bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adherence to the Atrial fibrillation Better Care pathway and the risk of adverse health outcomes in older care home residents with atrial fibrillation: a retrospective data linkage study 2003–18
Authors: Ritchie Leona A , Harrison Stephanie L , Penson Peter E , Akbari Ashley , Torabi Fatemeh , Hollinghurst Joe , Harris Daniel , Oke Oluwakayode B , Akpan Asangaedem , Halcox Julian P , Rodgers Sarah E , Lip Gregory Y H , Lane Deirdre A 
Published: February 2024

Abstract

Background
The Atrial fibrillation Better Care (ABC) pathway is the gold-standard approach to atrial fibrillation (AF) management, but the effect of implementation on health outcomes in care home residents is unknown.

Objective
To examine associations between ABC pathway adherence and stroke, transient ischaemic attack, cardiovascular hospitalisation, major bleeding, mortality and a composite of all these outcomes in care home residents.

Methods
A retrospective cohort study of older care home residents (≥65 years) in Wales with AF was conducted between 1 January 2003 and 31 December 2018 using the Secure Anonymised Information Linkage Databank. Adherence to the ABC pathway was assessed at care home entry using pre-specified definitions. Cox proportional hazard and competing risk models were used to estimate the risk of health outcomes according to ABC adherence.

Results
From 14,493 residents (median [interquartile range] age 87.0 [82.6–91.2] years, 35.2% male) with AF, 5,531 (38.2%) were ABC pathway adherent. Pathway adherence was not significantly associated with risk of the composite outcome (adjusted hazard ratio, 95% confidence interval [CI]: 1.01 [0.97–1.05]). There was a significant independent association observed between ABC pathway adherence and a reduced risk of myocardial infarction (0.70 [0.50–0.98]), but a higher risk of haemorrhagic stroke (1.59 [1.06–2.39]). ABC pathway adherence was not significantly associated with any other individual health outcomes examined.

Conclusion
An ABC adherent approach in care home residents was not consistently associated with improved health outcomes. Findings should be interpreted with caution owing to difficulties in defining pathway adherence using routinely collected data and an individualised approach is recommended.
Using name overlap analysis to understand medication name search safety
Authors: Flynn Allen , Mieure Katherine D , Myers Conor 
Published: February 2024

Abstract

Purpose
To examine the degree of left-to-right character overlap in medication names as they appear in real-world computer systems.

Methods
We programmed a computer to create and automatically analyze left-to-right character overlap in names appearing on 20,020 lists of real-world medication names. The lists varied in length from 100 to 500 medication names and were created by randomly drawing names from a pool of 2,249 medication names extracted from an operating medication use system database.

Results
Overall maximum left-to-right character overlap varied in lists of 100 to 500 medication names from 4 to 29 characters (mode of 14 characters). For a small subset of names for high-alert medications that must never be administered in error, overall maximum left-to-right character overlap varied from 3 to 10 characters (mode of 6 characters). Further, for users searching for medications by name in computer systems, the keystrokes that do the most work to disambiguate medication names on a list are always the initial few keystrokes.

Conclusion
Medication name left-to-right character overlap on lists of names searched ranges widely. Instead of requiring all users to type a set number of characters when searching for medications by name, search safety can potentially be improved by upgrading computer systems to dynamically respond to each keystroke entered. Using incremental dynamic search, searchers would often be able to type fewer than 5 characters to isolate a single medication by name but would sometimes have to type many more than 5 characters to do so.
Development of handling energy factors for use of dustiness data in exposure assessment modelling
Authors: Fonseca Ana Sofia , Ribalta Carla , Shandilya Neeraj , Fransman Wouter , Alstrup Jensen Keld 
Published: February 2024

Abstract
Several exposure assessment models use dustiness as an input parameter for scaling or estimating exposure during powder handling. Use of different dustiness methods will result in considerable differences in the dustiness values as they are based on different emission generation principles. EN17199:2019 offers 4 different dustiness test methods considering different dust release scenarios (e.g. powder pouring, mixing and gentle agitation, and vibration). Conceptually, the dustiness value by a given method can be multiplied with a scenario-specific modifier, called a handling energy factor (Hi), that allows conversion of a dustiness value to a release constant. Therefore, a Hi, scaling the effective mechanical energy in the process to the energy supplied in the specific dustiness test, needs to be applied. To improve the accuracy in predictive exposure modelling, we derived experimental Hi to be used in exposure algorithms considering both the mass- and number-based dust release fraction determined by the EN17199-3 continuous drop (CD) and the EN17199-4 small rotating drum (SRD) test methods. Three materials were used to evaluate the relationship between dustiness and dust levels during pouring powder from different heights in a controlled environment.
The results showed increasing scatter and difference between the Hi derived for the 2 test methods with increasing pouring height. Nearly all the Hi values obtained for both SRD and CD were &lt;1 indicating that the dustiness tests involved more energy input than the simulated pouring activity and consequently de-agglomeration and dust generation were higher. This effect was most pronounced in CD method showing that SRD mechanistically resembles more closely the powder pouring.
Do phylogenetic community metrics reveal the South African quartz fields as terrestrial-habitat islands?
Authors: Zhigila Daniel A , Elliott Tammy L , Schmiedel Ute , Muasya A Muthama 
Published: February 2024

Abstract

Background and Aims
The quartz fields of the Greater Cape Floristic Region (GCFR) are arid and island-like special habitats, hosting ~142 habitat-specialized plant species, of which 81 % are local endemics, characterized by a rapid turnover of species between and among sites. We use several phylogenetic community metrics: (1) to examine species diversity and phylogenetic structure within and among quartz fields; (2) to investigate whether quartz field specialists are evolutionarily drawn from local species pools, whereas the alternative hypothesis posits that there is no significant evolutionary connection between quartz field specialists and the local species pools; and (3) to determine whether there is an association between certain traits and the presence of species in quartz fields.

Methods
We sampled and developed dated phylogenies for six species-rich angiosperm families (Aizoaceae, Asteraceae, Crassulaceae, Cyperaceae, Fabaceae and Santalaceae) represented in the quartz field floras of southern Africa. Specifically, we focused on the flora of three quartz field regions in South Africa (Knersvlakte, Little Karoo and Overberg) and their surrounding species pools to address our research questions by scoring traits associated with harsh environments.

Key Results
We found that the Overberg and Little Karoo had the highest level of species overlap for families Aizoaceae and Fabaceae, whereas the Knersvlakte and the Overberg had the highest species overlap for families Asteraceae, Crassulaceae and Santalaceae. Although our phylogenetic community structure and trait analyses showed no clear patterns, relatively low pairwise phylogenetic distances between specialists and their local species pools for Aizoaceae suggest that quartz species could be drawn evolutionarily from their surrounding areas. We also found that families Aizoaceae and Crassulaceae in Knersvlakte and Little Karoo were phylogenetically even.

Conclusions
Despite their proximity to one another within the GCFR, the studied areas differ in their species pools and the phylogenetic structure of their specialists. Our work provides further justification for increased conservation focus on these unique habitats under future scenarios of global change.
CloudProteoAnalyzer: scalable processing of big data from proteomics using cloud computing
Authors: Li Jiancheng , Xiong Yi , Feng Shichao , Pan Chongle , Guo Xuan 
Published: February 2024

Abstract

Summary
Shotgun proteomics is widely used in many system biology studies to determine the global protein expression profiles of tissues, cultures, and microbiomes. Many non-distributed computer algorithms have been developed for users to process proteomics data on their local computers. However, the amount of data acquired in a typical proteomics study has grown rapidly in recent years, owing to the increasing throughput of mass spectrometry and the expanding scale of study designs. This presents a big data challenge for researchers to process proteomics data in a timely manner. To overcome this challenge, we developed a cloud-based parallel computing application to offer end-to-end proteomics data analysis software as a service (SaaS). A web interface was provided to users to upload mass spectrometry-based proteomics data, configure parameters, submit jobs, and monitor job status. The data processing was distributed across multiple nodes in a supercomputer to achieve scalability for large datasets. Our study demonstrated SaaS for proteomics as a viable solution for the community to scale up the data processing using cloud computing.

Availability and implementation
This application is available online at https://sipros.oscer.ou.edu/ or https://sipros.unt.edu for free use. The source code is available at https://github.com/Biocomputing-Research-Group/CloudProteoAnalyzer under the GPL version 3.0 license.
Sexual dimorphism in the Neotropical snakes genus Chironius (Serpentes: Colubridae)
Authors: dos Santos Marina Meireles , Klaczko Julia , Prudente Ana Lúcia da Costa 
Published: February 2024

Abstract
Sexual dimorphism is a common phenomenon among snakes, with female snakes being larger than male snakes as a recurrent pattern . However, species that show male-male combat behaviour may impose a selective advantage by developing larger bodies in male specimens, like the diurnal Chironius snakes, which display courtship and male-male combat behaviours. In this study, we analysed sexual dimorphism in body, tail, and head size, and skull size and shape in twelve species of Chironius. We investigated whether sexual dimorphism patterns could be a result of allometric growth. The absence of sexual dimorphism regarding body and head length was the main pattern revealed by our analyses. Sexual dimorphism characterized by larger body and head sizes in males was observed in Chironius bicarinatus, Chironius foveatus, and Chironius fuscus. Only females of Chironius exoletus exhibited larger body and head sizes than males. Regarding the shape of the head, six species showed sexual divergences, with enlarged or robust heads. Sexual dimorphism in skull shape seems related to selection in Chironius flavolineatus, with no allometric influences. Larger tails in males of C. fuscus, C. flavolineatus, and Chironius quadricarinatus may represent an advantageous defensive strategy. Finally, the lack of divergence in tail length in the remaining species probably evolved due to arboreal habits in Chironius.
Tree-informed Bayesian multi-source domain adaptation: cross-population probabilistic cause-of-death assignment using verbal autopsy
Authors: Wu Zhenke , Li Zehang R , Chen Irena , Li Mengbing 
Published: February 2024

Abstract
Determining causes of deaths (CODs) occurred outside of civil registration and vital statistics systems is challenging. A technique called verbal autopsy (VA) is widely adopted to gather information on deaths in practice. A VA consists of interviewing relatives of a deceased person about symptoms of the deceased in the period leading to the death, often resulting in multivariate binary responses. While statistical methods have been devised for estimating the cause-specific mortality fractions (CSMFs) for a study population, continued expansion of VA to new populations (or “domains”) necessitates approaches that recognize between-domain differences while capitalizing on potential similarities. In this article, we propose such a domain-adaptive method that integrates external between-domain similarity information encoded by a prespecified rooted weighted tree. Given a cause, we use latent class models to characterize the conditional distributions of the responses that may vary by domain. We specify a logistic stick-breaking Gaussian diffusion process prior along the tree for class mixing weights with node-specific spike-and-slab priors to pool information between the domains in a data-driven way. The posterior inference is conducted via a scalable variational Bayes algorithm. Simulation studies show that the domain adaptation enabled by the proposed method improves CSMF estimation and individual COD assignment. We also illustrate and evaluate the method using a validation dataset. The article concludes with a discussion of limitations and future directions.
Immune cell infiltrate in ductal carcinoma in situ and the risk of dying from breast cancer: case–control study
Authors: Rask Gunilla , Wadsten Charlotta , Acs Balazs , Hartman Johan , Fredriksson Irma , Garmo Hans , Wärnberg Fredrik , Sund Malin 
Published: February 2024

Abstract

Background
Studies identifying risk factors for death from breast cancer after ductal carcinoma in situ (DCIS) are rare. In this retrospective nested case–control study, clinicopathological factors in women treated for DCIS and who died from breast cancer were compared with those of patients with DCIS who were free from metastatic disease.

Methods
The study included patients registered with DCIS without invasive carcinoma in Sweden between 1992 and 2012. This cohort was linked to the National Cause of Death Registry. Of 6964 women with DCIS, 96 were registered with breast cancer as cause of death (cases). For each case, up to four controls (318; women with DCIS, alive and without metastatic breast cancer at the time of death of the corresponding case) were selected randomly by incidence density sampling. Whole slides of tumour tissue were evaluated for DCIS grade, comedo necrosis, and intensity of periductal lymphocytic infiltrate. Composition of the immune cell infiltrate, expression of oestrogen receptor, progesterone receptor, human epidermal growth factor receptor 2, and proliferation marker Ki-67 were scored on tissue microarrays. Clinical information was obtained from medical records. Information on date, site, and histological characteristics of local and distant recurrences was obtained from medical records for both cases and controls.

Results
Tumour tissue was analysed from 65 cases and 195 controls. Intense periductal lymphocytic infiltrate around DCIS was associated with an increased risk of later dying from breast cancer (OR 2.21. 95% c.i. 1.01 to 4.84). Tumours with more intense lymphocytic infiltrate had a lower T cell/B cell ratio. None of the other biomarkers correlated with increased risk of breast cancer death.

Conclusion
The immune response to DCIS may influence the risk of dying from breast cancer.
Ionized and total magnesium levels in patients with chronic kidney disease: associated factors and outcomes
Authors: Pluquet Maxime , Kamel Said , Alencar de Pinho Natalia , Mansencal Nicolas , Combe Christian , Metzger Marie , Massy Ziad A , Liabeuf Sophie , Laville Solène M 
Published: February 2024

ABSTRACT

Background
The association between hypo- and/or hypermagnesaemia and cardiovascular (CV) outcomes or mortality has shown conflicting results in chronic kidney disease (CKD) and has been conducted on total magnesium (tMg) levels. Thus, the objectives of the present study were to (i) describe the serum ionized Mg (iMg) concentration in patients at various CKD stages, (ii) measure the correlation between iMg and tMg concentrations, (iii) identify their associated factors and (iv) determine whether serum tMg and/or iMg concentrations are associated with major adverse cardiovascular events (MACE) and mortality before kidney replacement therapy in CKD patients.

Methods
Chronic Kidney Disease–Renal Epidemiology and Information Network (CKD-REIN) is a prospective cohort of CKD patients with an estimated glomerular filtration rate (eGFR) &lt;60 mL/min/1.73 m2. Baseline iMg and tMg serum concentrations were centrally measured. Adjusted cause-specific Cox proportional hazard models were used to estimate hazard ratios (HRs) for first MACE and for mortality.

Results
Of the 2419 included patients, median age was 68 years, and the mean eGFR was 34.8 mL/min/1.73 m2. Concentrations of serum iMg and tMg were strongly correlated (r = 0.89, P &lt; .001) and were independently associated with eGFR. The adjusted HR [95% confidence interval (CI)] for MACE associated with the baseline serum tMg level was 1.27 (0.95; 1.69) for patients in Tertile 1 and 1.56 (1.18; 2.06) for patients in Tertile 3, relative to patients in Tertile 2. The HR (95% CI) of death according to serum tMg concentration was increased in Tertile 3 [1.48 (1.11; 1.97)]. The adjusted risk for MACE and mortality (all-cause or CV) associated with the baseline serum iMg level was not significantly different between tertiles.

Conclusions
Our analysis of a large cohort of patients with moderate-to-advanced CKD demonstrated that individuals with higher serum tMg concentrations, although still within the normal range, had a greater likelihood of MACE and mortality. However, serum iMg levels were not associated with these outcomes.
The local topology of dynamical network models for biology
Authors: Borriello Enrico 
Published: February 2024

Abstract
The search for motifs—recurrent patterns in network topology—has led to the identification of universal classes of complex systems across diverse fields and has served as a quantitative tool to reveal common properties in both evolved and designed networks. In this study, we investigate the presence and significance of network superfamilies—previously identified through the census of triadic motifs—in the largest data set of dynamic, biological network models. We present triad significance profiles of 71 existing biological network models, all experimentally inspired. The generated data are treated in an unbiased manner and consistently clustered into two classes using several unsupervised techniques. The more prevalent class does exhibit a strong correlation with the superfamily of sensory transmission networks, which are characterized by the feedforward loop motif commonly found in signal-processing systems. Surprisingly, the remaining class shows a better correlation with the superfamily of word-adjacency networks. To better understand this, the results are analysed for varying network size thresholds, and their connection to the effect of model building activity is examined. It is highlighted that the more the model focuses on smaller portions of the regulatory network, as a result of the coarse-graining of the boundary dynamics and the peripheral regions of the network, the more its topology starts resembling that of ‘sentences’ of word-adjacency networks.
Meeting the Needs of Students and Families: Adapting Service Delivery of Special Education Social Workers during a Pandemic
Authors: Knox Kimberly M 
Published: February 2024

Abstract
During the COVID-19 pandemic, special education social workers (SESWs) had to adapt to meet the needs of families and students rapidly. Traditionally SESWs delivered services through in-person modalities in schools. However, as the world changed overnight to comply with stay-at-home orders, these social workers found themselves in a unique position to utilize social work skills to mitigate the challenges of remote schooling, the mental health needs of students, and technology scarcity all while maintaining their dedication of service to students, families, and schools. The experience of SESWs as they navigated through the changes and challenges the pandemic caused was explored through in-depth interviews. Via thematic analysis, themes emerged regarding being unprepared, bridging communication (a high priority for mental health services), finding the missing, privacy, eagerness for in-person services, and technology scarcity. The study highlights SESWs’ voices, experiences, and commitment to service.
Systematic Review of Interventions with Some School Involvement for School Refusal in High School–Age Adolescents
Authors: Fernandes Claudi-Santi F , Kannoth Sneha , Pendergrass Boomer Tyra M , Hieftje Kimberly D , Fiellin Lynn E 
Published: February 2024

Abstract
Chronic absenteeism is a public health concern. School refusal due to emotional distress is one reason students exhibit chronic absenteeism. The objective of this systematic review was to determine potential aspects of interventions, in school settings or involving a school-based component, that are successful in addressing school refusal among high school–age adolescents. After duplicated records were excluded, 1,864 studies were identified from searches. The abstracts and full text articles were independently reviewed and received two votes from each of the five reviewers using the eligibility criteria. Two reviewers independently evaluated the remaining articles and met to discuss findings with a third reviewer. The 10 articles included eight studies that noted techniques in cognitive–behavioral therapy (CBT) as promising and two studies that considered CBT as effective as other approaches. The study design for three studies were randomized controlled trials. The remaining seven studies were quasiexperimental. Only three of the 10 studies received a high rating using the Quality Appraisal Tool. There was a limited number of quality studies that used rigorous scientific methods and variation in how each study engaged schools. Further exploration and development of interventions with an integral school-based component are needed.