bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhanced CO2 Coordinates the Spatial Recruitment of Diazotrophs in Rice Via Root Development
Authors: Zhao Junwen , Chen Yuting , Tao Qi , Schreiber Lukas , Suresh Kiran , Frei Michael , Alam Muhammad Shahedul , Li Bing , Zhou Yaping , Baer Marcel , Hochholdinger Frank , Wang Changquan , Yu Peng 
Published: November 2024

ABSTRACTUnderstanding the reciprocal interaction between root development and coadapted beneficial microbes in response to elevated CO2 (eCO2) will facilitate the identification of nutrient‐efficient cultivars for sustainable agriculture.Here, systematic morphological, anatomical, chemical and gene expression assays performed under low‐nitrogen conditions revealed that eCO2 drove the development of the endodermal barrier with respect to L‐/S‐shaped lateral roots (LRs) in rice.Next, we applied metabolome and endodermal‐cell‐specific RNA sequencing and showed that rice adapts to eCO2 by spatially recruiting diazotrophs via flavonoid secretion in L‐shaped LRs. Using the rice Casparian strip mutant Oscasp1‐1, we confirmed that reduced lignin deposition selectively recruits the diazotrophic family of Oxalobacteraceae to confer tolerance to low nitrogen availability.
Modulation of Root Hydrotropism and Recovery From Drought by MIZ1‐like Genes in Tomato
Authors: Wexler Yonatan , Kiere Yvonne , Sobol Guy , Nuriel Roye , Azoulay‐Portal Shaked , Cohen Amir , Toporik Hila , Pasmanik‐Chor Metsada , Finkler Aliza , Shkolnik Doron 
Published: November 2024

ABSTRACTDrought limits crop performance worldwide. Plant roots' ability to grow toward moisture, termed hydrotropism, is considered one strategy for optimizing water recruitment from the growth medium. Based on the sequence of the hydrotropism‐indispensable MIZ1 protein in Arabidopsis thaliana, we identify hydrotropism and drought‐responsive genes in tomato. We utilized CRISPR/Cas9 genome‐editing technology for targeted mutagenesis of three hydrotropism‐associated loci (MIZ1‐like) in tomato (Solanum lycopersicum). We show that the three tomato MIZ1‐like genes are drought‐responsive and two of them are hydrostimulation‐responsive. Examination of the root hydrotropic response of triple and double mutants indicated the gene SlMIZ1‐1 as indispensable for tomato root hydrotropism. Moreover, expression of the SlMIZ1‐1 gene in the Arabidopsis miz1 mutant effectively complemented the lost MIZ1 functionality, including root hydrotropic bending and generation of hydrotropic Ca2+ signals. Transcriptome analysis of hydrostimulated tomato root tips under control gravity and continuous clinorotation conditions was performed to identify gravitropism‐ and hydrotropism‐responsive genes. This analysis suggested the involvement of ethylene and ABA signalling in modulating the interplay between hydrotropism and gravitropism. Unveiling the molecular mechanisms that underlie hydrotropism and drought response holds great potential for improving crop performance under limiting water availability due to global climate changes.
Reconsidering Martin Heidegger on the modern university
Authors: Ward Lee 
Published: November 2024

AbstractMartin Heidegger's 1933 Freiburg University Rector's Address is normally considered in terms of the horrors of its association with National Socialism. This study re‐frames the debate about the Address by situating it in the context of the tradition of philosophical reflection upon the political and historical significance of the modern research university. I highlight aspects of the Address that signified continuity with distinctively liberal presuppositions embedded in foundational ideas of the Humboldtian university. I conclude with reflections on how Heidegger's Address sheds light on the issues of university governance and academic freedom as the contemporary neoliberal university confronts its own challenges.
Toxoplasma gondii Infection of BALB/c Mice Perturbs Host Neurochemistry
Authors: Abdelati Abdelsalam Aisha A. , Woods Stuart , Henriquez Selina , Curran Lucy , Westrop Gareth , Roberts Craig W. 
Published: November 2024

ABSTRACTToxoplasma gondii infection has been associated with psychoneurological disease in humans and behavioural changes in rodents. However, the mechanisms accounting for this have not been fully described and in some cases could be argued to reflect the severe neuropathology that some mice suffer during infection. Herein we employ a multi‐omics approach to extensively examine BALB/c mice that are resistant to toxoplasmic encephalitis. Using a combination of LCMS (liquid chromatography–mass spectrometry) and RNAseq we demonstrate that infection alters the neurochemistry and the transcriptome of the brains of BALB/c mice. Notable changes to tryptophan, purine, arginine, nicotinamide and carnitine metabolism were observed in infected mice and this was accompanied with changes to the levels of a number of transcripts associated with enzymes these metabolic pathways. In addition, changes were seen in transcripts of many immunologically important genes known to contribute to immunity to T. gondii. Changes in the levels of additional transcripts during infection have previously been associated with psychoneurological diseases. The results demonstrate that the BALB/c mouse, with its relatively mild neurological disease, is a useful model for characterising the effects of T. gondii infection on murine neurochemistry. The results also implicate specific biochemical pathways in mediating these changes and should inform further mechanistic studies and suggest therapeutic targets.
Optimal sampling strategy for probability estimation: An application to the Agricultural Quarantine Inspection Monitoring program
Authors: Ma Huidi , Leibowicz Benjamin D. , Hasenbein John J. 
Published: November 2024

AbstractImported agricultural pests can cause substantial damage to agriculture, food security, and ecosystems. In the United States, the Agricultural Quarantine Inspection Monitoring (AQIM) program conducts random sampling to estimate the probabilities that cargo and passengers arriving at ports of entry carry pests. Assessing these risks accurately is critical to enable effective policies and operational procedures. This study introduces a pathway‐level analysis with an objective function aligned with AQIM's goal, offering a new perspective compared to the current container‐by‐container approach, which relies on heuristics to set inspection rates. We formulate an optimization model that minimizes the mean squared error of the probability estimates that AQIM obtains. The central decision‐making tradeoff that the model explores is whether it is preferable to sample more arriving containers (and fewer boxes per container) or more boxes per container (and fewer containers), given limited resources. We first derive an analytical solution for the optimal sampling strategy by leveraging several approximations. Then, we apply our model to a numerical case study of maritime cargo sampling at the Port of Long Beach. Across a wide range of parameter settings, the optimal strategy samples more containers (but fewer boxes per container) than the current AQIM protocol. The difference between the two strategies and the accuracy improvement with the optimal approach are larger if the pest statuses of boxes in the same container are more strongly correlated. We recommend that AQIM record box‐level (beyond only container‐level) inspection data, which could be used to estimate this correlation and other model parameters.
Rational surfaces with a non‐arithmetic automorphism group
Authors: Li Jennifer , Torres Sebastián 
Published: November 2024

AbstractIn [Algebraic surfaces and hyperbolic geometry, Cambridge University Press, Cambridge, 2012], Totaro gave examples of a K3 surface such that its automorphism group is not commensurable with an arithmetic group, answering a question of Mazur in Section 7 of [Bull. Amer. Math. Soc. (N.S.) 29 (1993), no. 1, 14–50]. We give examples of rational surfaces with the same property. Our examples are Looijenga pairs, that is, there is a connected singular nodal curve such that .
An Improved Direct Forcing Immersed Boundary Method With Integrated Mooring Algorithm for Floating Offshore Wind Turbines
Authors: Soydan Ahmet , Wang Widar Weizhi , Bihs Hans 
Published: November 2024

Abstract
An upgraded direct forcing immersed boundary method is implemented in the open-source hydrodynamic framework REEF3D::CFD for simulating the six-degrees-of-freedom motions of a floating offshore wind turbine (FOWT) based on the OC5 semi-submersible design. The direct forcing method is enhanced with a new density interpolation method across the fluid–structure interface that removes unphysical spurious phenomena and ensures stable and accurate wave load calculations on floating objects. A quasi-static algorithm is used for modeling the mooring system of the OC5 platform and restraining its motions in waves. The Navier–Stokes equations are solved on a staggered structured rectilinear grid for the hydrodynamic simulations. The level-set method is used to capture the free surface of the ocean waves. A ray-casting algorithm is employed to get inside–outside information near the fluid–solid interface while maintaining the underlying Cartesian grid in the hydrodynamic domain. The performance and accuracy of the mooring algorithm are compared to the widely-used mooring model MoorDyn, which is coupled to the hydrodynamic solver in REEF3D::CFD. The study demonstrates that the enhanced direct forcing method with the integrated quasi-static mooring algorithm in REEF3D::CFD provides a robust and accurate tool, suitable for the numerical analysis of the state-of-the-art FOWT in ocean waves.
Dissipation in Skewed Boundary Layers
Authors: Peacock Robert , Folk Masha , Pullan Graham 
Published: November 2024

Abstract
The entropy generation within a turbulent, collateral boundary layer is well understood and is characterized by a dissipation coefficient, Cd. However, it is common for the transverse pressure gradients in turbomachines to create highly skewed boundary layers, where the velocity varies in direction as well as magnitude. A combined experimental and high-fidelity computational approach is used to quantify the effect of skew on the dissipation coefficient for the first time. At a nominal condition of 14 deg of skew and Reθ of 1000, the increase in dissipation coefficient is 20% as determined from direct numerical simulation and 28% from experimental measurements, relative to the collateral boundary layer. Experimental data over a range of skew angles and Reθ values show that Cd increases approximately linearly with skew so that, at a skew of 25∘, loss is 70% greater than in the collateral boundary layer. The implications for loss estimation are examined by evaluating boundary layer loss, in the Harrison turbine cascade, with and without the influence of skew on Cd. By accounting for the skew in the boundary layer, a new proposed model has been used to calculate the loss coefficient in the Harrison cascade within 4% of the experimentally measured value.
Tensile, Flexural, and Fatigue Responses of Lightweight Pumice-Reinforced Magnesium Composite: Experimentation Followed by an Analytical Modeling
Authors: Nagarajan Bhuvanesh , Govindasamy Kumaresan , Chenrayan Venkatesh , Shahapurkar Kiran 
Published: November 2024

Abstract
Featherweight material to sustain mountainous loads is an extreme contrast. Still, in reality, the automobile and aerospace industries seek very light materials with high specific strength to survive in global competition. This study offers a timely answer to the problems faced by those sectors. Through the use of a stir-assisted squeeze casting method, the current investigation aims to generate a lightweight magnesium composite that is reinforced with porous low-density pumice particles at weight percentages of 5%, 10%, and 15%. An examination of the density indicates that there is a downward tendency in conjunction with the growing reinforcement. In comparison to the magnesium alloy in its natural state, the Pumice 15 coupon achieves a tensile strength increment of 47%, flexural strength increment of 35%, and a 10-time increment in service cycle at fatigue increase. The micromechanics model is implemented to justify the strengthening process in terms of the adhesion between the filler matrix and the interface shear strength. The property plots that were drafted provide evidence that the suggested material is lightweight while exhibiting a significant amount of strength in tensile, flexural, and fatigue. Post-fracture surface morphology analysis exhibits distinct tensile, flexural, and fatigue patterns.
Detection and quantification of human immunodeficiency virus-1 (HIV-1) total nucleic acids in wastewater settled solids from two California communities
Authors: Wolfe Marlene K. , Varkila Meri R. J. , Zulli Alessandro , Parsonnet Julie , Boehm Alexandria B. 
Published: November 2024

ABSTRACT

Wastewater surveillance for infectious agents has proved useful in identifying the circulation of viruses within populations. We investigated the presence and concentration of human immunodeficiency virus (HIV)-1 total nucleic acids (including both viral RNA and proviral DNA) in wastewater solids. We retrospectively measured HIV-1 nucleic acids in two samples per week for 26 months at two wastewater treatment plants serving populations with different prevalences of HIV infections in San Francisco and Santa Clara County, California, USA. We detected HIV nucleic acids in a majority of samples with concentrations ranging from non-detect to 3.9 × 10
5
cp/g (
N
= 459 samples total). Concentrations of HIV-1 were significantly higher in samples from the wastewater treatment plant serving a population with a higher prevalence of people living with HIV than in the plant serving a population with a lower prevalence. The HIV-1 nucleic acids amplified were primarily DNA and thus represented proviral DNA shedding into wastewater. Additionally, we found that HIV-1 nucleic acid concentrations in wastewater solids were orders of magnitude higher than those in liquid wastewater indicating that the HIV-1 target preferentially sorbs to solids. Whether concentrations of HIV-1 in wastewater solids can be used to identify the number of incident cases remains unknown. Additional work on HIV-1 shedding from individuals with viremia and people living with HIV is needed to translate wastewater measurements into quantitative information on infections. Additional work may also be needed to document non-human sources of HIV-1 nucleic acids in wastewater.

IMPORTANCE
Human immunodeficiency virus (HIV)-1 has infected nearly 100 million people since it emerged in the 1980s. Antiretroviral therapy prevents transmission of HIV and also allows infected individuals to live healthy lives with normal life expectancy. Consequently, identifying unrecognized cases of HIV is of paramount importance. Since wastewater represents a composite biological sample from a community, it may provide valuable information on HIV-1 prevalence that can be used to inform HIV testing and outreach.
Microbial consortia driving (ligno)cellulose transformation in agricultural woodchip bioreactors
Authors: Schiml Valerie C. , Walter Juline M. , Hagen Live H. , Varnai Aniko , Bergaust Linda L. , De Leon Arturo Vera Ponce , Elsgaard Lars , Bakken Lars R. , Arntzen Magnus Ø. 
Published: November 2024

ABSTRACT

Freshwater ecosystems can be largely affected by neighboring agriculture fields where potential fertilizer nitrate run-off may leach into surrounding water bodies. To counteract this eutrophic driver, farmers in certain areas are utilizing denitrifying woodchip bioreactors (WBRs) in which a consortium of microorganisms convert the nitrate into nitrogen gases in anoxia, fueled by the degradation of lignocellulose. Polysaccharide-degrading strategies have been well described for various aerobic and anaerobic systems, including the use of carbohydrate-active enzymes, utilization of lytic polysaccharide monooxygenases (LPMOs) and other redox enzymes, as well as the use of cellulosomes and polysaccharide utilization loci (PULs). However, for denitrifying microorganisms, the lignocellulose-degrading strategies remain largely unknown. Here, we have applied a combination of enrichment techniques, gas measurements, multi-omics approaches, and amplicon sequencing of fungal ITS and procaryotic 16S rRNA genes to identify microbial drivers for lignocellulose transformation in woodchip bioreactors and their active enzymes. Our findings highlight a microbial community enriched for (ligno)cellulose-degrading denitrifiers with key players from the taxa
Giesbergeria
,
Cellulomonas
,
Azonexus,
and UBA5070 (
Fibrobacterota
). A wide substrate specificity is observed among the many expressed carbohydrate-active enzymes (CAZymes) including PULs from Bacteroidetes. This suggests a broad degradation of lignocellulose subfractions, including enzymes with auxiliary activities whose functionality is still puzzling under strict anaerobic conditions.

IMPORTANCE

Freshwater ecosystems face significant threats from agricultural runoff, which can lead to eutrophication and subsequent degradation of water quality. One solution to mitigate this issue is using denitrifying woodchip bioreactors (WBRs), where microorganisms convert nitrate into nitrogen gases utilizing lignocellulose as a carbon source. Despite the well-documented polysaccharide-degrading strategies in various systems, the mechanisms employed by denitrifying microorganisms in WBRs remain largely unexplored. This study fills a critical knowledge gap by revealing the degrading strategies of denitrifying microbial communities in WBRs. By integrating state-of-the-art techniques, we have identified key microbial drivers including
Giesbergeria
,
Cellulomonas
,
Azonexus
, and UBA5070 (
Fibrobacterota
) playing significant roles in lignocellulose transformation and showcasing a broad substrate specificity and complex metabolic capability. Our findings advance the understanding of microbial ecology in WBRs and by revealing the enzymatic activities, this research may inform efforts to improve water quality, protect aquatic ecosystems, and reduce greenhouse gas emissions from WBRs.
Identification of
Veillonella parvula
and
Streptococcus gordonii
adhesins mediating co-aggregation and its impact on physiology and mixed biofilm structure
Authors: Dorison Louis , Béchon Nathalie , Martin-Gallausiaux Camille , Chamorro-Rodriguez Susan , Vitrenko Yakov , Ouazahrou Rania , Villa Romain , Deschamps Julien , Briandet Romain , Gribaldo Simonetta , Ghigo Jean-Marc , Beloin Christophe 
Published: November 2024

ABSTRACT

The dental plaque is a polymicrobial community where biofilm formation and co-aggregation, the ability to bind to other bacteria, play a major role in the construction of an organized consortium. One of its prominent members is the anaerobic diderm
Veillonella parvula,
considered a bridging species, which growth depends on lactate produced by oral streptococci. Understanding how
V. parvula
co-aggregates and the impact of aggregation has long been hampered due to the lack of appropriate genetic tools. Here we studied co-aggregation of the naturally competent strain
V. parvula
SKV38 with various oral bacteria and its effect on cell physiology. We show that
V. parvula
requires different trimeric autotransporters of the type V secretion system to adhere to oral streptococci and actinomyces. In addition, we describe a novel adhesin of
Streptococcus gordonii,
VisA (SGO_2004), as the protein responsible for co-aggregation with
V. parvula
. Finally, we show that co-aggregation does not impact cell-cell communication, which is mainly driven by environmental sensing, but plays an important role in the architecture and species distribution within the biofilm.

IMPORTANCE

Our research explores the mechanisms of bacterial adhesion within the dental plaque, focusing on
Veillonella parvula
, a key player in the oral microbiome. Dependent on lactate from streptococci,
V. parvula
plays a crucial bridging role in the formation of dental biofilms by co-aggregating with other bacteria. Despite its importance, the understanding of the underlying mechanisms of co-aggregation remains limited. Our study shows that
V. parvula
uses different trimeric autotransporters to adhere to oral Streptococci and Actinomyces. We additionally identify a novel adhesin from
S. gordonii
, VisA (SGO_2004) facilitating this interaction. We found that although co-aggregation does not affect cell-cell communication, it is critical for biofilm structure and species distribution. This research opens up new avenues for exploring microbial interactions in dental health and diseases.
Streptococcus agalactiae
strain COH1 transcriptome in association with stem cell-derived brain-like endothelial cells
Authors: Vollmuth Nadine , Sauerwein Till , Foerstner Konrad U. , Westermann Alexander J. , Schubert-Unkmeir Alexandra , Lam Daryl W. , Kim Brandon J. 
Published: November 2024

ABSTRACT

Streptococcus agalactiae
(Group
B Streptococcus
) strain COH1 is a representative strain of serotype III, multi-locus sequence type 17, which is disproportionately associated with neonatal meningitis. Here we report the transcriptome of COH1 when interacting with human brain endothelial cells compared with COH1 alone.
Metagenome-assembled genomes of 72
Escherichia coli
strains from vaginal samples collected from pregnant women
Authors: Boutouchent Nassim , Vu Thi Ngoc Anh , Landraud Luce , Kennedy Sean P. 
Published: November 2024

ABSTRACT

We report 72 metagenome-assembled genomes (MAGs) of
Escherichia coli
recovered from the vaginal microbiomes of pregnant women. The MAGs have an estimated median genome size of 5.1 Mb (IQR 4.9–5.3). The average number of unique genes identified per genome was 3,330 genes (IQR 3,356–3,501), with a mean of 1,708 per genome being annotated.
$$^{235}\text {U(n}_{\text {th}}\text {,f)}$$ mass yield evaluation with associated covariance matrix
Authors: Cheikh S. M. , Kessedjian G. , Serot O. , Chebboubi A. , Bernard D. , Vallet V. 
Published: November 2024

AbstractThe study of fission yields has a major impact on the characterization and understanding of the fission process and its applications. Mass yield evaluation represents a key element in order to perform the best estimation of independent and cumulative fission product yields. Today, the lack of analysis-based correlation matrix between the different fission observables induces many inconsistencies in the evaluations. In particular, the mass yield uncertainties are drastically overestimated in comparison to chain yields while these two quantities only differ from the emission of delayed neutrons. In this work, a new consistent process of mass yield evaluation is proposed taking into account the description of the covariance matrix. For $$^{235}\text {U(n}_{\text {th}}\text {,f)}$$

235

U(n
th

,f)

mass yields, existing data cover a large range of produced masses which makes it possible to propose an evaluation of mass yields independently of any model with a precision closed to $$1.5\%$$

1.5
%

for the high yields. This new precision brings the possibility to discuss the origin of the structures in the post-neutron mass yields, in particular the consistency with the pre-neutron mass yields and the prompt neutron multiplicity per mass. The work is the first part of the $$^{235}\text {U(n}_{\text {th}}\text {,f)}$$

235

U(n
th

,f)

thermal neutron induced fission yield evaluation which will be included in the new JEFF-4 library.