bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interaction between particle size and mixing ratio on porosity and properties of tea oil camellia (Camellia oleifera Abel.) shells-based particleboard
Authors: Choupani Chaydarreh Kamran , Lin Xiuyi , Guan Litao , Hu Chuanshuang 
Published: July 2022

AbstractThis study investigated the interaction between particle size and mixing ratio on the porosity of particleboard and in consequence its effect on the physical and mechanical properties of panels. Tea Oil Camellia Shell (TOCS), which could provide 1.8 million tons of lignocellulose raw material annually, can be a useful resource for particleboard production. In that regard, particleboards with different particle sizes (coarse and fine) and mixing ratios (wood and TOCS) bonded with Polymethylene polyphenyl polyisocyanate (pMDI) were investigated. The results showed that particleboard made with TOCS particles had higher densities than those of commercial wood particles. Furthermore, particleboards made with fine particles had lower porosity. The average values for physical and mechanical properties have shown that except for thickness swelling (TS), most properties were better with coarse particles. In terms of all properties, results showed that adding 50% of commercial wood in conjunction with TOCS particles regardless of particle size can offer acceptable results, which qualified all requirements of EN 312:2010 standard for P2-type particleboard (boards for interior fitments (including furniture) for use in dry conditions). In addition, due to the porous structure of the shells, TOCS-based particleboards have better thermal conductivity compared to wood-based particleboards.
orsum: a Python package for filtering and comparing enrichment analyses using a simple principle
Authors: Ozisik Ozan , Térézol Morgane , Baudot Anaïs 
Published: July 2022

Abstract
Background
Enrichment analyses are widely applied to investigate lists of genes of interest. However, such analyses often result in long lists of annotation terms with high redundancy, making the interpretation and reporting difficult. Long annotation lists and redundancy also complicate the comparison of results obtained from different enrichment analyses. An approach to overcome these issues is using down-sized annotation collections composed of non-redundant terms. However, down-sized collections are generic and the level of detail may not fit the user’s study. Other available approaches include clustering and filtering tools, which are based on similarity measures and thresholds that can be complicated to comprehend and set.

Result
We propose orsum, a Python package to filter enrichment results. orsum can filter multiple enrichment results collectively and highlight common and specific annotation terms. Filtering in orsum is based on a simple principle: a term is discarded if there is a more significant term that annotates at least the same genes; the remaining more significant term becomes the representative term for the discarded term. This principle ensures that the main biological information is preserved in the filtered results while reducing redundancy. In addition, as the representative terms are selected from the original enrichment results, orsum outputs filtered terms tailored to the study. As a use case, we applied orsum to the enrichment analyses of four lists of genes, each associated with a neurodegenerative disease.

Conclusion
orsum provides a comprehensible and effective way of filtering and comparing enrichment results. It is available at https://anaconda.org/bioconda/orsum.
EpiVisR: exploratory data analysis and visualization in epigenome-wide association analyses
Authors: Röder Stefan , Herberth Gunda , Zenclussen Ana C. , Bauer Mario 
Published: July 2022

AbstractBackgroundWith the widespread availability of microarray technology for epigenetic research, methods for calling differentially methylated probes or differentially methylated regions have become effective tools to analyze this type of data. Furthermore, visualization is usually employed for quality check of results and for further insights. Expert knowledge is required to leverage capabilities of these methods. To overcome this limitation and make visualization in epigenetic research available to the public, we designed EpiVisR.ResultsThe EpiVisR tool allows to select and visualize combinations of traits (i.e., concentrations of chemical compounds) and differentially methylated probes/regions. It supports various modes of enriched presentation to get the most knowledge out of existing data: (1) enriched Manhattan plot and enriched volcano plot for selection of probes, (2) trait-methylation plot for visualization of selected trait values against methylation values, (3) methylation profile plot for visualization of a selected range of probes against selected trait values as well as, (4) correlation profile plot for selection and visualization of further probes that are correlated to the selected probe. EpiVisR additionally allows exporting selected data to external tools for tasks such as network analysis.ConclusionThe key advantage of EpiVisR is the annotation of data in the enriched plots (and tied tables) as well as linking to external data sources for further integrated data analysis. Using the EpiVisR approach will allow users to integrate data from traits with epigenetic analyses that are connected by belonging to the same individuals. Merging data from various data sources among the same cohort and visualizing them will enable users to gain more insights from existing data.
Induction of iPSC-derived Prg4-positive cells with characteristics of superficial zone chondrocytes and fibroblast-like synovial cells
Authors: Satake Takashi , Komura Shingo , Aoki Hitomi , Hirakawa Akihiro , Imai Yuuki , Akiyama Haruhiko 
Published: July 2022

Abstract
Background
Lubricin, a proteoglycan encoded by the PRG4 gene, is synthesised by superficial zone (SFZ) chondrocytes and synovial cells. It reduces friction between joints and allows smooth sliding of tendons. Although lubricin has been shown to be effective against osteoarthritis and synovitis in animals, its clinical application remains untested. In this study, we aimed to induce lubricin-expressing cells from pluripotent stem cells (iPSCs) and applied them locally via cell transplantation.

Methods
To generate iPSCs, OCT3/4, SOX2, KLF4, and L-MYC were transduced into fibroblasts derived from Prg4-mRFP1 transgenic mice. We established a protocol for the differentiation of iPSC-derived Prg4-mRFP1-positive cells and characterised their mRNA expression profile. Finally, we injected Prg4-mRFP1-positive cells into the paratenon, surrounding the Achilles tendons and knee joints of severe combined immunodeficient mice and assessed lubricin expression.

Result
Wnt3a, activin A, TGF-β1, and bFGF were applied to induce the differentiation of iPSC-derived Prg4-mRFP1-positive cells. Markers related to SFZ chondrocytes and fibroblast-like synovial cells (FLSs) were expressed during differentiation. RNA-sequencing indicated that iPSC-derived Prg4-mRFP1-positive cells manifested expression profiles typical of SFZ chondrocytes and FLSs. Transplanted iPSC-derived Prg4-mRFP1-positive cells survived around the Achilles tendons and in knee joints.

Conclusions
The present study describes a protocol for the differentiation of iPSC-derived Prg4-positive cells with characteristics of SFZ chondrocytes and FLSs. Transplantation of lubricin-expressing cells offers promise as a therapy against arthritis and synovitis.
Revised eutherian gene collections
Authors: Premzl Marko 
Published: July 2022

Abstract
Objectives
The most recent research projects in scientific field of eutherian comparative genomics included intentions to sequence every extant eutherian species genome in foreseeable future, so that future revisions and updates of eutherian gene data sets were expected.

Data description
Using 35 public eutherian reference genomic sequence assemblies and free available software, the eutherian comparative genomic analysis protocol RRID:SCR_014401 was published as guidance against potential genomic sequence errors. The protocol curated 14 eutherian third-party data gene data sets, including, in aggregate, 2615 complete coding sequences that were deposited in European Nucleotide Archive. The published eutherian gene collections were used in revisions and updates of eutherian gene data set classifications and nomenclatures that included gene annotations, phylogenetic analyses and protein molecular evolution analyses.
The flax genome reveals orbitide diversity
Authors: Song Ziliang , Burbridge Connor , Schneider David J. , Sharbel Timothy F. , Reaney Martin J. T. 
Published: July 2022

Abstract
Background
Ribosomally-synthesized cyclic peptides are widely found in plants and exhibit useful bioactivities for humans. The identification of cyclic peptide sequences and their precursor proteins is facilitated by the growing number of sequenced genomes. While previous research largely focused on the chemical diversity of these peptides across various species, there is little attention to a broader range of potential peptides that are not chemically identified.

Results
A pioneering study was initiated to explore the genetic diversity of linusorbs, a group of cyclic peptides uniquely occurring in cultivated flax (Linum usitatissimum). Phylogenetic analysis clustered the 5 known linusorb precursor proteins into two clades and one singleton. Preliminary tBLASTn search of the published flax genome using the whole protein sequence as query could only retrieve its homologues within the same clade. This limitation was overcome using a profile-based mining strategy. After genome reannotation, a hidden Markov Model (HMM)-based approach identified 58 repeats homologous to the linusorb-embedded repeats in 8 novel proteins, implying that they share common ancestry with the linusorb-embedded repeats. Subsequently, we developed a customized profile composed of a random linusorb-like domain (LLD) flanked by 5 conserved sites and used it for string search of the proteome, which extracted 281 LLD-containing repeats (LLDRs) in 25 proteins. Comparative analysis of different repeat categories suggested that the 5 conserved flanking sites among the non-homologous repeats have undergone convergent evolution driven by functional selection.

Conclusions
The profile-based mining approach is suitable for analyzing repetitive sequences. The 25 LLDR proteins identified herein represent the potential diversity of cyclic peptides within the flax genome and lay a foundation for further studies on the functions and evolution of these protein tandem repeats.
Multiple-trait analyses improved the accuracy of genomic prediction and the power of genome-wide association of productivity and climate change-adaptive traits in lodgepole pine
Authors: Cappa Eduardo P. , Chen Charles , Klutsch Jennifer G. , Sebastian-Azcona Jaime , Ratcliffe Blaise , Wei Xiaojing , Da Ros Letitia , Ullah Aziz , Liu Yang , Benowicz Andy , Sadoway Shane , Mansfield Shawn D. , Erbilgin Nadir , Thomas Barb R. , El-Kassaby Yousry A. 
Published: July 2022

Abstract
Background
Genomic prediction (GP) and genome-wide association (GWA) analyses are currently being employed to accelerate breeding cycles and to identify alleles or genomic regions of complex traits in forest trees species. Here, 1490 interior lodgepole pine (Pinus contorta Dougl. ex. Loud. var. latifolia Engelm) trees from four open-pollinated progeny trials were genotyped with 25,099 SNPs, and phenotyped for 15 growth, wood quality, pest resistance, drought tolerance, and defense chemical (monoterpenes) traits. The main objectives of this study were to: (1) identify genetic markers associated with these traits and determine their genetic architecture, and to compare the marker detected by single- (ST) and multiple-trait (MT) GWA models; (2) evaluate and compare the accuracy and control of bias of the genomic predictions for these traits underlying different ST and MT parametric and non-parametric GP methods. GWA, ST and MT analyses were compared using a linear transformation of genomic breeding values from the respective genomic best linear unbiased prediction (GBLUP) model. GP, ST and MT parametric and non-parametric (Reproducing Kernel Hilbert Spaces, RKHS) models were compared in terms of prediction accuracy (PA) and control of bias.

Results
MT-GWA analyses identified more significant associations than ST. Some SNPs showed potential pleiotropic effects. Averaging across traits, PA from the studied ST-GP models did not differ significantly from each other, with generally a slight superiority of the RKHS method. MT-GP models showed significantly higher PA (and lower bias) than the ST models, being generally the PA (bias) of the RKHS approach significantly higher (lower) than the GBLUP.

Conclusions
The power of GWA and the accuracy of GP were improved when MT models were used in this lodgepole pine population. Given the number of GP and GWA models fitted and the traits assessed across four progeny trials, this work has produced the most comprehensive empirical genomic study across any lodgepole pine population to date.
Genome-wide analysis and identification of the PEBP genes of Brassica juncea var. Tumida
Authors: He Jing , Gu Linxin , Tan Quanqin , Wang Yu , Hui Fanfan , He Xiaohong , Chang Pingan , Gong Daping , Sun Quan 
Published: July 2022

Abstract
Background
Phosphatidylethanolamine-binding protein (PEBP) is widely present in animals, plants, and microorganisms. Plant PEBP genes are mainly involved in flowering transition and nutritional growth. These genes have been studied in several plants; however, to the best of our knowledge, no studies have explored them in Brassica juncea var. tumida. This study identified and characterized the entire PEBP gene family of Brassica juncea var. tumida.

Results
A total of 21 PEBP genes were identified from Brassica juncea var. tumida. Through phylogenetic analysis, the 21 corresponding proteins were classified into the following four clusters: TERMINAL FLOWER 1 (TFL1)-like proteins (n = 8), MOTHER OF FT AND TFL1 (MFT)-like proteins (n = 5), FLOWERING LOCUS T (FT)-like proteins (n = 6), and ybhB-like proteins (n = 2). A total of 18 genes contained four exons and had similar gene structures in each subfamily except BjMFT1, BjPYBHB1, and Arabidopsis thaliana CENTRORADIALIS homolog of Brassica juncea var. tumida (BjATC1). In the analysis of conserved motif composition, the BjPEBP genes exhibited similar characteristics, except for BjFT3, BjMFT1, BjPYBHB1, BjPYBHB2, and BjATC1. The BjPEBP promoter includes multiple cis-acting elements such as the G-box and I-box elements that respond to light, ABRE and GARE-motif elements that respond to hormones, and MBSI and CAT-box elements that are associated with plant growth and development. Analysis of RNA-Seq data revealed that the expression of a few BjPEBP genes may be associated with the development of a tumorous stem. The results of qRT–PCR showed that BjTFL1 and BjPYBHB1 were highly expressed in the flower tissue, BjFT1 and BjATC1 were mainly expressed in the root, and BjMFT4 were highly detected in the stem. The results of yeast two-hybrid screening suggested that BjFT interacts with Bj14-3-3. These results indicate that BjFT is involved in flowering regulation.

Conclusions
To the best of our knowledge, this study is the first to perform a genome-wide analysis of PEBP genes family in Brassica juncea var. tumida. The findings of this study may help improve the yield and molecular breeding of Brassica juncea var. tumida.
Genome characteristics of clinical Salmonella enterica population from a state public health laboratory, New Hampshire, USA, 2017–2020
Authors: Turcotte Madison R. , Smith Joshua T. , Li Jinfeng , Zhang Xinglu , Wolfe Kristin L. , Gao Fengxiang , Benton Christopher S. , Andam Cheryl P. 
Published: July 2022

Abstract
Background
The implementation of whole genome sequencing (WGS) by PulseNet, the molecular subtyping network for foodborne diseases, has transformed surveillance, outbreak detection, and public health laboratory practices in the United States. In 2017, the New Hampshire Public Health Laboratories, a member of PulseNet, commenced the use of WGS in tracking foodborne pathogens across the state. We present some of the initial results of New Hampshire’s initiative to transition to WGS in tracking Salmonella enterica, a bacterial pathogen that is responsible for non-typhoidal foodborne infections and enteric fever. We characterize the population structure and evolutionary history of 394 genomes of isolates recovered from human clinical cases in New Hampshire from 2017 to 2020.

Results
The New Hampshire S. enterica population is phylogenetically diverse, consisting of 78 sequence types (ST) and 67 serotypes. Six lineages dominate the population: ST 11 serotype Enteritidis, ST 19 Typhimurium, ST 32 Infantis, ST 118 Newport, ST 22 Braenderup, and ST 26 Thompson. Each lineage is derived from long ancestral branches in the phylogeny, suggesting their extended presence in the region and recent clonal expansion. We detected 61 genes associated with resistance to 14 antimicrobial classes. Of these, unique genes of five antimicrobial classes (aminocoumarins, aminoglycosides, fluoroquinolones, nitroimidazoles, and peptides) were detected in all genomes. Rather than a single clone carrying multiple resistance genes expanding in the state, we found multiple lineages carrying different combinations of independently acquired resistance determinants. We estimate the time to the most recent common ancestor of the predominant lineage ST 11 serotype Enteritidis (126 genomes) to be 1965 (95% highest posterior density intervals: 1927–1982). Its population size expanded until 1978, followed by a population decline until 1990. This lineage has been expanding since then. Comparison with genomes from other states reveal lack of geographical clustering indicative of long-distance dissemination.

Conclusions
WGS studies of standing pathogen diversity provide critical insights into the population and evolutionary dynamics of lineages and antimicrobial resistance, which can be translated to effective public health action and decision-making. We highlight the need to strengthen efforts to implement WGS-based surveillance and genomic data analyses in state public health laboratories.
Arbuscular mycorrhizal fungi reduce potassium, cadmium and ammonium losses but increases nitrate loss under high intensity leaching events
Authors: Xiao Yan , Chen Lu 
Published: July 2022

AbstractBackgroundNutrients and heavy metals can be lost from soilsvialeaching, and arbuscular mycorrhizal fungi (AMF) can influence these events. Soil column experiments were carried out to examine whether leaching intensity and AMF can alter nutrient and Cd uptake in white clover plants and the extent of their losses through leaching.ResultsThe presence of AMF significantly increased shoot and total biomass, as well as increased N, P, Cu and Zn uptake independent of water amount applied; while root P and Cu uptakes were promoted by AMF at any water amount treatments. Higher water amounts led to reductions in total N, K and Zn uptake for AMF-colonized plants in comparison to moderate water amount treatments. In the absence of AMF, white clover at low water amount treatment exhibited maximal root Cd uptake. At high water amount treatments, the presence of AMF significantly decreased leachate volumes and the amount of leached NH4+, K and Cd while AMF significantly increased the amounts of leached NO3−.ConclusionsOverall we found that AMF-colonized white clover plants reduced NH4+, K and Cd loss from soils but increased the risk of NO3−loss under high intensity leaching conditions.
Efficacy of intravascular imaging-guided drug-eluting stent implantation: a systematic review and meta-analysis of randomized clinical trials
Authors: Niu Ying , Bai Nan , Ma Ying , Zhong Peng-Yu , Shang Yao-Sheng , Wang Zhi-Lu 
Published: July 2022

Abstract
Background
Traditional angiography only displays two-dimensional images of the coronary arteries during stent implantation. However, intravascular imaging can show the structure of the vascular wall, plaque characteristics. This article aims to evaluate the efficacy of intravascular imaging-guided drug-eluting stent (DES) implantation.

Method
We conducted a systematic review and meta-analysis of randomized controlled trials of intravascular imaging-guided, including patients with DES implantation guided by intravascular ultrasound or optical coherence tomography and traditional angiography. The databases of PubMed, EMBASE, web of science, and Cochrane Library were searched. The primary outcome was target lesion revascularization (TLR). The secondary outcomes included the target vessel revascularization (TVR), myocardial infarction (MI), stent thrombosis (ST), cardiac death, all-cause death, and the major adverse cardiac events (MACE) during the 6–24 months follow-up. The fixed-effects model was used to calculate the relative risk (RR) and 95% confidence interval of the outcome event. Meanwhile, the trial sequence analysis was employed to evaluate the results.

Result
This meta-analysis included fourteen randomized controlled trials with 7307 patients. Compared with angiography-guided, intravascular imaging-guided DES implantation can significantly reduce the risk of TLR (RR 0.63, 0.49–0.82, P = 0.0004), TVR (RR 0.66, 0.52–0.85, P = 0.001), cardiac death (RR 0.58; 0.38–0.89; P = 0.01), MACE (RR 0.67, 0.57–0.79; P < 0.00001) and ST (RR 0.43, 0.24–0.78; P = 0.005). While there was no significant difference regarding MI (RR 0.77, 0.57–1.05, P = 0.10) and all-cause death (RR 0.87, 0.58–1.30, P = 0.50).

Conclusions
Compared with angiography, intravascular imaging-guided DES implantation is associated with better clinical outcomes in patients with coronary artery disease, especially complex lesions (Registered by PROSPERO, CRD 42021289205).
Nebulized budesonide combined with systemic corticosteroid vs systemic corticosteroid alone in acute severe asthma managed in the emergency department: a randomized controlled trial
Authors: Marghli Soudani , Bouhamed Chafiaa , Sghaier Amira , Chebbi Nabil , Dlala Insaf , Bettout Samia , Belkacem Achref , Kbaier Sarra , Jerbi Nahla , Bellou Abdelouahab 
Published: July 2022

Abstract
Background
The additive benefit of inhaled corticosteroid when used with systemic corticosteroid in acute asthma is still unclear. The objective of this study was to assess the effect of high and repeated doses of inhaled budesonide when combined with the standard treatment of adult acute asthma.

Methods
It was a prospective double-blind randomized controlled study performed in the emergency department (ED) from May 1, 2010 to February 28, 2011 (ClinicalTrials.gov, NCT04016220). Fifty patients were included and were randomized to receive intravenous hydrocortisone hemisuccinate in association with nebulized budesonide (n = 23, budesonide group) or normal saline (n = 27, control group). Nebulization of budesonide or saline was done in combination with 5 mg of terbutaline every 20 min the first hour, then at 2 h (H2), and 3 h (H3). All patients received standard treatment. Efficacy and safety of inhaled budesonide were evaluated every 30 min for 180 min.

Results
A significant increase in peak expiratory flow (PEF) was observed in both treatment groups at evaluation times. The increase in PEF persisted significantly compared to the previous measurement in both groups. There was no significant difference in the PEF between the two groups at evaluation times. There was no significant difference between the two groups in the evolution in the respiratory rate and heart rate. There was also no statistically significant difference between the two groups in the rate of hospitalization, the discharge criteria before the end of the protocol.

Conclusions
Considering its limited power, our study suggests that the association of nebulized budesonide with hydrocortisone hemisuccinate has no additional effect over the use of hydrocortisone alone in adults’ acute asthma managed in the ED.