bluuebunny/crossref_metadata_2025_split huggingface dataset:
Socioeconomic Disparities and the Prevalence of Antimicrobial Resistance
Authors: Cooper Lauren N , Beauchamp Alaina M , Ingle Tanvi A , Diaz Marlon I , Wakene Abdi D , Katterpalli Chaitanya , Keller Tony , Walker Clark , Blumberg Seth , Kanjilal Sanjat , Chen Jonathan H , Radunsky Alexander P , Most Zachary M , Hanna John J , Perl Trish M , Lehmann Christoph U , Medford Richard J 
Published: June 2024

Abstract

Background
The increased prevalence of antimicrobial-resistant (AMR) infections is a significant global health threat, resulting in increased disease, deaths, and costs. The drivers of AMR are complex and potentially impacted by socioeconomic factors. We investigated the relationships between geographic and socioeconomic factors and AMR.

Methods
We collected select patient bacterial culture results from 2015 to 2020 from electronic health records of 2 expansive healthcare systems within the Dallas–Fort Worth, Texas, metropolitan area. Among individuals with electronic health records who resided in the 4 most populous counties in Dallas–Fort Worth, culture data were aggregated. Case counts for each organism studied were standardized per 1000 persons per area population. Using residential addresses, the cultures were geocoded and linked to socioeconomic index values. Spatial autocorrelation tests identified geographic clusters of high and low AMR organism prevalence and correlations with established socioeconomic indices.

Results
We found significant clusters of AMR organisms in areas with high levels of deprivation, as measured by the area deprivation index (ADI). We found a significant spatial autocorrelation between ADI and the prevalence of AMR organisms, particularly for AmpC β-lactamase and methicillin-resistant Staphylococcus aureus, with 14% and 13%, respectively, of the variability in prevalence rates being attributable to their relationship with the ADI values of the neighboring locations.

Conclusions
We found that areas with a high ADI are more likely to have higher rates of AMR organisms. Interventions that improve socioeconomic factors such as poverty, unemployment, decreased access to healthcare, crowding, and sanitation in these areas of high prevalence may reduce the spread of AMR.
The private management of plant disease epidemics: infection levels and social inefficiencies
Authors: Martinez César , Courtois Pierre , Thébaud Gaël , Tidball Mabel 
Published: June 2024

Abstract
Plant disease control is often implemented at the private property level, and problems of cooperation and coordination between landowners can lead to social inefficiencies. Drawing on the private management problem of sharka on Prunus trees, we analyse an epidemic game and its outcomes according to initial infection levels. We show that, depending on the infection level in each farm, the nature of strategic interactions changes drastically, and a wide range of games can occur, including games with multiple or without pure strategy equilibria and games with coordination or anti-coordination patterns. We characterise the epidemic conditions for which private management produces social inefficiency and analyse the properties of uniform and differentiated subsidy schemes to solve it. We conclude with a discussion of the policy implications of the ongoing deregulation of sharka management in France.
Global transcriptome analysis of Pseudomonas aeruginosa NT06 response to potassium chloride, sodium lactate, sodium citrate, and microaerophilic conditions in a fish ecosystem
Authors: Tomaś Natalia , Myszka Kamila , Wolko Łukasz , Juzwa Wojciech 
Published: June 2024

Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that recently has been increasingly isolated from foods, especially from minimally processed fish-based products. Those are preserved by the addition of sodium chloride (NaCl) and packaging in a modified atmosphere. However, the current trends of minimizing NaCl content may result in an increased occurrence of P. aeruginosa. NaCl can be replaced with potassium chloride (KCl) or sodium salts of organic acids. Herein, we examined the antimicrobial effects of KCl, sodium lactate (NaL), sodium citrate (NaC), and sodium acetate (NaA) against P. aeruginosa NT06 isolated from fish. Transcriptome response of cells grown in medium imitating a fish product supplemented with KCl and KCl/NaL/NaC and maintained under microaerophilic conditions was analysed. Flow cytometry analysis showed that treatment with KCl and KCl/NaL/NaC resulted in changed metabolic activity of cells. In response to KCl and KCl/NaL/NaC treatment, genes related to cell maintenance, stress response, quorum sensing, virulence, efflux pump, and metabolism were differentially expressed. Collectively, our results provide an improved understanding of the response of P. aeruginosa to NaCl alternative compounds that can be implemented in fish-based products and encourage further exploration of the development of effective methods to protect foods against the P. aeruginosa, underestimate foodborne bacteria.
New robust remote reference estimator using robust multivariate linear regression
Authors: Usui Yoshiya , Uyeshima Makoto , Sakanaka Shin'ya , Hashimoto Tasuku , Ichiki Masahiro , Kaida Toshiki , Yamaya Yusuke , Ogawa Yasuo , Masuda Masataka , Akiyama Takahiro 
Published: June 2024

SUMMARY
The solution of the remote reference method, a frequently used technique in magnetotelluric (MT) data processing, can be viewed as a product of the two-input–multiple-output relationship between the local electromagnetic field and the reference field at a remote station. By applying a robust estimator to the two-input–multiple-output system, one can suppress the influence of outliers in the local magnetic field as well as those in the local electric field based on regression residuals. Therefore, this study develops a new robust remote reference estimator with the aid of robust multivariate linear regression. By applying the robust multivariate regression S-estimator to the multiple-output system, the present work derives a set of equations for robust estimates of the transfer function, noise variances, and the scale of the Mahalanobis distance simultaneously. The noise variances are necessary for the multivariate analysis to normalize the residuals of dependent variables. The Mahalanobis distance, a distance measure for multivariate data, is a commonly used indicator of outliers in multivariate statistics. By updating those robust estimates iteratively, the new robust remote reference estimator seeks the transfer function that minimizes the robust scale estimate of the Mahalanobis distance. The developed estimator can avoid bias in the MT transfer function even if there are significant noises in the reference magnetic field and handle outlying data more robustly than previously proposed robust remote reference estimators. The authors applied the developed method to a synthetic data set and real-world data. The test results demonstrate that the developed method downweights outliers in the local electric and magnetic fields and gives an unbiased transfer function.
Scm6A: A Fast and Low-cost Method for Quantifying m6A Modifications at the Single-cell Level
Authors: Li Yueqi , Li Jingyi , Li Wenxing , Liang Shuaiyi , Wei Wudi , Chu Jiemei , Lai Jingzhen , Lin Yao , Chen Hubin , Su Jinming , Hu Xiaopeng , Wang Gang , Meng Jun , Jiang Junjun , Ye Li , An Sanqi 
Published: June 2024

Abstract
It is widely accepted that N6-methyladenosine (m6A) exhibits significant intercellular specificity, which poses challenges for its detection using existing m6A quantitative methods. In this study, we introduced Single-cell m6A Analysis (Scm6A), a machine learning-based approach for single-cell m6A quantification. Scm6A leverages input features derived from the expression levels of m6A trans regulators and cis sequence features, and offers remarkable prediction efficiency and reliability. To further validate the robustness and precision of Scm6A, we first applied Scm6A to single-cell RNA sequencing (scRNA-seq) data from peripheral blood mononuclear cells (PBMCs) and calculated the m6A levels in CD4+ and CD8+ T cells. We also applied a winscore-based m6A calculation method to conduct N6-methyladenosine sequencing (m6A-seq) analysis on CD4+ and CD8+ T cells isolated through magnetic-activated cell sorting (MACS) from the same samples. Notably, the m6A levels calculated by Scm6A exhibited a significant positive correlation with those quantified through m6A-seq in different cells isolated by MACS, providing compelling evidence for Scm6A’s reliability. Additionally, we performed single-cell-level m6A analysis on lung cancer tissues as well as blood samples from patients with coronavirus disease 2019 (COVID-19), and demonstrated the landscape and regulatory mechanisms of m6A in different T cell subtypes from these diseases. In summary, Scm6A is a novel, dependable, and accurate method for single-cell m6A detection and has broad applications in the realm of m6A-related research.
Sustaining progress towards universal health coverage amidst a full-scale war: learning from Ukraine
Authors: Habicht Jarno , Hellowell Mark , Kutzin Joe 
Published: June 2024

Abstract
In the aftermath of Russia’s military response to the 2014 Revolution of Dignity, the government of Ukraine implemented a package of health financing reforms underpinned by universal health coverage (UHC) principles. By the time of Russia’s full-scale invasion of Ukraine in February 2022, the new systems and institutions envisaged in the reforms were largely established. In this Commentary article, we explain how these attributes strengthened the Ukrainian health system’s response to the impacts of the war. Ukraine’s experience highlights the role that health financing arrangements, designed in accordance with UHC principles, can play in strengthening health system resilience.
MdVQ17 negatively regulates apple resistance to Glomerella leaf spot by promoting MdWRKY17-mediated salicylic acid degradation and pectin lyase activity
Authors: Duan Dingyue , Yang Jie , Yi Ran , Dong Qinglong , Shi Mingrui , He Jingxuan , Mao Ke , Ma Fengwang 
Published: June 2024

Abstract
Glomerella leaf spot (GLS) is a fungal disease caused by Colletotrichum fructicola, which severely restricts the yield and quality of apples. Valine–glutamine (VQ) proteins are transcriptional regulators involved in the regulation of plant growth and stress responses. However, little is known about the role of VQ proteins in the biotic stress response in apple. Here, a VQ gene, MdVQ17, that was highly induced by C. fructicola infection was identified. Overexpression of MdVQ17 in apple increased susceptibility to C. fructicola and significantly reduced the salicylic acid content and β-1,3-glucanase and chitinase activities. Based on yeast two-hybrid screening, MdWRKY17, which promotes susceptibility to C. fructicola, was identified as an MdVQ17-interacting protein. Co-expression of MdVQ17 can promote the binding and transcriptional activation activity of MdWRKY17 on the promoter of Downy Mildew Resistant 6 (MdDMR6), thereby promoting MdWRKY17-mediated salicylic acid degradation. Based on DNA affinity purification sequencing, the pectin lyase-encoding gene MdPL-like was identified as a direct target of MdWRKY17. MdWRKY17 can directly bind to the promoter of MdPL-like and activate its transcription, and the binding and activation of MdWRKY17 on the MdPL-like promoter were significantly enhanced by MdVQ17 co-expression. Functional identification showed that MdPL-like promoted pectin lyase activity and susceptibility to C. fructicola. In sum, these results demonstrate that the MdVQ17-MdWRKY17 module mediates the response to C. fructicola infection by regulating salicylic acid accumulation and pectin lyase activity. Our findings provide novel insights into the mechanisms by which the VQ–WRKY complex modulates plant pathogen defense responses.
A near real-time interactive dashboard for monitoring and anticipating demands in emergency care in the Île-de-France region (France)
Authors: Hanf Matthieu , Salle Léopoldine , Mas Charline , Ghribi Saif Eddine , Huitorel Mathias , Mebarki Nabia , Larid Sonia , Mazué Jane-Lore , Wargon Mathias 
Published: June 2024

Abstract

Objective
To allow health professionals to monitor and anticipate demands for emergency care in the Île-de-France region of France.

Materials and Methods
Data from emergency departments and emergency medical services are automatically processed on a daily basis and visualized through an interactive online dashboard. Forecasting methods are used to provide 7 days predictions.

Results
The dashboard displays data at regional and departmental levels or for 5 different age categories. It features summary statistics, historical values, predictions, comparisons to previous years, and monitoring of common reasons for care and outcomes.

Discussion
A large number of health professionals have already requested access to the dashboard (n = 606). Although the quality of data transmitted may vary slightly, the dashboard has already helped improve health situational awareness and anticipation.

Conclusions
The high access demand to the dashboard demonstrates the operational usefulness of real-time visualization of multisource data coupled with advanced analytics.
Potential negative effects of genomic selection
Authors: Misztal Ignacy , Lourenco Daniela 
Published: June 2024

AbstractInitial findings on genomic selection (GS) indicated substantial improvement for major traits, such as performance, and even successful selection for antagonistic traits. However, recent unofficial reports indicate an increased frequency of deterioration of secondary traits. This phenomenon may arise due to the mismatch between the accelerated selection process and resource allocation. Traits explicitly or implicitly accounted for by a selection index move toward the desired direction, whereas neglected traits change according to the genetic correlations with selected traits. Historically, the first stage of commercial genetic selection focused on production traits. After long-term selection, production traits improved, whereas fitness traits deteriorated, although this deterioration was partially compensated for by constantly improving management. Adding these fitness traits to the breeding objective and the used selection index also helped offset their decline while promoting long-term gains. Subsequently, the trend in observed fitness traits was a combination of a negative response due to genetic antagonism, positive response from inclusion in the selection index, and a positive effect of improving management. Under GS, the genetic trends accelerate, especially for well-recorded higher heritability traits, magnifying the negatively correlated responses for fitness traits. Then, the observed trend for fitness traits can become negative, especially because management modifications do not accelerate under GS. Additional deterioration can occur due to the rapid turnover of GS, as heritabilities for production traits can decline and the genetic antagonism between production and fitness traits can intensify. If the genetic parameters are not updated, the selection index will be inaccurate, and the intended gains will not occur. While the deterioration can accelerate for unrecorded or sparsely recorded fitness traits, GS can lead to an improvement for widely recorded fitness traits. In the context of GS, it is crucial to look for unexpected changes in relevant traits and take rapid steps to prevent further declines, especially in secondary traits. Changes can be anticipated by investigating the temporal dynamics of genetic parameters, especially genetic correlations. However, new methods are needed to estimate genetic parameters for the last generation with large amounts of genomic data.
Genetic structure and diversity of the island-endemic freshwater prawn Macrobrachium shokitai Fujino & Baba, 1973 (Decapoda: Caridea: Palaemonidae) on Iriomote Island, Ryukyu Archipelago, southern Japan
Authors: Doi Wataru , Nohara Kenji , Inoue Hiroyuki , Kohno Hiroyoshi 
Published: June 2024

Abstract
Iriomote Island is a small continental island hosting approximately 40 rivers characterized by short, steep-gradient streams and small waterfalls. We examined the population genetic structure and diversity of the freshwater prawn Macrobrachium shokitaiFujino & Baba, 1973 (Palaemonidae) using the mitochondrial cytochrome c oxidase subunit I (COI) gene sequence. Specimens were collected from 19 sites along ten rivers on the island, covering the known geographic distribution of the species. Haplotype and nucleotide diversities were very low within each river on the island. Nearly all haplotypes were exclusive to a given river, confirming distinct population structures among rivers at a small geographical scale. Slight genetic differentiation was discerned between the upper and lower sites of waterfalls in only the Yuchin River. Phylogenetic tree reconstruction, haplotype network, and principle coordinate analysis classified five clades roughly correspond to geographical groups in the western, southern, central, and northern regions of the island. Extreme caution should therefore be taken when translocating individuals to other rivers to avoid introducing genetic disturbance, even during conservation and mitigation efforts.
Take your sunscreen: plant photoreceptor systems in Serritaenia testaceovaginata
Authors: Hess Wolfgang R , Hiltbrunner Andreas 
Published: June 2024

This article comments on:
Busch A, Gerbracht JV, Davies K, Hoecker U, Hess S. 2024. Comparative transcriptomics elucidates the cellular responses of an aeroterrestrial zygnematophyte to UV radiation. Journal of Experimental Botany 75, 3624–3642.
Introducing the BRAHMA simulation suite: signatures of low-mass black hole seeding models in cosmological simulations
Authors: Bhowmick Aklant K , Blecha Laura , Torrey Paul , Kelley Luke Zoltan , Weinberger Rainer , Vogelsberger Mark , Hernquist Lars , Somerville Rachel S , Evans Analis Eolyn 
Published: June 2024

ABSTRACT
While the first “seeds” of supermassive black holes (BH) can range from $\sim 10^2-10^6 \rm ~{\rm M}_{\odot }$, the lowest mass seeds ($\lesssim 10^3~\rm {\rm M}_{\odot }$) are inaccessible to most cosmological simulations due to resolution limitations. We present our new BRAHMA simulations that use a novel flexible seeding approach to predict the $z\ge 7$ BH populations for low-mass seeds. We ran two types of boxes that model $\sim 10^3~\rm {\rm M}_{\odot }$ seeds using two distinct but mutually consistent seeding prescriptions at different simulation resolutions. First, we have the highest resolution $[9~\mathrm{Mpc}]^3$ (BRAHMA-9-D3) boxes that directly resolve $\sim 10^3~\rm {\rm M}_{\odot }$ seeds and place them within haloes with dense, metal-poor gas. Second, we have lower resolution, larger volume $[18~\mathrm{Mpc}]^3$ (BRAHMA-18-E4), and $\sim [36~\mathrm{Mpc}]^3$ (BRAHMA-36-E5) boxes that seed their smallest resolvable $\sim 10^4~\&~10^5~\mathrm{{\rm M}_{\odot }}$ BH descendants using new stochastic seeding prescriptions calibrated using BRAHMA-9-D3. The three boxes together probe key BH observables between $\sim 10^3\,\mathrm{ and}\,10^7~\rm {\rm M}_{\odot }$. The active galactic nuclei (AGN) luminosity function variations are small (factors of $\sim 2-3$) at the anticipated detection limits of potential future X-ray facilities ($\sim 10^{43}~ \mathrm{ergs~s^{-1}}$ at $z\sim 7$). Our simulations predict BHs $\sim 10-100$ times heavier than the local $M_*$ versus $M_{\mathrm{ bh}}$ relations, consistent with several JWST-detected AGN. For different seed models, our simulations merge binaries at $\sim 1-15~\mathrm{kpc}$, with rates of $\sim 200-2000$ yr−1 for $\gtrsim 10^3~\rm {\rm M}_{\odot }$ BHs, $\sim 6-60$ yr−1 for $\gtrsim 10^4~\rm {\rm M}_{\odot }$ BHs, and up to $\sim 10$ yr−1 amongst $\gtrsim 10^5~\rm {\rm M}_{\odot }$ BHs. These results suggest that Laser Interferometer Space Antenna mission has promising prospects for constraining seed models.
Systematic analysis of jellyfish galaxy candidates in Fornax, Antlia, and Hydra from the S-PLUS survey: a self-supervised visual identification aid
Authors: Gondhalekar Yash , Chies-Santos Ana L , de Souza Rafael S , Queiroz Carolina , Lopes Amanda R , Ferrari Fabricio , Azevedo Gabriel M , Monteiro-Pereira Hellen , Overzier Roderik , Smith Castelli Analía V , Jaffé Yara L , Haack Rodrigo F , Rahna P T , Shen Shiyin , Mu Zihao , Lima-Dias Ciria , Barbosa Carlos E , Oliveira Schwarz Gustavo B , Riffel Rogério , Jimenez-Teja Yolanda , Grossi Marco , Mendes de Oliveira Claudia L , Schoenell William , Ribeiro Thiago , Kanaan Antonio 
Published: June 2024

ABSTRACT
We study 51 jellyfish galaxy candidates in the Fornax, Antlia, and Hydra clusters. These candidates are identified using the JClass scheme based on the visual classification of wide-field, twelve-band optical images obtained from the Southern Photometric Local Universe Survey. A comprehensive astrophysical analysis of the jellyfish (JClass &gt; 0), non-jellyfish (JClass = 0), and independently organized control samples is undertaken. We develop a semi-automated pipeline using self-supervised learning and similarity search to detect jellyfish galaxies. The proposed framework is designed to assist visual classifiers by providing more reliable JClasses for galaxies. We find that jellyfish candidates exhibit a lower Gini coefficient, higher entropy, and a lower 2D Sérsic index as the jellyfish features in these galaxies become more pronounced. Jellyfish candidates show elevated star formation rates (including contributions from the main body and tails) by $\sim$1.75 dex, suggesting a significant increase in the SFR caused by the ram-pressure stripping phenomenon. Galaxies in the Antlia and Fornax clusters preferentially fall towards the cluster’s centre, whereas only a mild preference is observed for Hydra galaxies. Our self-supervised pipeline, applied in visually challenging cases, offers two main advantages: it reduces human visual biases and scales effectively for large data sets. This versatile framework promises substantial enhancements in morphology studies for future galaxy image surveys.
The Alfvén transition zone observed by the Parker Solar Probe in young solar wind – global properties and model comparisons
Authors: Chhiber Rohit , Pecora Francesco , Usmanov Arcadi V , Matthaeus William H , Goldstein Melvyn L , Roy Sohom , Wang Jiaming , Thepthong Panisara , Ruffolo David 
Published: June 2024

ABSTRACT
The transition from subAlfvénic to superAlfvénic flow in the solar atmosphere is examined by means of Parker Solar Probe (PSP) measurements during solar encounters 8 to 14. Around 220 subAlfvénic periods with a duration ≥10 min are identified. The distribution of their durations, heliocentric distances, and Alfvén Mach number are analysed and compared with a global magnetohydrodynamic model of the solar corona and wind which includes turbulence effects. The results are consistent with a patchy and fragmented morphology, and suggestive of a turbulent Alfvén zone within which the transition from subAlfvénic to superAlfvénic flow occurs over an extended range of helioradii. These results inform and establish context for detailed analyses of subAlfvénic coronal plasma that are expected to emerge from PSP’s final mission phase, as well as for NASA’s planned PUNCH mission.