bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring patient experiences of cancer care in Northern Ireland: A thematic analysis of free-text responses to the 2018 Northern Ireland Patient Experience Survey (NICPES)
Authors: Prue Gillian , O’Connor Dominic , Brown Malcolm , Santin Olinda 
Published: June 2021

Abstract
Background
Cancer diagnosis, treatment and survivorship is multifaceted, and the cancer patient experience can serve as a key indicator of healthcare performance and quality. The purpose of this paper was to analyse free-text responses from the second Northern Ireland Cancer Patient Experience Survey (NICPES) in 2018, to understand experiences of care, emerging themes and identify areas for improvement.

Methods
A 72-item questionnaire (relating to clinical care experience, socio-demographics and 3 free-text questions) was distributed to all Health & Social Care Northern Ireland patients that met the inclusion criteria (≥ 16 years old; confirmed primary diagnosis of cancer and discharged between 1st May and 31st October 2017) in June 2018. Participants could complete the questionnaire online or access a free telephone support line if required. Open-ended free text responses were analysed thematically to identify common themes. Free text responses were divided into positive or negative comments.

Results
In total, 3,748 people responded to the survey, with 2,416 leaving at least one free text comment (69 %). Women aged 55–74 years were most likely to comment. Overall, 3,644 comments were left across the three comments boxes, which were categorised as either positive (2,462 comments; 68 %) or negative / area for improvement (1,182 comments; 32 %). Analysis of free text responses identified six common themes (staff; speed [diagnosis and treatment]; safety; system; support services and specific concerns), which were all related to the overarching theme of survival. Staff was the largest single theme (1,458 responses) with overwhelmingly positive comments (1,322 responses; 91 %), whilst safety (296 negative comments; 70 %) and system (340 negative comments; 81 %) were predominantly negative. Negative comments relating to primary care, aftercare and the cancer system were reported.

Conclusions
The high response rate to the free text comments indicates patients were motivated to engage. Analysis indicates most comments provided were positive in nature. Most survey respondents reported a positive experience in relation to staff. However, there were a number of areas for improvement including the aftercare experience, and a perceived disconnect between primary care and cancer services. These results can help inform the effective delivery of cancer services in Northern Ireland.
An analysis of school absences in England during the COVID-19 pandemic
Authors: Southall Emma , Holmes Alex , Hill Edward M. , Atkins Benjamin D. , Leng Trystan , Thompson Robin N. , Dyson Louise , Keeling Matt J. , Tildesley Michael J. 
Published: June 2021

Abstract
Background
The introduction of SARS-CoV-2, the virus that causes COVID-19 infection, in the UK in early 2020, resulted in the introduction of several control policies to reduce disease spread. As part of these restrictions, schools were closed to all pupils in March (except for vulnerable and key worker children), before re-opening to certain year groups in June. Finally, all school children returned to the classroom in September.

Methods
Here, we analyse data on school absences in late 2020 as a result of COVID-19 infection and how that varied through time as other measures in the community were introduced. We utilise data from the Department for Education Educational Settings database and examine how pupil and teacher absences change in both primary and secondary schools.

Results
Our results show that absences as a result of COVID-19 infection rose steadily following the re-opening of schools in September. Cases in teachers declined during the November lockdown, particularly in regions previously in tier 3, the highest level of control at the time. Cases in secondary school pupils increased for the first 2 weeks of the November lockdown, before decreasing. Since the introduction of the tier system, the number of absences with confirmed infection in primary schools was observed to be (markedly) lower than that in secondary schools. In December, we observed a large rise in the number of absences per school in secondary school settings in the South East and London, but such rises were not observed in other regions or in primary school settings. We conjecture that the increased transmissibility of the new variant in these regions may have contributed to this rise in secondary school cases. Finally, we observe a positive correlation between cases in the community and cases in schools in most regions, with weak evidence suggesting that cases in schools lag behind cases in the surrounding community.

Conclusions
We conclude that there is no significant evidence to suggest that schools are playing a substantial role in driving spread in the community and that careful monitoring may be required as schools re-open to determine the effect associated with open schools upon community incidence.
Involvement of the VEGF signaling pathway in immunosuppression and hypoxia stress: analysis of mRNA expression in lymphocytes mediating panting in Jersey cattle under heat stress
Authors: Wang Jian , Xiang Yang , Jiang Shisong , Li Hongchang , Caviezel Flurin , Katawatin Suporn , Duangjinda Monchai 
Published: June 2021

Abstract
Background
Extreme panting under heat stress threatens dairy cattle milk production. Previous research has revealed that the gas exchange-mediated respiratory drive in critically ill dairy cattle with low O2 saturation induces panting. Vascular endothelial growth factor (VEGF) signaling may play important roles in immunosuppression and oxidative stress during severe respiratory stress responses in heat-stressed cattle. The objectives of this study were to transcriptomically analyze mRNA expression mediating heat-induced respiratory stress-associated panting, evaluate gas exchange, screen hub genes, and verify the expression of proteins encoded by differentially expressed genes in lymphocyte pathways.

Results
Jersey cattle were naturally heat-exposed. Physiological data were collected for response evaluation, and blood was collected for gas exchange and gene expression assays at 06:00, 10:00 and 14:00 continuously for 1 week. Lymphocytes were isolated from whole-blood samples for mRNA-seq and expression analysis of key pathway genes/proteins. The cattle respiration rates differed with time, averaging 51 bpm at 06:00, 76 bpm at 10:00, and 121 bpm at 14:00 (p < 0.05). Gas exchange analysis showed that both pH and pCO2 differed with time: they were 7.41 and 41 mmHg at 06:00, 7.45 and 37.5 mmHg at 10:00, and 7.49 and 33 mmHg at 14:00, respectively (p < 0.01). Sixteen heat-related differentially expressed genes (DEGs; 13 upregulated and 3 downregulated) were screened between 212 DEGs and 1370 heat stress-affected genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) hub gene functional analysis annotated eleven genes to signal transduction, six genes to the immune response, and five genes to the endocrine response, including both prostaglandin-endoperoxide synthase 2 (PTGS2) and VEGF. Gene Ontology (GO) functional enrichment analysis revealed that oxygen regulation was associated with the phosphorus metabolic process, response to oxygen levels, response to decreased oxygen levels, response to hypoxia and cytokine activity terms. The main signaling pathways were the VEGF, hypoxia inducible factor-1(HIF-1), cytokine-cytokine receptor interaction and TNF pathways. Four genes involved Integrin beta 3 (ITBG3), PTGS2, VEGF, and myosin light chain 9 (MYL9) among the 16 genes related to immunosuppression, oxidative stress, and endocrine dysfunction were identified as participants in the VEGF signaling pathway and oxygenation.

Conclusion
These findings help elucidate the underlying immune and oxygen regulation mechanisms associated with the VEGF signaling pathway in heat-stressed dairy cattle.
In-situ muconic acid extraction reveals sugar consumption bottleneck in a xylose-utilizing Saccharomyces cerevisiae strain
Authors: Nicolaï Thomas , Deparis Quinten , Foulquié-Moreno María R. , Thevelein Johan M. 
Published: June 2021

Abstract
Background
The current shift from a fossil-resource based economy to a more sustainable, bio-based economy requires development of alternative production routes based on utilization of biomass for the many chemicals that are currently produced from petroleum. Muconic acid is an attractive platform chemical for the bio-based economy because it can be converted in chemicals with wide industrial applicability, such as adipic and terephthalic acid, and because its two double bonds offer great versatility for chemical modification.

Results
We have constructed a yeast cell factory converting glucose and xylose into muconic acid without formation of ethanol. We consecutively eliminated feedback inhibition in the shikimate pathway, inserted the heterologous pathway for muconic acid biosynthesis from 3-dehydroshikimate (DHS) by co-expression of DHS dehydratase from P. anserina, protocatechuic acid (PCA) decarboxylase (PCAD) from K. pneumoniae and oxygen-consuming catechol 1,2-dioxygenase (CDO) from C. albicans, eliminated ethanol production by deletion of the three PDC genes and minimized PCA production by enhancing PCAD overexpression and production of its co-factor. The yeast pitching rate was increased to lower high biomass formation caused by the compulsory aerobic conditions. Maximal titers of 4 g/L, 4.5 g/L and 3.8 g/L muconic acid were reached with glucose, xylose, and a mixture, respectively. The use of an elevated initial sugar level, resulting in muconic acid titers above 2.5 g/L, caused stuck fermentations with incomplete utilization of the sugar. Application of polypropylene glycol 4000 (PPG) as solvent for in situ product removal during the fermentation shows that this is not due to toxicity by the muconic acid produced.

Conclusions
This work has developed an industrial yeast strain able to produce muconic acid from glucose and also with great efficiency from xylose, without any ethanol production, minimal production of PCA and reaching the highest titers in batch fermentation reported up to now. Utilization of higher sugar levels remained conspicuously incomplete. Since this was not due to product inhibition by muconic acid or to loss of viability, an unknown, possibly metabolic bottleneck apparently arises during muconic acid fermentation with high sugar levels and blocks further sugar utilization.
Food marketing and gender among children and adolescents: a scoping review
Authors: Castronuovo Luciana , Guarnieri Leila , Tiscornia María Victoria , Allemandi Lorena 
Published: June 2021

AbstractBackgroundPervasive marketing of unhealthy foods is a contributing factor to the growth of the global epidemic of childhood and adolescent overweight and obesity. Sex and gender differences come into play in the design of and responses to these marketing strategies, contributing to the perpetuation of stereotyped behavior and generating disparities in food choices and health. The purpose of this paper is to review the current literature regarding gender differences in food marketing design and perception among children and adolescents to facilitate evidence-based policy dialogues to address gender-based health disparities in NCD prevention.MethodsScoping review of articles published in scientific journals in English and Spanish, from 2003 to 2018, that addressed the influence of food marketing among children and adolescents including a gender perspective. The methodological quality of each article was assessed following criteria specific to each study design.ResultsFrom a total of 37 articles (39 studies) included in the review, 17 were experimental and 22 had descriptive, cross-sectional designs. Twenty-one studies were found to have low methodological quality, while 10 and 8 were of medium and high quality, respectively. A total of 23 studies among children and adolescents found gender-based differences. Differences were found in the following dimensions: food marketing on intake; responses to specific marketing; perceptions and attitudes towards food marketing and marketing regulation initiatives; exposure to food advertising and gendered marketing content. The evidence was not conclusive in any of the dimensions.ConclusionsThe evidence suggests that food marketing has a similar impact on the consumption of unhealthy foods on boys and girls, but boys were found to be exposed to food advertising more intensively and their preferences to be more affected by this exposure, coinciding with a male-dominant advertising content. Limitations of these studies include taking gender as an unproblematic construct equivalent to biological sex and the lack of studies focused on developing countries. As gender is a cross-sectional dimension that interacts with other factors driving health disparities, an integrated gender perspective is needed to develop effective, evidence-based policies to control food marketing and tackle the childhood overweight and obesity pandemic.
Lesion segmentation in breast ultrasound images using the optimized marked watershed method
Authors: Shen Xiaoyan , Ma He , Liu Ruibo , Li Hong , He Jiachuan , Wu Xinran 
Published: June 2021

Abstract
Background
Breast cancer is one of the most serious diseases threatening women’s health. Early screening based on ultrasound can help to detect and treat tumours in the early stage. However, due to the lack of radiologists with professional skills, ultrasound-based breast cancer screening has not been widely used in rural areas. Computer-aided diagnosis (CAD) technology can effectively alleviate this problem. Since breast ultrasound (BUS) images have low resolution and speckle noise, lesion segmentation, which is an important step in CAD systems, is challenging.

Results
Two datasets were used for evaluation. Dataset A comprises 500 BUS images from local hospitals, while dataset B comprises 205 open-source BUS images. The experimental results show that the proposed method outperformed its related classic segmentation methods and the state-of-the-art deep learning model RDAU-NET. Its accuracy (Acc), Dice similarity coefficient (DSC) and Jaccard index (JI) reached 96.25%, 78.4% and 65.34% on dataset A, and its Acc, DSC and sensitivity reached 97.96%, 86.25% and 88.79% on dataset B, respectively.

Conclusions
We proposed an adaptive morphological snake based on marked watershed (AMSMW) algorithm for BUS image segmentation. It was proven to be robust, efficient and effective. In addition, it was found to be more sensitive to malignant lesions than benign lesions.

Methods
The proposed method consists of two steps. In the first step, contrast limited adaptive histogram equalization (CLAHE) and a side window filter (SWF) are used to preprocess BUS images. Lesion contours can be effectively highlighted, and the influence of noise can be eliminated to a great extent. In the second step, we propose adaptive morphological snake (AMS). It can adjust the working parameters adaptively according to the size of the lesion. Its segmentation results are combined with those of the morphological method. Then, we determine the marked area and obtain candidate contours with a marked watershed (MW). Finally, the best lesion contour is chosen by the maximum average radial derivative (ARD).
Personalised nutrition advice reduces intake of discretionary foods and beverages: findings from the Food4Me randomised controlled trial
Authors: Livingstone Katherine M. , Celis-Morales Carlos , Navas-Carretero Santiago , San-Cristobal Rodrigo , Forster Hannah , Woolhead Clara , O’Donovan Clare B. , Moschonis George , Manios Yannis , Traczyk Iwona , Gundersen Thomas E. , Drevon Christian A. , Marsaux Cyril F. M. , Fallaize Rosalind , Macready Anna L. , Daniel Hannelore , Saris Wim H. M. , Lovegrove Julie A. , Gibney Mike , Gibney Eileen R. , Walsh Marianne , Brennan Lorraine , Martinez J. Alfredo , Mathers John C. ,   on behalf of the Food4Me Study
Published: June 2021

Abstract
Background
The effect of personalised nutrition advice on discretionary foods intake is unknown. To date, two national classifications for discretionary foods have been derived. This study examined changes in intake of discretionary foods and beverages following a personalised nutrition intervention using these two classifications.

Methods
Participants were recruited into a 6-month RCT across seven European countries (Food4Me) and were randomised to receive generalised dietary advice (control) or one of three levels of personalised nutrition advice (based on diet [L1], phenotype [L2] and genotype [L3]). Dietary intake was derived from an FFQ. An analysis of covariance was used to determine intervention effects at month 6 between personalised nutrition (overall and by levels) and control on i) percentage energy from discretionary items and ii) percentage contribution of total fat, SFA, total sugars and salt to discretionary intake, defined by Food Standards Scotland (FSS) and Australian Dietary Guidelines (ADG) classifications.

Results
Of the 1607 adults at baseline, n = 1270 (57% female) completed the intervention. Percentage sugars from FSS discretionary items was lower in personalised nutrition vs control (19.0 ± 0.37 vs 21.1 ± 0.65; P = 0.005). Percentage energy (31.2 ± 0.59 vs 32.7 ± 0.59; P = 0.031), percentage total fat (31.5 ± 0.37 vs 33.3 ± 0.65; P = 0.021), SFA (36.0 ± 0.43 vs 37.8 ± 0.75; P = 0.034) and sugars (31.7 ± 0.44 vs 34.7 ± 0.78; P < 0.001) from ADG discretionary items were lower in personalised nutrition vs control. There were greater reductions in ADG percentage energy and percentage total fat, SFA and salt for those randomised to L3 vs L2.

Conclusions
Compared with generalised dietary advice, personalised nutrition advice achieved greater reductions in discretionary foods intake when the classification included all foods high in fat, added sugars and salt. Future personalised nutrition approaches may be used to target intake of discretionary foods.

Trial registration
Clinicaltrials.gov NCT01530139. Registered 9 February 2012.
Determining optimal clinical target volume margins in high-grade glioma based on microscopic tumor extension and magnetic resonance imaging
Authors: Nie Shulun , Zhu Yufang , Yang Jia , Xin Tao , Xue Song , Zhang Xianbin , Sun Jujie , Mu Dianbin , Gao Yongsheng , Chen Zhaoqiu , Ding Xingchen , Yu Jinming , Hu Man 
Published: June 2021

Abstract
Introduction
In this study, we performed a consecutive macropathologic analysis to assess microscopic extension (ME) in high-grade glioma (HGG) to determine appropriate clinical target volume (CTV) margins for radiotherapy.

Materials and methods
The study included HGG patients with tumors located in non-functional areas, and supratotal resection was performed. The ME distance from the edge of the tumor to the microscopic tumor cells surrounding brain tissue was measured. Associations between the extent of ME and clinicopathological characteristics were evaluated by multivariate linear regression (MVLR) analysis. An ME predictive model was developed based on the MVLR model.

Results
Between June 2017 and July 2019, 652 pathologic slides obtained from 30 HGG patients were analyzed. The mean ME distance was 1.70 cm (range, 0.63 to 2.87 cm). The MVLR analysis identified that pathologic grade, subventricular zone (SVZ) contact and O6-methylguanine-DNA methyltransferase (MGMT) methylation, isocitrate dehydrogenase (IDH) mutation and 1p/19q co-deletion status were independent variables predicting ME (all P < 0.05). A multivariable prediction model was developed as follows: YME = 0.672 + 0.513XGrade + 0.380XSVZ + 0.439XMGMT + 0.320XIDH + 0.333X1p/19q. The R-square value of goodness of fit was 0.780. The receiver operating characteristic curve proved that the area under the curve was 0.964 (P < 0.001).

Conclusion
ME was heterogeneously distributed across different grades of gliomas according to the tumor location and molecular marker status, which indicated that CTV delineation should be individualized. The model could predict the ME of HGG, which may help clinicians determine the CTV for individual patients.
Trial registration The trial was registered with Chinese Clinical Trial Registry (ChiCTR2100046106). Registered 4 May 2021-Retrospectively registered.
Outcomes with multi-disciplinary management of central lung tumors with CT-guided percutaneous high dose rate brachyablation
Authors: Yoon Stephanie M. , Suh Robert , Abtin Fereidoun , Moghanaki Drew , Genshaft Scott , Kamrava Mitchell , Drakaki Alexandra , Liu Sandy , Venkat Puja , Lee Alan , Chang Albert J. 
Published: June 2021

Abstract
Background
Centrally located lung tumors present treatment challenges given their proximity to mediastinal structures including the central airway, esophagus, major vessels, and heart. Therapeutic options can be limited for medically inoperable patients, particularly if they have received previous thoracic radiotherapy. High dose rate (HDR) brachyablation was developed to improve the therapeutic ratio for patients with central lung tumors. The purpose of this study is to report initial safety and efficacy outcomes with this treatment for central lung malignancies.

Methods
From September 2015 to August 2019, a total of 25 patients with 37 pulmonary tumors were treated with percutaneous HDR brachyablation. Treatment was delivered by a multi-disciplinary team of interventional radiologists, pulmonologists, and radiation oncologists. Twenty-three patients received a median dose of 21.5 Gy (range 15–27.5) in a single fraction, whereas two patients received median dose of 24.75 Gy (range 24–25.5) over 2–3 fractions. Tumor local control (LC) was evaluated by Response Evaluation Criteria in Solid Tumors v1.1. Treatment-related toxicities were graded by Common Terminology Criteria for Adverse Events v5.0, with adverse events less than 90 days defined as acute, and those occurring later were defined as late. LC, progression-free survival (PFS), and overall survival (OS) rates were estimated by the Kaplan–Meier method.

Results
Of 37 treated tumors, 88% were metastatic. Tumor location was central and ultra-central in 24.3% and 54.1%, respectively. Average tumor volume was 11.6 cm3 (SD 12.4, range 0.57–62.8). Median follow-up was 19 months (range 3–48). Two–year LC, PFS, and OS were 96.2%, 29.7%, and 65.5%, respectively. Thirteen of 39 (33.3%) catheter implantation procedures were associated with trace minor pneumothorax requiring no intervention, 1 (2.5%) procedure with minor radiographic pulmonary hemorrhage, and 4 (10.3%) with major pneumothorax requiring chest tube insertions. All procedural complications resolved within 24 h from treatment. Acute grade 1–2 toxicity was identified in 4 patients, whereas none developed late toxicity beyond 90 days of follow-up.

Conclusion
Percutaneous HDR brachyablation is a safe and promising treatment option for centrally located primary and metastatic lung tumors. Future comparisons with stereotactic body radiotherapy and other ablative techniques are warranted to expand multi-disciplinary management options.