bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mineral substrate quality determines the initial soil microbial development in front of the Nordenskiöldbreen, Svalbard
Authors: Luláková Petra , Šantrůčková Hana , Elster Josef , Hanáček Martin , Kotas Petr , Meador Travis , Tejnecký Václav , Bárta Jiří 
Published: September 2023

Abstract
Substrate geochemistry is an important factor influencing early microbial development after glacial retreat on nutrient-poor geological substrates in the High Arctic. It is often difficult to separate substrate influence from climate because study locations are distant. Our study in the retreating Nordenskiöldbreen (Svalbard) is one of the few to investigate biogeochemical and microbial succession in two adjacent forefields, which share the same climatic conditions but differ in their underlying geology. The northern silicate forefield evolved in a classical chronosequence, where most geochemical and microbial parameters increased gradually with time. In contrast, the southern carbonate forefield exhibited high levels of nutrients and microbial biomass at the youngest sites, followed by a significant decline and then a gradual increase, which caused a rearrangement in the species and functional composition of the bacterial and fungal communities. This shuffling in the early stages of succession suggests that high nutrient availability in the bedrock could have accelerated early soil succession after deglaciation and thereby promoted more rapid stabilization of the soil and production of higher quality organic matter. Most chemical parameters and bacterial taxa converged with time, while fungi showed no clear pattern.
Role of host ciliate Paramecium bursaria mitochondria and trichocysts for symbiotic Chlorella variabilis attachment beneath the host cell cortex
Authors: Kodama Yuuki , Fujishima Masahiro 
Published: September 2023

Abstract
Symbiotic Chlorella variabilis is encased in the perialgal vacuole (PV) membrane of ciliate Paramecium bursaria. The PV membrane is stably anchored below the host cell cortex by adhesion to host mitochondria. Host trichocysts, which are defensive organelles against predators, are present in the mitochondria and PV membrane vicinity. The mechanism by which PV attaches beneath the host cell cortex remains unknown. When P. bursaria is centrifuged at high speed, the symbiotic algae are displaced from the host cell cortex and concentrate at the posterior end. When centrifugation is stopped, the dislocated algae reattach beneath the host cell cortex with fast cytoplasmic streaming. The densities of mitochondria and trichocysts before and after centrifugation were compared using indirect immunofluorescence microscopy with monoclonal antibodies. Almost all trichocysts were shed by high-speed centrifugation, but dislocated algae could reattach even in the absence of trichocysts. In contrast, host mitochondria were unaffected in localization and number, and the dislocated algae also reattached. These findings suggest trichocysts are unnecessary for algal relocalization and that mitochondria are colocalized with the algae. However, many mitochondria were also present in the cell’s anterior region without symbiotic algae. Therefore, not all areas with mitochondria contained algae, but there was an algal localization bias within the host cell.
High prevalence of GR2 and GR4 plasmids in Acinetobacter baumannii strains from Brazil
Authors: de Melo Beatriz Souza Toscano , Xavier Danilo Elias , Leal Nilma Cintra , Campos Túlio de Lima 
Published: September 2023

Abstract
Acinetobacter baumannii is Gram-negative pathogen with extensive role in healthcare-associated infections (HAIs). Plasmids in this species are important carriers of antimicrobial resistance genes. In this work, we investigated the plasmids of 227 Brazilian A. baumannii genomes. A total of 389 plasmid sequences with 424 Rep proteins typed to 22 different homology groups (GRs) were identified. The GR2 plasmid group was the most predominant (40.6%), followed by the GR4 group (16.7%), representing ∼57% of all plasmids. There is a wide distribution of plasmids among the isolates and most strains carry more than one plasmid. Our analyses revealed a significant prevalence of GR4 plasmids in Brazilian A. baumannii genomes carrying several antimicrobial resistance genes, notably to carbapenem (39.43%). These plasmids harbor a MOBQ relaxase that might confer increased spreading potential in the environment. Most plasmids of the predominant groups belong to the same plasmid taxonomic unit (PTU-Pse7) and have a AbkA/AbkB toxin–antitoxin system that has a role in plasmid stability and dissemination of carbapenem resistance genes. The results of this work should contribute to our understanding of the molecular content of plasmids in a large and populous country, highlighting the importance of genomics for enhanced epidemiological surveillance.
An information theoretic Bayesian uncertainty analysis of AEM systems over Menindee Lake, Australia
Authors: Ray Anandaroop , Ley-Cooper Yusen , Brodie Ross C , Taylor Richard , Symington Neil , Moghaddam Negin F 
Published: September 2023

SUMMARYLong-range, active-source airborne electromagnetic (AEM) systems for near-surface conductivity imaging fall into two categories: helicopter (rotary-wing) borne or fixed-wing aircraft borne. A multitude of factors such as flying height, transmitter loop area and current, source waveforms, aerodynamic stability and data stacking times contribute to the geological resolvability of the subsurface. A comprehensive comparison of the relative merits of each system considering all such factors is difficult, but test flights over well-constrained subsurface geology with downhole induction logs are extremely useful for resolution studies. However, given the non-linear nature of the electromagnetic inverse problem, handling transmitter–receiver geometries in fixed-wing aircraft is especially challenging. As a consequence of this non-linearity, inspecting the closeness of downhole conductivities to deterministic inversion results is not sufficient for studying resolvability. A more comprehensive picture is provided by examining the variation in probability mass of the depth-wise Bayesian posterior conductivity distributions for each kind of AEM system within an information theoretic framework. For this purpose, probabilistic inversions of data must be carried out. Each acquiring system should fly over the same geology, survey noise levels must be measured and the same prior probabilities on conductivity must be used. With both synthetic models as well as real data from over the Menindee calibration range in New South Wales, Australia, we shed new light on the matter of AEM inverse model uncertainty. We do this using two information theoretic attributes derived from different Kullback–Leibler divergences—Bayesian information gain, and a strictly proper scoring rule, to assess posterior probabilities estimated by a novel Bayesian inversion scheme. The inversion marginalizes fixed-wing geometry attributes as generic nuisance parameters during Markov chain sampling. This is the first time-domain AEM study we know of, that compares nuisance marginalized subsurface posterior conductivities from a fixed-wing system, with rotary-wing derived posterior conductivities. We also compare field results with induction log data where available. Finally, we estimate the information gain in each case via a covariate shift adaptation technique that has not been used before in geophysical work. Our findings have useful implications in AEM system selection, as well as in the design of better deterministic AEM inversion algorithms.
An efficient algorithm to measure arrival times of weak seismic phases
Authors: Li Lei , Durand Stéphanie , Ricard Yanick , Debayle Eric 
Published: September 2023

SUMMARY
In seismic tomography, traveltime information of seismic body phases is commonly used to invert the seismic velocities of the subsurface structure. At long periods or for later seismic phases, the arrival time of seismic phases lack definitive onset and a direct picking of the absolute arrival time has large uncertainty and reproducibility. A common practice is to estimate the relative delay between the observed and synthetic signals that maximizes the correlation coefficient. For that aim, we must first select appropriate time windows around the candidate signals. To improve the ability to detect and extract weak signals, we develop a new morphological time window selection (MTWS) algorithm that adapts to the shape of signals and has robust performance in automated processing of massive data. The MTWS method consists of two successive steps. First, we detect the major peaks on the waveform envelope using a maximum filter. Secondly, we solve for the beginning and end of the time windows surrounding the peaks straightforwardly from simple geometrical equations. The efficiency and robustness of the MTWS algorithm make it very suitable for automated processing of huge data sets. We demonstrate the implementation of the method with both synthetic and observed long period (20–40 s) SH waves. From ∼100 000 traces of transverse-component seismograms recorded by global seismic networks over the course of a year, we obtain ∼15 000 Sdiff, ∼7500 ScS and also some ScS multiples. The global map of Sdiff correlation time delays shows consistent patterns with the shear wave velocity perturbations on the core–mantle boundary in the recent tomographic models.
Elastic deformation resulting from internal mass loading: semi-analytical solution
Authors: Tang He , Sun Wenke , Liu Tai 
Published: September 2023

SUMMARYNumerous physical processes are responsible for mass exchange between the surface and the interior of the Earth, including but not limited to the conversion of surface water and groundwater, volcanic eruptions and the consequent outflow of magma to the surface, and underground mining of mineral resources, among others. These mass transport phenomena influence the deformation of the Earth's crust. In this study, we extend the conventional loading theory to analyse the extent of crustal deformation by obtaining Green's functions due to internal mass loading in a layered elastic spherical earth model. For the surface source and internal source, the displacement and gravity change show significant differences within a specific horizontal range several times the source depth. Compared with other physical quantities, horizontal displacement is more sensitive to source depth. Furthermore, the utilization of a disc-like load example serves to illustrate the distinctions in displacement deformation between internal and surface loadings. We also published the code for calculating Green's function for internal mass loading in the public repository GitHub.
The impact of crustal scattering on body-wave reflection interferometry by cross-correlation and multidimensional deconvolution
Authors: Hartstra Iris , Wapenaar Kees 
Published: September 2023

SUMMARY
Previous studies indicate that scattering may pose a trade-off for the performance of seismic interferometry (SI) applications for retrieving body-wave reflections of a target reflector. While it has been demonstrated that a higher scattering strength of the overburden improves the Green’s function estimated by cross-correlation SI, other theoretical and empirical studies showed that multiple scattering also gives rise to more artefacts. The implications of this trade-off are analysed in this numerical study for a lithospheric scenario with varying crustal scattering strength and passive illumination conditions. In this scenario, we apply SI by cross-correlation to elastodynamic responses to double-couple sources to reconstruct virtual Moho primary reflections. We include multidimensional deconvolution (MDD) methods in the analysis to investigate whether scattering-induced artefacts affect MDD methods in a similar way as was shown for the cross-correlation method. Our results show that there indeed exists a trade-off between the quality of the virtual primary reflection of the target that can be obtained by SI and the scattering strength of the overburden. Furthermore, we find that the full-field MDD method proves to be most resilient to the negative effects of multiple scattering for all illumination conditions and scattering strengths analysed.
Mediastinal perigraft seroma after thoracic aortic surgery
Authors: Suzuki Ryo , Akita Masafumi , Miyazaki Suguru , Shimano Ryo 
Published: September 2023

Abstract

OBJECTIVES
We investigated pertinent factors associated with mediastinal perigraft seroma (PGS) after thoracic aortic surgery. In addition, we provided a clinical review of this entity, as reports reviewing abundant mediastinal PGS cases are rare.

METHODS
Eighty-two patients who underwent either ascending aortic replacement or aortic arch replacement between 2016 and 2022 in our institution were enrolled in the present study. Postoperative computed tomography scans were performed to detect fluid capsules with a diameter ≥3.0 cm and radiodensity ≤25 Hounsfield units. Patients who did and who did not develop PGS formation were compared. Variables with a statistically significant difference between these groups were included in a multiple logistic regression analysis along with other factors associated with PGS in the literature.

RESULTS
The incidence rate of PGS was 14.6% (12/82). The average radiodensity of the mass was 16.6 ± 6.3 Hounsfield units. The average onset of PGS was 8.5 months post-surgery. Multivariate logistic regression analysis revealed that ejection fraction [odds ratio (OR): 1.25, 95% confidence interval (CI): 1.03–1.50, P = 0.021], aortic dissection (versus degenerative aortic aneurysm) (OR: 6.61, 95% CI: 1.35–32.4, P = 0.02) and warfarin use (OR: 6.67, 95% CI: 1.19–37.1, P = 0.03) significantly contributed to mediastinal PGS after thoracic aortic surgery.

CONCLUSIONS
High ejection fraction, warfarin use and aortic dissection (versus degenerative aortic aneurysm) contributed significantly to mediastinal PGS formation after thoracic aortic surgery. Careful serial postoperative imaging studies and fluid analysis can be used to guide treatment plans.

Clinical trial registration
UMIN-CTR (University hospital Medical Information Network-Clinical Trial Registry) Registration number: UMIN000050764.
Genome-wide Association Study of Susceptibility to Respiratory Syncytial Virus Hospitalization in Young Children &lt;5 Years of age
Authors: Egeskov-Cavling Amanda Marie , van Wijhe Maarten , Yakimov Victor , Johannesen Caroline Klint , Pollard Andrew J , Trebbien Ramona , Bybjerg-Grauholm Jonas , Fischer Thea Kølsen ,   for the Respiratory Syncytial Virus Consortium in Europe (RESCEU) investigators, Nair Harish , Campbell Harry , Beutels Philippe , Bont Louis , Pollard Andrew , Openshaw Peter , Martinon-Torres Federico , Heikkinen Terho , Meijer Adam , Fischer Thea , van den Berge Maarten , Giaquinto Carlo , Abram Michael , Swanson Kena , Rizkalla Bishoy , Vernhes Charlotte , Gallichan Scott , Aerssens Jeroen , Kumar Veena , Molero Eva 
Published: September 2023

Abstract

Background
Worldwide, respiratory syncytial virus (RSV) infections are among the most common causes of infant hospitalization. Host genetic factors influencing the risk and severity of RSV infection are not well known.

Methods
We conducted a genome-wide association study (GWAS) to investigate single-nucleotide polymorphisms (SNPs) associated with severe RSV infections using a nested case-control design based on 2 Danish cohorts. We compared SNPs from 1786 children hospitalized with RSV to 45 060 controls without an RSV-coded hospitalization. We performed gene-based testing, tissue enrichment, gene-set enrichment, and a meta-analysis of the 2 cohorts. Finally, an analysis of potential associations between the severity of RSV infection and genetic markers was performed.

Results
We did not detect any significant genome-wide associations between SNPs and RSV infection or the severity of RSV. We did find potential loci associated with RSV infections on chromosome 5 in 1 cohort but failed to replicate any signals in both cohorts.

Conclusions
Despite being the largest GWAS of severe RSV infection, we did not detect any genome-wide significant loci. This may be an indication of a lack of power or an absence of signal. Future studies might include mild illness and need to be larger to detect any significant associations.
How to Survive a (Juvenile) Piranha Attack: An Integrative Approach to Evaluating Predator Performance
Authors: Lowe A , Kolmann M A , Paig-Tran E W M 
Published: September 2023

FiguresSynopsisThere is an evolutionary arms race between predators and prey. In aquatic environments, predatory fishes often use sharp teeth, powerful bites, and/or streamlined bodies to help capture their prey quickly and efficiently. Conversely, prey are often equipped with antipredator adaptations including: scaly armor, sharp spines, and/or toxic secretions. This study focused on the predator–prey interactions between the armored threestripe cory catfish (Corydoras trilineatus) and juvenile red-bellied piranha (Pygocentrus nattereri). Specifically, we investigated how resistant cory catfish armor is to a range of natural and theoretical piranha bite forces and how often this protection translated to survival from predator attacks by Corydoras. We measured the bite force and jaw functional morphology of P. nattereri, the puncture resistance of defensive scutes in C. trilineatus, and the in situ predatory interactions between the two. The adductor mandibulae muscle in juvenile P. nattereri is robust and delivers an average bite force of 1.03 N and maximum bite force of 9.71 N, yet its prey, C. trilineatus, survived 37% of confirmed bites without any damage. The C. trilineatus armor withstood an average of nine bites before puncture by P. nattereri. Predation was successful only when piranhas bit unarmored areas of the body, at the opercular opening and at the caudal peduncle. This study used an integrative approach to understand the outcomes of predator–prey interactions by evaluating the link between morphology and feeding behavior. We found that juvenile P. nattereri rarely used a maximal bite force and displayed a net predation success rate on par with other adult vertebrates. Conversely, C. trilineatus successfully avoided predation by orienting predator attacks toward their resilient, axial armor and behavioral strategies that reduced the predator's ability to bite in less armored regions of the body.
Turtle Shell Kinesis Underscores Constraints and Opportunities in the Evolution of the Vertebrate Musculoskeletal System
Authors: Cordero G A 
Published: September 2023

Synopsis
Species groups that feature traits with a low number of potentially variable (evolvable) character states are more likely to repeatedly evolve similar phenotypes, that is, convergence. To evaluate this phenomenon, this present paper addresses anatomical alterations in turtles that convergently evolved shell kinesis, for example, the movement of shell bones to better shield the head and extremities. Kinesis constitutes a major departure from the evolutionarily conserved shell of modern turtles, yet it has arisen independently at least 8 times. The hallmark signature of kinesis is the presence of shell bone articulations or “hinges,” which arise via similar skeletal remodeling processes in species that do not share a recent common ancestor. Still, the internal biomechanical components that power kinesis may differ in such distantly related species. Complex diarthrodial joints and modified muscle connections expand the functional boundaries of the limb girdles and neck in a lineage-specific manner. Some lineages even exhibit mobility of thoracic and sacral vertebrae to facilitate shell closure. Depending on historical contingency and structural correlation, a myriad of anatomical alterations has yielded similar functional outcomes, that is, many-to-one mapping, during the convergent evolution of shell kinesis. The various iterations of this intricate phenotype illustrate the potential for the vertebrate musculoskeletal system to undergo evolutionary change, even when constraints are imposed by the development and structural complexity of a shelled body plan. Based on observations in turtles and comparisons to other vertebrates, a hypothetical framework that implicates functional interactions in the origination of novel musculoskeletal traits is presented.
Metagenomic insights into the microbiota involved in lactate and butyrate production and manipulating their synthesis in alfalfa silage
Authors: Li Rongrong , Hu Ming , Jiang Xin , Xu Chuncheng 
Published: September 2023

Abstract

Aims
Lactate and butyrate are important indicators of silage quality. However, the microorganisms and mechanisms responsible for lactate and butyrate production in silage are not well documented.

Methods and results
whole-metagenomic sequencing was used to analyse metabolic pathways, microbiota composition, functional genes, and their contributions to lactate and butyrate production in alfalfa silage with (SA) and without (CK) sucrose addition. Carbon metabolism was the most abundant metabolic pathway. We identified 11 and 2 functional genes associated with lactate and butyrate metabolism, respectively. Among them, D-lactate dehydrogenase (ldhA) and L-lactate dehydrogenase (ldhB) were most important for the transition between D/L-lactate and pyruvate and were primarily related to Lactobacillus in the SA group. The genes encoding L-lactate dehydrogenase (lldD), which decomposes lactate, were the most abundant and primarily associated with Enterobacter cloacae. Butyrate-related genes, mainly encoding butyryl-CoA: acetate CoA-transferase (but), were predominantly associated with Klebsiella oxytoca and Escherichia coli in the CK group.

Conclusions
Enterobacteriaceae and Lactobacillaceae were mainly responsible for butyrate and lactate formation, respectively.
Enzymatic degradation of glucosaminoglucan and cellulase resistance of cellulose nanofiber coated with glucosaminoglucan
Authors: Morita Hiroki , Chida Shun , Takato Masaki , Kondo Keiko , Katahira Masato , Simao Luisa Brazão , Takeda Minoru 
Published: September 2023

Abstract

Aims
Enzymatic degradation of β-1,4-linked glucose and glucosamine (glucosaminoglucan, GG), which is prepared from Thiothrix nivea and can act as a cellulose-aminating agent with a strong affinity to cellulose, was attempted.

Methods and results
A chitosanase-secreting fungal strain was isolated as a GG-degrading microbe. GG was found to be degraded by not only chitosanases but also cellulases. Based on nuclear magnetic resonance spectroscopy, both enzymes were found to produce GlcN-Glc from GG. The cellulases also produced GlcN-Glc-GlcN-Glc as an additional final digest. Furthermore, aminated (GG-coated) cellulose nanofibers exhibited cellulase resistance. The flexibility of GG adsorbed onto a cellulose crystal was almost identical to that of cellulose, as estimated via the molecular dynamics calculations.

Conclusions
The chitosanase and cellulase hydrolyzed the β-1,4-linkage from Glc to GlcN and were expected to recognize the tetramer and hexamer units of GG depending on their final products. The cellulose nanofibers acquired cellulase resistance via amination with GG, probably because of the lower activity of cellulase to GG than cellulose.