bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantification of IgY to Erysipelothrix rhusiopathiae in serum from Swedish laying hens
Authors: Wattrang Eva , Eriksson Helena , Albihn Ann , Dalgaard Tina Sørensen 
Published: March 2021

Abstract
Background
Erysipelas, caused by Erysipelothrix rhusiopathiae (ER), is an important emerging disease in free-range and organic egg-production. The aim of the present study was to assess if quantification of ER specific IgY titers may aid the understanding of erysipelas in commercial laying hens. The methodology was validated with sequentially collected sera from experimentally ER infected SPF-chickens and subsequently applied on sera from Swedish commercial laying hens collected during and after outbreaks of erysipelas or collected at slaughter from healthy hens housed in furnished cages, barn production or in organic production (with outdoor access).

Results
In experimentally infected SPF-chickens, titers to ER were significantly increased approximately one week after infection while IgY to ER in uninfected age-matched controls remained low. Also chickens infected with low doses of ER, not displaying clinical signs of disease and with low recovery of ER in blood samples showed high titers of IgY to ER. For laying hens during and after erysipelas outbreaks the majority of samples were considered positive for antibodies to ER with a large variation in levels of IgY titers to ER between individuals. For healthy laying hens at slaughter all samples were deemed positive for antibodies to ER. An influence of flock on levels of IgY titers to ER was observed for both healthy hens and hens during erysipelas outbreaks. For healthy laying hens at slaughter no influence of the housing systems included in the study, history of erysipelas outbreaks at the farm or vaccination on levels of IgY titers to ER was noticed.

Conclusions
Taken together, these results show that high numbers of commercial laying hens showed high IgY titers to ER, comparable to those elicited by experimental ER infection, indicating that ER or bacteria that raises antibodies that cross-react with ER are common in this environment.
CDCA8 as an independent predictor for a poor prognosis in liver cancer
Authors: Shuai Yu , Fan Erxi , Zhong Qiuyue , Chen Qiying , Feng Guangyong , Gou Xiaoxia , Zhang Guihai 
Published: March 2021

Abstract
Background
Human cell division cycle associated 8 (CDCA8) a key regulator of mitosis, has been described as a potential prognostic biomarker for a variety of cancers, such as breast, colon and lung cancers. We aimed to evaluate the potential role of CDCA8 expression in the prognosis of liver cancer by analysing data from The Cancer Genome Atlas (TCGA).

Methods
The Wilcoxon rank-sum test was used to compare the difference in CDCA8 expression between liver cancer tissues and matched normal tissues. Then, we applied logistic regression and the Wilcoxon rank-sum test to identify the association between CDCA8 expression and clinicopathologic characteristics. Cox regression and the Kaplan–Meier method were used to examine the clinicopathologic features correlated with overall survival (OS) in patients from the TCGA. Gene set enrichment analysis (GSEA) was performed to explore possible mechanisms of CDCA8 according to the TCGA dataset.

Results
CDCA8 expression was higher in liver cancer tissues than in matched normal tissues. Logistic regression and the Wilcoxon rank-sum test revealed that the increased level of CDCA8 expression in liver cancer tissues was notably related to T stage (OR = 1.64 for T1/2 vs. T3/4), clinical stage (OR = 1.66 for I/II vs. III/IV), histologic grade (OR = 6.71 for G1 vs. G4) and histological type (OR = 0.24 for cholangiocarcinoma [CHOL] vs. hepatocellular carcinoma [LIHC]) (all P-values < 0.05). Kaplan–Meier survival analysis indicated that high CDCA8 expression was related to a poor prognosis in liver cancer (P = 2.456 × 10−6). Univariate analysis showed that high CDCA8 expression was associated with poor OS in liver cancer patients, with a hazard ratio (HR) of 1.85 (95% confidence interval [CI]: 1.47–2.32; P = 1.16 × 10–7). Multivariate analysis showed that CDCA8 expression was independently correlated with OS (HR = 1.74; CI: 1.25–12.64; P = 1.27 × 10–5). GSEA revealed that the apoptosis, cell cycle, ErbB, MAPK, mTOR, Notch, p53 and TGF-β signaling pathways were differentially enriched in the CDCA8 high expression phenotype.

Conclusions
High CDCA8 expression is a potential molecular predictor of a poor prognosis in liver cancer.
Validation of preimplantation genetic tests for aneuploidy (PGT-A) with DNA from spent culture media (SCM): concordance assessment and implication
Authors: Yin Baoli , Zhang Huijuan , Xie Juanke , Wei Yubao , Zhang Cuilian , Meng Li 
Published: March 2021

Abstract
Background
Spent culture medium (SCM) as a source of DNA for preimplantation genetic tests aneuploidy (PGT-A) has been widely discussed.

Methods
Seventy-five blastocysts that were donated for research provided a unique possibility in which multiple specimens, including trophectoderm (TE) biopsy, SCM, and paired corresponding whole blastocyst (WB) specimens from the same blastocyst source, could be utilized for the purpose of this preclinical validation.

Results
To conduct a validation ploidy concordance assessment, we evaluated the full chromosomal concordance rates between SCM and WB (SCM-to-WB), and between TE and WB (TE-to-WB) as well as sensitivity, specificity and overall diagnostic accuracy. 78.67% (59/75) of NGS results in the SCM group were interpretable, a significantly lower percentage than their corresponding TE and WB groups. This discrepancy manifests itself in intrinsically low quantity and poor integrity DNA from SCM. Subsequently, remarkable differences in full concordance rates (including mosaicism, and segmental aneuploidies) are seen as follows: 32.2% (SCM-to-WB, 19/59) and 69.33% (TE-to-WB, 52/75), (p < 0.001). In such cases, full concordance rates were 27.27% (15/55) in SCM-to-WB, and, 76% (57/75) in TE-to-WB (p < 0.001). Collectively, the NGS data from SCM also translated into lower sensitivities, Positive Predictive Value (PPV), Negative Predictive Value (NPV), overall diagnostic accuracies, and higher Negative Likelihood Ratio (NLR).

Conclusions
Our study reveals that DNA is detectable in the majority of SCM samples. Individual chromosomal aberration, such as segmental aneuploidy and mosaicism, can be quantitatively and qualitatively measured. However, TE still provides a more accurate and reliable high-throughput methodology for PGT-A. Meanwhile, cell-free DNA in SCM reporting lacks uniform diagnostic interpretations. Considering that this test is meant to determine which embryos are relegated to be discarded, PGT-A with cell-free DNA in SCM should not be permitted to be applied in routine clinical settings for diagnosis purpose.
Online art therapy in elementary schools during COVID-19: results from a randomized cluster pilot and feasibility study and impact on mental health
Authors: Malboeuf-Hurtubise Catherine , Léger-Goodes Terra , Mageau Geneviève A. , Taylor Geneviève , Herba Catherine M. , Chadi Nicholas , Lefrançois David 
Published: March 2021

Abstract
Background
Emerging literature on the current COVID-19 crisis suggests that children may experience increased anxiety and depression as a result of the pandemic. To prevent such school and mental health-related problems, there is a timely need to develop preventive strategies and interventions to address potential negative impacts of COVID-19 on children’s mental health, especially in school settings. Results from previous child clinical research indicate that art-based therapies, including mindfulness-based art therapy, have shown promise to increase children’s well-being and reduce psychological distress.

Objective
The goal of the present pilot and feasibility study was to compare the impact of an emotion-based directed drawing intervention and a mandala drawing intervention, on mental health in elementary school children (N = 22), in the context of the COVID-19 pandemic. Both interventions were group-based and delivered online and remotely. A pilot study using a randomized cluster design was implemented to evaluate and compare both interventions in relation to child anxiety, depression, inattention and hyperactivity symptoms.

Results
Analyses of covariance revealed a significant effect of the type of drawing intervention on levels of inattention, after controlling for baseline levels. Participants in the emotion-based directed drawing group showed lower inattention scores at post-test, when compared to participants in the mandala group. Post-hoc sensitivity analyses showed significant decreases in pre-to-post scores for levels of hyperactivity for the complete sample.

Conclusion
Overall, results from this pilot and feasibility study showed that both an emotion-based directed drawing intervention and a mandala drawing intervention may be beneficial to improve mental health in elementary school children, in the context of the current COVID-19 pandemic. From a feasibility standpoint, results indicate that the implementation of both interventions online and remotely, through a videoconference platform, is feasible and adequate in school-based settings. Further work incorporating larger sample sizes, longitudinal data and ensuring sufficient statistical power is warranted to evaluate the long-term impact of both interventions on children’s mental health.
An efficient system for intestinal on-site butyrate production using novel microbiome-derived esterases
Authors: Jung Dah Hyun , Yong Ji Hyun , Hwang Wontae , Yoon Mi Young , Yoon Sang Sun 
Published: March 2021

AbstractShort-chain fatty acids, especially butyrate, play beneficial roles in sustaining gastrointestinal health. However, due to limitations associated with direct consumption of butyrate, there has been interest in using prodrugs of butyrate. Tributyrin (TB), a triglyceride composed of three butyrate molecules and a glycerol, is a well-studied precursor of butyrate. We screened a metagenome library consisting of 5760 bacterial artificial chromosome clones, with DNA inserts originating from mouse microbiomes, and identified two clones that efficiently hydrolyse TB into butyrate. Nucleotide sequence analysis indicated that inserts in these two clones are derived from unknown microbes. BLASTp analysis, however, revealed that each insert contains a gene homologous to acetylesterase or esterase genes, from Clostridium spp. and Bacteroides spp., respectively. Predicted structures of these two proteins both contain serine-histidine-aspartate catalytic triad, highly conserved in the family of esterases. Escherichia coli host expressing each of the two candidate genes invariably produced greater amounts of butyrate in the presence of TB. Importantly, administration of TB together with cloned E. coli cells alleviated inflammatory symptoms in a mouse model of acute colitis. Based on these results, we established an efficient on-site and real-time butyrate production system that releases butyrate in a controlled manner inside the intestine.
Giotto: a toolbox for integrative analysis and visualization of spatial expression data
Authors: Dries Ruben , Zhu Qian , Dong Rui , Eng Chee-Huat Linus , Li Huipeng , Liu Kan , Fu Yuntian , Zhao Tianxiao , Sarkar Arpan , Bao Feng , George Rani E. , Pierson Nico , Cai Long , Yuan Guo-Cheng 
Published: March 2021

AbstractSpatial transcriptomic and proteomic technologies have provided new opportunities to investigate cells in their native microenvironment. Here we present Giotto, a comprehensive and open-source toolbox for spatial data analysis and visualization. The analysis module provides end-to-end analysis by implementing a wide range of algorithms for characterizing tissue composition, spatial expression patterns, and cellular interactions. Furthermore, single-cell RNAseq data can be integrated for spatial cell-type enrichment analysis. The visualization module allows users to interactively visualize analysis outputs and imaging features. To demonstrate its general applicability, we apply Giotto to a wide range of datasets encompassing diverse technologies and platforms.
Concept and development of an interactive tool for trial recruitment planning and management
Authors: Spies Ruan , Siegfried Nandi , Myers Bronwyn , Grobbelaar Sara S. 
Published: March 2021

AbstractBackgroundPredicting and monitoring recruitment in large, complex trials is essential to ensure appropriate resource management and budgeting. In a novel partnership between clinical trial investigators of the South African Medical Research Council and industrial engineers from the Stellenbosch University Health Systems Engineering and Innovation Hub, we developed a trial recruitment tool (TRT). The objective of the tool is to serve as a computerised decisions-support system to aid the planning and management phases of the trial recruitment process.MethodThe specific requirements of the TRT were determined in several workshops between the partners. A Poisson process simulation model was formulated and incorporated in the TRT to predict the recruitment duration. The assumptions underlying the model were made in consultation with the trial team at the start of the project and were deemed reasonable. Real-world data extracted from a current cluster trial, Project MIND, based in 24 sites in South Africa was used to verify the simulation model and to develop the monitoring component of the TRT.ResultsThe TRT comprises a planning and monitoring component. The planning component generates different trial scenarios for predicted trial recruitment duration based on user inputs, e.g. number of sites, initiation delays. The monitoring component uses and analyses the data retrieved from the trial management information system to generate different levels of information, displayed visually on an interactive, user-friendly dashboard. Users can analyse the results at trial or site level, changing input parameters to see the resultant effect on the duration of trial recruitment.ConclusionThis TRT is an easy-to-use tool that assists in the management of the trial recruitment process. The TRT has potential to expedite improved management of clinical trials by providing the appropriate information needed for the planning and monitoring of the trial recruitment phase. This TRT extends prior tools describing historic recruitment only to using historic data to predict future recruitment. The broader project demonstrates the value of collaboration between clinicians and engineers to optimise their respective skillsets.
A Community-enabled Readiness for first 1000 Days Learning Ecosystem (CRADLE) for first-time families: study protocol of a three-arm randomised controlled trial
Authors: Loy See Ling , Thilagamangai  , Teo Joyce , Chan Sze Wern , Razak Nurul Khairani Abdul , Chay Oh. Moh , Ng Kee Chong 
Published: March 2021

Abstract
Background
Enhanced parenting self-efficacy (PSE) contributes to positive parenting and future parental-child health. First-time parents, in particular, are in need of support since the pregnancy until post-delivery to strengthen their early PSE. However, there is a lack of effective and sustainable relevant programmes in the community. The Community-enabled Readiness for first 1000 Days Learning Ecosystem (CRADLE) aims to develop a self-learning eco-community throughout the pregnancy and early childhood to promote PSE among first-time parents. We apply choice architecture strategy using behavioural nudges and midwife-led continuity care during the first 1000 days, and test their effects on PSE and mother-child health for first-time families in Singapore.

Methods
This three-arm randomised controlled trial will recruit up to 750 pregnant women from the KK Women’s and Children’s Hospital, Singapore. Participants will be randomly assigned to receive: (1) standard routine care; (2) behavioural nudges (text messages) along with the use of a social media platform; or (3) midwife-led continuity care involving individualised teleconferencing sessions, during pregnancy and post-delivery. Using web-based questionnaires, participants will be assessed for baseline socio-demography and health status in the first visit, with follow-up assessments in the third trimester, at birth, 6-week (primary end-point), 6-, 12-, 18- and 24-month post-delivery. The primary outcome is PSE. Secondary outcomes include health and birth experience, mental wellness, feeding practice, maternal and child nutritional status. Intention-to-treat and per-protocol analyses will be performed using general linear models to test the effects of interventions across three arms. Recruitment has begun in June 2020 and is estimated to complete in September 2022.

Discussion
This study may identify a sustainable effective strategy in the community by helping first-time parents to have a positive experience during the pregnancy, childbirth and parenthood, leading to an enhanced PSE and health outcomes for both mother and child. Findings from this study will provide insight into the implementation of early parenting and mother-child care programmes.

Trial registration
ClinicalTrials.gov NCT04275765. Registered on 19 February 2020.
Physiological and transcriptional response to drought stress among bioenergy grass Miscanthus species
Authors: De Vega Jose J. , Teshome Abel , Klaas Manfred , Grant Jim , Finnan John , Barth Susanne 
Published: March 2021

AbstractBackgroundMiscanthusis a commercial lignocellulosic biomass crop owing to its high biomass productivity, resilience and photosynthetic capacity at low temperature. These qualities makeMiscanthusa particularly good candidate for temperate marginal land, where yields can be limited by insufficient or excessive water supply. Differences in response to water stress have been observed amongMiscanthusspecies, which correlated to origin. In this study, we compared the physiological and molecular responses amongMiscanthusspecies under excessive (flooded) and insufficient (drought) water supply in glasshouse conditions.ResultsA significant biomass loss was observed under drought conditions in all genotypes.M. x giganteusshowed a lower reduction in biomass yield under drought conditions compared to the control than the other species. Under flooded conditions, biomass yield was as good as or better than control conditions in all species. 4389 of the 67,789 genes (6.4%) in the reference genome were differentially expressed during drought among fourMiscanthusgenotypes from different species. We observed the same biological processes were regulated acrossMiscanthusspecies during drought stress despite the DEGs being not similar. Upregulated differentially expressed genes were significantly involved in sucrose and starch metabolism, redox, and water and glycerol homeostasis and channel activity. Multiple copies of the starch metabolic enzymes BAM and waxy GBSS-I were strongly up-regulated in drought stress in allMiscanthusgenotypes, and 12 aquaporins (PIP1, PIP2 and NIP2) were also up-regulated in drought stress across genotypes.ConclusionsDifferent phenotypic responses were observed during drought stress amongMiscanthusgenotypes from different species, supporting differences in genetic adaption. The low number of DEGs and higher biomass yield in flooded conditions supportedMiscanthususe in flooded land. The molecular processes regulated during drought were shared amongMiscanthusspecies and consistent with functional categories known to be critical during drought stress in model organisms. However, differences in the regulated genes, likely associated with ploidy and heterosis, highlighted the value of exploring its diversity for breeding.
RETRACTED ARTICLE: MicroRNA-29 mediates anti-inflammatory effects and alleviation of allergic responses and symptoms in mice with allergic rhinitis
Authors: Wang Jia , Yin Jinshu , Peng Hong , Liu Aizhu 
Published: March 2021

Abstract
Background
To investigate the role of microRNA-29 (miR-29) in mice with allergic rhinitis (AR) and its underlying mechanism.

Methods
AR model was established in BALB/c mice by intraperitoneal sensitization and intranasal challenge with ovalbumin (OVA). miRNA expression was examined in the nasal mucosa tissues of mice and patients with AR, and miRNA-29 was found to be downregulated. To unveil the role of miRNA-29 in AR, it was overexpressed in the nasal mucosa of AR mice by intranasal administration of miRNA-29 agomir. The symptoms of nasal rubbing and sneezing were recorded and evaluated. miR-29 expression, OVA-specific immunoglobulin E (IgE) concentration, pro-inflammatory cytokines levels, eosinophils number, and cleaved caspase-3 and CD276 expression were examined in nasal mucosa tissues and nasal lavage fluid (NALF) by qRT-PCR, ELISA, hematoxylin and eosin staining, western blotting, or immunohistochemistry, respectively. TUNEL assay was used to analyze nasal mucosa cells apoptosis.

Results
Decreased expression of miR-29 was observed in AR, the symptoms of which were alleviated by overexpressing miR-29. In addition, overexpression of miR-29 markedly reduced the concentration of OVA-specific IgE, the levels of IL-4, IL-6, IL-10, and IFN-γ, the pathological alterations and eosinophils infiltration in the nasal mucosa. Furthermore, restoration of miR-29 expression reduced nasal mucosa cell apoptosis. Moreover, overexpression of miR-29 significantly attenuated CD276 mRNA and protein levels in nasal mucosa cells.

Conclusion
MiR-29 mediated antiallergic effects in OVA-induced AR mice by decreasing inflammatory response, probably through targeting CD276. MiRNA-29 may serve as a potential novel therapeutic target for the treatment of AR.
On a reverse Mulholland-type inequality in the whole plane with general homogeneous kernel
Authors: Luo Ricai , Yang Bicheng , Huang Xingshou 
Published: March 2021

AbstractBy using the idea of introducing parameters and weight coefficients, a new reverse discrete Mulholland-type inequality in the whole plane with general homogeneous kernel is given, which is an extension of the reverse Mulholland inequality. The equivalent forms are obtained. The equivalent statements of the best possible constant factor related to several parameters and a few applied examples are presented.
Convergence and stability of modified multi-step Noor iterative procedure with errors for strictly hemicontractive-type mappings in Banach spaces
Authors: Asaduzzaman Md. 
Published: March 2021

AbstractIn this paper, we introduce and study a modified multi-step Noor iterative procedure with errors for two Lipschitz strictly hemicontractive-type mappings in arbitrary Banach spaces and constitute its convergence and stability. The obtained results in this paper generalize and extend the corresponding result of Hussainet al.(Fixed Point Theory Appl. 2012:160, 2012) and some analogous results of several authors in the literature. Finally, a numerical example is included to illustrate our analytical results and to display the efficiency of our proposed novel iterative procedure with errors.