bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reproducibility of mass spectrometry based metabolomics data
Authors: Ghosh Tusharkanti , Philtron Daisy , Zhang Weiming , Kechris Katerina , Ghosh Debashis 
Published: September 2021

AbstractBackgroundAssessing the reproducibility of measurements is an important first step for improving the reliability of downstream analyses of high-throughput metabolomics experiments. We define a metabolite to be reproducible when it demonstrates consistency across replicate experiments. Similarly, metabolites which are not consistent across replicates can be labeled as irreproducible. In this work, we introduce and evaluate the use (Ma)ximum (R)ank (R)eproducibility (MaRR) to examine reproducibility in mass spectrometry-based metabolomics experiments. We examine reproducibility across technical or biological samples in three different mass spectrometry metabolomics (MS-Metabolomics) data sets.ResultsWe apply MaRR, a nonparametric approach that detects the change from reproducible to irreproducible signals using a maximal rank statistic. The advantage of using MaRR over model-based methods that it does not make parametric assumptions on the underlying distributions or dependence structures of reproducible metabolites. Using three MS Metabolomics data sets generated in the multi-center Genetic Epidemiology of Chronic Obstructive Pulmonary Disease (COPD) study, we applied the MaRR procedure after data processing to explore reproducibility across technical or biological samples. Under realistic settings of MS-Metabolomics data, the MaRR procedure effectively controls the False Discovery Rate (FDR) when there was a gradual reduction in correlation between replicate pairs for less highly ranked signals. Simulation studies also show that the MaRR procedure tends to have high power for detecting reproducible metabolites in most situations except for smaller values of proportion of reproducible metabolites. Bias (i.e., the difference between the estimated and the true value of reproducible signal proportions) values for simulations are also close to zero. The results reported from the real data show a higher level of reproducibility for technical replicates compared to biological replicates across all the three different datasets. In summary, we demonstrate that the MaRR procedure application can be adapted to various experimental designs, and that the nonparametric approach performs consistently well.ConclusionsThis research was motivated by reproducibility, which has proven to be a major obstacle in the use of genomic findings to advance clinical practice. In this paper, we developed a data-driven approach to assess the reproducibility of MS-Metabolomics data sets. The methods described in this paper are implemented in the open-source R packagemarr, which is freely available from Bioconductor athttp://bioconductor.org/packages/marr.
Multivariate analysis of morphology, behaviour, growth and developmental timing in hybrids brings new insights into the divergence of sympatric Arctic charr morphs
Authors: Horta-Lacueva Quentin J.-B. , Snorrason Sigurður S. , Morrissey Michael B. , Leblanc Camille A.-L. , Kapralova Kalina H. 
Published: September 2021

AbstractBackgroundStudying the development of fitness related traits in hybrids from populations diverging in sympatry is a fundamental approach to understand the processes of speciation. However, such traits are often affected by covariance structures that complicate the comprehension of these processes, especially because the interactive relationships between traits of different nature (e.g. morphology, behaviour, life-history) remain largely unknown in this context. In a common garden setup, we conducted an extensive examination of a large suit of traits putatively involved in the divergence of two morphs of Arctic charr (Salvelinus alpinus), and investigated the consequences of potential patterns of trait covariance on the phenotype of their hybrids. These traits were measured along ontogeny and involved growth, yolk sac resorption, developmental timing (hatching and the onset of exogeneous feeding), head morphology and feeding behaviour.ResultsGrowth trajectories provided the strongest signal of phenotypic divergence between the two charr. Strikingly, the first-generation hybrids did not show intermediate nor delayed growth but were similar to the smallest morph, suggesting parental biases in the inheritance of growth patterns. However, we did not observe extensive multivariate trait differences between the two morphs and their hybrids. Growth was linked to head morphology (suggesting that morphological variations in early juveniles relate to simple allometric effects) but this was the only strong signal of covariance observed between all the measured traits. Furthermore, we did not report evidence for differences in overall phenotypic variance between morphs, nor for enhanced phenotypic variability in their hybrids.ConclusionOur study shed light on the multivariate aspect of development in a context of adaptive divergence. The lack of evidence for the integration of most traits into a single covariance structure suggested that phenotypic constraints may not always favour nor impede divergence toward ecological niches differing in numerous physical and ecological variables, as observed in the respective habitats of the two charr. Likewise, the role of hybridization as a disruptive agent of trait covariance may not necessarily be significant in the evolution of populations undergoing resource polymorphism.
The chloroplast genome of Amygdalus L. (Rosaceae) reveals the phylogenetic relationship and divergence time
Authors: Du Zhongyu , Lu Ke , Zhang Kai , He Yiming , Wang Haitao , Chai Guaiqiang , Shi Jianguo , Duan Yizhong 
Published: September 2021

AbstractBackgroundLimited access to genetic information has greatly hindered our understanding of the molecular evolution, phylogeny, and differentiation time of subg.Amygdalus. This study reported complete chloroplast (cp) genome sequences of subg.Amygdalus, which further enriched the available valuable resources of complete cp genomes of higher plants and deepened our understanding of the divergence time and phylogenetic relationships of subg.Amygdalus.ResultsThe results showed that subg.Amygdalusspecies exhibited a tetrad structure with sizes ranging from 157,736 bp (P. kansuensis) to 158,971 bp (P. davidiana), a pair of inverted repeat regions (IRa/IRb) that ranged from 26,137–26,467 bp, a large single-copy region that ranged from 85,757–86,608 bp, and a small single-copy region that ranged from 19,020–19,133 bp. The average GC content of the complete cp genomes in the 12 species was 36.80%. We found that the structure of the subg.Amygdaluscomplete cp genomes was highly conserved, and the 12 subg.Amygdalusspecies had anrps19 pseudogene. There was not rearrangement of the complete cp genome in the 12 subg.Amygdalusspecies. All 12 subg.Amygdalusspecies clustered into one clade based on both Bayesian inference and maximum likelihood. The divergence time analyses based on the complete cp genome sequences showed that subg.Amygdalusspecies diverged approximately 15.65 Mya.ConclusionOur results provide data on the genomic structure of subg.Amygdalusand elucidates their phylogenetic relationships and divergence time.
Genome-wide analysis of OSCA gene family members in Vigna radiata and their involvement in the osmotic response
Authors: Yin Lili , Zhang Meiling , Wu Ruigang , Chen Xiaoliang , Liu Fei , Xing Baolong 
Published: September 2021

Abstract
Background
Mung bean (Vigna radiata) is a warm-season legume crop and belongs to the papilionoid subfamily of the Fabaceae family. China is the leading producer of mung bean in the world. Mung bean has significant economic and health benefits and is a promising species with broad adaptation ability and high tolerance to environmental stresses. OSCA (hyperosmolality-gated calcium-permeable channel) gene family members play an important role in the modulation of hypertonic stress, such as drought and salinity. However, genome-wide analysis of the OSCA gene family has not been conducted in mung bean.

Results
We identified a total of 13 OSCA genes in the mung bean genome and named them according to their homology with AtOSCAs. All the OSCAs were phylogenetically split into four clades. Phylogenetic relationship and synteny analyses showed that the VrOSCAs in mung bean and soybean shared a relatively conserved evolutionary history. In addition, three duplicated VrOSCA gene pairs were identified, and the duplicated VrOSCAs gene pairs mainly underwent purifying selection pressure during evolution. Protein domain, motif and transmembrane analyses indicated that most of the VrOSCAs shared similar structures with their homologs. The expression pattern showed that except for VrOSCA2.1, the other 12 VrOSCAs were upregulated under treatment with ABA, PEG and NaCl, among which VrOSCA1.4 showed the largest increased expression levels. The duplicated genes VrOSCA2.1/VrOSCA2.2 showed divergent expression, which might have resulted in functionalization during subsequent evolution. The expression profiles under ABA, PEG and NaCl stress revealed a functional divergence of VrOSCA genes, which agreed with the analysis of cis-acting regulatory elements in the promoter regions of VrOSCA genes.

Conclusions
Collectively, the study provided a systematic analysis of the VrOSCA gene family in mung bean. Our results establish an important foundation for functional and evolutionary analysis of VrOSCAs and identify genes for further investigation of their ability to confer abiotic stress tolerance in mung bean.
High flow versus conventional nasal cannula for oxygenation and ventilation maintenance during surgery with intravenous deep sedation by propofol: a randomized controlled study
Authors: Vijitpavan Amorn , Kooncharoensuk Yanin 
Published: September 2021

Abstract
Background
The dead space washout and provision of some level of positive airway pressure by nasal high-flow (NHF) cannula could improve the efficiency of ventilation, oxygenation and maintenance of the upper airway in patients undergoing deep sedation. This study aimed to compare the incidences of events represented oxygenation and ventilation, i.e. desaturation and upper airway obstruction, and arterial blood gas (ABG) levels between using NHF cannula and conventional nasal cannula (NC2) during deep sedation of adult surgical patients.

Methods
In this prospective randomized single-blinded study, the patients who were 20–80 years old, ASA physical status of 1 to 3, scheduled for surgery under intravenous sedation (IVS) were included. The patients were randomly divided into two groups, i.e., NC2 or NHF groups. Propofol infusion was given to maintain deep sedation. The desaturation (SpO2 < 92%) and upper airway obstruction events (presence of snoring with paradoxical breathing) after application of NC2 or NHF were observed and collected. Other outcomes included interventions during IVS, such as jaw lifting or airway instrument insertion, mouth dryness, and post- ABG analyses were also collected and compared.

Results
Thirty-six patients undergoing endovascular surgery were randomized into NC2 or NHF groups (18 in each group). No patients dropped out of the study. There were no significant differences in age, sex, ASA physical status, pre-sedation and pre-application of NC2 and NHF ABG analyses (PaO2, SaO2, pH, PaCO2, and PaO2/FiO2). NHF group had significantly lower in the incidence of desaturation [5 (27.78%) vs 13 (72.22%), p = 0.008], upper airway obstruction [4 (22.22%) vs 13 (72.22%), p = 0.003], and airway maneuver [6 (33.33%) vs 13 (72.22%), p = 0.019] than NC2 group. There were no differences in the ABG analyses after oxygen supplementation and no significant differences in mouth dryness between groups.

Conclusion
The use of NHF cannula in patients undergoing endovascular surgery under deep sedation reduced desaturation events and required fewer airway interventions than NC2 with no difference in arterial blood gas analyses and mouth dryness.
Psychometric evaluation of the postpartum specific anxiety scale in an Iranian population (PSAS-IR)
Authors: Hasanzadeh Robab , Jafarabadi Mohammad Asghari , Hasanpour Shirin , Fallon Victoria , Silverio Sergio A. , Montazeri Reyhane , Mirghafourvand Mojgan 
Published: September 2021

Abstract
Background
Anxiety is one of the most prevalent mental health disorders among mothers during the postpartum period, which can lead to maternal and infant physical and psychological consequences. The Postpartum Specific Anxiety Scale (PSAS) predicts unique variance in postnatal outcomes over and above general anxiety tools. It has never been used in Iran and its validity and reliability have not been assessed either. Therefore, the present study aimed to translate and investigate the psychometric properties of the PSAS-IR.

Methods
510 women, from six weeks to six months postpartum, were selected through random sampling in 2020. After forward and back-translation, the face validity, content validity, and construct validity of PSAS (through confirmatory factor analysis) were examined. The reliability of the scale was assessed using both internal consistency (Cronbach’s alpha) and test-retest stability methods.

Results
CVI and CVR values of the PSAS tool were 0.89 and 0.88, respectively. The good fit indices confirmed the validity of four-factor structure. Cronbach’s alpha coefficient and Intra Correlation Coefficient (ICC) equaled 0.93 and 0.92, respectively.

Conclusion
The Persian version of PSAS is a valid and reliable four-factor scale, it will improve the measurement of postpartum anxiety in an Iranian setting. This will improve the measurement of postpartum anxiety in an Iranian setting.
Postpartum dietary and physical activity-related beliefs and behaviors among women with recent gestational diabetes mellitus: a qualitative study from Singapore
Authors: Teh Kailin , Quek Imm Pin , Tang Wern Ee 
Published: September 2021

Abstract
Background
A woman with a history of GDM has at least seven-fold increased lifetime risk of developing type 2 diabetes mellitus (T2DM), compared to women who have normoglycemic pregnancies. Postpartum lifestyle modification has been shown to reduce postpartum weight retention and prevent the progression to T2DM. The aim of this study was to explore the postpartum dietary and physical activity-related beliefs and behaviors among women in Singapore who had GDM in their most recent pregnancies.

Methods
Semi-structured in-depth interviews were conducted with 14 women, who were up to four months postpartum and had GDM in their most recent pregnancies. Interview data were analyzed using thematic analysis.

Results
Three themes were identified in the analysis: (1) risk perception and knowledge regarding future diabetes, (2) suboptimal diet and physical activity after delivery and (3) factors influencing the postpartum lifestyle.

Conclusions
The study findings provided useful information on the postpartum lifestyle beliefs and behaviors among women with a history of GDM. Most participants had low risk perception of future diabetes and their diet and physical activity after delivery were suboptimal due to various influences. These insights can be used to design tailored materials and programs to support women who have had GDM reduce their risk of developing future T2DM.
The role of education on Cancer amenable mortality among non-Hispanic blacks & non-Hispanic whites in the United States (1989–2018)
Authors: Barcelo Alberto , Duffett-Leger Linda , Pastor-Valero Maria , Pereira Juliana , Colugnati Fernando A. B. , Trapido Edward 
Published: September 2021

Abstract
Background
Cancer mortality in the U.S. has fallen in recent decades; however, individuals with lower levels of education experienced a smaller decline than more highly educated individuals. This analysis aimed to measure the influence of education lower than a high school diploma, on cancer amenable mortality among Non-Hispanic Whites (NHW) and Non-Hispanic Blacks (NHB) in the U.S. from 1989 to 2018.

Methods
We analyzed data from 8.2 million death certificates of men and women who died from cancer between 1989 and 2018. We examined 5-year and calendar period intervals, as well as annual percent changes (APC). APC was adjusted for each combination of sex, educational level, and race categories (8 models) to separate the general trend from the effects of age.

Results
Our study demonstrated an increasing mortality gap between the least and the most educated NHW and NHB males and females who died from all cancers combined and for most other cancer types included in this study. The gap between the least and the most educated was broader among NHW males and females than among NHB males and females, respectively, for most malignancies.

Conclusions
In summary, we reported an increasing gap in the age-adjusted cancer mortality among the most and the least educated NHW and NHB between 25 and 74 years of age. We demonstrated that although NHB exhibited the greatest age-adjusted mortality rates for most cancer locations, the gap between the most and the least educated was shown for NHW.
Topical gel based nanoparticles for the controlled release of oleanolic acid: design and in vivo characterization of a cubic liquid crystalline anti-inflammatory drug
Authors: Shi Zhiqi , Pan Shugang , Wang Luolin , Li Sha 
Published: September 2021

Abstract
Background
Oleanolic acid (OA) has multiple pharmaceutical applications including anti-inflammatory activity, but low permeability of the molecule limits its widespread use.

Methods
A cubic liquid crystalline nanoparticle (LCNP)-based gel was prepared as a potential topical delivery system for OA. The LCNP-based gel was optimized using rheological, drug release kinetic, and ex vivo permeation studies.

Results
The studies showed that the OA was trapped in the interior of the LCNP with a crystal form of Pn3m space. The optimized LCNP formulation performed well using in vitro release studies for up to 12 h (85.49 ± 0.21%). Ex vivo permeation studies showed that the LCNP-based gel formulation was superior to a standard gel formulation. The r2 value from the Peppas equation indicated good linearity, but showed irregular (non-Fickian) diffusion, suggesting that drug release was controlled by multiple processes.

Conclusions
In this study, OA-loaded LCNPs were prepared by the precursor method, resulting in a well-characterized OA-LCNP gel preparation. The gel was shown to be effective in a rodent carrageenan-induced hind paw inflammation model with sustained efficacy after a single application.
Patient participation in cancer network governance: a six-year case study
Authors: Tremblay Dominique , Touati Nassera , Usher Susan , Bilodeau Karine , Pomey Marie-Pascale , Lévesque Lise 
Published: September 2021

Abstract
Background
Patient participation in decision-making has become a hallmark of responsive healthcare systems. Cancer networks in many countries have committed to involving people living with and beyond cancer (PLC) at multiple levels. However, PLC participation in network governance remains highly variable for reasons that are poorly understood. This study aims to share lessons learned regarding mechanisms that enable PLC participation in cancer network governance.

Methods
This multiple case study, using a qualitative approach in a natural setting, was conducted over six years in three local cancer networks within the larger national cancer network in Quebec (Canada), where PLC participation is prescribed by the Cancer Directorate. Data were collected from multiple sources, including individual and focus group interviews (n = 89) with policymakers, managers, clinicians and PLC involved in national and local cancer governance committees. These data were triangulated and iteratively analysed according to a framework based on functions of collaborative governance in the network context.

Results
We identify three main mechanisms that enable PLC participation in cancer network governance: (1) consistent emphasis on patient-centred care as a network objective; (2) flexibility, time and support to translate mandated PLC representation into meaningful participation; and (3) recognition of the distinct knowledge of PLC in decision-making. The shared vision of person-centred care facilitates PLC participation. The quality of participation improves through changes in how committee meetings are conducted, and through the establishment of a national committee where PLC can pool their experience, develop skills and establish a common voice on priority issues. PLC knowledge is especially valued around particular challenges such as designing integrated care trajectories and overcoming barriers to accessing care. These three mechanisms interact to enable PLC participation in governance and are activated to varying extents in each local network.

Conclusions
This study reveals that mandating PLC representation on governance structures is a powerful context element enabling participation, but that it also delineates which governance functions are open to influence from PLC participation. While the activation of mechanisms is context dependent, the insights from this study in Quebec are transferable to cancer networks in other jurisdictions seeking to embed PLC participation in decision-making.