bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and validation of stemness-related lncRNA prognostic signature for breast cancer
Authors: Li Xiaoying , Li Yang , Yu Xinmiao , Jin Feng 
Published: August 2020

Abstract
Background
Long noncoding RNAs (lncRNAs) are emerging as crucial contributors to the development of breast cancer and are involved in the stemness regulation of breast cancer stem cells (BCSCs). LncRNAs are closely associated with the prognosis of breast cancer patients. It is critical to identify BCSC-related lncRNAs with prognostic value in breast cancer.

Methods
A co-expression network of BCSC-related mRNAs-lncRNAs from The Cancer Genome Atlas (TCGA) was constructed. Univariate and multivariate Cox proportional hazards analyses were used to identify a stemness risk model with prognostic value. Kaplan–Meier analysis, univariate and multivariate Cox regression analyses and receiver operating characteristic (ROC) curve analysis were performed to validate the risk model. Principal component analysis (PCA) and Gene Set Enrichment Analysis (GSEA) functional annotation were conducted to analyze the risk model.

Results
In this study, BCSC-related lncRNAs in breast cancer were identified. We evaluated the prognostic value of these BCSC-related lncRNAs and eventually obtained a prognostic risk model consisting of 12 BCSC-related lncRNAs (Z68871.1, LINC00578, AC097639.1, AP003119.3, AP001207.3, LINC00668, AL122010.1, AC245297.3, LINC01871, AP000851.2, AC022509.2 and SEMA3B-AS1). The risk model was further verified as a novel independent prognostic factor for breast cancer patients based on the calculated risk score. Moreover, based on the risk model, the low- risk and high-risk groups displayed different stemness statuses.

Conclusions
These findings suggested that the 12 BCSC-related lncRNA signature might be a promising prognostic factor for breast cancer and can promote the management of BCSC-related therapy in clinical practice.
Genomic landscape of the immune microenvironments of brain metastases in breast cancer
Authors: Lu Wei-cheng , Xie Hui , Yuan Ce , Li Jin-jiang , Li Zhao-yang , Wu An-hua 
Published: August 2020

AbstractBackgroundThis study was intended to investigate the genomic landscape of the immune microenvironments of brain metastases in breast cancer.MethodsThree gene expression profile datasets (GSE76714, GSE125989 and GSE43837) of breast cancer with brain metastases were downloaded from Gene Expression Omnibus (GEO) database. After differential expression analysis, the tumor immune microenvironment and immune cell infiltration were analyzed. Then immune-related genes were identified, followed by function analysis, transcription factor (TF)-miRNA–mRNA co-regulatory network analysis, and survival analysis of metastatic recurrence.ResultsThe present results showed that the tumor immune microenvironment in brain metastases was immunosuppressed compared with primary caner. Compared with primary cancer samples, the infiltration ratio of plasma cells in brain metastases samples was significantly higher, while the infiltration ratio of macrophages M2 cells in brain metastases samples was significantly lower. Total 42 immune-related genes were identified, such asTHY1andNEU2.CD1B,THY1andDOCK2were found to be implicated in the metastatic recurrence of breast cancer.ConclusionsTargeting macrophages or plasma cells may be new strategies for immunotherapy of breast cancer with brain metastases.THY1andNEU2may be potential therapeutic targets for breast cancer with brain metastases, andTHY1,CD1BandDOCK2may serve as potential prognostic markers for improvement of brain metastases survival.
Emerging of a SARS-CoV-2 viral strain with a deletion in nsp1
Authors: Benedetti Francesca , Snyder Greg A. , Giovanetti Marta , Angeletti Silvia , Gallo Robert C. , Ciccozzi Massimo , Zella Davide 
Published: August 2020

Abstract
Background
The new Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), which was first detected in Wuhan (China) in December of 2019 is responsible for the current global pandemic. Phylogenetic analysis revealed that it is similar to other betacoronaviruses, such as SARS-CoV and Middle-Eastern Respiratory Syndrome, MERS-CoV. Its genome is ∼ 30 kb in length and contains two large overlapping polyproteins, ORF1a and ORF1ab that encode for several structural and non-structural proteins. The non-structural protein 1 (nsp1) is arguably the most important pathogenic determinant, and previous studies on SARS-CoV indicate that it is both involved in viral replication and hampering the innate immune system response. Detailed experiments of site-specific mutagenesis and in vitro reconstitution studies determined that the mechanisms of action are mediated by (a) the presence of specific amino acid residues of nsp1 and (b) the interaction between the protein and the host’s small ribosomal unit. In fact, substitution of certain amino acids resulted in reduction of its negative effects.

Methods
A total of 17,928 genome sequences were obtained from the GISAID database (December 2019 to July 2020) from patients infected by SARS-CoV-2 from different areas around the world. Genomes alignment was performed using MAFFT (REFF) and the nsp1 genomic regions were identified using BioEdit and verified using BLAST. Nsp1 protein of SARS-CoV-2 with and without deletion have been subsequently modelled using I-TASSER.

Results
We identified SARS-CoV-2 genome sequences, from several Countries, carrying a previously unknown deletion of 9 nucleotides in position 686-694, corresponding to the AA position 241-243 (KSF). This deletion was found in different geographical areas. Structural prediction modelling suggests an effect on the C-terminal tail structure.

Conclusions
Modelling analysis of a newly identified deletion of 3 amino acids (KSF) of SARS-CoV-2 nsp1 suggests that this deletion could affect the structure of the C-terminal region of the protein, important for regulation of viral replication and negative effect on host’s gene expression. In addition, substitution of the two amino acids (KS) from nsp1 of SARS-CoV was previously reported to revert loss of interferon-alpha expression. The deletion that we describe indicates that SARS-CoV-2 is undergoing profound genomic changes. It is important to: (i) confirm the spreading of this particular viral strain, and potentially of strains with other deletions in the nsp1 protein, both in the population of asymptomatic and pauci-symptomatic subjects, and (ii) correlate these changes in nsp1 with potential decreased viral pathogenicity.
“They haven’t asked me. I haven’t told them either”: fertility plan discussions between women living with HIV and healthcare providers in western Ethiopia
Authors: Feyissa Tesfaye Regassa , Harris Melissa L. , Loxton Deborah 
Published: August 2020

AbstractBackgroundDespite the importance of women living with HIV (WLHIV) engaging in fertility plan discussions with their healthcare providers (HCPs), little research exists. This study explored perceptions surrounding fertility plan discussions between WLHIV and their HCPs in western Ethiopia, from the perspectives of both women and providers.MethodsThirty-one interviews (27 with WLHIV and 4 with HCPs) were conducted at four healthcare facilities in western Ethiopia in 2018. Data were transcribed verbatim and translated into English. Codes and themes were identified using inductive thematic analysis.ResultsThere was a discordance between HCPs and WLHIV’s perception regarding the delivery of fertility plan discussions. Only nine of the 27 WLHIV reported they had discussed their personal fertility plans with their HCPs. When discussions did occur, safer conception and contraceptive use were the primary focus. Referrals to mother support groups, adherence counsellors as well as family planning clinics (where they can access reproductive counselling) facilitated fertility discussions. However, lack of initiating discussions by either HCPs or women, high client load and insufficient staffing, and a poor referral system were barriers to discussing fertility plans. Where discussions did occur, barriers to good quality interactions were: (a) lack of recognizing women’s fertility needs; (b) a lack of time and being overworked; (c) mismatched fertility desire among couples; (d) non-disclosure of HIV-positive status to a partner; (e) poor partner involvement; (f) fear of repercussions of disclosing fertility desires to a HCP; and (g) HCPs fear of seroconversion.ConclusionsOur findings highlight the need for policies and guidelines to support fertility plan discussions. Training of HCPs, provision of non-judgmental and client-centered fertility counselling, improving integration of services along with increased human resources are crucial to counselling provision. Enhancing partner involvement, and supporting and training mother support groups and adherence counsellors in providing fertility plan discussions are crucial to improving safer conception and effective contraceptive use, which helps in having healthy babies and reducing HIV transmission.
Characterization of integrated prophages within diverse species of clinical nontuberculous mycobacteria
Authors: Glickman Cody , Kammlade Sara M. , Hasan Nabeeh A. , Epperson L. Elaine , Davidson Rebecca M. , Strong Michael 
Published: August 2020

Abstract
Background
Nontuberculous mycobacterial (NTM) infections are increasing in prevalence, with current estimates suggesting that over 100,000 people in the United States are affected each year. It is unclear how certain species of mycobacteria transition from environmental bacteria to clinical pathogens, or what genetic elements influence the differences in virulence among strains of the same species. A potential mechanism of genetic evolution and diversity within mycobacteria is the presence of integrated viruses called prophages in the host genome. Prophages may act as carriers of bacterial genes, with the potential of altering bacterial fitness through horizontal gene transfer. In this study, we quantify the frequency and composition of prophages within mycobacteria isolated from clinical samples and compare them against the composition of PhagesDB, an environmental mycobacteriophage database.

Methods
Prophages were predicted by agreement between two discovery tools, VirSorter and Phaster, and the frequencies of integrated prophages were compared by growth rate. Prophages were assigned to PhagesDB lettered clusters. Bacterial virulence gene frequency was calculated using a combination of the Virulence Factor Database (VFDB) and the Pathosystems Resource Integration Center virulence database (Patric-VF) within the gene annotation software Prokka. CRISPR elements were discovered using CRT. ARAGORN was used to quantify tRNAs.

Results
Rapidly growing mycobacteria (RGM) were more likely to contain prophage than slowly growing mycobacteria (SGM). CRISPR elements were not associated with prophage abundance in mycobacteria. The abundance of tRNAs was enriched in SGM compared to RGM.
We compared the abundance of bacterial virulence genes within prophage genomes from clinical isolates to mycobacteriophages from PhagesDB. Our data suggests that prophages from clinical mycobacteria are enriched for bacterial virulence genes relative to environmental mycobacteriophage from PhagesDB.

Conclusion
Prophages are present in clinical NTM isolates. Prophages are more likely to be present in RGM compared to SGM genomes. The mechanism and selective advantage of this enrichment by growth rate remain unclear. In addition, the frequency of bacterial virulence genes in prophages from clinical NTM is enriched relative to the PhagesDB environmental proxy. This suggests prophages may act as a reservoir of genetic elements bacteria could use to thrive within a clinical environment.
High intensity exercise downregulates FTO mRNA expression during the early stages of recovery in young males and females
Authors: Danaher Jessica , Stathis Christos G. , Wilson Robin A. , Moreno-Asso Alba , Wellard R. Mark , Cooke Matthew B. 
Published: August 2020

Abstract
Background
Physical exercise and activity status may modify the effect of the fat mass- and obesity-associated (FTO) genotype on body weight and obesity risk. To understand the interaction between FTO’s effect and physical activity, the present study investigated the effects of high and low intensity exercise on FTO mRNA and protein expression, and potential modifiers of exercise-induced changes in FTO in healthy-weighted individuals.

Methods
Twenty-eight untrained males and females (25.4 ± 1.1 years; 73.1 ± 2.0 kg; 178.8 ± 1.4 cm; 39.0 ± 1.2 ml.kg.min− 1 VO2peak) were genotyped for the FTO rs9939609 (T > A) polymorphism and performed isocaloric (400 kcal) cycle ergometer exercise on two separate occasions at different intensities: 80% (High Intensity (HI)) and 40% (Low Intensity (LO)) VO2peak. Skeletal muscle biopsies (vastus lateralis) and blood samples were taken pre-exercise and following 10 and 90 mins passive recovery.

Results
FTO mRNA expression was significantly decreased after HI intensity exercise (p = 0.003). No differences in basal and post-exercise FTO protein expression were evident between FTO genotypes. Phosphorylated adenosine monophosphate-activated protein kinase (AMPK) and Akt substrate of 160 kDa (AS160) were significantly increased following HI intensity exercise (p < 0.05). Multivariate models of metabolomic data (orthogonal two partial least squares discriminant analysis (O2PLS-DA)) were unable to detect any significant metabolic differences between genotypes with either exercise trial (p > 0.05). However, skeletal muscle glucose accumulation at 10 mins following HI (p = 0.021) and LO (p = 0.033) intensity exercise was greater in AA genotypes compared to TT genotypes.

Conclusion
Our novel data provides preliminary evidence regarding the effects of exercise on FTO expression in skeletal muscle. Specifically, high intensity exercise downregulates expression of FTO mRNA and suggests that in addition to nutritional regulation, FTO could also be regulated by exercise.

Trial registration
ACTRN12612001230842. Registered 21 November 2012 – Prospectively registered, https://www.anzctr.org.au/
An overview of the commercial determinants of health
Authors: Mialon Melissa 
Published: August 2020

Abstract
Background
Different terms are described in the literature that refer to commercial determinants as drivers of ill-health. The aim of the present review was to provide an overview of the commercial determinants of health, through a review of the literature on this subject. The review was conducted in December 2019 and updated in February 2020. Searches were conducted from peer-reviewed scientific articles, commentaries, books, and books chapters, with no restriction in their publication dates and languages.

Main body
The commercial determinants of health cover three areas. First, they relate to unhealthy commodities that are contributing to ill-health. Secondly, they include business, market and political practices that are harmful to health and used to sell these commodities and secure a favourable policy environment. Finally, they include the global drivers of ill-health, such as market-driven economies and globalisation, that have facilitated the use of such harmful practices.

Short conclusion
The discussion on the commercial determinants of health offers a unique opportunity to shift the dominant paradigm in public health, where individual behaviours are considered to be driven by inadequate environments. Ill-health, damages to the environment, and health and social inequalities, might be better understood through a commercial determinant lens.
An ethnoveterinary study on medicinal plants used by the Buyi people in Southwest Guizhou, China
Authors: Xiong Yong , Long Chunlin 
Published: August 2020

Abstract
Background
The Buyi (Bouyei) people in Qianxinan Buyi and Miao Autonomous Prefecture, Southwest Guizhou, China, have used medicinal plants and traditional remedies for ethnoveterinary practices, such as treating domestic animals during livestock breeding, since ancient times. However, the unique ethnoveterinary practices of the Buyi have rarely been recorded. This study aimed to identify the plants used in their traditional ethnoveterinary practices, and to propose suggestions for future conservation and sustainable use of this knowledge.

Methods
Ethnobotanical fieldwork was conducted in 19 villages/townships in Qianxinan Prefecture between 2017 and 2018. Data were collected from the local Buyi people through semi-structured interviews and participatory observations. The informant consensus factor (FIC) and use reports (URs) were utilized to evaluate the consent of the current ethnoveterinary practices among the local communities, and 83 informants were interviewed during the field investigations. Plant samples and voucher specimens were collected for taxonomic identification.

Results
A total of 122 plant species, belonging to 60 families and 114 genera, were recorded as being used in ethnoveterinary practices by the Buyi people. The most used ethnoveterinary medicinal plant (EMP) parts included the roots, whole plant, and bulb, and the most common preparation methods included decoction, crushing, and boiling. Some EMPs, such as Quisqualis indica and Paris polyphylla, have special preparation methods. The informant consensus factor (FIC) and use reports (URs) of the EMP species were analyzed. Twenty EMP species with the highest URs were noted as having particular importance in the daily lives of Buyi people in Qianxinan Prefecture.

Conclusion
In this study, we identified traditional ethnoveterinary knowledge of the medicinal plants among the Buyi communities in Qianxinan Prefecture. This knowledge has previously been limited to local vets, herders, and aged community members. Plants with important medicinal uses need to be validated phytochemically and pharmacologically in the future, to develop new alternative drugs for veterinary purposes.
Reconstruction method and optimum range of camera-shooting angle for 3D plant modeling using a multi-camera photography system
Authors: Lu Xingtong , Ono Eiichi , Lu Shan , Zhang Yu , Teng Poching , Aono Mitsuko , Shimizu Yo , Hosoi Fumiki , Omasa Kenji 
Published: August 2020

Abstract
Background
Measurement of plant structure is useful in monitoring plant conditions and understanding the responses of plants to environmental changes. 3D imaging technologies, especially the passive-SfM (Structure from Motion) algorithm combined with a multi-camera photography (MCP) system has been studied to measure plant structure due to its low-cost, close-range, and rapid image capturing ability. However, reconstruction of 3D plant models with complex structure is a time-consuming process and some systems have failed to reconstruct 3D models properly. Therefore, an MCP based SfM system was developed and an appropriate reconstruction method and optimal range of camera-shooting angles were investigated.

Results
An MCP system which utilized 10 cameras and a rotary table for plant was developed. The 3D mesh model of a single leaf reconstruction using a set of images taken at each viewing zenith angle (VZA) from 12° (C2 camera) to 60° (C6 camera) by the MCP based SfM system had less undetected or unstable regions in comparison with other VZAs. The 3D mesh model of a whole plant, which merged 3D dense point cloud models built from a set of images taken at each appropriate VZA (Method 1), had high accuracy. The Method 1 error percentages for leaf area, leaf length, leaf width, stem height, and stem width are in the range of 2.6–4.4%, 0.2–2.2%, 1.0–4.9%, 1.9–2.8%, and 2.6–5.7% respectively. Also, the error of the leaf inclination angle was less than 5°. Conversely, the 3D mesh model of a whole plant built directly from a set of images taken at all appropriate VZAs (Method 2) had lower accuracy than that of Method 1. For Method 2, the error percentages of leaf area, leaf length, and leaf width are in the range of 3.1–13.3%, 0.4–3.3%, and 1.6–8.6%, respectively. It was difficult to obtain the error percentages of stem height and stem width because some information was missing in this model. In addition, the calculation time for Method 2 was 1.97 times longer computational time in comparison to Method 1.

Conclusions
In this study, we determined the optimal shooting angles on the MCP based SfM system developed. We found that it is better in terms of computational time and accuracy to merge partial 3D models from images taken at each appropriate VZA, then construct complete 3D model (Method 1), rather than to construct 3D model by using images taken at all appropriate VZAs (Method 2). This is because utilization of incorporation of incomplete images to match feature points could result in reduced accuracy in 3D models and the increase in computational time for 3D model reconstruction.
Recent changes in trends of opioid overdose deaths in North America
Authors: Imtiaz Sameer , Shield Kevin D. , Fischer Benedikt , Elton-Marshall Tara , Sornpaisarn Bundit , Probst Charlotte , Rehm Jürgen 
Published: August 2020

Abstract
Background
As several regulatory and environmental changes have occurred in North America, trends in overdose deaths were examined in the United States (US), Ontario and British Columbia (BC), including changes in consumption levels of prescription opioids (PO) and overdose deaths, changes in correlations between consumption levels of PO and overdose deaths and modeled differences between observed and predicted overdose deaths if no changes had occurred.

Methods
Consumption levels of PO included defined daily doses for statistical purposes per million inhabitants per day for the US and Canada (2001–2015). Overdose deaths included opioid overdose deaths for the US (2001–2017) and Ontario (2003–2017) and illicit drug overdose deaths for BC (2001–2017). The analytic techniques included structural break point analyses, Pearson product-moment correlations and multivariate Gaussian state space modeling.

Results
Consumption levels of PO changed in the US in 2010 and in Canada in 2012. Overdose deaths changed in the US in 2014 and in Ontario and BC in 2015. Prior to the observed changes in consumption levels of PO, there were positive correlations between consumption levels of PO and overdose deaths in the US (r = 0.99, p < 0.001) and Ontario (r = 0.92, p = 0.003). After the observed changes in consumption levels of PO, there was a negative correlation between consumption levels of PO and overdose deaths in the US (r = − 0.99, p = 0.002). Observed overdose deaths exceeded predicted overdose deaths by 5.7 (95% Confidence Interval [CI]: 4.8–6.6), 3.5 (95% CI: 3.2–3.8) and 21.8 (95% CI: 18.6–24.9) deaths per 100,000 people in the US, Ontario and BC, respectively in 2017. These excess deaths corresponded to 37.7% (95% CI: 31.9–43.6), 39.2% (95% CI: 36.3–42.1) and 72.2% (95% CI: 61.8–82.6) of observed overdose deaths in the US, Ontario and BC, respectively in 2017.

Conclusions
The opioid crisis has evolved in North America, as a sizeable proportion of overdose deaths are now attributable to the several regulatory and environmental changes. These findings necessitate substance use policies to be conceptualized more broadly as well as the continued expansion of harm reduction services and types of pharmacotherapy interventions.