bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adherence with reporting of ethical standards in COVID-19 human studies: a rapid review
Authors: O’Sullivan Lydia , Killeen Ronan P. , Doran Peter , Crowley Rachel K. 
Published: June 2021

Abstract
Background
Patients with COVID-19 may feel under pressure to participate in research during the pandemic. Safeguards to protect research participants include ethical guidelines [e.g. Declaration of Helsinki and good clinical practice (GCP)], legislation to protect participants’ privacy, research ethics committees (RECs) and informed consent. The International Committee of Medical Journal Editors (ICMJE) advises researchers to document compliance with these safeguards. Adherence to publication guidelines has been suboptimal in other specialty fields. The aim of this rapid review was to determine whether COVID-19 human research publications report compliance with these ethical safeguards.

Methods
A rapid systematic literature review was conducted in MEDLINE using the search term ‘COVID-19’. The search was performed in April 2020 with no start date and repeated to include articles published in November 2020. Filters were ‘Full free text available’ and ‘English Language’. Two reviewers assessed article title, abstracts and full texts. Non-COVID-19 articles and non-clinical studies were excluded. Independent reviewers conducted a second assessment of a random 20% of articles. The outcomes included reporting of compliance with the Declaration of Helsinki and GCP, REC approval, informed consent and participant privacy.

Results
The searches yielded 1275 and 1942 articles of which 247 and 717 were deemed eligible, from the April search and November respectively. The majority of journals had editorial policies which purported to comply with ICMJE ethical standards. Reporting of compliance with ethical guidelines was low across all study types but was higher in the November search for case series and observational studies. Reporting of informed consent for case studies and observational studies was higher in the November search, but similar for case series. Overall, participant confidentiality was maintained but some case studies included a combination of details which would have enabled participant identification. Reporting of REC approval was higher in the November search for observational studies.

Conclusions
While the majority of journal’s editorial policies purported to support the ethical safeguards, many COVID-19 clinical research publications identified in this rapid review lacked documentation of these important safeguards for research participants. In order to promote public trust, ethical declarations should be included consistently.
Diabetes self-management in online health communities: an information exchange perspective
Authors: Min Jing , Chen Yan , Wang Li , He Ting , Tang Sha 
Published: June 2021

Abstract
Background
Online health communities (OHCs), with a wealth of multi-source information exchange, have provided a convenient way for people with diabetes to actively participate in their self-management and have been widely used. Information exchange assists people with diabetes with health-related decisions to actively engage in their care, and reduce the occurrence of potential complications of diabetes. However, there has been relatively little research on the information exchange behaviors and their effect on health in professional online medical platforms—OHCs.

Objective
Using a social exchange theory, this study focuses on two sources of information (doctors and people with diabetes) to investigate information exchange behaviors and consequences. Moreover, we also examine moderating effects of information price as patients need to pay prices for consulting with doctors to obtain medical information on OHCs.

Methods
By using the Python program, a rich dataset contained 22,746 doctor-patient dialogues from December 2017 to December 2018 is collected from the biggest OHC in China. Then the logistic and ordinal regression models are used to get empirical results.

Results
We found that first information sharing from doctors and other people with diabetes can promote their information sharing behavior. Second, the moderating effects of information price are heterogeneous and change with the exchange participants. Third, rich information exchange supports self-management of people with diabetes and improves their health status.

Conclusion
This study is among the first that tests the information exchange behavior and consequence for diabetes in OHCs and examines the moderating effects of the information price. The present study produces several insights, which have implications for social exchange, patient behavior, online health communities, and information technology in diabetes self-management literature.
On the predictability of postoperative complications for cancer patients: a Portuguese cohort study
Authors: Gonçalves Daniel , Henriques Rui , Santos Lúcio Lara , Costa Rafael S. 
Published: June 2021

AbstractPostoperative complications are still hard to predict despite the efforts towards the creation of clinical risk scores. The published scores contribute for the creation of specialized tools, but with limited predictive performance and reusability for implementation in the oncological context. This work aims to predict postoperative complications risk for cancer patients, offering two major contributions. First, to develop and evaluate a machine learning-based risk score, specific for the Portuguese population using a retrospective cohort of 847 cancer patients undergoing surgery between 2016 and 2018, for 4 outcomes of interest: (1) existence of postoperative complications, (2) severity level of complications, (3) number of days in the Intermediate Care Unit (ICU), and (4) postoperative mortality within 1 year. An additional cohort of 137 cancer patients from the same center was used for validation. Second, to improve the interpretability of the predictive models. In order to achieve these objectives, we propose an approach for the learning of risk predictors, offering new perspectives and insights into the clinical decision process. For postoperative complications the Receiver Operating Characteristic Curve (AUC) was 0.69, for complications’ severity AUC was 0.65, for the days in the ICU the mean absolute error was 1.07 days, and for 1-year postoperative mortality the AUC was 0.74, calculated on the development cohort. In this study, predictive models which could help to guide physicians at organizational and clinical decision making were developed. Additionally, a web-based decision support tool is further provided to this end.
Associations of GP practice characteristics with the rate of ambulatory care sensitive conditions in people living with dementia in England: an ecological analysis of routine data
Authors: Eyles Emily , Redaniel Maria Theresa , Purdy Sarah , Tilling Kate , Ben-Shlomo Yoav 
Published: June 2021

Abstract
Background
Hospital admissions for Ambulatory Care Sensitive Conditions (ACSCs) are potentially avoidable. Dementia is one of the leading chronic conditions in terms of variability in ACSC admissions by general practice, as well as accounting for around a third of UK emergency admissions.

Methods
Using Bayesian multilevel linear regression models, we examined the ecological association of organizational characteristics of general practices (ACSC n=7076, non-ACSC n=7046 units) and Clinical Commissioning Groups (CCG n=212 units) in relation to ACSC and non-ACSC admissions for people with dementia in England.

Results
The rate of hospital admissions are variable between GP practices, with deprivation and being admitted from home as risk factors for admission for ACSC and non-ACSC admissions. The budget allocated by the CCG to mental health shows diverging effects for ACSC versus non-ACSC admissions, so it is likely there is some geographic variation.

Conclusions
A variety of factors that could explain avoidable admissions for PWD at the practice level were examined; most were equally predictive for avoidable and non-avoidable admissions. However, a high amount of variation found at the practice level, in conjunction with the diverging effects of the CCG mental health budget, implies that guidance may be applied inconsistently, or local services may have differences in referral criteria. This indicates there is potential scope for improvement.
Conducting a psychosocial and lifestyle assessment as part of an integrated care approach for childhood obesity: experiences, needs and wishes of Dutch healthcare professionals
Authors: Koetsier L. W. , van Mil M. M. A. , Eilander M. M. A. , van den Eynde E. , Baan C. A. , Seidell J. C. , Halberstadt J. 
Published: June 2021

Abstract
Background
The causes and consequences of childhood obesity are complex and multifaceted. Therefore, an integrated care approach is required to address weight-related issues and improve children’s health, societal participation and quality of life. Conducting a psychosocial and lifestyle assessment is an essential part of an integrated care approach. The aim of this study was to explore the experiences, needs and wishes of healthcare professionals with respect to carrying out a psychosocial and lifestyle assessment of childhood obesity.

Methods
Fourteen semi-structured interviews were conducted with Dutch healthcare professionals, who are responsible for coordinating the support and care for children with obesity (coordinating professionals, ‘CPs’). The following topics were addressed in our interviews with these professionals: CPs’ experiences of both using childhood obesity assessment tools and their content, and CPs’ needs and wishes related to content, circumstances and required competences. The interviews comprised open-ended questions and were recorded and transcribed verbatim. The data was analysed using template analyses and complemented with open coding in MAXQDA.

Results
Most CPs experienced both developing a trusting relationship with the children and their parents, as well as establishing the right tone when engaging in weight-related conversations as important. CPs indicated that visual materials were helpful in such conversations. All CPs used a supporting assessment tool to conduct the psychosocial and lifestyle assessment but they also indicated that a more optimal tool was desirable. They recognized the need for specific attributes that helped them to carry out these assessments, namely: sufficient knowledge about the complexity of obesity; having an affinity with obesity-related issues; their experience as a CP; using conversational techniques, such as solution-focused counselling and motivational interviewing; peer-to-peer coaching; and finally, maintaining an open-minded, non-stigmatizing stance and harmonizing their attitude with that of the child and their parents.

Conclusions
Alongside the need for a suitable tool for conducting a psychosocial and lifestyle assessment, CPs expressed the need for requisite knowledge, skills and attitudes. Further developing a supporting assessment tool is necessary in order to facilitate CPs and thereby improve the support and care for children with obesity and their families.
Bronchial thermoplasty in asthma: an exploratory histopathological evaluation in distinct asthma endotypes/phenotypes
Authors: Papakonstantinou Eleni , Koletsa Triantafyllia , Zhou Liang , Fang Lei , Roth Michael , Karakioulaki Meropi , Savic Spasenija , Grize Leticia , Tamm Michael , Stolz Daiana 
Published: June 2021

Abstract
Background
Bronchial thermoplasty regulates structural abnormalities involved in airway narrowing in asthma. In the present study we aimed to investigate the effect of bronchial thermoplasty on histopathological bronchial structures in distinct asthma endotypes/phenotypes.

Methods
Endobronchial biopsies (n = 450) were collected from 30 patients with severe uncontrolled asthma before bronchial thermoplasty and after 3 sequential bronchial thermoplasties. Patients were classified based on blood eosinophils, atopy, allergy and smoke exposure. Tissue sections were assessed for histopathological parameters and expression of heat-shock proteins and glucocorticoid receptor. Proliferating cells were determined by Ki67-staining.

Results
In all patients, bronchial thermoplasty improved asthma control (p < 0.001), reduced airway smooth muscle (p = 0.014) and increased proliferative (Ki67 +) epithelial cells (p = 0.014). After bronchial thermoplasty, airway smooth muscle decreased predominantly in patients with T2 high asthma endotype. Epithelial cell proliferation was increased after bronchial thermoplasty in patients with low blood eosinophils (p = 0.016), patients with no allergy (p = 0.028) and patients without smoke exposure (p = 0.034).

In all patients, bronchial thermoplasty increased the expression of glucocorticoid receptor in epithelial cells (p = 0.018) and subepithelial mesenchymal cells (p = 0.033) and the translocation of glucocorticoid receptor in the nucleus (p = 0.036). Furthermore, bronchial thermoplasty increased the expression of heat shock protein-70 (p = 0.002) and heat shock protein-90 (p = 0.001) in epithelial cells and decreased the expression of heat shock protein-70 (p = 0.009) and heat shock protein-90 (p = 0.002) in subepithelial mesenchymal cells. The effect of bronchial thermoplasty on the expression of heat shock proteins -70 and -90 was distinctive across different asthma endotypes/phenotypes.

Conclusions
Bronchial thermoplasty leads to a diminishment of airway smooth muscle, to epithelial cell regeneration, increased expression and activation of glucocorticoid receptor in the airways and increased expression of heat shock proteins in the epithelium. Histopathological effects appear to be distinct in different endotypes/phenotypes indicating that the beneficial effects of bronchial thermoplasty are achieved by diverse molecular targets associated with asthma endotypes/phenotypes.
Effect and mechanisms of reproductive tract infection on oxidative stress parameters, sperm DNA fragmentation, and semen quality in infertile males
Authors: Liu Kang-Sheng , Mao Xiao-Dong , Pan Feng , An Rui Fang 
Published: June 2021

AbstractRecent years have seen a rising incidence of male infertility, mostly caused by the decline of sperm quality. The ratio of infertile males to infertile females has escalated from 3:7 in 2013 to current 5:5, which turns male infertility into the research focus of reproductive medicine. This study aimed to clarify the effect of reproductive tract infection by ureaplasma urealyticum (UU) and chlamydia trachomatis (CT) on the DNA integrity and routine semen parameters of infertile males. A retrospective study was performed. A total of 259 infertile males who were treated at the Andrological Laboratory Examination and Reproductive Medicine Center in our hospital were analyzed. qRT-PCR was used to examine the infection status of CT and UU. According to the eligibility criteria, we evaluated the semen parameters and biochemical data of 253 men. Based on the results of PCR, the subjects were divided into four groups: Group I (CT positive, 63 cases), Group II (UU positive, 60 cases), Group III (CT positive and UU positive, 62 cases), and Group IV (no infection, 68 cases). DNA fragmentation index (DFI), sperm count, vitality and morphology, elastase level, seminal plasma malondialdehyde (MDA), and total antioxidant capacity (TAC) were assessed. Compared to Group IV, three groups (Group I, Group II and Group III) showed difference in semen volume, proportion of sperm with normal morphology, sperm motility, progressive motility, and vitality (P < 0.05). Compared to Group IV, Group II and Group III showed difference in DFI (P < 0.05). Compared to Group IV, Group II and Group III showed difference in elastase level(P < 0.05). VCL, VSL, VAP, WOB, ROS, TM, HDS showed differences between groups of abnormal/normal WBC (*P < 0.01).UU infection significantly increased the level of seminal leukocytes only in Group II, but not in the other three groups, indicating that UU is a factor to increase the level of seminal leukocytes. Compared with the normal leukocyte group, there were significant differences in total motility, forward motility and normal sperm ratio between the two groups. The proportion of sperm with abnormal morphology (mostly in the head) showed obvious difference between groups of high and normal seminal leukocytic levels. At the same time, in this study, SCGE and SCD verified that leukocytes could damage sperm DNA by increasing ROS, which ultimately affects male fertility.
A novel surgical model for the preclinical assessment of the osseointegration of dental implants: a surgical protocol and pilot study results
Authors: AlOtaibi Noura M. , Dunne Michael , Ayoub Ashraf F. , Naudi Kurt B. 
Published: June 2021

AbstractBackgroundDental implants are considered the gold standard replacement for missing natural teeth. The successful clinical performance of dental implants is due to their ability to osseointegrate with the surrounding bone. Most dental implants are manufactured from Titanium and it alloys. Titanium does however have some shortcomings so alternative materials are frequently being investigated. Effective preclinical studies are essential to transfer the innovations from the benchtop to the patients. Many preclinical studies are carried out in the extra-oral bones of small animal models to assess the osseointegration of the newly developed materials. This does not simulate the oral environment where the dental implants are subjected to several factors that influence osseointegration; therefore, they can have limited clinical value.AimThis study aimed to develop an appropriatein-vivomodel for dental implant research that mimic the clinical setting. The study evaluated the applicability of the new model and investigated the impact of the surgical procedure on animal welfare.Materials and methodsThe model was developed in male New Zealand white rabbits. The implants were inserted in the extraction sockets of the secondary incisors in the maxilla. The model allows a split-mouth comparative analysis. The implants’ osseointegration was assessed clinically, radiographically using micro-computed tomography (µ-CT), and histologically. A randomised, controlled split-mouth design was conducted in 6 rabbits. A total of twelve implants were inserted. In each rabbit, two implants; one experimental implant on one side, and one control implant on the other side were applied. Screw-shaped implants were used with a length of 8 mm and a diameter of 2 mm.ResultsAll the rabbits tolerated the surgical procedure well. The osseointegration was confirmed clinically, histologically and radiographically. Quantitative assessment of bone volume and mineral density was measured in the peri-implant bone tissues. The findings suggest that the new preclinical model is excellent, facilitating a comprehensive evaluation of osseointegration of dental implants in translational research pertaining to the human application.ConclusionThe presented model proved to be safe, reproducible and required basic surgical skills to perform.
Interobserver variability in organ at risk delineation in head and neck cancer
Authors: van der Veen J. , Gulyban A. , Willems S. , Maes F. , Nuyts S. 
Published: June 2021

Abstract
Background
In radiotherapy inaccuracy in organ at risk (OAR) delineation can impact treatment plan optimisation and treatment plan evaluation. Brouwer et al. showed significant interobserver variability (IOV) in OAR delineation in head and neck cancer (HNC) and published international consensus guidelines (ICG) for OAR delineation in 2015. The aim of our study was to evaluate IOV in the presence of these guidelines.

Methods
HNC radiation oncologists (RO) from each Belgian radiotherapy centre were invited to complete a survey and submit contours for 5 HNC cases. Reference contours (OARref) were obtained by a clinically validated artificial intelligence-tool trained using ICG. Dice similarity coefficients (DSC), mean surface distance (MSD) and 95% Hausdorff distances (HD95) were used for comparison.

Results
Fourteen of twenty-two RO (64%) completed the survey and submitted delineations. Thirteen (93%) confirmed the use of delineation guidelines, of which six (43%) used the ICG. The OARs whose delineations agreed best with the OARref were mandible [median DSC 0.9, range (0.8–0.9); median MSD 1.1 mm, range (0.8–8.3), median HD95 3.4 mm, range (1.5–38.7)], brainstem [median DSC 0.9 (0.6–0.9); median MSD 1.5 mm (1.1–4.0), median HD95 4.0 mm (2.3–15.0)], submandibular glands [median DSC 0.8 (0.5–0.9); median MSD 1.2 mm (0.9–2.5), median HD95 3.1 mm (1.8–12.2)] and parotids [median DSC 0.9 (0.6–0.9); median MSD 1.9 mm (1.2–4.2), median HD95 5.1 mm (3.1–19.2)]. Oral cavity, cochleas, PCMs, supraglottic larynx and glottic area showed more variation. RO who used the consensus guidelines showed significantly less IOV (p = 0.008).

Conclusions
Although ICG for delineation of OARs in HNC exist, they are only implemented by about half of RO participating in this study, which partly explains the delineation variability. However, this study highlights that guidelines alone do not suffice to eliminate IOV and that more effort needs to be done to accomplish further treatment standardisation, for example with artificial intelligence.
New neural network classification method for individuals ancestry prediction from SNPs data
Authors: Soumare H. , Rezgui S. , Gmati N. , Benkahla A. 
Published: June 2021

AbstractArtificial Neural Network (ANN) algorithms have been widely used to analyse genomic data. Single Nucleotide Polymorphisms(SNPs) represent the genetic variations, the most common in the human genome, it has been shown that they are involved in many genetic diseases, and can be used to predict their development. DevelopingANNto handle this type of data can be considered as a great success in the medical world. However, the high dimensionality of genomic data and the availability of a limited number of samples can make the learning task very complicated. In this work, we propose a New Neural Network classification method based on input perturbation. The idea is first to useSVDto reduce the dimensionality of the input data and to train a classification network, which prediction errors are then reduced by perturbing theSVDprojection matrix. The proposed method has been evaluated on data from individuals with different ancestral origins, the experimental results have shown the effectiveness of the proposed method. Achieving up to96.23%of classification accuracy, this approach surpasses previous Deep learning approaches evaluated on the same dataset.
Direct long-read RNA sequencing identifies a subset of questionable exitrons likely arising from reverse transcription artifacts
Authors: Schulz Laura , Torres-Diz Manuel , Cortés-López Mariela , Hayer Katharina E. , Asnani Mukta , Tasian Sarah K. , Barash Yoseph , Sotillo Elena , Zarnack Kathi , König Julian , Thomas-Tikhonenko Andrei 
Published: June 2021

AbstractResistance to CD19-directed immunotherapies in lymphoblastic leukemia has been attributed, among other factors, to several aberrantCD19pre-mRNA splicing events, including recently reported excision of a cryptic intron embedded withinCD19exon 2. While “exitrons” are known to exist in hundreds of human transcripts, we discovered, using reporter assays and direct long-read RNA sequencing (dRNA-seq), that theCD19exitron is an artifact of reverse transcription. Extending our analysis to publicly available datasets, we identified dozens of questionable exitrons, dubbed “falsitrons,” that appear only in cDNA-seq, but never in dRNA-seq. Our results highlight the importance of dRNA-seq for transcript isoform validation.