bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of COVID-19-restrictive measures on ambient particulate matter pollution in Yangon, Myanmar
Authors: Aung Win-Yu , Paw-Min-Thein-Oo  , Thein Zaw-Lin , Matsuzawa Sadao , Suzuki Takehiro , Ishigaki Yo , Fushimi Akihiro , Mar Ohn , Nakajima Daisuke , Win-Shwe Tin-Tin 
Published: September 2021

Abstract
Background
Particulate matter (PM) is recognized as the most harmful air pollutant to the human health. The Yangon city indeed suffers much from PM-related air pollution. Recent research has interestingly been focused on the novel subject of changes in the air quality associated with the restrictive measures in place during the current coronavirus disease-2019 (COVID-19) pandemic. The first case of COVID-19 in Myanmar was diagnosed on March 23, 2020. In this article, we report on our attempt to evaluate any effects of the COVID-19-restrictive measures on the ambient PM pollution in Yangon.

Methods
We measured the PM concentrations every second for 1 week on four occasions at three study sites with different characteristics; the first occasion was before the start of the COVID-19 pandemic and the remaining three occasions were while the COVID-19-restrictive measures were in place, including Stay-At-Home and Work-From-Home orders. The Pocket PM2.5 Sensor [PRO] designed by the National Institute for Environmental Studies (NIES), Japan, in cooperation with Yaguchi Electric Co., Ltd., (Miyagi, Japan) was used for the measurement of the ambient PM2.5 and PM10 concentrations.

Results
The results showed that there was a significant reduction (P < 0.001) in both the PM2.5 and PM10 concentrations while the COVID-19-restrictive measures were in place as compared to the measured values prior to the pandemic. The city experienced a profound improvement in the PM-related air quality from the “unhealthy” category prior to the onset of the COVID-19 pandemic to the “good” category during the pandemic, when the restrictive measures were in place. The percent changes in the PM concentrations varied among the three study sites, with the highest percent reduction noted in a semi-commercial crowded area (84.8% for PM2.5; 88.6% for PM10) and the lowest percent reduction noted in a residential quiet area (15.6% for PM2.5; 12.0% for PM10); the percent reductions also varied among the different occasions during the COVID-19 pandemic that the measurements were made.

Conclusions
We concluded that the restrictive measures which were in effect to combat the COVID-19 pandemic had a positive impact on the ambient PM concentrations. The changes in the PM concentrations are considered to be largely attributable to reduction in anthropogenic emissions as a result of the restrictive measures, although seasonal influences could also have contributed in part. Thus, frequent, once- or twice-weekly Stay-At-Home or Telework campaigns, may be feasible measures to reduce PM-related air pollution. When devising such an action plan, it would be essential to raise the awareness of public about the health risks associated with air pollution and create a social environment in which Telework can be carried out, in order to ensure active compliance by the citizens.
KinOrtho: a method for mapping human kinase orthologs across the tree of life and illuminating understudied kinases
Authors: Huang Liang-Chin , Taujale Rahil , Gravel Nathan , Venkat Aarya , Yeung Wayland , Byrne Dominic P. , Eyers Patrick A. , Kannan Natarajan 
Published: September 2021

AbstractBackgroundProtein kinases are among the largest druggable family of signaling proteins, involved in various human diseases, including cancers and neurodegenerative disorders. Despite their clinical relevance, nearly 30% of the 545 human protein kinases remain highly understudied. Comparative genomics is a powerful approach for predicting and investigating the functions of understudied kinases. However, an incomplete knowledge of kinase orthologs across fully sequenced kinomes severely limits the application of comparative genomics approaches for illuminating understudied kinases. Here, we introduce KinOrtho, a query- and graph-based orthology inference method that combines full-length and domain-based approaches to map one-to-one kinase orthologs across 17 thousand species.ResultsUsing multiple metrics, we show that KinOrtho performed better than existing methods in identifying kinase orthologs across evolutionarily divergent species and eliminated potential false positives by flagging sequences without a proper kinase domain for further evaluation. We demonstrate the advantage of using domain-based approaches for identifying domain fusion events, highlighting a case between an understudied serine/threonine kinase TAOK1 and a metabolic kinase PIK3C2A with high co-expression in human cells. We also identify evolutionary fission events involving the understudied OBSCN kinase domains, further highlighting the value of domain-based orthology inference approaches. Using KinOrtho-defined orthologs, Gene Ontology annotations, and machine learning, we propose putative biological functions of several understudied kinases, including the role of TP53RK in cell cycle checkpoint(s), the involvement of TSSK3 and TSSK6 in acrosomal vesicle localization, and potential functions for the ULK4 pseudokinase in neuronal development.ConclusionsIn sum, KinOrtho presents a novel query-based tool to identify one-to-one orthologous relationships across thousands of proteomes that can be applied to any protein family of interest. We exploit KinOrtho here to identify kinase orthologs and show that its well-curated kinome ortholog set can serve as a valuable resource for illuminating understudied kinases, and the KinOrtho framework can be extended to any protein-family of interest.
The molecular interplay of the establishment of an infection – gene expression of Diaphorina citri gut and Candidatus Liberibacter asiaticus
Authors: Bento Flavia Moura Manoel , Darolt Josiane Cecília , Merlin Bruna Laís , Penã Leandro , Wulff Nelson Arno , Cônsoli Fernando Luis 
Published: September 2021

Abstract
Background
Candidatus Liberibacter asiaticus (CLas) is one the causative agents of greening disease in citrus, an unccurable, devastating disease of citrus worldwide. CLas is vectored by Diaphorina citri, and the understanding of the molecular interplay between vector and pathogen will provide additional basis for the development and implementation of successful management strategies. We focused in the molecular interplay occurring in the gut of the vector, a major barrier for CLas invasion and colonization.

Results
We investigated the differential expression of vector and CLas genes by analyzing a de novo reference metatranscriptome of the gut of adult psyllids fed of CLas-infected and healthy citrus plants for 1-2, 3-4 and 5-6 days. CLas regulates the immune response of the vector affecting the production of reactive species of oxygen and nitrogen, and the production of antimicrobial peptides. Moreover, CLas overexpressed peroxiredoxin, probably in a protective manner. The major transcript involved in immune expression was related to melanization, a CLIP-domain serine protease we believe participates in the wounding of epithelial cells damaged during infection, which is supported by the down-regulation of pangolin. We also detected that CLas modulates the gut peristalsis of psyllids through the down-regulation of titin, reducing the elimination of CLas with faeces. The up-regulation of the neuromodulator arylalkylamine N-acetyltransferase implies CLas also interferes with the double brain-gut communication circuitry of the vector. CLas colonizes the gut by expressing two Type IVb pilin flp genes and several chaperones that can also function as adhesins. We hypothesized biofilm formation occurs by the expression of the cold shock protein of CLas.

Conclusions
The thorough detailed analysis of the transcritome of Ca. L. asiaticus and of D. citri at different time points of their interaction in the gut tissues of the host led to the identification of several host genes targeted for regulation by L. asiaticus, but also bacterial genes coding for potential effector proteins. The identified targets and effector proteins are potential targets for the development of new management strategies directed to interfere with the successful utilization of the psyllid vector by this pathogen.
Genome sequencing of the neotype strain CBS 554.65 reveals the MAT1–2 locus of Aspergillus niger
Authors: Ellena Valeria , Seekles Sjoerd J. , Vignolle Gabriel A. , Ram Arthur F. J. , Steiger Matthias G. 
Published: September 2021

Abstract
Background
Aspergillus niger is a ubiquitous filamentous fungus widely employed as a cell factory thanks to its abilities to produce a wide range of organic acids and enzymes. Its genome was one of the first Aspergillus genomes to be sequenced in 2007, due to its economic importance and its role as model organism to study fungal fermentation. Nowadays, the genome sequences of more than 20 A. niger strains are available. These, however, do not include the neotype strain CBS 554.65.

Results
The genome of CBS 554.65 was sequenced with PacBio. A high-quality nuclear genome sequence consisting of 17 contigs with a N50 value of 4.07 Mbp was obtained. The assembly covered all the 8 centromeric regions of the chromosomes. In addition, a complete circular mitochondrial DNA assembly was obtained. Bioinformatic analyses revealed the presence of a MAT1-2-1 gene in this genome, contrary to the most commonly used A. niger strains, such as ATCC 1015 and CBS 513.88, which contain a MAT1-1-1 gene. A nucleotide alignment showed a different orientation of the MAT1–1 locus of ATCC 1015 compared to the MAT1–2 locus of CBS 554.65, relative to conserved genes flanking the MAT locus. Within 24 newly sequenced isolates of A. niger half of them had a MAT1–1 locus and the other half a MAT1–2 locus. The genomic organization of the MAT1–2 locus in CBS 554.65 is similar to other Aspergillus species. In contrast, the region comprising the MAT1–1 locus is flipped in all sequenced strains of A. niger.

Conclusions
This study, besides providing a high-quality genome sequence of an important A. niger strain, suggests the occurrence of genetic flipping or switching events at the MAT1–1 locus of A. niger. These results provide new insights in the mating system of A. niger and could contribute to the investigation and potential discovery of sexuality in this species long thought to be asexual.
Transcriptome and metabolome analysis reveals anthocyanin biosynthesis pathway associated with ramie (Boehmeria nivea (L.) Gaud.) leaf color formation
Authors: Feng Xinkang , Gao Gang , Yu Chunming , Zhu Aiguo , Chen Jikang , Chen Kunmei , Wang Xiaofei , Abubakar Aminu Shehu , Chen Ping 
Published: September 2021

Abstract
Background
The bast fiber crop ramie can be used as high-quality forage resources, especially in tropical or subtropical region where there is lack of high-quality protein feed. Hongxuan No.1 (HX_1) is a unique ramie variety with a light reddish brown leaf color, which is obviously different from elite cultivar, Zhongzhu No.1 (ZZ_1, green leaf). While, the regulatory mechanism of color difference or secondary metaboliates synthesis between these two varieties have not been studied.

Results
In this study, phenotypic, transcriptomic and metabolomic analysis of HX_1 and ZZ_1 were conducted to elucidate the mechanism of leaf color formation. Chromaticity value and pigment content measuring showed that anthocyanin was the main metabolites imparting the different leaf color phenotype between the two varieties. Based on LC/MS, at least 14 anthocyanins were identified in leaves of HX_1 and ZZ_1, and the HX_1 showed the higher relative content of malvidin-, pelargonidin-,and cyanidin-based anthocyanins. Transcriptome and metabolome co-analysis revealed that the up-regulated expression of flavonoids synthesis gene was positively correlated with total anthocyanins accumulation in ramie leaf, and the differentfially expression of “blue gene” (F3’5’H) and the “red gene” (F3’H) in leaves bring out HX_1 metabolic flow more input into the cyanidin branch. Furthermore, the enrichment of glycosylated modification pathway (UGT and AT) and the expression of flavonoid 3-O-glucosyl transferase (UFGT), anthocyanidin reductase (ANR), in leaves were significantly influenced the diversity of anthocyanins between HX_1 and ZZ_1.

Conclusions
Phenotypic, transcriptomic and metabolomic analysis of HX_1 and ZZ_1 indicated that the expression levels of genes related to anthocyanin metabolism contribute to the color formation of ramie variety. Anthocyanins are important plant secandary metabilates with many physiological functions, the results of this study will deepened our understanding of ramie leaf color formation, and provided basis for molecular breeding of functional forage ramie.
Reproductive tract microbiota of women in childbearing age shifts upon gynecological infections and menstrual cycle
Authors: Cheng Lijuan , Gao Yan , Xia Qing , Wang Hui , Xie Xiuzhen , Liu Yurong , Shang Heying , Diao Yutao 
Published: September 2021

Abstract
Background
This study was undertaken to discover whether the vaginal microbe of women at childbearing age is different among groups defined by urogenital tract infections, childbearing history and menstrual cycle, respectively.

Results
This was a multiple case-control study of women at childbearing age who were assigned to case or control groups according to their states of urogenital tract infections. The participants were also grouped by childbearing history and menstrual cycle. Vaginal swabs were collected and stored at − 70 °C until assayed. The V3-V4 region of 16S rRNA gene was amplified using PCR and sequenced on the Illumina MiSeq platform. We tested the hypothesis of whether the relative abundance of microbial species in vaginal microbiota was varied with urogenital tract infections, childbearing history and menstrual cycle. The vaginal microbial richness (Alpha diversity measured by PD_whole tree) was decreased in normal women (without reproductive tract infections) than in those with bacterial vaginosis (BV), and decreased in pregnant women than in other groups of non-pregnancy. Similarly, women from groups of normal and in pregnancy had lower beta diversity on measure of unweighted_unifrac distance in comparison to those of infected and non-pregnant. The top 10 genus relative abundance, especially Lactobacillus, which was the most dominant genus with the relative abundance of 71.55% among all samples, did not differ significantly between groups of childbearing history and menstrual cycle analyzed by ANOVA and nonparametric kruskal_wallis. Lactobacillus iners and Lactobacillus helveticus have the most abundance, totally account for 97.92% relative abundance of genus Lactobacillus. We also found that a higher L.helveticus/L.iners ratio is more likely to present in normal women than in the infected and in pregnant than in non-pregnant, although these comparisons lack statistical significance.

Conclusions
The relative abundance of dominant bacterial taxa in vaginal microbial communities of women at childbearing age were not different among groups of childbearing history and menstrual cycle. Women from groups of in pregnancy and without reproductive tract infections had lower alpha and beta diversity. The composition of the main lactobacillus species may shift upon phases of a menstrual cycle and the status of reproductive tract infections.
Recent amplification of microsatellite-associated miniature inverted-repeat transposable elements in the pineapple genome
Authors: Lin Lianyu , Sharma Anupma , Yu Qingyi 
Published: September 2021

Abstract
Background
Miniature inverted-repeat transposable elements (MITEs) are non-autonomous DNA transposable elements that play important roles in genome organization and evolution. Genome-wide identification and characterization of MITEs provide essential information for understanding genome structure and evolution.

Results
We performed genome-wide identification and characterization of MITEs in the pineapple genome. The top two MITE families, accounting for 29.39% of the total MITEs and 3.86% of the pineapple genome, have insertion preference in (TA) n dinucleotide microsatellite regions. We therefore named these MITEs A. comosus microsatellite-associated MITEs (Ac-mMITEs). The two Ac-mMITE families, Ac-mMITE-1 and Ac-mMITE-2, shared sequence similarity in the terminal inverted repeat (TIR) regions, suggesting that these two Ac-mMITE families might be derived from a common or closely related autonomous elements. The Ac-mMITEs are frequently clustered via adjacent insertions. Among the 21,994 full-length Ac-mMITEs, 46.1% of them were present in clusters. By analyzing the Ac-mMITEs without (TA) n microsatellite flanking sequences, we found that Ac-mMITEs were likely derived from Mutator-like DNA transposon. Ac-MITEs showed highly polymorphic insertion sites between cultivated pineapples and their wild relatives. To better understand the evolutionary history of Ac-mMITEs, we filtered and performed comparative analysis on the two distinct groups of Ac-mMITEs, microsatellite-targeting MITEs (mt-MITEs) that are flanked by dinucleotide microsatellites on both sides and mutator-like MITEs (ml-MITEs) that contain 9/10 bp TSDs. Epigenetic analysis revealed a lower level of host-induced silencing on the mt-MITEs in comparison to the ml-MITEs, which partially explained the significantly higher abundance of mt-MITEs in pineapple genome. The mt-MITEs and ml-MITEs exhibited differential insertion preference to gene-related regions and RNA-seq analysis revealed their differential influences on expression regulation of nearby genes.

Conclusions
Ac-mMITEs are the most abundant MITEs in the pineapple genome and they were likely derived from Mutator-like DNA transposon. Preferential insertion in (TA) n microsatellite regions of Ac-mMITEs occurred recently and is likely the result of damage-limiting strategy adapted by Ac-mMITEs during co-evolution with their host. Insertion in (TA) n microsatellite regions might also have promoted the amplification of mt-MITEs. In addition, mt-MITEs showed no or negligible impact on nearby gene expression, which may help them escape genome control and lead to their amplification.
The association between platelet-to-lymphocyte ratio with mortality among patients suffering from acute decompensated heart failure
Authors: Heidarpour Maryam , Bashiri Sepideh , Vakhshoori Mehrbod , Heshmat-Ghahdarijani Kiyan , Khanizadeh Farbod , Ferdowsian Shaghayegh , Shafie Davood 
Published: September 2021

AbstractBackgroundPlatelet-to-lymphocyte ratio (PLR) is an inflammation index suggested to have the prognostic capability in heart failure (HF). We sought to investigate the association of PLR with cardiovascular disease (CVD) mortality and creatinine (Cr) rise among Iranian individuals suffering from acute decompensated HF (ADHF).MethodsThis retrospective cohort study was in the context of the Persian Registry Of cardioVascular diseasE/Heart Failure (PROVE/HF) study. 405 individuals with ADHF admitted to the emergency department were recruited from April 2019 to March 2020. PLR was calculated by division of platelet to absolute lymphocyte counts and categorized based on quartiles. We utilized the Kaplan–Meier curve to show the difference in mortality based on PLR quartiles. Cr rise was defined as the increment of at least 0.3 mg/dl from baseline. Cox proportional hazard ratio (HR) was used to investigate the association of PLR with CVDs mortality.ResultsMean age of participants was 65.9 ± 13.49 years (males: 67.7%). The mean follow-up duration was 4.26 ± 2.2 months. CVDs mortality or re-hospitalization was not significantly associated with PLR status. Multivariate analysis of PLR quartiles showed a minimally reduced likelihood of CVDs death in 2nd quartile versus the first one (HR 0.40, 95% confidence interval (CI) 0.16–1.01, P = 0.054). Cr rise had no remarkable relation with PLR status in neither model.ConclusionPLR could not be used as an independent prognostic factor among ADHF patients. Several studies are required clarifying the exact utility of this index.
The short-term safety and effectiveness of a new distal perforating stent graft in Type B aortic dissection: a retrospective study
Authors: Liu Xunqiang , Ji Wenkai , Tian Min , Chen Huanjun , Li Cuihong , Zhang Liqiong , Yang Ying , Wang Jifeng , Ji Min , Yang Chunxin , Zhu Enshuai , Cong Lei , Zhang Xili , Zhou Xiaona , Liu Hailong , Wang Jiaping , Tan Jing , Zhang Jinhui 
Published: September 2021

Abstract
Background
Spinal artery ischemia (SCI) events can result from over coverage of the descending thoracic aorta with a coated stent during Thoracic Endovascular Aortic Repair (TEVAR). The aim of this study was to determine whether a new distal perforating stent could reduce the incidence of spinal cord ischemia while remodeling the true lumen.

Methods
TBAD patients treated with Talos stent in the vascular surgery Department of Yan 'an Hospital affiliated to Kunming Medical University between December 2017 and October 2019 were retrospectively analyzed to investigate the short-term safety and effectiveness of Talos stent.

Results
A total of the 20 patients, including 14 males and 6 females, with an average age of 52.65 ± 8.98 years (range 37–68 years), were included in the analysis. Stent-grafts were successfully implanted in all patients under local anesthesia, with a technical success rate of 100%. The average operation time was 50.75 ± 13.01 min. A total of 2 cases (10%) presented chest pain associated with intercostal artery ischemia that was relieved on the 3rd and 5th postoperative day, respectively. Postoperative mean follow-up was 16.15 ± 3.99 months. No paraplegia or other complications occurred. And stenting did not induce new tears. No migration, deformation, or fracture of the stents occurred. There was a significant difference in the remolding of the true lumen preoperatively and at 12 months postoperatively (P < 0.05).

Conclusions
Talos stent has achieved satisfactory clinical treatment results in short term.