bluuebunny/crossref_metadata_2025_split huggingface dataset:
Iodine value of tung biodiesel fuel using Wijs method is significantly lower than calculated value
Authors: Suzuki Toshisada , Sumimoto Kazuki , Fukada Kazuhiro , Katayama Takeshi 
Published: October 2021

AbstractThe tung tree (Vernicia fordii) is a non-edible oil plant native to southern China and was introduced in Japan in the nineteenth century. The tree produces tung oil, which is composed of approximately 80% α-eleostearic acid (9c, 11t, 13t-octadecatrienoic acid), 7% linoleic acid, and 6% oleic acid. Tung oil may be a non-edible source of biodiesel fuel (BDF) production. The iodine value (IV) is one of parameters to guarantee BDF quality, and the most common method for the determination of IV is the Wijs method. The IV can be calculated from the average molecular weight and the number of double bonds from the GC–MS data. In this study, the IVs of olive, castor, soybean, linseed, and perilla BDF using the Wijs method were found to be almost the same as the calculated IV. On the other hand, the IV of tung BDF by the Wijs method indicated a significantly lower value than that of the calculated value. To determine the cause of this discrepancy, the samples before and after halogenation using the Wijs method, were analyzed by 1H NMR. The conjugated double bond signals did not disappear, and a broad double bond signal remained in the tung BDF spectrum after halogenation. These results demonstrated that iodine, with a large atomic radius, could not react completely with the three conjugated double bonds in α-eleostearic acid. Therefore, the IV of tung BDF was significantly lower than the calculated value.
Impact of Working Together for adults with autism spectrum disorder: a multifamily group intervention
Authors: Smith DaWalt Leann , Hickey Emily , Hudock Rebekah , Esler Amy , Mailick Marsha 
Published: October 2021

AbstractBackgroundAdults with autism spectrum disorder (ASD) have lower engagement in their communities, higher rates of unemployment/underemployment, and continued difficulties with challenging behavior compared to their neurotypical peers. Multi-family psychoeducation emphasizes education and problem-solving with the goal of improving these outcomes for the individual with the disability.MethodsUsing a randomized waitlist control design, the present study evaluated a multi-family group psychoeducation intervention,Working Together,for adults on the autism spectrum without intellectual disability (n = 40). Five waves of data were collected at 3-month intervals. In this design, families in the intervention condition participated in intervention during the 6 months between baseline and time 3 data collection; the waitlist control condition received the intervention immediately after the time 3 data collection. We compared these two conditions, intervention group (n = 20) vs waitlist control group (n = 20), on key outcomes for the adults with ASD: engagement in work-related activities, engagement in meaningful activities, and behavior problems.ResultsResults indicated medium to large effect sizes associated with theWorking Togetherintervention across key outcomes, including adults on the spectrum experiencing significant increases in meaningful activities and decreases in internalizing problems. Although increases in work-related activities were not statistically significant, an observed one-half of a standard deviation difference from before to after the intervention indicated clinically significant change. We also found maintenance of the treatment effect through 6 months post-treatment for the intervention group and replication of the treatment effect within the control group after they received the intervention.ConclusionWorking Togetheris a promising multi-family group psychoeducation intervention designed to improve functioning during adulthood. These findings highlight the need for more intervention services research during adulthood and specifically the need for family-centered supports.
Associations between urinary heavy metal concentrations and blood pressure in residents of Asian countries
Authors: Mizuno Yuki , Shimizu-Furusawa Hana , Konishi Shoko , Inaoka Tsukasa , Ahmad Sk Akhtar , Sekiyama Makiko , Abdoellah Oekan S. , Gunawan Budhi , Parajuli Rajendra Prasad , Ikemoto Yukio , Lam Tran Dinh , Watanabe Chiho , Umezaki Masahiro 
Published: October 2021

Abstract
Background
Previous studies have suggested that exposures to heavy metals (arsenic, cadmium, lead, and selenium) may be associated with differences in blood pressure. However, the findings of these studies have been inconsistent. This study was performed to examine the associations between urinary heavy metal concentrations and blood pressure among residents of four Asian countries (Bangladesh, Indonesia, Nepal, and Vietnam).

Methods
This cross-sectional study examined 1899 adults in four Asian countries. Urinary concentrations of heavy metals were measured by inductively coupled plasma mass spectrometry. A questionnaire survey was administered regarding individual characteristics. Anthropometric measurements (height and weight) were performed. Systolic and diastolic blood pressures were measured after a short rest. Multiple linear regression models were applied to investigate associations between urinary heavy metal concentrations and blood pressure after adjustments for age, sex, and body mass index.

Results
The geometric means of the urinary concentrations of arsenic, cadmium, lead, and selenium were 84.6, 0.885, 2.09, and 16.5 μg/g creatinine, respectively. The urinary arsenic concentrations were slightly higher than those typically reported in non-polluted populations, while urinary cadmium, lead, and selenium concentrations were equivalent or slightly lower. The urinary lead concentrations were positively associated with both systolic and diastolic blood pressure, but urinary selenium concentrations were negatively associated with them.

Conclusions
Variations in the urinary concentrations of lead and selenium were associated with blood pressure at low levels of exposure/intake.
CorDiffViz: an R package for visualizing multi-omics differential correlation networks
Authors: Yu Shiqing , Drton Mathias , Promislow Daniel E. L. , Shojaie Ali 
Published: October 2021

AbstractBackgroundDifferential correlation networks are increasingly used to delineate changes in interactions among biomolecules. They characterize differences between omics networks under two different conditions, and can be used to delineate mechanisms of disease initiation and progression.ResultsWe present a new R package, , that facilitates the estimation and visualization of differential correlation networks using multiple correlation measures and inference methods. The software is implemented in , and , and is available athttps://github.com/sqyu/CorDiffViz. Visualization has been tested for the Chrome and Firefox web browsers. A demo is available athttps://diffcornet.github.io/CorDiffViz/demo.html.ConclusionsOur software offers considerable flexibility by allowing the user to interact with the visualization and choose from different estimation methods and visualizations. It also allows the user to easily toggle between correlation networks for samples under one condition and differential correlations between samples under two conditions. Moreover, the software facilitates integrative analysis of cross-correlation networks between two omics data sets.
Comparison of sequencing data processing pipelines and application to underrepresented African human populations
Authors: Breton Gwenna , Johansson Anna C. V. , Sjödin Per , Schlebusch Carina M. , Jakobsson Mattias 
Published: October 2021

Abstract
Background
Population genetic studies of humans make increasing use of high-throughput sequencing in order to capture diversity in an unbiased way. There is an abundance of sequencing technologies, bioinformatic tools and the available genomes are increasing in number. Studies have evaluated and compared some of these technologies and tools, such as the Genome Analysis Toolkit (GATK) and its “Best Practices” bioinformatic pipelines. However, studies often focus on a few genomes of Eurasian origin in order to detect technical issues. We instead surveyed the use of the GATK tools and established a pipeline for processing high coverage full genomes from a diverse set of populations, including Sub-Saharan African groups, in order to reveal challenges from human diversity and stratification.

Results
We surveyed 29 studies using high-throughput sequencing data, and compared their strategies for data pre-processing and variant calling. We found that processing of data is very variable across studies and that the GATK “Best Practices” are seldom followed strictly. We then compared three versions of a GATK pipeline, differing in the inclusion of an indel realignment step and with a modification of the base quality score recalibration step. We applied the pipelines on a diverse set of 28 individuals. We compared the pipelines in terms of count of called variants and overlap of the callsets. We found that the pipelines resulted in similar callsets, in particular after callset filtering. We also ran one of the pipelines on a larger dataset of 179 individuals. We noted that including more individuals at the joint genotyping step resulted in different counts of variants. At the individual level, we observed that the average genome coverage was correlated to the number of variants called.

Conclusions
We conclude that applying the GATK “Best Practices” pipeline, including their recommended reference datasets, to underrepresented populations does not lead to a decrease in the number of called variants compared to alternative pipelines. We recommend to aim for coverage of > 30X if identifying most variants is important, and to work with large sample sizes at the variant calling stage, also for underrepresented individuals and populations.
Combined nanopore adaptive sequencing and enzyme-based host depletion efficiently enriched microbial sequences and identified missing respiratory pathogens
Authors: Gan Mingyu , Wu Bingbing , Yan Gangfeng , Li Gang , Sun Li , Lu Guoping , Zhou Wenhao 
Published: October 2021

Abstract
Background
Enzyme-based host depletion significantly improves the sensitivity of clinical metagenomics. Recent studies found that real-time adaptive sequencing of DNA molecules was achieved using a nanopore sequencing machine, which enabled effective enrichment of microbial sequences. However, few studies have compared the enzyme-based host depletion and nanopore adaptive sequencing for microbial enrichment efficiency.

Results
To compare the host depletion and microbial enrichment efficiency of enzyme-based and adaptive sequencing methods, the present study collected clinical samples from eight children with respiratory tract infections. The same respiratory samples were subjected to standard methods, adaptive sequencing methods, enzyme-based host depletion methods, and the combination of adaptive sequencing and enzyme-based host depletion methods. We compared the host depletion efficiency, microbial enrichment efficiency, and pathogenic microorganisms detected between the four methods. We found that adaptive sequencing, enzyme-based host depletion and the combined methods significantly enriched the microbial sequences and significantly increased the diversity of microorganisms (p value < 0.001 for each method compared to standard). The highest microbial enrichment efficiency was achieved using the combined method. Compared to the standard method, the combined method increased the microbial reads by a median of 113.41-fold (interquartile range 23.32–327.72, maximum 1812), and the number of genera by a median of 70-fold (interquartile range 56.75–86.75, maximum 164). The combined method detected 6 pathogens in 4 samples with a median read of 547, compared to 5 pathogens in 4 samples with a median read of 4 using the standard method.

Conclusion
The combined method is an effective, easy-to-run method for enriching microbial sequences in clinical metagenomics from sputum and bronchoalveolar lavage fluid samples and may improve the sensitivity of clinical metagenomics for other host-derived clinical samples.
Manual Annotation Studio (MAS): a collaborative platform for manual functional annotation of viral and microbial genomes
Authors: Lueder Matthew R. , Cer Regina Z. , Patrick Miles , Voegtly Logan J. , Long Kyle A. , Rice Gregory K. , Bishop-Lilly Kimberly A. 
Published: October 2021

Abstract
Background
Functional genome annotation is the process of labelling functional genomic regions with descriptive information. Manual curation can produce higher quality genome annotations than fully automated methods. Manual annotation efforts are time-consuming and complex; however, software can help reduce these drawbacks.

Results
We created Manual Annotation Studio (MAS) to improve the efficiency of the process of manual functional annotation prokaryotic and viral genomes. MAS allows users to upload unannotated genomes, provides an interface to edit and upload annotations, tracks annotation history and progress, and saves data to a relational database. MAS provides users with pertinent information through a simple point and click interface to execute and visualize results for multiple homology search tools (blastp, rpsblast, and HHsearch) against multiple databases (Swiss-Prot, nr, CDD, PDB, and an internally generated database). MAS was designed to accept connections over the local area network (LAN) of a lab or organization so multiple users can access it simultaneously. MAS can take advantage of high-performance computing (HPC) clusters by interfacing with SGE or SLURM and data can be exported from MAS in a variety of formats (FASTA, GenBank, GFF, and excel).

Conclusions
MAS streamlines and provides structure to manual functional annotation projects. MAS enhances the ability of users to generate, interpret, and compare results from multiple tools. The structure that MAS provides can improve project organization and reduce annotation errors. MAS is ideal for team-based annotation projects because it facilitates collaboration.
Comparative transcriptomic analysis of races 1, 2, 5 and 6 of Fusarium oxysporum f.sp. pisi in a susceptible pea host identifies differential pathogenicity profiles
Authors: Achari Saidi R. , Edwards Jacqueline , Mann Ross C. , Kaur Jatinder K. , Sawbridge Tim , Summerell Brett A. 
Published: October 2021

Abstract
Background
The fungal pathogen Fusarium oxysporum f.sp. pisi (Fop) causes Fusarium wilt in peas. There are four races globally: 1, 2, 5 and 6 and all of these races are present in Australia. Molecular infection mechanisms have been studied in a few other F. oxysporum formae speciales; however, there has been no transcriptomic Fop-pea pathosystem study.

Results
A transcriptomic study was carried out to understand the molecular pathogenicity differences between the races. Transcriptome analysis at 20 days post-inoculation revealed differences in the differentially expressed genes (DEGs) in the Fop races potentially involved in fungal pathogenicity variations. Most of the DEGs in all the races were engaged in transportation, metabolism, oxidation-reduction, translation, biosynthetic processes, signal transduction, proteolysis, among others. Race 5 expressed the most virulence-associated genes. Most genes encoding for plant cell wall degrading enzymes, CAZymes and effector-like proteins were expressed in race 2. Race 6 expressed the least number of genes at this time point.

Conclusion
Fop races deploy various factors and complex strategies to mitigate host defences to facilitate colonisation. This investigation provides an overview of the putative pathogenicity genes in different Fop races during the necrotrophic stage of infection. These genes need to be functionally characterised to confirm their pathogenicity/virulence roles and the race-specific genes can be further explored for molecular characterisation.
Impact of human gene annotations on RNA-seq differential expression analysis
Authors: Hamaguchi Yu , Zeng Chao , Hamada Michiaki 
Published: October 2021

Abstract
Background
Differential expression (DE) analysis of RNA-seq data typically depends on gene annotations. Different sets of gene annotations are available for the human genome and are continually updated–a process complicated with the development and application of high-throughput sequencing technologies. However, the impact of the complexity of gene annotations on DE analysis remains unclear.

Results
Using “mappability”, a metric of the complexity of gene annotation, we compared three distinct human gene annotations, GENCODE, RefSeq, and NONCODE, and evaluated how mappability affected DE analysis. We found that mappability was significantly different among the human gene annotations. We also found that increasing mappability improved the performance of DE analysis, and the impact of mappability mainly evident in the quantification step and propagated downstream of DE analysis systematically.

Conclusions
We assessed how the complexity of gene annotations affects DE analysis using mappability. Our findings indicate that the growth and complexity of gene annotations negatively impact the performance of DE analysis, suggesting that an approach that excludes unnecessary gene models from gene annotations improves the performance of DE analysis.
Detection of viable and total fungal community in zaopei of Chinese strong-flavor baijiu using PMA combined with qPCR and HTS based on ITS2 region
Authors: Liu Huanming , Tan Guangxun , Chen Qitong , Dong Weiwei , Chen Ping , Cai Kaiyun , Hu Yuanliang , Zhang Weiyan , Peng Nan , Liang Yunxiang , Zhao Shumiao 
Published: October 2021

Abstract
Background
Chinese strong-flavor baijiu (CSFB), one of the three major baijiu types, is the most popular baijiu type among consumers in China. A variety of microbes are involved in metabolizing raw materials to produce ethanol and flavor substances during fermentation, which fundamentally determined the quality of baijiu. It is of great importance to study microbial community of fermented grains (zaopei) during baijiu brewing process for improving its quality. In this study, we firstly used propidium monoazide (PMA) to treat zaopei samples from 5-year pit and 20-year pit for removing the interference of non-viable fungi, and analyzed the diversity of total fungi and viable fungi by quantitative PCR (qPCR) and high-throughput sequencing (HTS) based on ITS2 gene.

Results
The results showed that total fungi and viable fungi displayed no significant differences at OTU, phylum, or genus levels during fermentation within two kinds of pits. A total of 6 phyla, 19 classes, and 118 genera in fungi were found based on OTUs annotation in zaopei samples from 5-year pit and 20-year pit. Besides, non-viable fungi had little effect on the fungal community diversity during the fermentation cycle. It was found that the most dominant viable fungi belonged to Saccharomyces, Kazachstania, Naumovozyma, and Trichosporon, and Naumovozyma was firstly detected in zaopei samples of CSFB. Moreover, based on the variation of flavor substances in zaopei samples, the quality of CSFB produced from older pit was better than that produced from younger pit.

Conclusion
The non-viable fungi had little effect on the fungal diversity, structure, and relative abundance in zaopei samples of CSFB, and Naumovozyma was firstly detected in zaopei samples of CSFB. Our findings can be applied as guidance for improving the quality and stability of CSFB.
Physiological and transcriptome analysis of Magnolia denudata leaf buds during long-term cold acclimation
Authors: Wu Kunjing , Duan Xiaojing , Zhu Zhonglong , Sang Ziyang , Duan Jie , Jia Zhongkui , Ma Luyi 
Published: October 2021

Abstract
Background
Magonlia denudata is an important perennial tree species of the Magnoliaceae family, known for its ornamental value, resistance to smoke pollution and wind, role in air purification, and robust cold tolerance. In this study, a high-throughput transcriptome analysis of leaf buds was performed, and gene expression following artificial acclimation 22 °C, 4 °C and 0 °C, was compared by RNA sequencing.

Results
Over 426 million clean reads were produced from three libraries (22 °C, 4 °C and 0 °C). A total of 74,503 non-redundant unigenes were generated, with an average length of 1173.7 bp (N50 = 1548). Based on transcriptional results, 357 and 235 unigenes were identified as being upregulated and downregulated under cold stress conditions, respectively. Differentially expressed genes were annotated using Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes pathway analyses. The transcriptomic analysis focused on carbon metabolism and plant hormone signal transduction associated with cold acclimation. Transcription factors such as those in the basic helix-loop-helix and AP2/ERF families were found to play an important role in M. denudata cold acclimation.

Conclusion
M. denudata exhibits responses to non-freezing cold temperature (4 °C) to increase its cold tolerance. Cold resistance was further strengthened with cold acclimation under freezing conditions (0 °C). Cold tolerance genes, and cold signaling transcriptional pathways, and potential functional key components for the regulation of the cold response were identified in M. denudata. These results provide a basis for further studies, and the verification of key genes involved in cold acclimation responses in M. denudata lays a foundation for developing breeding programs for Magnoliaceae species.
Comparative physiological and transcriptomic analyses reveal ascorbate and glutathione coregulation of cadmium toxicity resistance in wheat genotypes
Authors: Zhang Tao , Xiao Jingui , Zhao Yongsheng , Zhang Yifan , Jie Yaqi , Shen Dandan , Yue Caipeng , Huang Jinyong , Hua Yingpeng , Zhou Ting 
Published: October 2021

AbstractBackgroundCadmium (Cd) is a heavy metal with high toxicity that severely inhibits wheat growth and development. Cd easily accumulates in wheat kernels and enters the human food chain. Genetic variation in the resistance to Cd toxicity found in wheat genotypes emphasizes the complex response architecture. Understanding the Cd resistance mechanisms is crucial for combating Cd phytotoxicity and meeting the increasing daily food demand.ResultsUsing two wheat genotypes (Cd resistant and sensitive genotypes T207 and S276, respectively) with differing root growth responses to Cd, we conducted comparative physiological and transcriptomic analyses and exogenous application tests to evaluate Cd detoxification mechanisms. S276 accumulated more H2O2, O2−, and MDA than T207 under Cd toxicity. Catalase activity and levels of ascorbic acid (AsA) and glutathione (GSH) were greater, whereas superoxide dismutase (SOD) and peroxidase (POD) activities were lower in T207 than in S276. Transcriptomic analysis showed that the expression ofRBOHA,RBOHC, andRBOHEwas significantly increased under Cd toxicity, and two-thirds (22 genes) of the differentially expressedRBOHgenes had higher expression levels in S276 than inT207. Cd toxicity reshaped the transcriptional profiling of the genes involving the AsA-GSH cycle, and a larger proportion (74.25%) of the corresponding differentially expressed genes showed higher expression in T207 than S276. The combined exogenous application of AsA and GSH alleviated Cd toxicity by scavenging excess ROS and coordinately promoting root length and branching, especially in S276.ConclusionsThe results indicated that the ROS homeostasis plays a key role in differential Cd resistance in wheat genotypes, and the AsA-GSH cycle fundamentally and vigorously influences wheat defense against Cd toxicity, providing insight into the physiological and transcriptional mechanisms underlying Cd detoxification.