus megalanthus) in Peru has recently expanded (Verona-Ruiz et al. 2020). In August 2021, approximately 170 of 1,110 dragon fruit cuttings (15.3%) in the university's nursery (6°26'10'' S; 77°31'25'' W) showed basal rot symptoms. Initial symptoms included small brown spots on the base of stems, expanding towards the top that became soft and watery. All symptomatic plants eventually died, i.e., a severity of 100%. The disease was more prevalent on cuttings during the rooting phase than on well-established cuttings. We collected five symptomatic cuttings from throughout the nursery. Four sections of 1 × 1 cm2 of tissue adjacent to the diseased area were excised from each cutting, immersed for 1 min in 2% NaClO, rinsed twice with sterile distilled water, placed on potato dextrose agar (PDA) medium (four sections per Petri plate, five plates), and incubated at 25°C for 7 days. Morphologically similar mycelia grew from all sections, and five monosporic isolates were obtained, one per plate. Colonies grew fast, reaching 60 to 64 mm in 7 days, and produced violet-white cottony aerial mycelia with orange sporodochia on PDA, and abundant macro- and microconidia on synthetic nutrient-poor agar. Macroconidia were straight to slightly curved, typically with 2 to 3 septa, 16.6 to 23.3 × 1.7 to 3.7 µm (n = 30); microconidia were oval or kidney-shaped, and commonly hyaline, 6.7 to 16.4 × 2.5 to 4.7 µm (n = 40). Genomic DNA was extracted from isolate AFHP-100, then the ITS region and the TEF1 and RPB2 partial genes were amplified and sequenced (Accession numbers PP977433, OR437358, PP537149) following Gardes and Bruns (1993) and O'Donnell et al. (1998). We conducted a BLASTn search of ITS sequence against the NCBI "nr" database and local 'megablast' searches of TEF1 and RPB2 sequences against FUSARIUM-ID v.3.0 (Torres-Cruz et al. 2022). We found 100%, 98.19 to 99.84%, and 98.81 to 99.76% identities in ITS, TEF1, and RPB2 sequences, respectively, to the ex-epitype and other reference strains of Fusarium oxysporum (CBS 144134, NRRL26406, among others). A maximum likelihood phylogenetic analysis with a TEF1-RPB2 concatenated dataset with FUSARIUM-ID sequences also showed isolate AFHP-100 was F. oxysporum. A pathogenicity test was carried out by inoculating wounded healthy roots of three cuttings with submersion in a 5 × 106 conidia/ml suspension for 25 min. Then, the inoculated plants were planted in sterile soil. One cutting with wounded roots submerged in sterile water served as a control. In parallel, sterile soil was inoculated with 20 mL of the conidial suspension, and another three healthy cuttings were planted. A cutting planted in noninoculated soil also served as a control. Basal rot symptoms developed in all inoculated plants after 25 days. After re-isolation, the same fungus, corroborated based on micromorphology and TEF1 sequence (PP335689), was recovered, fulfilling Koch's postulates. The isolate was deposited in the KUELAP Herbarium (voucher KUELAP-3214), located and administered by the National University Toribio Rodriguez de Mendoza de Amazonas, in Chachapoyas, Peru. Fusarium oxysporum has been reported to cause basal stem rot in Bangladesh and Argentina (Mahmud et al. 2021; Wright et al. 2007), and stem blight in Malaysia (Mohd Hafifi et al. 2019) on dragon fruit. This is the first report of F. oxysporum causing basal rot in S. megalanthus in Peru. This fungus is among the most destructive plant pathogens, and the rapid expansion of the crop in Peru requires a comprehensive knowledge of the biotic factors influencing production. Therefore, this report is foundational to implementing proper control strategies.

The web of conflict-related interactions in Colombia: exploring causal linkages between ecological and social variables by the qualitative loop analysis.

In Colombia, the long-lasting internal conflict heavily shaped the socio-ecological context and imposed relationships that persisted after the peace agreement was signed in 2016. One question of interest is whether policies or interventions conceived to attain desirable goals for the post-conflict society may be effective or, rather, if the constraints imposed by the conflict scenario might produce unintended effects, either on the environmental or the social side. To explore this issue, we envisaged the socio-ecological system as a parsimonious set of characteristic ecological and social variables within the conflict-related framework and reconstructed their interactions, exploiting elicitation-based information and the literature. We visualized the resulting interactive networks as signed digraphs. Applying the qualitative technique of loop analysis combined with numerical simulations, we predicted the response of the system to policies as drivers of change, such as subsidized credit to capital-intensive activities or policies that increase small farming competitiveness and access to markets. Highlighting causal linkages reveals that the persistence of conflict factors may produce unexpected interdependencies between licit and illicit activities and that, only in a few cases, the persistence of these mechanisms allows synergies between desirable goals.This article is part of the theme issue 'Connected interactions: enriching food web research by spatial and social interactions'.

First report of Colletotrichum chlorophyti causing soybean anthracnose in Brazil.

Soybean [Glycine max (L.) Merr.] is one of the world's five major food crops, and Brazil produces the highest share at around 42%. Anthracnose caused by Colletotrichum is an important limiting factor to soybean production. In November 2013, anthracnose symptoms, characterized by brown irregular-shaped lesions on petioles, stems, and pods were observed in soybean fields (1% of incidence) in Vera, Mato Grosso State, Brazil. From the five plants gathered in the field, three leaves along with their corresponding petioles were meticulously chosen for the removal of symptomatic tissues. Sampling of these tissues involved carefully cutting a 0.5 × 0.5 cm fragment in the lesion area. The fragments were disinfected with 70% ethanol for 1 min, followed by 1% sodium hypochlorite for 2 min. Then the fragments were rinsed three times in sterile distilled water, placed on water-agar, and incubated at 25 °C for four days, in a 12/12 h photoperiod. Hyphal tips were transferred to potato dextrose agar (PDA) plates and incubated as previously described for seven days. A Colletotrichum sp. single-spore isolate (LFN0461) was selected, grown, preserved in filter paper, and stored at -80 °C. In 2023, it was reactivated for molecular characterization. On PDA, colony showed a rough-like mycelial growth, violaceous-black (front/reverse), with curved-shaped conidia 14.7 - 28.2 × 2.1 - 8.96 µm (average 18.4 × 4.7 µm). The DNA was extracted from 10-day-old mycelium using the cetyltrimethylammonium bromide (CTAB) method. The rDNA internal transcribed spacer (ITS), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), histone (HIS3), and ß-tubulin 2 (TUB2) regions were amplified by polymerase chain reaction (PCR), using the primer pairs ITS-1F + ITS-4 (Gardes and Bruns 1993; White et al. 1990), GDF1 + GDR1 (Guerber et al. 2003), CYLH3F + CYLH3R (Crous et al. 2006), and Bt2A + Bt2B (Glass and Donaldson 1995), respectively. The sequences were deposited in the GenBank database (accession numbers: PP209207 - ITS; PP213392 - GAPDH; PP213393 - HIS3; MN688797 - TUB2). The reconstruction of the multilocus phylogenetic tree revealed that the LFN0461 isolate clustered with C. cholorophyti reference strain (IMI 103806) with 99.9% of Bayesian probability. Given the seed-borne nature of soybean anthracnose (Boufleur et al. 2021; Yang et al. 2013), pathogenicity tests were carried out by soybean seeds inoculation. Fifty seeds of NS6220 IPRO (Nidera) cultivar were inoculated by water restriction method, with LFN0461 colonies grown on PDA amended with mannitol (Machado et al. 2004), while 50 seeds were placed on PDA amended with mannitol as negative control. Soybean seeds remained in contact with the inoculum for 48 hours. Subsequently, seeds were sown in 2 L pots (n = 10) containing sterilized substrate, which were placed in a greenhouse at 25 ± 5 ºC. After 10 days, inoculated soybean seedlings exhibited characteristic necrotic lesions on cotyledons and hypocotyls, while negative control plants remained asymptomatic. Colletotrichum chlorophyti was successfully reisolated from the symptomatic tissues. Currently, C. chlorophyti has been reported to cause soybean anthracnose and infect seeds in the United States (Yang et al. 2013, 2012). Although this pathogen has not been reported since our first observation in 2013 in Brazil, many Colletotrichum isolates are misidentified due to reliance on morphology (Boufleur et al. 2021). To our knowledge, this study is the first report of C. chlorophyti causing soybean anthracnose in Brazil, joining a new group of emergent Colletotrichum spp. associated with this disease.

First report of Colletotrichum plurivorum and Colletotrichum truncatum causing anthracnose on melon plants in Brazil.

Melon (Cucumis melo L.) is an economically important crop in Brazil, with an annual production of 699.281 tons (FAO 2024). Fungal diseases are one of the biggest problems in melon production, and melon growers in northeastern Brazil have reported over 80% of plants showing anthracnose symptoms in the fields during rainy seasons. Plants were wilted, displaying brown necrotic lesions and water-soaked spots with yellowish edges on the leaves and vines. Melon fruits displayed necrotic lesions on the outside. From June 2022 to June 2023, melon leaves (varieties Yellow, Galia, and Cantaloupe) from anthracnose-symptomatic plants were collected in four melon farms located in the municipalities of Afonso Bezerra, Mossoró, Tibau, and Upanema in the state of Rio Grande do Norte. Small fragments of symptomatic leaves were disinfected in 70% ethanol (30 sec) and 2.5 % sodium hypochlorite (1 min), rinsed in sterile distilled water, and plated on PDA Petri dishes with tetracycline (0.05g/liter). Plates were maintained in a bio-oxygen demand incubator (BOD) for 3 days at 28 ± 2 °C, under a 12 hr photoperiod. Eleven representative fungal colonies resembling Colletotrichum spp. were selected and monosporically grown on PDA for seven days for morphology, pathogenicity, and molecular analyses.ight colonies showed pinkish-dark brown with acervuli in the center and cottony mycelium, and showing black edges in some isolates, resembling C. plurivorum (Zhang et al. 2023). Conidia from those colonies were hyaline, cylindrical with obtuse ends, and 17.76 x 7.06 µm, n= 50. Three colonies developed pinkish-gray mycelia with numerous black microsclerotia, and the conidia were hyaline, falcate, and 27.38 x 4.10 µm, n= 50, resembling C. truncatum (Yu et al. 2023). The total DNA of the eleven isolates was extracted, and the internal transcribed space (ITS), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), actin (ACT), ß-tubulin (TUB), and chitin synthase 1 (CHS-1) regions were partially amplified by PCR. Amplicons were sequenced and deposited to Genbank (Table eXtra1). A phylogenetic tree was built with the Maximum likelihood method with the concatenated sequences of the five partial gene sequences on Software MEGA (Version 11.0.10) (Tamura et al. 2021). The isolates CML5, CML8, CML9, CML10, CML11, CML14, CML15, and CML25 were grouped with Colletotrichum plurivorum CBS 125474 (orchidearum complex), and the isolates CML26, CML27 and CML28 with Colletotrichum truncatum CBS 15:35 (truncatum complex) with 87 % e 97 % of Bootstrap support, respectively. C. plurivorum was detected in four farms visited (we selected two representative isolates per farm), while C. truncatum isolates were all from the farm in Afonso Bezerra municipality. A pathogenicity test was performed following the method of Baishuan et al. (2023), micro-injuries were made in leaves of melon seedlings 'Goldex Yellow' and inoculated with a spore suspension of colonies with seven days of growth (106 spore/mL) of each isolate and sprayed to the point of dripping. Sterile water was used as mock. After nine days, anthracnose symptoms similar to those observed in the field were seen in all inoculated leaves, while no symptom was observed in the leaves of the mock plants. The pathogens were reisolated and their identification was confirmed by morphology and sequencing. Five seedlings were inoculated per isolate and mock, the assay was repeated, and the same results were observed. The species C. plurivorum has already been reported to cause disease in Cucumbers in Brazil (Silva et al. 2023) and C. plurivorum and C. truncatum in Citrullus lanatus in China (Guo et al. 2022). To the best of our knowledge, this is the first report of C. plurivorum and C. truncatum causing anthracnose in melon plants in Brazil.

Pooled lagged effect of runoff on leptospirosis cases in Colombia.

Leptospirosis is a global zoonotic disease caused by spirochete bacteria of the genus Leptospira. The disease exhibits a notable incidence in tropical and developing countries, and in Colombia, environmental, economic, social, and cultural conditions favor disease transmission, directly impacting both mortality and morbidity rates. Our objective was to establish the pooled lagged effect of runoff on leptospirosis cases in Colombia. For our study, we included the top 20 Colombian municipalities with the highest number of leptospirosis cases. Monthly cases of leptospirosis, confirmed by laboratory tests and spanning from 2007 to 2022, were obtained from the National Public Health Surveillance System. Additionally, we collected monthly runoff and atmospheric and oceanic data from remote sensors. Multidimensional poverty index values for each municipality were sourced from the Terridata repository. We employed causal inference and distributed lag nonlinear models to estimate the lagged effect of runoff on leptospirosis cases. Municipality-specific estimates were combined through meta-analysis to derive a single estimate for all municipalities under study. The pooled results for the 20 municipalities suggest a lagged effect for the 0 to 2, and 0-3 months of runoff on leptospirosis when the runoff is < 120 g/m2. No effect was identified for longer lagged periods (0-1, 0 to 4, 0 to 5, and 0-6 months) or higher runoff values. Incorporation of the multidimensional poverty index into the meta-analysis of runoff contributed to the models for the lagged periods of 0-3, and 0-4 months.

Causal association between environmental variables and the excess cases of cutaneous leishmaniasis in Colombia: are we looking to the wrong side?

Our main aim was to estimate and compare the effects of six environmental variables (air temperature, soil temperature, rainfall, runoff, soil moisture, and the enhanced vegetation index) on excess cases of cutaneous leishmaniasis in Colombia. We used epidemiological data from the Colombian Public Health Surveillance System (January 2007 to December 2019). Environmental data were obtained from remote sensing sources including the National Oceanic and Atmospheric Administration, the Global Land Data Assimilation System (GLDAS), and the Moderate Resolution Imaging Spectroradiometer. Data on population were obtained from the TerriData dataset. We implemented a causal inference approach using a machine learning algorithm to estimate the causal association of the environmental variables on the monthly occurrence of excess cases of cutaneous leishmaniasis. The results showed that the largest causal association corresponded to soil moisture with a lag of 3 months, with an average increase of 8.0% (95% confidence interval [CI] 7.7-8.3%) in the occurrence of excess cases. The temperature-related variables (air temperature and soil temperature) had a positive causal effect on the excess cases of cutaneous leishmaniasis. It is noteworthy that rainfall did not have a statistically significant causal effect. This information could potentially help to monitor and control cutaneous leishmaniasis in Colombia, providing estimates of causal effects using remote sensor variables.

Association between inflammatory bowel disease and the risk of parenteral malignancies: A two-sample Mendelian randomization study.

AIM: Using Mendelian Randomization (MR) analysis to investigate the potential causal association between Inflammatory Bowel Disease (IBD) and the occurrence of parenteral malignancies, in order to provide some reference for the parenteral malignancy prevention in patients with IBD. METHODS: This was a two-sample MR study based on independent genetic variants strongly linked to IBD selected from the Genome-Wide Association Study (GWAS) meta-analysis carried out by the International Inflammatory Bowel Disease Genetics Consortium (IIBDGC). Parenteral malignancy cases and controls were obtained from the FinnGen consortium and the UK Biobank (UKB) release data. Inverse Variance Weighted (IVW), weighted median, MR-Egger, and strength test (F) were utilized to explore the causal association of IBD with parenteral malignancies. In addition, Cochran's Q statistic was performed to quantify the heterogeneity of Instrumental Variables (IVs). RESULTS: The estimates of IVW showed that patients with IBD had higher odds of diffuse large B-cell lymphoma (OR = 1.2450, 95% CI: 1.0311‒1.5034). UC had potential causal associations with non-melanoma skin cancer (all p < 0.05), melanoma (OR = 1.0280, 95% CI: 0.9860‒1.0718), and skin cancer (OR = 1.0004, 95% CI: 1.0001‒1.0006). Also, having CD was associated with higher odds of non-melanoma skin cancer (all p < 0.05) and skin cancer (OR = 1.0287, 95% CI: 1.0022‒1.0559). In addition, results of pleiotropy and heterogeneity tests indicated these results are relatively robust. CONCLUSIONS: IBD has potential causal associations with diffuse large B-cell lymphoma and skin cancers, which may provide some information on the prevention of parenteral malignancies in patients with IBD. Moreover, further studies are needed to explore the specific mechanisms of the effect of IBD on skin cancers.

Causal Forest Machine Learning Analysis of Parkinson's Disease in Resting-State Functional Magnetic Resonance Imaging.

In recent years, Artificial Intelligence has been used to assist healthcare professionals in detecting and diagnosing neurodegenerative diseases. In this study, we propose a methodology to analyze functional Magnetic Resonance Imaging signals and perform classification between Parkinson's disease patients and healthy participants using Machine Learning algorithms. In addition, the proposed approach provides insights into the brain regions affected by the disease. The functional Magnetic Resonance Imaging from the PPMI and 1000-FCP datasets were pre-processed to extract time series from 200 brain regions per participant, resulting in 11,600 features. Causal Forest and Wrapper Feature Subset Selection algorithms were used for dimensionality reduction, resulting in a subset of features based on their heterogeneity and association with the disease. We utilized Logistic Regression and XGBoost algorithms to perform PD detection, achieving 97.6% accuracy, 97.5% F1 score, 97.9% precision, and 97.7%recall by analyzing sets with fewer than 300 features in a population including men and women. Finally, Multiple Correspondence Analysis was employed to visualize the relationships between brain regions and each group (women with Parkinson, female controls, men with Parkinson, male controls). Associations between the Unified Parkinson's Disease Rating Scale questionnaire results and affected brain regions in different groups were also obtained to show another use case of the methodology. This work proposes a methodology to (1) classify patients and controls with Machine Learning and Causal Forest algorithm and (2) visualize associations between brain regions and groups, providing high-accuracy classification and enhanced interpretability of the correlation between specific brain regions and the disease across different groups.

First Report of White Mold Caused by Sclerotinia sclerotiorum on Hymenocallis glauca in Mexico.

In Mexico, there are 29 native species of the genus Hymenocallis, where H. glauca is one of the most cultivated bulbous plants. It holds economic importance as it is commercialized as a potted plant and cut flower (Leszczyñska and Borys, 2001). In October 2023, field sampling was conducted in the Research Center in Horticulture and Native Plants (18°55'55" N, 98°24'02.8"W) of UPAEP University. H. glauca diseased plants were found in an area of 0.4 ha, with an incidence of 35% and an estimated severity of 45% on infected plants in vegetative stage. The symptoms included chlorosis of foliage, necrosis at the base of the stem, and soft rot with abundant white to gray mycelium and abundant production of black, irregular sclerotia of approximately 3.5 mm diameter. Finally, the plants wilted and died. The fungus was isolated from 40 symptomatic plants. Sclerotia were collected, disinfested with 3% NaOCl for one minute, rinsed with sterile distilled water (SDW), and plated on Petri dishes containing potato dextrose agar (PDA) with sterile forceps. Subsequently, a sterile dissecting needle was used to place fragments of mycelium directly on Petri dishes with PDA. Plates were incubated at 23 °C in dark for 7 days. One isolate was obtained from each diseased plant by the hyphal-tip method (20 isolates from sclerotia and 20 from mycelium). After 7 days, colonies had fast-growing, dense, and cottony-white aerial mycelium forming irregular sclerotia of 3.57 ± 0.59 mm (mean ± standard deviation, n=100). In each Petri dish there were produced 21.5 ± 7.9 sclerotia (mean ± standard deviation, n=40), after 11 days; these were initially white and gradually turned black. The isolates were tentatively identified as Sclerotinia sclerotiorum based on morphological characteristics (Saharan and Mehta 2008). Two representative isolates were chosen for molecular identification and genomic DNA was extracted by the CTAB protocol. The ITS region and the glyceraldehyde 3-phosphate dehydrogenase (G3PDH) gene were amplified and sequenced (Staats et al. 2005; White et al. 1990). The sequences of a representative isolate (SsHg3) were deposited in GenBank (ITS- PP094578; G3PDH- PP101843). BLAST analysis of the partial sequences ITS (519 bp), and G3PDH (950 bp) showed 100% similarity to S. sclerotiorum isolates (GenBank: MG249967, MW082601). Pathogenicity was confirmed by inoculating 30 H. glauca plants in vegetative stage grown in pots with sterile soil. Ten sclerotia were deposited at the base of the stem, 10 mm below the soil surface. As control treatment, SDW was applied to 10 plants. The plants were placed in a greenhouse at 23 °C and 90% relative humidity. After 17 days, all inoculated plants displayed symptoms similar to those observed in the field, while no symptoms were observed on the controls. The fungus was re-isolated from the inoculated plants as described above, fulfilling Koch's postulates. The pathogenicity tests were repeated three times. S. sclerotiorum has been reported causing white mold on other bulbous plants, like fennel (Foeniculum vulgare) in Korea (Choi et al. 2015). To our knowledge, this is the first report of S. sclerotiorum causing white mold on H. glauca in Mexico. Information about diseases affecting this plant is very limited, so this research is essential for developing integrated management strategies and preventing spread to other production areas.

Insulin resistance potentiates the effect of remnant cholesterol on cardiovascular mortality in individuals without diabetes.

BACKGROUND AND AIMS: Remnant cholesterol (RC) and insulin resistance (IR) have been independently associated with cardiovascular risk. Here, we evaluated the role of IR and RC on cardiovascular disease (CVD) mortality. METHODS: We conducted an analysis of 16,113 individuals ≥20 years without diabetes from the National Health and Nutrition Examination Survey (NHANES-III/IV). RC levels were calculated using total cholesterol, non-HDL-c, and LDL-c; IR was defined as HOMA2-IR≥2.5 and CVD mortality as a composite of cardiovascular and cerebrovascular mortality. Multiple linear regression was used to assess the relationship between HOMA2-IR and RC and Cox regression models to assess their joint role in CVD mortality. Causally ordered mediation models were used to explore the mediating role of IR in RC-associated CVD mortality. RESULTS: We identified an association between higher HOMA2-IR and higher RC levels. The effect of IR on CVD mortality was predominant (HR 1.32, 95%CI 1.18-1.48) and decreased at older ages (HR 0.934, 95%CI 0.918-0.959) compared to RC (HR 0.983, 95%CI 0.952-1.014). Higher risk of CVD mortality was observed in individuals with IR but normal RC (HR 1.37, 95%CI 1.25-1.50) and subjects with IR and high RC (HR 1.24, 95%CI 1.13-1.37), but not in subjects without IR but high RC. In mediation models, HOMA2-IR accounted for 78.2% (95%CI 28.11-98.89) of the effect of RC levels on CVD mortality. CONCLUSIONS: Our findings suggest that RC potentiates the risk of CVD mortality through its effect on whole-body insulin sensitivity, particularly among younger individuals.