bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automatic segmentation of lung tumors on CT images based on a 2D & 3D hybrid convolutional neural network
Authors: Gan Wutian , Wang Hao , Gu Hengle , Duan Yanhua , Shao Yan , Chen Hua , Feng Aihui , Huang Ying , Fu Xiaolong , Ying Yanchen , Quan Hong , Xu Zhiyong 
Published: August 2021

Objective:
A stable and accurate automatic tumor delineation method has been developed to facilitate the intelligent design of lung cancer radiotherapy process. The purpose of this paper is to introduce an automatic tumor segmentation network for lung cancer on CT images based on deep learning.

Methods:
In this paper, a hybrid convolution neural network (CNN) combining 2D CNN and 3D CNN was implemented for the automatic lung tumor delineation using CT images. 3D CNN used V-Net model for the extraction of tumor context information from CT sequence images. 2D CNN used an encoder–decoder structure based on dense connection scheme, which could expand information flow and promote feature propagation. Next, 2D features and 3D features were fused through a hybrid module. Meanwhile, the hybrid CNN was compared with the individual 3D CNN and 2D CNN, and three evaluation metrics, Dice, Jaccard and Hausdorff distance (HD), were used for quantitative evaluation. The relationship between the segmentation performance of hybrid network and the GTV volume size was also explored.

Results:
The newly introduced hybrid CNN was trained and tested on a dataset of 260 cases, and could achieve a median value of 0.73, with mean and stand deviation of 0.72 ± 0.10 for the Dice metric, 0.58 ± 0.13 and 21.73 ± 13.30 mm for the Jaccard and HD metrics, respectively. The hybrid network significantly outperformed the individual 3D CNN and 2D CNN in the three examined evaluation metrics (p &lt; 0.001). A larger GTV present a higher value for the Dice metric, but its delineation at the tumor boundary is unstable.

Conclusions:
The implemented hybrid CNN was able to achieve good lung tumor segmentation performance on CT images.

Advances in knowledge:
The hybrid CNN has valuable prospect with the ability to segment lung tumor.
Perceived stress and generalized anxiety in the Indian population due to lockdown during the COVID-19 pandemic: a cross-sectional study
Authors: Wakode Naina , Wakode Santosh , Santoshi John 
Published: August 2021

Background: Research on the psychosocial toll of the COVID-19 pandemic is being conducted in various countries. This study aimed to examine stress levels and causal stressors for perceived stress and generalized anxiety in the Indian population related to the lockdown during the COVID-19 pandemic. Methods: A total of 300 adults were invited to participate in the online study via snowball and virtual snowball sampling. They were requested to complete electronic survey forms for assessing perceived stress and anxiety, and questions related to psychosocial stressors. Frequency and percentage were used for categorical variables. Unpaired t-test was applied to compare responses based on gender, level of education, employment, and place of residence. A p-value of <0.05 was considered statistically significant. Result: In total, 257 out of the 300 invited, responded and completed the survey. Men accounted for 58% (n=149) of the respondents. Overall, 84% (n=217) of participants had moderate to severe levels of perceived stress and 88% (n=228) had moderate to severe levels of anxiety. Women, as well as those not employed, reported significantly higher perceived stress and anxiety, urban residents reported higher perceived stress, while level of education had no difference in terms of perceived stress as well as anxiety. Fear of contracting COVID-19 was the highest stressor followed by difficulties in executing a routine exercise schedule and worry about the future. Conclusion: The psychosocial impact of the nationwide lockdown on the Indian population has been high. Vulnerable groups for increased stress and anxiety include women, younger ages, and the unemployed. The stressors recognized include fear of contracting COVID-19, inability to execute a routine exercise schedule and worry about the future.
Using citation tracking for systematic literature searching - study protocol for a scoping review of methodological studies and a Delphi study
Authors: Hirt Julian , Nordhausen Thomas , Appenzeller-Herzog Christian , Ewald Hannah 
Published: August 2021

Background: Up-to-date guidance on comprehensive study identification for systematic reviews is crucial. According to current recommendations, systematic searching should combine electronic database searching with supplementary search methods. One such supplementary search method is citation tracking. It aims at collecting directly and/or indirectly cited and citing references from "seed references". Tailored and evidence-guided recommendations concerning the use of citation tracking are strongly needed. Objective: We intend to develop recommendations for the use of citation tracking in systematic literature searching for health-related topics. Our study will be guided by the following research questions: What is the benefit of citation tracking for systematic literature searching for health-related topics? Which methods, citation indexes, and other tools are used for citation tracking? What terminology is used for citation tracking methods? Methods: Our study will have two parts: a scoping review and a Delphi study. The scoping review aims at identifying methodological studies on the benefit and use of citation tracking in systematic literature searching for health-related topics with no restrictions on study design, language, and publication date. We will perform database searching in MEDLINE (Ovid), CINAHL (EBSCOhost), Web of Science Core Collection, two information science databases, web searching, and contact experts in the field. Two reviewers will independently perform study selection. We will conduct direct backward and forward citation tracking on included articles. Data from included studies will be extracted using a prespecified extraction sheet and presented in both tabular and narrative form. The results of the scoping review will inform the subsequent Delphi study through which we aim to derive consensus recommendations for the future practice and research of citation tracking.
Tissue-dependent transcriptional and bacterial associations in primary sclerosing cholangitis-associated inflammatory bowel disease
Authors: Ilott Nicholas E. , Neyazi Mastura ,   Oxford Translational Gastroenterology Unit Investigators, Arancibia-Cárcamo Carolina V. , Powrie Fiona , Geremia Alessandra 
Published: August 2021

Background: Primary sclerosing cholangitis (PSC) is a disease of the bile duct and liver. However, patients frequently have co-morbidities including inflammatory bowel disease (IBD) and colorectal cancer. Colorectal cancer risk in patients with PSC-associated ulcerative colitis (PSC/UC) is elevated relative to patients with ulcerative colitis (UC) alone, reasons for which remain obscure. Further, clinical and immunological features, and involved intestinal sites differ between PSC/UC and UC. Understanding the molecular and microbial basis for differences in cancer risk between these two patient groups and how these differ across intestinal sites is important for the development of therapies to prevent colorectal cancer development in at-risk individuals. Methods: We employed ribonucleic acid sequencing (RNA-seq) analysis of biopsy samples across three intestinal tissue locations (ileum, caecum and rectum) in patients with PSC/UC (n = 8), UC (n = 10) and healthy controls (n = 12) to determine tissue-dependent transcriptional alterations in PSC/UC. We also performed 16S ribosomal RNA (rRNA) amplicon sequencing to determine bacterial associations with PSC/UC and host-microbiome associations. Results: Tissue-defining transcriptional signatures revealed that the ileum was enriched for genes involved in lipid and drug metabolism, the caecum for activated immune cells and the rectum for enteric neurogenesis. Transcriptional alterations relative to healthy control samples were largely shared between patients with PSC/UC or UC although were distinct across tissue locations. Nevertheless, we observed reduced expression of gamma-glutamyl transferase 1 (GGT1) specifically in the ileum and caecum of patients with PSC/UC. Analysis of the bacterial component of the microbiome revealed high inter-individual variability of microbiome composition and little evidence for tissue-dependency. We observed a reduction in Parabacteroides relative abundance in the rectum of patients with PSC/UC. Conclusions: The role of gamma-glutamyl transferase in maintaining the redox environment through the glutathione salvage pathway makes our observed alterations a potential pathway to PSC-associated colorectal cancer.
Social media reactions of nurses to the documentary Stacey Dooley: On the Psych Ward
Authors: Porter Cody Normitta 
Published: August 2021

Background/Aims Mental health nursing is becoming a more transparent discipline. Increasingly, documentaries have provided the general public with insights regarding these therapeutic ward environments. The opinions of staff working in such places is important for ensuring the accuracy of the information, and the usefulness of what is publicly aired. This study explored the social media comments of nursing staff (as the experts) who viewed the Stacey Dooley: On the Psych Ward documentary. Methods Social media (Facebook and Twitter) were searched for comments on the documentary 3 weeks after the documentary was aired. In total, 4008 Facebook comments and 604 tweets were downloaded and assessed. Comments that did not relate to the documentary were excluded. A total of 31 Facebook comments and 54 tweets were used for analysis. Results Some evidence of criticism towards the presenter was found, as well as the use of an award-winning hospital as a non-representative – and unrealistic – example of psychiatric care. In general, healthcare staff felt that the documentary was useful for informing the general public, as well as students. Conclusions Documentaries such as this one that capture the realities of working on mental health wards have educational merit.
Compressive ultrafast pulse measurement via time-domain single-pixel imaging
Authors: Zhao Jiapeng , Dai Jianming , Braverman Boris , Zhang Xi-Cheng , Boyd Robert W. 
Published: August 2021

In contrast to imaging using position-resolving cameras, single-pixel imaging uses a bucket detector along with spatially structured illumination to compressively recover images. This emerging imaging technique is a promising candidate for a broad range of applications due to the high signal-to-noise ratio (SNR) and sensitivity, and applicability in a wide range of frequency bands. Here, inspired by single-pixel imaging in the spatial domain, we demonstrate a time-domain single-pixel imaging (TSPI) system that covers frequency bands including both terahertz (THz) and near-infrared (NIR) regions. By implementing a programmable temporal fan-out gate based on a digital micromirror device, we can deterministically prepare temporally structured pulses with a temporal sampling size down to

16.00
±
0.01

f
s

. By inheriting the advantages of detection efficiency and sensitivity from spatial single-pixel imaging, TSPI enables the recovery of a 5 fJ THz pulse and two NIR pulses with over

97
%

fidelity via compressive sensing. We demonstrate that the TSPI is robust against temporal distortions in the probe pulse train as well. As a direct application, we apply TSPI to machine-learning-aided THz spectroscopy and demonstrate a high sample identification accuracy (97.5%) even under low SNRs (SNR

∼

10

).
Clinical and biological clusters of sepsis patients using hierarchical clustering
Authors: Papin Grégory , Bailly Sébastien , Dupuis Claire , Ruckly Stéphane , Gainnier Marc , Argaud Laurent , Azoulay Elie , Adrie Christophe , Souweine Bertrand , Goldgran-Toledano Dany , Marcotte Guillaume , Gros Antoine , Reignier Jean , Mourvillier Bruno , Forel Jean-Marie , Sonneville Romain , Dumenil Anne-Sylvie , Darmon Michael , Garrouste-Orgeas Maité , Schwebel Carole , Timsit Jean-François ,   OUTCOMEREA study group
Published: August 2021

Background
Heterogeneity in sepsis expression is multidimensional, including highly disparate data such as the underlying disorders, infection source, causative micro-organismsand organ failures. The aim of the study is to identify clusters of patients based on clinical and biological characteristic available at patients’ admission.

Methods
All patients included in a national prospective multicenter ICU cohort OUTCOMEREA and admitted for sepsis or septic shock (Sepsis 3.0 definition) were retrospectively analyzed. A hierarchical clustering was performed in a training set of patients to build clusters based on a comprehensive set of clinical and biological characteristics available at ICU admission. Clusters were described, and the 28-day, 90-day, and one-year mortality were compared with log-rank rates. Risks of mortality were also compared after adjustment on SOFA score and year of ICU admission.

Results
Of the 6,046 patients with sepsis in the cohort, 4,050 (67%) were randomly allocated to the training set. Six distinct clusters were identified: young patients without any comorbidities, admitted in ICU for community-acquired pneumonia (n = 1,603 (40%)); young patients without any comorbidities, admitted in ICU for meningitis or encephalitis (n = 149 (4%)); elderly patients with COPD, admitted in ICU for bronchial infection with few organ failures (n = 243 (6%)); elderly patients, with several comorbidities and organ failures (n = 1,094 (27%)); patients admitted after surgery, with a nosocomial infection (n = 623 (15%)); young patients with immunosuppressive conditions (e.g., AIDS, chronic steroid therapy or hematological malignancy) (n = 338 (8%)). Clusters differed significantly in early or late mortality (p < .001), even after adjustment on severity of organ dysfunctions (SOFA) and year of ICU admission.

Conclusions
Clinical and biological features commonly available at ICU admission of patients with sepsis or septic shock enabled to set up six clusters of patients, with very distinct outcomes. Considering these clusters may improve the care management and the homogeneity of patients in future studies.
Assessing the healthiness of UK food companies’ product portfolios using food sales and nutrient composition data
Authors: Bandy Lauren Kate , Hollowell Sven , Harrington Richard , Scarborough Peter , Jebb Susan , Rayner Mike 
Published: August 2021

Background
The provision and over-consumption of foods high in energy, saturated fat, free sugars or salt are important risk factors for poor diet and ill-health. In the UK, policies seek to drive improvement through voluntary reformulation of single nutrients in key food groups. There has been little consideration of the overall progress by individual companies. This study assesses recent changes in the nutrient profile of brands and products sold by the top 10 food and beverage companies in the UK.

Methods
The FSA/Ofcom nutrient profile model was applied to the nutrient composition data for all products manufactured by the top 10 food and beverage companies and weighted by volume sales. The mean nutrient profiling score, on a scale of 1–100 with thresholds for healthy products being 62 for foods and 68 for drinks, was used to rank companies and food categories between 2015 and 2018, and to calculate the proportion of individual products and sales that are considered by the UK Government to be healthy.

Results
Between 2015 and 2018 there was little change in the sales-weighted nutrient profiling score of the top 10 companies (49 to 51; p = 0.28) or the proportion of products classified as healthy (46% to 48%; p = 0.23). Of the top five brands sold by each of the ten companies, only six brands among ten companies improved their nutrient profiling score by 20% or more. The proportion of total volume sales classified as healthy increased from 44% to 51% (p = 0.07) driven by an increase in the volume sales of bottled water, low/no calorie carbonates and juices, but after removing soft drinks, the proportion of foods classified as healthy decreased from 7% to 6% (p = 33).

Conclusions
The UK voluntary reformulation policies, setting targets for reductions in calories, sugar and salt, do not appear to have led to significant changes in the nutritional quality of foods, though there has been progress in soft drinks where the soft drink industry levy also applies. Further policy action is needed to incentivise companies to make more substantive changes in product composition to support consumers to achieve a healthier diet.
Initiation of domiciliary care and nursing home admission following first hospitalization for heart failure, stroke, chronic obstructive pulmonary disease or cancer
Authors: Rørth Rasmus , Clausen Marianne F. , Fosbøl Emil L. , Mogensen Ulrik M. , Kragholm Kristian , Jhund Pardeep S. , Petrie Mark C. , Torp-Pedersen Christian , Gislason Gunnar H. , McMurray John J. V. , Køber Lars , Kristensen Søren L. 
Published: August 2021

Background
Patients with chronic diseases are at higher risk of requiring domiciliary and nursing home care, but how different chronic diseases compare in terms of risk is not known. We examined initiation of domiciliary care and nursing home admission among patients with heart failure (HF), stroke, COPD and cancer.

Methods
Patients with a first-time hospitalization for HF, stroke, COPD or cancer from 2008–2016 were identified. Patients were matched on age and sex and followed for five years.

Results
111,144 patients, 27,786 with each disease, were identified. The median age was 69 years and two thirds of the patients were men. The 5-year risk of receiving domiciliary care was; HF 20.9%, stroke 25.2%, COPD 24.6% and cancer 19.3%. The corresponding adjusted hazard ratios (HRs), with HF patients used as reference, were: stroke 1.35[1.30–1.40]; COPD 1.29[1.25–1.34]; and cancer 1.19[1.14–1.23]. The five-year incidence of nursing home admission was 6.6% for stroke, and substantially lower in patients with HF(2.6%), COPD(2.6%) and cancer (1.5%). The adjusted HRs were (HF reference): stroke, 2.44 [2.23–2.68]; COPD 1.01 [0.91–1.13] and cancer 0.76 [0.67–0.86]. Living alone, older age, diabetes, chronic kidney disease, depression and dementia predicted a higher likelihood of both types of care.

Conclusions
In patients with HF, stroke, COPD or cancer 5-year risk of domiciliary care and nursing home admission, ranged from 19–25% and 1–7%, respectively. Patients with stroke had the highest rate of domiciliary care and were more than twice as likely to be admitted to a nursing home, compared to patients with the other conditions.
Community’s experience and perceptions of maternal health services across the continuum of care in Ethiopia: A qualitative study
Authors: Tiruneh Gizachew Tadele , Demissie Meaza , Worku Alemayehu , Berhane Yemane 
Published: August 2021

Background
Continuum of care is an effective strategy to ensure that every woman receives a series of maternal health services continuously from early pregnancy to postpartum stages. The community perceptions regarding the use of maternal services across the continuum of care are essential for utilization of care in low-income settings but information in that regard is scanty. This study explored the community perceptions on the continuum of care for maternal health services in Ethiopia.

Methods
This study employed a phenomenological qualitative research approach. Four focus group discussions involving 26 participants and eight in-depth interviews were conducted with women who recently delivered, community health workers, and community leaders that were purposively selected for the study in West Gojjam zone, Amhara region. All the interviews and discussions were audio-taped; the records were transcribed verbatim. Data were coded and analyzed thematically using ATLAS.ti software.

Results
We identified three primary themes: practice of maternal health services; factors influencing the decision to use maternal health services; and reasons for discontinuation across the continuum of maternal health services. The study showed that women faced multiple challenges to continuously uptake maternal health services. Late antenatal care booking was the main reasons for discontinuation of maternal health services across the continuum at the antepartum stage. Women’s negative experiences during care including poor quality of care, incompetent and unfriendly health providers, disrespectful care, high opportunity costs, difficulties in getting transportation, and timely referrals at healthcare facilities, particularly at health centers affect utilization of maternal health services across the continuum of care. In addition to the reverberation effect of the intrapartum care factors, the major reasons mentioned for discontinuation at the postpartum stage were lack of awareness about postnatal care and service delivery modality where women are not scheduled for postpartum consultations.

Conclusion
This study showed that rural mothers still face multiple challenges to utilize maternal health services as recommended by the national guidelines. Negative experiences women encountered in health facilities, community perceptions about postnatal care services as well as challenges related to service access and opportunity costs remained fundamental to be reasons for discontinuation across the continuum pathways.
Application of manual aspiration thrombectomy in the treatment of deep vein thrombosis in cancer patients: Descriptive retrospective cohort study
Authors: Kim Eu Hyun , Lee Hae Giu , Oh Jung Suk , Chun Ho Jong , Choi Byung Gil , Lee Myung Ah 
Published: August 2021

Objectives
To determine the outcomes and feasibility of endovascular treatment, mainly based on manual aspiration thrombectomy (MAT) with adjunctive percutaneous balloon angioplasty with or without stent deployment, for treatment of symptomatic ilio-femoral deep vein thrombosis (IFDVT) in cancer patients.

Materials and methods
In this retrospective cohort study, 135 consecutive patients (56 men; mean age, 63 years; 149 limbs) with acute (n = 113; 83.7%) and subacute to chronic (n = 22; 16.3%) symptomatic IFDVT underwent MAT-based endovascular treatment. Among them, adjunctive balloon angioplasty and stent placement was performed in 94 patients. Technical and clinical success regarding stage and cause of DVT was assessed.

Results
Technical success (complete thrombus removal without residual thrombus or stenosis) was achieved in 89.6%, and subjective symptom improvement was stated by 71.5% of treated patients. The primary patency rates were 88.1%, 81.6%, 76.0%, 74.1% and 69.1% at 1, 3, 6, 12, and 30 months, respectively. Recurrent IFDVT occurred in 19.3% (26/135) of patients, 0.79 cases per patients-years of follow up. According to the analysis by causes of IFDVT, recurrence rate was 19.3% (11/57), 21.2% (12/57), and 14.3% (3/21) in unknown, compression/invasion of the vein by cancerous mass, and May-Thurner syndrome groups, respectively (p = 0.798). No procedure-related complication developed.

Conclusions
Endovascular treatment based on MAT is a feasible treatment option with favorable outcomes and minimal risk of complication in cancer patients with symptomatic IFDVT.