bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic endoscopic staging of mediastinum to determine impact on radiotherapy for locally advanced lung cancer (SEISMIC): protocol for a prospective single arm multicentre interventional study
Authors: Steinfort Daniel P. , Siva Shankar , Rangamuwa Kanishka , Lee Percy , Fielding David , Nguyen Phan , Jennings Barton R. , Yo Shaun , Hardcastle Nick , Kothari Gargi , Crombag Laurence , Annema Jouke , Yasufuku Kazuhiro , Ost David E. , Irving Louis B. 
Published: September 2022

Abstract
Background
Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is established as the preferred method of mediastinal lymph node (LN) staging in non-small cell lung cancer (NSCLC). Selective (targeted) LN sampling is most commonly performed however studies in early stage NSCLC and locally advanced NSCLC confirm systematic EBUS-TBNA evaluation improves accuracy of mediastinal staging. This study aims to establish the rate of detection of positron emission tomography (PET)-occult LN metastases following systematic LN staging by EBUS-TBNA, and to determine the utility of systematic mediastinal staging for accurate delineation of radiation treatment fields in patients with locally advanced NSCLC.

Methods
Consecutive patients undergoing EBUS-TBNA for diagnosis/staging of locally advanced NSCLC will be enrolled in this international multi-centre single arm study. Systematic mediastinal LN evaluation will be performed, with all LN exceeding 6 mm to be sampled by TBNA. Where feasible, endoscopic ultrasound staging (EUS-B) may also be performed. Results of minimally invasive staging will be compared to FDG-PET. The primary end-point is proportion of patients in whom systematic LN staging identified PET-occult NSCLC metastases. Secondary outcome measures include (i) rate of nodal upstaging, (ii) false positive rate of PET for mediastinal LN assessment, (iii) analysis of clinicoradiologic risk factors for presence of PET-occult LN metastases, (iv) impact of systematic LN staging in patients with discrepant findings on PET and EBUS-TBNA on target coverage and dose to organs at risk (OAR) in patients undergoing radiotherapy.

Discussion
With specificity of PET of 90%, guidelines recommend tissue confirmation of positive mediastinal LN to ensure potentially early stage patients are not erroneously denied potentially curative resection. However, while confirmation of pathologic LN is routinely sought, the exact extent of mediastinal LN involvement in NSCLC in patient with Stage III NSCLC is rarely established. Studies examining systematic LN staging in early stage NSCLC report a significant discordance between PET and EBUS-TBNA. In patients with locally advanced disease this has significant implications for radiation field planning, with risk of geographic miss in the event of PET-occult mediastinal LN metastases. The SEISMIC study will examine both diagnostic outcomes following systematic LN staging with EBUS-TBNA, and impact on radiation treatment planning.

Trial registration

ACTRN12617000333314, ANZCTR, Registered on 3 March 2017.
New Moms Wellness Study: the randomized controlled trial study protocol for an intervention study to increase fruit and vegetable intake and lower breast cancer risk through weekly counseling and supplemental fruit and vegetable box delivery in breastfeeding women
Authors: Sturgeon Susan R. , Sibeko Lindiwe , Balasubramanian Raji , Arcaro Kathleen F. 
Published: September 2022

Abstract
Background
Laboratory studies indicate that chemicals in fruits and vegetables have anti-carcinogenic and anti-inflammatory activities that can lower breast cancer risk. However, epidemiologic studies of the association between fruit and vegetable intake and breast cancer risk have produced mixed results. Measurement error, confounding, and an emphasis on diet in later adulthood may contribute to weak associations. This paper describes a randomized controlled diet intervention trial in breastfeeding women to examine the effect of high fruit and vegetable intake on breast cancer risk factors, including weight, DNA methylation and inflammatory markers.

Methods
Eligible breastfeeding women who reside within a 35-mile radius of Amherst, MA are enrolled at five to six weeks postpartum and randomly assigned to a Fruit and Vegetable Intervention Arm (target n = 200) or to a USDA MyPlate Control Arm (target n = 200). The Fruit and Vegetable Intervention group receives weekly telephone or video-based counseling to encourage intake of at least eight to ten daily servings of fruits and vegetables and a weekly delivery of a supplemental box of fruits and vegetables for 20 weeks, and less intensive counseling for up to one year. Breastmilk and infant fecal specimens are collected at baseline, 10 and 20 weeks. Anthropometric measurements are obtained at these timepoints and at the 1-year follow-up. The primary outcomes are change in DNA methylation in breast epithelial cells and change in inflammatory markers in breastmilk from randomization to 20 weeks; and change in weight, waist circumference, and fruit and vegetable intake for the period from randomization to 20 weeks and 1 year.

Discussion
This 1-year randomized diet intervention trial in breastfeeding women will assess whether intake of at least eight to ten daily servings of fruits and vegetables per day improves biomarkers of breast cancer risk directly in the breast (i.e., DNA methylation and inflammatory markers) and helps women maintain a healthy weight.
Trial registration: ClinicalTrials.gov Identifier: NCT04374747. Registered May 5, 2020. https://www.clinicaltrials.gov/ct2/show/NCT04374747.
The PIER framework for healthcare simulation integration in undergraduate physiotherapy education
Authors: van der Merwe Anke , Barnes Roline Yvette , Labuschagne Mathys Jacobus 
Published: September 2022

Abstract
Background
The need for healthcare curricula renewal to facilitate a continuum in education from classrooms to diverse healthcare settings is undeniable. Simulation has been recognized as an educational strategy to address healthcare education challenges, with limited reporting on the integration of simulation-based learning experiences in physiotherapy education. The study aimed to describe the finalisation of a framework for integration of healthcare simulation in an undergraduate physiotherapy program.

Methods
A qualitative descriptive research design was utilized. Five South African experts in the fields of healthcare simulation and/or physiotherapy education contributed to the finalization of the framework during a consensus meeting. Content analysis was employed and credibility was ensured through double coding.

Results
Structural coding yielded five themes- Planning, Implementation, Program Evaluation, Program Revision and Framework. The five themes consisted of fifteen categories, two sub-categories and 44 codes. The planning theme was most robust with seven categories. The Planning, Implementation, Evaluation, Revision (PIER) framework was developed and finalized by expert participants. following the consensus meeting.

Conclusion
Needs analyses when planning and incorporating simulation is essential. Collaboration through resource and knowledge sharing is vital in developing a responsive curriculum integrating simulation. Furthermore, facilitator and student preparation are paramount in ensuring active engagement in simulated-based learning experiences. The interconnectedness of all framework elements and integration phases, as well as the implied importance of competent facilitators and prepared students is crucial and highlights careful consideration to be given to these aspects. The PIER framework is generic in nature and represents the continuous process of simulation integration for any healthcare program.
Parental waivers to enable adolescent participation in certain forms of health research: lessons from a South African case study
Authors: Strode Ann , Essack Zaynab 
Published: September 2022

Abstract
Background
The South African legal framework requires mandatory parental/legal guardian consent for all research with children. Ethics guidelines provide some reprieve by allowing RECs to grant waivers of parental or guardianship consent in certain defined circumstances. In the first instance, consent may be provided by a proxy when parents or guardians are unavailable, for example with orphaned children. In the second instance, guidelines permit adolescent self-consent when the nature of the study justifies this approach, for example, research on sensitive issues like sexual behaviour or substance use.

Discussion
South African guidelines set several conditions that must be met for waivers to be granted. These norms overlap with those in international guidelines. However, the ethical norms, especially related to self-consent are sometimes vague. This article critically evaluates the consent norms in the national ethics guidelines and makes recommendations for reform to ethics guidelines in a way that recognises the value of child participation in research, their evolving decision-making capacity and their best interests.

Conclusion
Recommendations are made to harmonise ethics guidelines and law in a way that promotes child participation in research, to ensure additional protections for adolescents when self-consent is allowed, and to withdraw procedural requirements for the community endorsement of self-consent strategies.
Implementation barriers and remedial strategies for community-based health insurance in Bangladesh: insights from national stakeholders
Authors: Sheikh Nurnabi , Tagoe Eunice Twumwaa , Akram Raisul , Ali Nausad , Howick Susan , Morton Alec 
Published: September 2022

Abstract
Background
Community-based health insurance (CBHI) is a part of the health system in Bangladesh, and overcoming the obstacles of CBHI is a significant policy concern that has received little attention. The purpose of this study is to analyze the implementation barriers of voluntary CBHI schemes in Bangladesh and the strategies to overcome these barriers from the perspective of national stakeholders.

Methods
This study is exploratory qualitative research, specifically case study design, using key informant interviews to investigate the barriers of CBHI that are faced during the implementation. Using a topic guide, we conducted thirteen semi-structured in-depth interviews with key stakeholders directly involved in the CBHI implementation process. The data were analyzed using the Framework analysis method.

Results
The implementation of CBHI schemes in Bangladesh is being constrained by several issues, including inadequate population coverage, adverse selection and moral hazard, lack of knowledge about health insurance principles, a lack of external assistance, and insufficient medical supplies. Door-to-door visits by local community-health workers, as well as regular promotional and educational campaigns involving community influencers, were suggested by stakeholders as ways to educate and encourage people to join the schemes. Stakeholders emphasized the necessity of external assistance and the design of a comprehensive benefits package to attract more people. They also recommended adopting a public–private partnership with a belief that collaboration among the government, microfinance institutions, and cooperative societies will enhance trust and population coverage in Bangladesh.

Conclusions
Our research concludes that systematically addressing implementation barriers by including key stakeholders would be a significant reform to the CBHI model, and could serve as a foundation for the planned national health protection scheme for Bangladesh leading to universal health coverage.
Improved biomarker discovery through a plot twist in transcriptomic data analysis
Authors: Sánchez-Baizán Núria , Ribas Laia , Piferrer Francesc 
Published: September 2022

AbstractBackgroundTranscriptomic analysis is crucial for understanding the functional elements of the genome, with the classic method consisting of screening transcriptomics datasets for differentially expressed genes (DEGs). Additionally, since 2005, weighted gene co-expression network analysis (WGCNA) has emerged as a powerful method to explore relationships between genes. However, an approach combining both methods, i.e., filtering the transcriptome dataset by DEGs or other criteria, followed by WGCNA (DEGs + WGCNA), has become common. This is of concern because such approach can affect the resulting underlying architecture of the network under analysis and lead to wrong conclusions. Here, we explore a plot twist to transcriptome data analysis: applying WGCNA to exploit entire datasets without affecting the topology of the network, followed with the strength and relative simplicity of DEG analysis (WGCNA + DEGs). We tested WGCNA + DEGs against DEGs + WGCNA to publicly available transcriptomics data in one of the most transcriptomically complex tissues and delicate processes: vertebrate gonads undergoing sex differentiation. We further validate the general applicability of our approach through analysis of datasets from three distinct model systems: European sea bass, mouse, and human.ResultsIn all cases, WGCNA + DEGs clearly outperformed DEGs + WGCNA. First, the network model fit and node connectivity measures and other network statistics improved. The gene lists filtered by each method were different, the number of modules associated with the trait of interest and key genes retained increased, and GO terms of biological processes provided a more nuanced representation of the biological question under consideration. Lastly, WGCNA + DEGs facilitated biomarker discovery.ConclusionsWe propose that building a co-expression network from an entire dataset, and only thereafter filtering by DEGs, should be the method to use in transcriptomic studies, regardless of biological system, species, or question being considered.
Berberine supplementation modulates the somatotropic axis and ameliorates glucose tolerance in dairy goats during late gestation and early lactation
Authors: Ghavipanje Navid , Fathi Nasri Mohammad Hasan , Farhangfar Seyyed Homayoun , Ghiasi Seyyed Ehsan , Vargas-Bello-Pérez Einar 
Published: September 2022

Abstract
Background
Pregnancy, parturition, and the onset of lactation represent an enormous physiological and hormonal challenge to the homeostasis of dairy animals, being a risk for their health and reproduction. Thus, as a part of the homothetic changes in preparturition period, goats undergo a period of IR as well as uncoupled GH/IGF-1 axis. The objective for this study was to determine the effect of berberine (BBR) during the peripartal period on hormonal alteration and somatotropic axis in dairy goats as well as glucose and insulin kinetics during an intravenous glucose tolerance test (IVGTT). At 21 days before the expected kidding date, 24 primiparous Saanen goats were assigned randomly to 4 dietary treatments. Goats were fed a basal diet from wk. 3 antepartum (AP) until wk. 3 postpartum (PP) supplemented with 0 (CTRL), 1 (BBR1), 2 (BBR2), and 4 (BBR4) g/d BBR. Blood samples were collected on days − 21, − 14, − 7, 0, 7, 14, and 21 relative to the expected kidding date. An IVGTT was also performed on day 22 PP.

Results
Compared with CTRL, supplementation with either BBR2 or BBR4 increased DMI at kidding day and PP, as well as body conditional score (BCS) and milk production (p ≤ 0.05). On d 7 and 14 PP plasma glucose was higher in BBR2- and BBR4-treated than in CTRL. The glucagon concentration was not affected by BBR during the experimental period. However, supplemental BBR indicated a tendency to decrease in cortisol concentration on days 7 (p = 0.093) and 14 (p = 0.100) PP. Lower plasma GH was observed in BBR than in non-BBR goats (p ≤ 0.05). Plasma IGF-1 concentration was enhanced in both BBR2 and BBR4 at kidding and day 7 PP (p ≤ 0.05). During the IVGTT, glucose area under the curve (AUC), clearance rate (CR), T1/2, and Tbasal was lower (p ≤ 0.05) in both BBR2 and BBR4 goats as compared with CTRL. Likewise, the insulin CR was higher (p ≤ 0.05) in goats receiving either BBR2 or BBR4 which was accompanied by a lower insulin T1/2 and AUC.

Conclusions
Altogether, our results indicated an improved glucose and insulin status along with the modulation of the somatotropic axis and glucose and insulin response to IVGTT in dairy goats supplemented with 2 and 4 g/d BBR.
Metabolic engineering of Escherichia coli for efficient production of L-5-hydroxytryptophan from glucose
Authors: Zhang Zhen , Yu Zichen , Wang Jinduo , Yu Yifa , Li Lanxiao , Sun Pengjie , Fan Xiaoguang , Xu Qingyang 
Published: September 2022

Abstract
Background
5-hydroxytryptophan (5-HTP), the direct biosynthetic precursor of the neurotransmitter 5-hydroxytryptamine, has been shown to have unique efficacy in the treatment of a variety of disorders, including depression, insomnia, and chronic headaches, and is one of the most commercially valuable amino acid derivatives. However, microbial fermentation for 5-HTP production continues to face many challenges, including low titer/yield and the presence of the intermediate L-tryptophan (L-Trp), owing to the complexity and low activity of heterologous expression in prokaryotes. Therefore, there is a need to construct an efficient microbial cell factory for 5-HTP production.

Results
We describe the systematic modular engineering of wild-type Escherichia coli for the efficient fermentation of 5-HTP from glucose. First, a xylose-induced T7 RNA polymerase-PT7 promoter system was constructed to ensure the efficient expression of each key heterologous pathway in E. coli. Next, a new tryptophan hydroxylase mutant was used to construct an efficient tryptophan hydroxylation module, and the cofactor tetrahydrobiopterin synthesis and regeneration pathway was expressed in combination. The L-Trp synthesis module was constructed by modifying the key metabolic nodes of tryptophan biosynthesis, and the heterologous synthesis of 5-HTP was achieved. Finally, the NAD(P)H regeneration module was constructed by the moderate expression of the heterologous GDHesi pathway, which successfully reduced the surplus of the intermediate L-Trp. The final engineered strain HTP11 was able to produce 8.58 g/L 5-HTP in a 5-L bioreactor with a yield of 0.095 g/g glucose and a maximum real-time productivity of 0.48 g/L/h, the highest values reported by microbial fermentation.

Conclusion
In this study, we demonstrate the successful design of a cell factory for high-level 5-HTP production, combined with simple processes that have potential for use in industrial applications in the future. Thus, this study provides a reference for the production of high-value amino acid derivatives using a systematic modular engineering strategy and a basis for an efficient engineered strain development of 5-HTP high-value derivatives.
Multifaceted characterization of the biological and transcriptomic signatures of natural killer cells derived from cord blood and placental blood
Authors: Gao Haibo , Liu Min , Zhang Yawei , Zhang Leisheng , Xie Baoguo 
Published: September 2022

Abstract
Background
Perinatal blood including umbilical cord blood and placental blood are splendid sources for allogeneic NK cell generation with high cytotoxicity of combating pathogenic microorganism and malignant tumor. Despite the generation of NK cells from the aforementioned perinatal blood, yet the systematical and detailed information of the biological and transcriptomic signatures of UC-NKs and P-NKs before large-scale clinical applications in disease remodeling is still largely obscure.

Methods
Herein, we took advantage of the “3IL”-based strategy for high-efficient generation of NK cells from umbilical cord blood and placental blood (UC-NKs and P-NKs), respectively. On the one hand, we conducted flow cytometry (FCM) assay and coculture to evaluate the subpopulations, cellular vitality and cytotoxic activity of the aforementioned NK cells. On the other hand, with the aid of RNA-SEQ and multiple bioinformatics analyses, we further dissected the potential diversities of UC-NKs and P-NKs from the perspectives of transcriptomes.

Results
On the basis of the “3IL” strategy, high-efficient NKs were generated from mononuclear cells (MNCs) in perinatal blood. P-NKs revealed comparable ex vivo expansion but preferable activation and cytotoxicity upon K562 cells over UC-NKs. Both of the two NKs showed diversity in cellular vitality and transcriptome including apoptotic cells, cell cycle, gene expression profiling and the accompanied multifaceted biological processes.

Conclusions
Our data revealed the multifaceted similarities and differences of UC-NKs and P-NKs both at the cellular and molecular levels. Our findings supply new references for allogeneic NK cell-based immunotherapy in regenerative medicine and will benefit the further exploration for illuminating the underlying mechanism as well.
Identification and validation of a ferroptosis-related gene to predict survival outcomes and the immune microenvironment in lung adenocarcinoma
Authors: Deng Biao , Xiang Jing , Liang Zhu , Luo Lianxiang 
Published: September 2022

Abstract
Background
Lung adenocarcinoma (LUAD) is a leading cause of cancer-related death worldwide. Ferroptosis, a form of cell death characterized by iron-dependent lipid peroxidation. However, the involvement of ferroptosis in the regulation of immune cell infiltration and its immunotherapeutic efficacy in LUAD remain unclear.

Methods
The Cancer Genome Atlas (TCGA) LUAD cohort was used to assess the survival prognosis of FRGs and construct a seven-gene risk signature. Correlation tests, difference tests, and a cluster analysis were performed to explore the role of FRGs in the immune microenvironment and their immunotherapeutic efficacy in LUAD. The effects of FRGs on LUAD cells were assessed by Western blot, iron assay, and lipid peroxidation assay.

Results
The seven-gene risk signatures of patients with LUAD were established and validated. FRG clustering based on 70 differentially expressed FRGs was associated with the immune microenvironment and indicated potential immune subtypes of LUAD. The seven-gene risk signature was an independent prognostic factor for LUAD and was used to divide the LUAD cohort into a high-risk and a low-risk group. Immunocyte infiltration levels, immune checkpoints, and immunotherapy response rates were significantly different between the two groups. Patients with high risk scores had lower overall levels of immunocyte infiltration but higher immunotherapy response rates. The key gene ribonucleotide reductase subunit M2 (RRM2) was associated with LUAD prognosis, which may be related to its ability to regulate the infiltration levels of activated mast cells and activated CD4 memory T cells. In addition, RRM2 was involved in ferroptosis, and its expression was up regulated in lung cancer tissues and the LUAD cell lines. Silencing RRM2 can inhibit the proliferation and induce ferroptosis of H1975 cells suggesting that silencing RRM2 could promote ferroptosis in H1975 cells.

Conclusion
Our results revealed RRM2 as a promising biomarker and therapeutic target associated with tumor immune infiltration in patients with LUAD.