bluuebunny/crossref_metadata_2025_split huggingface dataset:
ExplaiNN: interpretable and transparent neural networks for genomics
Authors: Novakovsky Gherman , Fornes Oriol , Saraswat Manu , Mostafavi Sara , Wasserman Wyeth W. 
Published: June 2023

AbstractDeep learning models such as convolutional neural networks (CNNs) excel in genomic tasks but lack interpretability. We introduce ExplaiNN, which combines the expressiveness of CNNs with the interpretability of linear models. ExplaiNN can predict TF binding, chromatin accessibility, and de novo motifs, achieving performance comparable to state-of-the-art methods. Its predictions are transparent, providing global (cell state level) as well as local (individual sequence level) biological insights into the data. ExplaiNN can serve as a plug-and-play platform for pretrained models and annotated position weight matrices. ExplaiNN aims to accelerate the adoption of deep learning in genomic sequence analysis by domain experts.
CrebH protects against liver injury associated with colonic inflammation via modulation of exosomal miRNA
Authors: Lee Sang-Hee , Moon Sung-Je , Woo Seung Hee , Ahn Gwangsook , Kim Won Kon , Lee Chul-Ho , Hwang Jung Hwan 
Published: June 2023

Abstract
Background
Hepatic liver disease, including primary sclerosing cholangitis (PSC), is a serious extraintestinal manifestations of colonic inflammation. Cyclic adenosine monophosphate (cAMP)-responsive element-binding protein H (CrebH) is a transcription factor expressed mostly in the liver and small intestine. However, CrebH’s roles in the gut–liver axis remain unknown.

Methods
Inflammatory bowel disease (IBD) and PSC disease models were established in wild-type and CrebH−/− mice treated with dextran sulfate sodium, dinitrobenzene sulfonic acid, and diethoxycarbonyl dihydrocollidine diet, respectively. RNA sequencing were conducted to investigate differential gene expression. Exosomes were isolated from plasma and culture media. miRNA expression profiling was performed using the NanoString nCounter Mouse miRNA Panel. Effects of miR-29a-3p on adhesion molecule expression were investigated in bEnd.3 brain endothelial cells.

Results
CrebH−/− mice exhibited accelerated liver injury without substantial differences in the gut after administration of dextran sulfate sodium (DSS), and had similar features to PSC, including enlarged bile ducts, enhanced inflammation, and aberrant MAdCAM-1 expression. Furthermore, RNA-sequencing analysis showed that differentially expressed genes in the liver of CrebH−/− mice after DSS overlapped significantly with genes changed in PSC-liver. Analysis of plasma exosome miRNA isolated from WT and CrebH−/− mice indicates that CrebH can contribute to the exosomal miRNA profile. We also identified miR-29a-3p as an effective mediator for MAdCAM-1 expression. Administration of plasma exosome from CrebH−/− mice led to prominent inflammatory signals in the liver of WT mice with inflammatory bowel disease (IBD).

Conclusions
CrebH deficiency led to increased susceptibility to IBD-induced liver diseases via enhanced expression of adhesion molecules and concomitant infiltration of T lymphocytes. Exosomes can contribute to the progression of IBD-induced liver injury in CrebH−/− mice. These study provide novel insights into the role of CrebH in IBD-induced liver injury.
Gender and racial differences in first and senior authorship of high-impact critical care randomized controlled trial studies from 2000 to 2022
Authors: Chander Subhash , Luhana Sindhu , Sadarat Fnu , Leys Lorenzo , Parkash Om , Kumari Roopa 
Published: June 2023

Abstract
Background
Females and ethnic minorities are underrepresented in the first and senior authorships positions of academic publications. This stems from various structural and systemic inequalities and discrimination in the journal peer-review process, as well as educational, institutional, and organizational cultures.

Methods
A retrospective bibliometric study design was used to investigate the representation of gender and racial/ethnic groups in the authorship of critical care randomized controlled trials in 12 high-impact journals from 2000 to 2022.

Results
In the 1398 randomized controlled trials included in this study, only 24.61% of the first authors and 16.6% of the senior authors were female. Although female authorship increased during the study period, authorship was significantly higher for males throughout (Chi-square for trend, p < 0.0001). The educational attainment [χ2(4) = 99.2, p < 0.0001] and the country of the author's affiliated institution [χ2(42) = 70.3, p = 0.0029] were significantly associated with gender. Male authorship was significantly more prevalent in 10 out of 12 journals analyzed in this study [χ2(11) = 110.1, p < 0.0001]. The most common race/ethnic group in our study population was White (85.1% women, 85.4% males), followed by Asians (14.3% females, 14.3% males). Although there was a significant increase in the number of non-White authors between 2000 and 2022 [χ2(22) = 77.3, p < 0.0001], the trend was driven by an increase in non-White male and not non-White female authors. Race/ethnicity was significantly associated with the country of the author’s affiliated institution [χ2(41) = 1107, p < 0.0001] but not with gender or educational attainment.

Conclusions
Persistent gender and racial disparities in high-impact medical and critical care journals underscore the need to revise policies and strategies to encourage greater diversity in critical care research.
A kind of bivariate Bernoulli-type multiquadric quasi-interpolation operator with higher approximation order
Authors: Wu Ruifeng 
Published: June 2023

AbstractIn this paper, a kind of bivariate Bernoulli-type multiquadric quasi-interpolation operator is studied by combining the known multiquadric quasi-interpolation operator with the generalized Taylor polynomial as the expansion in the bivariate Bernoulli polynomials. Some error bounds and convergence rates of the combined operators are studied. A selection of numerical examples is presented to compare the performances of the obtained scheme. Furthermore, our method can be applied to time-dependent differential equations. Its advantage is that the algorithm is very simple and easy to implement.
Sand dune movement and flooding risk analysis for the pyramids of Meroe, Al Bagrawiya archaeological site, Sudan
Authors: Fahmy Abdelrhman , Domínguez-Bella Salvador , Martínez-López Javier , Molina-Piernas Eduardo 
Published: June 2023

Abstract
The pyramids of Meroe are a significant archaeological place at the Al Bagrawiya archaeological site (Sudan) with hundreds of pyramids dating back to the kingdom of Kush (1070 BC–550 AD). In this area, winds, heavy rains, and flooding events are the main geohazards that need assessments and solutions because pyramids are subjected to an accumulation of sand dunes around them and the risk of flooding, affecting their durability. This research aims to assess the impacts of sand dunes on the stability of pyramid structures in addition to assessing the risk of flooding using satellite image observations, and damage and decay assessments of pyramid building materials were carried out through digital mapping. The results from satellite image analysis and monitoring showed that sand dunes along with heavy rains and flooding are the main decay factors, causing the collapse, disintegration, crumbling, alveolarization, loss of materials, and cracking of the sandstone ashlars, detecting an increase in deterioration, even considering only the last three decades.
Dog breeds and conformations predisposed to osteosarcoma in the UK: a VetCompass study
Authors: O’Neill Dan G. , Edmunds Grace L. , Urquhart-Gilmore Jade , Church David B. , Rutherford Lynda , Smalley Matthew J. , Brodbelt Dave C. 
Published: June 2023

Abstract
Background
Osteosarcoma is a malignant bone neoplasia that has high welfare consequences for affected dogs. Awareness of breed and canine conformational risk factors for osteosarcoma can assist with earlier diagnosis and improved clinical management. Study of osteosarcoma in dogs also offers translational value for humans. Anonymised clinical data within VetCompass on dogs under primary veterinary care in the UK were searched for osteosarcoma cases. Descriptive statistics reported overall and breed-specific prevalence. Risk factor analysis used multivariable logistic regression modelling.

Results
From 905,552 study dogs, 331 osteosarcoma cases were confirmed yielding a one-year period prevalence of 0.037% (95% CI: 0.033–0.041). Breeds with the highest annual prevalence were the Scottish Deerhound (3.28%, 95% CI 0.90–8.18), Leonberger (1.48%, 95% CI 0.41- 3.75), Great Dane (0.87%, 95% CI 0.43- 1.55) and Rottweiler (0.84%, 95% CI 0.64–1.07). The median age at diagnosis was 9.64 years (IQR: 7.97–11.41).
Following multivariable modelling, 11 breeds showed increased odds of osteosarcoma compared with crossbred dogs. Breeds with the highest odds included Scottish Deerhound (OR 118.40, 95% CI 41.12–340.95), Leonberger (OR 55.79, 95% CI 19.68–158.15), Great Dane (OR 34.24, 95% CI 17.81–65.83) and Rottweiler (OR 26.67, 95% CI 18.57–38.29). Compared with breeds with mesocephalic skull conformation, breeds with dolichocephalic skull conformation (OR 2.72, 95% CI 2.06–3.58) had increased odds while breeds with brachycephalic skull conformation showed reduced odds (OR 0.50, 95% CI 0.32–0.80). Chondrodystrophic breeds had 0.10 times the odds (95% CI 0.06–0.15) compared with non-chondrodystrophic breeds. Increasing adult bodyweight was associated with increasing odds of osteosarcoma.

Conclusions
The current study cements the concept that breed, bodyweight and longer leg or longer skull length are all strong risk factors for osteosarcoma in dogs. With this awareness, veterinarians can update their clinical suspicion and judgement, breeders can select towards lower-risk animals, and researchers can robustly define more useful study populations for fundamental and translational bioscience.
The microbial composition of larval airways from Drosophila melanogaster differ between specimens from laboratory and natural habitats
Authors: Angstmann Hanna , Pfeiffer Stefan , Kublik Susanne , Ehrhardt Birte , Uliczka Karin , Rabe Klaus F. , Roeder Thomas , Wagner Christina , Schloter Michael , Krauss-Etschmann Susanne 
Published: June 2023

Abstract
Background
The fruit fly Drosophila melanogaster lives in natural habitats and has also long been used as a model organism in biological research. In this study, we used a molecular barcoding approach to analyse the airways microbiome of larvae of D. melanogaster, which were obtained from eggs of flies of the laboratory strain w1118 and from immune deficient flies (NF-kB-K), and from wild-caught flies. To assess intergenerational transmission of microbes, all eggs were incubated under the same semi-sterile conditions.

Results
The airway microbiome of larvae from both lab-strains was dominated by the two families Acetobacteraceae and Lactobacillaceae, while larvae from wild-caught flies were dominated by Lactobacillaceae, Anaplasmataceae and Leuconostocaceae. Barcodes linked to Anaplasmataceae could be further assigned to Wolbachia sp., which is a widespread intracellular pathogen in arthropods. For Leuconostoceae, the most abundant reads were assigned to Weissella sp. Both Wolbachia and Weissella affect the development of the insects. Finally, a relative high abundance of Serratia sp. was found in larvae from immune deficient relish−/− compared to w1118 and wild-caught fly airways.

Conclusions
Our results show for the first time that larvae from D. melanogaster harbor an airway microbiome, which is of low complexity and strongly influenced by the environmental conditions and to a lesser extent by the immune status. Furthermore, our data indicate an intergenerational transmission of the microbiome as shaped by the environment.
Down the brain drain: a rapid review exploring physician emigration from West Africa
Authors: Ebeye Tega , Lee HaEun 
Published: June 2023

Abstract
Background
The emigration of physicians from low- and middle-income countries (LMICs) to high-income countries (HICs), colloquially referred to as the “brain drain”, has been a topic of discussion in global health spheres for years. With the call to decolonize global health in mind, and considering that West Africa, as a region, is a main source of physicians emigrating to HICs, this rapid review aims to synthesize the reasons for, and implications of, the brain drain, as well as recommendations to mitigate physician emigration from West African countries to HICs.

Methods
A literature search was conducted on PubMed, EMBASE and The Cochrane Library. Main inclusion criteria were the inclusion of West African trained physicians' perspectives, the reasons and implications of physician emigration, and recommendations for management. Data on the study design, reasons for the brain drain, implications of brain drain, and proposed solutions to manage physician emigration were extracted using a structured template. The Hawker Tool was used as a risk of bias assessment tool to evaluate the included articles.

Results
A total of 17 articles were included in the final review. Reasons for physician emigration include poor working conditions and remuneration, limited career opportunities, low standards of living, and sociopolitical unrest. Implications of physician emigration include exacerbation of low physician to population ratios, and weakened healthcare systems. Recommendations include development of international policies that limit HICs’ recruitment from LMICs, avenues for HICs to compensate LMICs, collaborations investing in mutual medical education, and incorporation of virtual or short-term consultation services for physicians working in HICs to provide care for patients in LMICs.

Conclusions
The medical brain drain is a global health equity issue requiring the collaboration of LMICs and HICs in implementing possible solutions. Future studies should examine policies and innovative methods to involve both HICs and LMICs to manage the brain drain.
Arabic translation, cultural adaptation, and validation of the Bristol Impact of Hypermobility questionnaire
Authors: Alsiri Najla , Alhadhoud Meshal , Alhumaid Asma , Palmer Shea 
Published: June 2023

Abstract
Background
The Bristol Impact of Hypermobility questionnaire (BIoH) is the first condition-specific patient reported outcome measure for people with hypermobility-related conditions. The BIoH original version is in English, which limits its use for patients who speak other languages. The study aimed to translate and culturally adapt the BIoH into Arabic and determine its concurrent validity, reliability, internal consistency and smallest detectable change.

Methods
Forward-backward translation and cross-sectional designs were used. The Ethics Committee of Kuwait Ministry of Health approved the study. Spearman correlation coefficient, intraclass correlation coefficient (ICC), and Cronbach’s α were used for statistical analysis. Patients with hypermobility spectrum disorders (HSD) were included, diagnosed using the 2017 classification framework.

Results
55 HSD patients were included, aged 26.0 (18.0) years old; median (IQR), and 85.5% were women. The BIoH showed very good concurrent validity when correlated with the SF-12 total and physical component scores; r = -0.743 and − 0.740, respectively (p < 0.05). Good correlation was identified between the BIoH and the SF-12 mental component score; r = -0.496 (p < 0.05). The BIoH demonstrated excellent test-retest reliability; ICC = 0.934 (0.749–0.983 95% CI) (p < 0.05), and high internal consistency (Cronbach’s α = 0.933). The smallest detectable change was 30.90 points, representing 19.8% of the mean baseline score.

Conclusions
The study successfully translated the BIoH into Arabic and demonstrated high psychometric properties. The translated score can help Arabic patients with HSD in their clinical evaluation process. Future research needs to determine the responsiveness of the Arabic version and translate the BIoH to other languages.
Adaptation and validation of the Hungarian version of Thyroid-Related Patient-Reported Outcome-39 (ThyPro-39) questionnaire: testing factor structure, known-group validity with the comparison of quality of life in Hashimoto’s thyroiditis and Graves’ disease
Authors: Rigó Adrien , Malkov Katalin , Szabó Alexandra , Bognár Virág Katalin , Urbán Róbert 
Published: June 2023

Abstract
Background
Living with autoimmune thyroid disease is a longstanding challenge and can seriously affect the quality of life. We aimed to adapt and validate the Hungarian version of the Thyroid-Related Patient-Reported Outcome-39 (ThyPro-39) questionnaire, test its factor structure, and compare two frequent autoimmune thyroid diseases, Hashimoto’s thyroiditis, and Graves’ disease. We tested the factor structure of ThyPro-39 with a series of confirmatory factor analyses (CFAs). To examine the validity of ThyPro-39 and to compare the quality of life of the two groups — Hashimoto’s thyroiditis (N = 240), Graves’ disease (N = 51) — CFA with covariates were used.

Results
Our results supported a bifactor model with psychosocial and somatic symptoms as general factors, and 12 symptom-specific factors. Based on the analysis of omega hierarchical indices ranging between 0.22 and 0.66, the specific scales also carry information besides the composite scores and should be used when a more detailed analysis is required. In the multivariate analysis, perceived stress was significantly associated with the general psychosocial factor (β = 0.80), symptom factors (β = 0.34), anxiety (β = 0.43), depressivity (β = 0.37), and emotional susceptibility (β = 0.38) specific factors. Graves’ patients reported more eye symptoms (d = 0.45) and cosmetic complaints (d = 0.40), while Hashimoto patients had more cognitive problems (d = 0.36) and more severe hypothyroid symptoms (d = 0.35). These group differences confirm the known-group validity of the questionnaire.

Conclusions
The validity of the Hungarian version of ThyPRO-39 is supported. We recommend using two composite scores of psychosocial and somatic symptoms and the specific symptoms scores to measure the quality of life in clinical practice and research.
Reliability of mathematical regression models for age estimation in the mixed dentition stage for Egyptian children
Authors: Salma Rehab Samir , AbdElfatah Omnia M. 
Published: June 2023

Abstract
Background
The purpose of this study was to evaluate the accuracy of established mathematical regression models for estimating the age of Egyptian children, develop new models that would better match this population and to evaluate the validity and reliability of these new models.

Results
One thousand one hundred fifteen children ranging in age between 6–14 years participated in the study. Group I consisted of 1000 children; 513 (51.3%) children were of the age group 6–< 9 years and 487 (48.7%) children were 9–14 years. Male children were 484 (48.4%) while female children were 516 (51.6%). Group II consisted of 115 children; 84 (73%) children were of the age group 6–< 9 years and 31 (27%) children were 9–14 years. Male children were 58 (50.4%) while Female children were 57 (49.6%). Foti regression models showed poor agreement of Intraclass Correlation Coefficient (ICC) with chronological age of children in the mixed dentition stage. The new regression models for estimating dental age showed ICC of more than 0.7 with chronological age suggesting better accuracy in age estimation than Foti models.

Conclusions
The newly formulated regression models are reliable for estimating the age of Egyptian children during the mixed dentition stage. A good agreement was found between the estimated age obtained from the first two models and the chronological age. However, the third model had the least agreement, suggesting that age estimation may be more accurate using only the first two models.
Remote terahertz spectroscopy from extended two-color plasma filaments: The ALTESSE 2 project
Authors: Talbi A. , Zhou B. , Jepsen P. U. , Skupin S. , Courjaud A. , Bergé L. 
Published: June 2023

Abstract
Coherent time-domain spectroscopy (TDS) using terahertz radiation is valuable for fundamental science, security, and medical applications. This study investigates the performance of air-biased coherent detection terahertz spectroscopy (ABCD-THz) when an extended plasma filament is created in the air over long distances. We report on the latest results obtained within the follow-up of the ALTESSE project (Bergé L. et al., EPL, 126 (2019) 24001) whose objective is to measure a set of spectral signatures characterizing suspicious materials over meter-long distances. As one of the most critical steps towards routinely applying this technique, we verified the feasibility of a remote THz time-domain spectroscopy by loosely focusing two-color ultrashort laser pulses at more than 3 meters from the laser source. The absorption spectra of amino acids and explosives analyzed in such a filamentation geometry are compared with those obtained using a standard ABCD scheme where the plasma is generated at much shorter distances of

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Acoustic bound states in continuum protected by crystalline symmetry
Authors: Pan Jincheng , Lu Jiuyang , Deng Weiyin , Huang Xueqin , Liu Zhengyou 
Published: June 2023

Abstract
Bound states in continuum (BICs) are highly localized resonant states embedded in the continuum background. Recently, crystalline symmetries have been exploited as a new mechanism in generating BICs. Here we propose crystalline-symmetry–protected BICs in a two-dimensional bilayer phononic crystal. Our system possesses a D
4 point group symmetry and provides isolated quadratic degeneracies in momentum space to support defect localized BICs. Such BICs are forbidden to leak to the background due to the symmetry mismatch between the defect and the bulk modes. We also provide a rigorous tight-binding model to demonstrate the crystalline-symmetry–protected BICs. Our findings enrich the formation approach of BICs in phononic crystals and may inspire possible applications related to wave confinement, such as energy harvesting and particle manipulation.
Working Paper 46: Incrementando el impacto de los Pactos de Integridad en la contratación pública
Authors: Arribas Reyes Esteban 
Published: June 2023

Este documento de trabajo analiza cuatro Pactos de Integridad en España implementados entre abril de 2017 y enero de 2019. Basándose en el análisis, ofrece recomendaciones específicas para medir y mejorar el impacto de los Pactos de Integridad, especialmente para lograr cambios a largo plazo.
***English***
Enhancing the impact of Integrity Pacts in public procurement: an analysis from Spain‘s experience
This Working Paper analyses four Integrity Pacts in Spain implemented between April 2017 and January 2019. Based on the analysis, it offers specific recommendations to measure and enhance the impact of Integrity Pacts, especially in achieving long-term change.