bluuebunny/crossref_metadata_2025_split huggingface dataset:
Digi-Do: a digital information tool to support patients with breast cancer before, during, and after start of radiotherapy treatment: an RCT study protocol
Authors: Fristedt Sofi , Smith Frida , Grynne Annika , Browall Maria 
Published: February 2021

Abstract
Background
Radiation Therapy (RT) is a common treatment after breast cancer surgery and a complex process using high energy X-rays to eradicate cancer cells, important in reducing the risk of local recurrence. The high-tech environment and unfamiliar nature of RT can affect the patient’s experience of the treatment. Misconceptions or lack of knowledge about RT processes can increase levels of anxiety and enhance feelings of being unprepared at the beginning of treatment. Moreover, the waiting time is often quite long. The primary aim of this study will be to evaluate whether a digital information tool with VR-technology and preparatory information can decrease distress as well as enhance the self-efficacy and health literacy of patients affected by breast cancer before, during, and after RT. A secondary aim will be to explore whether the digital information tool increase patient flow while maintaining or increasing the quality of care.

Method
The study is a prospective and longitudinal RCT study with an Action Research participatory design approach including mixed-methods data collection, i.e., standardised instruments, qualitative interviews (face-to-face and telephone) with a phenomenological hermeneutical approach, diaries, observations, and time measurements, and scheduled to take place from autumn 2020 to spring 2022. The intervention group (n = 80), will receive standard care and information (oral and written) and the digital information tool; and the control group (n = 80), will receive standard care and information (oral and written). Study recruitment and randomisation will be completed at two centres in the west of Sweden.

Discussion
Research in this area is scarce and, to our knowledge, only few previous studies examine VR as a tool for increasing preparedness for patients with breast cancer about to undergo RT that also includes follow-ups six months after completed treatment. The participatory approach and design will safeguard the possibilities to capture the patient perspective throughout the development process, and the RCT design supports high research quality. Digitalisation brings new possibilities to provide safe, person-centred information that also displays a realistic picture of RT treatment and its contexts. The planned study will generate generalisable knowledge of relevance in similar health care contexts.
Trial registration: ClinicalTrials.gov Identifier: NCT04394325. Registered May 19, 2020. Prospectively registered.
The practice environment’s influence on patient participation in intermediate healthcare services – the perspectives of patients, relatives and healthcare professionals
Authors: Kvæl Linda Aimée Hartford , Bergland Astrid 
Published: February 2021

AbstractBackgroundIntermediate care (IC) bridges the clinical pathway of older patients transitioning from the hospital to home. Currently, there is a strong consensus that the practice environment is an important factor in helping older people overcome their limitations and regain function after illness or injury. Regardless of the arising attention related to person-centred care, the practice environment is yet to be recognised as a vital part of care, and a small extent of focus has been given the environmental dimensions of IC services. Thus, more research is required regarding the complex relationships between older people and the practice environment. This study explores the perspectives of older patients, their relatives and healthcare professionals related to the practice environment’s influence on patient participation among older people in the context of intermediate healthcare services.MethodsUsing purposive sampling and theoretical approaches, including frameworks of patient participation, the practices environment and person-centred care, semi-structured interviews were conducted with 15 older patients, 12 relatives and 18 healthcare professionals from three different IC institutions in Norway to discuss their experiences and preferences regarding patient participation. A thematic analysis was used to explore patterns across the interviews.ResultsThree main themes were identified: ‘location and access to physical facilities’, ‘symbolic expression of patients’ and professionals’ possibilities’ and ‘participating in meaningful activities’. The findings show that both the physical and the psychosocial environments influenced older patients’ various types of participation in IC services.ConclusionsTo optimise rehabilitation care for older people, the ward configuration should focus on supportive environments that facilitate patient participation and provide options for the patients and relatives to independently access the facilities, balancing the personal capabilities with the environmental demands. To foster patient participation, the practice environment should thus align with the model of person-centred rehabilitation.
20E-mediated regulation of BmKr-h1 by BmKRP promotes oocyte maturation
Authors: Zhu Zidan , Tong Chunmei , Qiu Binbin , Yang Hongguang , Xu Jiahui , Zheng Sichun , Song Qisheng , Feng Qili , Deng Huimin 
Published: February 2021

Abstract
Background
Krüppel homolog 1 (Kr-h1) is a critical transcription factor for juvenile hormone (JH) signaling, known to play a key role in regulating metamorphosis and adult reproduction in insects. Kr-h1 can also be induced by molting hormone 20-hydroxyecdysone (20E), however, the underlying mechanism of 20E-induced Kr-h1 expression remains unclear. In the present study, we investigated the molecular mechanism of Kr-h1 induction by 20E in the reproductive system of a model lepidopteran insect, Bombyx mori.

Results
Developmental and tissue-specific expression analysis revealed that BmKr-h1 was highly expressed in ovaries during the late pupal and adult stages and the expression was induced by 20E. RNA interference (RNAi)-mediated depletion of BmKr-h1 in female pupae severely repressed the transcription of vitellogenin receptor (VgR), resulting in the reduction in vitellogenin (Vg) deposition in oocytes. BmKr-h1 specifically bound the Kr-h1 binding site (KBS) between − 2818 and − 2805 nt upstream of BmVgR and enhanced the transcription of BmVgR. A 20E cis-regulatory element (CRE) was identified in the promoter of BmKr-h1 and functionally verified using luciferase reporter assay, EMSA and DNA-ChIP. Using pull-down assays, we identified a novel transcription factor B. mori Kr-h1 regulatory protein (BmKRP) that specifically bound the BmKr-h1 CRE and activated its transcription. CRISPR/Cas9-mediated knockout of BmKRP in female pupae suppressed the transcription of BmKr-h1 and BmVgR, resulting in arrested oogenesis.

Conclusion
We identified BmKRP as a new transcription factor mediating 20E regulation of B. mori oogenesis. Our data suggests that induction of BmKRP by 20E regulates BmKr-h1 expression, which in turn induces BmVgR expression to facilitate Vg uptake and oogenesis.
Glycolysis-associated lncRNAs identify a subgroup of cancer patients with poor prognoses and a high-infiltration immune microenvironment
Authors: Ho Kuo-Hao , Huang Tzu-Wen , Shih Chwen-Ming , Lee Yi-Ting , Liu Ann-Jeng , Chen Peng-Hsu , Chen Ku-Chung 
Published: February 2021

Abstract
Background
Long noncoding (lnc)RNAs and glycolysis are both recognized as key regulators of cancers. Some lncRNAs are also reportedly involved in regulating glycolysis metabolism. However, glycolysis-associated lncRNA signatures and their clinical relevance in cancers remain unclear. We investigated the roles of glycolysis-associated lncRNAs in cancers.

Methods
Glycolysis scores and glycolysis-associated lncRNA signatures were established using a single-sample gene set enrichment analysis (GSEA) of The Cancer Genome Atlas pan-cancer data. Consensus clustering assays and genomic classifiers were used to stratify patient subtypes and for validation. Fisher’s exact test was performed to investigate genomic mutations and molecular subtypes. A differentially expressed gene analysis, with GSEA, transcription factor (TF) activity scoring, cellular distributions, and immune cell infiltration, was conducted to explore the functions of glycolysis-associated lncRNAs.

Results
Glycolysis-associated lncRNA signatures across 33 cancer types were generated and used to stratify patients into distinct clusters. Patients in cluster 3 had high glycolysis scores and poor survival, especially in bladder carcinoma, low-grade gliomas, mesotheliomas, pancreatic adenocarcinomas, and uveal melanomas. The clinical significance of lncRNA-defined groups was validated using external datasets and genomic classifiers. Gene mutations, molecular subtypes associated with poor prognoses, TFs, oncogenic signaling such as the epithelial-to-mesenchymal transition (EMT), and high immune cell infiltration demonstrated significant associations with cluster 3 patients. Furthermore, five lncRNAs, namely MIR4435-2HG, AC078846.1, AL157392.3, AP001273.1, and RAD51-AS1, exhibited significant correlations with glycolysis across the five cancers. Except MIR4435-2HG, the lncRNAs were distributed in nuclei. MIR4435-2HG was connected to glycolysis, EMT, and immune infiltrations in cancers.

Conclusions
We identified a subgroup of cancer patients stratified by glycolysis-associated lncRNAs with poor prognoses, high immune infiltration, and EMT activation, thus providing new directions for cancer therapy.
A CTSA One Health Alliance (COHA) survey of clinical trial infrastructure in North American veterinary institutions
Authors: Moore Sarah A. , McCleary-Wheeler Angela , Coates Joan R , Olby Natasha , London Cheryl 
Published: February 2021

AbstractWhile a necessary step toward enhancing rigor and reproducibility of veterinary clinical trials conducted on the translational spectrum includes understanding the current state of the field, no broad assessment of existing veterinary clinical trial resources has been previously conducted. Funded by a CTSA One Health Alliance (COHA) pilot award, the goal of this project was to conduct an electronic survey of North American Veterinary Colleges regarding practices in veterinary clinical trial review, approval, conduct, and support in order to identify opportunities to leverage existing resources and develop new ones to enhance the impact of veterinary and translational health research.A total of 30 institutions were invited to participate in the survey and the survey response rate was 73 %. The most common source of funding noted for veterinary clinical research was industry (33 %); however, respondents reported that only 5 % (3.7–11.0) of studies were FDA-regulated. Respondents indicated that most studies (80 %); conducted at their institution were single site studies. Study review and approval involved the IACUC either solely, or in combination with a hospital review board, at 95.5 % of institutions. Workforce training related to clinical research best practices was variable across institutions. Opportunities were identified to strengthen infrastructure through harmonization of clinical research review and approval practices. This might naturally lead to expansion of multi-site studies. Based on respondent feedback, future workforce development initiatives might center on training in the specifics of conducting FDA-sponsored research, Good Clinical Practice (GCP), clinical study budget design, grants management, adverse event reporting, study monitoring and use of electronic data capture platforms.
Integrated CNV-seq, karyotyping and SNP-array analyses for effective prenatal diagnosis of chromosomal mosaicism
Authors: Ma Na , Xi Hui , Chen Jing , Peng Ying , Jia Zhengjun , Yang Shuting , Hu Jiancheng , Pang Jialun , Zhang Yanan , Hu Rong , Wang Hua , Liu Jing 
Published: February 2021

Abstract
Background
Emerging studies suggest that low‐coverage massively parallel copy number variation sequencing (CNV-seq) more sensitive than chromosomal microarray analysis (CMA) for detecting low-level mosaicism. However, a retrospective back-to-back comparison evaluating accuracy, efficacy, and incremental yield of CNV-seq compared with CMA is warranted.

Methods
A total of 72 mosaicism cases identified by karyotyping or CMA were recruited to the study. There were 67 mosaic samples co-analysed by CMA and CNV-seq, comprising 40 with sex chromosome aneuploidy, 22 with autosomal aneuploidy and 5 with large cryptic genomic rearrangements.

Results
Of the 67 positive mosaic cases, the levels of mosaicism defined by CNV-seq ranged from 6 to 92% compared to the ratio from 3 to 90% by karyotyping and 20% to 72% by CMA. CNV-seq not only identified all 43 chromosomal aneuploidies or large cryptic genomic rearrangements detected by CMA, but also provided a 34.88% (15/43) increased yield compared with CMA. The improved yield of mosaicism detection by CNV-seq was largely due to the ability to detect low level mosaicism below 20%.

Conclusion
In the context of prenatal diagnosis, CNV-seq identified additional and clinically significant mosaicism with enhanced resolution and increased sensitivity. This study provides strong evidence for applying CNV-seq as an alternative to CMA for detection of aneuploidy and mosaic variants.
Airway gene-expression classifiers for respiratory syncytial virus (RSV) disease severity in infants
Authors: Wang Lu , Chu Chin-Yi , McCall Matthew N. , Slaunwhite Christopher , Holden-Wiltse Jeanne , Corbett Anthony , Falsey Ann R. , Topham David J. , Caserta Mary T. , Mariani Thomas J. , Walsh Edward E. , Qiu Xing 
Published: February 2021

AbstractBackgroundA substantial number of infants infected with RSV develop severe symptoms requiring hospitalization. We currently lack accurate biomarkers that are associated with severe illness.MethodWe defined airway gene expression profiles based on RNA sequencing from nasal brush samples from 106 full-tem previously healthy RSV infected subjects during acute infection (day 1–10 of illness) and convalescence stage (day 28 of illness). All subjects were assigned a clinical illness severity score (GRSS). Using AIC-based model selection, we built a sparse linear correlate of GRSS based on 41 genes (NGSS1). We also built an alternate model based upon 13 genes associated with severe infection acutely but displaying stable expression over time (NGSS2).ResultsNGSS1 is strongly correlated with the disease severity, demonstrating a naïve correlation (ρ) of ρ = 0.935 and cross-validated correlation of 0.813. As a binary classifier (mild versus severe), NGSS1 correctly classifies disease severity in 89.6% of the subjects following cross-validation. NGSS2 has slightly less, but comparable, accuracy with a cross-validated correlation of 0.741 and classification accuracy of 84.0%.ConclusionAirway gene expression patterns, obtained following a minimally-invasive procedure, have potential utility for development of clinically useful biomarkers that correlate with disease severity in primary RSV infection.
Identification of key genes involved in tumor immune cell infiltration and cetuximab resistance in colorectal cancer
Authors: Liang Li , Liu Mengling , Sun Xun , Yuan Yitao , Peng Ke , Rashid Khalid , Yu Yiyi , Cui Yuehong , Chen Yanjie , Liu Tianshu 
Published: February 2021

Abstract
Background
The anti-epidermal growth factor receptor (EGFR) antibody introduces adaptable variations to the transcriptome and triggers tumor immune infiltration, resulting in colorectal cancer (CRC) treatment resistance. We intended to identify genes that play essential roles in cetuximab resistance and tumor immune cell infiltration.

Methods
A cetuximab-resistant CACO2 cellular model was established, and its transcriptome variations were detected by microarray. Meanwhile, public data from the Gene Expression Omnibus and The Cancer Genome Atlas (TCGA) database were downloaded. Integrated bioinformatics analysis was applied to detect differentially expressed genes (DEGs) between the cetuximab-resistant and the cetuximab-sensitive groups. Then, we investigated correlations between DEGs and immune cell infiltration. The DEGs from bioinformatics analysis were further validated in vitro and in clinical samples.

Results
We identified 732 upregulated and 1259 downregulated DEGs in the induced cellular model. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses, along with Gene Set Enrichment Analysis and Gene Set Variation Analysis, indicated the functions of the DEGs. Together with GSE59857 and GSE5841, 12 common DEGs (SATB-2, AKR1B10, ADH1A, ADH1C, MYB, ATP10B, CDX-2, FAR2, EPHB2, SLC26A3, ORP-1, VAV3) were identified and their predictive values of cetuximab treatment were validated in GSE56386. In online Genomics of Drug Sensitivity in Cancer (GDSC) database, nine of twelve DEGs were recognized in the protein-protein (PPI) network. Based on the transcriptome profiles of CRC samples in TCGA and using Tumor Immune Estimation Resource Version 2.0, we bioinformatically determined that SATB-2, ORP-1, MYB, and CDX-2 expressions were associated with intensive infiltration of B cell, CD4+ T cell, CD8+ T cell and macrophage, which was then validated the correlation in clinical samples by immunohistochemistry. We found that SATB-2, ORP-1, MYB, and CDX-2 were downregulated in vitro with cetuximab treatment. Clinically, patients with advanced CRC and high ORP-1 expression exhibited a longer progression-free survival time when they were treated with anti-EGFR therapy than those with low ORP-1 expression.

Conclusions
SATB-2, ORP-1, MYB, and CDX-2 were related to cetuximab sensitivity as well as enhanced tumor immune cell infiltration in patients with CRC.
Human drug efflux transporter ABCC5 confers acquired resistance to pemetrexed in breast cancer
Authors: Chen Jihui , Wang Zhipeng , Gao Shouhong , Wu Kejin , Bai Fang , Zhang Qiqiang , Wang Hongyu , Ye Qin , Xu Fengjing , Sun Hong , Lu Yunshu , Liu Yan 
Published: February 2021

Abstract
Aim
Pemetrexed, a new generation antifolate drug, has been approved for the treatment of locally advanced or metastatic breast cancer. However, factors affecting its efficacy and resistance have not been fully elucidated yet. ATP-binding cassette (ABC) transporters are predictors of prognosis as well as of adverse effects of several xenobiotics. This study was designed to explore whether ABC transporters affect pemetrexed resistance and can contribute to the optimization of breast cancer treatment regimen.

Methods
First, we measured the expression levels of ABC transporter family members in cell lines. Subsequently, we assessed the potential role of ABC transporters in conferring resistance to pemetrexed in primary breast cancer cells isolated from 34 breast cancer patients and the role of ABCC5 in mediating pemetrexed transport and apoptotic pathways in MCF-7 cells. Finally, the influence of ABCC5 expression on the therapeutic effect of pemetrexed was evaluated in an in vivo xenograft mouse model of breast cancer.

Results
The expression levels of ABCC2, ABCC4, ABCC5, and ABCG2 significantly increased in the pan-resistant cell line, and the ABCC5 level in the MCF-7-ADR cell line was 5.21 times higher than that in the control group. ABCC5 expression was inversely correlated with pemetrexed sensitivity (IC50, r = 0.741; p < 0.001) in breast cancer cells derived from 34 patients. Furthermore, we found that the expression level of ABCC5 influenced the efflux and cytotoxicity of pemetrexed in MCF-7 cells, with IC50 values of 0.06 and 0.20 μg/mL in ABCC5 knockout and over-expression cells, respectively. In the in vivo study, we observed that ABCC5 affected the sensitivity of pemetrexed in breast tumor-bearing mice, and the tumor volume was much larger in the ABCC5-overexpressing group than in the control group when compared with their own initial volumes (2.7-fold vs. 1.3-fold).

Conclusions
Our results indicated that ABCC5 expression was associated with pemetrexed resistance in vitro and in vivo, and it may serve as a target or biomarker for the optimization of pemetrexed regimen in breast cancer treatment.
Genetic characterization of Plasmodium vivax isolates from Pakistan using circumsporozoite protein (pvcsp) and merozoite surface protein-1 (pvmsp-1) genes as genetic markers
Authors: Bibi Zainab , Fatima Anam , Rani Rehana , Maqbool Ayesha , Khan Samea , Naz Shumaila , Waseem Shahid 
Published: February 2021

Abstract
Background
Plasmodium vivax contributes to over 70% malaria burden in Pakistan, but limited data exists on various aspects including genetic diversity of the parasite as compared to other parts of the world. Since the information about the genetic diversity of P. vivax assists to understand the population dynamics of the parasite, the current study was designed to understand population divergence of P. vivax in Pakistan using circumsporozoite protein (pvcsp) and merozoite surface protein-1 (pvmsp-1) genes as molecular markers.

Methods
The PCR for pvcsp and pvmsp-1 genes was carried out for 150 P. vivax isolates, followed by DNA sequencing of 35 and 30, respectively. Genetic diversity and polymorphism were analysed using ChromasPro, ClustalW, MEGA7, DnaSP v.5 and WebLogo programs.

Results
The PCR for pvcsp and pvmsp-1 genes was carried out for 150 P. vivax isolates and resulting the PCR products of 1100 bp for pvcsp and ~ 400 bp for pvmsp-1 genes, respectively. In the central-repeat region (CRR) of pvcsp gene, sequences comprised of four variable repeats of PRMs, out of which GDRADGQPA (PRM1), GDRAAGQPA (PRM2) were more extensively dispersed among the P. vivax isolates. Partial sequences (~ 400 bp) of block 2 of pvmsp-1 gene depicted high level of diversity.

Conclusion
The results revealed the polymorphism and genetic diversity especially at the CRR of pvcsp and block 2 of pvmsp-1 genes, respectively. The base-line data presented here warrants future studies to investigate more into the genetic diversity of P. vivax with large sample size from across the country for better understanding of population dynamics of P. vivax that will help to control malaria at individual and community level.