bluuebunny/crossref_metadata_2025 huggingface dataset:
Simulation of lahar flow potensial hazards in seulawah agam volcano eruption-aceh
Authors: Masyithah  , Ismail N , Nizamuddin
Published: July 2024

Seulawah Agam volcano is an active stratovolcanic volcano located on Sumatra Island. During the decade following the phreatic eruption in 1839 up to now, there have only been a few small-scale increases in activity. The hazards associated with volcanic eruptions can be divided into primary hazards and secondary hazards. One type of significant secondary hazard is lahar flow. The consequences of this volcanic eruption must be overcome because the impact is the same as the main hazard, especially if efforts to overcome it are not taken seriously. Therefore, simulations are needed to understand the lahar flow patterns that can occur due to the eruption of the Seulawah Agam volcano. This lahar flow simulation is based on Digital Elevation Model (DEM) data, namely DEMNAS, and uses the LAHARZ application, which is based on Geographic Information Systems (GIS). The LAHARZ software is designed to calculate potential hazard zones exposed to lahar flows based on volume parameters. Lahar flow simulations were made in hydrological channels with several lahar volume scenarios, such as 1 x 105 m3, 1 x 106 m3, and 5 x 106 m3. The lahar volume estimate used is based on information from historical data on volcanic eruptions whose characteristics are almost the same as the Seulawah Agam volcano. This volume scenario shows differences in the extent of lahar flows and the size of the affected area. The results of this lahar flow simulation can be one of the first steps in efforts to mitigate the hazards of volcanic eruptions in the future.
Experimental study of calcium carbonate solution saturation in the separation process of palm kernel-shell mixtures using water clay bath systems
Authors: Syarifuddin S , Husin H , Mahidin M , Jakfar J , Nurhazanah N , Nasution F , Nasri F R , Ramadhan H D
Published: July 2024

Continual use of CaCO3in the separation of the palm kernel-shell mixture causes CaCO3solution saturation. In this study, we aimed to evaluate the causes of CaCO3solution saturation during the separation process of palm kernel-shell mixtures. The process was carried out in the laboratory clay bath system using several factors in the separation process, including calcium carbonate to water ratios (1:2 and 1:3), palm kernel-shell mixture feed rates (2.5, 3.0, and 3.5 kg/batch), and times (1, 2, 3, 4, and 5 h) with density, pH, and oil content as the quantitative control. The results show that the density and pH of the separating solution dropped per unit length of processing, with the lowest values being around 1.0916 g/ml and 6.65 (CaCO3to H2O ratios of 1:3; feed rates 3.0 kg/batch; and times 5 h), respectively. In addition, the oil content of the separating solution was raised from 0.145 mg/L to 571.87 mg/L. Owing to the results, the dissolved oil in the solution was discovered as the cause of the saturation of the separating solution (decanting agent) during the process, corresponding to the inefficient separation of palm kernels and shells.
Efficient hygro-thermal and ammonia control in day-old chick brooding box using internet of things and Tsukamoto Fuzzy controller
Authors: Adek R T , Ula M , Bustami B
Published: July 2024

Day-old chick brooding box systems play a pivotal role in optimizing chicken production by providing ideal environmental conditions. Controlling hygro-thermal parameters (temperature and relative humidity) and ammonia levels in poultry buildings is paramount. In this study, we introduce a novel approach where an Internet of Things (IoT) based prototype for day-old chick brooding box management is integrated with an Android application for real-time monitoring and control. The prototype incorporates an innovative hybrid control strategy, combining a Tsukamoto (TSUKAMOTO) fuzzy logic controller (FLC) with IoT. This approach is rigorously tested through experimental measures and studies over a 90-day period, encompassing both rainy and drought seasons. Comparative analysis reveals that the T-FLC controller outperforms conventional methods, exhibiting lower root mean square errors for temperature and relative humidity response (0.9°C, 1.35%) compared to the FLC (1.18°C, 1.89%) and On/Off controller (2.08°C, 3.07%). Importantly, all controllers maintain ammonia concentrations below 4 ppm. Furthermore, the T-FLC system demonstrates superior efficiency, achieving a daily weight gain rate of 95%, surpassing the FLC (89%) and On/Off controller (81%). Additionally, the T-FLC controller significantly reduces energy consumption, saving up to 40% compared to the On/Off controller and 16% compared to the fuzzy controller. These findings underscore the exceptional efficiency and effectiveness of the proposed control strategy for day-old chick brooding box applications, promising enhanced poultry production and sustainability.
Elemental analysis of “kampong” chicken egg shell content using a Nd-YAG laser induced breakdown spectroscopy
Authors: Putri A , Mitaphonna R , Rajibussalim  , Lahna K , Idris N
Published: July 2024

Distinguishing between eggs laid by chickens fed organic versus chemical feed poses a formidable challenge, particularly when relying on eggshell characteristics alone. As such, this investigation was undertaken to conduct a qualitative exploration of the eggshell composition in free-range chickens, employing laser induced breakdown spectroscopy (LIBS) to discern varying feed treatments within the samples. To initiate the formation of micro-plasma, a Nd:YAG LIBS system has been utilized as the excitation source. The eggshells used in the study were sourced from seven distinct chicken groups subjected to diverse feeding protocols, including 100% industrial feed, 100% village feed, and its combination, and also along with eggshells from purebred chickens purchased from traditional markets. Based on the spectroscopic analysis, the seven samples utilized in this study exhibit a uniform chemical composition, encompassing both organic and inorganic elements, specifically C, O, H, Ca, Mg, Fe, Al, K, Si, and S.
The impact of corrosion due to salinity levels in the eastern zone of krueng aceh on the service life of steel frame building structural elements
Authors: Farhan R. , Bermansyah S. , Fikri R. , Hayati Y.
Published: July 2024

The use of profile steel as the main element in construction has gained significant popularity due to its mechanical strength and ease of workability. Corrosion is a problem that occurs within steel as a result of the chemical interaction between the steel and its surrounding environment. The purpose of this research is to assess the impact of corrosion rate on the service life of steel frame structures in the East Zone of Krueng Aceh based on varying levels of salinity. This study employs direct observation and an experimental method that carry out testing on-site for 30 days on test objects/items. The test specimens consist of steel plates measuring 50mm x 25mm x 5mm with BJ45 quality, which were cut and buried in soil excavated to a depth of approximately 1 to 2 meters for one month while submerged. Subsequently, calculations were made using the Weight Loss Method to obtain the corrosion rate value.The results obtained in Zone II, which has the highest salinity level of 6788 ppm, yielded a corrosion rate value of 0.145 mm/year. In this study, the structural element under consideration is the column. Remaining service life analysis is based on the reduction in the cross-sectional area of the column profile after corrosion, thus assessing the decrease in its strength while referring back to the requirements outlined in SNI 1729:2020. The remaining service life of the steel frame structure in Zone II after corrosion is 21 years. For the test specimens placed in Zone IV, which has the lowest salinity level of 941 ppm.
Robust high-Q quasi-BICs in double-layer high-contrast metagrating with temperature self-compensation for refractive index sensing
Authors: Sun Jiaxi , Hu Jinhua , Li Lei , Zhao Jijun
Published: July 2024

We propose a double-layer high-contrast metagrating structure with robust high-quality (Q) and temperature self-compensation for four-band refractive index sensing. The structure supports four-band symmetry-protected bound states in the continuum (SP-BICs) that transform into quasi-BICs as a result of structural symmetry breaking. However, the Q-factor of these quasi-BICs are limited by perturbation parameters, hampering practical fabrication. Interestingly, tuning the cavity length, we implement four-band Fabry–Pérot bound states in the continuum (FP-BICs) to transform the resonance mode back into high-Q quasi-BICs even at large perturbations. This approach is conducive to improving robustness and modulation freedom of Q-factors. In addition, we achieve temperature self-compensation by using the double-layer high-contrast metagrating consists of two materials with opposite thermo-optic (TO) dispersions. The simulation results indicate that the largest refractive index sensitivity is 470.9 nm RIU−1, its figure of merit is 427 818.2, and its Q-factor up to 9.3 × 105. The proposed double-layer high-contrast metagrating has potential application prospects for multiplex and high-performance sensing.
rAbDesFlow: a novel workflow for computational recombinant antibody design for healthcare engineering
Authors: Krishnan Sowmya Ramaswamy , Sharma Divya , Nazeer Yasin , Bose Mayilvahanan , Rajkumar Thangarajan , Jayaraman Guhan , Madaboosi Narayanan , Gromiha M Michael
Published: July 2024

Recombinant antibodies (rAbs) have emerged as a promising solution to tackle antigen specificity, enhancement of immunogenic potential and versatile functionalization to treat human diseases. The development of single chain variable fragments has helped accelerate treatment in cancers and viral infections, due to their favorable pharmacokinetics and human compatibility. However, designing rAbs is traditionally viewed as a genetic engineering problem, with phage display and cell free systems playing a major role in sequence selection for gene synthesis. The process of antibody engineering involves complex and time-consuming laboratory techniques, which demand substantial resources and expertise. The success rate of obtaining desired antibody candidates through experimental approaches can be modest, necessitating iterative cycles of selection and optimization. With ongoing advancements in technology, in silico design of diverse antibody libraries, screening and identification of potential candidates for in vitro validation can be accelerated. To meet this need, we have developed rAbDesFlow, a unified computational workflow for recombinant antibody engineering with open-source programs and tools for ease of implementation. The workflow encompasses five computational modules to perform antigen selection, antibody library generation, antigen and antibody structure modeling, antigen–antibody interaction modeling, structure analysis, and consensus ranking of potential antibody sequences for synthesis and experimental validation. The proposed workflow has been demonstrated through design of rAbs for the ovarian cancer antigen Mucin-16 (CA-125). This approach can serve as a blueprint for designing similar engineered molecules targeting other biomarkers, allowing for a simplified adaptation to different cancer types or disease-specific antigens.
Exposure to metal mixtures and telomere length in Bangladeshi children
Authors: Farzan Shohreh F , Niu Zhongzheng , Guo Fangqi , Shahriar Mohammad , Kibriya Muhammad G , Jasmine Farzana , Sarwar Golam , Jackson Brian P , Ahsan Habibul , Argos Maria
Published: July 2024

Telomere length is associated with chronic diseases and, in younger populations, may represent a biomarker of disease susceptibility. As growing evidence suggests that environmental factors, including metals, may impact telomere length. We investigated the association between 17 metals measured in toenail samples and leukocyte relative telomere length (RTL), among 472 5- to 7-year-old children enrolled in the Bangladesh Environmental Research in Children’s Health (BiRCH) cohortIn single-exposure linear regression models, a doubling of arsenic (As) and mercury (Hg) (μg/g) were associated with a −0.21 (95% CI, −0.032 to −0.010; P = .0005) and −0.017 (95% CI, −0.029 to −0.004; P = .006) difference in RTL, respectively. In Bayesian Kernel Machine Regression (BKMR) mixture models, the overall metal mixture was inversely associated with RTL (P-for-trend < 0.001). Negative associations with RTL were observed with both log2-As and log2-Hg, while an inverted U-shaped association was observed for log2-zinc (Zn) with RTL. We found little evidence of interaction among metals. Sex-stratification identified stronger associations of the overall mixture and log2-As with RTL among females compared to males. Our study suggests that As and Hg may independently influence RTL in mid-childhood. Further studies are needed to investigate potential long-term impacts of metal-associated telomere shortening in childhood on health outcomes in adult life.
Evaluating recommendation-based dietary and physical activity strategies for prostate cancer prevention: a target trial emulation in the Health Professionals Follow-up Study
Authors: Guo Fuyu , McGee Emma E , Chiu Yu-Han , Giovannucci Edward , Mucci Lorelei A , Dickerman Barbra A
Published: July 2024

The 2018 World Cancer Research Fund/American Institute for Cancer Research recommends sustained strategies of physical activity and diet for cancer prevention, but evidence for long-term prostate cancer risk is limited. Using observational data from 27 859 men in the Health Professionals Follow-up Study, we emulated a target trial of recommendation-based physical activity and dietary strategies and 26-year risks of prostate cancer, adjusting for risk factors via the parametric g-formula. Compared with no intervention, limiting sugar-sweetened beverages showed a 0.4% (0.0%-0.9%) lower risk of lethal (metastatic or fatal) disease and 0.5% (0.1%-0.9%) lower risk of fatal disease. Restricting consumption of processed foods showed a 0.4% to 0.9% higher risk of all prostate cancer outcomes. Estimated risk differences for clinically significant disease were close to null for strategies involving fruits and nonstarchy vegetables, whole grains and legumes, red meat, and processed meat, as well as under a joint strategy of physical activity and diet. Compared with a “low-adherence” strategy, maintaining recommended physical activity levels showed a 0.4% (0.1%-0.8%) lower risk of lethal and 0.5% (0.2%-0.8%) lower risk of fatal disease. Adhering to specific components of current physical activity and dietary recommendations may help to prevent lethal and fatal prostate cancer over 26 years.
A simple Cox approach to estimating risk ratios without sharing individual-level data in multisite studies
Authors: Shu Di , Zou Guangyong , Hou Laura , Petrone Andrew B , Maro Judith C , Fireman Bruce H , Toh Sengwee , Connolly John G
Published: July 2024

Epidemiologic studies frequently use risk ratios to quantify associations between exposures and binary outcomes. When the data are physically stored at the sites of multiple data partners, it can be challenging to perform individual-level analysis if data cannot be pooled centrally due to privacy constraints. Existing methods either require multiple file transfers between each data partner and an analysis center (eg, distributed regression) or only provide approximate estimation of the risk ratio (eg, meta-analysis). Here we develop a practical method that requires a single transfer of 8 summary-level quantities from each data partner. Our approach leverages an existing risk-set method and software originally developed for Cox regression. Sharing only summary-level information, the proposed method provides risk ratio estimates and 95% CIs identical to those that would be provided—if individual-level data were pooled—by the modified Poisson regression. We justify the method theoretically, confirm its performance using simulated data, and implement it in a distributed analysis of COVID-19 data from the US Food and Drug Administration’s Sentinel System.

This article is part of a Special Collection on Pharmacoepidemiology.
A rapid literature review of the effect of alcohol marketing on people with, or at increased risk of, an alcohol problem
Authors: Murray Rachael L , Leonardi-Bee Jo , Barker Alexander , Brown Olivia , Langley Tessa
Published: July 2024

Aims

To explore the effect or potential effect of alcohol marketing in people with an alcohol use disorder, in recovery from an alcohol use disorder, and hazardous and harmful drinkers.

Methods

Relevant literature was identified by searching Medline (OVID), EMBASE (OVID), and PsycINFO (OVID) and relevant websites. Both quantitative and qualitative studies were eligible for inclusion. A narrative approach was used to synthesize the findings.

Results

The review included 10 studies. Two quantitative and three qualitative studies focused on participants recovering from an alcohol use disorder and five quantitative studies on those with hazardous or harmful consumption levels of alcohol. The effect of alcohol advertising on alcohol use was only assessed in one study, a small experimental study of young adult heavy drinkers, which found no significant association. Studies looking at other outcomes found that people with or at risk of alcohol problems were likely to notice alcohol advertisements and find them appealing, and that advertisements may have an effect on positive alcohol-related emotions and cognitions. Among people in recovery from an alcohol use disorder, findings suggested that there could be an effect on craving, and that alcohol marketing may be perceived to trigger a desire to drink.

Conclusions

Alcohol marketing is likely to have an effect on alcohol consumption in people with, or at increased risk of, an alcohol problem. Studies have also found that alcohol marketing is perceived to act as a trigger by people in recovery from alcohol problems.

A rapid review explored the effect of alcohol marketing in people with an alcohol use disorder, in recovery from an alcohol use disorder, and hazardous and harmful drinkers. The findings of the 10 included studies suggest that an effect of alcohol marketing in these populations is likely.
Characterizing efficient feature selection for single-cell expression analysis
Authors: Cho Juok , Baik Bukyung , Nguyen Hai C T , Park Daeui , Nam Dougu
Published: July 2024

Unsupervised feature selection is a critical step for efficient and accurate analysis of single-cell RNA-seq data. Previous benchmarks used two different criteria to compare feature selection methods: (i) proportion of ground-truth marker genes included in the selected features and (ii) accuracy of cell clustering using ground-truth cell types. Here, we systematically compare the performance of 11 feature selection methods for both criteria. We first demonstrate the discordance between these criteria and suggest using the latter. We then compare the distribution of selected genes in their means between feature selection methods. We show that lowly expressed genes exhibit seriously high coefficients of variation and are mostly excluded by high-performance methods. In particular, high-deviation- and high-expression-based methods outperform the widely used in Seurat package in clustering cells and data visualization. We further show they also enable a clear separation of the same cell type from different tissues as well as accurate estimation of cell trajectories.
Spatial proximity and gene function: a new dimension in prokaryotic gene association network analysis with 3D-GeneNet
Authors: Gao Yuan , Ma Bin , Xu Qianshuai , Peng Yuna , Gong Huimin , Guan Aohan , Hua Kexin , Langford Paul R , Jin Hui , Luo Rui
Published: July 2024

Understanding the biological functions and processes of genes, particularly those not yet characterized, is crucial for advancing molecular biology and identifying therapeutic targets. The hypothesis guiding this study is that the 3D proximity of genes correlates with their functional interactions and relevance in prokaryotes. We introduced 3D-GeneNet, an innovative software tool that utilizes high-throughput sequencing data from chromosome conformation capture techniques and integrates topological metrics to construct gene association networks. Through a series of comparative analyses focused on spatial versus linear distances, we explored various dimensions such as topological structure, functional enrichment levels, distribution patterns of linear distances among gene pairs, and the area under the receiver operating characteristic curve by utilizing model organism Escherichia coli K-12. Furthermore, 3D-GeneNet was shown to maintain good accuracy compared to multiple algorithms (neighbourhood, co-occurrence, coexpression, and fusion) across multiple bacteria, including E. coli, Brucella abortus, and Vibrio cholerae. In addition, the accuracy of 3D-GeneNet’s prediction of long-distance gene interactions was identified by bacterial two-hybrid assays on E. coli K-12 MG1655, where 3D-GeneNet not only increased the accuracy of linear genomic distance tripled but also achieved 60% accuracy by running alone. Finally, it can be concluded that the applicability of 3D-GeneNet will extend to various bacterial forms, including Gram-negative, Gram-positive, single-, and multi-chromosomal bacteria through Hi-C sequencing and analysis. Such findings highlight the broad applicability and significant promise of this method in the realm of gene association network. 3D-GeneNet is freely accessible at https://github.com/gaoyuanccc/3D-GeneNet.
GALEON: a comprehensive bioinformatic tool to analyse and visualize gene clusters in complete genomes
Authors: Pisarenco Vadim A , Vizueta Joel , Rozas Julio
Published: July 2024

Motivation

Gene clusters, defined as a set of genes encoding functionally related proteins, are abundant in eukaryotic genomes. Despite the increasing availability of chromosome-level genomes, the comprehensive analysis of gene family evolution remains largely unexplored, particularly for large and highly dynamic gene families or those including very recent family members. These challenges stem from limitations in genome assembly contiguity, particularly in repetitive regions such as large gene clusters. Recent advancements in sequencing technology, such as long reads and chromatin contact mapping, hold promise in addressing these challenges.

Results

To facilitate the identification, analysis, and visualization of physically clustered gene family members within chromosome-level genomes, we introduce GALEON, a user-friendly bioinformatic tool. GALEON identifies gene clusters by studying the spatial distribution of pairwise physical distances among gene family members along with the genome-wide gene density. The pipeline also enables the simultaneous analysis and comparison of two gene families and allows the exploration of the relationship between physical and evolutionary distances. This tool offers a novel approach for studying the origin and evolution of gene families.

Availability and implementation

GALEON is freely available from https://www.ub.edu/softevol/galeon and https://github.com/molevol-ub/galeon
scMaSigPro: differential expression analysis along single-cell trajectories
Authors: Srivastava Priyansh , Benegas Coll Marta , Götz Stefan , Nueda María José , Conesa Ana
Published: July 2024

Motivation

Understanding the dynamics of gene expression across different cellular states is crucial for discerning the mechanisms underneath cellular differentiation. Genes that exhibit variation in mean expression as a function of Pseudotime and between branching trajectories are expected to govern cell fate decisions. We introduce scMaSigPro, a method for the identification of differential gene expression patterns along Pseudotime and branching paths simultaneously.

Results

We assessed the performance of scMaSigPro using synthetic and public datasets. Our evaluation shows that scMaSigPro outperforms existing methods in controlling the False Positive Rate and is computationally efficient.

Availability and implementation

scMaSigPro is available as a free R package (version 4.0 or higher) under the GPL(≥2) license on GitHub at ‘github.com/BioBam/scMaSigPro’ and archived with version 0.03 on Zenodo at ‘zenodo.org/records/12568922’.
Testing independence for sparse longitudinal data
Authors: Zhu Changbo , Yao Junwen , Wang Jane-Ling
Published: July 2024

With the advance of science and technology, more and more data are collected in the form of functions. A fundamental question for a pair of random functions is to test whether they are independent. This problem becomes quite challenging when the random trajectories are sampled irregularly and sparsely for each subject. In other words, each random function is only sampled at a few time-points, and these time-points vary with subjects. Furthermore, the observed data may contain noise. To the best of our knowledge, there exists no consistent test in the literature to test the independence of sparsely observed functional data. We show in this work that testing pointwise independence simultaneously is feasible. The test statistics are constructed by integrating pointwise distance covariances (Székely et al., 2007) and are shown to converge, at a certain rate, to their corresponding population counterparts, which characterize the simultaneous pointwise independence of two random functions. The performance of the proposed methods is further verified by Monte Carlo simulations and analysis of real data.
Party Politics in Austria: From Proporz to Populism?
Authors: Roesel Felix
Published: July 2024

Party politics in Austria has two distinctive features: institutionalized power sharing between the two main parties, known as Proporz, and a longstanding tradition of far-right populism. I examine whether these two phenomena are connected: Does reduced political competition correlate with vote shares for the far right? The results do not support the hypothesis that populist parties are stronger in places with reduced political competition and with Proporz institutions. Instead, the results show that Austrian populism has very deep historical roots. Historical party preferences in the 1930s explain a substantial part of the variation in far-right populist vote shares across Austrian regions today. Populism may also have economic consequences. Descriptive evidence shows that economic growth was 2 percentage points lower in Austria when far-right populists were in the national government, whereas no partisan differences can be found for the two main parties.
In vitro accuracy of ultra-low dose cone-beam CT for detection of proximal caries
Authors: Taeby Aria , Seyyedi Seyyed Amir , Mostafavi Maryam
Published: July 2024

Objectives

This study aimed to assess the accuracy of ultra-low dose (ULD) cone-beam CT (CBCT) for detection of proximal caries.

Methods

This in vitro study evaluated 104 molar and premolar teeth. The teeth were mounted in dry skulls and underwent CBCT with 4 protocols of high-resolution (HR), normal (NORM), ULD-HR, and ULD-NORM; 78 CBCT images were scored by 3 observers for the presence and penetration depth of caries twice with a 2-week interval using a 5-point Likert scale. The teeth were then sectioned and observed under a stereomicroscope (gold standard). The 4 protocols were compared with each other and with the gold standard. The receiver operating characteristic curve was drawn, and the area under the curve (AUC) was calculated and compared by the Chi-square test (alpha = .05).

Results

The interobserver agreement ranged from 0.5233 to 0.6034 for ULD-NORM, 0.5380 to 0.6279 for NORM, 0.5856 to 0.6300 for ULD-HR, and 0.6614 to 0.7707 for HR images. The intra-observer agreement ranged from 0.6027 to 0.8812 for ULD-HR, 0.7083 to 0.7556 for HR, 0.6076 to 0.9452 for ULD-NORM, and 0.7012 to 0.9221 for NORM images. Comparison of AUC revealed no significant difference between NORM and ULD-NORM (P > .05), or HR and ULD-HR (P > .05). The highest AUC belonged to HR (0.8529) and the lowest to NORM (0.7774).

Conclusions

Considering the significant reduction in radiation dose in ULD CBCT and its acceptable diagnostic accuracy for detection of proximal caries, this protocol may be used for detection of proximal carious lesions and assessment of their depth.
Lumican promotes calcific aortic valve disease through H3 histone lactylation
Authors: Huang Yuming , Wang Chunli , Zhou Tingwen , Xie Fei , Liu Zongtao , Xu Haiying , Liu Ming , Wang Shunshun , Li Lanqing , Chi Qingjia , Shi Jiawei , Dong Nianguo , Xu Kang
Published: July 2024

Background and Aims

Valve interstitial cells (VICs) undergo a transition to intermediate state cells before ultimately transforming into the osteogenic cell population, which is a pivotal cellular process in calcific aortic valve disease (CAVD). Herein, this study successfully delineated the stages of VIC osteogenic transformation and elucidated a novel key regulatory role of lumican (LUM) in this process.

Methods

Single-cell RNA-sequencing (scRNA-seq) from nine human aortic valves was used to characterize the pathological switch process and identify key regulatory factors. The in vitro, ex vivo, in vivo, and double knockout mice were constructed to further unravel the calcification-promoting effect of LUM. Moreover, the multi-omic approaches were employed to analyse the molecular mechanism of LUM in CAVD.

Results

ScRNA-seq successfully delineated the process of VIC pathological transformation and highlighted the significance of LUM as a novel molecule in this process. The pro-calcification role of LUM is confirmed on the in vitro, ex vivo, in vivo level, and ApoE−/−//LUM−/− double knockout mice. The LUM induces osteogenesis in VICs via activation of inflammatory pathways and augmentation of cellular glycolysis, resulting in the accumulation of lactate. Subsequent investigation has unveiled a novel LUM driving histone modification, lactylation, which plays a role in facilitating valve calcification. More importantly, this study has identified two specific sites of histone lactylation, namely, H3K14la and H3K9la, which have been found to facilitate the process of calcification. The confirmation of these modification sites’ association with the expression of calcific genes Runx2 and BMP2 has been achieved through ChIP-PCR analysis.

Conclusions

The study presents novel findings, being the first to establish the involvement of lumican in mediating H3 histone lactylation, thus facilitating the development of aortic valve calcification. Consequently, lumican would be a promising therapeutic target for intervention in the treatment of CAVD.
Who cares? Elucidating parental care evolution in extant birds
Authors: Lavaniegos-Puebla Pablo , Rincón-Rubio Verónica A , Gonzalez-Voyer Alejandro
Published: July 2024

Extant birds stand out among vertebrates in the diversity of parental care types they present, spanning absence of care to uniparental care by either sex, biparental care, or even cooperative care. Despite years of research, key questions remain regarding parental care evolution in birds. Firstly, the parental care type in the most recent ancestor of extant birds is a matter of controversy, with proposed ancestral states including no care, uniparental male or female care, and biparental care. Another unsolved question is the direction, order, and frequency of transitions between parental care types. We address these key questions using a database of 5,438 bird species (~50% of extant diversity) and modern phylogenetic comparative methods controlling simultaneously for model and phylogenetic uncertainty as well as potential confounding effects of state-dependent diversification. Our results indicate that the most likely ancestral state for extant birds is male-only care, with a posterior probability of 0.8. Transition rates across parental care types were generally low and heterogeneous; loss of parental care virtually never occurs and transitions away from female-only or cooperative care most often lead to biparental care. Given the low transition rates, future research should analyze the factors favoring the maintenance of care types.
Total RNA analysis of the active microbiome on moving bed biofilm reactor carriers under incrementally increasing micropollutant concentrations
Authors: Martin Joseph Donald , Tisler Selina , Scheel Maria , Svendsen Sif , Anwar Muhammad Zohaib , Zervas Athanasios , Ekelund Flemming , Bester Kai , Hansen Lars Hestbjerg , Jacobsen Carsten Suhr , Ellegaard-Jensen Lea
Published: July 2024

Micropollutants are increasingly prevalent in the aquatic environment. A major part of these originates from wastewater treatment plants since traditional treatment technologies do not remove micropollutants sufficiently. Moving bed biofilm reactors (MBBRs), however, have been shown to aid in micropollutant removal when applied to conventional wastewater treatment as a polishing step. Here, we used Total RNA sequencing to investigate both the active microbial community and functional dynamics of MBBR biofilms when these were exposed to increasing micropollutant concentrations over time. Concurrently, we conducted batch culture experiments using biofilm carriers from the MBBRs to assess micropollutant degradation potential. Our study showed that biofilm eukaryotes, in particular protozoa, were negatively influenced by micropollutant exposure, in contrast to prokaryotes that increased in relative abundance. Further, we found several functional genes that were differentially expressed between the MBBR with added micropollutants and the control. These include genes involved in aromatic and xenobiotic compound degradation. Moreover, the biofilm carrier batch experiment showed vastly different alterations in benzotriazole and diclofenac degradation following the increased micropollutant concentrations in the MBBR. Ultimately, this study provides essential insights into the microbial community and functional dynamics of MBBRs and how an increased load of micropollutants influences these dynamics.
Global Change in a Material World
Authors: Burnett Nicholas P , Moore Talia Y
Published: July 2024

Synopsis

The biological structures that fill the environment around us are derived from materials produced by organisms. These biological materials are key to the mechanical function of organisms. The pathways and growth processes that produce biological materials can influence the mechanical properties of the materials, which can in turn shape the higher level function of the system into which the materials are incorporated. Characterizing a biological system requires thorough knowledge of the underlying materials, including their mechanical function, diversity, evolution, and sensitivity to the environment. Anthropogenic activity is driving rapid and widespread changes to the natural environment and global climate, which are influencing organismal growth and physiology in myriad ways. Here, we briefly introduce a collection of articles that focus on the intersection of anthropogenic activity and the mechanical function of biological materials, as part of the “Global Change in a Material World” bundle for Integrative and Comparative Biology. In addition, we provide an analysis of the current scientific literature in this field, highlighting an urgent need to better understand how changes to our world, driven by human activity, are influencing the fundamental architecture and mechanical performance of organisms across the globe.
Pulmonary artery catheter use and in-hospital outcomes in cardiac surgery: a systematic review and meta-analysis
Authors: Rong Lisa Q , Luhmann Grant , Di Franco Antonino , Dimagli Arnaldo , Perry Luke A , Martinez Andrew P , Demetres Michelle , Mazer C David , Bellomo Rinaldo , Gaudino Mario
Published: July 2024

OBJECTIVES

To determine the association of intraoperative pulmonary artery catheter (PAC) use with in-hospital outcomes in cardiac surgical patients.

METHODS

MEDLINE, Embase, and Cochrane Library (Wiley) databases were screened for studies that compared cardiac surgical patients receiving intraoperative PAC with controls and reporting in-hospital mortality. Secondary outcomes included intensive care unit length of stay, cost of hospitalization, fluid volume administered, intubation time, inotropes use, acute kidney injury (AKI), stroke, myocardial infarction (MI), and infections.

RESULTS

Seven studies (25 853 patients, 88.6% undergoing coronary artery bypass graft surgery) were included. In-hospital mortality was significantly increased with PAC use [odds ratio (OR) 1.57; 95% confidence interval (CI) 1.12–2.20, P = 0.04]; PAC use was also associated with greater intraoperative inotrope use (OR 2.61; 95% CI 1.54–4.41) and costs [standardized mean difference (SMD) = 0.20; 95% CI 0.16–0.23], longer intensive care unit stay (SMD = 0.29; 95% CI 0.25–0.33), and longer intubation time (SMD = 0.44; 95% CI 0.12–0.76).

CONCLUSIONS

PAC use is associated with significantly increased odds of in-hospital mortality, but the amount and quality of the available evidence is limited. Prospective randomized trials testing the effect of PAC on the outcomes of cardiac surgical patients are urgently needed.
The Geopolitics of Disinformation: Worldviews, Media Consumption and the Adoption of Global Strategic Disinformation Narratives
Authors: Madrid-Morales Dani , Wasserman Herman , Ahmed Saifuddin
Published: July 2024

Concerns over the existence of a global “information disorder” marked by the contamination of the public sphere with deception campaigns have grown in recent years. This “disorder” has domestic and international dimensions, with multiple state actors standing accused of malicious influence abroad. Previous research, focused on the Global North, has neglected the potential role of anti-colonial and anti-imperialist sentiments in shaping public opinion in the Global South, where problems with foreign influence operations have persisted for decades. Using survey data (N = 4,613) collected in Angola, Ethiopia, South Africa, and Zambia in late 2022, this paper addresses this knowledge gap by exploring the relationship between individuals’ worldviews and news consumption, and their support of strategic disinformation narratives favored by Russia and China, both of which have been active in trying to use the news media to influence public opinion. At a country level, we find that support for these narratives is most pronounced in Ethiopia and South Africa, while at an individual level, we find limited evidence that news consumption is connected to the adoption of these narratives. In discussing these findings, we argue that African public opinion is simultaneously shaped by global, geopolitical shifts and domestic, and local contestations.
What Makes Fact-Checking Effective? Exploratory Research into the Role of Linguistic Politeness
Authors: Lee Hogeun , Kim Hyun Suk
Published: July 2024

This study examined how the linguistic politeness of fact-checking messages affects audiences’ belief accuracy and message acceptance by shaping their perceived face threat and psychological reactance. In 2 experiments with national convenience samples of South Korean adults, we manipulated linguistic politeness by using either honorific or non-honorific sentence endings—a well-established marker of linguistic politeness in Korean—in fact-checking news articles correcting misinformation about COVID-19 (Study 1) and refugees (Study 2). Study 1 (N = 240) found that fact-checking articles using honorific sentence endings were perceived as less face-threatening than those presenting identical content with non-honorific endings, which in turn increased belief accuracy and the perceived persuasiveness of the articles. Study 2 (N = 296) replicated the findings of Study 1 and extended them by demonstrating: (1) the effect of using honorific (vs. non-honorific) sentence endings on recipients’ perceived face threat was not moderated by their conspiratorial predisposition or need for cognition; (2) the effects of perceived face threat were mediated by psychological reactance; and (3) the sequential mediation also produced attitudinal effects. The findings are discussed in light of their theoretical and practical implications for designing effective fact-checking messages to combat misinformation in non-Western languages.
Strategic Storytelling: Russian State-Backed Media Coverage of the Ukraine War
Authors: Bradshaw Samantha , Elswah Mona , Haque Monzima , Quelle Dorian
Published: July 2024

Strategic narratives help shape wars. In modern history, strategic narratives were used during the Cold War, the War in Afghanistan, and the Iraq War to justify military invasions and manipulate opponents. During the 2022 Russian invasion of Ukraine, Russia was accused of weaponizing its state-backed media outlets to promote a pro-Russian version of the war. Consequently, Russian state-backed media faced a series of new sanctions from Western governments and technology companies. While some studies have sought to identify disinformation about the war, less research has focused on understanding how these stories come together as narratives, particularly in non-English language contexts. Grounded in strategic narrative theory, we analyze Russian state-backed media coverage of the Ukraine war across 12 languages. Using topic modeling and narrative analysis, we find that Russian state-backed media focused primarily on promoting identity narratives, forming an image that Russia is powerful, Ukraine is evil, and the West is hypocritical. Russian strategic narratives both converged and diverged across languages and outlets in ways that met Russia’s desired image and objectives in each region. This paper allows us to better theorize the evolving and transformative role of strategic narrative in Russian state-backed news media during times of conflict.
Analyzing Misinformation Claims During the 2022 Brazilian General Election on WhatsApp, Twitter, and Kwai
Authors: Hale Scott A , Belisario Adriano , Mostafa Ahmed Nasser , Camargo Chico
Published: July 2024

This study analyzes misinformation claims sent to fact-checking organizations on WhatsApp during the 2022 Brazilian general election and compares them with content from Twitter and Kwai (a popular video-sharing application similar to TikTok). Given the democratic importance of accurate information during elections, multiple fact-checking organizations collaborated to collect and respond to misinformation via WhatsApp tiplines and power a fact-checking feature within a chatbot operated by Brazil’s election authority, the Tribunal Superior Eleitoral (TSE). We partnered with TSE and three fact-checking organizations and collected social media data to study how misinformation claims propagate across platforms. We observed little overlap between the users of different fact-checking tiplines and a high correlation between the number of users and the amount of unique content, suggesting that WhatsApp tiplines are far from reaching a saturation point. Similarly, we also found little overlap in content across platforms, indicating the need for further research with cross-platform approaches to identify misinformation dynamics.
A Comparison Theorem For The Pro-étale Fundamental Group
Authors: Yu Jiu-Kang , Zhang Lei
Published: July 2024

Let $X$ be a connected scheme locally of finite type over ${\mathbb{C}}$, and let $X^{\textrm{an}}$ be its associated analytic space. In this paper, we define a comparison map from the topological fundamental group of $X^{\textrm{an}}$ to the pro-étale fundamental group of $X$.
Combined Treatment of Severe Acute Respiratory Syndrome Coronavirus 2 Reduces Molnupiravir-Induced Mutagenicity and Prevents Selection for Nirmatrelvir/Ritonavir Resistance Mutations
Authors: Zhou Shuntai , Long Nathan , Rosenke Kyle , Jarvis Michael A , Feldmann Heinz , Swanstrom Ronald
Published: July 2024

We investigated the mutation profiles of severe acute respiratory syndrome coronavirus 2 in samples collected from a molnupiravir and nirmatrelvir/ritonavir combination therapy in macaques. We found that molnupiravir induced several nirmatrelvir resistance mutations at low abundance that were not further selected in combination therapy. Coadministration of nirmatrelvir/ritonavir lowered the magnitude of the mutagenetic effect of molnupiravir.
Severe West Nile Virus and Severe Acute Respiratory Syndrome Coronavirus 2 Infections in a Patient With Thymoma and Anti–Type I Interferon Antibodies
Authors: Barzaghi Federica , Visconti Camilla , Pipitone Giovanni Battista , Bondesan Simone , Molli Giulia , Giannelli Stefania , Sartirana Claudia , Lampasona Vito , Bazzigaluppi Elena , Brigatti Cristina , Gervais Adrian , Bastard Paul , Tassan Din Chiara , Molinari Chiara , Piemonti Lorenzo , Casanova Jean-Laurent , Carrera Paola , Casari Giorgio , Aiuti Alessandro
Published: July 2024

Main point

Patients with severe West Nile virus and SARS-CoV-2 infections deserve accurate diagnosis of underlying diseases, determining possible anti-interferon autoantibody production, since they must receive antiviral and immunological therapies to enhance antiviral response.

The current study aimed to investigate determinants of severity in a previously healthy patient who experienced 2 life-threatening infections, from West Nile Virus (WNV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV2). During coronavirus disease 2019 (COVID-19) hospitalization he was diagnosed with a thymoma, retrospectively identified as already present at the time of WNV infection. Heterozygosity for p.Pro554Ser in the TLR3 gene, which increases susceptibility to severe COVID-19, and homozygosity for CCR5 c.554_585del, associated with severe WNV infection, were found. Neutralizing anti-interferon (IFN)-α and anti-IFN-ω autoantibodies were detected, likely induced by the underlying thymoma and increasing susceptibility to both severe COVID-19 pneumonia and West Nile encephalitis.
Low rates of complications and β-lactam resistance in viridans group streptococci bloodstream infection among cancer patients receiving chemotherapy
Authors: Sheehy Joshua , Scott Ashleigh P , Henden Andrea S , Kennedy Glen , Redmond Andrew M , Stewart Adam G
Published: July 2024

Background

Viridans group streptococci (VGS) bloodstream infection (BSI) frequently occurs in cancer patients receiving chemotherapy, and is associated with infective endocarditis (IE) in up to 20% of cases in the general population.

Objectives

In cancer patients receiving chemotherapy with VGS BSI, we aimed to: (i) determine the incidence of infective complications including IE, (ii) assess the utility of echocardiography in this patient population, (iii) determine the duration and type of antimicrobial therapy received for monomicrobial infections, and (iv) determine the evolution of antimicrobial resistance.

Methods

VGS BSIs (excluding Streptococcus pneumoniae and Streptococcus pseudopneumoniae) in cancer patients receiving chemotherapy were identified from a statewide public pathology database between 2013 and 2022 at our tertiary centre. Medical records were accessed for clinical, microbiological and radiological data.

Results

Of 581 patient episodes screened, 183 episodes involving 171 patients met inclusion criteria. Of these, 51% were bone marrow transplantation (BMT) patients, 40% were non-BMT haematology patients, and 8% were solid organ malignancy patients. The median age was 55 years, and 96% were neutropenic at the time of blood culture collection. A transthoracic echocardiogram was performed for 71% of episodes, and one patient met modified Duke’s criteria for definite IE, although this diagnosis was not suspected on clinical grounds. Other complications were uncommon. Benzylpenicillin resistance was rare (2.9%) and did not change over time. Most episodes (75%) were treated with piperacillin/tazobactam. For monomicrobial BSIs, the median antibiotic duration was 5 days (IQR 2–7) post-neutropenia resolution.

Conclusions

Infective complications and antimicrobial resistance are rare in cancer patients with VGS BSI. This may provide a safe opportunity to limit both investigations (e.g. echocardiogram) and prolonged exposure to broad-spectrum antimicrobials.