bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gut microbiome modulates tacrolimus pharmacokinetics through the transcriptional regulation of ABCB1
Authors: Degraeve Alexandra Louise 
Published: September 2024

Background. Following solid organ transplantation, tacrolimus (TAC) is an essential drug in the immunosuppressive strategy. Its use constitutes a challenge due to its narrow therapeutic index and its high inter- and intra- pharmacokinetic (PK) variability. As the contribution of the gut microbiota to drug metabolism is now emerging, it might be explored as one of the factors explaining TAC PK variability. Herein, we studied the contribution of the gut microbiota to TAC PK, using a combination of in vivo and in vitro models. Results. TAC oral administration was performed in mice. Compared to controls, mice with a lower intestinal microbial load due to antibiotics administration exhibit a 33% reduction in TAC whole blood exposure and a lower inter-individual variability. This reduction in TAC levels was strongly correlated with higher expression of the efflux transporter ABCB1 (also known as the p-glycoprotein (P-gp) or the multidrug resistance protein 1 (MDR1)) in the small intestine. Conventionalization of germ-free mice confirmed the ability of the gut microbiota to downregulate ABCB1 expression in a site-specific fashion. The functional inhibition of ABCB1 in vivo by zosuquidar formally established the implication of this efflux transporter in the modulation of TAC PK by the gut microbiota. Furthermore, we showed that polar bacterial metabolites could recapitulate the transcriptional regulation of ABCB1 by the gut microbiota, without affecting its functionality. Finally, whole transcriptome analyses pinpointed, among others, the Constitutive Androstane Receptor (CAR) as a transcription factor likely to mediate the impact of the gut microbiota on ABCB1 transcriptional regulation. Conclusions. We highlight for the first time how the modulation of ABCB1 expression by bacterial metabolites results in changes in TAC PK, affecting not only blood levels but also the inter-individual variability. More broadly, considering the high number of drugs with unexplained PK variability transported by ABCB1, our work is of clinical importance and paves the way for incorporating the gut microbiota in prediction algorithms for dosage of such drugs.Link to OA paper: http://dx.doi.org/10.1186/s40168-023-01578-y
Surgical Treatment for Colorectal Cancer Partially Restores Gut Microbiome and Metabolome Traits
Authors: Shiroma Hirotsugu 
Published: September 2024

Accumulating evidence indicates that the gut microbiome and metabolites are associated with colorectal cancer (CRC). However, the influence of surgery for CRC treatment on the gut microbiome and metabolites and how it relates to CRC risk in postoperative CRC patients remain partially understood. Here, we collected 170 fecal samples from 85 CRC patients pre- and approximately 1 year postsurgery and performed shotgun metagenomic sequencing and capillary electrophoresis-time of flight mass spectrometry (CE-TOFMS)-based metabolomics analyses to characterize alterations between pre- and postsurgery. We determined that the relative abundance of 114 species was altered postsurgery (P lower than 0.005). CRC-associated species, such as Fusobacterium nucleatum, were decreased postsurgery. On the other hand, Clostridium scindens, carcinogenesis-associated deoxycholate (DCA)-producing species, and its biotransformed genes (bai operon) were increased postsurgery. The concentration of 60 fecal metabolites was also altered postsurgery (P lower than 0.005). Two bile acids, cholate and DCA, were increased postsurgery. We developed methods to estimate postoperative CRC risk based on the gut microbiome and metabolomic compositions using a random forest machine-learning algorithm that classifies large adenoma or early-stage CRC and healthy controls from publicly available data sets. We applied methods to preoperative samples and then compared the estimated CRC risk between the two groups according to the presence of large adenoma or tumors 5 years postsurgery (P lower than 0.05). Overall, our results show that the gut microbiome and metabolites dynamically change from pre- to postsurgery. In postoperative CRC patients, potential CRC risk derived from gut microbiome and metabolites still remains, which indicates the importance of follow-up assessments.Link to OA paper: https://journals.asm.org/doi/10.1128/msystems.00018-22
Reporting guidelines for human microbiome research: the STORMS checklist
Authors: Mirzayi Chloe 
Published: September 2024

The particularly interdisciplinary nature of human microbiome research makes the organization and reporting of results spanning epidemiology, biology, bioinformatics, translational medicine and statistics a challenge. Commonly used reporting guidelines for observational or genetic epidemiology studies lack key features specific to microbiome studies. Therefore, a multidisciplinary group of microbiome epidemiology researchers adapted guidelines for observational and genetic studies to culture-independent human microbiome studies, and also developed new reporting elements for laboratory, bioinformatics and statistical analyses tailored to microbiome studies. The resulting tool, called Strengthening The Organization and Reporting of Microbiome Studies (STORMS), is composed of a 17-item checklist organized into six sections that correspond to the typical sections of a scientific publication, presented as an editable table for inclusion in supplementary materials. The STORMS checklist provides guidance for concise and complete reporting of microbiome studies that will facilitate manuscript preparation, peer review, and reader comprehension of publications and comparative analysis of published results. Link to OA paper: https://www.nature.com/articles/s41591-021-01552-x
Variation and transmission of the human gut microbiota across multiple familial generations
Authors: Colomer Mireia Vallès 
Published: September 2024

Although the composition and functional potential of the human gut microbiota evolve over the lifespan, kinship has been identified as a key covariate of microbial community diversification. However, to date, sharing of microbiota features within families has mostly been assessed between parents and their direct offspring. Here we investigate the potential transmission and persistence of familial microbiome patterns and microbial genotypes in a family cohort (n = 102) spanning 3 to 5 generations over the same female bloodline. We observe microbiome community composition associated with kinship, with seven low abundant genera displaying familial distribution patterns. While kinship and current cohabitation emerge as closely entangled variables, our explorative analyses of microbial genotype distribution and transmission estimates point at the latter as a key covariate of strain dissemination. Highest potential transmission rates are estimated between sisters and mother–daughter pairs, decreasing with increasing daughter’s age and being higher among cohabiting pairs than those living apart. Although rare, we detect potential transmission events spanning three and four generations, primarily involving species of the genera Alistipes and Bacteroides. Overall, while our analyses confirm the existence of family-bound microbiome community profiles, transmission or co-acquisition of bacterial strains appears to be strongly linked to cohabitation. Link to the OA paper: https://www.nature.com/articles/s41564-021-01021-8
Different Effects of Mineral Versus Vegetal Granular Activated Carbon Filters on the Microbial Community Composition of a Drinking Water Treatment Plant
Authors: Bruno Antonia 
Published: September 2024

Drinking water quality and safety is strictly regulated and constantly monitored, but little is known about the microorganisms inhabiting drinking water treatment plants (DWTPs). This lack of knowledge prevents optimization of designs and operational controls. Here we investigated the drinking water microbial community harbored by a groundwater-derived DWTP, involving mineral and vegetal granular activated carbon filters (GACs). We used 16S rRNA gene sequencing to analyze water microbiome variations through the potabilization process, considering (i) different GAC materials and (ii) time from GAC regeneration. Our results revealed the predominance of Cand. Patescibacteria, uncultivable bacteria with limited metabolic capacities and small genomes, from source to downstream water. Microbial communities clustered per sampling date, with the noteworthy exception of groundwater samples. If the groundwater microbiome showed no significant variations over time, the community structure of water downstream GACs (both mineral and vegetal) seemed to be affected by time from GAC regeneration. Looking at a finer scale, different GAC material affected microbiome assembly over time with significant variation in the relative abundances of specific taxa. The significance of our research is in identifying the environmental microorganisms intrinsic of deep groundwater and the community shift after the perturbations induced by potabilization processes. Which microorganisms colonize different GACs and become abundant after GACs regeneration and over time is a first step toward advanced control of microbial communities, improving drinking water safety and management of operational costs.Link to OA paper: https://www.frontiersin.org/articles/10.3389/fevo.2021.615513/full
Steamed broccoli sprouts alleviate gut inflammation and retain gut microbiota against DSS-induced dysbiosis
Authors: Holman Johanna M 
Published: September 2024

Inflammatory Bowel Diseases (IBD) are devastating conditions of the gastrointestinal tract with limited treatments, and dietary intervention may be effective, affordable, and safe for managing symptoms. Ongoing research has identified inactive compounds in broccoli sprouts, like glucoraphanin, and that mammalian gut microbiota play a role in metabolizing it to the anti-inflammatory sulforaphane. The objectives were to identify biogeographic location of participating microbiota and correlate that to health outcomes. We fed specific pathogen free C57BL/6 mice either a control diet or a 10% steamed broccoli sprout diet, and gave a three-cycle regimen of 2.5% dextran sodium sulfate (DSS) in drinking water over a 40-day experiment to simulate chronic, relapsing ulcerative colitis. We monitored body weight, fecal characteristics, fecal lipocalin, and sequenced bacterial communities from the contents and mucosa in the jejunum, cecum, and colon. Mice fed the broccoli sprout diet while receiving DSS performed better than mice fed the control diet while receiving DSS for all disease parameters, including significantly more weight gain (2-way ANOVA, p lower than 0.05), lower Disease Activity Index scores (2-way ANOVA, p lower than 0.001), and higher bacterial richness in all gut locations (linear regression model, p lower than 0.01 for all locations measured). Bacterial communities were assorted by gut location except in the mice receiving the control diet and DSS treatment (Beta-diversity, ANOVA, p lower than 0.05 for each). Importantly, our results suggested that broccoli sprout feeding completely abrogated the effects of DSS on gut microbiota, as bacterial communities were similar between mice receiving broccoli sprouts with and without DSS. Spatially resolved microbial communities provide greater insight when investigating host-microbe interactions. Here, we show that a 10% broccoli sprout diet protects mice from the negative effects of dextran sodium sulfate induced colitis, that colitis erases biogeographical patterns of bacterial communities in the gut, and that the cecum is not likely to be a significant contributor to colonic bacteria of interest in the DSS mouse model of ulcerative colitis.Link to OA paper: https://www.biorxiv.org/content/10.1101/2023.01.27.522641v2
Rapid and accurate identification of ribosomal RNA sequences using deep learning
Authors: Deng Zhi Luo 
Published: September 2024

Advances in transcriptomic and translatomic techniques enable in-depth studies of RNA activity profiles and RNA-based regulatory mechanisms. Ribosomal RNA (rRNA) sequences are highly abundant among cellular RNA, but if the target sequences do not include polyadenylation, these cannot be easily removed in library preparation, requiring their post-hoc removal with computational techniques to accelerate and improve downstream analyses. Here we describe RiboDetector, a novel software based on a Bi-directional Long Short-Term Memory (BiLSTM) neural network, which rapidly and accurately identifies rRNA reads from transcriptomic, metagenomic, metatranscriptomic, noncoding RNA, and ribosome profiling sequence data. Compared with state-of-the-art approaches, Ribodetector can produce one order of magnitude fewer misclassifications. Importantly, the few false positives of RiboDetector on the benchmark dataset were not enriched in certain Gene Ontology (GO) terms, suggesting a low bias for downstream functional profiling. RiboDetector also demonstrated a remarkable generalization ability for detecting novel rRNA sequences divergent from the training data with sequence identities of less than 90%. On a personal computer, RiboDetector can process 40M reads in less than 6 minutes, which is about 50 times faster in GPU mode and about 15 times in CPU mode than other methods.RiboDetector is available under a GPL v3.0 license at https://github.com/hzi-bifo/RiboDetector.
Financial Development, Economic Growth, and the African Union’s Agenda 2063
Authors: Houeninvo Toussaint , Lankoande and Germain 
Published: September 2024

ABSTRACT
This article evaluates the role of financial development in achieving the objectives of the African Union’s Agenda 2063, especially its income per capita growth goal and leveraging domestic resource mobilization to finance the continent’s development needs. It uses panel data for 1995–2020 and applies a system generalized method of moments as the econometric technique. The findings indicate that promoting financial development can speed up the achievement of key Agenda 2063 expected transformational outcomes, in particular the continent’s real income per capita growth. Based on the estimation of short-term and long-term elasticities of financial development with respect to economic growth, a counterfactual simulation shows that if credit to the private sector as a percentage of GDP could increase from 4.36%, one of the lowest country values in the sample, to 54.03%, the corresponding GDP per capita could increase from its current level of USD 523 to USD 633.18 in the short-term and to USD 4,840 by the end of 2063. The article contributes to closing the gap of empirical studies on Agenda 2063.
BLACK’S SELF-RESILIENCE IN MAYA ANGELOU’S POEM STILL I RISE: A MIMETIC ANALYSIS
Authors: Aulia Ela Manikam , Rasiah Rasiah , Putra Ansor , Koso Halijah 
Published: September 2024

This research is intended to showcase the reflection of Black self-resilience through Still I Rise poem written by Maya Angelou. Mimetic approach and the concept of self-resilience were used to analyze the problem of this research. Self-resilience was seen in two points; physical and psychological ones. Black self-resilient performed in the poem is considered as the mimetic rendition of the dynamic process of black struggle that leads to the positive adaptations within the context of significant adversity in their life context of the US. Type of this research is included in library research with using descriptive qualitative-interpretive method in analyzing the data. It suggests that Maya Angelou in the poem Still I Rise pictured two kinds of Black self-resilience; physical resilience is showed through some selected words, like; dust, sun, moon, tide, they still arise in their place and time. Black did not and could not be destroyed by the bitter treatment of racism. These words also represented the psychological resilience by adding some other words; having gold mine, walk like I've got oil wells, certainty of tides, and the repeating word, I rise, to show their inner self-motivation, affection, and actualization. This study concluded that Black self-resilience both physically and psychologically reflected by Maya Angelou in her Poem Still I Rise is dealing with the racism. Blacks are destroyed not only physically but also mentality, so, they have to endure themselves by leading to a positive adaptation to exist in the United States.
ANALISA PERANCANGAN SISTEM PENGENDALIAN KUALITAS FILM RADIOGRAPHY DENGAN METODE TOTAL QUALITY MANAGEMENT
Authors: Larisang Larisang , Bora M. Ansyar , Sumarni Sumarni 
Published: September 2024

Dalam era global persaingan menjadi semakin tajam. Hanya perusahaan yang dapat menghasilkan kualitas barang atau jasa yang sesuai dengan tuntutan pelanggan yang dapat memenangkan persaingan. Mengacu pada data PT. Astar Testing & Inspection Batam dalam satu bulan minimal terdapat 20% cacat pada photo radiography sampai ditolak pelanggan. Dari cacat tersebut terdapat masalah yang sangat merugikan perusahaan juga orang lain seperti tertundanya pembayaran invoice, waktu yang terbuang sia-sia, dan hilangnya kepercayaan client terhadap kinerja operator RT perusahaan tersebut. Untuk menganalisa suatu kegagalan/cacat dalam film radiography, dilakukan pengolahan data dengan menggunakan alat bantu Statistical Processing Control (SPC) dimulai dengan pengumpulan data check sheet, histogram, diagram pareto, menghitung uji keseragaman dan kecukupan data, batas kontrol, diagram alir, dan diagram sebab akibat. Piranti TQM (Total Quality Manajement) diterapkan dalam langkah-langkah siklus PDCA (Plan, Do, Check, Action) untuk menyelesaikan persoalan kerja yang dihadapi dan mengadakan perbaikan secara terus-menerus. Hasil penelitian yang diperoleh dari cacat radiography antara lain diperlukannya perbaikan kualitas manusia, bahan baku, mesin, metode kerja,dan lingkungan. Untuk film 4’’x10’’ terdapat 64% cacat karena kegagalan pencucian dan penegringan dan film 4’’x15’’ terdapat 49% cacat karena kegagalan pencucian dan pengeringan. Usulan perbaikan yang disarankan adalah pelatihan, pengawasan, perbaikan sarana ruang proses pencucian, pembelian bahan baku sesuai standar kualitas, dan membuat instruksi kerja secara tertulis dan rinci kepada setiap team sebelum memulai pekerjaan.
Jogos digitais e educação matemática: perspectivas do game “O paradeiro de Euclides” para a aprendizagem de geometria
Authors: Santos William de Souza , Souza João Paulo de Araujo , Bonifácio Francisco Tiago , Silva Leonardo Macaulay Bernardo da 
Published: September 2024

Um dos principais objetivos da Educação Matemática é resgatar a arte de fazer Matemática e buscar uma ressignificação da importância da Geometria, que tempos atrás foi deixada de lado. O cenário brasileiro atual vem mostrando a grande dificuldade dos estudantes quanto a aprendizagem matemática, e o uso dos jogos digitais educacionais surgem como uma proposta de chamar à atenção dos discentes e contribuir para seu aprendizado. Nessa perspectiva, por meio de uma abordagem qualitativa, este artigo tem como objetivo apresentar o jogo “O Paradeiro de Euclides” e como ele aborda conteúdos de geometria. Como resultado, são apresentados o enredo e as situações-problemas que possuem como foco principal atribuir significação quanto às aplicações do conteúdo, levando-os a refletir sobre a importância dos conceitos matemáticos, em especial, os de Geometria, para a formação plena de um indivíduo. Como conclusão, espera-se que este artigo possa contribuir para a discussão da aprendizagem baseada em jogos digitais por parte da comunidade científica da área da Educação Matemática, e que o jogo possa contribuir para a aprendizagem de conceitos de Geometria.
CONDIÇÕES DE TRABALHO E QUALIDADE DE VIDA DOS PROFISSIONAIS DE ENFERMAGEM NO CONTEXTO DA COVID-19: REVISÃO INTEGRATIVA DA LITERATURA
Authors: Santos Jeniffer Dayane Duarte dos , Reis Meillyne Alves dos , Biella Ana Flávia de Carvalho Lima , Rezende Wender Lopes , Pereira Ana Claudia Souza 
Published: September 2024

A pandemia da covid-19, declarada em março de 2020 é considerada o problema de saúde pública mais grave dos últimos 100 anos, levou ao colapso dos sistemas de saúde afetando principalmente os profissionais de enfermagem por ser a maior categoria entre os profissionais da saúde. Identificar as evidências científicas disponíveis na literatura em relação às condições de trabalho e qualidade de vida dos profissionais de enfermagem no contexto da covid-19. Revisão integrativa (RI) de literatura, a busca de dados foi realizada no mês de agosto de 2020 no portal da BVS e PUBMED. Foram selecionados 6 artigos indexados nas bases de dados LILACS, BDENF e PUBMED. Os estudos revelaram que condições de trabalho inadequadas dos profissionais de enfermagem se intensificaram durante a pandemia da covid-19 gerando muitas vezes transtornos psicológicos e afetando diretamente na qualidade da assistência prestada. A realidade aponta que é fundamental que governantes e gestores se sensibilizem e implementem medidas de proteção à saúde desses profissionais, garantindo no mínimo o direito de trabalhar sob condições adequadas, seguras e que preservem a saúde dos mesmos.
Determination of Radon-222 (222Rn) in Well and Borehole Water at Nasarawa LG, Kano State, Nigeria
Authors: Abubakar Abdulkadir Abubakar , Garba Nuraddeen Nasir , Nasiru Rabi’u , Tijani Abdulkadir Shehu , Bello Suleiman , Ado Abbati Muhammad , Aliyu Abubakar Sadiq 
Published: September 2024

Study’s Excerpt/Novelty

This study provides radiological assessment of Radon-222 concentrations in groundwater sources within Nassarawa LG, Kano, highlighting significant public health concerns.
The findings reveal that the mean radon activity concentration in both well and borehole water samples exceeds the maximum permissible limits set by USEPA and WHO, with 70% of the samples surpassing these thresholds.
This research underscores the urgent need for continuous monitoring and implementation of mitigation measures to ensure safe drinking water and protect public health in densely populated areas reliant on groundwater sources.

Full Abstract
Nassarawa LG is one of Kano's most densely populated local government areas and depends solely on groundwater (well and borehole) for drinking and other domestic purposes. Radon, one of the most important radioactive elements, is abundant due to the presence of uranium and radium. It can dissolve in underground water, leading to internal exposure if ingested. Therefore, there is a need for a radiological assessment of Radon-222 in the water and an evaluation of the health hazards associated with the level (high or low) of radon and background radioactivity. A total of one hundred (100) water samples were collected from the study area. The samples were analysed using a liquid scintillation counter from the Center for Energy Research (CERT), Ahmadu Bello University, Zaria. The mean radon activity concentration in the water was found to be 12.78±0.04 Bq/L, which is higher than the maximum permissible limits of 11.1 Bq/L and 10 Bq/L set by the USEPA and WHO, respectively (WHO, 2004; USEPA, 2003). The mean radon activity concentration in well and borehole water was 11.946±0.04Bq/L and 13.612±0.04Bq/L, respectively, with a range from 3.634±0.04Bq/L to 44.952±0.04Bq/L. The highest recorded radon activity concentration was 44.952±0.04Bq/L in borehole water from Giginyu, and the lowest was recorded in well water from Kawo. 70% of the total samples had a high radon concentration, exceeding the maximum contaminant levels of 11.1 Bq/L set by USEPA and 10 Bq/L set by WHO, as also reported by UNSCEAR. The concentration level was found to be higher in borehole water compared to well water. In conclusion, many of the samples from the study area exceeded the maximum contaminant levels of 11.1 Bq/L (USEPA) and 10 Bq/L (WHO), indicating a significant public health concern that warrants further investigation and mitigation measures. It recommended that continuous monitoring and assessment of Radon-222 levels in drinking water should be implemented to protect public health.