bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nutrient intake and dietary adequacy among infants in Kongwa District, Tanzania: A sub-study of the Mycotoxin Mitigation Trial
Authors: Kayanda Rosemary Alphonce , Phillips Erica , Kassim Neema , Ngure Francis , Stoltzfus Rebecca 
Published: April 2023

Abstract

Background: Early exposure to aflatoxin, a common toxin in global food systems, has been associated with child growth faltering. The Mycotoxin Mitigation Trial was a community-based cluster-randomized trial designed to assess the effect of dietary aflatoxin on stunting. The study provided low aflatoxin pre- blended porridge flour and groundnuts flour to the Intervention arm, while the same porridge recipe from home ingredients was promoted through education to the Standard of Care (SOC) arm. The objective was to isolate the effect of aflatoxin consumption while keeping dietary intake otherwise the same between the two arms.
Methods: To assess dietary intake, we performed a cross-sectional study on trial participants to evaluate and compare nutrient intake and adequacy of protein, energy, lipid, iron, zinc, calcium, and vitamin A between the randomized arms of the study. Twenty paired clusters (10 per trial arm) were selected, with up to 15 households per cluster randomly selected for a structured, multi-pass 24-h recall in three different rounds of data collection at 12 months of age.
Results: A total of 282 children participated. Nutrient intake was estimated from mixed models to account for clusters. The mean daily intakes of energy and lipid were 505 kcal and 13 mg respectively in the intervention and SOC while intervention children consumed slightly more proteins (13.7 g v 12.3 g, p= 0.02). There were no differences between the arms regarding the consumption of iron, zinc, calcium, or vitamin A. Generally, Iron and zinc consumption was very low.
Conclusion: At the midpoint of the trial intervention only protein consumption differed between arms. Both arms met RNI for energy, protein, and vitamin A but not for other nutrients assess.
Trial registration ClinicalTrials.gov: NCT03940547, registered April 24, 2019
Functional Janus liquids
Authors: Ghaffarkhah Ahmadreza , Hashemi Seyyed Alireza , Ahmadijokani Farhad , Goodarzi Milad , Riazi Hossein , Mhatre Sameer E. , Zaremba Orysia , Rojas Orlando , Soroush Masoud , Russell Thomas , Wuttke Stefan , Kamkar Milad , Arjmand Mohammad 
Published: April 2023

Abstract
Janus structures have unique properties due to their distinct functionalities on opposing faces, but have yet to be realized with flowing liquids. We demonstrate such Janus liquids with a programmable distribution of nanoparticles (NPs) throughout their structures by joining two aqueous streams of NP dispersions in an apolar liquid. Using this anisotropic integration platform, different magnetic, conductive, or non-responsive NPs can be spatially confined to opposite sides of the original interface using magnetic graphene oxide (mGO)/GO, Ti3C2Tx/GO, or GO suspensions. The resultant Janus liquids can be used as templates for programmable, responsive, and mechanically robust aerogels suitable for piezoresistive sensing, human motion monitoring, and electromagnetic interference (EMI) shielding with a tuned absorption mechanism. The EMI shields outperform their current counterparts in terms of wave absorption, i.e., SET≈51 dB, SER≈0.4 dB, A = 0.91, due to their multi-scale porosity along with non-interfering magnetic and conductive networks imparted by the Janus architecture.
Co-creation of a complex, multicomponent rehabilitation intervention and feasibility trial protocol for the PostUraL tachycardia Syndrome Exercise (PULSE) study
Authors: Pearce Gemma , Holliday Nikki , Sandhu Harbinder , Eftekhari Helen , Bruce Julie , Timms Emma , Ablett Laura , Kavi Lesley , Simmonds Jane , Evans Rebecca , Magee Paul , Powell Richard , Keogh Shane , McGregor Gordon 
Published: April 2023

Abstract
Background: There is a dearth of research to support the treatment of people with Postural Tachycardia Syndrome (PoTS). Despite expert consensus suggesting exercise is recommended for this patient group, there are no randomised control trials examining this rigorously. The aim was to co-create a feasibility trial protocol and a rehabilitation intervention for people living with PoTS.
Methods: The intervention and feasibility trial design were co-created as part of the PostUraL tachycardia Syndrome Exercise (PULSE) study. We used the ‘three co’s framework’ of co-define, co-design and co-refine. Recruitment included key national charities and National Health Service Trusts treating people living with PoTS in the United Kingdom.18 Patient and Public Involvement members attended the co-define session, and 16 co-creators with a mix of expertise attended the subsequent co-design and co-refine sessions. Seven intervention practitioners were trained in the rehabilitation intervention, providing feedback for further co-refinement.
Results: The final co-created intervention comprises online physical activity, and lifestyle and behaviour change support sessions. It is based on functional movement activities using a patient-centred approach tailored to individual needs. Physical activity intensity is guided by individuals’ perception of effort rather than by objective measures. Recumbent bikes are provided for home use. Patients deemed randomisation to be acceptable because research in this area was considered important.
Conclusions: An innovative approach was used to co-create the PULSE intervention and feasibility trial protocol to meet the evidence-based and logistical needs of people living with PoTS, clinicians, service deliverers, third sector organisations, academics and funders. This can be used as a successful example and template for future research internationally. People living with PoTS were recognised as experts and involved in every aspect of conceptualisation, design and refinement. This complex rehabilitation intervention is currently being tested in a randomised feasibility trial comparing the PULSE intervention with best-practice usual care for people living with PoTS.
Trial registration: ISRCTN45323485 registered on 7 April 2020.
Application of Kernel-based Learning Algorithms in Survival Analysis: A Systematic Review
Authors: Rezaei Mansour , Montaseri Maryam , Mostafaei Shayan , Taheri Mohammad 
Published: April 2023

Abstract

BackgroundThe time until an event happens is the outcome variable of interest in the statistical data analysis method known as survival analysis. Some researchers have created kernel statistics for various types of data and kernels that allow the association of a set of markers with survival data. Multiple Kernel Learning (MKL) is often considered a linear or convex combination of multiple kernels. This paper aims to provide a comprehensive overview of the application of kernel learning algorithms in survival analysis.MethodsWe conducted a systematic review which involved an extensive search for relevant literature in the field of biomedicine. After using the keywords in literature searching, 435 articles were identified based on the title and abstract screening.ResultIn this review, out of a total of 56 selected articles, only 20 articles that have used MKL for high-dimensional data, were included. In most of these articles, the MKL method has been expanded and has been introduced as a novel method. In these studies, the extended MKL models due to the nature of classification or regression have been compared with SVM, Cox PH (Cox), Extreme Learning (ELM), MKCox, Gradient Boosting (GBCox), Parametric Censored Regression Models (PCRM), Elastic-net Cox (EN-Cox), LASSO-Cox, Random Survival Forests (RSF), and Boosting Concordance Index (BoostCI). In most of these articles, the optimal model’s parameters are estimated by 10-fold cross-validation. In addition, the Concordance index (C-index) and the area under the ROC curve (AUC) were calculated to quantitatively measure the performance of all methods for validation. Predictive accuracy is improved by using kernels.ConclusionOur findings suggest that using multiple kernels instead of one single kernel can make decision functions more interpretable and can improve performance.
Uncovering plant microbiomes using long-read metagenomic sequencing
Authors: Masuda Sachiko , Gan Pamela , Kiguchi Yuya , Anda Mizue , Sasaki Kazuhiro , Shibata Arisa , Iwasaki Wataru , Suda Wataru , Shirasu Ken 
Published: April 2023

Abstract
The microbiome of plants plays a pivotal role in their growth and health. Despite its importance, many fundamental questions about the microbiome remain largely unanswered, such as the identification of colonizing bacterial species, the genes they carry, and the location of these genes on chromosomes or plasmids. To gain insights into the genetic makeup of the rice leaf microbiome, we performed a metagenomic analysis using long-read sequences, and developed a genomic DNA extraction method that provides relatively intact DNA for long-read sequencing. 1.8 Gb reads were assembled into 26,067 contigs, including 136 circular sequences of less than 1 Mbp, as well as 172 large (≥ 1 Mbp) sequences, six of which were circularized. Within these contigs, 669 complete 16S rRNA genes were clustered into 166 bacterial species, 130 of which showed low identity to previously defined sequences, suggesting that they represent novel species. The large circular contigs contain novel chromosomes and a megaplasmid, and most of the smaller circular contigs (<1 Mbp) were defined as novel plasmids or bacteriophages. One circular contig represents the complete chromosome of an uncultivated bacterium in the candidate phylum Candidatus Saccharibacteria. Our findings demonstrate the efficacy of long-read-based metagenomics for profiling microbial communities and discovering novel sequences in plant-microbiome studies.
Genome-wide gene expression profiling analysis reveals bisphenol A interacts with seven prognosis-related genes to promote the progression of osteosarcoma
Authors: Liu Jin , Zhang Peng , Xu Meng , Chen Fan , Yu Wenjing , Xia Ting 
Published: April 2023

Abstract
With more and more application of the endocrine disruptors (EDCs) in the daily use, there is evidence that EDCs can cause cancer, and they can cause a variety of deleterious effects. It has been known for many years that bisphenol A (BPA), a xenoestrogen found in many consumer products, dysregulates a wide array of signaling pathways in the body. In this work, we discovered a new method to evaluate the role of BPA in human osteosarcoma (OS). An analysis of genes previously identified as associated with BPA was conducted from the CTD database, and we hypothesized that these genes might be useful as biomarkers, which was proved by protein-protein interactive network. In addition, the KEGG enrichment analysis demonstrated many cancers, including OS, are closely associated with the BPA. The single sample gene set enrichment analysis algorithm was further used to explore the genes that may play a key role in the OS. An in silico analysis was performed based on gene expression data extracted from Target database. On the basis of the BPA-based prognostic prediction model in OS cohort, we discovered that seven BPA-related genes (IHH, ELFN1-AS1, AL161909.1, IGHV4-39, CSAG1, ACTA2 and SSX1) are closely associated with the prognosis of the OS patients. The enrichment pathways analysis reveals these seven genes are closely associated with the many tumor-related pathways, such as TNFA signaling via NFKB, interferon alpha response, inflammatory response, IL6 JAK STAT3 signaling and IL2 STAT5 signaling pathways. Additionally, the exposure of 10 µM BPA was found to promote the proliferation ability of OS cells in vitro. Our findings suggest that BPA can promote the proliferation of osteosarcoma cells. IHH, ELFN1-AS1, AL161909.1, IGHV4-39, CSAG1, ACTA2 and SSX1 are among the most critical targets for BPA to act as a carcinogen.
Identification of novel spatially resolved markers of malignant transformation in Intraductal Papillary Mucinous Neoplasms
Authors: Carbone Carmine , Agostini Antonio , Piro Geny , Inzani Frediano , Quero Giuseppe , Esposito Annachiara , Caggiano Alessia , Priori Lorenzo , Larghi Alberto , Alfieri Sergio , Casolino Raffaella , Scaglione Giulia , Tondolo Vincenzo , Cammarota Giovanni , Ianiro Gianluca , Corbo Vincenzo , Biankin Andrew , Tortora Giampaolo 
Published: April 2023

Abstract
Objective The current IPMN risk stratification is based on clinical and histological features rather than molecular markers. We aimed to improve the current diagnostic criteria of IPMN performing spatial transcriptomic (ST) on lesions of different grade to identify novel markers that define IPMN degeneration to PDAC.
Design We performed ST on two independent cohorts of IPMN samples grouped by morphology and degree of dysplasia using two innovative technologies:
Visium ST on a discovery cohort of 18 samples from 14 patients: 4 low-grade IPMN (3 low-grade dysplasia (LGD), 1 intermediate dysplasia/Borderline), 9 high-grade IPMN characterized by a high-grade of dysplasia (HGD), including 4 invasive IPMN with associated PDAC, and 1 PDAC-associated normal duct).
GeoMx ST on a validation cohort of 57 IPMN samples: 23 low-grade IPMN (6 low-grade dysplasia (LGD), 17 intermediate dysplasia/Borderline), 34 High-grade IPMN (13 HGD Gastric IPMN and 21 HGD Intestinal IPMN) from 40 patients.
Results Novel subtype-specific markers were identified in the discovery cohort: HOXB3 and ZNF117 in LGD ; SPDEF, and gastric neck cell markers in Borderline; NKX6-2 and gastric isthmus cell markers in HGD Gastric IPMN. The spatial trajectory inference implicated NKX6-2 in progression of Gastric IPMN. Transcriptomic dissection highlighted the role of TNFα signalling and Myc activation in IPMN progression. The findings were confirmed in the independent validation cohort by GeoMx analysis.
Conclusions Our results identify novel markers associated with IPMN morphology and dysplasia to be explored for clinical utility, to better delineate progression in patients, improve risk stratification and clinical management.
Evolutionary games on multilayer networks: coordination and equilibrium selection
Authors: Raducha Tomasz , Miguel Maxi San 
Published: April 2023

Abstract
We study mechanisms of synchronisation, coordination, and equilibrium selectionin two-player coordination games on multilayer networks. We apply the approach from evolutionary game theory with threepossible update rules: the replicator dynamics (RD), the best response (BR), and the unconditional imitation (UI). Players interact on a two-layer random regular network. The population on each layer plays a different game, with layer I preferring the opposite strategy to layer II. We measure the difference between the two games played on the layersby a difference in payoffs ∆ S while the inter-connectedness is measured by a node overlap parameter q. We discover a critical value qc(∆ S) below whichlayers do not synchronise. For q>qc in general both layerscoordinate on the same strategy. Surprisingly, there is a symmetry breakingin the selection of equilibrium -- for RD and UI there isa phase where only the payoff-dominant equilibrium is selected. Our work is an example of previously observed differences between the update rules on a single network. However, we took a novel approach with the game being playedon two inter-connected layers. As we show, the multilayer structure enhances the abundance of the Pareto-optimal equilibrium in coordination games with imitative update rules.
Perceptions, knowledge and practices related to oral health in a group of pregnant women: A qualitative study
Authors: Velosa-Porras Juliana , Malagón Nelcy Rodríguez 
Published: April 2023

Abstract

Background It is known that the prevalence of dental caries and periodontal disease is increasing in pregnant women. Dental care is sufficient to prevent oral diseases and perform timely interventions. However, few pregnant women go to the dental office during this period due to a lack of knowledge. The perceptions, knowledge and oral health practices of pregnant women have been scarcely explored and should be taken into account to propose assertive interventions in this population.Aims To identify and explore the perceptions, knowledge, and practices in oral health in a group of pregnant women in Colombia.Methods Twenty-four semistructured interviews were conducted in different areas of Colombia. The interviews were conducted via telephone, and the calls were recorded with the consent of the participants. The recordings were transcribed in Word and checked for typing and transcription errors. The transcripts were analyzed using a hybrid approach combining inductive and deductive coding. The information was organized and encoded using NVivo12 software. We followed the SRQR checklist.Results Pregnant women reported having good oral health. One limitation mentioned for occupation was pregnancy. The appearance of the oral cavity has not negatively affected the relationships of the pregnant women.Conclusions The pregnant women had good oral hygiene habits but did not receive dental check-ups. Knowledge in this group was limited and diverse. The information given by health professionals should be standardized, and some beliefs should be demystified.
Molecular Epidemiology of Sars-CoV-2 in the Pityusic Islands, a Touristic Worldwide Hotspot in the Western Mediterranean
Authors: Viver Tomeu , López-Causapé Carla , Fraile-Ribot Pablo , Pérez-Mazón Carmen , López-Solé Dolors , Jiménez-Guerra Gemma , Taltavull Biel , López-López Aránzazu 
Published: April 2023

Abstract
The public health emergency caused by the Covid-19 outbreak in March 2020 encouraged worldwide initiatives to monitor the genetic diversity and features of the SARS-CoV-2 circulating variants, mainly based on the genomic surveillance. However, due to the impossibility to carry out extensive sequencing in resource-limited
hospitals, other PCR-based strategies could be applied to efficiently monitor the circulating variants without the need to greatly expand the sequencing capacity. In our case, overpassing the technical limitations inherent to a second level hospital, we were able to characterize the weekly distribution of SARS-CoV-2 by the amplification patterns visualization, genotyping, and sequencing of randomly selected samples. All these molecular approaches allowed us to trace the epidemiology of SARS-CoV-2 viruses circulating in Ibiza and Formentera (Balearic Islands, Spain) during the third to the sixth pandemic waves, in which three major lineages that were considered as VoCs (alpha, delta, and omicron), and many other non-VoC variants were detected and tracked.
Role of the Nrf2/ARE downregulation and mtDNA damage in the cognitive impairments in APP/PS1 mice
Authors: Gureev Artem P. , Babenkova Polina I. , Nesterova Veronika V. , Tsvetkova Arina D. , Sadovnikova Irina S. , Eremina Anna A. , Kryukova Vera A. , Popov Vasily N. 
Published: April 2023

Abstract
Mitochondrial dysfunction is one of the key events in the pathogenesis of Alzheimer's disease (AD) that mediates cognitive impairment. In this study, we examined the extent to which the mitochondrial DNA (mtDNA) of APP/PS1 mouse strain is susceptible to damage accumulation and explored the potential relationship between mtDNA integrity and other physiological processes. The gut microbiome is known to largely determine the inflammatory status of the organism. However, although we found no significant differences in the bacterial composition of the gut microbiome at the phylum level between APP/PS1 and C57BL/6 mice strains, we found increased expression of the gene encoding the proinflammatory factor TNFα in the brain. This coincided with a decrease in expression of the transcription factor Nrf2, which is responsible for antioxidant protection of cells. We found decreased expression of genes responsible for glutathione and thioredoxin pathways of H2O2 utilization. In addition, we observed a decrease in the expression of some genes responsible for DNA repair. These processes appear to be the reason for the accumulation of oxidative damage in the mtDNA of the brain, and the damage accumulates predominantly in the cerebellum. Suppression of cerebellar output may facilitate freezing behavior, which we observed using the Barnes test. Freezing in APP/PS1 mice was a main reason for the increased average latency time to find the escape hole compared to C57BL/6 mice. Therefore, mitochondrial dysfunction at the level of changes in transcriptome and mtDNA integrity in some brain compartments may facilitate cognitive dysfunction in APP/PS1 mice.
Determinants of Household Payments for Drinking Water in Mexico, with Equity Considerations
Authors: Revollo-Fernández Daniel 
Published: April 2023

Abstract
The situation with non-payment of the drinking water services that households receive is an increasingly common problem with significant financial implications. The principal determinants of this lack of payment was estimated using a probabilistic model for the case of Mexico, with consideration of equity among household deciles. The results show that while this problem can be associated with households belonging to lower deciles, those in upper deciles are responsible for nearly the same share of the financial impact on water management organizations, and consequently, on the wellbeing of society. Nevertheless, households in the first deciles have more reasonable motives for deciding not to pay. Therefore, when wanting to develop policy incentives for households to pay for drinking water services, the incentives should be differentiated according to socioeconomic strata.
Determining the clinicopathological significance of the VI-RADS true-positive group: A retrospective study
Authors: Ikuma Shunsuke , Akatsuka Jun , Takeda Hayato , Endo Yuki , Hamasaki Tsutomu , Kimura Go , Kondo Yukihiro 
Published: April 2023

Abstract
Background The Vesical Imaging Reporting and Data System (VI-RADS) is widely used as a diagnostic method for predicting muscle-invasive bladder cancer (MIBC). This study aimed to determine the clinicopathological significance of the VI-RADS true-positive (TP) group.Methods We performed 333 transurethral resections of bladder tumors (TURBT) at our hospital between January 2019 and April 2021, and included 125 patients who underwent preoperative Magnetic resonance imaging (MRI) into this study. The patients were pathologically diagnosed with urothelial carcinoma (UC). We first compared the results of patients with VI-RADS scores of 3 and 4 to determine the cut-off values for MIBC; thereafter, the 125 patients were divided into TP, false-positive (FP), true-negative (TN), and false-negative (FN) groups using VI-RADS. The clinicopathological significance of the TP group was examined by retrospectively comparing the characteristics of each group.Results A total of 125 cases were examined, out of which 29 were pathologically diagnosed with MIBC. Of the 29 MIBC cases, 4 (13.8%) had a VI-RADS score of ≤ 3 and 25 (86.2%) had a VI-RADS score of ≥ 4. Of the 96 Non-muscle-invasive bladder cancer (NMIBC) cases, 83 (86.5%) had a VI-RADS score of ≤ 3 and 13 (13.5%) had a VI-RADS score of ≥ 4. The diagnostic performance of the VI-RADS with a cutoff value of 4 was 87.1% for sensitivity, 86.5% for specificity, and an area under the curve (AUC) of 0.87. In contrast, for a cutoff value of 3, the sensitivity was 90.3%, specificity was 61.5%, and AUC was 0.76. In this study, a VI-RADS score of ≥ 4 could predict MIBC. In the TP group, all 25 patients had high-grade tumors. The TP group had significantly more high-grade bladder cancers than the other groups (TP vs. TN, p = 0.001; TP vs. FP, p = 0.009; and TP vs. FN, p = 0.0278). In addition, the TP group had more tumor necrosis (TP vs. TN, p = 0.001; TP vs. FP, p = 0.0045) and more UC variant cases (TP vs. TN, p = 0.0012; TP vs. FP, p = 0.0217) than the TN and FP groups.Conclusion This study suggests that VI-RADS has a high diagnostic performance in predicting MIBC, and that VI-RADS could diagnose high-grade tumors, necrosis, and UC variants.