bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validity of a New Prediction Model to Identify Patients at Risk for Obstructive Sleep Apnea Hypopnea Syndrome
Authors: Tawaranurak Krongthong , Kamolphiwong Sinchai , Sae-wong Suthon , Vasupongayya Sangsuree , Kamolphiwong Thossaporn , Bumrungsena Chuanchom , Chaiyarukjirakun Varaned 
Published: January 2021

Objectives: To develop and validate a new clinical prediction model for screening patients at risk for obstructive sleep apnea–hypopnea syndrome (OSAHS). Methods: This study used 2 data sets to develop and validate the model. To build the model, the first data set comprised 892 patients who had diagnostic polysomnography (PSG); data were assessed by multivariate logistic regression analysis. To validate the new model, the second data set comprised 374 patients who were enrolled to undergo overnight PSG. Receiver operating characteristic analysis and all predictive parameters were validated. Results: In the model development phase, univariate analysis showed 6 parameters were significant for prediction apnea–hypopnea index ≥15 events/hour: male sex, choking or apnea, high blood pressure, neck circumference >16 inches (female) or 17 inches (male), waist circumference ≥80 (female) or 90 cm (male), and body mass index >25 kg/m2. Estimated coefficients showed an area under the curve of 0.753. In the model validation phase, the sensitivity and specificity were approximately 93% and 26%, respectively, for identifying OSAHS. Comparison with the Epworth Sleepiness Scale score of ≥10 and STOP-Bang score ≥3 showed sensitivity of 42.26% and 56.23%, respectively, for detecting patients at risk. Conclusions: This new prediction model gives a better result on identifying patients at risk for OSAHS than Epworth Sleepiness Scale and STOP-Bang in terms of sensitivity. Moreover, this model may play a role in clinical decision-making for a comprehensive sleep evaluation to prioritize patients for PSG.
Fuel and material utilization of a waste shiitake (Lentinula edodes) mushroom bed derived from hardwood chips I: characteristics of calorific value in terms of elemental composition and ash content
Authors: Sekino Noboru , Jiang Zhuoqiu 
Published: January 2021

AbstractTo understand the fuel characteristics of a waste shiitake mushroom bed derived from hardwood chips, the moisture content at the time of disposal and after 1 month, as well as its calorific value, ash content, and elemental composition, were investigated. The moisture content on a wet basis (MCw) was 78% at the time of disposal and was as high as 63% even 1 month after disposal. It is considered that the slow drying process is caused by the low moisture permeability of the skin of mushroom bed, and therefore, it is preferable to crush the waste mushroom bed before drying. Comparing the gross calorific value on a dry basis of the waste mushroom bed with that of the cultivation bed wood chips, the value inside of the waste mushroom bed was similar, while that of its skin was significantly lower (by 11%). The reason for this lies in the significantly higher ash content and nitrogen content compared to those of wood. When analyzed from the combustion heat of the contained elements, it was found that both the cultivation bed wood chips and the waste mushroom bed had almost no hydrogen contributing to combustion due to their high oxygen content, and they were dependent on the heat generation of carbon. As a result of finding the relationship between the net calorific value that can be used as a boiler fuel and MCw, for example, the value at an MCw of 50% was calculated to be 7.6 MJ/kg, which was almost the same as that of sugi (Cryptomeria Japonica) sapwood and bark. The ash content of the waste mushroom bed was about 7%, which is close to that of bark and about ten times that of the wood used for the cultivation bed. When the waste mushroom bed is used as boiler fuel, appropriate ash treatment is required as in the case of using bark.
Generation and Starch Characterization of Non-Transgenic BEI and BEIIb Double Mutant Rice (Oryza sativa) with Ultra-High Level of Resistant Starch
Authors: Miura Satoko , Koyama Nana , Crofts Naoko , Hosaka Yuko , Abe Misato , Fujita Naoko 
Published: January 2021

Abstract
Background
Cereals high in resistant starch (RS) are gaining popularity, as their intake is thought to help manage diabetes and prediabetes. Number of patients suffering from diabetes is also increasing in Asian countries where people consume rice as a staple food, hence generation of practically growable high RS rice line has been anticipated. It is known that suppression of starch branching enzyme (BE) IIb increases RS content in cereals. To further increase RS content and for more practical use, we generated a non-transgenic be1 be2b double mutant rice (Oryza sativa) line, which completely lacked both proteins, by crossing a be1 mutant with a be2b mutant.

Results
The be1 be2b mutant showed a decrease in intermediate amylopectin chains and an increase in long amylopectin chains compared with be2b. The amylose content of be1 be2b mutant (51.7%) was the highest among all pre-existing non-transgenic rice lines. To understand the effects of chewing cooked rice and cooking rice flour on RS content, RS content of mashed and un-mashed cooked rice as well as raw and gelatinized rice flour were measured using be1 be2b and its parent mutant lines. The RS contents of mashed cooked rice and raw rice flour of be1 be2b mutant (28.4% and 35.1%, respectively) were 3-fold higher than those of be2b mutant. Gel-filtration analyses of starch treated with digestive enzymes showed that the RS in be1 be2b mutant was composed of the degradation products of amylose and long amylopectin chains. Seed weight of be1 be2b mutant was approximately 60% of the wild type and rather heavier than that of be2b mutant.

Conclusions
The endosperm starch in be1 be2b double mutant rice were enriched with long amylopectin chains. This led to a great increase in RS content in cooked rice grains and rice flour in be1 be2b compared with be2b single mutant. be1 be2b generated in this study must serve as a good material for an ultra-high RS rice cultivar.
Analysis of the polyester clothing value chain to identify key intervention points for sustainability
Authors: Palacios-Mateo Cristina , van der Meer Yvonne , Seide Gunnar 
Published: January 2021

AbstractClothing is one of the primary human needs, and the demand is met by the global production of thousands of tons of textile fibers, fabrics and garments every day. Polyester clothing manufactured from oil-based polyethylene terephthalate (PET) is the market leader. Conventional PET creates pollution along its entire value chain—during the production, use and end-of-life phases—and also contributes to the unsustainable depletion of resources. The consumption of PET garments thus compromises the quality of land, water and air, destroys ecosystems, and endangers human health. In this article, we discuss the different stages of the value chain for polyester clothing from the perspective of sustainability, describing current environmental challenges such as pollution from textile factory wastewater, and microfibers released from clothing during the laundry cycle. We also consider potential solutions such as enhanced reuse and recycling. Finally, we propose a series of recommendations that should be applied to polyester clothing at all stages along the value chain, offering the potential for meaningful and effective change to improve the environmental sustainability of polyester textiles on a global scale.
DISTEVAL: a web server for evaluating predicted protein distances
Authors: Adhikari Badri , Shrestha Bikash , Bernardini Matthew , Hou Jie , Lea Jamie 
Published: January 2021

AbstractBackgroundProtein inter-residue contact and distance prediction are two key intermediate steps essential to accurate protein structure prediction. Distance prediction comes in two forms: real-valued distances and ‘binned’ distograms, which are a more finely grained variant of the binary contact prediction problem. The latter has been introduced as a new challenge in the 14th Critical Assessment of Techniques for Protein Structure Prediction (CASP14) 2020 experiment. Despite the recent proliferation of methods for predicting distances, few methods exist for evaluating these predictions. Currently only numerical metrics, which evaluate the entire prediction at once, are used. These give no insight into the structural details of a prediction. For this reason, new methods and tools are needed.ResultsWe have developed a web server for evaluating predicted inter-residue distances. Our server, DISTEVAL, accepts predicted contacts, distances, and a true structure as optional inputs to generate informative heatmaps, chord diagrams, and 3D models. All of these outputs facilitate visual and qualitative assessment. The server also evaluates predictions using other metrics such as mean absolute error, root mean squared error, and contact precision.ConclusionsThe visualizations generated by DISTEVAL complement each other and collectively serve as a powerful tool for both quantitative and qualitative assessments of predicted contacts and distances, even in the absence of a true 3D structure.
Effect of inorganic phosphate on migration and osteogenic differentiation of bone marrow mesenchymal stem cells
Authors: Lin Hengzhang , Zhou Yong , Lei Qun , Lin Dong , Chen Jiang , Wu Chuhuo 
Published: January 2021

Abstract
Background
Phosphate is the major ingredient of bone tissue, and is also an important component of commercial bone substitute materials, bone scaffolds, and implant surface coatings. With the dissolution of the bone substitute materials and the degradation by cells, local ion concentrations will change and affect bone tissue reconstruction. Bone marrow -derived mesenchymal stem cells (BM-MSCs) are main autologous cells to repair injured bone. When bone injure occurs, BM-MSCs migrate to the damaged area, differentiate into osteoblasts, and secrete bioactive factors to promote bone tissue repaired. This study aimed to investigate the effect of inorganic phosphate (Pi) at a series of concentration on migration and osteogenic differentiation of human bone marrow -derived mesenchymal stem cells(hBM-MSCs).

Methods
The culture of hBM-MSCs in mediums with different concentration of Pi from 2 mM to 10 mM were performed. HBM-MSCs migration were examined with transwell assays. HBM-MSCs proliferation were evaluated by cell counting kit-8 colorimetric method. Osteogenic genes expression were analyzed by real-time reverse transcriptase polymerase chain reaction. Mineralized nodules formation were demonstrated by Alizarin red staining.

Result
4–10 mM Pi could effectively promote the migration of hBM-MSCs at 12 h and 18 h. There was no significant difference in the migration number of hBM-MSCs in Pi culture mediums at a concentration of 6, 8, and10mM. 2–10 mM Pi could promote the proliferation of hBM-MSCs to varying degrees in the observation period, while 4–10 mM Pi could promote the osteogenic differentiation and mineralization of hBM-MSCs.

Conclusion
The findings in our study showed 4-10 mM Pi could promote the migration, osteogenic differentiation, and mineralization of hBM-MSCs.
Ion channel profiling of the Lymnaea stagnalis ganglia via transcriptome analysis
Authors: Dong Nancy , Bandura Julia , Zhang Zhaolei , Wang Yan , Labadie Karine , Noel Benjamin , Davison Angus , Koene Joris M. , Sun Hong-Shuo , Coutellec Marie-Agnès , Feng Zhong-Ping 
Published: January 2021

Abstract
Background
The pond snail Lymnaea stagnalis (L. stagnalis) has been widely used as a model organism in neurobiology, ecotoxicology, and parasitology due to the relative simplicity of its central nervous system (CNS). However, its usefulness is restricted by a limited availability of transcriptome data. While sequence information for the L. stagnalis CNS transcripts has been obtained from EST libraries and a de novo RNA-seq assembly, the quality of these assemblies is limited by a combination of low coverage of EST libraries, the fragmented nature of de novo assemblies, and lack of reference genome.

Results
In this study, taking advantage of the recent availability of a preliminary L. stagnalis genome, we generated an RNA-seq library from the adult L. stagnalis CNS, using a combination of genome-guided and de novo assembly programs to identify 17,832 protein-coding L. stagnalis transcripts. We combined our library with existing resources to produce a transcript set with greater sequence length, completeness, and diversity than previously available ones. Using our assembly and functional domain analysis, we profiled L. stagnalis CNS transcripts encoding ion channels and ionotropic receptors, which are key proteins for CNS function, and compared their sequences to other vertebrate and invertebrate model organisms. Interestingly, L. stagnalis transcripts encoding numerous putative Ca2+ channels showed the most sequence similarity to those of Mus musculus, Danio rerio, Xenopus tropicalis, Drosophila melanogaster, and Caenorhabditis elegans, suggesting that many calcium channel-related signaling pathways may be evolutionarily conserved.

Conclusions
Our study provides the most thorough characterization to date of the L. stagnalis transcriptome and provides insights into differences between vertebrates and invertebrates in CNS transcript diversity, according to function and protein class. Furthermore, this study provides a complete characterization of the ion channels of Lymnaea stagnalis, opening new avenues for future research on fundamental neurobiological processes in this model system.
Meta-Apo improves accuracy of 16S-amplicon-based prediction of microbiome function
Authors: Jing Gongchao , Zhang Yufeng , Cui Wenzhi , Liu Lu , Xu Jian , Su Xiaoquan 
Published: January 2021

Abstract
Background
Due to their much lower costs in experiment and computation than metagenomic whole-genome sequencing (WGS), 16S rRNA gene amplicons have been widely used for predicting the functional profiles of microbiome, via software tools such as PICRUSt 2. However, due to the potential PCR bias and gene profile variation among phylogenetically related genomes, functional profiles predicted from 16S amplicons may deviate from WGS-derived ones, resulting in misleading results.

Results
Here we present Meta-Apo, which greatly reduces or even eliminates such deviation, thus deduces much more consistent diversity patterns between the two approaches. Tests of Meta-Apo on > 5000 16S-rRNA amplicon human microbiome samples from 4 body sites showed the deviation between the two strategies is significantly reduced by using only 15 WGS-amplicon training sample pairs. Moreover, Meta-Apo enables cross-platform functional comparison between WGS and amplicon samples, thus greatly improve 16S-based microbiome diagnosis, e.g. accuracy of gingivitis diagnosis via 16S-derived functional profiles was elevated from 65 to 95% by WGS-based classification. Therefore, with the low cost of 16S-amplicon sequencing, Meta-Apo can produce a reliable, high-resolution view of microbiome function equivalent to that offered by shotgun WGS.

Conclusions
This suggests that large-scale, function-oriented microbiome sequencing projects can probably benefit from the lower cost of 16S-amplicon strategy, without sacrificing the precision in functional reconstruction that otherwise requires WGS. An optimized C++ implementation of Meta-Apo is available on GitHub (https://github.com/qibebt-bioinfo/meta-apo) under a GNU GPL license. It takes the functional profiles of a few paired WGS:16S-amplicon samples as training, and outputs the calibrated functional profiles for the much larger number of 16S-amplicon samples.
Comparative Analysis of Genome of Ehrlichia sp. HF, a Model Bacterium to Study Fatal Human Ehrlichiosis
Authors: Lin Mingqun , Xiong Qingming , Chung Matthew , Daugherty Sean C. , Nagaraj Sushma , Sengamalay Naomi , Ott Sandra , Godinez Al , Tallon Luke J. , Sadzewicz Lisa , Fraser Claire , Dunning Hotopp Julie C. , Rikihisa Yasuko 
Published: January 2021

AbstractBackgroundThe genusEhrlichiaconsists of tick-borne obligatory intracellular bacteria that can cause deadly diseases of medical and agricultural importance.Ehrlichiasp. HF, isolated fromIxodes ovatusticks in Japan [also referred to asI. ovatus Ehrlichia(IOE) agent], causes acute fatal infection in laboratory mice that resembles acute fatal human monocytic ehrlichiosis caused byEhrlichia chaffeensis. As there is no small laboratory animal model to study fatal human ehrlichiosis,Ehrlichiasp. HF provides a needed disease model. However, the inability to cultureEhrlichiasp. HF and the lack of genomic information have been a barrier to advance this animal model. In addition,Ehrlichiasp. HF has several designations in the literature as it lacks a taxonomically recognized name.ResultsWe stably culturedEhrlichiasp. HF in canine histiocytic leukemia DH82 cells from the HF strain-infected mice, and determined its complete genome sequence.Ehrlichiasp. HF has a single double-stranded circular chromosome of 1,148,904 bp, which encodes 866 proteins with a similar metabolic potential asE. chaffeensis.Ehrlichiasp. HF encodes homologs of all virulence factors identified inE. chaffeensis, including 23 paralogs of P28/OMP-1 family outer membrane proteins, type IV secretion system apparatus and effector proteins, two-component systems, ankyrin-repeat proteins, and tandem repeat proteins.Ehrlichiasp. HF is a novel species in the genusEhrlichia, as demonstrated through whole genome comparisons with six representativeEhrlichiaspecies, subspecies, and strains, using average nucleotide identity, digital DNA-DNA hybridization, and core genome alignment sequence identity.ConclusionsThe genome ofEhrlichiasp. HF encodes all known virulence factors found inE. chaffeensis, substantiating it as a modelEhrlichiaspecies to study fatal human ehrlichiosis. Comparisons betweenEhrlichiasp. HF andE. chaffeensiswill enable identification ofin vivovirulence factors that are related to host specificity, disease severity, and host inflammatory responses. We propose to nameEhrlichiasp. HF asEhrlichia japonicasp. nov. (type strain HF), to denote the geographic region where this bacterium was initially isolated.
Unbiased RNA-Seq-driven identification and validation of reference genes for quantitative RT-PCR analyses of pooled cancer exosomes
Authors: Dai Yao , Cao Yumeng , Köhler Jens , Lu Aiping , Xu Shaohua , Wang Haiyun 
Published: January 2021

Abstract
Background
Exosomes are extracellular vesicles (EVs) derived from endocytic compartments of eukaryotic cells which contain various biomolecules like mRNAs or miRNAs. Exosomes influence the biologic behaviour and progression of malignancies and are promising candidates as non-invasive diagnostic biomarkers or as targets for therapeutic interventions. Usually, quantitative real-time polymerase chain reaction (qRT-PCR) is used to assess gene expression in cancer exosomes, however, the ideal reference genes for normalization yet remain to be identified.

Results
In this study, we performed an unbiased analysis of high-throughput mRNA and miRNA-sequencing data from exosomes of patients with various cancer types and identify candidate reference genes and miRNAs in cancer exosomes. The expression stability of these candidate reference genes was evaluated by the coefficient of variation “CV” and the average expression stability value “M”. We subsequently validated these candidate reference genes in exosomes from an independent cohort of ovarian cancer patients and healthy control individuals by qRT-PCR.

Conclusions
Our study identifies OAZ1 and hsa-miR-6835-3p as the most reliable individual reference genes for mRNA and miRNA quantification, respectively. For superior accuracy, we recommend the use of a combination of reference genes - OAZ1/SERF2/MPP1 for mRNA and hsa-miR-6835-3p/hsa-miR-4468-3p for miRNA analyses.
Physical mapping and InDel marker development for the restorer gene Rf2 in cytoplasmic male sterile CMS-D8 cotton
Authors: Feng Juanjuan , Zhang Xuexian , Zhang Meng , Guo Liping , Qi Tingxiang , Tang Huini , Zhu Haiyong , Wang Hailin , Qiao Xiuqin , Xing Chaozhu , Wu Jianyong 
Published: January 2021

Abstract
Background
Cytoplasmic male sterile (CMS) with cytoplasm from Gossypium Trilobum (D8) fails to produce functional pollen. It is useful for commercial hybrid cotton seed production. The restore line of CMS-D8 containing Rf2 gene can restore the fertility of the corresponding sterile line. This study combined the whole genome resequencing bulked segregant analysis (BSA) with high-throughput SNP genotyping to accelerate the physical mapping of Rf2 locus in CMS-D8 cotton.

Methods
The fertility of backcross population ((sterile line×restorer line)×maintainer line) comprising of 1623 individuals was investigated in the field. The fertile pool (100 plants with fertile phenotypes, F-pool) and the sterile pool (100 plants with sterile phenotypes, S-pool) were constructed for BSA resequencing. The selection of 24 single nucleotide polymorphisms (SNP) through high-throughput genotyping and the development insertion and deletion (InDel) markers were conducted to narrow down the candidate interval. The pentapeptide repeat (PPR) family genes and upregulated genes in restore line in the candidate interval were analysed by qRT-PCR.

Results
The fertility investigation results showed that fertile and sterile separation ratio was consistent with 1:1. BSA resequencing technology, high-throughput SNP genotyping, and InDel markers were used to identify Rf2 locus on candidate interval of 1.48 Mb on chromosome D05. Furthermore, it was quantified in this experiment that InDel markers co-segregated with Rf2 enhanced the selection of the restorer line. The qRT-PCR analysis revealed PPR family gene Gh_D05G3391 located in candidate interval had significantly lower expression than sterile and maintainer lines. In addition, utilization of anther RNA-Seq data of CMS-D8 identified that the expression level of Gh_D05G3374 encoding NB-ARC domain-containing disease resistance protein in restorer lines was significantly higher than that in sterile and maintainer lines.

Conclusions
This study not only enabled us to precisely locate the restore gene Rf2 but also evaluated the utilization of InDel markers for marker assisted selection in the CMS-D8 Rf2 cotton breeding line. The results of this study provide an important foundation for further studies on the mapping and cloning of restorer genes.