bluuebunny/crossref_metadata_2025_split huggingface dataset:
Blood transcriptomics to facilitate diagnosis and stratification in pediatric rheumatic diseases – a proof of concept study
Authors: Ha My Kieu , Bartholomeus Esther , Van Os Luc , Dandelooy Julie , Leysen Julie , Aerts Olivier , Siozopoulou Vasiliki , De Smet Eline , Gielen Jan , Guerti Khadija , De Maeseneer Michel , Herregods Nele , Lechkar Bouchra , Wittoek Ruth , Geens Elke , Claes Laura , Zaqout Mahmoud , Dewals Wendy , Lemay Annelies , Tuerlinckx David , Weynants David , Vanlede Koen , van Berlaer Gerlant , Raes Marc , Verhelst Helene , Boiy Tine , Van Damme Pierre , Jansen Anna C. , Meuwissen Marije , Sabato Vito , Van Camp Guy , Suls Arvid , Werff ten Bosch Jutte Van der , Dehoorne Joke , Joos Rik , Laukens Kris , Meysman Pieter , Ogunjimi Benson 
Published: October 2022

Abstract
Background
Transcriptome profiling of blood cells is an efficient tool to study the gene expression signatures of rheumatic diseases. This study aims to improve the early diagnosis of pediatric rheumatic diseases by investigating patients’ blood gene expression and applying machine learning on the transcriptome data to develop predictive models.

Methods
RNA sequencing was performed on whole blood collected from children with rheumatic diseases. Random Forest classification models were developed based on the transcriptome data of 48 rheumatic patients, 46 children with viral infection, and 35 controls to classify different disease groups. The performance of these classifiers was evaluated by leave-one-out cross-validation. Analyses of differentially expressed genes (DEG), gene ontology (GO), and interferon-stimulated gene (ISG) score were also conducted.

Results
Our first classifier could differentiate pediatric rheumatic patients from controls and infection cases with high area-under-the-curve (AUC) values (AUC = 0.8 ± 0.1 and 0.7 ± 0.1, respectively). Three other classifiers could distinguish chronic recurrent multifocal osteomyelitis (CRMO), juvenile idiopathic arthritis (JIA), and interferonopathies (IFN) from control and infection cases with AUC ≥ 0.8. DEG and GO analyses reveal that the pathophysiology of CRMO, IFN, and JIA involves innate immune responses including myeloid leukocyte and granulocyte activation, neutrophil activation and degranulation. IFN is specifically mediated by antibacterial and antifungal defense responses, CRMO by cellular response to cytokine, and JIA by cellular response to chemical stimulus. IFN patients particularly had the highest mean ISG score among all disease groups.

Conclusion
Our data show that blood transcriptomics combined with machine learning is a promising diagnostic tool for pediatric rheumatic diseases and may assist physicians in making data-driven and patient-specific decisions in clinical practice.
Environmental and health-related research on application and production of rare earth elements under scrutiny
Authors: Klingelhöfer Doris , Braun Markus , Dröge Janis , Fischer Axel , Brüggmann Dörthe , Groneberg David A. 
Published: October 2022

Abstract
Background
Unlike most other commodities, rare earth elements (REEs) are part of a wide range of applications needed for daily life all over the world. These applications range from cell phones to electric vehicles to wind turbines. They are often declared as part of “green technology” and, therefore, often called “green elements”. However, their production and use are not only useful but also risky to the environment and human health, as many studies have shown. Consequently, the range of global research efforts is broad and highly variable, and therefore difficult to capture and assess. Hence, this study aims to assess the global parameters of global research on REE in the context of environment and health (REEeh). In addition to established bibliometric parameters, advanced analyses using market driver and scientific infrastructure values were carried out to provide deep insight into incentives, necessities, and barriers to international research.

Results
The focus of REE research is in line with national aspirations, especially from the major global players, China and the USA. Whereas globally, regional research interests are related to market interests, as evidenced by the inclusion of drivers such as electric vehicles, wind turbines, and permanent magnets. The topics receiving the most attention are related to gadolinium used for magnetic resonance imaging and the use of ceria nanoparticles. Since both are used for medical purposes, the medical research areas are equally profiled and mainly addressed in high-income countries. Nevertheless, environmental issues are increasingly in focus.

Conclusions
There is still a need for research that is independent and open-ended. For this, market-independent technologies, substitutes and recycling of REEs need to be addressed scientifically. The results of this study are relevant for all stakeholders, from individual scientists to planners to funders, to improve future research strategies in line with these research mandates.

Graphical Abstract
Tarsal coalition resections: a long-term retrospective analysis of 97 resections in 78 patients
Authors: Saxena Amol , Allen Ryan , Wright Anthony , Migliorini Filippo , Maffulli Nicola 
Published: October 2022

Abstract
Background
Resection of tarsal coalitions provides good patient satisfaction scores, reduced pain, and improved long-term function in both athletic and non-athletic populations. This study aimed to determine when athletic patients undergoing resection of a tarsal coalition were able to return to their desired activity, and whether they experienced a decreased desired activity level (DDA).

Methods
Data on a total of 78 patients who underwent 97 tarsal coalition resections (49 talocalcaneal coalitions, 47 calcaneo-navicular, 14 cuboid-navicular, and three cuneo-navicular; some patients had more than one coalition) operated between January 2001 and June 2020 were prospectively collected. To subjectively assess outcomes, the Roles and Maudsley score (RM) was utilized.

Results
At an average follow-up from the index procedure of 33.6 ± 41.5 months, return to activity for the entire cohort was 18.3 ± 9.6 weeks. Post-RM was 1.3 ± 0.6.

Conclusion
Surgical excision of tarsal coalitions produced favorable results, with most patients able to return to their desired activity level.

Level of evidence
IV.
Long-term safety and efficacy of gene-corrected autologous keratinocyte grafts for recessive dystrophic epidermolysis bullosa
Authors: So Jodi Y. , Nazaroff Jaron , Iwummadu Chinonso V. , Harris Nicki , Gorell Emily S. , Fulchand Shivali , Bailey Irene , McCarthy Daniel , Siprashvili Zurab , Marinkovich M. Peter , Tang Jean Y. , Chiou Albert S. 
Published: October 2022

Abstract
Background
Recessive dystrophic epidermolysis bullosa (RDEB) is a rare, devastating blistering genodermatosis caused by mutations in the COL7A1 gene, which encodes for type VII collagen and is necessary for dermal-epidermal adhesion and integrity. Disease manifestations include severe and debilitating wounds, aggressive squamous cell carcinomas, and premature death; however, there are currently no approved therapies. This Phase 1/2a, open-label study evaluated the long-term efficacy and safety of gene-corrected autologous keratinocyte grafts (EB-101) for chronic RDEB wounds.

Methods
Autologous keratinocytes were harvested from participants with severe RDEB, transduced with a retrovirus containing the full-length COL7A1 gene, and grown into 5 × 7 cm (35 cm2) sheets. Gene-corrected keratinocyte sheets were then transplanted onto chronic RDEB wounds present for ≥ 12 weeks.

Results
Seven adult participants with severe RDEB were grafted with six sheets each (42 total sheets) onto wounds and followed for a mean of 5.9 years (range 4–8 years). Long-term improvements in wound healing and symptoms were observed. At year five, 70% (21/30) of treated sites demonstrated ≥ 50% wound healing compared to baseline by investigator global assessment. No sites with ≥ 50% wound healing were painful or pruritic, compared to 67% (6/9) of sites with < 50% wound healing (p < 0.001) at year five. Grafts were well-tolerated throughout long-term follow-up. No serious adverse events related to treatment were reported over a mean of 5.9 years of follow-up. No persistent systemic autoimmunity against type VII collagen or replication-competent retrovirus infections were identified, and no participants developed squamous cell carcinomas related to treatment during long-term follow-up.

Conclusions
Treatment with EB-101 appears safe and efficacious, and produces long-term improvements in wound healing, pain, and itch for RDEB patients. Results from the Phase 3 randomized controlled trial are forthcoming.

Trial registration

ClinicalTrials.gov, NCT01263379. Registered December 15, 2010. https://clinicaltrials.gov/ct2/show/NCT01263379
The epidemiology and outcomes of prolonged trauma care (EpiC) study: methodology of a prospective multicenter observational study in the Western Cape of South Africa
Authors: Suresh Krithika , Dixon Julia M. , Patel Chandni , Beaty Brenda , del Junco Deborah J. , de Vries Shaheem , Lategan Hendrick J. , Steyn Elmin , Verster Janette , Schauer Steven G. , Becker Tyson E. , Cunningham Cord , Keenan Sean , Moore Ernest E. , Wallis Lee A. , Baidwan Navneet , Fosdick Bailey K. , Ginde Adit A. , Bebarta Vikhyat S. , Mould-Millman Nee-Kofi 
Published: October 2022

AbstractBackgroundDeaths due to injuries exceed 4.4 million annually, with over 90% occurring in low-and middle-income countries. A key contributor to high trauma mortality is prolonged trauma-to-treatment time. Earlier receipt of medical care following an injury is critical to better patient outcomes. Trauma epidemiological studies can identify gaps and opportunities to help strengthen emergency care systems globally, especially in lower income countries, and among military personnel wounded in combat. This paper describes the methodology of the “Epidemiology and Outcomes of Prolonged Trauma Care (EpiC)” study, which aims to investigate how the delivery of resuscitative interventions and their timeliness impacts the morbidity and mortality outcomes of patients with critical injuries in South Africa.MethodsThe EpiC study is a prospective, multicenter cohort study that will be implemented over a 6-year period in the Western Cape, South Africa. Data collected will link pre- and in-hospital care with mortuary reports through standardized clinical chart abstraction and will provide longitudinal documentation of the patient’s clinical course after injury. The study will enroll an anticipated sample of 14,400 injured adults. Survival and regression analysis will be used to assess the effects of critical early resuscitative interventions (airway, breathing, circulatory, and neurologic) and trauma-to-treatment time on the primary 7-day mortality outcome and secondary mortality (24-h, 30-day) and morbidity outcomes (need for operative interventions, secondary infections, and organ failure).DiscussionThis study is the first effort in the Western Cape of South Africa to build a standardized, high-quality, multicenter epidemiologic trauma dataset that links pre- and in-hospital care with mortuary data. In high-income countries and the U.S. military, the introduction of trauma databases and registries has led to interventions that significantly reduce post-injury death and disability. The EpiC study will describe epidemiology trends over time, and it will enable assessments of how trauma care and system processes directly impact trauma outcomes to ultimately improve the overall emergency care system.Trial Registration: Not applicable as this study is not a clinical trial.
Role of ursodeoxycholic acid in neonatal indirect hyperbilirubinemia: a systematic review and meta-analysis of randomized controlled trials
Authors: Lazarus Glen , Francie Jerrell , Roeslani Rosalina Dewi , Saldi Siti Rizny Fitriana , Oswari Hanifah 
Published: October 2022

Abstract
Background
Neonatal jaundice is a transitional phenomenon affecting three out of five full-term newborns globally. Ursodeoxycholic acid could be beneficial in neonatal jaundice needing phototherapy.

Methods
We searched PubMed, EBSCO, ProQuest, and Cochrane Library up to August 21st, 2021, for articles to be reviewed. Meta-analysis using random-effects model was performed.

Results
Eight studies involving 1116 neonates were chosen in this review; however, only five studies were included for meta-analysis. Phototherapy duration was significantly lower in the interventional group with high heterogeneities. Subgroup analysis of the phototherapy duration based on the risk of bias resulted in a shorter duration (mean difference (MD) = –17.82; 95% CI = –20.17 to –15.47; p =  < 0.001) with low heterogeneity in the treatment group. Secondary outcome focusing on mean total serum bilirubin showed a lower mean total serum bilirubin in 48 h post-treatment (MD = –0.43; 95% CI = –0.64 to –0.22; p =  < 0.0001) with low heterogeneities in Asian countries.”

Conclusions
Ursodeoxycholic acid might be considered as a novel adjuvant therapy in neonatal indirect hyperbilirubinemia to shorten the phototherapy duration and lower the mean total serum bilirubin.
Can erythema multiforme be an immune sequela of IgM nephropathy? A case report
Authors: Messina Francesco , Fagotto Laura , Caroppo Francesca , Salmaso Roberto , Belloni Fortina Anna 
Published: October 2022

AbstractA 13-year-old Chinese girl attended to our Pediatric Dermatology Unit for the appearance of itchy targetoid lesions on the trunk, face and upper limbs. A skin biopsy showed histological findings typical of erythema multiforme minor. A month earlier she was admitted for the onset of a nephrotic syndrome and the renal biopsy showed an IgM nephropathy with a diffuse mesangial cell proliferation. There was no medical history of recent infections, fever, muscle or joint pain, drugs intake related to erythema multiforme and viral serology were negative.The role of antibodies in erythema multiforme could be more relevant than suspected and the severity of erythema multiforme was reported to be proportional to the antibody-mediated complement-dependent cytotoxicity, supporting the potential pathogenetic role for humoral immunity in this subtype of erythema multiforme.We reported the first association of erythema multiforme and IgM nephropathy in a pediatric patient providing an additional hint that an antibody-mediated process, rather than T-cell cytotoxicity, might represent the main pathogenetic mechanism in certain subtypes of erythema multiforme.
iDNA-ABF: multi-scale deep biological language learning model for the interpretable prediction of DNA methylations
Authors: Jin Junru , Yu Yingying , Wang Ruheng , Zeng Xin , Pang Chao , Jiang Yi , Li Zhongshen , Dai Yutong , Su Ran , Zou Quan , Nakai Kenta , Wei Leyi 
Published: October 2022

AbstractIn this study, we propose iDNA-ABF, a multi-scale deep biological language learning model that enables the interpretable prediction of DNA methylations based on genomic sequences only. Benchmarking comparisons show that our iDNA-ABF outperforms state-of-the-art methods for different methylation predictions. Importantly, we show the power of deep language learning in capturing both sequential and functional semantics information from background genomes. Moreover, by integrating the interpretable analysis mechanism, we well explain what the model learns, helping us build the mapping from the discovery of important sequential determinants to the in-depth analysis of their biological functions.
Indicators for local policies of cultural welfare: content, dimensions, and quality criteria
Authors: Cicerchia Annalisa 
Published: October 2022

AbstractWellbeing measures are gaining consensus as complementary to the traditional GDP approach when it comes to assessing the development of countries and communities. Cultural Welfare is a new, integrated approach aimed at promoting the wellbeing and health of individuals and communities through practices rooted in the arts and in cultural heritage. Recently, experimental tools have been devised and applied, with reference to either specific target groups of beneficiaries or individual cultural/artistic disciplines, the purpose of which is to measure and assess the contribution to individual and societal wellbeing, as well as the health of cultural and artistic participation and practice in general. Policies aimed at promoting cultural welfare need a robust body of evidence, and indicators may contribute to supporting them. While measures for the assessment of the culture-and-wellbeing relationship have been proposed at the national level or at the level of individual organizations or programmes, the level of local policies appears still largely unexplored. The article discusses a few theoretical and methodological issues and proposes a set of quality criteria for designing cultural welfare indicators on a local scale.
Building bridges: a review and synthesis of research on teaching knowledge for undergraduate instruction in science, engineering, and mathematics
Authors: Andrews Tessa C. , Speer Natasha M. , Shultz Ginger V. 
Published: October 2022

AbstractHere, we systematically review research on teaching knowledge in the context of undergraduate STEM education, with particular attention to what this research reveals about knowledge that is important for evidence-based teaching. Evidence-based teaching can improve student outcomes in undergraduate STEM education. However, the enactment of promising evidence-based teaching strategies depends greatly on the instructor and potentially on the teaching knowledge they are able to deploy. The review includes an overview of prevalent teaching knowledge theory, including pedagogical content knowledge, mathematical knowledge for teaching, and pedagogical knowledge. We compare and contrast teaching knowledge theory and terminology across STEM disciplines in order to build bridges for researchers across disciplines. Our search for peer-reviewed investigations of teaching knowledge in undergraduate science, engineering and mathematics yielded 45 papers. We examined the theoretical frameworks used in each study and analyzed study approaches, comparing across disciplines. Importantly, we also synthesized findings from research conducted in the context of evidence-based teaching. Overall, teaching knowledge research is sparse and siloed by discipline, and we call for collaborative work and better bridge-building across STEM disciplines. Though disciplinary divergences are common in discipline-based education research, the effect is magnified in this research area because the theoretical frameworks are themselves siloed by discipline. Investigations of declarative knowledge were common, and we call for increased attention to knowledge used in the practice of teaching. Finally, there are not many studies examining teaching knowledge in the context of evidence-based teaching, but the existing work suggests that components of pedagogical content knowledge, pedagogical knowledge, and content knowledge influence the implementation of evidence-based teaching. We describe implications for future teaching knowledge research. We also call on those who develop and test evidence-based strategies and curriculum to consider, from the beginning, the teaching knowledge needed for effective implementation.
Spatial dissimilarity of zooplankton and hydrodynamic conditions in a Patagonian channel used intensely by aquaculture: the influence of a geomorphological constriction
Authors: Hernández-Miranda Eduardo , Betancourt Ignacio , Sobarzo Marcus , Vergara Odette , Iturra Claudio , Quiñones Renato A. 
Published: October 2022

Abstract
Background
Marine aquaculture is a very important economic and food production activity in Patagonian channels. The biophysical mechanisms through which farms interact with surrounding areas is poorly understood. A better understanding of the relationship between zooplankton distribution, hydrodynamics and aquaculture farms in Patagonian channels can contribute to the environmental sustainability of this activity.

Methods
The study was conducted in winter in the Caucahué Channel (Chiloé Island, southern Chile), which is composed of two asymmetric northern and southern sections separated by a geomorphological constriction (a narrows) and hosts 55 aquaculture farms. Intensive zooplankton and water column sampling (time scale: 12 h) was carried out, together with current measurements as a background of the channel hydrodynamics (time scale: 30 days).

Results
Spatial dissimilarities in composition and abundances of zooplankton communities and in water column variables were identified between the two sections of the channel in this short-term time scale. In the southern section we found higher abundances of holo- and meroplankton and higher species richness. No differences in zooplankton community were found between sampling sites near and far from aquaculture farms. Southward asymmetrical residual flow and semidiurnal tidal excursion were verified in the central part of the channel during two tidal fortnightly time periods.

Conclusions
(i) Clear dissimilarity in zooplankton composition were found between the two sections of Caucahué Channel in the time scale studied; and (ii) Quemchi geomorphological constriction and the asymmetrical southward residual flow could act as a physical barrier favoring the spatial dissimilarities found in biotic and abiotic variables between the two sections of the channel.
The association between dietary glycemic index and cardio-metabolic risk factors in obese individuals
Authors: Siri Goli , Mahmoudinezhad Mahsa , Alesaeidi Samira , Farhangi Mahdieh Abbasalizad , Ardekani Abnoos Mokhtari 
Published: October 2022

Abstract
Background:
The dietary glycemic index (GI) has been introduced as a novel index to elucidate the potential of foods to increase postprandial glucose. According to the limited available data about the association of GI with cardio-metabolic risk factors such as lipid profile, blood glucose markers, and blood pressure in developing countries, the current study was conducted to investigate this association in apparently obese individuals.

Method and material:
Three hundred forty-seven obese adults were recruited in the present cross-sectional study. A validated 147-food item semi-quantitative food frequency questionnaire (FFQ) was used to evaluate the usual dietary intake of study participants. Dietary GI was calculated using the international GI database. Fatty acid desaturase (FADs)2 gene variants were determined according to polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). ANOVA was used to compare study variables across different tertile of GI.

Results:
We found significant differences in terms of anthropometric parameters [weight (P = 0.038), waist circumference (WC) (P = 0.023), weight to hip ratio (WHR) (P = 0.007), and fat-free mass (FFM) (P < 0.001)] between different tertiles of GI. Similarly, energy and macronutrient intakes had a significant difference across dietary GI, and subjects with a higher dietary intake of energy and macronutrients (carbohydrate, protein, and total fat) were assigned to the third tertile of dietary GI (P < 0.001). While there was no significant difference in terms of cardio-metabolic risk factors in different dietary GI tertiles. Moreover, the total GI score was non-significantly higher in the TT genotype of FADS2 gene polymorphism compared with other genotypes. While no significant difference was observed between FADS2 genotype frequencies in different GI tertiles.

Conclusion:
Calculated dietary GI was associated with several cardio-metabolic risk factors in obese individuals. However, further prospective studies and clinical trials are needed to confirm our findings.