bluuebunny/crossref_metadata_2025_split huggingface dataset:
Objective evaluation of postoperative changes in real-life activity levels in the postoperative course of lumbar spinal surgery using wearable trackers
Authors: Inoue Masahiro , Orita Sumihis , Inage Kazuhide , Suzuki Miyako , Fujimoto Kazuki , Shiga Yasuhiro , Kanamoto Hirohito , Abe Koki , Kinoshita Hideyuki , Norimoto Masaki , Umimura Tomotaka , Sato Takashi , Sato Masashi , Suzuki Masahiro , Enomoto Keigo , Eguchi Yawara , Akazawa Tsutomu , Aoki Yasuchika , Kawasaki Yohei , Ohtori Seiji 
Published: January 2020

Abstract
Background: Lumbar spinal disease causes disabilities in performing daily activities. Operative treatments are aimed at pain relief and rapid return to routine activity. Patient-based outcome measures are used to evaluate pathologies and therapeutic effects associated with lumbar spinal disease. Nevertheless, it remains unknown as to how much such treatment improves activity levels. The purpose of the current study was to measure changes in activity levels before and after lumbar spinal surgery using a wearable activity tracker and to analyze the differences between results and patient-based outcomes. Methods: Sixty patients who underwent lumbar surgery were studied. The physical activity of participants was objectively evaluated using a wearable Micro-Motion logger system (Actigraph). We measured the amount of activity before and at 1, 3, 6, and 12 months after the surgery to evaluate postoperative changes. The Japanese Orthopaedic Association Back Pain Evaluation Questionnaire, Oswestry Disability Index, Roland-Morris Disability Questionnaire and visual analog scale were used to assess patient-based outcomes of pain and activities of daily living-related scores; we analyzed the relationships between scores and actual activity levels. Results: The amount of actual activity decreased significantly 1 month after the surgery compared to that during the preoperative period, which then improved after 3 months postoperatively ( p <0.01). Furthermore, there was a significant improvement 6 months after the surgery compared to that during the preoperative period ( p < 0.05). The changes in activity for each period were strongly correlated, regardless of the period. In contrast, a significant improvement was observed at 1 month after the surgery in almost all items of the patient-based questionnaires ( p < 0.05). Conclusions: The objective activity tracker demonstrated that lumbar surgery results in the amount of activity decreasing 1 month just after surgery followed by gradual postoperative recovery within 3 months. By contrast, patient-based outcomes showed improvement in 1 month that was significantly different from the change in actual activity, indicating a gap between patient-oriented clinical scores and their actual activities.
Low red/far-red ratio as a signal promotes carbon assimilation of soybean seedlings by increasing the photosynthetic capacity
Authors: Yang Feng , Liu Qinlin , Cheng Yajiao , Feng Lingyang , Wu Xiaoling , Fan Yuanfang , Raza Muhammad Ali , Wang Xiaochun , Yong Taiwen , Liu Weiguo , Liu Jiang , Du Junbo , Shu Kai , Yang Wenyu 
Published: January 2020

Abstract
Background: Shading includes low light intensity and varying quality. However, a low red/far-red (R/Fr) ratio of light is a signal that affects plant growth in intercropping and close- planting systems. Thus, the low R/Fr ratio uncoupling from shading conditions was assessed to identify the effect of light quality on photosynthesis and CO2 assimilation. Soybean plants were grown in a growth chamber with natural solar radiation under four treatments, that is, normal (N, sunlight), N+Fr, Low (L) +Fr, and L light.

Results: Low R/Fr ratio significantly increased the total biomass, leaf area, starch and sucrose contents, chlorophyll content, net photosynthetic rate, and quantum efficiency of the photosystem II compared with normal R/Fr ratio under the same light level (P < 0.05). Proteomic analysis of soybean leaves under different treatments was performed to quantify the changes in photosynthesis and CO2 assimilation in the chloroplast. Among the 7834 proteins quantified, 12 showed a > 1.3-fold change in abundance, of which 1 was related to porphyrin and chlorophyll metabolism, 2 were involved in photosystem I (PS I), 4 were associated with PS II, 3 proteins participated in photosynthetic electron transport, and 2 were involved in starch and sucrose metabolism. The dynamic change in these proteins indicates that photosynthesis and CO2 assimilation were maintained in the L treatment by up-regulating the component protein levels compared with those in N treatment. Although low R/Fr ratio increased the photosynthetic CO2 assimilation parameters, the differences in most protein expression levels in N+Fr and L+Fr treatments compared with those in N treatment were insignificant. Similar trends were found in gene expression through quantitative reverse transcription polymerase chain reaction excluding the gene expression of sucrose synthase possible because light environment is one of the factors affecting carbon assimilation.

Conclusions: Low R/Fr ratio (high Fr light) can increase the photosynthetic CO2 assimilation in the same light intensity by improving the photosynthetic efficiency of the photosystems.
A novel insight into nitrogen and auxin signaling in lateral root formation in tea plant [Camellia sinensis (L.) O. Kuntze]
Authors: Author) Shunkai Hu(Former Corresponding , Zhang Mi , Yang Yiqing , Xuan Wei , Zou Zhongwei , Arkorful Emmanuel , Chen Yi , Ma Qingping , Jeyaraj Anburaj , Chen Xuan , Author) Xinghui Li(New Corresponding 
Published: January 2020

Abstract
Background: Tea plant (Camellia sinensis) is one of the most popular non-alcoholic beverage worldwide. Lateral roots (LRs) of tea plant are the main organ used for tea plant to absorb soil moisture and nutrients. Lateral roots formation and development are tightly regulated by the nitrogen and auxin signaling pathway. In order to understand the function of auxin and nitrogen signaling in LRs formation and development, transcriptome analysis was applied to investigate the differentially expressed genes involved in lateral roots of tea plants treated with indole-3-butyric acid (IBA), N-1-naphthylphthalamic acid (NPA), low and high nitrogen concentration. Results: A total of 296 common differentially expressed genes were mainly identified and annotated to four signaling pathways, such as nitrogen metabolism, plant hormone signal transduction, Glutathione metabolism and transcription factors. RNA-sequencing results revealed that majority of differentially expressed genes play important roles in nitrogen metabolism and hormonal signal transduction. Low nitrogen condition induced the biosynthesis of auxin and accumulation of transcripts, thereby regulating lateral roots formation. Furthermore, metabolism of cytokinin and ethylene biosynthesis were also involved in lateral roots development. Transcription factors like MYB genes also contributed to the lateral roots formation of tea plants through secondary cell wall biosynthesis. Reversed phase ultra performance liquid chromatography (RP-UPLC) results showed that the auxin concentration in lateral roots was increased, while the nitrogen level decreased. Thus, tea plant lateral roots formation could be induced by low nitrogen concentration via auxin biosynthesis and accumulation. Conclusion: This study provides new insights into the mechanisms associated with nitrogen and auxin signaling pathways to regulate LRs formation and arises new clues for the efficient utilization of nitrogen in tea plant at the genetic level.
Transcriptome Ortholog Alignment Sequence Tools (TOAST) for Phylogenomic Dataset Assembly
Authors: dornburg alex , Wcisel Dustin J. , Howard J. Thomas , Yoder Jeffrey A. 
Published: January 2020

Abstract
Background: Advances in next-generation sequencing technologies have reduced the cost of whole transcriptome analyses, allowing characterization of non-model species at unprecedented levels. The rapid pace of transcriptomic sequencing has driven the public accumulation of a wealth of data for phylogenomic analyses, however lack of tools aimed towards phylogeneticists to efficiently identify orthologous sequences currently hinders effective harnessing of this resource.Results: We introduce TOAST, an open source R software package that can utilize the ortholog searches based on the software Benchmarking Universal Single-Copy Orthologs (BUSCO) to assemble multiple sequence alignments of orthologous loci from transcriptomes for any group of organisms. By streamlining search, query, and alignment, TOAST automates the generation of locus and concatenated alignments, and also presents a series of outputs from which users can not only explore missing data patterns across their alignments, but also reassemble alignments based on user-defined acceptable missing data levels for a given research question.Conclusions: TOAST provides a comprehensive set of tools for assembly of sequence alignments of orthologs for comparative transcriptomic and phylogenomic studies. This software empowers easy assembly of public and novel sequences for any target database of candidate orthologs, and fills a critically needed niche for tools that enable quantification and testing of the impact of missing data. As open-source software, TOAST is fully customizable for integration into existing or novel custom informatic pipelines for phylogenomic inference. Software, a detailed manual, and example data files are available through github carolinafishes.github.io
Indole -3-acetic acid improves drought tolerance of white clover associated with activating auxin-related genes, abscisic acid and jasmonic acid-induced stress responsive transcription factors, and inhibiting senescence genes
Authors: Zhang Youzhi , Li Yaping , Hassan Muhammad Jawad , Li Zhou , Peng Yan 
Published: January 2020

Abstract
Auxin plays an important role in regulating plant development. To idenfity what effects IAA has in white clover under drought stress and how IAA regulates white clover response to drought. Relative water content, chlorophyll content, six phytohormones content, expression of gene-related to IAA signal perception and synthesis, transcription factor genes related to drought-resistance and senescence genes were investigated in white clover pretreated with 1µM exogenous IAA or 100µM L-AOPP (inhibitor of IAA synthesis) under 15% polyethylene glycol-6000 (PEG-6000). Compared to control, drought stress significantly diminished stem dry weight (g/10 plant), relative water content (RWC, %) and total chlorophyll content (Chl, mg/g). Exogenous IAA significantly increased RWC and Chl, however, L-AOPP decreased stem dry weight, RWC and Chl compared with direct drought treatment. Besides that, compared with direct drought set, exogenous IAA significantly improved ABA content and JA content, up-regulated expression levels of some auxin-responsive genes ( GH3.1 , GH3.9 , IAA8 ) , transcription factor genes ( bZIP11 , DREB2 , MYB14 , MYB48 , WRKY2 , WRKY56 , WRKY108715 ) related to drought-resistance and drought resistance gene ( RD22 ). Meanwhile, exogenous IAA down-regulated expression levels of several auxin-responsive genes ( GH3.3 , GH3.6 , IAA27 ) and leaf senescence genes ( SAG101 and SAG102 ). Contrarily, L-AOPP significantly reduced ABA, GA3 and JA content, down-regulated expression levels of GH3.1 , GH3.9 , IAA8 , bZIP11 , DREB2 , MYB14 , MYB48 , WRKY2 , WRKY56 , WRKY108715 , ERD and RD22 , and up-regulated expression levels of SAG101 and SAG102 . Collectively, these data suggested a positive role of exogenous IAA in alleviating drought damage through many involved physiological processes in white clover.
Influence of pupil dilation on the Barrett Universal II (new generation), Haigis (4th generation), and SRK/T (3rd generation) intraocular lens calculation formulas: a retrospective study
Authors: Teshigawara Takeshi , Meguro Akira , Mizuki Nobuhisa 
Published: January 2020

Abstract
Background: We investigated the effect of pupil dilation on predicted postoperative refraction (PPR) and recommended intraocular lens (IOL) power calculated using three different generations of IOL power calculation formulas: Barrett Universal II (Barrett) (new generation), Haigis (4th generation), and SRK/T (3rd generation).
Methods: This retrospective study included 150 eyes. All variables were measured and calculated using a ZEISS IOL Master 700. The following variables were measured before and after dilation: anterior chamber depth (ACD), lens thickness (LT), white-to-white (WTW). PPR and recommended IOL power were calculated by Barrett, Haigis, and SRK/T IOL calculation formulas. The change in each variable before and after dilation, and correlations between all changes were analyzed using the Wilcoxon signed-rank test and the Spearman’s rank-order correlation test, respectively. The influence of pupil dilation on recommended IOL power calculated by each formula was also analyzed.
Results: The mean absolute change (MAC) in PPR before and after dilation was highest in Barrett, followed by Haigis and SRK/T. Significant differences were found among each MACs (P < 0.0001). Significant changes were observed before and after dilation in ACD and LT (P < 0.0001) but not in WTW. In Barrett and Haigis, there was a significant positive correlation between change in PPR and change in ACD (P < 0.0001) and a negative correlation between change in PPR and change in LT (P < 0.0001). Correlations were strongest in Barret followed by Haigis, especially in LT. Change in PPR in Barrett also demonstrated a significant positive correlation with change in WTW (P = 0.022). The recommended IOL power using Barrett and Haigis changed before and after dilation in 23.3% and 19.3% cases; SRK/T showed no change.
Conclusions: In PPR and recommended IOL power, pupil dilation influenced Barrett most strongly, followed by Haigis and SRK/T. Given the stronger correlation between the change in PPR in Barrett and the change in ACD, LT, and WTW, the change of ACD, LT, and WTW is more important to the influence of dilation on Barrett. The influence of dilation on each formula and variable, including ACD, LT, and WTW, is key to improving IOL calculation.
Fatty acid biosynthesis and transcriptional regulation of Stearoyl-CoA Desaturase 1 (SCD1) in Buffalo milk
Authors: Li Zhipeng , Lu Suyu , Cui Kuiqing , Shafique Laiba , Rehman Saif ur , Luo Chan , Wang Zhiqiang , Ruan Jue , Qian Qian , Liu Qingyou 
Published: January 2020

Abstract
Background: Buffalo milk is considered as a highly nutritious food owing to its higher contents of fatty acids (FA)and rich nutrient profile. Higher fat contents of buffalo milk make it suitable for processing to develop various healthy and nutritious products. Moreover, buffalo milk contains more unsaturated FAs (UFA) such as oleic and linolenic acid, which are important from the human health point of view owing to their desirable physiological effects. However, inadequate information is available about the chemical composition and mechanism of FA synthesis in buffalo milk. In this study, we hypothesized that expression of SCD 1 gene could alter the biosynthesis of FA in epithelial cells of mammary gland and subsequently affect the FA contents in b uffalo milk. We investigated the transcriptional and biological role of Stearoyl-CoA Desaturase 1 ( SCD 1) in the buffalo mammary epithelial cells (BMECs) during FA and triacylglycerol (TAG) synthesis. Results : Results revealed that unsaturated fatty acid contents were much higher in concentration in buffalo milk as compared to Holstein cow. Significant increase in the expression level of FAS , ACACA , SREBP 1, PPARG , GPAT , and AGPAT genes was observed in response to altered expression of SCD 1 in buffalo milk . Moreover, change in SCD1 gene in BMECs also mediated the expression of genes related to FA biosynthesis subsequently leading to alter the FA composition. Overexpression of SCD1 significantly increased the expression of genes associated with FA and TAG synthesis leading to enhance FA and unsaturated FA contents in BMECs. However, down-regulation of SCD1 exhibited opposite consequences. Conclusion: Our study provides mechanistic insights on transcriptional regulation of SCD 1 to alter FA and TAG synthesis through directly or indirectly mediating biosynthesis and metabolic pathways in BMECs. We provide preliminary findings regarding engineering of FA contents in buffalo milk through SCD 1 signaling.
Effects of Lactobacillus plantarum on intestinal integrity and immune responses of egg-laying chickens infected with Clostridium perfringens under the free-range or the specific pathogen free environment
Authors: Xu Tianyue , Chen Yan , Yu Longfei , Wang Jun , Huang Mingxing , Zhu Nianhua 
Published: January 2020

Abstract
Background Necrotic enteritis, which is caused by Clostridium perfringens, has resulted in more than $2 billion losses in the poultry industry every year. Due to the ban of antibiotics in feed industry, alternatives like environment improvement and probiotics have been found to be effective as well. In our study, we aim to explore the protective effect of Lactobacillus plantarum supplementation on CP infected chickens in two environments. Results The results showed that the Clostridium perfringens administration led to visible and histomorphological gut lesions. In the specific pathogen free or free-range system environment, dietary supplementation with LP obvious increased the ratio of intestinal villus height to crypt depth and the expression of MUC2 mRNA in ileum mucosa, then reduced the mRNA expression level of TNF-α gene in the ileum mucosa. LP treatment significantly reduced the contents of total protein, total superoxide dismutase and glutamic oxaloacetic transaminase in serum of the chickens. Conclusions The specific pathogen free environment contributed to the recovery of pre-inflammation of the chickens, and free-range system environment contributed to the repair of damage in the later stages of chicken inflammation. Supplementation of LP in FRS environment was more conducive to the recovery of CP infected in chickens.
Complete genome sequencing and comparative genomic analyses of Bacillus sp. S3, a novel hyper Sb(III)-oxidizing bacterium
Authors: Li Jiaokun , Gu Tianyuan , Zeng Weimin , Yu Runlan , Liu Yuandong , Wu Xueling , Shen Li , Qiu Guanzhou , Li Liang Zhi 
Published: January 2020

Abstract
Background: Antimonite [Sb(III)]-oxidizing bacterium has great potential in the environmental bioremediation of Sb-polluted sites. Bacillus sp. S3 that was previously isolated from antimony-contaminated soil displayed high Sb(III) resistance and Sb(III) oxidation efficiency. However, the genomic information and evolutionary feature of Bacillus sp. S3 are very scarce. Results: Here, we identified a 5,579,638 bp chromosome with 40.30% GC content and a 241,339 bp plasmid with 36.74% GC content in the complete genome of Bacillus sp. S3. Genomic annotation showed that Bacillus sp. S3 contained a key aioB gene potentially encoding As(III)/Sb(III) oxidase, which was not shared with other Bacillus strains. Further, a series of genes associated with Sb(III) and other heavy metal(loid)s were also ascertained in Bacillus sp. S3, reflecting its adaptive advantage for growth in the harsh eco-environment. Based on the analysis of phylogenetic relationship and the average nucleotide identities (ANI), we found that Bacillus sp. S3 was a novel species within the Bacillus genus. The majority of mobile genetic elements (MGEs) mainly distributed on chromosomes within the Bacillus genus. Pan-genome analysis showed that the 45 genomes contained 554 core genes and many unique genes were dissected in analyzed genomes. Whole genomic alignment showed that Bacillus genus underwent frequently large-scale evolutionary events. In addition, the origin and evolution analysis of Sb(III)-resistance genes revealed that evolutionary relationships and horizontal gene transfer (HGT) events among the Bacillus genus. The assessment of functionality of heavy metal(loid)s resistance genes emphasized its indispensable roles in the harsh eco-environment of Bacillus genus. The real-time Quantitative PCR (RT-qPCR) results of Sb(III)-related genes indicated that the Sb(III) resistance was constantly increased under the Sb(III) stress. Conclusions: The results in this study shed light on the molecular mechanisms of Bacillus sp. S3 coping with Sb(III), extended our understanding on the evolutionary relationship between Bacillus sp. S3 and other closely related species, and further enriched the Sb(III) resistance genetic data sources.
Classification of Andrographis paniculata extracts by solvent extraction using HPLC fingerprint and chemometric analysis
Authors: Rafi Mohamad , Devi Anggun Fenika , Syafitri Utami Dyah , Heryanto Rudi , Suparto Irma Herawati , Amran Muhammad Bachri , Rohman Abdul , Prajogo Bambang , Lim Lee Wah 
Published: January 2020

Abstract
Objective: Andrographis paniculata, widely used as an antidiabetic in Indonesian traditional medicines (jamu), contains chemical compounds whose concentration is related to its therapeutic effects. The concentration of solvents used for extraction will also affect the number of compounds extracted. Therefore, a quality control method is needed to ensure consistency in quantifying these compounds in A. paniculata to improve its therapeutic application. High-performance liquid chromatography fingerprint analysis combined with chemometrics was used to evaluate extracts from different solvent extraction treatments. The content of andrographolide, the main bioactive compound in A. paniculata, and the level of α-glucosidase inhibition activity, an indicator of its antidiabetic activity, were also determined.
Results: Fingerprint chromatograms of A. paniculata extracts from different treatments exhibited a similar pattern with several peaks in common, only differing in area and intensity value. The A. paniculata extracts were classified using HPLC fingerprint and principal component analysis to allow grouping according to their respective solvent extraction treatments. The highest andrographolide content and α-glucosidase inhibition activity occurred in the 50% ethanol extract and the lowest in the water extract. HPLC fingerprint analysis could be used for identifying A. paniculata extracts based on solvent extraction, thus improving quality control for their therapeutic application.