bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling and cleaning RNA-seq data significantly improve detection of differentially expressed genes
Authors: Deyneko Igor V. , Mustafaev Orkhan N. , Tyurin Alexander А. , Zhukova Ksenya V. , Varzari Alexander , Goldenkova-Pavlova Irina V. 
Published: November 2022

Abstract
Background
RNA-seq has become a standard technology to quantify mRNA. The measured values usually vary by several orders of magnitude, and while the detection of differences at high values is statistically well grounded, the significance of the differences for rare mRNAs can be weakened by the presence of biological and technical noise.

Results
We have developed a method for cleaning RNA-seq data, which improves the detection of differentially expressed genes and specifically genes with low to moderate transcription. Using a data modeling approach, parameters of randomly distributed mRNA counts are identified and reads, most probably originating from technical noise, are removed. We demonstrate that the removal of this random component leads to the significant increase in the number of detected differentially expressed genes, more significant pvalues and no bias towards low-count genes.

Conclusion
Application of RNAdeNoise to our RNA-seq data on polysome profiling and several published RNA-seq datasets reveals its suitability for different organisms and sequencing technologies such as Illumina and BGI, shows improved detection of differentially expressed genes, and excludes the subjective setting of thresholds for minimal RNA counts. The program, RNA-seq data, resulted gene lists and examples of use are in the supplementary data and at https://github.com/Deyneko/RNAdeNoise.
Impact of a prospective feedback loop on care review activities in older patients at the end of life. A stepped-wedge randomised trial
Authors: Brown Christine , Lee Xing J. , Farrington Alison , Shield Carla , Carter Hannah E. , McPhail Steven M. , Cardona Magnolia , Hillman Kenneth , Callaway Leonie , Willmott Lindy , White Ben P. , Harvey Gillian , Graves Nicholas , Barnett Adrian G. 
Published: November 2022

Abstract
Background
Hospitalisation rates for older people are increasing, with end-of-life care becoming a more medicalised experience. Innovative approaches are warranted to support early identification of the end-of-life phase, communicate prognosis, provide care consistent with people’s preferences, and improve the use of healthcare resources. The Intervention for Appropriate Care and Treatment (InterACT) trial aimed to increase appropriate care and treatment decisions for older people at the end of life, through implementation of a prospective feedback loop. This paper reports on the care review outcomes.

Methods
A stepped-wedge randomised controlled trial was conducted in three large acute hospitals in Queensland, Australia between May 2020 and June 2021. The trial identified older people nearing the end of life using two validated tools for detecting deterioration and short-term death. Admitting clinical teams were provided with details of patients identified as at-risk with the goal of increasing awareness that end of life was approaching to facilitate appropriate patient centred care and avoid non-beneficial treatment. We examined the time between when the patient was identified as ‘at-risk’ and three outcomes: clinician-led care review discussions, review of care directive measures and palliative care referrals. These were considered useful indicators of appropriate care at the end of life.

Results
In two hospitals there was a reduction in the review of care directive measures during the intervention compared with usual care at 21 days (reduced probability of − 0.08; 95% CI: − 0.12 to − 0.04 and − 0.14; 95% CI: − 0.21 to − 0.06). In one hospital there was a large reduction in clinician-led care review discussions at 21 days during the intervention (reduced probability of − 0.20; 95% CI: − 0.28 to − 0.13). There was little change in palliative care referrals in any hospital, with average probability differences at 21 days of − 0.01, 0.02 and 0.04.

Discussion
The results are disappointing as an intervention designed to improve care of hospitalised older people appeared to have the opposite effect on care review outcomes. The reasons for this may be a combination of the intervention design and health system challenges due to the pandemic that highlight the complexity of providing more appropriate care at the end of life.

Trial registration
Australia New Zealand Clinical Trial Registry, ACTRN12619000675123 (registered 6 May 2019).
Exploring the connection between parental bonding and smartphone addiction in Chinese medical students
Authors: Xin Chunyu , Ding Ning , Jiang Nan , Li Honghe , Wen Deliang 
Published: November 2022

Abstract
Background
Smartphone addiction bodes adverse consequences, affecting different populations, including medical students. Parental bonding in childhood had been associated with addiction and recovery in later life. Therefore, this study aimed to examine the associations between parental bonding and smartphone addiction among Chinese medical students.

Method
Binary logistic regressions were used to investigate the associations between parental bonding with mothers and fathers, respectively, and smartphone addiction. Interaction terms of care and protection were included in the models.

Results
A total of 517 medical students were included in the study. The prevalence of smartphone addiction was 48.16% (n = 249). The estimated effects of maternal and paternal parenting on smartphone addiction differed. Maternal protection was positively associated with smartphone addiction (OR, 1.046;95% CI, 1.005-1.087), and maternal care enhanced the estimated effect of protection on smartphone addiction. Paternal care was negatively associated with smartphone addiction (OR, 0.954;95% CI, 0.919-0.989).

Conclusions
Chinese medical students with overprotective mothers or with indifferent fathers tended to exhibit traits of smartphone addiction. Further studies on factors influencing the associations between parental bonding and smartphone addiction may pave the way for potential family-oriented interventions for smartphone addiction.
Unlocking the potential for engaging men to improve reproductive, maternal, and neonatal health in Karnali Province, Nepal
Authors: Pokhrel Khem Narayan , Thakuri Dipendra Singh , Dagadu Nana Apenem , Balami Roma , Sharma Matrika , Bhandari Rajan 
Published: November 2022

Abstract
Background
Adolescent girls and young women (AGYW) often experience early childbearing and have poor utilization of reproductive, maternal, and neonatal health (RMNH) services in Nepal. Involving men in such services has been increasingly recognized globally to improve gender-equitable reproductive health behaviour in husbands. This qualitative study assessed the implementation of Healthy Transitions’ male engagement interventions in Karnali Province, Nepal which were implemented to improve gender-equitable attitudes, and supportive RMNH care-seeking behaviors among the husbands of young women.

Methods
We conducted a summative qualitative study that included in-depth interviews with 12 AGYW as primary beneficiaries and their husbands (N = 12) and in-laws (N = 8). In addition, key informant interviews were conducted with health workers (N = 8), local government representatives (N = 4), members of Health Facility Operation and Management Committee (N = 8) and project implementers (N = 12). Due to COVID-19-related travel restrictions and lockdowns, all interviews were conducted via phone calls and online consultation. Data were analyzed using multistage coding and thematic content analysis.

Results
AGYW, their husbands, in-laws and health workers were receptive to the Healthy transitions’ male engagement initiatives. They perceived that the project contributed a momentum to facilitate men’s gender-responsive behaviour. Many participants reported that male engagement interventions, including home visits, community dialogues, and social events improved husbands’ support for their wives during menstruation, pregnancy, and childbirth. The activities also facilitated spousal communication and improved the couple’s decision-making for family planning use. Women reported that improved support from their husbands increased their self-confidence.

Conclusions
This study sheds light on the role of male engagement strategies to improve RMNH in a context where inequitable gender norms and roles are highly prevalent. Our findings highlight the potential to improve RMNH by addressing barriers to male engagement.
Aspergillus tracheobronchitis with Birt-Hogg-Dubè syndrome as a rare cause of chronic cough
Authors: Huang Lianrong , Yi Fang , Zhan Chen , Lai Kefang 
Published: November 2022

Abstract
Background
Aspergillus tracheobronchitis (ATB) is confined as a condition of chronic superficial infection of tracheobronchial tree. Its diagnosis is difficult due to atypical manifestations and low detective rate of Aspergillus thus far.

Case presentation:
Herein, we presented a 45-year-old male patient with a sole chronic productive cough for five years referred to our cough specialist clinic. Chest high-resolution computed tomography showed multiple lung cysts predominantly located in the subpleural lesions and near the mediastinum. Neither bacteria nor fungi were identified by sputum culture. However, metagenomic next-generation sequencing in sputum detected Aspergillus fumigatus DNA. The genetic testing of whole blood suggested the germline mutation of the tumor suppressor gene folliculin, supporting a diagnosis of Birt-Hogg-Dubé (BHD) syndrome. His productive cough symptom significantly improved after receiving itraconazole treatment for 2 months. After discontinuation of antifungal treatment, there was no relapse for four months follow-up. A diagnosis of ATB with BHD syndrome was eventually established in this patient.

Conclusion
ATB should be considered in any patient with prolonged unexplained productive cough. Next-generation sequencing technologies may be useful to identify ATB which is uncommon and easily ignored in clinical practice.
Association between metabolic control and oral health in children with type 1 diabetes mellitus
Authors: Ferizi Lulëjeta , Bimbashi Venera , Kelmendi Jeta 
Published: November 2022

Abstract
Background
Type 1 diabetes mellitus is the most common chronic disease and can be reflected in the oral cavity. The aim of this study was to analyze the impact of metabolic control on saliva, dental caries, dental plaque, gingival inflammation, and cariogenic bacteria in saliva.

Methods
A case–control epidemiologic study was performed on children with type 1 diabetes (ages 10–15 years) separated into two groups: 34 children with good metabolic control of glycated hemoglobin (HbA1c < 7.5%) and 46 children with poor metabolic control of glycated hemoglobin (HbA1c > 7.5%). Oral status was assessed using the Decay, Missing, and Filled Teeth index for permanent teeth (DMFT), plaque index and gingival index. The stimulated salivary flow rate was measured, and the colonies of Streptococcus mutans and Lactobacillus in saliva were determined. The observed children answered questions related to their frequency of brushing habits, dental visits and parents’ education. Mann–Whitney U Test, Chi-Square test and Fisher’s exact test were used in the statistical analyses. The significance level was set at p < 0.05.

Results
The children with diabetes with poor metabolic control had significantly higher values of the DMFT index, plaque index, and gingival index, more colonies, and a higher risk of Streptococcus mutans and Lactobacillus than the children with diabetes with good metabolic control (p < 0.001). The level of metabolic control of diabetes had no influence on salivary flow rates (p > 0.05). The majority of both groups with good and poor metabolic control brushed their teeth once per day, and they visited the dentist only when necessary (61.3%). However, the parents of children in both groups had medium to low levels of education, without any significant difference between groups (p > 0.05).

Conclusion
The results indicate that children with diabetes have a lower level of oral hygiene and are potentially to dental caries and periodontal diseases, mainly when their metabolic disorder is uncontrolled.
Access to oral health care for children with fetal alcohol spectrum disorder: a cross-sectional study
Authors: Hu Katie , Da Silva Keith 
Published: November 2022

Abstract
Background
Individuals with developmental disabilities, including Fetal Alcohol Spectrum Disorder (FASD), often suffer from poorer oral health than the general population as they experience challenges with accessing care. However, few studies have investigated access to oral health care specific to children diagnosed with FASD. Thus, the objective of this cross-sectional study is to examine the use of oral health care services by children diagnosed with FASD in Saskatchewan, Canada, and to identify perceived barriers that affect their access to oral health care.

Methods
Parents or caregivers for children with FASD under the age of 16 were recruited through community organizations. Between July 2020 and January 2021, 189 participants completed a 64-item questionnaire that assessed sociodemographic characteristics, oral health care utilization, and perceived barriers to care.

Results
Most children (85%) had visited the dentist within the last 24 months. 55% of children had required sedation for some treatment. 43% of caregivers experienced frustration trying to access care for their child. Common barriers were cost (63%), location (55%), the child’s behaviour (78%) and caregiver anxiety (60%). 35% of caregivers believed their dentist lacked adequate knowledge of FASD. Univariate analysis reveals that income, caregiver education, residence location, and insurance status were significantly associated with reporting barriers. Multivariate logistic regression analysis reveals that caregivers who reported a high school education (OR=1.23; 95% CI 1.03 – 1.38); or public insurance (OR=1.33; 95% CI 1.24 – 1.42) or out-of-pocket payments (OR=1.37, 95% CI 1.20 – 1.46); or rural (OR=1.19, 95% CI 1.07 – 1.26) or remote (OR=1.23; 95% CI=1.12 – 1.31) residences were more likely to report difficulties accessing oral health care.

Conclusion
Our findings indicate that children with FASD experience various barriers to accessing oral health care. Social determinants of health were significant variables that increased likelihood of barriers. Like other vulnerable populations, cost and clinic location are notable barriers. Oral health care providers’ assessment and management of children with FASD are noteworthy for future research.
Dental pedagogy in the ‘new normal’ COVID-19 era: a transition template of teaching protocols
Authors: Khalifa Nadia , Samaranayake Lakshman , Fakhruddin Kausar Sadia 
Published: November 2022

Abstract
Aims
Delivery of clinical dental education, as opposed to clinical medicine, is particularly challenging due to the obligatory aerosol-generating procedures (AGPs) used in dentistry, which are known to facilitate the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Hence, using AGPs and working in close proximity to patients for extended periods in dental hospital/university settings with multiple teaching clinics have been a formidable prospect for all stake holders. Therefore, several professional and governmental organizations have promulgated variations of infection control guidelines for general practice dentistry in the pandemic era to mitigate SARS-CoV-2 transmission.

Materials and methods
In the absence of unified guidelines for modified infection control/clinical procedures for dental education. We implemented a clinical protocol template and modified operating procedures (MOP) for teaching clinical dentistry to fit the infection control requirements during the pandemic/post-pandemic period at the Sharjah University, College of Dentistry, UAE. MOPs ranged from various engineering control measures (e.g., negative-pressure ventilation systems in operatories) to administrative control measures featuring post-procedure fallow periods of treatment-abeyance between patient sessions.

Results
The new MOPs for clinical dentistry in the COVID-19 pandemic era, trialled in a UAE dental teaching hospital, have successfully eliminated infection transmission amongst the students, clinicians, ancillary staff, or attending patients, thus far.

Conclusions
The proposed MOPs that complement the standard operating protocols in clinical dentistry were an attempt to mitigate nosocomial infection transmission and protect four different groups of stakeholders, i) the patients, ii) the dental students, iii) the clinical academics, and iv) the para-dental personnel/assistants. Due to the endemicity of the COVID-19 in many regions of the World, the suggested MOPs need periodic review and revision, to fit the emerging data on the disease. Finally, as there are no studies to date comparing the relative efficacy of the MOPs in various dental academic institutions, there is an urgent need for future workers to address this issue.
Home care nurses’ perception of the challenges they faced during the COVID-19 pandemic: a qualitative study
Authors: Ghezeljeh Tahereh Najafi , Shahrestanaki Sahar Keyvanloo , Majdabadi kohne Zahra Amrollah , Fakhari Ehsan 
Published: November 2022

Abstract
Background
Despite the significant role they play in the whole health care system, home care nurses are not paid the attention they deserve. Besides highlighting their significant role in the health care system, the COVID-19 pandemic also posed several challenges for home care nurses.

Objective
The purpose of this study is to explain the nurses’ perception of the challenges of home care during the Covid-19 pandemic.

Methods
The present study was a qualitative study with a conventional content analysis approach conducted from November 2020 to September 2021. Participants included 16 home care nurses who were purposefully selected based on the eligibility criteria. After obtaining ethical authorization, the data were collected through semi-structured interviews. MAXQDA Version 10 software was used for data mangement. Data analysis was performed using the Granheim and Lundman five-step method. Guba and Lincoln criteria were utilized for trustworthiness.

Findings
The seven main categories obtained in this study included “the onset of a new chapter: from avoidance to relapse”, “burnout”, “vortex of moral distress”, “social stigma”, “difficulty in breaking the transmission chain”, “care inhibitors related to the patient and family” and “support deficiency: the crisis of home care nursing agencies during the crisis”.

Conclusion
The results showed that nurses working in home care during the Covid-19 pandemic experienced several challenges in various fields. This study captured the nurses’ perception of the challenges of home care during the Covid-19 pandemic, a period of unprecedented change and difficulty. These challenges included lack of support, psychological problems, and dealing with new experiences. Identifying these challenges can help improve the quality of home care nursing and planning in this area.
Effect of gamified flipped classroom on improving nursing students’ skills competency and learning motivation: a randomized controlled trial
Authors: Elzeky Mohamed E. H. , Elhabashy Heba M. M. , Ali Wafaa G. M. , Allam Shaimaa M. E. 
Published: November 2022

Abstract
Background
Flipped learning excessively boosts the conceptual understanding of students through the reversed arrangement of pre-learning and in classroom learning events and challenges students to independently achieve learning objectives. Using a gamification method in flipped classrooms can help students stay motivated and achieve their goals.

Methods
This study adopted a randomized controlled study design with a pre-test and post-test and involved 128 nursing students at Mansoura University. This study randomly divided the students into the study and control groups. Data were collected at three time points using six tools. In the intervention group, Moodle was gamified for 6 weeks.

Results
A significant difference in the students’ self-confidence (p = 0.021), skills knowledge (p < 0.001), intensity of preparation (p < 0.001), and motivation (p < 0.001) was observed between the two groups; however, no difference in the students’ skills performance (p = 0.163) was observed between the two groups after using gamified flipped classrooms.

Conclusions
Compared with the traditional flipped classrooms, gamified flipped classrooms improved nursing students’ motivation, intensity of preparation, skills knowledge, and self-confidence during laboratory clinical practice. Thus, gamification is a learning approach that can be implemented in conjunction with the flipped classroom model to motivate students to participate in the learning process.
Trial registration.
Prospectively registered with ClinicalTrials.gov on 26/04/2021; registration number NCT04859192.
Malaria among under-five children in Ethiopia: a systematic review and meta-analysis
Authors: Biset Gebeyaw , Tadess Abay Woday , Tegegne Kirubel Dagnaw , Tilahun Lehulu , Atnafu Natnael 
Published: November 2022

Abstract
Background
Globally, malaria is among the leading cause of under-five mortality and morbidity. Despite various malaria elimination strategies being implemented in the last decades, malaria remains a major public health concern, particularly in tropical and sub-tropical regions. Furthermore, there have been limited and inconclusive studies in Ethiopia to generate information for action towards malaria in under-five children. Additionally, there is a considerable disparity between the results of the existing studies. Therefore, the pooled estimate from this study will provide a more conclusive result to take evidence-based interventional measures against under-five malaria.

Methods
The protocol of this review is registered at PROSPERO with registration number CRD42020157886. All appropriate databases and grey literature were searched to find relevant articles. Studies reporting the prevalence or risk factors of malaria among under-five children were included. The quality of each study was assessed using the Newcastle–Ottawa Quality Assessment Scale (NOS). Data was extracted using Microsoft Excel 2016 and analysis was done using STATA 16.0 statistical software. The pooled prevalence and its associated factors of malaria were determined using a random effect model. Heterogeneity between studies was assessed using the Cochrane Q-test statistics and I2 test. Furthermore, publication bias was checked by the visual inspection of the funnel plot and using Egger’s and Begg’s statistical tests.

Results
Twelve studies with 34,842 under-five children were included. The pooled prevalence of under-five malaria was 22.03% (95% CI 12.25%, 31.80%). Lack of insecticide-treated mosquito net utilization (AOR: 5.67, 95% CI 3.6, 7.74), poor knowledge of child caretakers towards malaria transmission (AOR: 2.79, 95% CI 1.70, 3.89), and living near mosquito breeding sites (AOR: 5.05, 95% CI 2.92, 7.19) were risk factors of under-five malaria.

Conclusion
More than one in five children aged under five years were infected with malaria. This suggests the rate of under-five malaria is far off the 2030 national malaria elimination programme of Ethiopia. The Government should strengthen malaria control strategies such as disseminating insecticide-treated mosquito nets (ITNs), advocating the utilization of ITNs, and raising community awareness regarding malaria transmission.