bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recent progress in the application of omics technologies in the study of bio-mining microorganisms from extreme environments
Authors: Li Min , Wen Jianping 
Published: September 2021

AbstractBio-mining microorganisms are a key factor affecting the metal recovery rate of bio-leaching, which inevitably produces an extremely acidic environment. As a powerful tool for exploring the adaptive mechanisms of microorganisms in extreme environments, omics technologies can greatly aid our understanding of bio-mining microorganisms and their communities on the gene, mRNA, and protein levels. These omics technologies have their own advantages in exploring microbial diversity, adaptive evolution, changes in metabolic characteristics, and resistance mechanisms of single strains or their communities to extreme environments. These technologies can also be used to discover potential new genes, enzymes, metabolites, metabolic pathways, and species. In addition, integrated multi-omics analysis can link information at different biomolecular levels, thereby obtaining more accurate and complete global adaptation mechanisms of bio-mining microorganisms. This review introduces the current status and future trends in the application of omics technologies in the study of bio-mining microorganisms and their communities in extreme environments.
Molecular epidemiology of blaCTX-M gene-producing uropathogenic Escherichia coli among Iranian kidney transplant patients: clonal dissemination of CC131 and CC10
Authors: Halaji Mehrdad , Shahidi Shahrzad , Ataei Behrooz , Atapour Abdolamir , Feizi Awat , Havaei Seyed Asghar 
Published: September 2021

Abstract
Background
This study aimed to investigate the phylogenetic characterization and virulence traits of uropathogenic Escherichia coli (UPEC) isolated from kidney transplant patients (KTPs) as well as non-KTPs and analyze the clonal distribution of Extended spectrum β-lactamases (ESBLs)-producing UPEC containing blaCTX-M gene.

Methods
To this end, we determined virulence marker and the phylogenetic characterization of UPEC in non-KTPs (n = 65) and KTPs (n = 46). The non-KTPs were considered the control group of the study. Also, according to the Achtman scheme, we performed multilocus sequence typing to assess the relationship between twenty-nine of ESBL-producing isolates containing blaCTX-M gene.

Results
According to the results of PCR assay, the prevalence of virulence factor genes ranged from 0% (cnf and papG III) to 93.7% (fimH). Also, KTP isolates significantly differed from non-KTP isolates only in terms of the prevalence of pap GI elements. Moreover, the most frequent UPEC isolates were in phylogenetic group B2, followed by group D (18.9%), and group A (13.5%). Furthermore, except for phylogenetic group C, there was no significant correlation between phylogenetic distribution in KTPs and non-KTPs. Additionally, MLST analysis of blaCTX-M carrying isolates identified 18 unique sequence types (ST) the most common of which was ST131 (24.1%), followed by ST1193 (10.3%), while fourteen STs were detected only once.

Conclusions
The results further revealed significant differences between the UPEC isolates from KTPs and non-KTPs regarding the phylogroups C and PAI gene. Based on MLST analysis, we also observed a relatively high diversity in UPEC isolates obtained from KTPs and non-KTPs. Moreover, clonal complex (CC) 131 and ST131 were found to be the most prevalent clones and ST types, respectively. Besides, for the first time, ST8503 were reported in KTPs. These results suggested regular studies on characterization of UPEC isolates among KTPs.
An ADAR1-dependent RNA editing event in the cyclin-dependent kinase CDK13 promotes thyroid cancer hallmarks
Authors: Ramírez-Moya Julia , Miliotis Christos , Baker Allison R. , Gregory Richard I. , Slack Frank J. , Santisteban Pilar 
Published: September 2021

AbstractBackgroundAdenosine deaminases acting on RNA (ADARs) modify many cellular RNAs by catalyzing the conversion of adenosine to inosine (A-to-I), and their deregulation is associated with several cancers. We recently showed that A-to-I editing is elevated in thyroid tumors and that ADAR1 is functionally important for thyroid cancer cell progression. The downstream effectors regulated or edited by ADAR1 and the significance of ADAR1 deregulation in thyroid cancer remain, however, poorly defined.MethodsWe performed whole transcriptome sequencing to determine the consequences of ADAR1 deregulation for global gene expression, RNA splicing and editing. The effects of gene silencing or RNA editing were investigated by analyzing cell viability, proliferation, invasion and subnuclear localization, and by protein and gene expression analysis.ResultsWe report an oncogenic function forCDK13in thyroid cancer and identify a new ADAR1-dependent RNA editing event that occurs in the coding region of its transcript.CDK13was significantly over-edited (c.308A > G) in tumor samples and functional analysis revealed that this editing event promoted cancer cell hallmarks. Finally, we show thatCDK13editing increases the nucleolar abundance of the protein, and that this event might explain, at least partly, the global change in splicing produced by ADAR1 deregulation.ConclusionsOverall, our data support A-to-I editing as an important pathway in cancer progression and highlight novel mechanisms that might be used therapeutically in thyroid and other cancers.
The role of lncRNAs and circRNAs in the PD-1/PD-L1 pathway in cancer immunotherapy
Authors: Jiang Wenxiao , Pan Shuya , Chen Xin , Wang Zhi-wei , Zhu Xueqiong 
Published: September 2021

AbstractCancer immunotherapy has recently shown promising antitumor effects in various types of tumors. Among all immune checkpoints, the PD-1/PD-L1 pathway plays an important role in the immune evasion of tumor cells, making it a potent target in antitumor immunity. Accordingly, antibodies targeting the PD-1/PD-L1 pathway have been developed to attack tumor cells; however, resistance to immune therapy remains to be solved. Hence, identification of the underlying modulators of the PD-1/PD-L1 pathway is of significant importance to understand the mechanisms of antitumor immunotherapy. Long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) have been identified to regulate the PD-1/PD-L1 pathway, leading to participation in the immune response and immunotherapy. Therefore, this review focuses on the functions of lncRNAs and circRNAs in regulation of the PD-1/PD-L1 axis in tumorigenesis and tumor progression. We hope this review will stimulate research to supply more precise and effective cancer immune checkpoint therapies for a large number of tumors.
Extracellular vesicles derived from CD73 modified human umbilical cord mesenchymal stem cells ameliorate inflammation after spinal cord injury
Authors: Zhai Xiao , Chen Kai , Yang Huan , Li Bo , Zhou Tianjunke , Wang Haojue , Zhou Huipeng , Chen Shaofeng , Zhou Xiaoyi , Wei Xiaozhao , Bai Yushu , Li Ming 
Published: September 2021

Abstract
Background
Spinal cord injury (SCI) is an inflammatory condition, and excessive adenosine triphosphate (ATP) is released into the extracellular space, which can be catabolized into adenosine by CD73. Extracellular vesicles have been designed as nano drug carriers in many diseases. However, their impacts on delivery of CD73 after SCI are not yet known. We aimed to construct CD73 modified extracellular vesicles and explore the anti-inflammatory effects after SCI.

Methods
CD73 engineered extracellular vesicles (CD73+ hucMSC-EVs) were firstly established, which were derived from human umbilical cord mesenchymal stem cells (hucMSCs) transduced by lentiviral vectors to upregulate the expression of CD73. Effects of CD73+ hucMSC-EVs on hydrolyzing ATP into adenosine were detected. The polarization of M2/M1 was verified by immunofluorescence. Furthermore, A2aR and A2bR inhibitors and A2bR knockdown cells were used to investigate the activated adenosine receptor. Biomarkers of microglia and levels of cAMP/PKA were also detected. Repetitively in vivo study, morphology staining, flow cytometry, cytokine analysis, and ELISA assay, were also applied for verifications.

Results
CD73+ hucMSC-EVs reduced concentration of ATP and promoted the level of adenosine. In vitro experiments, CD73+ hucMSC-EVs increased macrophages/microglia M2:M1 polarization, activated adenosine 2b receptor (A2bR), and then promoted cAMP/PKA signaling pathway. In mice using model of thoracic spinal cord contusion injury, CD73+ hucMSC-EVs improved the functional recovery after SCI through decreasing the content of ATP in cerebrospinal fluid and improving the polarization from M1 to M2 phenotype. Thus, the cascaded pro-inflammatory cytokines were downregulated, such as TNF-α, IL-1β, and IL-6, while the anti-inflammatory cytokines were upregulated, such as IL-10 and IL-4.

Conclusions
CD73+ hucMSC-EVs ameliorated inflammation after spinal cord injury by reducing extracellular ATP, promoting A2bR/cAMP/PKA pathway and M2/M1 polarization. CD73+ hucMSC-EVs might be promising nano drugs for clinical application in SCI therapy.

Graphical Abstract
Development, characteristics and impact of quality improvement casebooks: a scoping review
Authors: Anderson Natalie N. , Gagliardi Anna R. 
Published: September 2021

Abstract
Background
Quality improvement (QI) casebooks, compilations of QI experiences, are one way to share experiential knowledge that healthcare policy-makers, managers and professionals can adapt to their own contexts. However, QI casebook use, characteristics and impact are unknown. We aimed to synthesize published research on QI prevalence, development, characteristics and impact.

Methods
We conducted a scoping review by searching MEDLINE, EMBASE, CINAHL and SCOPUS from inception to 4 February 2021. We extracted data on study characteristics and casebook definitions, development, characteristics (based on the WIDER [Workgroup for Intervention Development and Evaluation Research] framework) and impact. We reported findings using summary statistics, text and tables.

Results
We screened 2999 unique items and included five articles published in Canada from 2011 to 2020 describing three studies. Casebooks focused on promoting positive weight-related conversations with children and parents, coordinating primary care-specialist cancer management, and showcasing QI strategies for cancer management. All defined casebooks similarly described real-world experiences of developing and implementing QI strategies that others could learn from, emulate or adapt. In all studies, casebook development was a multistep, iterative, interdisciplinary process that engages stakeholders in identifying, creating and reviewing content. While casebooks differed in QI topic, level of application and scope, cases featured common elements: setting or context, QI strategy details, impacts achieved, and additional tips for implementing strategies. Cases were described with a blend of text, graphics and tools. One study evaluated casebook impact, and found that it enhanced self-efficacy and use of techniques to improve clinical care. Although details about casebook development and characteristics were sparse, we created a template of casebook characteristics, which others can use as the basis for developing or evaluating casebooks.

Conclusion
Future research is needed to optimize methods for developing casebooks and to evaluate their impact. One approach is to assess how the many QI casebooks available online were developed. Casebooks should be evaluated alone or in combination with other interventions that support QI on a range of outcomes.
Mobility and muscle strength trajectories in old age: the beneficial effect of Mediterranean diet in combination with physical activity and social support
Authors: Saadeh Marguerita , Prinelli Federica , Vetrano Davide L. , Xu Weili , Welmer Anna-Karin , Dekhtyar Serhiy , Fratiglioni Laura , Calderón-Larrañaga Amaia 
Published: September 2021

Abstract
Introduction
Decline in physical function varies substantially across older individuals due to several extrinsic modifiable factors such as dietary patterns, physical activity and social support. We aimed to determine the association of these factors and their interaction with mobility and muscle strength decline.

Methods
We analyzed data from 1686 functionally healthy individuals aged 60 + from the population-based Swedish National study on Aging and Care in Kungsholmen (SNAC-K). The Mediterranean Diet Score (MDS) was calculated based on a validated food frequency questionnaire. Self-reported physical activity was categorized based on current recommendations, and social support was measured according to participants’ perceived material and psychological support from relatives and friends. Participants’ physical function was assessed over 12 years through changes in walking speed (m/s) and chair stand time (s). Linear mixed models adjusted for socio-demographic and clinical factors were used. In order to explore the combined effect of the different exposures, two indicator variables were created by cross-classifying individuals' levels of Mediterranean diet adherence and social support or physical activity.

Results
Participants with a high adherence to Mediterranean diet were primarily < 78 years (82.3%), women (56.1%), married (61.1%), with university education (52.8%), high levels of social support (39.3%) and health-enhancing levels of physical activity (51.5%). A one-point increase in MDS (score range 0–9) was associated with less annual deterioration in walking speed (β*time[year] = 0.001; p = 0.024) and chair-stand time (β*time[year] = -0.014; p = 0.008). The potential protective effect of Mediterranean diet was highest among participants reporting high social support (β*time[year] = -0.065, p = 0.026 for chair stands) and high physical activity (β*time[year] = 0.010, p = 0.001 for walking speed), beyond the effect of each exposure individually.

Conclusion
A higher adherence to Mediterranean diet, especially in combination with recommended levels of physical activity and high social support, may contribute to delay the decline in physical function observed with aging.
Establishment of a novel glycolysis-related prognostic gene signature for ovarian cancer and its relationships with immune infiltration of the tumor microenvironment
Authors: Bi Jianlei , Bi Fangfang , Pan Xue , Yang Qing 
Published: September 2021

Abstract
Background
Glycolysis affects tumor growth, invasion, chemotherapy resistance, and the tumor microenvironment. In this study, we aimed to construct a glycolysis-related prognostic model for ovarian cancer and analyze its relationship with the tumor microenvironment’s immune cell infiltration.

Methods
We obtained six glycolysis-related gene sets for gene set enrichment analysis (GSEA). Ovarian cancer data from The Cancer Genome Atlas (TCGA) database and two Gene Expression Omnibus (GEO) datasets were divided into two groups after removing batch effects. We compared the tumor environments' immune components in high-risk and low-risk groups and analyzed the correlation between glycolysis- and immune-related genes. Then, we generated and validated a predictive model for the prognosis of ovarian cancer using the glycolysis-related genes.

Results
Overall, 27/329 glycolytic genes were associated with survival in ovarian cancer, 8 of which showed predictive value. The tumor cell components in the tumor microenvironment did not differ between the high-risk and low-risk groups; however, the immune score differed significantly between groups. In total, 13/24 immune cell types differed between groups, including 10 T cell types and three other immune cell types. Eight glycolysis-related prognostic genes were related to the expression of multiple immune-related genes at varying degrees, suggesting a relationship between glycolysis and immune response.

Conclusions
We identified eight glycolysis-related prognostic genes that effectively predicted survival in ovarian cancer. To a certain extent, the newly identified gene signature was related to the tumor microenvironment, especially immune cell infiltration and immune-related gene expression. These findings provide potential biomarkers and therapeutic targets for ovarian cancer.
Muscle activation strategies of people with early-stage Parkinson’s during walking
Authors: Keloth Sana M. , Arjunan Sridhar P. , Raghav Sanjay , Kumar Dinesh Kant 
Published: September 2021

Abstract
Introduction
Some people with Parkinson’s disease (PD) frequently have an unsteady gait with shuffling, reduced strength, and increased rigidity. This study has investigated the difference in the neuromuscular strategies of people with early-stage PD, healthy older adults (HOA) and healthy young adult (HYA) during short-distance walking.

Method
Surface electromyogram (sEMG) was recorded from tibialis anterior (TA) and medial gastrocnemius (MG) muscles along with the acceleration data from the lower leg from 72 subjects—24 people with early-stage PD, 24 HOA and 24 HYA during short-distance walking on a level surface using wearable sensors.

Results
There was a significant increase in the co-activation, a reduction in the TA modulation and an increase in the TA-MG lateral asymmetry among the people with PD during a level, straight-line walking. For people with PD, the gait impairment scale was low with an average postural instability and gait disturbance (PIGD) score = 5.29 out of a maximum score of 20. Investigating the single and double support phases of the gait revealed that while the muscle activity and co-activation index (CI) of controls modulated over the gait cycle, this was highly diminished for people with PD. The biggest difference between CI of controls and people with PD was during the double support phase of gait.

Discussion
The study has shown that people with early-stage PD have high asymmetry, reduced modulation, and higher co-activation. They have reduced muscle activity, ability to inhibit antagonist, and modulate their muscle activities. This has the potential for diagnosis and regular assessment of people with PD to detect gait impairments using wearable sensors.
Analysis of intercondylar notch size and shape in patients with cyclops syndrome after anterior cruciate ligament reconstruction
Authors: Ficek Krzysztof , Rajca Jolanta , Cholewiński Jerzy , Racut Agnieszka , Gwiazdoń Paweł , Przednowek Krzysztof , Hajduk Grzegorz 
Published: September 2021

Abstract
Background
Cyclops lesion is the second most common cause of extension loss after anterior cruciate ligament reconstruction. This study focused on the correlation between the anatomy of the intercondylar notch and the incidence of cyclops lesion. To determine whether the size and shape of the intercondylar notch are related to cyclops lesion formation following anterior cruciate ligament reconstruction according to magnetic resonance imaging (MRI) findings.

Methods
One hundred twenty-five (125) patients were retrospectively evaluated. The notch width index (NWI) and notch shape index (NSI) were measured based on coronal and axial MRI sections in patients diagnosed with cyclops syndrome (n = 25), diagnosed with complete anterior cruciate ligament (ACL) tears (n = 50), and without cyclops lesions or ACL ruptures (n = 50).

Results
Imaging analysis results showed that the cyclops and ACL groups had lower mean NWI and NSI values than the control group. Significant between-group differences were found in NSI (p = 0.0140) based on coronal cross-sections and in NWI (p = 0.0026) and NSI (p < 0.0001) based on axial sections.

Conclusions
The geometry of the intercondylar notch was found to be associated with the risk of cyclops lesion formation and ACL rupture.
Risk factor analysis of clinical outcomes of total aortic arch replacement and frozen elephant trunk with aortic balloon occlusion
Authors: Wang Luchen , Li Yunfeng , Dun Yaojun , Sun Xiaogang 
Published: September 2021

Abstract
Background
Total aortic arch replacement (TAR) with frozen elephant trunk (FET) requires hypothermic circulatory arrest (HCA) for 20 min, which increases the surgical risk. We invented an aortic balloon occlusion (ABO) technique that requires 5 min of HCA on average to perform TAR with FET and investigated the possible merit of this new method in this study.

Methods
This retrospective study included consecutive patients who underwent TAR and FET (consisting of 130 cases of ABO group and 230 cases of conventional group) in Fuwai Hospital between August 2017 and February 2019. In addition to the postoperative complications, the alterations of blood routine tests, alanine transaminase (ALT) and aspartate transaminase (AST) during in-hospital stay were also recorded.

Results
The 30-day mortality rates were similar between ABO group (4.6%) and conventional group (7.8%, P = 0.241). Multivariate analysis showed ABO reduced postoperative acute kidney injury (23.1% vs. 35.7%, P = 0.013) and hepatic injury (12.3% vs. 27.8%, P = 0.001), and maintained similar cost to patients (25.5 vs. 24.9 kUSD, P = 0.298). We also found that AST was high during intensive care unit (ICU) stay and recovered to normal before discharge, while ALT was not as high as AST in ICU but showed a rising tendency before discharge. The platelet count showed a rising tendency on postoperative day 3 and may exceed the preoperative value before discharge.

Conclusions
The ABO achieved the surgical goal of TAR with FET with an improved recovery process during the in-hospital stay.
Long-term efficacy of lipoprotein apheresis and lomitapide in the treatment of homozygous familial hypercholesterolemia (HoFH): a cross-national retrospective survey
Authors: D’Erasmo Laura , Gallo Antonio , Cefalù Angelo Baldassare , Di Costanzo Alessia , Saheb Samir , Giammanco Antonina , Averna Maurizio , Buonaiuto Alessio , Iannuzzo Gabriella , Fortunato Giuliana , Puja Arturo , Montalcini Tiziana , Pavanello Chiara , Calabresi Laura , Vigna Giovanni Battista , Bucci Marco , Bonomo Katia , Nota Fabio , Sampietro Tiziana , Sbrana Francesco , Suppressa Patrizia , Sabbà Carlo , Fimiani Fabio , Cesaro Arturo , Calabrò Paolo , Palmisano Silvia , D’Addato Sergio , Pisciotta Livia , Bertolini Stefano , Bittar Randa , Kalmykova Olga , Béliard Sophie , Carrié Alain , Arca Marcello , Bruckert Eric 
Published: September 2021

Abstract

Background
Homozygous familial hypercholesterolemia (HoFH) is a rare life-threatening condition that represents a therapeutic challenge. The vast majority of HoFH patients fail to achieve LDL-C targets when treated with the standard protocol, which associates maximally tolerated dose of lipid-lowering medications with lipoprotein apheresis (LA). Lomitapide is an emerging therapy in HoFH, but its place in the treatment algorithm is disputed because a comparison of its long-term efficacy versus LA in reducing LDL-C burden is not available. We assessed changes in long-term LDL-C burden and goals achievement in two independent HoFH patients’ cohorts, one treated with lomitapide in Italy (n = 30) and the other with LA in France (n = 29).

Results
The two cohorts differed significantly for genotype (p = 0.004), baseline lipid profile (p < 0.001), age of treatment initiation (p < 0.001), occurrence of cardiovascular disease (p = 0.003) as well as follow-up duration (p < 0.001). The adjunct of lomitapide to conventional lipid-lowering therapies determined an additional 58.0% reduction of last visit LDL-C levels, compared to 37.1% when LA was added (padj = 0.004).
Yearly on-treatment LDL-C < 70 mg/dl and < 55 mg/dl goals were only achieved in 45.5% and 13.5% of HoFH patients treated with lomitapide. The long-term exposure to LDL-C burden was found to be higher in LA than in Lomitapide cohort (13,236.1 ± 5492.1 vs. 11,656.6 ± 4730.9 mg/dL-year respectively, padj = 0.002). A trend towards fewer total cardiovascular events was observed in the Lomitapide than in the LA cohort.

Conclusions
In comparison with LA, lomitapide appears to provide a better control of LDL-C in HoFH. Further studies are needed to confirm this data and establish whether this translates into a reduction of cardiovascular risk.