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Researchers have become increasingly aware that data-analysis decisions affect results. Here, we examine this issue systematically for multinomial processing tree (MPT) models, a popular class of cognitive models for categorical data. Specifically, we examine the robustness of MPT model parameter estimates that arise from two important decisions: the level of data aggregation (complete-pooling, no-pooling, or partial-pooling) and the statistical framework (frequentist or Bayesian). These decisions span a multiverse of estimation methods. We synthesized the data from 13,956 participants (164 published data sets) with a meta-analytic strategy and analyzed the magnitude of divergence between estimation methods for the parameters of nine popular MPT models in psychology (e.g., process-dissociation, source monitoring). We further examined moderators as potential sources of divergence. We found that the absolute divergence between estimation methods was small on average (

Plasmodium vivax is the predominant malaria parasite in Latin America. Its colonization history in the region is rich and complex, and is still highly debated, especially about its origin(s). Our study employed cutting-edge population genomic techniques to analyze whole genome variation from 620 P. vivax isolates, including 107 newly sequenced samples from West Africa, Middle East, and Latin America. This sampling represents nearly all potential source populations worldwide currently available. Analyses of the genetic structure, diversity, ancestry, coalescent-based inferences, including demographic scenario testing using Approximate Bayesian Computation, have revealed a more complex evolutionary history than previously envisioned. Indeed, our analyses suggest that the current American P. vivax populations predominantly stemmed from a now-extinct European lineage, with the potential contribution also from unsampled populations, most likely of West African origin. We also found evidence that P. vivax arrived in Latin America in multiple waves, initially during early European contact and later through post-colonial human migration waves in the late 19th-century. This study provides a fresh perspective on P. vivax's intricate evolutionary journey and brings insights into the possible contribution of West African P. vivax populations to the colonization history of Latin America.

Urbanization is a driving factor for biodiversity loss and potential climate change by reducing carbon stocks. Understanding how urban development, as mitigated by socio-economic factors alters urban biodiversity is crucial for effective urban planning that maintains or improves environmental resilience. The luxury effect hypothesis predicts that wealthier parts of a city will have higher levels of biodiversity. This effect has been tested widely but we still have limited understanding of how wealth influences urban biodiversity in tropical regions of developing countries where plant species play profound sociocultural roles beyond aesthetics. This study investigates links between household income and the diversity of cultivated plants distribution within neighborhoods of two growing cities in Benin. We conducted a survey of 936 randomly selected households to record their socioeconomic characteristics and survey the cultivated plant species found in household gardens’. This enabled us to estimate household-level diversity metrics including taxonomic diversity and phylogenetic diversity. We found no global support for the luxury effect on phylogenetic diversity but rented properties had lower plant taxonomic diversity along with less phylogenetic diversity than privately owned houses. Taxonomic diversity is higher in the less urbanized areas while phylogenetic diversity is weakened. Household’s cultural connection to plants has a negative effect on both diversity indices. Our results highlight the complex relationships between socioeconomic traits and urban plant diversity distribution in two tropical African cities, which only partly confirmed the luxury effect hypothesis. Disentangling these complex relationships can help city planners and policymakers to take informed decisions to promote sustainable cities.

The Bacillus Calmette Guerin (BCG) vaccine has been shown to induce non-specific protection against diseases other than tuberculosis in vaccinated individuals, attributed to the induction of trained immunity. We have previously demonstrated that BCG administration induces innate immune training in mixed peripheral blood mononuclear cells and monocytes in calves. Gamma Delta (γδ) T cells are non-conventional T cells that exhibit innate and adaptive immune system features. They are in higher proportion in the peripheral blood of cattle than humans or rodents and play an essential role in bovine immune response to pathogens. In the current study, we determined if BCG administration induced innate immune training in bovine γδ T cells. A group of 16 pre-weaned Holstein calves (2-4 d age) were enrolled in the study and randomly assigned to vaccine and control groups (n=8/group). The vaccine group received two doses of 106 colony forming units (CFU) BCG Danish strain subcutaneously, separated by 2 weeks. The control group remained unvaccinated. Gamma delta T cells were purified from peripheral blood using magnetic cell sorting three weeks after receiving the 1st BCG dose. We observed functional changes in the γδ T cells from BCG-treated calves shown by increased IL-6 and TNF-α cytokine production in response to in vitro stimulation with Escherichia coli LPS and PAM3CSK4. ATAC-Seq analysis of 78,278 regions of open chromatin (peaks) revealed that γδ T cells from BCG-treated calves had an altered epigenetic status compared to cells from the control calves. Differentially accessible peaks (DAP) found near the promoters of innate immunity-related genes like Siglec14, Irf4, Ifna2, Lrrfip1, and Tnfrsf10d were 1 to 4-fold more accessible in cells from BCG-treated calves. MOTIF enrichment analysis of the sequences within DAPs, which explores transcription factor binding motifs (TFBM) upstream of regulatory elements, revealed TFBM for Eomes and IRF-5 were among the most enriched transcription factors. GO enrichment analysis of genes proximal to the DAPs showed enrichment of pathways such as regulation of IL-2 production, T-cell receptor signaling pathway, and other immune regulatory pathways. In conclusion, our study shows that subcutaneous BCG administration in pre-weaned calves can induce innate immune memory in the form of trained immunity in γδ T cells. This memory is associated with increased chromatin accessibility of innate immune response-related genes, thereby inducing a functional trained immune response evidenced by increased IL-6 and TNF-α cytokine production.

La leptospirosis es una infección sistémica zoonótica, transmitida a través de la piel, mucosas o ingesta de agua contaminada por espiroquetas patógenas del género Leptospira en mamíferos y roedores infectados. Se presenta con sintomatología inespecífica de aparición aguda asociada a dolor abdominal, hemorragia subconjuntival e ictericia, que suele tener una resolución completa en la mayoría de los pacientes; sin embargo, en menor porcentaje puede progresar causando complicaciones sistémicas graves, con alto riesgo de mortalidad principalmente por nefropatía aguda, disfunción hepática asociada a ictericia y hemorragias, llamada síndrome de Weil o fiebre icterohemorrágica. Se presenta una serie de casos de pacientes que cursaron con síndrome biliar obstructivo como principal manifestación de infección grave por leptospirosis.

Plasmodium vivax is the predominant malaria parasite in Latin America. Its colonization history in the region is rich and complex, and is still highly debated, especially about its origin(s). Our study employed cutting-edge population genomic techniques to analyze whole genome variation from 620 P. vivax isolates, including 107 newly sequenced samples from West Africa, Middle East, and Latin America. This sampling represents nearly all potential source populations worldwide currently available. Analyses of the genetic structure, diversity, ancestry, coalescent-based inferences, including demographic scenario testing using Approximate Bayesian Computation, have revealed a more complex evolutionary history than previously envisioned. Indeed, our analyses suggest that the current American P. vivax populations predominantly stemmed from a now-extinct European lineage, with the potential contribution also from unsampled populations, most likely of West African origin. We also found evidence that P. vivax arrived in Latin America in multiple waves, initially during early European contact and later through post-colonial human migration waves in the late 19th-century. This study provides a fresh perspective on P. vivax's intricate evolutionary journey and brings insights into the possible contribution of West African P. vivax populations to the colonization history of Latin America. Author summary: Our study investigates the origins and spread of Plasmodium vivax in Latin America, the primary malaria parasite in this region. By analyzing genetic data from 620 P. vivax samples worldwide, including new samples from West Africa, the Middle East, and Latin America, we were able to reconstruct the evolutionary history of the parasite in this region. Our findings indicate that the current P. vivax strains in Latin America mainly descended from a now-extinct European lineage. Additionally, we found evidence suggesting that several migration waves following human migrations waves may have contributed to the parasite diversity, with possible contributions from West African populations during the transatlantic slave trade (16th to 19th century) and further input from Europe during post-colonial human migrations in the late 19th century. This study offers a fresh perspective on how historical human migrations have shaped the genetic landscape of P. vivax in Latin America. These insights are valuable for understanding the parasite evolution and may help inform strategies for malaria control and prevention in the future. [ABSTRACT FROM AUTHOR]

Urbanization is a driving factor for biodiversity loss and potential climate change by reducing carbon stocks. Understanding how urban development, as mitigated by socio-economic factors alters urban biodiversity is crucial for effective urban planning that maintains or improves environmental resilience. The luxury effect hypothesis predicts that wealthier parts of a city will have higher levels of biodiversity. This effect has been tested widely but we still have limited understanding of how wealth influences urban biodiversity in tropical regions of developing countries where plant species play profound sociocultural roles beyond aesthetics. This study investigates links between household income and the diversity of cultivated plants distribution within neighborhoods of two growing cities in Benin. We conducted a survey of 936 randomly selected households to record their socioeconomic characteristics and survey the cultivated plant species found in household gardens'. This enabled us to estimate household-level diversity metrics including taxonomic diversity and phylogenetic diversity. We found no global support for the luxury effect on phylogenetic diversity but rented properties had lower plant taxonomic diversity along with less phylogenetic diversity than privately owned houses. Taxonomic diversity is higher in the less urbanized areas while phylogenetic diversity is weakened. Household's cultural connection to plants has a negative effect on both diversity indices. Our results highlight the complex relationships between socioeconomic traits and urban plant diversity distribution in two tropical African cities, which only partly confirmed the luxury effect hypothesis. Disentangling these complex relationships can help city planners and policymakers to take informed decisions to promote sustainable cities. [ABSTRACT FROM AUTHOR]

Listeria monocytogenes hijacks host actin to promote its intracellular motility and intercellular spread. While L. monocytogenes virulence hinges on cell-to-cell spread, little is known about the dynamics of bacterial spread in epithelia at a population level. Here, we use live microscopy and statistical modeling to demonstrate that L. monocytogenes cell-to-cell spread proceeds anisotropically in an epithelial monolayer in culture. We show that boundaries of infection foci are irregular and dominated by rare pioneer bacteria that spread farther than the rest. We extend our quantitative model for bacterial spread to show that heterogeneous spreading behavior can improve the chances of creating a persistent L. monocytogenes infection in an actively extruding epithelium. Thus, our results indicate that L. monocytogenes cell-to-cell spread is heterogeneous, and that rare pioneer bacteria determine the frontier of infection foci and may promote bacterial infection persistence in dynamic epithelia. Editorial note:This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).

The analytical validation is reported for a targeted methylation-based cell-free DNA multi-cancer early detection test designed to detect cancer and predict the cancer signal origin (tissue of origin). A machine-learning classifier was used to analyze the methylation patterns of >105 genomic targets covering >1 million methylation sites. Analytical sensitivity (limit of detection [95% probability]) was characterized with respect to tumor content by expected variant allele frequency and was determined to be 0.07%-0.17% across five tumor cases and 0.51% for the lymphoid neoplasm case. Test specificity was 99.3% (95% confidence interval, 98.6-99.7%). In the reproducibility and repeatability study, results were consistent in 31/34 (91.2%) pairs with cancer and 17/17 (100%) pairs without cancer; between runs, results were concordant for 129/133 (97.0%) cancer and 37/37 (100%) non-cancer sample pairs. Across 3- to 100-ng input levels of cell-free DNA, cancer was detected in 157/182 (86.3%) cancer samples but not in any of the 62 non-cancer samples. In input titration tests, cancer signal origin was correctly predicted in all tumor samples detected as cancer. No cross-contamination events were observed. No potential interferent (hemoglobin, bilirubin, triglycerides, genomic DNA) affected performance. The results of this analytical validation study support continued clinical development of a targeted methylation cell-free DNA multi-cancer early detection test.

Introduction: All cosmetic ingredients must be evaluated for their safety to consumers. In the absence of in vivo data, systemic concentrations of ingredients can be predicted using Physiologically based Pharmacokinetic (PBPK) models. However, more examples are needed to demonstrate how they can be validated and applied in Next-Generation Risk Assessments (NGRA) of cosmetic ingredients. We used a bottom-up approach to develop human PBPK models for genistein and daidzein for a read-across NGRA, whereby genistein was the source chemical for the target chemical, daidzein. Methods: An oral rat PBPK model for genistein was built using PK-Sim® and in vitro ADME input data. This formed the basis of the daidzein oral rat PBPK model, for which chemical-specific input parameters were used. Rat PBPK models were then converted to human models using human-specific physiological parameters and human in vitro ADME data. In vitro skin metabolism and penetration data were used to build the dermal module to represent the major route of exposure to cosmetics. Results: The initial oral rat model for genistein was qualified since it predicted values within 2-fold of measured in vivo PK values. This was used to predict plasma concentrations from the in vivo NOAEL for genistein to set test concentrations in bioassays. Intrinsic hepatic clearance and unbound fractions in plasma were identified as sensitive parameters impacting the predicted Cmax values. Sensitivity and uncertainty analyses indicated the developed PBPK models had a moderate level of confidence. An important aspect of the development of the dermal module was the implementation of first-pass metabolism, which was extensive for both chemicals. The final human PBPK model for daidzein was used to convert the in vitro PoD of 33 nM (from an estrogen receptor transactivation assay) to an external dose of 0.2% in a body lotion formulation. Conclusion: PBPK models for genistein and daidzein were developed as a central component of an NGRA read-across case study. This will help to gain regulatory confidence in the use of PBPK models, especially for cosmetic ingredients. [ABSTRACT FROM AUTHOR]

Author(s): Andrew S. Moore [sup.1] [sup.2] [sup.3] , Stephen M. Coscia [sup.1] [sup.2] [sup.4] , Cory L. Simpson [sup.1] [sup.2] [sup.5] , Fabian E. Ortega [sup.6] , Eric C. Wait [...], Symmetric cell division requires the even partitioning of genetic information and cytoplasmic contents between daughter cells. Whereas the mechanisms coordinating the segregation of the genome are well known, the processes that ensure organelle segregation between daughter cells remain less well understood.sup.1. Here we identify multiple actin assemblies with distinct but complementary roles in mitochondrial organization and inheritance in mitosis. First, we find a dense meshwork of subcortical actin cables assembled throughout the mitotic cytoplasm. This network scaffolds the endoplasmic reticulum and organizes three-dimensional mitochondrial positioning to ensure the equal segregation of mitochondrial mass at cytokinesis. Second, we identify a dynamic wave of actin filaments reversibly assembling on the surface of mitochondria during mitosis. Mitochondria sampled by this wave are enveloped within actin clouds that can spontaneously break symmetry to form elongated comet tails. Mitochondrial comet tails promote randomly directed bursts of movement that shuffle mitochondrial position within the mother cell to randomize inheritance of healthy and damaged mitochondria between daughter cells. Thus, parallel mechanisms mediated by the actin cytoskeleton ensure both equal and random inheritance of mitochondria in symmetrically dividing cells. During mitosis, complementary actin-based mechanisms ensure equal and random distributions of mitochondria among daughter cells following symmetrical cell division.

La producción de café en Colombia hace parte de uno de los renglones más importantes de su economía, de este producto dependen miles de personas directa e indirectamente que se han visto afectados por la volatilidad de su precio en los mercados locales e internacionales. El presente estudio consiste en analizar un modelo predictivo de los precios internos del café que ayudará a mitigar el impacto económico producto de su cotización en bolsa. Para ello se empleó el análisis de series de tiempo, lo que permitió formular un modelo autorregresivo de media móvil heterocedástico cuya ventana de tiempo comprende las cotizaciones del precio que van desde el año 2010 hasta el 2019, tiempo que incluyó su respectivo periodo de entrenamiento y validación. Se obtiene como resultado un modelo que cumplió satisfactoriamente con la etapa de diagnóstico, así como de validación. Se concluye de los resultados que el análisis y construcción del modelo permitió realizar una predicción de los precios del café para el mes de enero del 2020 cuyo comportamiento presentó estabilidad con una disminución lenta pero sostenida de la volatilidad.