bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Translational Science Conundrum for Junior Investigators
Authors: Calderon S.J. , Momeni S.S. , Coker M.O. 
Published: January 2023

Translational research is the integration of 2 broad categories of biomedical science—basic science and applied science. However, in dentistry, this effort has been concentrated among a few researchers and must expand to keep pace with other disciplines. This commentary discusses the ongoing challenges faced by translational researchers (particularly early-career investigators) as they conduct oral and dental research, disseminate work, and contribute to science in general. This commentary also provides some recommendations/initiatives that could potentially address or alleviate these challenges. Knowledge Transfer Statement: The challenges and recommendations outlined in this commentary will serve as steppingstones to process the concepts of translational science, facilitate training for future scientists, and serve as an approach for the early investigators in the field of translational science.
Real-world efficacy of the intrascleral ciliary sulcus suprachoroidal microtube technique in Black and Afro-Latinx patients with glaucoma: a 1-year retrospective study
Authors: Laroche Daniel , Nkrumah Gideon , Ng Chester 
Published: January 2023

Background: Suprachoroidal surgery can lower intraocular pressure and medication use. There is currently no commercial suprachoroidal product on the market. Here, we report our 1 year results of a novel ciliary sulcus suprachoroidal microtube technique. Purpose: To determine the real-world efficacy of intrascleral ciliary sulcus suprachoroidal microtube technique in Black and Afro-Latinx patients with glaucoma refractory to topical ocular hypertensive medications. Methods: A retrospective non-comparative single center study of 36 Black and Afro-Latinx patients with glaucoma and pseudophakia who underwent intrascleral ciliary sulcus suprachoroidal microtube surgery for glaucoma as a stand-alone procedure at a single practice. Investigated parameters were number of medications, visual acuity (VA), intraocular pressure (IOP), mean deviation on visual field (VF) test. Success was defined as (a) IOP ⩽ 15 mmHg and or ⩾ 20% reduction in IOP and (b) a reduction in number of medications. We used paired t-test to compare baseline and follow-up parameters. Results: We reviewed a total of 36 patients who had undergone the procedure. Twenty had success with 12-month follow-up in the study. The mean number of medications decreased significantly from 4.2 ± 1.0 preoperatively to 2.4 ± 1.7 in 12 months ( p = 0.021) with five patients being medication free. In addition, the IOP decreased significantly from 21 ± 8.2 to 13.5 ± 4.4 mmHg ( p = 0.032). In the 20 patients who had 12-month follow-up, the VA remained stable from Log Mar 0.62 ± 0.6–0.46 ± 0.6 ( p = 0.052). VF in patients with successful procedure (no further interventions) remained stable from baseline mean deviation of –16.53 ± 10.04 to –16.82 ± 9.80 dB at 6–12 months. Adverse effects were transient and included IOP spike, hypotony, hyphema, and cornea edema that were treated and resolved. Conclusions: This 12-month retrospective study demonstrated that intrascleral ciliary sulcus suprachoroidal microtube surgery can reduce IOP and medication burden in pseudophakic patients with glaucoma. However, despite several successes, surveillance should take place for IOP spikes, possible tube obstruction, and need for additional glaucoma surgery.
Fighting Pandemic: The Mobile Application Way (a Case of the Aarogya Setu App)
Authors: Tabeck Pooja Sehgal , Jain Vinamra 
Published: January 2023

The world of the COVID-19 pandemic is an anomalous biosphere with nothing to be forecasted. The main concern of every individual is focused on keeping themselves safe from infection. This need of keeping oneself safe has raised an alarming situation and resulted into quasi self-quarantines and self-imposed seclusion. The pandemic has increasingly put pressure on the healthcare system of different countries, wherein the countries with the limited number of doctors and health staff are finding it increasingly difficult for all intent and purposes to treat the patients. To lay off the load of medical staff all around the world, different countries have adopted their own unique technique of handling the calamity. One of the creations is applications on smartphones. This has resulted in increasing awareness, self-detection of coronavirus symptoms among the population. These applications were designed to increase awareness among individuals of any risk in their surroundings. It has been developed by corporates, governments and NGOs. The Indian government also launched its own indigenous app named Aarogya Setu (Bridge of Health) to capacitate people to handle and self-detect coronavirus symptoms. The present case is an effort to understand the adoption of Aarogya Setu app from the eye of diffusion of innovation. Case Objective Objectives of the case are to make readers aware about the coronavirus-related applications launched during pandemic, criteria for diffusion of innovation and the concepts of adoption.
Gene targeting in amyotrophic lateral sclerosis using causality-based feature selection and machine learning
Authors: Founta Kyriaki , Dafou Dimitra , Kanata Eirini , Sklaviadis Theodoros , Zanos Theodoros P. , Gounaris Anastasios , Xanthopoulos Konstantinos 
Published: January 2023

Abstract
Background
Amyotrophic lateral sclerosis (ALS) is a rare progressive neurodegenerative disease that affects upper and lower motor neurons. As the molecular basis of the disease is still elusive, the development of high-throughput sequencing technologies, combined with data mining techniques and machine learning methods, could provide remarkable results in identifying pathogenetic mechanisms. High dimensionality is a major problem when applying machine learning techniques in biomedical data analysis, since a huge number of features is available for a limited number of samples. The aim of this study was to develop a methodology for training interpretable machine learning models in the classification of ALS and ALS-subtypes samples, using gene expression datasets.

Methods
We performed dimensionality reduction in gene expression data using a semi-automated preprocessing systematic gene selection procedure using Statistically Equivalent Signature (SES), a causality-based feature selection algorithm, followed by Boosted Regression Trees (XGBoost) and Random Forest to train the machine learning classifiers. The SHapley Additive exPlanations (SHAP values) were used for interpretation of the machine learning classifiers. The methodology was developed and tested using two distinct publicly available ALS RNA-seq datasets. We evaluated the performance of SES as a dimensionality reduction method against: (a) Least Absolute Shrinkage and Selection Operator (LASSO), and (b) Local Outlier Factor (LOF).

Results
The proposed methodology achieved 85.18% accuracy for the classification of cerebellum or frontal cortex samples as C9orf72-related familial ALS, sporadic ALS or healthy samples. Importantly, the genes identified as the most determinative have also been reported as disease-associated in ALS literature. When tested in the evaluation dataset, the methodology achieved 88.89% accuracy for the classification of sporadic ALS motor neuron samples. When LASSO was used as feature selection method instead of SES, the accuracy of the machine learning classifiers ranged from 74.07 to 96.30%, depending on tissue assessed, while LOF underperformed significantly (77.78% accuracy for the classification of pooled cerebellum and frontal cortex samples).

Conclusions
Using SES, we addressed the challenge of high dimensionality in gene expression data analysis, and we trained accurate machine learning ALS classifiers, specific for the gene expression patterns of different disease subtypes and tissue samples, while identifying disease-associated genes.
nf-core/circrna: a portable workflow for the quantification, miRNA target prediction and differential expression analysis of circular RNAs
Authors: Digby Barry , Finn Stephen P. , Ó Broin Pilib 
Published: January 2023

Abstract
Background
Circular RNAs (circRNAs) are a class of covalenty closed non-coding RNAs that have garnered increased attention from the research community due to their stability, tissue-specific expression and role as transcriptional modulators via sequestration of miRNAs. Currently, multiple quantification tools capable of detecting circRNAs exist, yet none delineate circRNA–miRNA interactions, and only one employs differential expression analysis. Efforts have been made to bridge this gap by way of circRNA workflows, however these workflows are limited by both the types of analyses available and computational skills required to run them.

Results
We present nf-core/circrna, a multi-functional, automated high-throughput pipeline implemented in nextflow that allows users to characterise the role of circRNAs in RNA Sequencing datasets via three analysis modules: (1) circRNA quantification, robust filtering and annotation (2) miRNA target prediction of the mature spliced sequence and (3) differential expression analysis. nf-core/circrna has been developed within the nf-core framework, ensuring robust portability across computing environments via containerisation, parallel deployment on cluster/cloud-based infrastructures, comprehensive documentation and maintenance support.

Conclusion
nf-core/circrna reduces the barrier to entry for researchers by providing an easy-to-use, platform-independent and scalable workflow for circRNA analyses. Source code, documentation and installation instructions are freely available at https://nf-co.re/circrna and https://github.com/nf-core/circrna.
Breast abscess due to Nannizziopsis obscura in an immunocompromised renal transplant patient after travel to Nigeria: case report and review
Authors: Jiménez-García Nicolás , Fernández Sánchez Fernando , Guillén Rodríguez Celeste María , Castilla Castellano María del Mar , Del Arco Jiménez Alfonso 
Published: January 2023

Abstract
Background
Nannizziopsis is a genus of fungi with several known cases in reptiles of pyogranulomatous infections at cutaneous and musculoskeletal level, of rapid and fatal evolution. There are few cases of this genus described in humans, mainly skin affection but also with visceral abcesses, typically in immunosuppressed patients, with a recent visit to Africa.

Case presentation
A 45-year-old woman immunosuppressed after renal transplantation and with a recent visit to Nigeria presented with a painless breast abcess, ulceration to the skin and bleeding, and non hematic telorrhea. The mammogram, also completed with an ultrasound scan, showed a polylobulated nodule, BI-RADS 4C. Due to the suspicion of breast cancer, a core needle biopsy was performed and the pathology study showed abundant presence of fungal spores and hyphae. It was identified by genomic amplification of the internal transcription spacer region-2 and a percentage of similarity with sequences of Nannizziopsis obscura from GenBank of 98% was obtained. An empiric treatment with anidulafungin was initiated, and after the surgical resection, it was replaced by isavuconazole, with a total time of treatment of one month.

Conclusions
This is the first case report of a successful treatment of Nannizziopsis obscura with isavuconazole, with the shortest time of treatment published for this fungi. We highlighted the importance of referring difficult to diagnose species to reference centers, as well as achieving the most complete resection in order to shorten the antibiotic therapy.
Effectiveness of brief alcohol interventions for pregnant women: a systematic literature review and meta-analysis
Authors: Popova Svetlana , Dozet Danijela , Pandya Ekta , Sanches Marcos , Brower Krista , Segura Lidia , Ondersma Steven J. 
Published: January 2023

Abstract
Background
Prenatal alcohol exposure (PAE) can result in a range of adverse neonatal outcomes, including Fetal Alcohol Spectrum Disorder (FASD). This systematic review and meta-analysis sought to investigate the effectiveness of brief interventions (BIs) in eliminating or reducing 1) alcohol consumption during pregnancy; and 2) PAE-related adverse neonatal outcomes; and 3) cost-effectiveness of BIs.

Method
We conducted a systematic literature search for original controlled studies (randomized control trials (RCTs); quasi-experimental) in any setting, published from 1987 to 2021. The comparison group was no/minimal intervention, where a measure of alcohol consumption was reported. Studies were critically appraised using the Centre for Evidence-based Medicine Oxford critical appraisal tool for RCTs (1). The certainty in the evidence for each outcome was assessed using the GRADE (Grading of Recommendations Assessment, Development and Evaluation) (2). Meta-analysis of continuous and binary estimates of effect-size for similar outcome measures for BIs versus control groups were pooled and reported as mean difference (MD) Hedges’ g and odds ratios (ORs), respectively.

Results
In total, 26 studies, all from high income countries, met inclusion criteria. Alcohol abstinence outcome available in 12 studies (n = 2620) found modest effects in favor of BIs conditions by increasing the odds of abstinence by 56% (OR = 1.56, 95% confidence interval (CI) = 1.15–2.13, I2 = 46.75%; p = 0.04). BIs effects for reduction in mean drinks/week (Cohen’s d = − 0.21, 95%CI = - 0.78 to 0.36; p = 0.08) and AUDIT scores (g = 0.10, 95%CI = − 0.06 to 0.26; p = 0.17) were not statistically significant. Among seven studies (n = 740) reporting neonatal outcomes, BI receipt was associated with a modest and significant reduction in preterm birth (OR = 0.67, 95% CI = 0.46–0.98, I2 = 0.00%; p = 0.58). No statistically significant differences were observed for mean birthweight or lower likelihood of low birth weight (LBW). Certainty in the evidence was rated as ‘low’. No eligible studies were found on cost-effectiveness of BIs.

Conclusion
BIs are moderately effective in increasing abstinence during pregnancy and preventing preterm birth. More studies on the effectiveness of BIs are needed from low- and middle-income countries, as well as with younger mothers and with a broader range of ethnic groups.
Maternal periconceptional environmental exposure and offspring with congenital heart disease: a case–control study in Guangzhou, China
Authors: Xiao Di , Li Weidong , Zhang Wei-Hong , Wen Zihao , Mo Weijian , Lu Ciyong , Guo Lan , Yang Li 
Published: January 2023

Abstract
Background
Congenital heart defects (CHDs) are a major global health problem, yet their crucial environmental risk factors are still unclear. We aimed to explore the associations between maternal periconceptional environmental exposures and all CHDs, isolated and multiple CHDs and CHDs subtypes.

Method
A case–control study including 675 infants with CHDs and 1545 healthy controls was conducted. Participating mothers who delivered in Guangzhou from October 2019 to November 2021 were recruited. To examine the independent associations between maternal periconceptional environmental exposure and offspring with CHDs, we calculated odds ratios (ORs) and 95% confidence intervals (CIs) using multivariable logistic regression model.

Results
Maternal exposure to living near main roads [adjusted OR (aOR) = 1.94, 95% CI = 1.06–3.56] and housing renovation (aOR = 1.94, 95% CI = 1.03–3.67) during the periconceptional period were positively related to a greater risk of all CHDs, similar results were also found in isolated CHDs rather than multiple CHDs. Additionally, living near main roads was positively associated with secundum atrial septal defect/patent foramen ovale (aOR = 2.65, 95% CI = 1.03–6.81) and housing renovation was strongly positively associated with ventricular septal defect (aOR = 5.08, 95% CI = 2.05–12.60). However, no association was observed between incense burning and family relationships and all CHDs, isolated and multiple CHDs and CHDs subtypes.

Conclusion
Living near main roads and housing renovation during the periconceptional period are significantly associated with the increased risks for all CHDs and isolated CHDs. Further study is needed to extend sample size to explore the effects of time and frequency of burning incense and family relationships on CHDs in offspring.
Examining the usefulness of the brain network marker program using fMRI for the diagnosis and stratification of major depressive disorder: a non-randomized study protocol
Authors: Okada Go , Sakai Yuki , Shibakawa Maki , Yoshioka Toshinori , Itai Eri , Shinzato Hotaka , Yamamoto Osamu , Kurata Kenichi , Tamura Tatsuji , Jitsuiki Hiroaki , Yamashita Hidehisa , Mantani Akio , Yokota Norio , Kawato Mitsuo , Okamoto Yasumasa 
Published: January 2023

Abstract
Background
Although many studies have reported the biological basis of major depressive disorder (MDD), none have been put into practical use. Recently, we developed a generalizable brain network marker for MDD diagnoses (diagnostic marker) across multiple imaging sites using resting-state functional magnetic resonance imaging (rs-fMRI). We have planned this clinical trial to establish evidence for the practical applicability of this diagnostic marker as a medical device. In addition, we have developed generalizable brain network markers for MDD stratification (stratification markers), and the verification of these brain network markers is a secondary endpoint of this study.

Methods
This is a non-randomized, open-label study involving patients with MDD and healthy controls (HCs). We will prospectively acquire rs-fMRI data from 50 patients with MDD and 50 HCs and anterogradely verify whether our diagnostic marker can distinguish between patients with MDD and HCs. Furthermore, we will longitudinally obtain rs-fMRI and clinical data at baseline and 6 weeks later in 80 patients with MDD treated with escitalopram and verify whether it is possible to prospectively distinguish MDD subtypes that are expected to be effectively responsive to escitalopram using our stratification markers.

Discussion
In this study, we will confirm that sufficient accuracy of the diagnostic marker could be reproduced for data from a prospective clinical study. Using longitudinally obtained data, we will also examine whether the “brain network marker for MDD diagnosis” reflects treatment effects in patients with MDD and whether treatment effects can be predicted by “brain network markers for MDD stratification”. Data collected in this study will be extremely important for the clinical application of the brain network markers for MDD diagnosis and stratification.

Trial registration
Japan Registry of Clinical Trials (jRCTs062220063). Registered 12/10/2022.
COVID-19 prevention at institutions of higher education, United States, 2020–2021: implementation of nonpharmaceutical interventions
Authors: Moreland Sarah , Zviedrite Nicole , Ahmed Faruque , Uzicanin Amra 
Published: January 2023

Abstract
Background
In early 2020, following the start of the coronavirus disease 2019 (COVID-19) pandemic, institutions of higher education (IHEs) across the United States rapidly pivoted to online learning to reduce the risk of on-campus virus transmission. We explored IHEs’ use of this and other nonpharmaceutical interventions (NPIs) during the subsequent pandemic-affected academic year 20202021.

Methods
From December 2020 to June 2021, we collected publicly available data from official webpages of 847 IHEs, including all public (n = 547) and a stratified random sample of private four-year institutions (n = 300). Abstracted data included NPIs deployed during the academic year such as changes to the calendar, learning environment, housing, common areas, and dining; COVID-19 testing; and facemask protocols. We performed weighted analysis to assess congruence with the October 29, 2020, US Centers for Disease Control and Prevention (CDC) guidance for IHEs. For IHEs offering ≥50% of courses in person, we used weighted multivariable linear regression to explore the association between IHE characteristics and the summated number of implemented NPIs.

Results
Overall, 20% of IHEs implemented all CDC-recommended NPIs. The most frequently utilized NPI was learning environment changes (91%), practiced as one or more of the following modalities: distance or hybrid learning opportunities (98%), 6-ft spacing (60%), and reduced class sizes (51%). Additionally, 88% of IHEs specified facemask protocols, 78% physically changed common areas, and 67% offered COVID-19 testing. Among the 33% of IHEs offering ≥50% of courses in person, having < 1000 students was associated with having implemented fewer NPIs than IHEs with ≥1000 students.

Conclusions
Only 1 in 5 IHEs implemented all CDC recommendations, while a majority implemented a subset, most commonly changes to the classroom, facemask protocols, and COVID-19 testing. IHE enrollment size and location were associated with degree of NPI implementation. Additional research is needed to assess adherence to NPI implementation in IHE settings.
Health-related quality of life decreases in young people with asthma during the transition from adolescence to young adulthood: a birth cohort study
Authors: Ödling Maria , Andersson Niklas , Janson Christer , Melén Erik , Bergström Anna , Kull Inger 
Published: January 2023

AbstractBackgroundDuring the transition from paediatric to adult healthcare there is a gap between asthma guidelines and actual management with decreased healthcare consultations and dispensations of asthma medications after the transition to adult healthcare among young people with asthma. How health-related quality of life (HRQoL) develops during the transition from adolescence to young adulthood is unclear. Our aim was therefore to investigate HRQoL among young people with asthma during the transition to adulthood. Further, to assess if level of asthma control and physical activity influence any potential association between asthma and HRQoL.MethodsThe study population consisted of 2268 participants from the ongoing Swedish population-based prospective birth cohort BAMSE (Barn/Child, Allergy, Milieu, Stockholm, Epidemiology). HRQoL was measured using the instrument EQ-5D-3 L and three general questions. The EQ-5D-3 L consists of the EQ-5D descriptive system and the EQ visual analogue scale (EQ VAS). The EQ-5D-3 L instrument and questions on general health, symptoms and treatment of asthma, and lifestyle factors were based on data from follow-ups at 16 and 24 years. Cross-sectional analyses were made.ResultsAt the 24-year follow-up, the adjusted median values of EQ VAS were lower compared with at the 16-year follow-up; among both participants with asthma (80 vs. 85,p < 0.01) and those without asthma (80 vs. 87,p < 0.01). At the 24-year follow-up, participants with uncontrolled asthma had a lower adjusted median EQ VAS score than peers with controlled/partly controlled asthma (75 vs. 80,p = 0.03). Further, young adults with asthma who did not fulfil the WHO recommendations on physical activity had lower EQ VAS scores than peers who did (70 vs. 80,p < 0.01).ConclusionHRQoL is lower in young adulthood than in adolescence. Young adults with asthma having uncontrolled disease or who are physically inactive appear to be particularly vulnerable.