bluuebunny/crossref_metadata_2025_split huggingface dataset:
Kidney function before and after acute kidney injury: a nationwide population-based cohort study
Authors: Jensen Simon Kok , Heide-Jørgensen Uffe , Vestergaard Søren Viborg , Gammelager Henrik , Birn Henrik , Nitsch Dorothea , Christiansen Christian Fynbo 
Published: November 2022

ABSTRACTBackgroundAcute kidney injury (AKI) is a common and serious condition defined by a rapid decline in kidney function. Data on changes in long-term kidney function following AKI are sparse and conflicting. Therefore, we examined the changes in estimated glomerular filtration rate (eGFR) from before to after AKI in a nationwide population-based setting.MethodsUsing Danish laboratory databases, we identified individuals with first-time AKI defined by an acute increase in plasma creatinine (pCr) during 2010 to 2017. Individuals with three or more outpatient pCr measurements before and after AKI were included and cohorts were stratified by baseline eGFR (≥/&lt;60 mL/min/1.73 m2). Linear regression models were used to estimate and compare individual eGFR slopes and eGFR levels before and after AKI.ResultsAmong individuals with a baseline eGFR ≥60 mL/min/1.73 m2 (n = 64 805), first-time AKI was associated with a median difference in eGFR level of −5.6 mL/min/1.73 m2 [interquartile range (IQR) −16.1 to 1.8] and a median difference in eGFR slope of −0.4 mL/min/1.73 m2/year (IQR −5.5 to 4.4). Correspondingly, among individuals with a baseline eGFR &lt;60 mL/min/1.73 m2 (n = 33 267), first-time AKI was associated with a median difference in eGFR level of −2.2 mL/min/1.73 m2 (IQR −9.2 to 4.3) and a median difference in eGFR slope of 1.5 mL/min/1.73 m2/year (IQR −2.9 to 6.5).ConclusionAmong individuals with first-time AKI surviving to have repeated outpatient pCr measurements, AKI was associated with changes in eGFR level and eGFR slope for which the magnitude and direction depended on baseline eGFR.
Bacterial communities vary across populations and tissue type in red mangroves (Rhizophora mangle, Rhizophoraceae) along an expanding front
Authors: Scherer Brendan P , Mason Olivia U , Mast Austin R 
Published: November 2022

Abstract
Plant-associated microbial communities may be important sources of functional diversity and genetic variation that influence host evolution. Bacteria provide benefits for their hosts, yet in most plant systems we know little about their taxonomic composition or variation across tissues and host range. Red Mangrove (Rhizophora mangle L.) is a vital coastal plant species that is currently expanding poleward and with it, perhaps, its microbiome. We explored variability in bacterial communities across tissues, individuals, and populations. We collected samples from six sample types from 5 to 10 individuals at each of three populations and used 16S rRNA gene (iTag) sequencing to describe their bacterial communities. Core community members and dominant bacterial classes were determined for each sample type. Pairwise PERMANOVA of Bray–Curtis dissimilarity and Indicator Species Analysis revealed significant differences in bacterial communities between sample types and populations. We described the previously unexplored microbiome of the reproductive tissues of R. mangle. Populations and most sample types were associated with distinct communities. Bacterial communities associated with R. mangle are influenced by host geography and sample type. Our study provides a foundation for future work exploring the functional roles of these microbes and their relevance to biogeochemical cycling.
Improved microbial genomes and gene catalog of the chicken gut from metagenomic sequencing of high-fidelity long reads
Authors: Zhang Yan , Jiang Fan , Yang Boyuan , Wang Sen , Wang Hengchao , Wang Anqi , Xu Dong , Fan Wei 
Published: November 2022

Abstract

Background
Due to the importance of chicken production and the remarkable influence of the gut microbiota on host health and growth, tens of thousands of metagenome-assembled genomes (MAGs) have been constructed for the chicken gut microbiome. However, due to the limitations of short-read sequencing and assembly technologies, most of these MAGs are far from complete, are of lower quality, and include contaminant reads.

Results
We generated 332 Gb of high-fidelity (HiFi) long reads from the 5 chicken intestinal compartments and assembled 461 and 337 microbial genomes, of which 53% and 55% are circular, at the species and strain levels, respectively. For the assembled microbial genomes, approximately 95% were regarded as complete according to the “RNA complete” criteria, which requires at least 1 full-length ribosomal RNA (rRNA) operon encoding all 3 types of rRNA (16S, 23S, and 5S) and at least 18 copies of full-length transfer RNA genes. In comparison with the short-read-derived chicken MAGs, 384 (83% of 461) and 89 (26% of 337) strain-level and species-level genomes in this study are novel, with no matches to previously reported sequences. At the gene level, one-third of the 2.5 million genes in the HiFi-derived gene catalog are novel and cannot be matched to the short-read-derived gene catalog. Moreover, the HiFi-derived genomes have much higher continuity and completeness, as well as lower contamination; the HiFi-derived gene catalog has a much higher ratio of complete gene structures. The dominant phylum in our HiFi-assembled genomes was Firmicutes (82.5%), and the foregut was highly enriched in 5 genera: Ligilactobacillus, Limosilactobacillus, Lactobacillus, Weissella, and Enterococcus, all of which belong to the order Lactobacillales. Using GTDB-Tk, all 337 species-level genomes were successfully classified at the order level; however, 2, 35, and 189 genomes could not be classified into any known family, genus, and species, respectively. Among these incompletely classified genomes, 9 and 49 may belong to novel genera and species, respectively, because their 16S rRNA genes have identities lower than 95% and 97% to any known 16S rRNA genes.

Conclusions
HiFi sequencing not only produced metagenome assemblies and gene structures with markedly improved quality but also recovered a substantial portion of novel genomes and genes that were missed in previous short-read-based metagenome studies. The novel genomes and species obtained in this study will facilitate gut microbiome and host–microbiota interaction studies, thereby contributing to the sustainable development of poultry resources.
Utilizing an artificial intelligence system to build the digital structural proteome of reef-building corals
Authors: Zhu Yunchi , Liao Xin , Han Tingyu , Chen J-Y , He Chunpeng , Lu Zuhong 
Published: November 2022

Abstract

Background
Reef-building corals play an important role in the marine ecosystem, and analyzing their proteomes from a structural perspective will exert positive effects on exploring their biology. Here we integrated mass spectrometry with newly published ColabFold to obtain digital structural proteomes of dominant reef-building corals.

Results
Of the 8,382 homologous proteins in Acropora muricata, Montipora foliosa, and Pocillopora verrucosa identified, 8,166 received predicted structures after about 4,060 GPU hours of computation. The resulting dataset covers 83.6% of residues with a confident prediction, while 25.9% have very high confidence.

Conclusions
Our work provides insight-worthy predictions for coral research, confirms the reliability of ColabFold in practice, and is expected to be a reference case in the impending high-throughput era of structural proteomics.
How to do (or not to do)… health resource allocations using constrained mathematical optimization
Authors: Stuart Robyn M , Fraser-Hurt Nicole , Shubber Zara , Vu Lung , Cheik Nejma , Kerr Cliff C , Wilson David P 
Published: November 2022

Abstract
Despite the push towards evidence-based health policy, decisions about how to allocate health resources are all too often made on the basis of political forces or a continuation of the status quo. This results in wastage in health systems and loss of potential population health. However, if health systems are to serve people best, then they must operate efficiently and equitably, and appropriate valuation methods are needed to determine how to do this. With the advances in computing power over the past few decades, advanced mathematical optimization algorithms can now be run on personal computers and can be used to provide comprehensive, evidence-based recommendations for policymakers on how to prioritize health spending considering policy objectives, interactions of interventions, real-world system constraints and budget envelopes. Such methods provide an invaluable complement to traditional or extended cost-effectiveness analyses or league tables. In this paper, we describe how such methods work, how policymakers and programme managers can access them and implement their recommendations and how they have changed health spending in the world to date.
Exploring how social inequalities in health have influenced the design of Mali’s SARS-CoV-2 testing policy: a qualitative study
Authors: Boivin Pauline , Gautier Lara , Coulibaly Abdourahmane , Zinszer Kate , Ridde Valéry 
Published: November 2022

AbstractIn the fight against infectious diseases, social inequalities in health (SIH) are generally forgotten. Mali, already weakened by security and political unrest, has not been spared by the COVID-19 pandemic. Although the country was unprepared, the authorities were quick to implement public health measures, including a SARS-CoV-2 testing programme. This study aimed to understand if and how social inequalities in health were addressed in the design and planning for the national COVID-19 testing policy in Mali. A qualitative survey was conducted between March and April 2021 in Bamako, the capital of Mali. A total of 26 interviews were conducted with key government actors and national and international partners. A document review of national reports and policy documents complemented this data collection. The results demonstrated that the concept of SIH was unclear to the participants and was not a priority. The authorities focused on a symptom-based testing strategy that was publicly available. Participants also mentioned some efforts to reduce inequalities across geographical territories. The reflection and consideration of SIH within COVID-19 interventions was difficult given the governance approach to response efforts. The urgency of the situation, the perceptions of COVID-19 and the country’s pre-existing fragility were factors limiting this reflection. Over time, little action has been taken to adapt to the specific needs of certain groups in the Malian population. This study (re)highlights the need to consider SIH in the planning stages of a public health intervention, to adapt its implementation and to limit the negative impact on SIH.
The role of the family in health promotion: a scoping review of models and mechanisms
Authors: Ho Yi-Ching Lynn , Mahirah Dhiya , Ho Clement Zhong-Hao , Thumboo Julian 
Published: November 2022

Summary
The family is an important contributor to the cultural conditions that support health. Current challenges in family health promotion interventions include programme design that is not always guided by theory and change mechanisms. Multifaceted programmes also make it hard to examine what works for whom, given different family roles and the range of lifestyle behaviour and mechanisms examined within diverse conceptual frameworks and cultures. We performed a scoping review on the heterogeneous literature to map and categorize the models and mechanisms by which a family may promote health behaviours among its members. We searched five electronic databases and grey literature up to 2020. Publications were included if they examined health-promoting behaviours, influences at the family level, and outlined the behavioural mechanisms involved. Two hundred and forty studies were identified. Ecological systems theory, social cognitive theory, family systems theory and the theory of planned behaviour were the frameworks most widely used in explaining either study context and/or mechanism. The most frequently studied family mechanisms involved aspects of family support, supervision and modelling, while some studies also included individual-level mechanisms. Majority of the studies investigated parental influence on the child, while few studies assessed the elderly family member as a recipient or actor of the influences. Studies on African, Asian and Middle Eastern populations were also in the minority, highlighting room for further research. Improving the understanding of context and behavioural mechanisms for family health promotion will aid the development of public health policy and chronic disease prevention programmes, complementing efforts targeted at individuals.
Predicting non-response in patient-reported outcome measures: results from the Swiss quality assurance programme in cardiac inpatient rehabilitation
Authors: KÖhn Stefanie , Schlumbohm Anna , Marquardt Manuela , Scheel-Sailer Anke , Tobler Stephan , Vontobel Jan , Menzi Luise 
Published: November 2022

Abstract

Background
Quality assurance programmes measure and compare certain health outcomes to ensure high-quality care in the health-care sector. The outcome of health-related quality of life is typically measured by patient-reported outcome measures (PROMs). However, certain patient groups are less likely to respond to PROMs than others. This non-response bias can potentially distort results in quality assurance programmes.

Objective
Our study aims to identify relevant predictors of non-response during assessment using the PROM MacNew Heart Disease questionnaire in cardiac rehabilitation.

Methods
This is a cross-sectional study based on data from the Swiss external quality assurance programme. All patients aged 18 years or older who underwent inpatient cardiac rehabilitation in 16 Swiss rehabilitation clinics between 2016 and 2019 were included. Patients’ socio-demographic and basic medical data were analysed descriptively by comparing two groups: non-responders and responders. We used a random intercept logistic regression model to estimate the associations of patient characteristics and clinic differences with non-response.

Results
Of 24 572 patients, there were 33.3% non-responders and 66.7% responders. The mean age was 70 years, and 31.0% were women. The regression model showed that being female was associated with non-response [odds ratio (OR) 1.22; 95% confidence interval (CI) 1.14–1.30], as well as having no supplementary health insurance (OR 1.49; 95% CI 1.39–1.59). Each additional year of age increased the chance of non-response by an OR of 1.02 (95% CI 1.02–1.02). Not being a first language speaker of German, French or Italian increased the chance of non-response by an OR of 6.94 (95% CI 6.03–7.99). Patients admitted directly from acute care had a higher chance of non-response (OR 1.23; 95% CI 1.10–1.38), as well as patients being discharged back into acute care after rehabilitation (OR 3.89; 95% CI 3.00–5.04). Each point on the cumulative illness rating scale total score increased the chance of non-response by an OR of 1.05 (95% CI 1.04–1.05). Certain diagnoses also influenced the chance of non-response. Even after adjustment for known confounders, response rates differed substantially between the 16 clinics.

Conclusion
We have found significant non-response bias among certain patient groups, as well as across different treatment facilities. Measures to improve response rates among patients with known barriers to participation, as well as among different treatment facilities, need to be considered, particularly when PROMs are being used for comparison of providers in quality assurance programmes or outcome evaluation.
Monkeypox Emergence and the Eradication of Smallpox: An Historical Review
Authors: Shulman Stanford T 
Published: November 2022

AbstractBackgroundHuman monkeypox infection was first identified in 1970 in African. Small rodents were the natural reservoir of this orthopoxvirus, with humans and primates as incidental hosts. Smallpox vaccination induces cross protection against monkeypox. In Africa monkeypox overlapped with the Global Smallpox Eradication Program (GSEP) six decades ago. The 2022 human monkeypox epidemic prompted literature review re potential impact of monkeypox upon GSEP efforts.MethodsLiterature review from 1960 to present related to GSEP launched in 1969 with particular focus on monkeypox epidemiology during planning of GSEP in the 1960’s through 1989 including surveillance years later.ResultsEstablishing the lack of a non-human reservoir of smallpox was essential to assessing the GSEP because of the similarity of the two orthopoxviruses. It was found that a non-human smallpox reservoir was highly remote. Human monkeypox did not occur in smallpox-vaccinated humans and was limited to non-vaccinees. Surveillance in Democratic Republic of the Congo (DRC) until 1989 found monkeypox was very unlikely to persist in humans and unlikely to become a major public health problem. From 2005–2007, decades after cessation of smallpox vaccination, monkeypox surveillance in DRC revealed 20-fold higher incidence of human monkeypox correlated with much lower rates of prior smallpox vaccination.ConclusionsHuman monkeypox rates in DRC were 20-fold higher decades after cessation of smallpox vaccination compared to when smallpox vaccination was still used. The resultant decreased cross-protection against monkeypox contributed to the 2022 multinational outbreak of human monkeypox.
First Light And Reionization Epoch Simulations (FLARES) VII: The star formation and metal enrichment histories of galaxies in the early Universe
Authors: Wilkins Stephen M , Vijayan Aswin P , Lovell Christopher C , Roper William J , Zackrisson Erik , Irodotou Dimitrios , Seeyave Louise T C , Kuusisto Jussi K , Thomas Peter A , Caruana Joseph , Conselice Christopher J 
Published: November 2022

ABSTRACT
The star formation and metal enrichment histories of galaxies – at any epoch – constitute one of the key properties of galaxies, and their measurement is a core aim of observational extragalactic astronomy. The lack of deep rest-frame optical coverage at high redshift has made robust constraints elusive, but this is now changing thanks to JWST. In preparation for the constraints provided by JWST, we explore the star formation and metal enrichment histories of galaxies at z = 5–13 using the First Light And Reionization Epoch Simulations (flares) suite. Built on the EAGLE model, the unique strategy of flares allows us to simulate galaxies with a wide range of stellar masses (and luminosities) and environments. While we predict significant redshift evolution of average ages and specific star formation rates, our core result is mostly a flat relationship of age and specific star formation rate with stellar mass. We also find that galaxies in this epoch predominantly have strongly rising star formation histories, albeit with the normalization dropping with redshift and stellar mass. In terms of chemical enrichment, we predict a strong stellar mass–metallicity relation present at z = 10 and beyond alongside significant α-enhancement. Finally, we find no large-scale environmental dependence of the relationship between age, specific star formation rate, or metallicity with stellar mass.
Morphological signatures of mergers in the TNG50 simulation and the Kilo-Degree Survey: the merger fraction from dwarfs to Milky Way-like galaxies
Authors: Guzmán-Ortega Alejandro , Rodriguez-Gomez Vicente , Snyder Gregory F , Chamberlain Katie , Hernquist Lars 
Published: November 2022

ABSTRACT
Using the TNG50 cosmological simulation and observations from the Kilo-Degree Survey (KiDS), we investigate the connection between galaxy mergers and optical morphology in the local Universe over a wide range of galaxy stellar masses (8.5 ≤ log (M*/M⊙) ≤ 11). To this end, we have generated over 16 000 synthetic images of TNG50 galaxies designed to match KiDS observations, including the effects of dust attenuation and scattering, and used the statmorph code to measure various image-based morphological diagnostics in the r-band for both data sets. Such measurements include the Gini–M20 and concentration–asymmetry–smoothness statistics. Overall, we find good agreement between the optical morphologies of TNG50 and KiDS galaxies, although the former are slightly more concentrated and asymmetric than their observational counterparts. Afterwards, we trained a random forest classifier to identify merging galaxies in the simulation (including major and minor mergers) using the morphological diagnostics as the model features, along with merger statistics from the merger trees as the ground truth. We find that the asymmetry statistic exhibits the highest feature importance of all the morphological parameters considered. Thus, the performance of our algorithm is comparable to that of the more traditional method of selecting highly asymmetric galaxies. Finally, using our trained model, we estimate the galaxy merger fraction in both our synthetic and observational galaxy samples, finding in both cases that the galaxy merger fraction increases steadily as a function of stellar mass.
SuperNatural 3.0—a database of natural products and natural product-based derivatives
Authors: Gallo Kathleen , Kemmler Emanuel , Goede Andrean , Becker Finnja , Dunkel Mathias , Preissner Robert , Banerjee Priyanka 
Published: November 2022

AbstractNatural products (NPs) are single chemical compounds, substances or mixtures produced by a living organism - found in nature. Evolutionarily, NPs have been used as healing agents since thousands of years and still today continue to be the most important source of new potential therapeutic preparations. Natural products have played a key role in modern drug discovery for several diseases. Furthermore, following consumers’ increasing demand for natural food ingredients, many efforts have been made to discover natural low-calorie sweeteners in recent years. SuperNatural 3.0 is a freely available database of natural products and derivatives. The updated version contains 449 058 natural compounds along with their structural and physicochemical information. Additionally, information on pathways, mechanism of action, toxicity, vendor information if available, drug-like chemical space prediction for several diseases as antiviral, antibacterial, antimalarial, anticancer, and target specific cells like the central nervous system (CNS) are also provided for the natural compounds. The updated version of the database also provides a valuable pool of natural compounds in which potential highly sweet compounds are expected to be found. The possible taste profile of the natural compounds was predicted using our published VirtualTaste models. The SuperNatural 3.0 database is freely available via http://bioinf-applied.charite.de/supernatural_3, without any login or registration.