bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chikungunya virus infection: molecular biology, clinical characteristics, and epidemiology in Asian countries
Authors: Khongwichit Sarawut , Chansaenroj Jira , Chirathaworn Chintana , Poovorawan Yong 
Published: December 2021

AbstractChikungunya virus (CHIKV) is a re-emerging mosquito-borne human pathogen that causes chikungunya fever, which is typically accompanied by severe joint pain. In Asia, serological evidence indicated that CHIKV first emerged in 1954. From the 1950’s to 2005, sporadic CHIKV infections were attributed to the Asian genotype. However, the massive outbreak of CHIKV in India and the Southwest Indian Ocean Islands in 2005 has since raised chikungunya as a worldwide public health concern. The virus is spreading globally, but mostly in tropical and subtropical regions, particularly in South and Southeast Asia. The emergence of the CHIKV East/Central/South African genotype-Indian Ocean lineage (ECSA-IOL) has caused large outbreaks in South and Southeast Asia affected more than a million people over a decade. Notably, the massive CHIKV outbreaks before 2016 and the more recent outbreak in Asia were driven by distinct ECSA lineages. The first significant CHIKV ECSA strains harbored the Aedes albopictus-adaptive mutation E1: A226V. More recently, another mass CHIKV ECSA outbreak in Asia started in India and spread beyond South and Southeast Asia to Kenya and Italy. This virus lacked the E1: A226V mutation but instead harbored two novel mutations (E1: K211E and E2: V264A) in an E1: 226A background, which enhanced its fitness in Aedes aegypti. The emergence of a novel ECSA strain may lead to a more widespread geographical distribution of CHIKV in the future. This review summarizes the current CHIKV situation in Asian countries and provides a general overview of the molecular virology, disease manifestation, diagnosis, prevalence, genotype distribution, evolutionary relationships, and epidemiology of CHIKV infection in Asian countries over the past 65 years. This knowledge is essential in guiding the epidemiological study, control, prevention of future CHIKV outbreaks, and the development of new vaccines and antivirals targeting CHIKV.
Prevalence of potential mediators of artemisinin resistance in African isolates of Plasmodium falciparum
Authors: Owoloye Afolabi , Olufemi Michael , Idowu Emmanuel T. , Oyebola Kolapo M. 
Published: December 2021

Abstract
Background
The devastating public health impact of malaria has prompted the need for effective interventions. Malaria control gained traction after the introduction of artemisinin-based combination therapy (ACT). However, the emergence of artemisinin (ART) partial resistance in Southeast Asia and emerging reports of delayed parasite sensitivity to ACT in African parasites signal a gradual trend towards treatment failure. Monitoring the prevalence of mutations associated with artemisinin resistance in African populations is necessary to stop resistance in its tracks. Mutations in Plasmodium falciparum genes pfk13, pfcoronin and pfatpase6 have been linked with ART partial resistance.

Methods
Findings from published research articles on the prevalence of pfk13, pfcoronin and pfatpase6 polymorphisms in Africa were collated. PubMed, Embase and Google Scholar were searched for relevant articles reporting polymorphisms in these genes across Africa from 2014 to August 2021, for pfk13 and pfcoronin. For pfatpase6, relevant articles between 2003 and August 2021 were retrieved.

Results
Eighty-seven studies passed the inclusion criteria for this analysis and reported 742 single nucleotide polymorphisms in 37,864 P. falciparum isolates from 29 African countries. Five validated-pfk13 partial resistance markers were identified in Africa: R561H in Rwanda and Tanzania, M476I in Tanzania, F446I in Mali, C580Y in Ghana, and P553L in an Angolan isolate. In Tanzania, three (L263E, E431K, S769N) of the four mutations (L263E, E431K, A623E, S769N) in pfatpase6 gene associated with high in vitro IC50 were reported. pfcoronin polymorphisms were reported in Senegal, Gabon, Ghana, Kenya, and Congo, with P76S being the most prevalent mutation.

Conclusions
This meta-analysis provides an overview of the prevalence and widespread distribution of pfk13, pfcoronin and pfatpase6 mutations in Africa. Understanding the phenotypic consequences of these mutations can provide information on the efficacy status of artemisinin-based treatment of malaria across the continent.

Graphical Abstract
Global health diplomacy in Mexico: insights from key actors in the field
Authors: Guerra German , Orozco Emanuel , Jiménez Paulina , Ruckert Arne , Labonté Ronald , Snyder Nelly Salgado de 
Published: December 2021

Abstract
Background
Global health diplomacy (GHD) focuses on the actions taken by diverse stakeholders from different nations –governments, multilateral agents, and civil society– to phenomena that can affect population health and its determinants beyond national borders. Although the literature on conceptual advancements of GHD exists, empirical studies about how health becomes an issue of relevance for foreign policy are scarce. We present an analysis of the entry processes of health into the foreign policy and diplomatic domains in Mexico from the perspective of key informants of three different sectors.

Methods
A purposive sample of high-rank representatives of three sectors involved in GHD was designed: Two from Health Sector (HS), four from Foreign Affairs Sector (FAS), and three from Non-governmental organizations (NGOs). Nine semi-structured interviews were conducted exploring the topics of: (1) Health concerns entering diplomatic and foreign policy; (2) Processes that allow actors to influence foreign policy and negotiation and; (3) Impact of multilateral negotiations on decision-making at the national level.

Results
Our analysis suggests that GHD in Mexico is hierarchically driven by the FAS and health concerns only enter foreign policy when they are relevant to national priorities (such as trade or security). HS possesses a lesser degree of influence in GHD, serving as an instance of consultation for the FAS when deciding on health-related issues at global meetings (i.e., World Health Assembly). NGOs resort to lobbying, advocacy, networking, and coalition-working practices with other sectors (academy, think-tanks) to prevent harmful impacts on local health from multilateral decisions and as a mean to compensate its power asymmetry for influencing GHD processes in relation to the government.

Conclusions
GHD in Mexico occurs in a context of asymmetric power relationships where government actors have the strongest influence. However, NGOs’ experience in raising awareness of health risks needs to be weighted by government decision-makers. This situation calls for capacity building on intersectoral communication and coordination to create formal mechanisms of GHD practices, including the professionalization and training on GHD among government agencies.
Circ-ATAD1 is overexpressed in osteosarcoma (OS) and suppresses the maturation of miR-154-5p to increase cell invasion and migration
Authors: Zhou Jihui , Xu Li , Yang Peng , Lin Shibang , Huang Haizhou 
Published: December 2021

Abstract
Background
Circ-ATAD1 plays an oncogenic role in gastric cancer. However, its roles in other cancers are unclear. We aimed to analyze the role of circ-ATAD1 in osteosarcoma (OS).

Methods
The expression levels of circ-ATAD1, mature miR-154-5p, and premature miR-154-5p in paired OS and non-tumor tissues from 56 OS patients were determined using RT-qPCR. Nuclear fractionation assay was performed to analyze the subcellular location of circ-ATAD1. The interaction between circ-ATAD1 and premature miR-154-5p was analyzed using RNA pull-down assay. The role of circ-ATAD1 in regulating miR-154-5p maturation was analyzed using RT-qPCR in cells with overexpression. Transwell assays were performed to analyze the roles of circ-ATAD1 and miR-154-5p in regulating OS cell invasion and migration.

Results
Circ-ATAD1 was overexpressed in OS compared to non-tumor tissues and was detected in the nuclei of OS cells. Mature miR-154-5p, but not premature miR-154-5p, was downregulated in OS tissues compared to non-tumor tissues and was inversely correlated with circ-ATAD1. In OS cells, circ-ATAD1 overexpression decreased the expression of mature miR-154-5p, but not premature miR-154-5p. Transwell assay analysis showed that circ-ATAD1 overexpression increased cell invasion and migration, and mature miR-154-5p overexpression suppressed these cell behaviors. In addition, circ-ATAD1 overexpression reduced the effects of mature miR-154-5p overexpression on cell behaviors.

Conclusions
Circ-ATAD1 is overexpressed in OS and suppresses miR-154-5p maturation to increase cell invasion and migration.
GSK3-beta as a candidate therapeutic target in soft tissue sarcomas
Authors: Verbeke S. , Perret R. , Chaire V. , Richard E. , Velasco V. , Giles F. , Cavalcante L. , Italiano A. 
Published: December 2021

AbstractSoft tissue sarcoma (STS) is a predominantly fatal rare malignancy with inadequate treatment options. Glycogen synthase kinase 3β (GSK-3β) is an emerging target in human malignancies. Its therapeutic relevance in STS is unknown. We analyzed the prognostic impact of GSK-3β gene and protein expression in two independent cohorts of patients with STS. We then treated STS cell lines and mice xenografts with a novel GSK-3 inhibitor 9-ING-41 alone or in combination with chemotherapy. We demonstrated that 9-ING-41 treatment induced significant STS cells apoptosis and was synergistic in vivo when combined with chemotherapy. Mechanistically, 9-ING-41 induces significant apoptosis of STS cells via suppression of NF-κB-mediated X-linked inhibitor of apoptosis protein (XIAP) expression. These data support the inclusion of patients with STS in clinical studies of 9-ING-41 alone and in combination with chemotherapy.
Estimating the risk of malignancy of adnexal masses: validation of the ADNEX model in the hands of nonexpert ultrasonographers in a gynaecological oncology centre in China
Authors: He Ping , Wang Jing-jing , Duan Wei , Song Chao , Yang Yu , Wu Qing-qing 
Published: December 2021

Abstract
Background
This study aims to validate the diagnostic accuracy of the International Ovarian Tumor Analysis (IOTA) the Assessment of Different NEoplasias in the adneXa (ADNEX) model in the preoperative diagnosis of adnexal masses in the hands of nonexpert ultrasonographers in a gynaecological oncology centre in China.

Methods
This was a single oncology centre, retrospective diagnostic accuracy study of 620 patients. All patients underwent surgery, and the histopathological diagnosis was used as a reference standard. The masses were divided into five types according to the ADNEX model: benign ovarian tumours, borderline ovarian tumours (BOTs), stage I ovarian cancer (OC), stage II-IV OC and ovarian metastasis. Receiver operating characteristic (ROC) curve analysis was used to evaluate the ability of the ADNEX model to classify tumours into different histological types with and without cancer antigen 125 (CA 125) results.

Results
Of the 620 women, 402 (64.8%) had a benign ovarian tumour and 218 (35.2%) had a malignant ovarian tumour, including 86 (13.9%) with BOT, 75 (12.1%) with stage I OC, 53 (8.5%) with stage II-IV OC and 4 (0.6%) with ovarian metastasis. The AUC of the model to differentiate benign and malignant adnexal masses was 0.97 (95% CI, 0.96–0.98). Performance was excellent for the discrimination between benign and stage II-IV OC and between benign and ovarian metastasis, with AUCs of 0.99 (95% CI, 0.99–1.00) and 0.99 (95% CI, 0.98–1.00), respectively. The model was less effective at distinguishing between BOT and stage I OC and between BOT and ovarian metastasis, with AUCs of 0.54 (95% CI, 0.45–0.64) and 0.66 (95% CI, 0.56–0.77), respectively. When including CA125 in the model, the performance in discriminating between stage II–IV OC and stage I OC and between stage II–IV OC ovarian metastasis was improved (AUC increased from 0.88 to 0.94, P = 0.01, and from 0.86 to 0.97, p = 0.01).

Conclusions
The IOTA ADNEX model has excellent performance in differentiating benign and malignant adnexal masses in the hands of nonexpert ultrasonographers with limited experience in China. In classifying different subtypes of ovarian cancers, the model has difficulty differentiating BOTs from stage I OC and BOTs from ovarian metastases.
Malignancy and NF-κB signalling strengthen coordination between expression of mitochondrial and nuclear-encoded oxidative phosphorylation genes
Authors: Perez Marcos Francisco , Sarkies Peter 
Published: December 2021

Abstract
Background
Mitochondria are ancient endosymbiotic organelles crucial to eukaryotic growth and metabolism. The mammalian mitochondrial genome encodes for 13 mitochondrial proteins, and the remaining mitochondrial proteins are encoded by the nuclear genome. Little is known about how coordination between the expression of the two sets of genes is achieved.

Results
Correlation analysis of RNA-seq expression data from large publicly available datasets is a common method to leverage genetic diversity to infer gene co-expression modules. Here we use this method to investigate nuclear-mitochondrial gene expression coordination. We identify a pitfall in correlation analysis that results from the large variation in the proportion of transcripts from the mitochondrial genome in RNA-seq data. Commonly used normalisation techniques based on total read counts, such as FPKM or TPM, produce artefactual negative correlations between mitochondrial- and nuclear-encoded transcripts. This also results in artefactual correlations between pairs of nuclear-encoded genes, with important consequences for inferring co-expression modules beyond mitochondria. We show that these effects can be overcome by normalizing using the median-ratio normalisation (MRN) or trimmed mean of M values (TMM) methods. Using these normalisations, we find only weak and inconsistent correlations between mitochondrial and nuclear-encoded mitochondrial genes in the majority of healthy human tissues from the GTEx database.

Conclusions
We show that a subset of healthy tissues with high expression of NF-κB show significant coordination, suggesting a role for NF-κB in ensuring balanced expression between mitochondrial and nuclear genes. Contrastingly, most cancer types show robust coordination of nuclear and mitochondrial OXPHOS gene expression, identifying this as a feature of gene regulation in cancer.
DropletQC: improved identification of empty droplets and damaged cells in single-cell RNA-seq data
Authors: Muskovic Walter , Powell Joseph E. 
Published: December 2021

Abstract
Background
Advances in droplet-based single-cell RNA-sequencing (scRNA-seq) have dramatically increased throughput, allowing tens of thousands of cells to be routinely sequenced in a single experiment. In addition to cells, droplets capture cell-free “ambient” RNA predominantly caused by lysis of cells during sample preparation. Samples with high ambient RNA concentration can create challenges in accurately distinguishing cell-containing droplets and droplets containing ambient RNA. Current methods to separate these groups often retain a significant number of droplets that do not contain cells or empty droplets. Additionally, there are currently no methods available to detect droplets containing damaged cells, which comprise partially lysed cells, the original source of the ambient RNA.

Results
Here, we describe DropletQC, a new method that is able to detect empty droplets, damaged, and intact cells, and accurately distinguish them from one another. This approach is based on a novel quality control metric, the nuclear fraction, which quantifies for each droplet the fraction of RNA originating from unspliced, nuclear pre-mRNA. We demonstrate how DropletQC provides a powerful extension to existing computational methods for identifying empty droplets such as EmptyDrops.

Conclusions
We implement DropletQC as an R package, which can be easily integrated into existing single-cell analysis workflows.
Structural changes and expression of hepatic fibrosis-related proteins in coculture of Echinococcus multilocularis protoscoleces and human hepatic stellate cells
Authors: Cao Deping , Shamsan Emad , Jiang Bofan , Fan Haining , Zhang Yaogang , Dehwah Mustafa Abdo Saif 
Published: December 2021

Abstract
Background
Echinococcus multilocularis is the causative agent of human hepatic alveolar echinococcosis (AE). AE can cause damage to several organs, primarily the liver, and have severe outcomes, such as hepatic failure and encephalopathy. The main purpose of this study was to explore the interactions between hepatic stellate cells (HSCs) and E. multilocularis protoscoleces (PSCs). The results of this study provide an experimental basis for further examination of the pathogenesis of hepatic fibrosis due to AE infection.

Methods
We investigated the role of Echinococcus multilocularis (Echinococcus genus) PSCs in hepatic fibrosis by examining structural changes and measuring hepatic fibrosis-related protein levels in cocultures of PSCs and human HSCs. Structural changes were detected by transmission electron microscopy (TEM), and levels of the hepatic fibrosis-related proteins collagen I (Col-I), alpha-smooth muscle actin (α-SMA) and osteopontin (OPN) were measured by western blotting and enzyme-linked immunosorbent assay (ELISA).

Results
Under coculture (1) both PSCs and HSCs exhibited morphological changes, as observed by TEM; (2) Col-I, α-SMA, and OPN expression levels, which were determined by western blotting and ELISA, significantly increased after 3 days of incubation.

Conclusions
The results of this study provide insights into the molecular mechanisms of AE-induced hepatic fibrosis.

Graphical abstract
Anti-tumor effect of polysaccharide from Pleurotus ostreatus on H22 mouse Hepatoma ascites in-vivo and hepatocellular carcinoma in-vitro model
Authors: Khinsar Kavish Hasnain , Abdul Sattar , Hussain Akbar , Ud Din Riaz , Lei Liu , Cao Jing , Abbasi Majid , Ur Rehman Ata , Farooqui Nabeel , Yi Xin , Min Huang , Wang Liang , Mintao Zhong 
Published: December 2021

AbstractHepatocellular carcinoma is one of the leading causes of cancer-associated death across the globe. Malignant ascites are the major clinical attributes in cancer patients. Despite the advancements in HCC treatments such as chemotherapy, radiotherapy, surgery, and hormonal therapy, researchers are pursuing novel natural edible compounds for the treatment of cancer to eliminate dreadful side effects. Pleurotus ostreatus is one of the most edible cuisines in Asia as well as all over the world. It has been a source of nutritious diet since it was classified as an edible mushroom with no or negligible side effects. The present study focused on the natural anti-cancerous and anti-ascites capabilities of polysaccharides extracted from Pleurotus ostreatus in-vivo as well as in-vitro. Administration of polysaccharide Pleurotus ostreatus showed a significant decrease in tumor cell metastasis while the increase in the survival period among mice models of H22 malignant ascites. Downregulation of regenerative genes Foxp3 and Stat3 and secretion of immunological factors such as IL-2, TNF α, and INF γ were observed after treating with the partially pure extracted polysaccharide. Twining with the hypothesis of tumor suppression in-vivo model polysaccharide showed a decrease in invasion and migration abilities and henceforth responsible for the gene regulation such Cytochrome C which supposedly induced the chain of gene regulation process resulting in apoptosis in HCC cell lines observed in-vitro experiments. Collective research findings manifested that polysaccharide extracted from Pleurotus ostreatus bears anti-proliferative activity and thus influence tumor suppression in-vivo and in-vitro against hepatocellular carcinoma and can be used for therapeutic purposes as a potential anti-cancerous source in the future.
A DNA adductome analysis revealed a reduction in the global level of C5-hydroxymethyl-2′-deoxycytidine in the non-tumoral upper urinary tract mucosa of urothelial carcinoma patients
Authors: Matsushita Yuto , Iwashita Yuji , Ohtsuka Shunsuke , Ohnishi Ippei , Yamashita Takashi , Miyake Hideaki , Sugimura Haruhiko 
Published: December 2021

Abstract
Background
DNA adducts, covalent modifications to DNA due to exposure to specific carcinogens, cause the mispairing of DNA bases, which ultimately results in DNA mutations. DNA methylation in the promoter region, another type of DNA base modification, alters the DNA transcription process, and has been implicated in carcinogenesis in humans due to the down-regulation of tumor suppressor genes. Difficulties are associated with demonstrating the existence of DNA adducts or chemically modified bases in the human urological system. Apart from aristolochic acid-DNA adducts, which cause urothelial carcinoma and endemic nephropathy in a particular geographical area (Balkan), limited information is currently available on DNA adduct profiles in renal cell carcinoma and upper urinary tract urothelial carcinoma, including renal pelvic cancer and ureteral cancer.

Method
To elucidate the significance of DNA adducts in carcinogenesis in the urothelial system, we investigated 53 DNA adducts in the non-tumoral renal parenchyma and non-tumoral renal pelvis of patients with renal cell carcinoma, upper urinary tract urothelial carcinoma, and other diseases using liquid chromatography coupled with tandem mass spectrometry. A comparative analysis of tissue types, the status of malignancy, and clinical characteristics, including lifestyle factors, was performed.

Results
C5-Methyl-2′-deoxycytidine, C5-hydroxymethyl-2′-deoxycytidine (5hmdC), C5-formyl-2′-deoxycytidine, 2′-deoxyinosine, C8-oxo-2′-deoxyadenosine, and C8-oxo-2′-deoxyguanosine (8-OHdG) were detected in the renal parenchyma and renal pelvis. 8-OHdG was more frequently detected in the renal pelvis than in the renal cortex and medulla (p = 0.048 and p = 0.038, respectively). 5hmdC levels were significantly lower in the renal pelvis of urothelial carcinoma patients (n = 10) than in the urothelium of patients without urothelial carcinoma (n = 15) (p = 0.010). Regarding 5hmdC levels in the renal cortex and medulla, Spearman’s rank correlation test revealed a negative correlation between age and 5hmdC levels (r = − 0.46, p = 0.018 and r = − 0.45, p = 0.042, respectively).

Conclusions
The present results revealed a reduction of 5hmdC levels in the non-tumoral urinary tract mucosa of patients with upper urinary tract urothelial carcinoma. Therefore, the urothelial cell epithelia of patients with upper urinary tract cancer, even in non-cancerous areas, may be predisposed to urothelial cancer.