Bootstrap Replicates Research Articles

BootGSEA: a bootstrap and rank aggregation pipeline for multi-study and multi-omics enrichment analyses.

Introduction: Gene set enrichment analysis (GSEA) subsequent to differential expression analysis is a standard step in transcriptomics and proteomics data analysis. Although many tools for this step are available, the results are often difficult to reproduce because set annotations can change in the databases, that is, new features can be added or existing features can be removed. Finally, such changes in set compositions can have an impact on biological interpretation. Methods: We present bootGSEA, a novel computational pipeline, to study the robustness of GSEA. By repeating GSEA based on bootstrap samples, the variability and robustness of results can be studied. In our pipeline, not all genes or proteins are involved in the different bootstrap replicates of the analyses. Finally, we aggregate the ranks from the bootstrap replicates to obtain a score per gene set that shows whether it gains or loses evidence compared to the ranking of the standard GSEA. Rank aggregation is also used to combine GSEA results from different omics levels or from multiple independent studies at the same omics level. Results: By applying our approach to six independent cancer transcriptomics datasets, we showed that bootstrap GSEA can aid in the selection of more robust enriched gene sets. Additionally, we applied our approach to paired transcriptomics and proteomics data obtained from a mouse model of spinal muscular atrophy (SMA), a neurodegenerative and neurodevelopmental disease associated with multi-system involvement. After obtaining a robust ranking at both omics levels, both ranking lists were combined to aggregate the findings from the transcriptomics and proteomics results. Furthermore, we constructed the new R-package "bootGSEA," which implements the proposed methods and provides graphical views of the findings. Bootstrap-based GSEA was able in the example datasets to identify gene or protein sets that were less robust when the set composition changed during bootstrap analysis. Discussion: The rank aggregation step was useful for combining bootstrap results and making them comparable to the original findings on the single-omics level or for combining findings from multiple different omics levels.

First Report of Chocolate Spot Caused by Botrytis eucalypti on Faba bean in China.

Faba bean (Vicia faba) is one of the characteristic economic crops in Qinghai Province of China, which has multiple uses as grain, vegetable, fodder, fertilizer and medicine. Chocolate spot is a critical disease of faba bean in the world, and it is widely spread in all production areas of Qinghai. In August 2021, a severe occurrence of chocolate spot was found in a faba bean field in Xunhua County, Qinghai Province (35°52'N, 102°22'E, alt. 1890m). All plants in the field were affected by this disease. A voucher specimen was deposited in the Herbarium of Plant Pathology, College of Agricultural and Forestry Sciences at Qinghai University under accession No. PY015. The pathogen infected the leaves and stems, causing small irregular red spots to appear, which later coalesce into larger spots and faded green lesions appear around the spots. Diseased leaf pieces 5 mm2 were surface sterilized with 75% ethyl alcohol for 30s, 1.2% NaOCl for 30s, and rinsed three times with sterile water. They were then plated on potato dextrose agar (PDA) at 22℃ for 10 days in the dark. Fungal colonies are initially white, then gray, and have produced spores by 5 days. Conidia are clusters, ellipsoidal or ovoid, 9-14 × 6-9 μm. The conidiophore is straight, terminally enlarged, septate, 300-1500 μm long, 8-13 μm wide. No sclerotia were observed during culture. DNA of the strain PY015 was extracted by CTAB method. Molecular identification was first performed using the universal region of ITS (ITS1/ITS4). The PCR product was sequenced, the sequence was deposited in GenBank under the accession number OR739575. The results showed 100% similarity to Botrytis spp. (KX301016, MT250940, LC519322) in BLAST search. Molecular characterization was continued using five specific primer pairs: RPB2 (DNA-dependent RNA polymerase subunit II, RPB2-5F/RPB2-7cR), NEP1 and NEP2 (necrosis and ethylene-inducing proteins, NEP1for/ NEP1revB and NEP2forD/NEP2revD), HSP60 (heat-shock protein 60, HSP60for/HSP60rev), G3PDH (glyceraldehyde-3-phosphate dehydrogenase, G3PDHfor/G3PDHrev). The sequences of PY015 were deposited in GenBank (accession numbers: OR731179, OR731180, OR731181, OR731182, OR731183), and all five sequences showed 100% similarity to Botrytis eucalypti YZU171088 (accession numbers: MH614610 MH614611, MH614612, MH614613 MH614614). A phylogenetic tree based on these five genes was constructed using Mega7.0 (1000 bootstrap replicates, neighbor-joining method), and PY015 was placed in the same clade as YZU171088 with 100% bootstrap values. Morphological and molecular biological results confirmed that isolate PY015 was B. eucalypti. To fulfill Koch's postulates, the spore suspension (2 × 105 conidia/ml) was sprayed on healthy faba bean (Yun-122) plants at the 10-leaf stage, while an equal amount of sterile distilled water was applied to controls. After 7 days, the inoculated plants showed symptoms consistent with field infection and B. eucalypti was re-isolated using the same protocol, while the control remained asymptomatic. The pathogenicity test was repeated twice. The same isolates were recovered from symptomatic leaves and identified by NEP1 sequence. B. eucalypti was morphologically and molecularly identical to the original isolates, completing Koch's postulates. Currently, Botrytis fabae, Botrytis fabiopsis, and Botrytis cinerea are the main pathogens of chocolate spot on faba bean that have been identified and reported nationally and internationally. B. eucalypti is a new species discovered from eucalyptus in southern China in 2016, and its current hosts are only eucalyptus and citrus. To our knowledge, the present study is the first report of chocolate spot caused by B. eucalypti on faba bean in China.

Lifestyle Factors Associated With Frequent Recurrent Headaches in Children and Adolescents: A Canadian Population-Based Study.

Lifestyle behaviors have been postulated to affect headache frequency in youth and are often the primary target of self-management recommendations. Our study aimed to assess the association between various lifestyle factors and frequent recurrent headaches in children and youth. Children and adolescents aged 5-17 years were enrolled in a large cross-sectional Canadian population-based health survey, completed on January 31, 2019. Headache frequency was dichotomized into "approximately once/week or less" or ">once/week" (defined as frequent recurrent headaches). The association between frequent headaches and meal schedules, screen exposure, physical activity, chronotype, and frequent substance use/exposure (alcohol, cigarettes, electronic cigarettes, and cannabis) was assessed using both unadjusted logistic regression models and models adjusted for age/sex. Fully adjusted models examined the odds of frequent headaches according to all exposures. Survey design effects were accounted for using bootstrap replicate weighting. There were an estimated nweighted = 4,978,370 eligible participants in the population. The mean age was 10.9 years (95% CI 10.9-11.0); 48.8% were female; 6.1% had frequent headaches. Frequent headaches were associated with older age (odds ratio [OR] = 1.31, 95% CI 1.28-1.34, p < 0.001) and female sex (OR = 2.39, 95% CI 2.08-2.75, p < 0.001). In models adjusted for age/sex, the odds of frequent headaches decreased with meal regularity (adjusted OR [aOR] = 0.90, 95% CI 0.89-0.92, p < 0.001) and increased with later chronotype (aOR = 1.10, 95% CI 1.05-1.15, p < 0.001) and excess screen exposure (≥21 hours vs none in past week: aOR = 2.97, 95% CI 1.53-5.77, p = 0.001); there was no significant association with reported physical activity (aOR = 0.95, 95% CI 0.67-1.34, p = 0.77). In 12- to 17-year-olds, frequent headaches were associated with frequent alcohol use (≥1/wk vs never: aOR = 3.50, 95% CI 2.18-5.62, p < 0.001), binge drinking (≥5 times in past month vs never: aOR = 5.52, 95% CI 2.95-10.32, p < 0.001), smoking cigarettes (daily vs never: aOR = 3.81, 95% CI 1.91-7.62, p < 0.001), using e-cigarettes (daily vs never: aOR = 3.10, 95% CI 2.29-4.20, p < 0.001), and cannabis use (daily vs never: aOR = 3.59, 95% CI 2.0-6.45, p < 0.001). In the entire sample, daily exposure to smoking inside the house was associated with frequent headaches (aOR = 2.00, 95% CI 1.23-3.27, p = 0.005). Several lifestyle behaviors were associated with frequent headaches in children and youth, such as meal irregularity, late chronotype, prolonged screen exposure, and frequent substance use/exposure, suggesting that these are potential modifiable risk factors to target in this population.

Occurence of leaf spot on Narrow-head ragwort (Ligularia stenocephala) caused by Alternaria cinerariae in Korea.

Narrow-head ragwort (Ligularia stenocephala (Maxim.) Matsum. & Koidz.) has been used for medicinal purposes and a leafy vegetable in South Korea (Choi et al., 2007; Debnath et al., 2017). In May 2022, brown spots and blight were observed on the leaves in a farmer's field in Namwon (35°26'58.9"N, 127°28'55.9"E), Korea. About 80% of the plants in a 3000 m2 cultivation area were infected. To isolate the causal agent, small pieces (1 mm2) surface-sterilized (1% NaOCl for 1 min) symptomatic leaf tissues were put onto a water agar (WA) plate and incubated in the dark at 25℃. After five days of incubation, two isolates (FD00021, FD00022) were obtained from diseased leaves using a single spore isolation technique. Morphological characteristics were examined after seven days of incubation at 25℃ in the dark. Colonies were 51.6 to 65.3 mm in diameter, gray-green in the center, and ivory at the edge. Conidiophores were straight or curved and 10 - 34 × 4 - 5 μm. Conidia were solitary or two to four in a chain, long ellipsoid to obclavate, one to thirteen transverse septa, 52 - 169 ×14 - 34 μm, blunt-tapered beak variable in size 4 - 56 × 3 - 10 μm (n=75). The morphological and cultural characteristics of the isolates were consistent with that of Alternaria cinerariae (Nishikawa and Nakashima, 2015; Simmons, 2007). For molecular identification, genomic DNA was extracted from 5-day-old cultures using the Maxwell® RSC PureFood GMO and Authentication Kit (Promega). Five gene regions, including rDNA ITS, GPD, Alt a, RPB2, and EF1-α were amplified and sequenced using ITS1/ITS4, gpd1/gpd2, Alt-a1-for/ Alt-a1-rev, RPB2-5F2/RPB2-7cR, and EF1-728F/EF1-986R primer sets respectively (Wang et al., 2022; Garibaldi et al., 2022). The resulting sequences were deposited in GenBank with accession no. OP785152, OP785153 and OP832000 to OP832007). The concatenated genes (rDNA ITS, GPD, Alt a, RPB2, and EF1-α) sequence identity of the FD00021 and FD00022 against the reference strain A. cinerariae CBS 116495 is 99.92% (2572/2574) and 99.84% (2570/2574), respectively. Maximum Likelihood tree was inferred based on the concatenated sequences of the five gene regions using the Kimura 2-parameter model with 1,000 bootstrap replications. The phylogenetic tree showed that the present strains and A. cinerariae CBS 116495 fell into the same clade with high bootstrap support (100%). Based on morphological characteristics and molecular analysis, the isolates were identified as A. cinerariae. To confirm their pathogenicity, drops (70 μl) of conidial suspension (1×104 spores/ml) were applied on intact healthy leaves (3 leaves/plant) of plants (3 plants/isolate) that had been cultivated for one month after transplantation as seedlings. Controls were treated with sterile distilled water. The treated plants were covered with plastic boxes to maintain humidity around 90% and were maintained in an incubator at 25℃ in a 12-hour light-dark cycle. Symptoms appeared only on inoculated leaves after four days of inoculation, while controls remained asymptomatic. The A. cinerariae isolates were re-isolated from infected tissue of the inoculated leaves, thus fulfilling Koch's postulates. Alternaria cinerariae is an important plant pathogen that can cause leaf spot and blight on a variety of host plants including Cineraria spp. and Tussilago farfara (He et al. 2020). This is the first report on leaf spot on Narrow-head ragwort caused by A. cinerariae in the world. Leaf spot disease caused by Alternaria cinerariae is a significant threat to narrow-head ragwort agriculture in South Korea. Therefore, its control strategies are necessary for increasing productivity.

Prediction of cognitive impairment using higher order item response theory and machine learning models.

Timely detection of cognitive impairment (CI) is critical for the wellbeing of elderly individuals. The MyCog assessment employs two validated iPad-based measures from the NIH Toolbox® for Assessment of Neurological and Behavioral Function (NIH Toolbox). These measures assess pivotal cognitive domains: Picture Sequence Memory (PSM) for episodic memory and Dimensional Change Card Sort Test (DCCS) for cognitive flexibility. The study involved 86 patients and explored diverse machine learning models to enhance CI prediction. This encompassed traditional classifiers and neural-network-based methods. After 100 bootstrap replications, the Random Forest model stood out, delivering compelling results: precision at 0.803, recall at 0.758, accuracy at 0.902, F1 at 0.742, and specificity at 0.951. Notably, the model incorporated a composite score derived from a 2-parameter higher order item response theory (HOIRT) model that integrated DCCS and PSM assessments. The study's pivotal finding underscores the inadequacy of relying solely on a fixed composite score cutoff point. Instead, it advocates for machine learning models that incorporate HOIRT-derived scores and encompass relevant features such as age. Such an approach promises more effective predictive models for CI, thus advancing early detection and intervention among the elderly.

Fear of COVID-19 as a mediator within the impact of presenteeism on social loafing1.

The coronavirus disease 2019 (COVID-19) pandemic caused employees to be mentally absent at work and decreased their motivation and effort when they work collaboratively rather than individually due to the fear of transmission. The study aims to test the effect of fear caused by COVID-19 on levels of presenteeism and social loafing from job tasks of employees. Data were collected from 522 white-collar and blue-collar workers in Turkey by the snowball sampling method. Before testing the hypotheses, CFA was performed. Reliability analysis was assessed via Cronbach Alpha (FCV-19S = 0.941; PS = 0.713; SLS = 0.974), AVE (FCV-19S = 0.686; PS = 0.524; SLS = 0.725), and CR (FCV-19S = 0.734; PS = 0.722; SLS = 0.856) values. The mediating effect of fear of COVID-19 within the impact on presenteeism on social loafing was evaluated through Process Macro for SPSS. The coefficients for both direct and indirect effects were calculated in the 95% confidence interval using 5,000 bootstrap replicates. The results show that presenteeism has a significant positive impact on social loafing. Fear of COVID-19 has a statistically significant impact on presenteeism and social loafing. Also, fear of COVID-19 partially mediates within the impact of presenteeism on social loafing in the study. Organizations should consider employees' views to increase the level of well-being and productivity. A high level of inventiveness from organizations is compulsory to explore which organizational roles and workflow are at least remotely operated during this period.

First Report of Charcoal Rot on Soybean Caused by Macrophomina phaseolina in Manitoba, Canada.

First Report of Charcoal Rot on Soybean Caused by Macrophomina phaseolina in Manitoba, Canada.

Modeling the Spatial Distribution of Acacia decurrens Plantation Forests Using PlanetScope Images and Environmental Variables in the Northwestern Highlands of Ethiopia

Small-scale Acacia decurrens plantation forests, established by farmers on degraded lands, have become increasingly prevalent in the Northwestern Highlands of Ethiopia. This trend has been particularly notable in Fagita Lekoma District over the past few decades. Such plantations play a significant role in addressing concerns related to sustainable agricultural land use, mitigating the adverse effects of deforestation, and meeting the livelihood and energy requirements of a growing population. However, the spatial distribution of Acacia decurrens and the essential remote sensing and environmental variables that determine its distribution are not well understood. This study aimed to model the spatial distribution of Acacia decurrens plantation forests using PlanetScope data and environmental variables combined with a species distribution model (SDM). Employing 557 presence/absence points, noncollinear variables were identified and utilized as input for six SDM algorithms, with a 70:30 split between training and test data, and 10-fold bootstrap replication. The model performance was evaluated using the receiver operation characteristic curve (AUC) and true skill statics (TSS). The ensemble model, which combined results from six individual algorithms, was implemented to predict the spatial distribution of Acacia decurrens. The highest accuracy with the values of 0.93 (AUC) and 0.82 (TSS) was observed using random forest (RF), followed by SVM with values of 0.89 (AUC) and 0.71 (TSS), and BRT with values of 0.89 (AUC) and 0.7 (TSS). According to the ensemble model result, Acacia decurrens plantation forests cover 22.44% of the district, with the spatial distribution decreasing towards lower elevation areas in the northeastern and western parts of the district. The major determinant variables for identifying the species were vegetation indices, specifically CVI, ARVI, and GI, with AUC metric values of 39.3%, 16%, and 7.1%, respectively. The findings of this study indicate that the combination of high-resolution remote sensing-derived vegetation indices and environmental variables using SDM could play a vital role in identifying Acacia decurrens plantations, offering valuable insights for land use planning and management strategies. Moreover, comprehending the spatial distribution’s extent is crucial baseline information for assessing its environmental implications at a local scale.

Comparing Two Bootstrapped Regions in Images: The D-Test

ObjectivesMany molecular imaging diagnoses involve comparing two regions of interest (ROIs) in the image or different images. Since the images are obtained by measuring a random phenomenon, such comparisons should be based on a statistical test to ensure reliability. Recent studies have shown that use of the bootstrap approach provides access to the statistical variability of reconstructed values in molecular images. However, although there is general agreement that this increase in information should make diagnosis based on molecular images more reliable, no approach has been proposed in the relevant literature to use bootstrap replicates to enhance the reliability of comparisons of two ROIs. In this paper, we propose to fill this gap by introducing the first statistical test that allows us to compare two sets of pixels/voxels for which bootstrap replicates are available. Material and methodsAfter presenting the theoretical basis of this non-parametric statistical test, this article describes how to calculate it in practice. Finally, it proposes two experiments based on quantitative comparisons and expert judgment to assess its relevance. ResultsThe results obtained are consistent with expert diagnosis on synthetic data. This validates the relevance of the D-test. ConclusionThis paper presents the first statistical test to compare two ROIs in reconstructed images for which the statistical variability information is accessible.

Unbiased Proxy Calibration

The linear calibration model is a powerful statistical tool that can be utilized to predict an unknown response variable, Y, through observations of a proxy or predictor variable, X. Since calibration involves estimation of regression model parameters on the basis of a limited amount of noisy data, an unbiased calibration slope estimation is of utmost importance. This can be achieved by means of state-of-the-art, data-driven statistical techniques. The present paper shows that weighted least-squares for both variables estimation (WLSXY) is able to deliver unbiased slope estimations under heteroscedasticity. In the case of homoscedasticity, besides WLSXY, ordinary least-squares (OLS) estimation with bias correction (OLSBC) also performs well. For achieving unbiasedness, it is further necessary to take the correct regression direction (i.e., of Y on X) into account. The present paper introduces a pairwise moving block bootstrap resampling approach for obtaining accurate estimation confidence intervals (CIs) under real-world climate conditions (i.e., non-Gaussian distributional shapes and autocorrelations in the noise components). A Monte Carlo simulation experiment confirms the feasibility and validity of this approach. The parameter estimates and bootstrap replications serve to predict the response with CIs. The methodological approach to unbiased calibration is illustrated for a paired time series dataset of sea-surface temperature and coral oxygen isotopic composition. Fortran software with implementation of OLSBC and WLSXY accompanies this paper.

First Report of Wilt Disease of Ginger Caused by Achromobacter xylosoxidans in China

Ginger (Zingiber officinale) is an important commercial crop that has been widely cultivated in China for more than 2500 years. One variety, Tongling white ginger, has been grown in the Yi'an District of Tongling city, Anhui province (30°45 N, 117°43 E), China. In August 2022, symptoms of yellowing and wilting were observed on ginger plants, with a disease incidence rate exceeding 20% in the field. The stem base of the diseased plants became soft, brown and water-soaked. Additionally, the rhizomes displayed symptoms of browning and water-soaked rot, resembling those caused by Ralstonia solanacearum and Enterobacter cloacae (Yu et al. 2003; Nishijima et al. 2004; Liu et al. 2021). Consequently, ginger bacterial wilt disease may potentially emerge from a combination of infections by diverse pathogenic bacteria. To identify novel pathogens causing the wilt disease, stem tissues of the diseased plants from different locations were sterilized with 1% sodium hypochlorite (NaOCl) for 10 min, followed by at least three time rinses with sterile water. The sterilized samples were then ground with 0.9% saline solution and left at room temperature for 30 min. A 20 μL aliquot of the suspension was serially diluted and cultured on Luria-Bertani (LB) medium at 28°C. A total of 217 isolates was picked and purified for taxonomic identification by 16S rRNA gene analyses with the primer 27F/1492R (Weisburg et al. 1991). Among these isolates, 23 single colony isolates were identified as A. xylosoxidans through NCBI BLASTn analyses. Furthermore, three single isolates from different locations were randomly selected for further experiments. The growing colonies appeared opaque white and round. Microscopic evaluation revealed that cells were rod-shaped with an average length of 1.95 µm and average width of 0.46 µm. The three isolates shared identical 16S rRNA sequences, displayed 99.72% identity with the sequence from A. xylosoxidans strain SeqID2 (GenBank accession NO. MH266081.1). The glutamate synthase (gltB), GTP-binding membrane protein (lepA), NADH:ubiquinone oxidoreductase subunit L (nuoL), RNA polymerase beta-subunit (rpoB), and the enolase (eno) genes of the three isolates were amplified by PCR using primer pairs gltB-F/gltB-R, lepA-F/lepA-R, nuoL-F/nuoL-R, rpoB-F/rpoB-R and eno-F/eno-R, respectively (Spilker et al. 2012; Vandamme et al. 2016). The gene sequences of 16S rRNA (OQ711945, OQ740153 and OR230037), gltB (OR242732, OQ737692 and OR262112), lepA (OR233727, OQ737693 and OR262113), nuoL (OR233726, OQ737694 and OR262114), ropB (OR233725, OQ737695 and OR262115) and eno (OR242733, OQ737696 and OR262116) for the isolates ZOR02, ZOR05 and ZOR12 were deposited in GenBank database. The gltB, lepA, nuoL, rpoB and eno sequences of the isolates ZOR02, ZOR05 and ZOR12 showed 98.66-99.16%, 98.9-100%, 96.28%-97.34%, 98.47-99.44% and 99.27-99.82% similarity to A. xylosoxidans strain AX27, respectively. Phylogenetic trees were constructed based on the 16S rRNA and gltB-lepA-nuoL-rpoB-eno multilocus using the Neighbor-Joining (NJ) method with 1000 bootstrap replicates in MEGA11.0 software (Álvarez et al. 2018). For pathogenicity tests, bacterial suspensions were initially prepared in sterile water at a final concentration of 108 CFU mL-1. Subsequently, 10 μL of bacterial suspensions was injected into the stem base of two-month-old ginger plants, while sterile water was used as a control (Wang et al. 2022). These plants were then incubated at 28°C and 70% relative humidity. There were three replicates for each treatment, and each replicate contained five plants. After six days of inoculation, the ginger plants injected with bacterial suspensions alone exhibited severe wilting symptoms similar to those observed in the field. However, water-soaked symptoms were not observed on rhizome tissues from the pathogen-infected plants. Bacterial pathogens were re-isolated from the diseased plants and identified using the morphological and molecular methods to meet Koch's hypothetical tests. To our knowledge, this is the first report of A. xylosoxidans causing wilt disease of ginger in China. In 2022, the average yield loss due to wilt disease in the Yi'an District of Tongling exceeded 20%, posing a major threat to local ginger cultivation. Effective disease management strategies are needed to develop for the control and prevention of the disease.

What makes a great invader? Anatomical traits as predictors of locomotor performance and metabolic rate in an invasive frog.

Invasive species are characterized by their ability to establish and spread in a new environment. In alien populations of anurans, dispersal and fitness-related traits such as endurance, burst performance and metabolism are key to their success. However, few studies have investigated inter-individual variation in these traits and more specifically have attempted to understand the drivers of variation in these traits. Associations of anatomical features may be excellent predictors of variation in performance and could be targets for selection or subject to trade-offs during invasions. In this study, we used marsh frogs (Pelophylax ridibundus), a species that has been introduced in many places outside its native range and which is now colonizing large areas of Western Europe. We first measured the inter-individual variation in resting metabolism, the time and distance they were able to jump until exhaustion, and their peak jump force, and then measured the mass of specific organs and lengths of body parts suspected to play a role in locomotion and metabolism. Among the 5000 bootstrap replicates on body size-corrected variables, our statistical models most often selected the stomach (75.42%), gonads (71.46%) and the kidneys (67.26%) as predictors of inter-individual variation in metabolism, and the gluteus maximus muscle (97.24%) mass was the most frequently selected predictor of jump force. However, endurance was poorly associated with the anatomical traits (R2distance=0.42, R2time=0.37). These findings suggest that selection on these predictors may lead to physiological changes that may affect the colonization, establishment and dispersal of these frogs.

Genetic characterization and lineage analysis of Pasundan (Rancah) cattle in West Java, Indonesia: Insights from ZFY gene sequencing

&lt;p class="MDPI17abstract"&gt;&lt;strong&gt;Objective: &lt;/strong&gt;This study was carried out to characterize Pasundan (Rancah) cattle from West Java of Indonesia based on a partial Zinc Finger Y-linked (ZFY) gene sequence.&lt;/p&gt;&lt;p class="MDPI17abstract"&gt;&lt;strong&gt;Methods:&lt;/strong&gt; Total of fourteen (14) DNA samples of unrelated Pasundan bulls at the breeding station (BPPIBT-SP Ciamis, West Java) were used for sequencing analysis. The blood samples were collected from jugular vein of each bull for the DNA extraction analysis. Along 979 bp of ZFY gene was amplified using primer pairs of forward: 5’- GGT GAG GGC ACA TGA GTT C -3’and reverse: 5’- CTC TGC AGG TGG TTG TGT AA -3’. Therefore, a forward sequencing method was performed in the present study to obtain the ZFY gene sequences. Along 714 bp of &lt;em&gt;bovine &lt;/em&gt;ZFY gene sequences were used for determining the Neighbor-Joining (NJ) tree for Pasundan bulls with 1000 × bootstrap replications using a MEGA computer program. The genetic diversity parameters of haplotype diversity (H&lt;sub&gt;d&lt;/sub&gt;), nucleotide diversity (p&lt;sub&gt;i&lt;/sub&gt;), Tajima’s D test and Fu’s Fs statistics were calculated using a DNAsp computer program.&lt;/p&gt;&lt;p class="MDPI17abstract"&gt;&lt;strong&gt;Results:&lt;/strong&gt; Total of fourteen (14) haplotypes of ZFY gene and seventy (70) mutation sites were detected in the Pasundan bulls. The haplotype diversity (H&lt;sub&gt;d&lt;/sub&gt;) and nucleotide diversity (p&lt;sub&gt;i&lt;/sub&gt;) in Pasundan’s ZFY gene diversity were 1.00 (high) and 0.01 (low), respectively. The neutrality test of Tajima’s D and Fu’s Fs statistic values were -1.42 and -6.47, respectively. &lt;em&gt;Bovine &lt;/em&gt;ZFY gene can be classified into two clades of ZFY-1 and ZFY-2. Therefore, the Neighbor-joining (NJ) tree (1000×bootstrap) revealed that the Pasundan cattle are classified into clade ZFY-1 together with &lt;em&gt;Bos taurus &lt;/em&gt;(AF241273, AF465179). Meanwhile, a clade ZFY-2 consisted of &lt;em&gt;Bos taurus &lt;/em&gt;(AF465181, DQ336536), &lt;em&gt;Bos indicus &lt;/em&gt;(DQ336537), and &lt;em&gt;Bos javanicus &lt;/em&gt;(DQ336578).&lt;/p&gt;&lt;p class="MDPI17abstract"&gt;&lt;strong&gt;Conclusion:&lt;/strong&gt; The ZFY gene of Pasundan bulls were polymorphic with seventy mutation sites. Therefore, Pasundan bulls were characterized into ZFY-1 clade or &lt;em&gt;Taurine &lt;/em&gt;lineage based on ZFY gene sequence variaton. The crossbreeding program with &lt;em&gt;Bos taurus&lt;/em&gt; straw to increase meat production of cattle may affecting the genetic structure of Pasundan bulls since this program is widely applied in West Java through many years ago.&lt;/p&gt;

Bootstrapping multiple systems estimates to account for model selection

Multiple systems estimation using a Poisson loglinear model is a standard approach to quantifying hidden populations where data sources are based on lists of known cases. Information criteria are often used for selecting between the large number of possible models. Confidence intervals are often reported conditional on the model selected, providing an over-optimistic impression of estimation accuracy. A bootstrap approach is a natural way to account for the model selection. However, because the model selection step has to be carried out for every bootstrap replication, there may be a high or even prohibitive computational burden. We explore the merit of modifying the model selection procedure in the bootstrap to look only among a subset of models, chosen on the basis of their information criterion score on the original data. This provides large computational gains with little apparent effect on inference. We also incorporate rigorous and economical ways of approaching issues of the existence of estimators when applying the method to sparse data tables.

Income-Related Inequality Changes in Osteoarthritis First-Line Interventions: A Cohort Study

ObjectiveTo examine income-related inequality changes in the outcomes of an osteoarthritis (OA) first-line intervention. DesignRetrospective cohort study. SettingSwedish health care system. ParticipantsWe included 115,403 people (age: 66.2±9.7 years; females 67.8%; N=115,403) with knee (67.8%) or hip OA (32.4%) recorded in the “Swedish Osteoarthritis Registry” (SOAR). InterventionsExercise and education. Main Outcome MeasuresErreygers’ concentration index (E) measured income-related inequalities in “Pain intensity,” “Self-efficacy,” “Use of NSAIDs,” and “Desire for surgery” at baseline, 3-month, and 12-month follow-ups and their differences over time. E-values range from -1 to +1 if the health variables are more concentrated among people with lower or higher income. Zero represents perfect equality. We used entropy balancing to address demographic and outcome imbalances and bootstrap replications to estimate confidence intervals for E differences over time. ResultsComparing baseline to 3 months, “pain” concentrated more among individuals with lower income initially (E=-0.027), intensifying at 3 months (difference with baseline: E=-0.011 [95% CI: -0.014; -0.008]). Similarly, the “Desire for surgery” concentrated more among individuals with lower income initially (E=-0.009), intensifying at 3 months (difference with baseline: E=-0.012 [-0.018; -0.005]). Conversely, “Self-efficacy” concentrated more among individuals with higher income initially (E=0.058), intensifying at 3 months (difference with baseline: E=0.008 [0.004; 0.012]). Lastly, the “Use of NSAIDs” concentrated more among individuals with higher income initially (E=0.068) but narrowed at 3 months (difference with baseline: E=-0.029 [-0.038; -0.021]). Comparing baseline with 12 months, “pain” concentrated more among individuals with lower income initially (E=-0.024), intensifying at 12 months (difference with baseline: E=-0.017 [-0.022; -0.012]). Similarly, the “Desire for surgery” concentrated more among individuals with lower income initially (E=-0.016), intensifying at 12 months (difference with baseline: E=-0.012 [-0.022; -0.002]). Conversely, “Self-efficacy” concentrated more among individuals with higher income initially (E=0.059), intensifying at 12 months (difference with baseline: E=0.016 [0.011; 0.021]). The variable 'Use of NSAIDs' was not recorded in the SOAR at 12-month follow-up. ConclusionOur results highlight the increase of income-related inequalities in the SOAR over time.

First report of Zymoseptoria tritici causing Septoria tritici blotch in wheat in Paraguay.

Wheat (Triticum aestivum) is the third most cultivated field crop in Paraguay; it is grown on over 450,000 hectares with an annual production of 927,776 tons (fao.org/faostat). In 1952, Septoria tritici blotch (STB) was associated with the fungus Septoria tritici solely based on microscopic observation of conidia (Viedma and Delgado 1987). However, no morphometric or molecular studies have been performed in Paraguay up to date. Over the following decades, STB epidemic outbreaks were recorded, with a reduction in wheat production of up to 70% (Viedma and Delgado 1987). During winter 2021, leaf blotch symptoms were observed with an incidence above 50% in wheat fields in Capitán Miranda, Itapúa, Paraguay. Scattered, spherical, buried, and light brown necrotic spots with dark edges were observed on the leaves. Pycnidia with prominent central ostiole were observed. Leaves with symptoms were washed with 1% sodium hypochlorite for 1 min, rinsed with sterile distilled water, and incubated in wet chambers to induce sporulation of the fungus. Pycnidia produced greyish to white cirri. Isolated conidia were thin, elongated, and hyaline, ranging from 26.9-72.7 × 1.5-2.9 μm with one to three septa. Monosporic colonies on potato dextrose agar (PDA, ; Difco laboratories, Detroit, MI) media varied in color from white to pink, dark gray to black, or black with stroma-like structures. Based on morphology, the fungus was characterized as Zymoseptoria tritici (Hoorne et al. 2002; Gilchrist-Saavedra et al. 2005). Fungal DNA was extracted from mycelia, and the internal transcribed spacer (ITS), translation elongation factor 1-α (TEF1-α), 28S rRNA gene (LSU), actin gene (act), calmodulin (CaM) were amplified using ITS1/ITS4, EF1-728F/EF-2, LSU1Fd/ LR5, ACT-512F/ACT-783R, CAL-228F/CAL737R primers, respectively. PCR amplicons were sequenced at Macrogen (Seoul, Republic of Korea) and deposited in the NCBI GenBank database (ITS: OQ360718; TEF1-α: OQ999044, LSU: OQ996413, act: OQ999046, CaM: OQ999045). Sequences were aligned with several isolates of Septoria spp. previously reported (Verkley et al. 2013; Stukenbrock et al. 2012) using ClustalW. The alignments were concatenated with Bioedit (Hall 1999). The UPGMA method with 1,000 bootstrap replications, was used to construct the phylogenetic tree using MEGA11 with Readeriella mirabilis as the outgroup. The isolate from Paraguay grouped into the Zymoseptoria tritici clade with 96% bootstrap support. To confirm pathogenicity, ten wheat plants cv. Itapúa 80 were grown in pots for three weeks in growth chambers (22 ± 2°C; 16 h photoperiod). Subsequently, these plants were inoculated with 1×107 conidia ml-1 suspension, and ten non-inoculated plants served as control. Seven days after inoculation (DAI), symptoms were observed displaying oval necrotic lesions and approximately 14 DAI abundant pycnidia were observed on and around the lesions. Segments of symptomatic leaves were placed in moisture chambers overnight to enhance cirri development. Conidia were mounted on a slide and observed under the compound microscope. Individual cirrhus were transferred to plates containing PDA and produced colonies like those used in the inoculation (Hoorne et al. 2002). We confirmed that the causal agent of STB from wheat fields in Paraguay was Zymoseptoria tritici. This pathogen causes annual wheat disease epidemics in Paraguay; therefore, optimizing surveillance for early detection and understanding its distribution will improve integrated management.

First Report of Pestalotiopsis trachicarpicola Causing Apothecium Wither on Cultivated Morchella sextelata in Sichuan, China.

Morel (Morchella sextelata) is a valuable medicinal and edible mushroom, but the wild yield is seriously insufficient, so several artificial varieties have been developed to alleviate the shortage of wild yield. However, in 2020-2022, apothecium wither symptoms were observed in Nanchong, Sichuan. A total of 30.80% of the morels in the planting base (1.3 km2) showed these symptoms. The initial symptoms were slight white lesions on the surface of apothecium, then the mycelia gradually invaded the interior of the fruiting body, and eventually leading to black and wilt apothecium (Fig. 1a). Fifteen symptomatic morels were collected and ten isolates were obtained using the single spore isolation technique developed by Chomnunti et al. (2014). The morphological characteristics of the ten isolates were similar, which showed dense aerial white mycelia colony texture on PDA, and later forming concentric black mucus (Fig. 1c). The reverse side was yellow (Fig. 1d). The acervulus was floral-shaped and discrete, with smooth walls and measured 120.0 to 400.5 × 15.5 to 40.0 μm (n=10) (Fig. 1e); the conidia were fusiform and hyaline, 21.0 to 28.6 × 6.0 to 7.6 μm in size (n=50), each contained five cells. The apical cell was hyaline, conic and with 2 to 4 tubular apical appendages on the top. The three intermediate cells were brown to olivaceous, doliform to cylindrical, constricted at septa. The basal cell was conic to acute (Fig. 1f). The morphological characteristics were consistent with the published description of Pestalotiopsis trachicarpicola (Maharachchikumbura et al., 2012). PCR was performed with primers ITS1/ITS4 for internal transcribed spacer (ITS) (White et al., 1990), BT2A/BT2B for β-tubulin gene (TUB) (Glass and Donaldson, 1995), and EF1-526F/EF1-1567R for translation elongation factor 1-alpha (TEF-1α) (Roger et al., 1999). The pairwise alignments of ITS, TUB, and TEF-1α sequences was nearly 100% identical to P. trachicarpicola with GenBank accession numbers MT889666.1 (579/585 bp, 99%), MT884145.1 (445/450 bp, 99%), and MW149930.1 (946/958 bp, 99%), respectively. The resulting sequences were deposited in GenBank (Accession no. ITS: OL362082; TUB: OL828342; and TEF-1α: OL905009). Phylogenetic analysis performed with maximum likelihood method used MEGA 7.0 (1000 bootstrap replications) classified WLM5 into the P. trachicarpicola clade (Fig. 2), so we finally confirmed the identity of WLM5 as P. trachicarpicola. To fulfill Koch's postulates, twenty morels were surface disinfected with 2% sodium hypochlorite and then artificially wounded (diameter of 0.5 mm) prior to inoculation with 200 μL conidial suspension (105 conidia/mL), while an equal amount of sterile distilled water was applied to controls. After 4 days, the inoculated fruiting bodies showed symptoms consistent with field infection (Fig. 1b) and P. trachicarpicola was re-isolated using the same protocol, while the control remained asymptomatic. This first report of P. trachicarpicola causing apothecium wither on morel will help develop robust disease management strategies against this emerging fungal pathogen.

Validation of Globorisk in Turkish people and development of a new model for cardiovascular diseases

Abstract Background Cardiovascular diseases (CVD) is a major cause of death globally, and accurate risk assessment is important for identifying high-risk individuals. This study aimed to validate the laboratory-based Globorisk score for predicting CVD in the Turkish population and to develop a Turkish population-specific model. Methods We analyzed data from Turkey's Chronic Diseases and Risk Factors study, which examined CVD incidence from 2011 until 2017. After excluding those with prior CVD history, a total of 7239 individuals aged 40 to 80 years were included in the analysis. The performance of Globorisk in predicting CVD was assessed using the C-index. With demographic, dietary, anthropometric and Globorisk variables; we used backward stepwise logistic regression to select the final model (Turkish CVD-TCVD). Lastly, the TCVD model was internally validated and calibrated with 200 bootstrap replicates. Results Out of 7239 participants (mean age: 53.9±10.3), women: 52.3%); 766 developed CVD within six years (cumulative incidence rate: 10.6%). The C-index of the Globorisk was 0.72 with sensitivity and specificity being 68.2% and 67.3%. In the final TCVD model, backward stepwise selection identified age (odds ratio-OR: 1.06, 95% Cl: 1.05-1.07), diabetes (OR:1.83, 1.47-2.28), body mass index (OR:1.02, 1.01-1.04), high waist-hip ratio (OR:1.37, 1.13-1.66) and systolic blood pressure (OR:1.01, 1.00-1.01) as significant predictors for CVD. C-index was 0.73 with sensitivity and specificity being 72.9%, and 62.9%. Examination of the calibration plot showed signs of overprediction when the actual CVD probability was &amp;gt;20%. Conclusions Laboratory-based Globorisk score had a good fit in the Turkish population. TCVD model had better sensitivity than Globorisk. Adding of waist-hip ratio to the Globorisk score could improve predictive CVD models in the Turkish population. Key messages • External validation of laboratory-based Globorisk showed good predictive accuracy in the Turkish population. • Although more challenging to measure, adding of waist-hip ratio to the laboratory-based Globorisk score could improve predictive cardiovascular disease models in the Turkish population.

Haplotype Diversity in the Mitochondrial COI Gene of Barred Rainbowfish (Chilaterina fasciata) from Mamberamo River of Western New Guinea, Indonesia

A Barred rainbowfish (Chilatherina fasciata) is one of the native fish species found in Western New Guinea of Indonesia. This study aimed to observe the levels of haplotype diversity in the partial Cytochrome-c oxidase subunit I (COI) gene of Barred rainbowfish. For the DNA analysis, thirty (30) Barred rainbowfishes were caught from the Mamberamo River. Three (3) molecular packages of BioEdit, MEGA, and DNAsp were used to analyze twenty (30) forward sequences of the COI gene (502 bp). The research showed four (4) haplotypes for the examined population, a total of seven (7) mutations, and low genetic diversity detected in the partial COI gene with the haplotype diversity (Hd) = 0.405 and nucleotide diversity (pi) = 0.003. Meanwhile, the Fu's and Tajima's tests were 1.21 and -0.69, respectively. The UPGMA tree with 1,000 × bootstrap replications revealed that Barred rainbowfishes are grouped into similar clusters with Melanotaenia vanheurni, Chilatherina alleni, and Chilatherina bleheri. In conclusion, haplotype 3 (77%) was detected as the common haplotype for Barred rainbowfishes at the Mamberamo River of Western New Guinea.

New Report of Endophytic Sordariomycetes from the Seagrasses of Cebu, Central Philippines

Sordariomycete is one of the dominant components of the endophytic community in seagrasses. However, there are still many species under this group that still need to be described. Among the tropical seagrasses, the Philippines had the least number of endophytic Sordariomycete reported. This study reports the isolation of endophytic Sordariomycete from Enhalus acoroides, Cymodocea serrulata, and Thalassia hemprichii. Seagrass samples were collected from the coastal areas of Hilutungan Channel, Cebu, Central Philippines using a sterilized razor. Explants from seagrass samples were surface-sterilized, inoculated in culture plates, and incubated for 14 days at 27±2°C. Fungi that grew from the edge of explants were purified and identified through morphological and molecular methods using ITS sequences. Molecular phylogeny was inferred by neighbor-joining with 1000 bootstrap replications. Three species of Sordariomycete were identified in this study. Fungal isolates from the rhizomes and roots of Cymodocea serrulata had 99.84% nucleotide similarity with Eutypella sp. Isolates from the rhizomes and roots of Enhalus acoroides had a 100% match identity with Beauveria bassiana. While the isolate from the leaf of Thalassia hemprichii had a 99% nucleotide affinity to Xylaria apoda. These isolates formed a well-supported clade with their closest match taxa at 100% bootstrap support. The estimate of evolutionary divergence between the isolates’ sequences and their reference taxa was 0.0, suggesting no nucleotide base substitutions per site. The identification of seagrass isolates as Eutypella sp., Beauveria bassiana, and Xylaria apoda is hereby supported. Phylogenetic analysis revealed that endophytic fungi from the Philippine seagrass did not cluster with any fungal species previously reported from the Philippines, suggesting different species. To our knowledge, Eutypella sp., Beauveria bassiana, and Xylaria apoda were the first reports of endophytic Sordariomycete in Philippine seagrasses. The isolation of these endophytes is promising because these genera are a rich source of novel compounds and biocontrol agents.