bluuebunny/crossref_metadata_2025_split huggingface dataset:
Internal carotid artery patency after mechanical thrombectomy for stroke due to occlusive dissection: Impact on outcome
Authors: Scopelliti Giuseppe , Karam Arnaud , Labreuche Julien , Bricout Nicolas , Marrama Federico , Diomedi Marina , Ben Hassen Wagih , Leclerc Xavier , Cordonnier Charlotte , Henon Hilde , Casolla Barbara 
Published: December 2022

Introduction: Internal carotid artery dissection (ICAD) is a rare cause of acute ischemic stroke with large vessel occlusion (AIS-LVO). We aimed investigating the impact on outcome of internal carotid artery (ICA) patency after mechanical thrombectomy (MT) for AIS-LVO due to occlusive ICAD. Patients and methods: We included consecutive patients with AIS-LVO due to occlusive ICAD treated with MT from January 2015 to December 2020 in three European stroke centers. We excluded patients with unsuccessful intracranial reperfusion after MT (modified Thrombolysis in Cerebral Infarction (mTICI) score < 2b). We compared 3-month favorable clinical outcome rate, defined as a modified Rankin scale (mRS) score ⩽2, according to ICA status (patency vs occlusion) at the end of MT and at 24-h follow-up imaging, using univariate and multivariable models. Results: Among 70 included patients, ICA was patent in 54/70 (77%) at the end of MT, and in 36/66 (54.5%) patients with 24-h follow-up imaging. Among patients with ICA patency at the end of MT, 32% presented ICA occlusion at 24-h control imaging. Favorable 3-month outcome occurred in 41/54 (76%) patients with ICA patency post-MT and in 9/16 (56%) patients with occluded ICA post-MT ( p = 0.21). Rates of favorable outcome were significantly higher in patients with 24-h ICA patency compared to patients with 24-h ICA occlusion (32/36 [89%] vs 15/30 [50%]), with an adjusted odds ratio of 4.67 (95% CI: 1.26–17.25). Discussion and conclusion: Obtaining sustained (24-h) ICA patency after MT could be a therapeutic target for improving functional outcome in patients with AIS-LVO due to ICAD.
The Relationship between Bacterial Load and Initial Run Time of a Surgical Helmet
Authors: Lynch Brian C , Swanson David R , Marmor William A , Gibb Bryan , Komatsu David E , Wang Edward D 
Published: December 2022

Background Periprosthetic joint infection (PJI) is a complication of arthroplasty surgery with significant morbidity and mortality. Surgical helmets are a possible source of infection. Pre-existing dust and microorganisms on its surface may be blown into the surgical field by the helmet ventilation system. Methods Twenty surgical helmets at our institution were assessed through microscopy and polymerase chain reaction testing. Helmets were arranged with agar plates under the front and rear outflow vents. Helmets ran while plates were exchanged at different time points. Bacterial growth was assessed via colony counts and correlated with fan operating time. Gram staining and 16S sequencing were performed to identify bacterial species. Results The primary microbiological contaminate identified was Burkholderia. There was an inverse relationship between colony formation and fan operating time. The highest number of colonies was found within the first minute of fan operating time. There was a significant decrease in the number of colonies formed from the zero-minute to the three (27 vs 5; P = <.01), four (27 vs 3; P = <.01), and five-minute (27 vs 4; P = <.01) time points for the front outflow plates. A significant difference was also observed between the one-minute and four-minute time points ( P = .046). Conclusion We observed an inverse relationship between bacterial spread helmet fan operation time, which may correlate with dispersion of pre-existing contaminates. To decrease contamination risk, we recommend that helmets are run for at least 3 min prior to entering the operating room.
Circadian gene CSNK1D promoted the progression of hepatocellular carcinoma by activating Wnt/β-catenin pathway via stabilizing Dishevelled Segment Polarity Protein 3
Authors: Zhu Mengqi , Zhang Jianping , Bian Saiyan , Zhang Xue , Shen Yiping , Ni Zhiyu , Xu Shiyu , Cheng Chun , Zheng Wenjie 
Published: December 2022

Abstract
Purpose
A variety of studies have connected circadian rhythm to the initiation and progression of hepatocellular carcinoma (HCC). The purpose of this study was to figure out about the circadian genes' profile characteristics, prognostic significance, and targeted values in HCC.

Methods
The expression profiles and prognostic significance of circadian genes in the cancer genome atlas liver hepatocellular carcinoma (TCGA-LIHC) database were investigated using bioinformatics analysis. The expression features of Casein Kinase 1 Delta (CSNK1D), a robust signature gene, was further detected by immunohistochemistry, western blotting and Real-time quantitative PCR (RT-qPCR) in a local HCC cohort. The effect of CSNK1D on corresponding phenotypes of HCC cells was evaluated using Cell Counting Kit-8 (CCK8), flowcytometry, clone assay, Transwell assay, and xenograft assay. In addition, the underlying mechanisms of CSNK1D in the Wnt/β-catenin signaling were validated by multiple molecular experiments.

Results
Abnormal expression of the Circadian genome was associated with the malignant clinicopathological characteristics of HCC patients. A 10 circadian gene-based signature with substantial prognostic significance was developed using Cox regression and least absolute shrinkage and selection operator (LASSO) analysis. Of them, CSNK1D, significantly elevated in a local HCC cohort, was chosen for further investigation. Silencing or overexpression of CSNK1D significantly reduced or increased proliferation, invasion, sorafenib resistance, xenograft development, and epithelial-mesenchymal transformation (EMT) of HCC cells, respectively. Mechanically, CSNK1D exacerbated the aggressiveness of HCC cells by activating Wnt/β-catenin signaling through interacting with Dishevelled Segment Polarity Protein 3 (DVL3).

Conclusions
The Circadian gene CSNK1D was found to contribute to HCC progression by boosting the Wnt/β-catenin pathway, hinting that it could be a prospective therapeutic target for HCC.
Characterization of the Dicranostigma leptopodum chloroplast genome and comparative analysis within subfamily Papaveroideae
Authors: Wang Lei , Li Fuxing , Wang Ning , Gao Yongwei , Liu Kangjia , Zhang Gangmin , Sun Jiahui 
Published: December 2022

AbstractBackgroundDicranostigma leptopodum(Maxim.) Fedde is a perennial herb with bright yellow flowers, well known as "Hongmao Cao" for its medicinal properties, and is an excellent early spring flower used in urban greening. However, its molecular genomic information remains largely unknown. Here, we sequenced and analyzed the chloroplast genome ofD. leptopodumto discover its genome structure, organization, and phylogenomic position within the subfamily Papaveroideae.ResultsThe chloroplast genome size ofD. leptopodumwas 162,942 bp, andD. leptopodumexhibited a characteristic circular quadripartite structure, with a large single-copy (LSC) region (87,565 bp), a small single-copy (SSC) region (18,759 bp) and a pair of inverted repeat (IR) regions (28,309 bp). TheD. leptopodumchloroplast genome encoded 113 genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The dynamics of the genome structures, genes, IR contraction and expansion, long repeats, and single sequence repeats exhibited similarities, with slight differences observed among the eight Papaveroideae species. In addition, seven interspace regions and three coding genes displayed highly variable divergence, signifying their potential to serve as molecular markers for phylogenetic and species identification studies. Molecular evolution analyses indicated that most of the genes were undergoing purifying selection. Phylogenetic analyses revealed thatD. leptopodumformed a clade with the tribe Chelidonieae.ConclusionsOur study provides detailed information on theD. leptopodumchloroplast genome, expanding the available genomic resources that may be used for future evolution and genetic diversity studies.
Description of a novel species of Leclercia, Leclercia tamurae sp. nov. and proposal of a novel genus Silvania gen. nov. containing two novel species Silvania hatchlandensis sp. nov. and Silvania confinis sp. nov. isolated from the rhizosphere of oak
Authors: Maddock Daniel , Arnold Dawn , Denman Sandra , Brady Carrie 
Published: December 2022

AbstractBackgroundAcute Oak Decline (AOD) is a decline disease first reported on native oaks in the UK, but in recent years reports from further afield such as Europe and the Middle East, indicate that the distribution and host range is increasing at an alarming rate. The stem weeping symptoms of the disease partially develop due to polymicrobial-host interaction, caused by several members of the order Enterobacterales. While investigating the rhizosphere soil of AOD-unaffected trees, termed ‘healthy’ trees, and diseased oaks suffering from Acute Oak Decline (AOD), an enrichment method designed for enhanced recovery of Enterobacterales led to the recovery of several isolates that could not be classified as any existing species. These isolates showed a close relationship to the genusLeclercia, of which both species are of clinical importance, but the type speciesLeclercia adecarboxylataalso displays plant growth-promoting properties in the rhizosphere.ResultsPartial sequencing of four housekeeping genes revealed similarity to the genusLeclerciawith varying degrees of relatedness. As such a complete polyphasic approach was used to determine the true taxonomic position of these isolates. This involved whole genome sequencing, phylogenomic analysis, phylogenetic analysis of both the 16S rRNA and four housekeeping gene sequences, combined with phenotypic testing and fatty acid analysis. Both the phylogenomic and phylogenetic analyses separated the isolates into four clusters, two of which were contained in theLeclerciaclade. The remaining two clusters formed a separate lineage far removed from any currently defined species. Further investigation into the role of the isolates as plant growth-promoting bacteria as well as plant pathogens was investigated computationally, revealing a number of plant growth-promoting traits as well as virulence genes related to motility, adhesion and immune modulation.ConclusionBased on the genotypic and phenotypic data presented here, these isolates could be differentiated from each other and their closest neighbours. As such we propose the description ofLeclercia tamuraesp. nov. (type strain H6S3T = LMG 32609T = CCUG 76176T),Silvaniagen. nov.,Silvania hatchlandensissp. nov. (type strain H19S6T = LMG 32608T = CCUG 76185T) andSilvania confinissp. nov. (type strain H4N4T = LMG 32607T = CCUG 76175T). Due to their interesting protein annotations and alignments, these species warrant further investigation for their role in relation to plant health.
Transcriptome profiling of two Moringa species and insights into their antihyperglycemic activity
Authors: Shafi K. Mohamed , Sajeevan Radha Sivarajan , Kouser Sania , Vishnuprasad Chethala N , Sowdhamini Ramanathan 
Published: December 2022

Abstract
Background
Moringa concanensis Nimmo (MC), a plant that resembles Moringa oleifera Lam. (MO), has less scientific information but has traditionally been used as a medicinal plant. Moringa species have long been known for their medicinal qualities, which include antioxidant, anti-inflammatory, anticancer, and antihyperglycemic effects. We investigated the antidiabetic potential of MC and MO species in this study by using transcriptome profiling, metabolite analysis, and in vitro assay studies.

Results
Our transcriptome analysis revealed the expression of enzymes involved in the biosynthesis of quercetin, chlorogenic acid, and benzylamine, all of which have previously been shown to have antidiabetic activity. We compared the expression patterns of five different tissues from MC and MO and it was found that the key enzymes involved in the biosynthesis of these compounds were highly expressed in leaf tissue. The expression estimated by MC transcriptome data in different tissues was verified using RT-qPCR analysis. The amount of these compounds was further quantified in the crude leaf extract of both species and found that MC had a higher abundance of quercetin and chlorogenic acid than MO. The crude leaf extract from both MC and MO were further tested in vitro, and the results demonstrated strong inhibitory activity for α-glucosidase and DPP-IV enzymes. Our findings suggest that compounds in leaf tissue, such as quercetin, benzylamine, and chlorogenic acid, could play a significant role in this antidiabetic activity. In addition, when comparing MO plants, we found that MC had a slightly higher effect in expression, abundance, and inhibitory activity.

Conclusions
This study presents the first report of MC transcriptome data, as well as a comparison of its anti-diabetic activity to MO. Our analysis discussed the significance of leaf tissue in antidiabetic activity compared to other tissues of both species. Overall, this study not only provides transcriptome resources for Moringa species, but also sheds light on antidiabetic potential of both species.
OrchidBase 5.0: updates of the orchid genome knowledgebase
Authors: Chen You-Yi , Li Chung‐I , Hsiao Yu-Yun , Ho Sau-Yee , Zhang Zhe-Bin , Liao Chien-Chi , Lee Bing-Ru , Lin Shao-Ting , Wu Wan-Lin , Wang Jeen-Shing , Zhang Diyang , Liu Ke-Wei , Liu Ding-Kun , Zhao Xue-Wei , Li Yuan-Yuan , Ke Shi-Jie , Zhou Zhuang , Huang Ming-Zhong , Wu Yong-Shu , Peng Dong-Hui , Lan Si-Ren , Chen Hong-Hwa , Liu Zhong-Jian , Wu Wei-Sheng , Tsai Wen-Chieh 
Published: December 2022

AbstractContaining the largest number of species, the orchid family provides not only materials for studying plant evolution and environmental adaptation, but economically and culturally important ornamental plants for human society. Previously, we collected genome and transcriptome information of Dendrobium catenatum, Phalaenopsis equestris, and Apostasia shenzhenica which belong to two different subfamilies of Orchidaceae, and developed user-friendly tools to explore the orchid genetic sequences in the OrchidBase 4.0. The OrchidBase 4.0 offers the opportunity for plant science community to compare orchid genomes and transcriptomes and retrieve orchid sequences for further study.In the year 2022, two whole-genome sequences of Orchidoideae species, Platanthera zijinensis and Platanthera guangdongensis, were de novo sequenced, assembled and analyzed. In addition, systemic transcriptomes from these two species were also established. Therefore, we included these datasets to develop the new version of OrchidBase 5.0. In addition, three new functions including synteny, gene order, and miRNA information were also developed for orchid genome comparisons and miRNA characterization.OrchidBase 5.0 extended the genetic information to three orchid subfamilies (including five orchid species) and provided new tools for orchid researchers to analyze orchid genomes and transcriptomes. The online resources can be accessed at https://cosbi.ee.ncku.edu.tw/orchidbase5/
Proteome profiles during early stage of somatic embryogenesis of two Eucalyptus species
Authors: Chen Bowen , Li Changrong , Chen Yingying , Chen Shengkan , Xiao Yufei , Wu Qi , Zhong Lianxiang , Huang Kaiyong 
Published: December 2022

Abstract
Background
Somatic embryogenesis (SE) was recognized as an important tool for plants to propagate. However, our knowledge about the proteins involved in early SE including the callus dedifferentiation is still limited, especially in the economic woody tree – Eucalyptus.

Results
We used the data-independent acquisition mass-spectrometry to study the different proteome profiles of early SE of two Eucalyptus species—E. camaldulensis (high regeneratively potential) and E. grandis x urophylla (low regenerative potential). Initially, 35,207 peptides and 7,077 proteins were identified in the stem and tissue-culture induced callus of the two Eucalyptus species. MSstat identified 2,078 and 2,807 differentially expressed proteins (DEPs) in early SE of E. camaldulensis and E. grandis x urophylla, respectively. They shared 760 upregulated and 420 downregulated proteins, including 4 transcription factors, 31 ribosomal proteins, 1 histone, 3 zinc finger proteins (ZFPs), 16 glutathione transferases, 10 glucosyltransferases, ARF19, WOX8 and PIN1. These proteins might be involved in the early SE of Eucalyptus. By combining the miRNA and RNA-Seq results, some miRNA ~ gene/protein regulatory networks were identified in early SE of Eucalyptus, such as miR160 ~ TPP2, miR164 ~ UXS2, miR169 ~ COX11 and miR535 ~ Eucgr.E01067. Further, we found SERK, WRKY, ZFP and ABC transporter might be related with high SE potential.

Conclusions
Overall, our study identified proteins involved in the early SE and related to the high regeneration potential of Eucalyptus. It greatly enhanced our understanding of the early SE and the SE capacity of Eucalyptus.
Positive end-expiratory pressure and prone position alter the capacity of force generation from diaphragm in acute respiratory distress syndrome: an animal experiment
Authors: Firstiogusran Andi Muhammad Fadlillah , Yoshida Takeshi , Hashimoto Haruka , Iwata Hirofumi , Fujino Yuji 
Published: December 2022

Abstract
Background
Spontaneous breathing potentially injures lungs and diaphragm when spontaneous effort is vigorous in acute respiratory distress syndrome (ARDS) while immobility also has risks of Intensive Care Unit (ICU) acquired weakness and diaphragm atrophy. Thus, ventilatory strategy to mitigate strong spontaneous effort should be promptly established without a systemic use of neuromuscular blocking agent. Here, we investigated the impacts of positive end-expiratory pressure (PEEP) and body position on the capacity of force generation from diaphragm following bilateral phrenic nerve stimulations in a rabbit ARDS model.

Methods
Using lung-injured rabbits, we measured 1) transdiaphragmatic pressure by bilateral phrenic nerve stimulation and 2) end-expiratory lung volume using computed tomography, under two different levels of PEEP (high, low) and body positions (supine, prone).

Results
Overall, transdiaphragmatic pressure was the highest at low PEEP in supine position and the lowest at high PEEP in prone position. Compared to values in low PEEP + supine, transdiaphragmatic pressure was significantly reduced by either prone alone (the same PEEP) or increasing PEEP alone (the same position) or both combinations. End-expiratory lung volume was significantly increased with increasing PEEP in both positions, but it was not altered by body position.

Interpretation
The capacity of force generation from diaphragm was modulated by PEEP and body position during mechanical ventilation in ARDS. Higher PEEP or prone position per se or both was effective to decrease the force generation from diaphragm.
Effect of triage training on the knowledge application and practice improvement among the practicing nurses of the emergency departments of the National Referral Hospitals, 2018; a pre-post study in Asmara, Eritrea
Authors: Bahlibi Teklu Tsegai , Tesfamariam Eyasu Habte , Andemeskel Yonatan Mehari , Weldegiorgis Ghidey Gebreyohannes 
Published: December 2022

Abstract
Background
Triage starts at the front door of the Emergency Department (ED), and repeatedly performed by the responsible duty nurses with the aim of facilitating a timely and appropriate treatment of patients. A triage system called the Orotta Triage System was implemented in the emergency settings of the selected hospitals in 2006, with the emergency nurses trained to triage using the system. Since the introduction, a majority of nurses have been replaced by new untrained nurses. This study was conducted to assess the impact of an educational intervention on the triage nurses knowledge and performance.

Methods
A single group pre-posttest study design was performed in the adult EDs of the National Referral Eritrean Referral Hospitals, from January to July of 2018. All staff members in the ED were involved. Data collection tools utilized were, a self-administered knowledge assessing questionnaire and a practice observation checklist. Analysis was done in SPSS (version 22) using repeated measures ANOVA. Statistical significance level was set at P < 0.05.

Results
The mean knowledge scores at Time 1(prior to the intervention), Time 2 (following the intervention) and Time 3 (three month follow up) were 6.23 (SD = 2.29), 10.55 (SD = 1.79), and 9.39(SD = 2.67) respectively. During the pre-intervention phase, only one (3%) nurse was determined to have adequate knowledge. Two days post training (immediate post-intervention), the percentage possessing adequate knowledge increased to 39% but dropped back to 19% three months later. Mean knowledge difference scores (95% CI) of immediate post and pre-intervention (Diff. = 4.32, 1 95%CI: 3.08–5.56), three months later and pre-intervention (Diff. = 3.16, 95%CI: 1.71–4.62) and immediate post and three months later (Diff. = 1.16, 95%CI: 0.12–2.20) were found to be statistically significant. The median score of appropriate triage practice at pre-intervention (Md = 6, IQR = 3) was not significantly different (p = 0.053) from that at post-intervention (Md = 8, IQR = 5).

Conclusion
The level of triage knowledge and appropriate application was low among the emergency nurses prior to training. The training provided an initial improvement in knowledge, but no significant improvement in triage nursing performance. To optimize ED triage performance, appropriate, timely in-service training is required to ensure new staff are educated and experienced staff have their knowledge and skills refreshed.