bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying signature features of epidemic diseases from 19th century all-cause mortality data
Authors: Pedersen Rasmus Kristoffer , Ingholt Mathias Mølbak , Van Wijhe Maarten , Andreasen Viggo , Simonsen Lone 
Published: July 2024

Abstract
Deadly epidemics leave distinct marks on all-cause mortality. When cause-specific health data are unavailable, studies of all-cause mortality may be necessary for understanding epidemic and pandemic diseases in history. Here, we identify and catalog every major epidemic in Denmark during the 100-year period between 1815 and 1915, based on a recently digitized and compiled data set of all 4 million burials during the period. Although the data set lacks specific information on cause of death, we were able to determine plausible etiology for the majority of 418 identified mortality crises that had more than 50 excess deaths. Epidemiologic methods, data analysis, consultation of historical sources, and investigation of the signature features of age patterns, seasonality, timing, and geography were used. The identified epidemics included, among others, pandemic influenza, cholera outbreaks in 1853 and 1857, and annually repeating epidemics during the period 1826-1832. Although these epidemics have been discussed elsewhere, our work presents a different view of these epidemics, based solely on all-cause mortality. Some of the identified epidemics were caused by pathogens that still affect us in modern times. In low-income modern settings for which representative population health data may be unavailable, the use of mortality data to determine the signature features may guide policy and improve future mitigation strategies.
Studying the association between longitudinal nondense breast tissue measurements and the risk of breast cancer: a joint modeling approach
Authors: Illipse Maya , Gasparini Alessandro , Christoffersen Benjamin , Hall Per , Czene Kamila , Humphreys Keith 
Published: July 2024

Abstract
Conflicting results have appeared in the literature on whether the amount of nondense, adipose tissue in the breast is a risk factor or a protective factor for breast cancer (BC), and biological hypotheses supporting both have been proposed. We suggest here that limitations in study design and statistical methodology could potentially explain the inconsistent results. Specifically, we exploit recent advances in methodology and software developed for the joint analysis of multiple longitudinal outcomes and time-to-event data to jointly analyze dense and nondense tissue trajectories and the risk of BC in a large Swedish screening cohort. We also perform extensive sensitivity analyses by mimicking analyses/designs of previously published studies—for example, ignoring available longitudinal data. Overall, we do not find strong evidence supporting an association between nondense tissue and the risk of incident BC. We hypothesize that (1) previous studies have not been able to isolate the effect of nondense tissue from dense tissue or adipose tissue elsewhere in the body, that (2) estimates of the effect of nondense tissue on risk are strongly sensitive to modeling assumptions, or that (3) the effect size of nondense tissue on BC risk is likely to be small/not clinically relevant.
Impact of connected dispensing technology with advanced analytics in a multicenter health system
Authors: Freeman-Muhammad Steven , Chipman-Ashley Regina , Martin Richard E , Williams Jennifer , Prochazka Amanda , Dumitru Doina , Greszler Craig 
Published: July 2024

Abstract

Purpose
This study was designed to evaluate the impact of enterprise inventory optimization (EIO) technology and analytics on pharmacy labor, costs, and medication availability within a large integrated delivery network (IDN).

Methods
This article describes a mixed-methods, postmarket observational study assessing the impact of a solution of disparate technologies including automated dispensing cabinets (ADCs), centralized pharmacy inventory software, and controlled substance vaults connected by an inventory optimization analytics (IOA) tool. Four study modules were implemented over a 10-month period. The intervention consisted of implementation of the IOA software, linking the disparate automated technologies. Transactional data was collected and aggregated with user perception survey data in both the pre- and postintervention periods. Descriptive and comparative statistical testing was used to assess outcomes.

Results
A total of 11 facilities with bed counts ranging between 22 and 908 beds were included in this study. At an enterprise level, users were able to complete an average of 2.8 times more periodic automated replenishment (PAR) level changes post intervention, resulting in an estimated enterprise labor avoidance of over 1 full-time equivalent (2,099 labor hours) annually. Despite an enterprise decision to increase ADC inventory on hand from a 3-day supply to a 5-day supply, 5 sites (45%) had a decrease in total inventory, while 9 sites (82%) saw a decrease in ADC inventory costs. Additionally, 7 sites (64%) saw a reduction in the ADC stockout percentage and all 11 sites (100%) saw a decrease in the central pharmacy stockout percentage post intervention.

Conclusion
Integration and optimization of connected inventory management technology was observed to have positive impacts on improving labor productivity, reducing ADC inventory carrying costs, and increasing medication availability.
Systemic inflammatory markers in ageing, Alzheimer's disease and other dementias
Authors: Cai Huimin , Zhao Tan , Pang Yana , Fu Xiaofeng , Ren Ziye , Quan Shuiyue , Jia Longfei 
Published: July 2024

Abstract
Systemic inflammation with alterations in inflammatory markers is involved in ageing and Alzheimer's disease. However, few studies have investigated the longitudinal trajectories of systemic inflammatory markers during ageing and Alzheimer's disease, and specific markers contributing to Alzheimer's disease remain undetermined. In this study, a longitudinal cohort (cohort 1: n = 290; controls, 136; preclinical Alzheimer's disease, 154) and a cross-sectional cohort (cohort 2: n = 351; controls, 62; Alzheimer's disease, 63; vascular dementia, 58; Parkinson's disease dementia, 56; behavioural variant frontotemporal dementia, 57; dementia with Lewy bodies, 55) were included. Plasma levels of inflammatory markers were measured every 2 years during a 10-year follow-up in the longitudinal cohort and once in the cross-sectional cohort.
The study demonstrated that the inflammatory markers significantly altered during both ageing and the development of Alzheimer's disease. However, only complement C3, interleukin-1β and interleukin-6 exhibited significant changes in participants with preclinical Alzheimer's disease, and their longitudinal changes were significantly associated with the development of Alzheimer's disease compared to controls over the 10-year follow-up. In the cross-sectional cohort, complement C3 demonstrated specificity to Alzheimer's disease, while interleukin-1β and interleukin-6 were also altered in other dementias.
The study provides a new perspective on the involvement of inflammatory markers in the ageing process and the development of Alzheimer's disease, implying that regulating inflammation may have a pivotal role in promoting successful ageing and in the prevention and treatment of Alzheimer's disease.
Still to ARRIVE at adequate reporting of orthodontic studies involving animal models
Authors: Flitti Dihya , Pandis Nikolaos , Seehra Jadbinder 
Published: July 2024

Abstract

Background
The ARRIVE 2.0 guidelines were introduced to improve the reporting of animal studies. The aim of this study was to assess the reporting adherence of orthodontic speciality animal studies in relation to ARRIVE 2.0 guidelines. Associations between the reporting and study characteristics were explored.

Materials and method
An electronic database search was undertaken using Medline via PubMed (www.pubmed.ncbi.nlm.nih.gov) to identify studies meeting the eligibility criteria published between 1 January 2018 and 31 December 2023. Data extraction was performed in duplicate and independently. Descriptive statistics and frequency distributions for the responses to each checklist item were calculated. Mean values for adequate reporting per ARRIVE item were calculated. A sum score was calculated by adding the responses (0 = not reported, 1 = inadequate reporting, 2 = adequate reporting) per item and sub-questions. On an exploratory basis, univariable linear regression between summary score and study characteristics (year of publication, continent of authorship, type of centre, and number of authors) was performed.

Results
Three hundred and eighty-four studies were analysed. Variability in the adequate reporting of the ARRIVE 2.0 guideline items was evident. In particular, in 32% of studies, there was a lack of reporting of the priori sample size calculation. Overall, the mean reporting score for the sample was 57.9 (SD 6.7 and range 34–74). There were no associations between score and study characteristics except for a weak association for year of publication with a small improvement over time (each additional year).

Conclusions
The reporting of animal studies relevant to the speciality of orthodontics is sub-optimal in relation to the ARRIVE 2.0 guidelines. There was a tendency for the non-reporting of items pertaining to study sample size, eligibility, methods to reduce bias and interpretation/scientific implications. Greater awareness and reporting adherence to the ARRIVE 2.0 guidelines are required to reduce research waste involving animal models.
Waveform modelling of hydroacoustic teleseismic earthquake records from autonomous Mermaid floats
Authors: Pipatprathanporn Sirawich , Simons Frederik J 
Published: July 2024

SUMMARY
We present a computational technique to model hydroacoustic waveforms from teleseismic earthquakes recorded by mid-column Mermaid floats deployed in the Pacific, taking into consideration bathymetric effects that modify seismo-acoustic conversions at the ocean bottom and acoustic wave propagation in the ocean layer, including reverberations. Our approach couples axisymmetric spectral-element simulations performed for moment-tensor earthquakes in a 1-D solid Earth to a 2-D Cartesian fluid–solid coupled spectral-element simulation that captures the conversion from displacement to acoustic pressure at an ocean-bottom interface with accurate bathymetry. We applied our workflow to 1129 seismograms for 682 earthquakes from 16 Mermaids (short for Mobile Earthquake Recording in Marine Areas by Independent Divers) owned by Princeton University that were deployed in the Southern Pacific as part of the South Pacific Plume Imaging and Modeling (SPPIM) project. We compare the modelled synthetic waveforms to the observed records in individually selected frequency bands aimed at reducing local noise levels while maximizing earthquake-generated signal content. The modelled waveforms match the observations very well, with a median correlation coefficient of 0.72, and some as high as 0.95. We compare our correlation-based traveltime measurements to measurements made on the same data set determined by automated arrival-time picking and ray- traced traveltime predictions, with the aim of opening up the use of Mermaid records for global seismic tomography via full-waveform inversion.
Real-time dual-parameter full-waveform inversion of GPR data based on robust deep learning
Authors: Xue Jiyan , Huang Qinghua , Wu Sihong , Zhao Li , Ma Bowen 
Published: July 2024

SUMMARY
Ground penetrating radar (GPR) is becoming an increasingly important tool for understanding the shallow electrical structures of the Earth and planets due to its adaptability to harsh detection environments, efficient data acquisition and accurate detection results. GPR full-waveform can simultaneously constrain the permittivity and resistivity of the medium, providing more comprehensive geophysical information and reducing the non-uniqueness of inversion. However, given the highly non-linear inverse problem and the massive data resulted from high temporal and spatial samplings, traditional full-waveform inversion algorithms are prohibitively costly. Inspired by Google's vision semantic segmentation system, we develop a robust deep learning-guided network that integrates geology and geophysics knowledge to support the real-time translation of zero-offset GPR data into dual-parameter electrical structures. We test our proposed network using synthetic data, which demonstrates that the algorithm can provide an accurate dual-parameter electrical model from a GPR sounding in milliseconds on a common laptop PC, exhibiting high robustness and adaptability to noise interference and extreme values of model parameters. We also apply our network to field data gathered for pollutant investigation in the United States. The resulting dual-parameter structure provides a more comprehensive and realistic depiction of subsurface electrical properties and reveals the migration and ageing of pollutants. Our algorithm's real-time and accurate advantages are expected to further unleash the potential of GPR technology and enable it to play a more significant role in earth and planetary exploration.
Pneumococcal Carriage and Disease in Adults in England, 2011–2019: The Importance of Adults as a Reservoir for Pneumococcus in Communities
Authors: El Safadi Dima , Hitchins Lisa , Howard Ashleigh , Aley Parvinder , Bowman Jaclyn , Bertran Marta , Collins Andrea , Colin-Jones Rachel , Elterish Filora , Fry Norman K , Gordon Stephen S , Gould Kate , Hinds Jason , Horn Emilie , Hyder-Wright Angela , Kandasamy Rama , Ladhani Shamez , Litt David , Mitsi Elena , Murphy Annabel , Pollard Andrew J , Plested Emma , Pojar Sherin , Ratcliffe Helen , Robertson Maria C , Robinson Hannah , Snape Matthew D , Solórzano Carla , Voysey Merryn , Begier Elizabeth , Catusse Julie , Lahuerta Maria , Theilacker Christian , Gessner Bradford D , Tiley Karen S , Ferreira Daniela M 
Published: July 2024

Abstract

Background
Pneumococcal carriage in healthy adults and its relationship to invasive pneumococcal disease (IPD) is not well understood.

Methods
Nasal wash samples from adults without close contact with young children (Liverpool, UK), 2011–2019, were cultured, and culture-negative samples tested by polymerase chain reaction (PCR). Pneumococcal carriage in adults 18–44 years was compared with carriage among pneumococcal conjugate vaccine–vaccinated children aged 13–48 months (nasopharyngeal swabs, Thames Valley, UK) and national IPD data, 2014–2019. Age group–specific serotype invasiveness was calculated and used with national IPD data to estimate carriage serotype distributions for ≥65 years.

Results
Overall, 98 isolates (97 carriers) were identified (3 solely by PCR) from 1631 ≥18 years adults (standardized carriage prevalence 6.4%). Despite different carriage and IPD serotype distributions between adults and children, serotype invasiveness was highly correlated (R = 0.9). Serotypes 3, 37, and 8 represented a higher proportion of adult carriage than expected. Predicted carriage serotype distributions for ≥65 years aligned closest with the young adult carriage serotype distribution.

Conclusions
Nasal wash technique is highly sensitive. For some serotypes carried by adults aged ≥65 years, other adults may be an important reservoir for transmission. Age groups such as older children should also be considered.
Molecular Methods Enhance the Detection of Pyoderma-Related Streptococcus pyogenes and emm-Type Distribution in Children
Authors: Hall Jennifer N , Armitage Edwin P , Senghore Elina , Darboe Saffiatou , Barry Momodou , Camara Janko , Bah Sulayman , Keeley Alexander J , McCarthy James S , Smeesters Pierre , Turner Claire E , Darton Thomas C , Marks Michael , Angyal Adrienn , de Silva Thushan I 
Published: July 2024

Abstract

Background
Streptococcus pyogenes–related skin infections are increasingly implicated in the development of rheumatic heart disease (RHD) in lower-resource settings, where they are often associated with scabies. The true prevalence of S pyogenes–related pyoderma may be underestimated by bacterial culture.

Methods
A multiplex quantitative polymerase chain reaction (qPCR) assay for S pyogenes, Staphylococcus aureus, and Sarcoptes scabiei was applied to 250 pyoderma swabs from a cross-sectional study of children aged &lt;5 years in The Gambia. Direct PCR-based emm-typing was used to supplement previous whole genome sequencing (WGS) of cultured isolates.

Results
Pyoderma lesions with S pyogenes increased from 51% (127/250) using culture to 80% (199/250) with qPCR. Compared to qPCR, the sensitivity of culture was 95.4% for S pyogenes (95% confidence interval {CI}, 77.2%–99.9%) in samples with S pyogenes alone (22/250 [9%]), but 59.9% (95% CI, 52.3%–67.2%) for samples with S aureus coinfection (177/250 [71%]). Direct PCR-based emm-typing was successful in 50% (46/92) of cases, identifying 27 emm-types, including 6 not identified by WGS (total 52 emm-types).

Conclusions
Bacterial culture significantly underestimates the burden of S pyogenes in pyoderma, particularly with S aureus coinfection. Molecular methods should be used to enhance the detection of S pyogenes in surveillance studies and clinical trials of preventive measures in RHD-endemic settings.
Prevalence of MRSA in canine and feline clinical samples from one-third of veterinary practices in Germany from 2019–2021
Authors: Feuer Leonie , Frenzer Stefanie Katharina , Merle Roswitha , Leistner Rasmus , Bäumer Wolfgang , Bethe Astrid , Lübke-Becker Antina , Klein Babette , Bartel Alexander 
Published: July 2024

AbstractBackgroundMRSA is a major contributor to AMR-related deaths. The WHO’s global action plan emphasizes a One Health approach, acknowledging the connection between humans and their companion animals. It is agreed on that comprehensive AMR surveillance is needed.ObjectivesThis study provides a large-scale overview of MRSA occurrence in cats and dogs in Germany, serving as a foundation for continuous surveillance.MethodsThe study analysed all results of canine and feline bacterial diagnostic samples from a large laboratory, encompassing samples received from veterinary practices between January 2019 and December 2021. MRSA prevalence between host species, sample types and geographical distribution were compared. Additionally, data were contrasted with human MRSA surveillance data from Germany.ResultsSamples originated from 3491 German veterinary practices, representing 33.1% of practices and clinics nationally. Bacterial examination results from 175 171 samples were analysed, identifying S. aureus in 5526 of these samples (3.2% isolation rate). S. aureus in clinical samples was more prevalent in cats (5.6%) than dogs (2.0%). Methicillin resistance was found in 17.8% of S. aureus samples and was higher in dogs (20.4%, 95%CI 18.9–22.0) than cats (15.6%, 95%CI 14.3–17.0). The highest MRSA prevalence was found in canine wound samples (32%), compared to skin/soft tissue, respiratory tract and other (&lt;23% respectively).ConclusionThe study reveals a 17.8% MRSA prevalence, which is higher than the human outpatient MRSA prevalence (5.4%). Restriction and regulation of veterinary antibiotic use should be validated with AMR surveillance. Our study shows that this is feasible in companion animals with significant coverage.
Estimation of (Consumer) Sustainability Benefits from Horizontal Agreements: A Quasi Ex Post Analysis
Authors: Bartels Andy , Inderst Roman , Wentzien Christoph 
Published: July 2024

Abstract
The European Commission’s new horizontal guidelines create scope for sustainability agreements and, to calculate efficiencies, suggest the estimation of consumers’ willingness to pay (WTP) for so-called “nonuse value.” We contrast estimates obtained from a hypothetical choice experiment conducted for the Netherlands’ competition authority (the “Chicken of Tomorrow” case) with estimates based on homescan data documenting consumers’ real choices between more or less animal-friendly meat, ensuring that the respective alternatives are made highly comparable. Still, the estimated WTP for the animal-friendly alternative is several times higher in the choice experiment. Given observed prices and the WTP estimated in the choice experiment, the animal-friendly alternative should have already crowded out the conventional variant. We use our findings to inform about several pitfalls both when using experimental data and when using data from true purchases.
Comprehensive analysis of the eclipsing binaries V527 Dra and V2846 Cyg
Authors: Čeki Atila , Şenavcı Hakan Volkan , Latković Olivera , Uzunçam Ebru , Yorulmaz Eda Burcu , Bahar Engin 
Published: July 2024

ABSTRACT
This is the first comprehensive study of the eclipsing binaries V527 Dra and V2846 Cyg, based on radial velocities and ground- and space-based light curves. We perform detailed modeling of these data to derive the absolute parameters and the orbital properties of the two systems. V527 Dra is found to be a semidetached, and V2846 Cyg a contact binary. Both show continual out-of-eclipse variations that can be explained by migrating dark spots of magnetic origin. We also perform the eclipse timing variation (ETV) analysis which reveals that V527 Dra has a tertiary companion whose mass (${\sim} 1 \,{\rm M}_{\odot }$) and orbital inclination (${\sim} 70^{\circ }$) are additionally constrained by radial velocities. The ETV diagram of V2846 Cyg displays a quadratic trend accompanied by a low-amplitude cyclic variation, likely due to a magnetic cycle, although further eclipse times are needed to provide a clearer explanation. Lastly, we demonstrate a correlation between the variations in spot parameters obtained via light curve modelling for individual orbital cycles and the residual ETVs, essentially confirming the assumption of magnetic activity in both systems.
Impact of a Switch From Ciprofloxacin to Ceftriaxone Prophylaxis on Infectious Complications After Transrectal Ultrasound-Guided Biopsy of the Prostate
Authors: Mendo-Lopez Rafael , Lengu Irma , Nguyen Carvell , Wilson Brigid M , Donskey Curtis J , Hecker Michelle T 
Published: July 2024

Abstract
In a 12-year single-center quasi-experimental study, a switch from ciprofloxacin to ceftriaxone prophylaxis for transrectal ultrasound-guided prostate biopsy procedures was associated with a significant reduction in 30-day postprocedure urinary tract infection, urinary tract infection–related hospitalizations, antibiotic prescriptions, and isolation of fluoroquinolone-resistant organisms from urine or blood cultures.