bluuebunny/crossref_metadata_2025_split huggingface dataset:
CAD systems for COVID-19 diagnosis and disease stage classification by segmentation of infected regions from CT images
Authors: Alshayeji Mohammad H. , ChandraBhasi Sindhu Silpa , Abed Sa’ed 
Published: July 2022

Abstract
Background
Here propose a computer-aided diagnosis (CAD) system to differentiate COVID-19 (the coronavirus disease of 2019) patients from normal cases, as well as to perform infection region segmentation along with infection severity estimation using computed tomography (CT) images. The developed system facilitates timely administration of appropriate treatment by identifying the disease stage without reliance on medical professionals. So far, this developed model gives the most accurate, fully automatic COVID-19 real-time CAD framework.

Results
The CT image dataset of COVID-19 and non-COVID-19 individuals were subjected to conventional ML stages to perform binary classification. In the feature extraction stage, SIFT, SURF, ORB image descriptors and bag of features technique were implemented for the appropriate differentiation of chest CT regions affected with COVID-19 from normal cases. This is the first work introducing this concept for COVID-19 diagnosis application. The preferred diverse database and selected features that are invariant to scale, rotation, distortion, noise etc. make this framework real-time applicable. Also, this fully automatic approach which is faster compared to existing models helps to incorporate it into CAD systems. The severity score was measured based on the infected regions along the lung field. Infected regions were segmented through a three-class semantic segmentation of the lung CT image. Using severity score, the disease stages were classified as mild if the lesion area covers less than 25% of the lung area; moderate if 25–50% and severe if greater than 50%. Our proposed model resulted in classification accuracy of 99.7% with a PNN classifier, along with area under the curve (AUC) of 0.9988, 99.6% sensitivity, 99.9% specificity and a misclassification rate of 0.0027. The developed infected region segmentation model gave 99.47% global accuracy, 94.04% mean accuracy, 0.8968 mean IoU (intersection over union), 0.9899 weighted IoU, and a mean Boundary F1 (BF) contour matching score of 0.9453, using Deepabv3+ with its weights initialized using ResNet-50.

Conclusions
The developed CAD system model is able to perform fully automatic and accurate diagnosis of COVID-19 along with infected region extraction and disease stage identification. The ORB image descriptor with bag of features technique and PNN classifier achieved the superior classification performance.
Change point detection for clustered expression data
Authors: Sieg Miriam , Sciesielski Lina Katrin , Kirschner Karin Michaela , Kruppa Jochen 
Published: July 2022

Abstract
Background
To detect changes in biological processes, samples are often studied at several time points. We examined expression data measured at different developmental stages, or more broadly, historical data. Hence, the main assumption of our proposed methodology was the independence between the examined samples over time. In addition, however, the examinations were clustered at each time point by measuring littermates from relatively few mother mice at each developmental stage. As each examination was lethal, we had an independent data structure over the entire history, but a dependent data structure at a particular time point. Over the course of these historical data, we wanted to identify abrupt changes in the parameter of interest - change points.

Results
In this study, we demonstrated the application of generalized hypothesis testing using a linear mixed effects model as a possible method to detect change points. The coefficients from the linear mixed model were used in multiple contrast tests and the effect estimates were visualized with their respective simultaneous confidence intervals. The latter were used to determine the change point(s). In small simulation studies, we modelled different courses with abrupt changes and compared the influence of different contrast matrices. We found two contrasts, both capable of answering different research questions in change point detection: The Sequen contrast to detect individual change points and the McDermott contrast to find change points due to overall progression. We provide the R code for direct use with provided examples. The applicability of those tests for real experimental data was shown with in-vivo data from a preclinical study.

Conclusion
Simultaneous confidence intervals estimated by multiple contrast tests using the model fit from a linear mixed model were capable to determine change points in clustered expression data. The confidence intervals directly delivered interpretable effect estimates representing the strength of the potential change point. Hence, scientists can define biologically relevant threshold of effect strength depending on their research question. We found two rarely used contrasts best fitted for detection of a possible change point: the Sequen and McDermott contrasts.
Research on the frailty status and adverse outcomes of elderly patients with multimorbidity
Authors: Lv Jing , Li Rao , Yuan Li , Yang Xiao-ling , Wang Yi , Ye Zi-Wei , Huang Feng-Mei 
Published: July 2022

Abstract
Background
As patients age, the frailty of those with multimorbidity increases, often resulting in adverse health outcomes. The current study investigated the frailty status and the factors which influence it in elderly patients with multimorbidity in Chinese hospitals. The relationship between the frailty of patients with multimorbidity and adverse outcomes was explored.

Methods
The current prospective cohort study investigated inpatients in the internal medicine department of 5 tertiary hospitals in Sichuan Province, China. A total of 3836 elderly patients with multimorbidity were enrolled. Frailty was assessed using the FRAIL scale and adverse outcome events occurring during hospitalization were tracked. Descriptive statistics and logistic regressions were used for data analysis.

Results
The prevalence of frailty was 27.2% and of pre-frailty, 58.9%. Logistic regression analysis showed that increasing age, low BMI, low education level, lack of exercise, multiple types of medications and multiple numbers of chronic diseases were the main risk factors for frailty in elderly patients with multimorbidity (OR values: 1.020, 1.469, 2.350, 2.836, 1.156 and 1.308, respectively). The incidence of adverse outcomes was 13.9% among the cohort with the most common being deep vein thrombosis (42.4%), followed by pressure injury (38.8%). Regression analysis showed a significant correlation of frailty with adverse outcome (OR: 1.496; p < 0.01).

Conclusions
The prevalence of frailty and pre-frailty in hospitalized elderly patients with multimorbidity was high. Increasing age, low BMI, low education level, lack of exercise, multiple types of medications and multiple numbers of chronic diseases were factors which influenced frailty and frailty was an important factor in the occurrence of adverse outcomes. The most common adverse outcome of elderly multimorbidity patients during hospitalization was deep vein thrombosis.
Staff-to-resident abuse in nursing homes: a scoping review
Authors: Hirt Julian , Adlbrecht Laura , Heinrich Steffen , Zeller Adelheid 
Published: July 2022

Abstract
Background
Elder abuse in long-term care is an important public health concern with social,
health-related, and economic implications. Staff-to-resident abuse is of particular interest since institutions should protect residents’ rights and prevent harm. To provide an up-to date comprehensive overview of staff-to-resident abuse in nursing homes, we performed a scoping review considering types of abuse, their prevalence and associated factors, descriptions, experiences, and preventive interventions.

Methods
We performed a scoping review following the framework provided by Arksey and O’Malley. We searched MEDLINE (via PubMed), CINAHL, PsycINFO via Ovid, and Cochrane Library.
Additionally, we performed free web searching using Google Scholar and checked relevant reviews. Two reviewers independently selected studies. We narratively synthesised the results.

Results
Out of 3876 references retrieved by our search, we included 46 studies in 47 reports. The prevalence rates of abuse varied widely, ranging from 0 to 93% depending on the type of abuse. Associated factors of abuse at the staff, resident, and nursing home level were evaluated inconsistently. Abuse was perceived ambiguous: even though it was considered unacceptable, it was underreported. We found only four studies addressing preventive interventions. Of these, four made recommendations for intervention development. Only one study with an experimental design examined a multi-component intervention including education and mutual support.

Conclusions
The review yielded heterogenous evidence not allowing a concrete conclusion on prevalence and associated factors. However, the results show the significance of the problem and indicate that there are associate factors of abuse that can be influenced by appropriate interventions. These are amongst other staff education, organisational culture, and conditions. Further research should investigate the composition and content of preventive interventions and their potential to reduce abusive behaviours.
Development of an online patient decision aid for kidney failure treatment modality decisions
Authors: Engels Noel , van der Nat Paul B. , Ankersmid Jet W. , Prick Janine C. M. , Parent Ellen , The Regina , Takahashi Asako , Bart Hans A. J. , van Uden-Kraan Cornelia F. , Stiggelbout Anne M. , Bos Willem J. W. , van den Dorpel Marinus A. 
Published: July 2022

Abstract
Background
Patient decision aids (PtDAs) support patients and clinicians in shared decision-making (SDM). Real-world outcome information may improve patients’ risk perception, and help patients make decisions congruent with their expectations and values. Our aim was to develop an online PtDA to support kidney failure treatment modality decision-making, that: 1) provides patients with real-world outcome information, and 2) facilitates SDM in clinical practice.

Methods
The International Patient Decision Aids Standards (IPDAS) development process model was complemented with a user-centred and convergent mixed-methods approach. Rapid prototyping was used to develop the PtDA with a multidisciplinary steering group in an iterative process of co-creation. The results of an exploratory evidence review and a needs-assessment among patients, caregivers, and clinicians were used to develop the PtDA. Seven Dutch teaching hospitals and two national Dutch outcome registries provided real-world data on selected outcomes for all kidney failure treatment modalities. Alpha and beta testing were performed to assess the prototype and finalise development. An implementation strategy was developed to guide implementation of the PtDA in clinical practice.

Results
The ‘Kidney Failure Decision Aid’ consists of three components designed to help patients and clinicians engage in SDM: 1) a paper hand-out sheet, 2) an interactive website, and 3) a personal summary sheet. A ‘patients-like-me’ infographic was developed to visualise survival probabilities for each treatment modality on the website. Other treatment outcomes were incorporated as event rates (e.g. hospitalisation rates) or explained in text (e.g. the flexibility of each treatment modality). No major revisions were needed after alpha and beta testing. During beta testing, some patients ignored the survival probabilities because they considered these too confronting. Nonetheless, patients agreed that every patient has the right to choose whether they want to view this information. Patients and clinicians believed that the PtDA would help patients make informed decisions, and that it would support values- and preferences-based decision-making. Implementation of the PtDA has started in October 2020.

Conclusions
The ‘Kidney Failure Decision Aid’ was designed to facilitate SDM in clinical practice and contains real-world outcome information on all kidney failure treatment modalities. It is currently being investigated for its effects on SDM in a clinical trial.
Sleep patterns and psychosocial health of parents of preterm and full-born infants: a prospective, comparative, longitudinal feasibility study
Authors: Marthinsen Gunhild Nordbø , Helseth Sølvi , Småstuen Milada , Bjorvatn Bjørn , Bandlien Signe Marie , Fegran Liv 
Published: July 2022

Abstract
Background
The early birth and hospitalization of a preterm infant in neonatal intensive care unit can produce several emotional and behavioural responses including sleep problems for parents. Few studies have explored sleep and its associations with health and HRQoL over time in this vulnerable parent population. This purpose of this study was to evaluate the feasibility of a prospective, comparative, longitudinal study of the sleep patterns and psychosocial health of preterm and full-born infants’ parents during the first postpartum year.

Methods
A prospective, comparative, longitudinal feasibility study was conducted. Parents of preterm infants were compared to parents of full-born infants to identify if there were differences in outcomes between the groups. The parents were instructed to wear actigraphs and complete sleep diaries for two consecutive weeks, and responded to a digital questionnaire covering stress, insomnia, fatigue, depression, social support, self-efficacy, and health-related quality of life. Survey data were collected at infant ages of 2, 6, and 12 months, actigraphy and sleep diary data were collected at infant age of 2 months only. Descriptive analysis was used to describe recruitment and attrition rates. Differences between completers and dropouts were analysed with a chi-square test (categorical data) and Mann–Whitney–Wilcoxon test for two independent samples (continuous variables).

Results
Between June 2019 and March 2020, 25 parents of a preterm infant and 78 parents of a full-born infant were recruited from four neonatal intensive care units and two maternity wards, respectively, in four Norwegian hospitals. Feasibility was predefined as recruiting ≥ 75 parents each of preterm and full-born infants. The target for the full-born group was reached. However, the preterm group recruitment was challenging. Actigraphs, sleep diaries, and questionnaires were evaluated as feasible for use in a future study. Attrition rates were high in both groups at 6 and 12 months. No parent-related characteristics were associated with participation at 6 months. At 12 months, dropouts had a statistically significantly lower age in the full-born group (both parents) and higher age and body mass index in the preterm group (fathers).

Conclusions
A longitudinal study is feasible; however, procedural changes, including using active methods and contacting participants, are necessary to increase the recruitment of preterm infants’ parents.
Characteristics and in-hospital morbidity trends associated with oral and oropharyngeal cancers in Brazil
Authors: de Miranda Vargas Deborah Gomes , da Cunha Amanda Ramos , Probst Livia Fernandes , Zafalon Edílson José , Pereira Paulo Zárate , da Silva Tagliaferro Elaine Pereira , De-Carli Alessandro Diogo 
Published: July 2022

Abstract
Background
Brazil experienced an expansion of the population's access to oral health policies after the creation of the Unified Health System (SUS, Sistema Único de Saúde). Through public policies, the consolidation of Primary Health Care (PHC) and the incorporation of dental care into primary and hospital care took place. The objective of this study was to identify epidemiological aspects, including the temporal trend, of hospital morbidity from oral and oropharyngeal cancer in Brazil, considering hospitalizations for this neoplasm in a hospital network linked to the public care system.

Methods
Observational study based on information on hospital admissions for oral cancer throughout Brazil. The research used data from the Brazilian Cancer Registry Information System. For the temporal series analysis, generalized linear regression model was used with the Prais-Winsten method.

Results
Of the 121,971 patients hospitalized with oral and oropharyngeal cancers, 76.40% were male and 23.60% were female, resulting in a M:F ratio of 3.24:1. Regarding the anatomical region of involvement among hospitalized patients with oral cavity neoplastic lesions, there was a predominance in non-specific places in the mouth, such as the floor of the mouth, soft and hard palate, among others (32.68%), followed by lesions in the region of tongue (28.89%). In this population, the predominant age group was between the fifth decade (31.09%) and sixth decade of life (24.99%); men presented neoplastic lesions of oral and oropharyngeal cancers at an earlier age than women. In all regions of the country, the staging of cases diagnosed in the tertiary health network accredited to the José Alencar Gomes da Silva National Cancer Institute (INCA) was late, with higher tendency for metastasis. The temporal trend of the adjusted in-hospital morbidity rates showed to be increasing in the Northeast, South and Midwest regions for the male gender. For females, they were increasing in the Northeast and South regions.

Conclusions
It is concluded that the distribution of in-hospital morbidity rates of oral and oropharyngeal cancers in the country is irregular. There is a greater number of cases identified by the study in male patients and in the Southeast and South regions; with an increasing tendency of this coefficient in both genders.
Enhanced production of terrein in marine-derived Aspergillus terreus by refactoring both global and pathway-specific transcription factors
Authors: Yao Guangshan , Bai Xinfeng , Zhang Bingxin , Wang Lu , Chen Songbiao , Wang Zonghua 
Published: July 2022

Abstract
Background
Terrein, a major secondary metabolite from Aspergillus terreus, shows great potentials in biomedical and agricultural applications. However, the low fermentation yield of terrein in wild A. terreus strains limits its industrial applications.

Results
Here, we constructed a cell factory based on the marine-derived A. terreus RA2905, allowing for overproducing terrein by using starch as the sole carbon source. Firstly, the pathway-specific transcription factor TerR was over-expressed under the control of a constitutive gpdA promoter of A. nidulans, resulting in 5 to 16 folds up-regulation in terR transcripts compared to WT. As expected, the titer of terrein was improved in the two tested terR OE mutants when compared to WT. Secondly, the global regulator gene stuA, which was demonstrated to suppress the terrein synthesis in our analysis, was deleted, leading to greatly enhanced production of terrein. In addition, LS-MS/MS analysis showed that deletion of StuA cause decreased synthesis of the major byproduct butyrolactones. To achieve an optimal strain, we further refactored the genetic circuit by combining deletion of stuA and overexpression of terR, a higher terrein yield was achieved with a lower background of byproducts in double mutants. In addition, it was also found that loss of StuA (both ΔstuA and ΔstuA::OEterR) resulted in aconidial morphologies, but a slightly faster growth rate than that of WT.

Conclusion
Our results demonstrated that refactoring both global and pathway-specific transcription factors (StuA and TerR) provides a high-efficient strategy to enhance terrein production, which could be adopted for large-scale production of terrein or other secondary metabolites in marine-derived filamentous fungi.
Birch pollen, air pollution and their interactive effects on airway symptoms and peak expiratory flow in allergic asthma during pollen season – a panel study in Northern and Southern Sweden
Authors: Carlsen Hanne Krage , Haga Susanna Lohman , Olsson David , Behndig Annelie F , Modig Lars , Meister Kadri , Forsberg Bertil , Olin Anna-Carin 
Published: July 2022

AbstractBackgroundEvidence of the role of interactions between air pollution and pollen exposure in subjects with allergic asthma is limited and need further exploration to promote adequate preventive measures. The objective of this study was to assess effects of exposure to ambient air pollution and birch pollen on exacerbation of respiratory symptoms in subjects with asthma and allergy to birch.MethodsThirty-seven subjects from two Swedish cities (Gothenburg and Umeå) with large variation in exposure to both birch-pollen and air pollutants, participated in the study. All subjects had confirmed allergy to birch and self-reported physician-diagnosed asthma. The subjects recorded respiratory symptoms such as rhinitis or eye irritation, dry cough, dyspnoea, the use of any asthma or allergy medication and peak respiratory flow (PEF), daily for five consecutive weeks during two separate pollen seasons and a control season without pollen. Nitrogen oxides (NOx), ozone (O3), particulate matter (PM2.5), birch pollen counts, and meteorological data were obtained from an urban background monitoring stations in the study city centres. The data were analysed using linear mixed effects models.ResultsDuring pollen seasons all symptoms and medication use were higher, and PEF was reduced in the subjects. In regression analysis, exposure to pollen at lags 0 to 2 days, and lags 0 to 6 days was associated with increased ORs of symptoms and decreased RRs for PEF. Pollen and air pollution interacted in some cases; during low pollen exposure, there were no associations between air pollution and symptoms, but during high pollen exposure, O3concentrations were associated with increased OR of rhinitis or eye irritation, and PM2.5concentrations were associated with increased ORs of rhinitis or eye irritation, dyspnea and increased use of allergy medication.ConclusionsPollen and air pollutants interacted to increase the effect of air pollution on respiratory symptoms in allergic asthma. Implementing the results from this study, advisories for individuals with allergic asthma could be improved, minimizing the morbidities associated with the condition.
Rhein attenuates angiotensin II-induced cardiac remodeling by modulating AMPK–FGF23 signaling
Authors: Lu Wei , Zhu Hongqiao , Wu Jiawen , Liao Sheng , Cheng Guobing , Li Xiaoyang 
Published: July 2022

Abstract
Background
Increasing evidence indicates that myocardial oxidative injury plays a crucial role in the pathophysiology of cardiac hypertrophy (CH) and heart failure (HF). The active component of rhubarb, rhein exerts significant actions on oxidative stress and inflammation. Nonetheless, its role in cardiac remodeling remains unclear.

Methods
CH was induced by angiotensin II (Ang II, 1.4 mg/kg/d for 4 weeks) in male C57BL/6 J mice. Then, rhein (50 and 100 mg/kg) was injected intraperitoneally for 28 days. CH, fibrosis, oxidative stress, and cardiac function in the mice were examined. In vitro, neonatal rat cardiomyocytes (CMs) and cardiac fibroblasts (CFs) pre-treated with rhein (5 and 25 μM) were challenged with Ang II. We performed RNA sequencing to determine the mechanistic role of rhein in the heart.

Results
Rhein significantly suppressed Ang II-induced CH, fibrosis, and reactive oxygen species production and improved cardiac systolic dysfunction in vivo. In vitro, rhein significantly attenuated Ang II-induced CM hypertrophy and CF collagen expression. In addition, rhein obviously alleviated the increased production of superoxide induced by Ang II. Mechanistically, rhein inhibited FGF23 expression significantly. Furthermore, FGF23 overexpression abolished the protective effects of rhein on CMs, CFs, and cardiac remodeling. Rhein reduced FGF23 expression, mostly through the activation of AMPK (AMP-activated protein kinase). AMPK activity inhibition suppressed Ang II-induced CM hypertrophy and CF phenotypic transformation.

Conclusion
Rhein inhibited Ang II-induced CH, fibrosis, and oxidative stress during cardiac remodeling through the AMPK–FGF23 axis. These findings suggested that rhein could serve as a potential therapy in cardiac remodeling and HF.