bluuebunny/crossref_metadata_2025_split huggingface dataset:
CardioGraph: a platform to study variations associated with familiar cardiopathies
Authors: García S. Alberto , Costa Mireia , Perez Ana , Pastor Oscar 
Published: October 2024

Abstract
Background
Familiar cardiopathies are genetic disorders that affect the heart. Cardiologists face a significant problem when treating patients suffering from these disorders: most DNA variations are novel (i.e., they have not been classified before). To facilitate the analysis of novel variations, we present CardioGraph, a platform specially designed to support the analysis of novel variations and help determine whether they are relevant for diagnosis. To do this, CardioGraph identifies and annotates the consequence of variations and provides contextual information regarding which heart structures, pathways, and biological processes are potentially affected by those variations.

Methods
We conducted our work through three steps. First, we define a data model to support the representation of the heterogeneous information. Second, we instantiate this data model to integrate and represent all the genomics knowledge available for familiar cardiopathies. In this step, we consider genomic data sources and the scientific literature. Third, the design and implementation of the CardioGraph platform. A three-tier structure was used: the database, the backend, and the frontend.

Results
Three main results were obtained: the data model, the knowledge base generated with the instantiation of the data model, and the platform itself. The platform code has been included as supplemental material in this manuscript. Besides, an instance is publicly available in the following link: https://genomics-hub.pros.dsic.upv.es:3090.

Conclusion
CardioGraph is a platform that supports the analysis of novel variations. Future work will expand the body of knowledge about familiar cardiopathies and include new information about hotspots, functional studies, and previously reported variations.
Provider and community perceptions of integrated COVID-19 and routine childhood immunisation programmes in Nigeria: a qualitative exploratory study
Authors: Bakare Ayobami A. , Akinsola Kofoworola O. , King Carina , Sogbesan Abiodun A. , Bakare Oluwabunmi R. , Fadahunsi Opeyemi Y. , Salako Julius , Falade Adegoke G. , Herzig van Wees Sibylle 
Published: October 2024

Abstract
Background
In Nigeria, COVID-19 vaccines were delivered through outreach activities, as well as integrated within routine immunisation. However, evaluations of integrated approaches for novel vaccines are scarce. We aimed to understand the perceived benefits and challenges of integrating the COVID-19 vaccine within routine immunisation in Nigeria, and identify ways to strengthen this approach.

Methods
We conducted 30 semi-structured interviews with community members and healthcare workers in primary healthcare facilities (PHCs) in Jigawa (n = 16) and Oyo (n = 14) states, Nigeria from 08 August to 13 September 2022. Participants were selected purposively from PHCs. We obtained information on participants’ perception about routine immunisation, and perceived benefits and challenges associated with integrated COVID-19 vaccine delivery. Healthcare worker and community interviews were analysed separately following a thematic analysis approach.

Results
We identified four themes that describe the community and healthcare workers’ responses, perceived impact, and the health system adaptions to the challenges associated with the integrated vaccine delivery approach. Community members expressed concern that children might be given COVID-19 vaccines instead of routine immunisations, while others appreciated the integrated approach due to their trust in the efficacy of COVID-19 vaccines, government, and healthcare providers. Healthcare providers perceived the integrated approach as improving vaccination coverage and awareness but noted additional problems of increased workload, vaccine scarcity, and prolonged clinic visits. Insufficient resources were subsisting barriers to effective integration in both states, but the provider’s gender was also a challenge in Jigawa state. Additionally, the use of incentives to generate demand had ambiguous effects in Jigawa state.

Conclusion
Taking an integrated approach to deliver COVID-19 vaccines was acceptable by healthcare providers but community members expressed concerns. Given existing vaccination programmes have persistent challenges, it is pertinent to address these barriers to enhance effectiveness of an integrated approach.
Cost-effectiveness of screening and treating alcohol use and depression among people living with HIV in Zimbabwe: a mathematical modeling study
Authors: Su Jasmine I-Shin , Yeo Yao-rui , Jeetoo Mellesia , Morojele Neo K. , Francis Joel M. , Shenoi Sheela , Braithwaite R. Scott 
Published: October 2024

AbstractBackgroundAlcohol use disorder (AUD) and major depressive disorder (MDD) drive HIV transmission in many sub-Saharan African settings. The impact of screening and treating AUD and MDD on HIV outcomes is unknown. We aimed to identify the cost-effectiveness of AUD and MDD interventions in Zimbabwe, and their potential contribution to reaching Zimbabwe’s Ending the HIV Epidemic 2030 goal.MethodsUsing a validated HIV compartmental transmission model in Zimbabwe, we compared four policy scenarios: prevention as usual (baseline); implement AUD screening (using AUDIT) and treatment (motivational interviewing and cognitive-behavioral therapy); implement MDD screening (using PHQ-9) and treatment (cognitive-behavioral therapy); and implement screening and treatment for both. Outcomes were HIV incidence projections, infections averted through 2030, quality-adjusted life-years gained, cost per infection averted, and cost per QALY gained. Analyses considered “spillover,” when treatment for AUD also results in an improvement in MDD and the converse. Sensitivity analyses identified cost reductions necessary for AUD and MDD interventions to be as cost-effective as other HIV interventions, particularly the scale-up of long-acting PrEP.ResultsAUD and MDD combined will be responsible for 21.1% of new HIV infections in Zimbabwe by 2030.Without considering spillover, compared to the baseline, MDD intervention can reduce new infections by 5.4% at $2039/infection averted and $3186/QALY. AUD intervention can reduce new infections by 5.8%, but at $2,968/infection averted and $4753/QALY, compared to baseline. Both MDD and AUD interventions can reduce new infections by 11.1% at $2810/infection averted and $4229/QALY, compared to baseline.Considering spillover, compared to the baseline, MDD intervention can reduce new infections by 6.4% at $1714/infection averted and $2630/QALY. AUD intervention can reduce new infections by 7.4%, but at $2299/infection averted and $3560/QALY compared to baseline. Both MDD and AUD interventions can reduce new infections by 11.9% at $2247/infection averted and $3382/QALY compared to baseline. For MDD intervention to match the cost-effectiveness of scaling long-acting PrEP, the cost of MDD intervention would need to be reduced from $16.64 to $12.88 per person.ConclusionsImplementing AUD and MDD interventions can play an important role in HIV reduction in Zimbabwe, particularly if intervention cost can be decreased while preserving effectiveness.
Isolation and evaluation of the pathogenicity of a hybrid shiga toxin-producing and Enterotoxigenic Escherichia coli in pigs
Authors: Nammuang Danaya , Shen Yi-Wen , Ke Chiao-Hsu , Kuan Nan-Ling , Lin Chao-Nan , Yeh Kuang-Sheng , Chang Yen-Chen , Chang Chia-Yu , Chang Hui-Wen 
Published: October 2024

Abstract
Background
Porcine pathogenic Escherichia coli (E. coli), the globally recognized important pathogen, causes significant economic loss in the field. Enterotoxigenic E. coli (ETEC) causes porcine neonatal and post-weaning diarrhea (PWD), frequently carrying F4 adhesin, F18 adhesin, Heat-Stable toxin (ST), and Heat-Labile toxin (LT). Shiga Toxin-Producing E. coli (STEC) produces F18 adhesin and Shiga toxin type 2e (stx2e), majorly leading to systemic endothelial cell damage and edema disease. In this study, hemolytic pathogenic hybrid STEC/ETEC strains carrying ST and LT genes of ETEC and the Stx2e gene of STEC isolated from pigs with PWD in Taiwan were identified. The pathogenicity of a Taiwan hybrid STEC/ETEC strain was evaluated by oral inoculation in post-weaning pigs.

Results
Next generation sequencing and multilocus sequence typing of two hybrid Taiwan porcine STEC/ETEC isolates indicated that these two isolates were closely related to the ST88 porcine hybrid STEC/ETEC isolated from pigs with watery diarrhea. Furthermore, the two hybrid Taiwan porcine STEC/ETEC isolates also displayed combinations of multiple resistance genes encoding mechanisms for target modification and antibiotic inactivation. Animal experiments confirmed that the Taiwan hybrid STEC/ETEC could cause watery diarrhea in post-weaning pigs with no signs of edema disease and minimal histopathological lesions.

Conclusion
To the best of the authors’ knowledge, the present study is the first study demonstrating intestinal pathogenicity of the hybrid STEC/ETEC in pigs. The result suggests that the hybrid STEC/ETEC should be considered as a new emerging pathogen and a new target for vaccine development.
Transcriptional pathways of terminal differentiation in high- and low-density blood granulocytes in sepsis
Authors: Guenther Tobias , Coulibaly Anna , Velásquez Sonia Y. , Schulte Jutta , Fuderer Tanja , Sturm Timo , Hahn Bianka , Thiel Manfred , Lindner Holger A. 
Published: October 2024

Abstract
Background
Trauma and infection induce emergency granulopoiesis. Counts of immature granulocytes and transcriptional pathways of terminal granulocytic differentiation in blood are elevated in sepsis but correlate with disease severity. This limits their performance as sepsis biomarkers in critically ill patients. We hypothesized that activation of these pathways in sepsis is attributable to immature low-density (LD) rather than mature high-density (HD) granulocytes.

Methods
We included patients with sepsis and systemic inflammatory response syndrome (SIRS) of comparable disease severity, and additionally septic shock, on intensive or intermediate care unit admission. Blood granulocyte isolation by CD15 MicroBeads was followed by density-gradient centrifugation. Flow cytometry was used to determine counts of developmental stages (precursors) and their relative abundancies in total, HD, and LD granulocytes. Five degranulation markers were quantified in plasma by multiplex immunoassays. A set of 135 genes mapping granulocyte differentiation was assayed by QuantiGene™ Plex. CEACAM4, PLAC8, and CD63 were analyzed by qRT-PCR. Nonparametric statistical tests were applied.

Results
Precursor counts appeared higher in sepsis than SIRS but did not correlate with disease severity for early immature and mature granulocytes. Precursor subpopulations were enriched at least ten-fold in LD over HD granulocytes without sepsis-SIRS differences. Degranulation markers in blood were comparable in sepsis and SIRS. Higher expression of early developmental genes in sepsis than SIRS was more pronounced in LD and less in HD than total granulocytes. Only the cell membrane protein encoding genes CXCR2 and CEACAM4 were more highly expressed in SIRS than sepsis. By qRT-PCR, the azurophilic granule genes CD63 and PLAC8 showed higher sepsis than SIRS levels in LD granulocytes and PLAC8 also in total granulocytes where its discriminatory performance resembled C-reactive protein (CRP).

Conclusions
Transcriptional programs of early terminal granulocytic differentiation distinguish sepsis from SIRS due to both higher counts of immature granulocytes and elevated expression of early developmental genes in sepsis. The sustained expression of PLAC8 in mature granulocytes likely accounts for its selection in the whole blood SeptiCyte™ LAB test. Total granulocyte PLAC8 rivals CRP as sepsis biomarker. However, infection-specific transcriptional pathways, that differentiate sepsis from sterile stress-induced granulocytosis more reliably than CRP, remain to be identified.
Massive citizen science sampling and integrated taxonomic approach unravel Danish cryptogam-dwelling tardigrade fauna
Authors: Gąsiorek Piotr , Sørensen Martin V. , Lillemark Marie Rathcke , Leerhøi Frederik , Tøttrup Anders P. 
Published: October 2024

AbstractTardigrade diversity and distribution are enigmatic in most parts of the globe, and only some European countries can boast of a relatively well-studied water bear fauna. However, even these suffer from the lack of genetic data, which would substantiate faunistic data and make biogeographic comparisons easier. Denmark has never been intensively and systematically researched in this regard, thus a citizen science sampling of cryptogams (mosses, liverworts, and lichens) was launched in spring 2023, aiming at a comprehensive biodiversity survey across this insular country. Nearly 700 samples were selected out of 8.000 sent to NHMD, based on the quality of samples, representativeness of various regions of Denmark, and the type of substrate to allow unravelling of potential ecological associations between tardigrades and cryptogams. Importantly, a large fraction of morphological identifications was backed up by DNA barcode data based on ITS-2 (1001 sequences), and in some cases also on COI (93 sequences) and ITS-1 (22 sequences) molecular markers, which are recognised DNA fragments used in species delimitation. We quadruple the number of known Danish limno-terrestrial tardigrade species (55 spp. reported in this paper vs. 14 spp. reported in literature so far, most of which were contentious due to the insufficient knowledge on tardigrade taxonomy), demonstrating the power of integrative taxonomy. No fewer than nine spp. are new to science. This is the first case where tardigrade fauna of an entire country is examined both from morphological and DNA barcoding data perspective.
Greenness and whiteness appraisal for bioanalysis of quetiapine, levodopa and carbidopa in spiked human plasma by high performance thin layer chromatography
Authors: Hindam Finan T. , Abou Al Alamein Amal M. , Arafa Reham M. , Ahmed Neven , Eltanany Basma M. 
Published: October 2024

AbstractA sustainable HPTLC-densitometric method was developed for quantitative determination of Quetiapine (QUET), Levodopa (LD) and Carbidopa (CD) in presence of Dopamine (DOP) as an internal standard. This applicable technique was achieved by spiking human plasma and extraction was performed using the protein precipitation approach. The mobile phase used was acetone, dichloromethane, n-butanol, glacial acetic acid and water (3: 2.5: 2: 2: 1.75, by volume). Method validation was done according to US-FDA guidelines and was able to quantify Quetiapine, Levodopa and Carbidopa in the ranges of 100–4000, 200–8000 and 30–1300 ng/mL, respectively. Bioanalytical method validation parameters were assessed for the studied drugs. Finally, the analytical suggested methodology was evaluated using various green and white analytical chemistry metrics and other tools, such as the green solvent selection tool, analytical eco-scale, green analytical procedure index, analytical greenness metric approach and the red–green–blue algorithm tool. The results revealed that the applied analytical method had a minor impact on the environment and is a relatively greener option than other previously reported chromatographic methods.
Graphical Abstract
Model-based estimation of heart movements using microwave Doppler radar sensor
Authors: Ota Takashi , Okusa Kosuke 
Published: October 2024

Abstract
Background
Heart rate is one of the most crucial vital signs and can be measured remotely using microwave Doppler radar. As the distance between the body and the Doppler radar sensor increases, the output signal weakens, making it difficult to extract heartbeat waveforms. In this study, we propose a new template-matching method that addresses this issue by simulating Doppler radar signals. This method extracts the heartbeat waveform with higher accuracy while the participant is naturally sitting in a chair.

Methods
An extended triangular wave model was created as a mathematical representation of cardiac physiology, taking into account heart movements. The Doppler radar output signal was then simulated based on this model to automatically obtain a template for one cycle. The validity of the proposed method was confirmed by calculating the PPIs using the template and comparing their accuracy to the R-R intervals (RRIs) of the electrocardiogram for five participants and by analyzing the signals of eight participants in their natural state using the mathematical model of heart movements. All measurements were conducted from a distance of 500 mm.

Results
The correlation coefficients between the RRIs of the electrocardiogram and the PPIs using the proposed method were examined for five participants. The correlation coefficients were 0.93 without breathing and 0.70 with breathing. This demonstrates a higher correlation considering the long distance of 500 mm, and the fact that body movements were not specifically restricted, suggesting that the proposed method can successfully estimate RRI. The average correlation coefficients, calculated between the Doppler output signals and the templates for each of the eight participants, exceeded 0.95. Overall, the proposed method showed higher correlation coefficients than those reported in previous studies, indicating that our method performed well in extracting heartbeat waveforms.

Conclusions
Our results indicate that the proposed method of remote heart monitoring using microwave Doppler radar demonstrates higher accuracy in estimating the RRI of the electrocardiogram while at rest sitting in a chair, and the ability to extract the heartbeat waveforms from the measured Doppler output signal, eliminating the need to create templates in advance as required by conventional template matching methods. This approach offers more flexibility in the measurement environment than conventional methods.
Comparison of AI-assisted cephalometric analysis and orthodontist-performed digital tracing analysis
Authors: Bor Sabahattin , Ciğerim Saadet Çınarsoy , Kotan Seda 
Published: October 2024

Abstract
Background
The aim of this study was to compare and evaluate three AI-assisted cephalometric analysis platforms—CephX, WeDoCeph, and WebCeph—with the traditional digital tracing method using NemoCeph software.

Material and method
A total of 1500 lateral cephalometric films that met the inclusion criteria were classified as Class I, Class II, and Class III. Subsequently, 40 patients were randomly selected from each class. These selected films were uploaded to 3 AI-assisted cephalometric analysis platforms and analyzed without any manual intervention. The same films were also analyzed by an orthodontist using the NemoCeph program.

Results
The results revealed significant differences in key angular measurements (ANB, FMA, IMPA, and NLA) across Class I, II, and III patients when comparing the four cephalometric analysis methods (WebCeph, WeDoCeph, CephX, and NemoCeph). Notably, ANB (p < 0.05), FMA (p < 0.001), IMPA (p < 0.001), and NLA (p < 0.001) varied significantly. Linear measurements also differed, with significant differences in U1-NA (p = 0.002) and Co-A (p = 0.002) in certain classes. Repeated measurement analysis revealed variation in SNA (p = 0.011) and FMA (p = 0.030), particularly in the Class II NemoCeph group, suggesting method-dependent variability.

Conclusion
AI-assisted cephalometric analysis platforms such as WebCeph, WeDoCeph, and CephX give rise to notable variation in accuracy and reliability compared to traditional manual digital tracing, specifically in terms of angular and linear measurements. These results emphasize the importance of meticulous selection and assessment of analysis methods in orthodontic diagnostics and treatment planning.
Comments on the paper “Data-driven gating (DDG)-based motion match for improved CTAC registration. EJNMMI Physics. 2024;11(1):42.”
Authors: Pan Tinsu 
Published: October 2024

AbstractMisregistration between CT and PET in PET/CT is mainly caused by respiratory motion or irregular respiration during the CT scan in PET/CT. Other than repeat CT, repeat PET/CT, or data-driven gated (DDG) CT, there is no practical approach to mitigate the misregistration artifacts and subsequent CT attenuation correction (CTAC) of the PET data. DDG PET derives a respiratory motion model based on the multiple phases of PET images without hardware gating and it allows for a potential correction of the misregistration artifacts based on the respiratory motion model. The purpose of this commentary was to compare the recent two publications on matching the random phase of helical CT with one of the PET phases derived from the motion model of DDG PET and warping the misregistered helical CT for CTAC of and registration with PET or DDG PET. The two publications were similar in methodology. However, the data sets used for the comparison were different and could potentially impact their conclusions.
Assessing the measurement properties of PROMIS Computer Adaptive Tests, short forms and legacy patient reported outcome measures in patients undergoing total hip arthroplasty
Authors: Braaksma C. , Wolterbeek N. , Veen M. R. , Poolman R. W. , Pronk Y. , Klaassen A. D. , Ostelo R. W. J. G. , Terwee C. B. 
Published: October 2024

Abstract
Background
The commonly used (‘legacy’) PROMs evaluating outcomes of total hip arthroplasty (THA), have several limitations regarding their measurement properties and interpretation of scores. One innovation in PROMs is the use of Computerized Adaptive Testing (CAT). The Patient-Reported Outcomes Measurement Information System (PROMIS®) is a validated system of CATs. The aim of this study was to assess the measurement properties of PROMIS and legacy instruments in patients undergoing THA.

Methodology
Patients in this multicenter study filled out a questionnaire twice, including Dutch-Flemish PROMIS v1.2 Physical Function (PROMIS-PF) and v1.1 Pain Interference (PROMIS-PI) CATs and short forms, PROMIS v1.0 Pain Intensity, and legacy PROMs (Hip disability and Osteoarthritis Outcome Score (HOOS), HOOS-Physical function Shortform (HOOS-PS), Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC), Oxford Hip Score (OHS), and two numeric rating scales measuring pain). The reliability, measurement precision (Standard Error of Measurement (SEM)), smallest detectable change (SDC), and burden of PROMIS instruments were presented head-to-head to legacy PROMs. Furthermore, construct validity was assessed.

Results
208 patients were included. All instruments had a sufficient test-retest reliability (range ICC: 0.83–0.96). The SEM of PROMIS CATs and short forms ranged from 1.8 to 2.2 T-score points, the SEM of legacy instruments 2.6–11.1. The SDC of PROMIS instruments ranged from 2.1 to 7.3 T-score points, the SDC of legacy instruments 7.2–30.9. The construct validity of PROMIS CAT and short forms were found sufficient, except for the PROMIS-PI short form. The burden of PROMIS CATs was smaller than PROMIS short forms (range 4.8–5.2 versus 8–20 items, respectively). The burden of legacy instruments measuring physical functioning ranged from 5 to 40 items.

Conclusions
The PROMIS-PF is less burdensome, with high measurement precision, and almost no minimal or maximal scores, and an equal reliability compared to legacy instruments measuring physical functioning in patients undergoing THA. The PROMIS Pain Intensity 1a is comparable to the legacy pain instruments in terms of burden, reliability and SDC. Measuring the construct Pain Interference may not have additional value in this population because of its high correlation with instruments measuring physical functioning. The SDC values presented in this study can be used for individual patient monitoring.