bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extending Association Rule Mining to Microbiome Pattern Analysis: Tools and Guidelines to Support Real Applications
Authors: Agostinetto Giulia 
Published: September 2024

Boosted by the exponential growth of microbiome-based studies, analyzing microbiome patterns is now a hot-topic, finding different fields of application. In particular, the use of machine learning techniques is increasing in microbiome studies, providing deep insights into microbial community composition. In this context, in order to investigate microbial patterns from 16S rRNA metabarcoding data, we explored the effectiveness of Association Rule Mining (ARM) technique, a supervised-machine learning procedure, to extract patterns (in this work, intended as groups of species or taxa) from microbiome data. ARM can generate huge amounts of data, making spurious information removal and visualizing results challenging. Our work sheds light on the strengths and weaknesses of pattern mining strategy into the study of microbial patterns, in particular from 16S rRNA microbiome datasets, applying ARM on real case studies and providing guidelines for future usage. Our results highlighted issues related to the type of input and the use of metadata in microbial pattern extraction, identifying the key steps that must be considered to apply ARM consciously on 16S rRNA microbiome data. To promote the use of ARM and the visualization of microbiome patterns, specifically, we developed microFIM (microbial Frequent Itemset Mining), a versatile Python tool that facilitates the use of ARM integrating common microbiome outputs, such as taxa tables. microFIM implements interest measures to remove spurious information and merges the results of ARM analysis with the common microbiome outputs, providing similar microbiome strategies that help scientists to integrate ARM in microbiome applications. With this work, we aimed at creating a bridge between microbial ecology researchers and ARM technique, making researchers aware about the strength and weaknesses of association rule mining approach.Link to OA paper: https://www.frontiersin.org/articles/10.3389/fbinf.2021.794547/full
Metabolic diversity in commensal protists regulates intestinal immunity and trans-kingdom competition
Authors: Gerrick Elias 
Published: September 2024

Commensal protists have historically been overlooked as members of the gut microbiota, but recent studies have highlighted the dominant effects of these commensals on the gut ecosystem. In particular, protists in the Parabasalia phylum reshape the intestinal immune landscape and influence host susceptibility to both infectious and inflammatory diseases. However, the mechanisms used by these protists to shape the gut environment remain poorly understood. Here, we identify a new species of commensal parabasalid in the mouse intestine, Tritrichomonas casperi. We find that metabolic differences between T. casperi and the closely related species Tritrichomonas musculis modulate their effects on host immunity and determine their ecological niche within the microbiota. First, we investigate metabolic output of these commensal parabasalids using genomic and metabolomic analysis. This reveals species-level differences in excretion of the tuft cell activating metabolite succinate, which causes differential remodeling of the immune system in the small intestine. Next, we investigate protist metabolic input by manipulating dietary fiber intake, as well as developing in vitro culture. This reveals that whereas T. musculis preferentially relies on dietary polysaccharides, T. casperi uses host mucus glycans as a carbon source. These carbon source preferences lead to differential competition with commensal bacteria in the intestine, including Bacteroidales spp. and Akkermansia muciniphila. These trans-kingdom interactions can in turn suppress protist-induced intestinal immune responses in a diet-dependent manner. Finally, we explore the diversity of commensal protists in humans by examining parabasalids in the microbiomes of both industrialized and non-industrialized populations. We identify multiple new species of commensal parabasalids in the microbiomes of non-industrialized populations, including novel human-associated tritrichomonads that are closely related T. musculis and T. casperi. Altogether, our findings elucidate how commensal parabasalid metabolism acts as a focal point for complex interactions with the host immune system, commensal bacteria, and diet, to impact intestinal immunity and host health.Link to OA paper: https://www.biorxiv.org/content/10.1101/2022.08.26.505490v2
Prebiotic intervention with HAMSAB in untreated essential hypertensive patients assessed in a phase II randomized trial
Authors: Jama Hamdi 
Published: September 2024

Fibers remain undigested until they reach the colon, where some are fermented by gut microbiota, producing metabolites called short-chain fatty acids (SCFAs), such as acetate and butyrate1. SCFAs lower blood pressure in experimental models2,3,4,5, but their translational potential is unknown. Here we present the results of a phase II, randomized, placebo-controlled, double-blind cross-over trial (Australian New Zealand Clinical Trials Registry ACTRN12619000916145) using prebiotic acetylated and butyrylated high-amylose maize starch (HAMSAB) supplementation6. Twenty treatment-naive participants with hypertension were randomized to 40 g per day of HAMSAB or placebo, completing each arm for 3 weeks, with a 3-week washout period between them. The primary endpoint was a reduction in ambulatory systolic blood pressure. Secondary endpoints included changes to circulating cytokines, immune markers and gut microbiome modulation. Patients receiving the HAMSAB treatment showed a clinically relevant reduction in 24-hour systolic blood pressure independent of age, sex and body mass index without any adverse effects. HAMSAB increased levels of acetate and butyrate, shifted the microbial ecosystem and expanded the prevalence of SCFA producers. In summary, a prebiotic intervention with HAMSAB could represent a promising option to deliver SCFAs and lower blood pressure in patients with essential hypertension.Link to paper: https://www.nature.com/articles/s44161-022-00197-4
Co-diversification of an intestinal Mycoplasma and its salmonid host
Authors: Rasmussen Jacob Agerbo 
Published: September 2024

Understanding the evolutionary relationships between a host and its intestinal resident bacteria can transform how we understand adaptive phenotypic traits. The interplay between hosts and their resident bacteria inevitably affects the intestinal environment and, thereby, the living conditions of both the host and the microbiota. Thereby this co-existence likely influences the fitness of both bacteria and host. Whether this co-existence leads to evolutionary co-diversification in animals is largely unexplored, mainly due to the complexity of the environment and microbial communities and the often low host selection. We present the gut metagenome from wild Atlantic salmon (Salmo salar), a new wild organism model with an intestinal microbiota of low complexity and a well-described population structure, making it well-suited for investigating co-evolution. Our data reveal a strong host selection of a core gut microbiota dominated by a single Mycoplasma species. We found a clear co-diversification between the population structure of Atlantic salmon and nucleotide variability of the intestinal Mycoplasma populations conforming to expectations from co-evolution between host and resident bacteria. Our results show that the stable microbiota of Atlantic salmon has evolved with its salmonid host populations while potentially providing adaptive traits to the salmon host populations, including defence mechanisms, biosynthesis of essential amino acids, and metabolism of B vitamins. We highlight Atlantic salmon as a novel model for studying co-evolution between vertebrate hosts and their resident bacteria.Link to OA paper: https://www.nature.com/articles/s41396-023-01379-z
Incorporating information from reference genomes with semi-supervised deep learning leads to better metagenomic assembled genomes (MAGs)
Authors: Pan Shaojun 
Published: September 2024

High-throughput sequencing is commonly used to study microorganisms in the environment without a need for culturing. Computational analysis of metagenomic has enabled the construction of large compendia of metagenome-assembled genomes (MAGs) from human-, animal-associated and environmental samples. Metagenomic binning is the step in the standard pipeline which groups the contigs into bins such that each bin is predicted to contain only contigs from the same genome.Binning methods can be divided into reference-dependent (based on reference genomes) and reference-independent methods (operating de novo). Compared to reference-dependent methods, reference-independent methods can discover new species or even new phyla, but completely ignore any background information. To combine the advantages of these two categories, we propose a novel binning method called SemiBin which uses a semi-supervised neural network to incorporate information from reference genomes, while still being capable of finding novel species. SemiBin outperforms existing state-of-the-art binning methods in simulated and real microbiome datasets across three different environments (human gut, dog gut, and marine environments). SemiBin returns more high-quality bins (48.0-99.2% more in single-sample mode; 11.0-30.7% more in multi-sample mode, compared to the second-best alternative). Compared to the alternatives, SemiBin captures a larger taxonomic diversity, including more distinct genera and species. In particular, we verified that SemiBin can retrieve more genomes from both known and novel species.SemiBin is available as open source software at https://github.com/BigDataBiology/SemiBin/.
Do you see what I see? Improving color accessibility and organization of microbiome data visualizations with the microshades R package
Authors: Dahl Erin 
Published: September 2024

Background: Color Vision Deficiency (CVD), commonly known as colorblindness, affects approximately 300 million people worldwide. Individuals with CVD do not experience complete loss of color vision, but have reduced ability to distinguish different colors. When creating scientific figures, it is important to consider that individuals with CVD may not perceive all colors as intended. While there are several CVD friendly color palettes available, they are often insufficient for visualizing complex data that is often generated in microbiome studies. Methods: To overcome CVD accessibility for microbiome datasets, we developed an R package, microshades. Microshades includes CVD accessible color palettes and data organization functions. To construct the palettes, hue (type of color), chroma (colorfulness), and luminance (brightness) were adjusted for optimal visual distinction and CVD accessibility. All shades were tested with a CVD simulator (cvdemulator) for accessibility. In addition to accessible color palettes, we also provide data organization functions. These include grouping data by taxonomic ranking, sorting the data vertically and horizontally, and restructuring the plot legends. Results: Each microshades color palette contains six hues with five sequential variations of chroma and luminance per hue, for a total of 30 available colors per palette. The microshades_cvd_palettes colors are universally CVD accessible to individuals with the three most common types of CVD (Deuteranope, Protanope, and Tritanope). The individual hues of the microshades_palettes colors are CVD friendly, but when used in conjunction with multiple hues, may not be universally accessible to all forms of CVD. Discussion: The microshades R package is a visualization tool designed for microbiome researchers. The package contains two CVD accessible palettes, along with several organization features. The microshades package can be used in conjunction with common microbiome R packages, such as phyloseq, to enhance microbiome data visualization.Link to paper: https://journals.asm.org/doi/10.1128/mra.00795-22
Analyzing microbial evolution through gene and genome phylogenies
Authors: Teichman Sarah 
Published: September 2024

Microbiome scientists critically need modern tools to explore and analyze microbial evolution. Often this involves studying the evolution of microbial genomes as a whole. However, different genes in a single genome can be subject to different evolutionary pressures, which can result in distinct gene-level evolutionary histories. To address this challenge, we propose to treat estimated gene-level phylogenies as data objects, and present an interactive method for the analysis of a collection of gene phylogenies. We use a local linear approximation of phylogenetic tree space to visualize estimated gene trees as points in low-dimensional Euclidean space, and address important practical limitations of existing related approaches, allowing an intuitive visualization of complex data objects. We demonstrate the utility of our proposed approach through microbial data analyses, including by identifying outlying gene histories in strains of Prevotella, and by contrasting Streptococcus phylogenies estimated using different gene sets. Our method is available as an open-source R package, and assists with estimating, visualizing, and interacting with a collection of bacterial gene phylogenies.Link to OA paper: https://doi.org/10.1093/biostatistics/kxad025
Investigating Long-Run Money Demand and Its Policy Implications for the Proposed Monetary Union in West Africa: Evidence from Macro Panel Data Techniques
Authors: Tucker Joseph Ansu 
Published: September 2024

ABSTRACT
At the nucleus of the ongoing process of establishing a monetary union in West Africa are the harmonization of the institutional and operational mechanisms of monetary policy across member states and the determination of an appropriate monetary policy regime that would ensure the effective conduct of a common monetary policy. In-depth knowledge of the demand for money balances in the region is crucial in making an informed decision on the choice of the policy regime. This study investigates long-run money demand in the region and its implications for the conduct of a common monetary policy in the proposed monetary union. It employs a range of macro panel data methods, including pooled mean group (PMG), mean group (MG), and dynamic fixed effects (DFE) estimators. The baseline analysis is predicated on the common correlated effects mean group (CCEMG) estimator that accommodates heterogeneity and cross-sectional dependence. The robustness of the results is ascertained by adopting the augmented mean group (AMG) estimator and using a higher frequency dataset. The study finds that income levels and inflation exert significant influence on people’s desire to hold money balances in the region. Recursive estimations of the panel model reveal that the money demand function exhibits instability.
¿Por qué enseñar ciencias sociales y humanidades en la actualidad?
Authors: Morales Carrero Jesús Alfredo 
Published: September 2024

El escrito es resultado de una revisión documental con enfoque cualitativo, tiene como propósito establecer un diálogo en torno a las razones que fundamentan la necesidad de enseñar ciencias sociales y humanidades en la actualidad; para la construcción de argumentos se tomaron aportes de los autores Martha Nussbaum y Hugo Zemelman, en quienes se precisan los referentes teóricos, conceptuales y metodológicos que sustentan la formación de un ciudadano capaz de leer, valorar interpretativamente y pensar su realidad asistido tanto por la actitud crítico-reflexiva como por el espíritu analítico, cualidades que por sus implicaciones cognitivas e intelectuales favorecen la comprensión explicativa profunda de los elementos que entretejen el mundo. Los resultados indican que la interacción con contenidos humanísticos y de las ciencias sociales, da lugar al afloramiento de actitudes democráticas asociadas con la sensibilidad para convivir dentro de los parámetros de la ética y la moral universal, pero además, desde el sentido de apertura a la valoración acuciosa de las circunstancias más allá de los parámetros establecidos, en los cuales se precisa la adherencia al reduccionismo, a las visiones monádicas y a la reproducción de planteamientos que no estiman lo inédito. En conclusión, lograr la capacidad de agencia como ideal global requiere de esfuerzos enfocados en promover el diálogo razonable, la independencia de criterios, la autonomía de pensamiento y la actitud cuestionadora como requerimientos desde los cuales zambullirse en la realidad en la búsqueda de nuevos significados, que al ser integrados y organizados coherentemente den lugar a la producción de conocimiento.
Estrategias de organización interna de las unidades económicas de las familias campesinas en las colonias Yolaina y La Esperanza de Nueva Guinea, Nicaragua
Authors: Díaz Torres Kettys Raquel , Mccune Nils 
Published: September 2024

La investigación consiste en la caracterización de las estrategias de vida de las familias campesinas de las colonias de Yolaina y La Esperanza del municipio de nueva Guinea de la Región Autónoma de la Costa Caribe Sur (RAACS). La organización de las familias campesinas determina en gran medida la capacidad que tiene para alcanzar metas, desarrollar sus sistemas productivos y mejorar su calidad de vida. Este documento presenta una revisión bibliográfica sobre cómo están organizadas las familias de colonos del Pacífico en las zonas rurales del Caribe Sur, complementada con la información obtenida de campo, destacándose las principales organizaciones internas: producción agrícola comercial (monocultivos), producción para autoconsumo, producción pecuaria (ganadería mayor y menor), servicios complementarios y migratorios. Siendo la producción comercial y la pecuaria los que más generan ingresos tradicionalmente, un aporte valioso en algunas familias son las remesas que se obtienen de los miembros que han emigrado, principalmente a Costa Rica, España y Estados Unidos. La migración se da temporalmente e indefinido. La familia campesina tiene grandes retos, para satisfacer sus necesidades económicas, productivas, sociales, uno de ellos es el aumento de los precios de los insumos agropecuarios, por otro lado, los bajos precios en el mercado, de lo que producen, que son determinantes en la economía familiar, para mejorar sus estrategias de organización
Patient Factors Associated With Reimplantation After Girdlestone Resection Arthroplasty for Treatment of Periprosthetic Joint Infections of the Hip
Authors: Okewunmi Jeffrey , Yendluri Avanish , Cordero John K. , Zubizarreta Nicole , Chen Darwin , Moucha Calin S. , Poeran Jashvant , Hayden Brett L. 
Published: September 2024

Introduction:
For patients unsuitable for prosthesis reimplantation or temporary spacer placement, Girdlestone resection arthroplasty (GRA) is a suitable option to eliminate infection. Using a large-scale database, this study aims to determine factors associated with reimplantation.

Methods:
This study included patients who underwent GRA and subsequent total hip arthroplasty (2012 to 2015 Medicare Limited Data Set with ≥5-year follow-up). A mixed-effects model measured associations between patient characteristics and reimplantation. Odds ratios (OR) with 95% confidence intervals (CI) were reported.

Results:
Among 2,772 GRA cases, 2,025 (73.1%) were reimplanted (median time to reimplantation 3.0 months). In multivariable analysis, patient factors associated with reduced odds of reimplantation were increased age (OR 0.96; CI, 0.94 to 0.97; P < 0.0001), Black race (OR, 0.58; CI, 0.37 to 0.90; P = 0.0149), obesity (OR, 0.74; CI, 0.58 to 0.94; P = 0.0150), and increased Deyo-Charlson comorbidities (1 comorbidity: OR, 0.78; CI, 0.61 to 0.99; P = 0.0453; two comorbidities: OR, 0.53; CI, 0.39 to 0.71; P < 0.0001; ≥3 comorbidities: OR, 0.69; CI, 0.49 to 0.95; P = 0.0244). Male (versus female) patients, however, had increased odds of reimplantation (OR, 1.64; CI, 1.32 to 2.02; P < 0.0001).

Discussion:
Age, race, and comorbidities influence the likelihood of reimplantation after GRA. Owing to variability in patients who undergo additional surgery, additional studies should be conducted to determine the rationale of patient selection.
Social Media Use by American Association of Hip and Knee Surgeons Members
Authors: Culp Hunter , Cieremans David , Schuett Dustin 
Published: September 2024

Introduction:
Social media offers physicians marketing opportunities previously unavailable. We sought to evaluate social media use and its correlation with public rankings among Association of Hip and Knee Surgeons members.

Methods:
A list of members and demographics was collected. Social media sites were reviewed for each surgeon, and a score was calculated based on active use. The US News and World Report (NWR) was used to determine rating and number of reviews. The Spearman correlation coefficient and independent samples t-test were used to measure correlation and compare means between the groups, respectively.

Results:
A total of 2436 members were analyzed. The average social media score was 4.14. The average US NWR score was 4.25. A strong correlation was observed between social media and US NWR scores (r = 0.74, P < 0.01) but not with the number of reviews (r = 0.40, P = 0.17). A strong association with US NWR rating (r = 0.74, P = 0.04) and a weak correlation with the total number of reviews (r = 0.61, P = 0.06) were found.

Conclusions:
Social media use is correlated with US NWR scores. Association of Hip and Knee Surgeons members may be underutilizing social media for the promotion of their practices. Future studies are needed to evaluate whether it affects patient volume and outcomes.
Quantification of chlorpyrifos in aqueous samples by liquid-liquid microextraction and gas chromatography using a µ-ecd detector
Authors: Reyes Tatiana Garrido , Escobar Nicol Campos , Crisosto Jorge Mendoza 
Published: September 2024

The evaluation of contaminants present in the environment is a recurring theme at the international level, which is why it is imperative to develop new methodologies for the extraction of analytes from matrices such as surface water, with a low impact on the environment. Chlorpyrifos (CP) is an organophosphate compound widely used for pest control, toxic to living organisms, which can be mobilized from soils to different water sources. Dispersive liquid-liquid microextraction (DLLME) can be considered as a methodology with green analytical chemistry characteristics, due to its low solvent and time consumption. The objective of this work was to optimize DLLME for the analysis of CP in water samples. For the extraction, methanol was used as dispersing agent and CS2 as extracting agent, and five extraction times were evaluated: 5, 10, 15, 15, 20 and 25 min. The extracts were analyzed by gas chromatography with electron microcapture detector (GC-μECD). The results of the shaking time evaluation showed that, for the shaking times of 10 and 15 min, a CP recovery percentage of 108% and 88% was obtained, respectively, with a detection and quantification limit of 18.3 and 22.4 μg/L, respectively, and a precision expressed as relative standard deviation of less than 14.2%, which is acceptable for this type of extraction. It can be concluded that the DLLME methodology associated with GC-μECD is a suitable alternative for the quantification of CP in aqueous matrices with a low environmental impact.