bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oral Health in Rheumatoid Arthritis: Listening to Patients
Authors: Protudjer J.L.P. , Billedeau C. , Hurst K. , Schroth R. , Stavropoulou C. , Kelekis-Cholakis A. , Hitchon C.A. 
Published: May 2021

Introduction: Rates of periodontal disease and tooth loss are increased in individuals with rheumatoid arthritis (RA). Understanding factors that contribute to the increased burden of periodontal disease in RA is critical to improving oral health and arthritis outcomes. Objectives: To determine the perceptions held by people with RA relating to their oral health, to identify patient-centered priorities for oral health research, and to inform optimal strategies for delivering oral health knowledge. Methods: Semistructured interviews were conducted with patients with RA. Recorded interview transcripts were iteratively reviewed to reveal surface and latent meaning and to code for themes. Constructs were considered saturated when no new themes were identified in subsequent interviews. We report themes with representative quotes. Results: Interviews were conducted with 11 individuals with RA (10 women [91%]; mean age, 68 y), all of whom were taking RA medication. Interviews averaged 19 min (range, 8 to 31 min) and were mostly conducted face-to-face. Three overall themes were identified: 1) knowledge about arthritis and oral health links; 2) oral health care in RA is complicated, both in personal hygiene practices and in professional oral care; and 3) poor oral health is a source of shame. Participants preferred to receive oral health education from their rheumatologists or dentists. Conclusions: People with RA have unique oral health perceptions and experience significant challenges with oral health care due to their arthritis. Adapting oral hygiene recommendations and professional oral care delivery to the needs of those with arthritis are patient priorities and are required to improve satisfaction regarding their oral health. Knowledge Translation Statement: Patients living with long-standing rheumatoid arthritis described poor oral health–related quality of life and multiple challenges with maintaining optimal oral health. Study findings indicate a need for educational materials addressing oral health maintenance for patients with rheumatic diseases and their providers.
Molecular and morphological clocks for estimating evolutionary divergence times
Authors: Barba-Montoya Jose , Tao Qiqing , Kumar Sudhir 
Published: May 2021

Abstract
Background
Matrices of morphological characters are frequently used for dating species divergence times in systematics. In some studies, morphological and molecular character data from living taxa are combined, whereas others use morphological characters from extinct taxa as well. We investigated whether morphological data produce time estimates that are concordant with molecular data. If true, it will justify the use of morphological characters alongside molecular data in divergence time inference.

Results
We systematically analyzed three empirical datasets from different species groups to test the concordance of species divergence dates inferred using molecular and discrete morphological data from extant taxa as test cases. We found a high correlation between their divergence time estimates, despite a poor linear relationship between branch lengths for morphological and molecular data mapped onto the same phylogeny. This was because node-to-tip distances showed a much higher correlation than branch lengths due to an averaging effect over multiple branches. We found that nodes with a large number of taxa often benefit from such averaging. However, considerable discordance between time estimates from molecules and morphology may still occur as some intermediate nodes may show large time differences between these two types of data.

Conclusions
Our findings suggest that node- and tip-calibration approaches may be better suited for nodes with many taxa. Nevertheless, we highlight the importance of evaluating the concordance of intrinsic time structure in morphological and molecular data before any dating analysis using combined datasets.
A short-term evaluation of a prototype disposable Oscillating Positive Expiratory Pressure (OPEP) device in a cohort of children with cystic fibrosis
Authors: O’Sullivan Kevin J. , Power Valerie , Linnane Barry , McGrath Deirdre , Mulligan Magdalena , White Rebecca , O’Sullivan Leonard W. , Dunne Colum P. 
Published: May 2021

Abstract
Background
Oscillating Positive Expiratory Pressure (OPEP) devices are important adjuncts to airway clearance therapy in patients with cystic fibrosis (CF). Current devices are typically reusable and require daily, or often more frequent, cleaning to prevent risk of infection by acting as reservoirs of potentially pathogenic organisms. In response, a daily disposable OPEP device, the UL-OPEP, was developed to mitigate the risk of contamination and eliminate the burdensome need for cleaning devices.

Methods
A convenience sample of 36 participants, all current OPEP device users, was recruited from a paediatric CF service. For one month, participants replaced their current OPEP device with a novel daily disposable device. Assessment included pre- and post-intervention lung function by spirometry, as well as Lung Clearance Index. Quality of life was assessed using the Cystic Fibrosis Questionnaire – Revised, while user experience was evaluated with a post-study survey.

Results
31 participants completed the study: 18 males; median age 10 years, range 4–16 years. Lung function (mean difference ± SD, %FEV1 = 1.69 ± 11.93; %FVC = 0.58 ± 10.04; FEV1: FVC = 0.01 ± 0.09), LCI (mean difference ± SD, 0.08 ± 1.13), six-minute walk test, and CFQ-R were unchanged post-intervention. Participant-reported experiences of the device were predominantly positive.

Conclusions
The disposable OPEP device maintained patients’ lung function during short term use (≤ 1 month), and was the subject of positive feedback regarding functionality while reducing the risk of airway contamination associated with ineffective cleaning.

Registration
The study was approved as a Clinical Investigation by the Irish Health Products Regulatory Authority (CRN-2209025-CI0085).
Echinacea purpurea (L.) Moench treatment of monocytes promotes tonic interferon signaling, increased innate immunity gene expression and DNA repeat hypermethylated silencing of endogenous retroviral sequences
Authors: Declerck Ken , Novo Claudina Perez , Grielens Lisa , Van Camp Guy , Suter Andreas , Vanden Berghe Wim 
Published: May 2021

Abstract
Background
Herbal remedies of Echinacea purpurea tinctures are widely used today to reduce common cold respiratory tract infections.

Methods
Transcriptome, epigenome and kinome profiling allowed a systems biology level characterisation of genomewide immunomodulatory effects of a standardized Echinacea purpurea (L.) Moench extract in THP1 monocytes.

Results
Gene expression and DNA methylation analysis revealed that Echinaforce® treatment triggers antiviral innate immunity pathways, involving tonic IFN signaling, activation of pattern recognition receptors, chemotaxis and immunometabolism. Furthermore, phosphopeptide based kinome activity profiling and pharmacological inhibitor experiments with filgotinib confirm a key role for Janus Kinase (JAK)-1 dependent gene expression changes in innate immune signaling. Finally, Echinaforce® treatment induces DNA hypermethylation at intergenic CpG, long/short interspersed nuclear DNA repeat elements (LINE, SINE) or long termininal DNA repeats (LTR). This changes transcription of flanking endogenous retroviral sequences (HERVs), involved in an evolutionary conserved (epi) genomic protective response against viral infections.

Conclusions
Altogether, our results suggest that Echinaforce® phytochemicals strengthen antiviral innate immunity through tonic IFN regulation of pattern recognition and chemokine gene expression and DNA repeat hypermethylated silencing of HERVs in monocytes. These results suggest that immunomodulation by Echinaforce® treatment holds promise to reduce symptoms and duration of infection episodes of common cold corona viruses (CoV), Severe Acute Respiratory Syndrome (SARS)-CoV, and new occurring strains such as SARS-CoV-2, with strongly impaired interferon (IFN) response and weak innate antiviral defense.
Notch-ing up knowledge on molecular mechanisms of skin fibrosis: focus on the multifaceted Notch signalling pathway
Authors: Condorelli Angelo Giuseppe , El Hachem May , Zambruno Giovanna , Nystrom Alexander , Candi Eleonora , Castiglia Daniele 
Published: May 2021

AbstractFibrosis can be defined as an excessive and deregulated deposition of extracellular matrix proteins, causing loss of physiological architecture and dysfunction of different tissues and organs. In the skin, fibrosis represents the hallmark of several acquired (e.g. systemic sclerosis and hypertrophic scars) and inherited (i.e. dystrophic epidermolysis bullosa) diseases. A complex series of interactions among a variety of cellular types and a wide range of molecular players drive the fibrogenic process, often in a context-dependent manner. However, the pathogenetic mechanisms leading to skin fibrosis are not completely elucidated. In this scenario, an increasing body of evidence has recently disclosed the involvement of Notch signalling cascade in fibrosis of the skin and other organs. Despite its apparent simplicity, Notch represents one of the most multifaceted, strictly regulated and intricate pathways with still unknown features both in health and disease conditions. Starting from the most recent advances in Notch activation and regulation, this review focuses on the pro-fibrotic function of Notch pathway in fibroproliferative skin disorders describing molecular networks, interplay with other pro-fibrotic molecules and pathways, including the transforming growth factor-β1, and therapeutic strategies under development.
COVID19-CT-dataset: an open-access chest CT image repository of 1000+ patients with confirmed COVID-19 diagnosis
Authors: Shakouri Shokouh , Bakhshali Mohammad Amin , Layegh Parvaneh , Kiani Behzad , Masoumi Farid , Ataei Nakhaei Saeedeh , Mostafavi Sayyed Mostafa 
Published: May 2021

Abstract
Objectives
The ongoing Coronavirus disease 2019 (COVID-19) pandemic has drastically impacted the global health and economy. Computed tomography (CT) is the prime imaging modality for diagnosis of lung infections in COVID-19 patients. Data-driven and Artificial intelligence (AI)-powered solutions for automatic processing of CT images predominantly rely on large-scale, heterogeneous datasets. Owing to privacy and data availability issues, open-access and publicly available COVID-19 CT datasets are difficult to obtain, thus limiting the development of AI-enabled automatic diagnostic solutions. To tackle this problem, large CT image datasets encompassing diverse patterns of lung infections are in high demand.

Data description
In the present study, we provide an open-source repository containing 1000+ CT images of COVID-19 lung infections established by a team of board-certified radiologists. CT images were acquired from two main general university hospitals in Mashhad, Iran from March 2020 until January 2021. COVID-19 infections were ratified with matching tests including Reverse transcription polymerase chain reaction (RT-PCR) and accompanying clinical symptoms. All data are 16-bit grayscale images composed of 512 × 512 pixels and are stored in DICOM standard. Patient privacy is preserved by removing all patient-specific information from image headers. Subsequently, all images corresponding to each patient are compressed and stored in RAR format.
An analytical study of the Huexotzinco Codex using X-ray fluorescence, fiber optic reflectance spectroscopy, and portable Fourier-transform infrared spectroscopy
Authors: Villafana Tana Elizabeth , Haude Mary Elizabeth , Satorius Amanda 
Published: May 2021

Abstract
The Huexotzinco Codex is one of the earliest surviving manuscripts from the early colonial period of Mexico. The codex pertains to the legal case of conquistador Hernán Cortés and contains paintings and documents detailing the seizure of Cortés’ personal properties and over-taxation of his Huexotzincan allies by the colonial government in New Spain (present-day Mexico). Eight paintings within the manuscript were subjected to non-invasive analytical techniques revealing the pigment palette and production methodology. The findings of this study show a mixture of pre- and colonial codex production practices as well a unique Maya blue formulation and the identification of a silicate material used as a matrix for an organic yellow dye.
Arm activity measure (ArmA): psychometric evaluation of the Swedish version
Authors: Ramström Therese , Bunketorp-Käll Lina , Wangdell Johanna 
Published: May 2021

Abstract
Background
Patient Reported Outcomes Measure (PROM) are commonly used in research and essential to understand the patient experience when receiving treatment. Arm Activity Measure (ArmA) is a valid and reliable self-report questionnaire for assessing passive (section A) and active (section B) real-life arm function in patients with disabling spasticity. The original English version of ArmA has been psychometrically tested and translated into Thai.

Aims
Translate and cross-culturally adapt ArmA to Swedish language and context. Further, to evaluate the reliability, validity and sensitivity of the Swedish version of the questionnaire (ArmA-S) in patients with disabling upper limb spasticity caused by injuries to the central nervous system (CNS).

Materials and methods
ArmA was translated and cross-culturally adapted according to established guidelines. Validity and reliability were evaluated in 61 patients with disabling spasticity. Face and content validity was evaluated by expert opinions from clinicians and feedback from patients with upper limb spasticity. Internal consistency reliability was assessed with Cronbach’s alpha and test-retest reliability was assessed using the quadratic weighted kappa.

Results
ArmA-S was shown to be clinically feasible, with good face and content validity and no floor or ceiling effects. Internal consistency of ArmA-S was high and equivalent to ArmA; with Chronbach´s alpha coefficients values of 0.94 and 0.93 for section A and B, respectively. Test-retest reliability was good, with kappa values of 0.86 and 0.83 for section A and B, respectively. Some layout modifications of ArmA-S were made to further increase the user-friendliness, test-retest reliability, and responsiveness.

Conclusion
ArmA-S was shown to be a reliable and valid self-report questionnaire for use in clinical practice and research to assess improvements in passive and active upper limb function in patients with disabling spasticity.
Large-scale wildfire reduces population growth in a peripheral population of sage-grouse
Authors: Dudley Ian F. , Coates Peter S. , Prochazka Brian G. , O’Neil Shawn T. , Gardner Scott , Delehanty David J. 
Published: May 2021

Abstract
Background
Drastic increases in wildfire size and frequency threaten western North American sagebrush (Artemisia L. spp.) ecosystems. At relatively large spatial scales, wildfire facilitates type conversion of sagebrush-dominated plant communities to monocultures of invasive annual grasses (e.g., Bromus tectorum L.). Annual grasses provide fine fuels that promote fire spread, contributing to a positive grass–fire feedback cycle that affects most sagebrush ecosystems, with expected habitat loss for resident wildlife populations. Greater sage-grouse (Centrocercus urophasianus Bonaparte, 1827) are sagebrush obligate species that are indicators of sagebrush ecosystem function because they rely on different components of sagebrush ecosystems to meet seasonal life history needs. Because wildfire cannot be predicted, chronic impacts of wildfire on sage-grouse populations have been largely limited to correlative studies. Thus, evidence from well-designed experiments is needed to understand the specific mechanisms by which wildfire is detrimental to sage-grouse population dynamics.

Results
Following a significant wildfire event in the southwest periphery of sage-grouse range, we implemented a before-after-control-impact study with long-term paired (BACIP) datasets of male sage-grouse surveyed from traditional breeding grounds (leks) within and outside the wildfire boundary. We estimated sage-grouse population rate of change in apparent abundance ($$ \hat{\uplambda} $$

λ
̂

) at burned and unburned areas before and after wildfire and derived BACIP ratios, which provide controlled evidence of wildfire impact. We found that $$ \hat{\uplambda} $$

λ
̂

at leks within the wildfire boundary decreased approximately 16% relative to leks at control sites. Furthermore, we estimated a 98.5% probability that the observed change in $$ \hat{\uplambda} $$

λ
̂

could be attributed to the wildfire.

Conclusions
We demonstrated adverse wildfire impacts on sage-grouse population growth using an experimental BACIP design, which disentangled the effect of wildfire disturbance from natural population fluctuations. Our results underscore the importance of active and comprehensive management actions immediately following wildfire (i.e., seeding coupled with planting sagebrush), that might offset short-term impacts of wildfire by timing rapid recovery of sagebrush to meet short-term species’ habitat requirements. Burned leks likely have substantial immediate impacts that may extend beyond wildfire boundaries, especially if critical source habitats are removed. Such impacts could fragment habitat and disrupt connectivity, thereby affecting larger populations and possibly contributing to more widespread declines in sage-grouse populations.
A systematic review of the case findings, testing and management of COVID-19
Authors: Susanna Dewi , Pratiwi Dian , Purnama Sang Gede 
Published: May 2021

Background: Mass testing and adequate management are essential to terminate the spread of coronavirus disease 2019 (COVID-19). This testing is due to the possibility of unidentified cases, especially ones without COVID-19 related symptoms. This review aimed to examine the outcome of the existing studies on the ways of identifying COVID-19 cases, and determine the populations at risk, symptom and diagnostic test management of COVID-19. Methods: The articles reviewed were scientific publications on the PubMed, Science Direct, ProQuest, and Scopus databases. The keywords used to obtain the data were COVID-19, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and case detection, case management or diagnostic test. We applied the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) and Population, Intervention, Control and Outcomes (PICO) approaches. Results: A total of 21 articles from 13 countries met the inclusion criteria and were further analyzed qualitatively. However, 62% of the articles used a rapid antibody test for screening rather than a rapid antigen test. According to the rapid antigen test, 51.3% were positive, with men aged above 50 years recording the highest number of cases. Furthermore, 57.1% of patients were symptomatic, while diagnostic tests' sensitivity and specificity increased to 100% in 14 days after the onset. Conclusions: Real-time polymerase chain reaction (RT-PCR) is recommended by the World Health Organization for detection of COVID-19. Suppose it is unavailable, the rapid antigen test is used as an alternative rather than the rapid antibody test. Diagnosis is expected to be confirmed using the PCR and serological assay to achieve an early diagnosis of COVID-19, according to disease progression, gradual rapid tests can be used, such as rapid antigen in an earlier week and antibody tests confirmed by RT–PCR and serological assay in the second week of COVID-19.
Assessing fitness-for-purpose and comparing the suitability of COVID-19 multi-country models for local contexts and users
Authors: Clapham Hannah , Gad Mohamed , Gheorghe Adrian , Hutubessy Raymond , Megiddo Itamar , Painter Christopher , Ruiz Francis , Cheikh Nejma , Gorgens Marelize , Wilkinson Thomas , Brisson Marc , Gay Nigel , Labadin Jane , McVernon Jodie , Luz Paula M. , Ndifon Wilfred , Nichols Brooke E. , Prinja Shankar , Salomon Joshua , Tshangela Akhona 
Published: May 2021

Background: Mathematical models have been used throughout the COVID-19 pandemic to inform policymaking decisions. The COVID-19 Multi-Model Comparison Collaboration (CMCC) was established to provide country governments, particularly low- and middle-income countries (LMICs), and other model users with an overview of the aims, capabilities and limits of the main multi-country COVID-19 models to optimise their usefulness in the COVID-19 response. Methods: Seven models were identified that satisfied the inclusion criteria for the model comparison and had creators that were willing to participate in this analysis. A questionnaire, extraction tables and interview structure were developed to be used for each model, these tools had the aim of capturing the model characteristics deemed of greatest importance based on discussions with the Policy Group. The questionnaires were first completed by the CMCC Technical group using publicly available information, before further clarification and verification was obtained during interviews with the model developers. The fitness-for-purpose flow chart for assessing the appropriateness for use of different COVID-19 models was developed jointly by the CMCC Technical Group and Policy Group. Results: A flow chart of key questions to assess the fitness-for-purpose of commonly used COVID-19 epidemiological models was developed, with focus placed on their use in LMICs. Furthermore, each model was summarised with a description of the main characteristics, as well as the level of engagement and expertise required to use or adapt these models to LMIC settings. Conclusions: This work formalises a process for engagement with models, which is often done on an ad-hoc basis, with recommendations for both policymakers and model developers and should improve modelling use in policy decision making.