bluuebunny/crossref_metadata_2025 huggingface dataset:
Long‐term methylome changes after experimental seed demethylation and their interaction with recurrent water stress in Erodium cicutarium (Geraniaceae)
Authors: Balao F. , Medrano M. , Bazaga P. , Paun O. , Alonso C.
Published: September 2024

The frequencies and lengths of drought periods are increasing in subtropical and temperate regions worldwide. Epigenetic responses to water stress could be key for plant resilience to these largely unpredictable challenges. Experimental DNA demethylation, together with application of a stress factor is an appropriate strategy to reveal the contribution of epigenetics to plant responses to stress.

We analysed leaf cytosine methylation changes in adult plants of the annual Mediterranean herb, Erodium cicutarium, in a greenhouse, after seed demethylation with 5‐Azacytidine and/or recurrent water stress. We used bisulfite RADseq (BsRADseq) and a newly reported reference genome for E. cicutarium to characterize methylation changes in a 2 × 2 factorial design, controlling for plant relatedness.

In the long term, 5‐Azacytidine treatment alone caused both hypo‐ and hyper‐methylation at individual cytosines, with substantial hypomethylation in CG contexts. In control conditions, drought resulted in a decrease in methylation in all but CHH contexts. In contrast, the genome of plants that experienced recurrent water stress and had been treated with 5‐Azacytidine increased DNA methylation level by ca. 5%.

Seed demethylation and recurrent drought produced a highly significant interaction in terms of global and context‐specific cytosine methylation. Most methylation changes occurred around genic regions and within Transposable Elements. The annotation of these Differentially Methylated Regions associated with genes included several with a potential role in stress responses (e.g., PAL, CDKC, and ABCF), confirming an epigenetic contribution in response to stress at the molecular level.
Plant Growth Promoting Rhizobacteria (PGPR) induced protection: A plant immunity perspective
Authors: Kumari Rinkee , Pandey Ekta , Bushra Sayyada , Faizan Shahla , Pandey Saurabh
Published: September 2024

Plant‐environment interactions, particularly biotic stress, are increasingly essential for global food security due to crop losses in the dynamic environment. Therefore, understanding plant responses to biotic stress is vital to mitigate damage. Beneficial microorganisms and their association with plants can reduce the damage associated with plant pathogens. One such group is PGPR (Plant growth‐promoting rhizobacteria), which influences plant immunity significantly by interacting with biotic stress factors and plant signalling compounds. This review explores the types, metabolism, and mechanisms of action of PGPR, including their enzyme pathways and the signalling compounds secreted by PGPR that modulate gene and protein expression during plant defence. Furthermore, the review will delve into the crosstalk between PGPR and other plant growth regulators and signalling compounds, elucidating the physiological, biochemical, and molecular insights into PGPR's impact on plants under multiple biotic stresses, including interactions with fungi, bacteria, and viruses. Overall, the review comprehensively adds to our knowledge about PGPR's role in plant immunity and its application for agricultural resilience and food security.
Which Novel Ingredient Should be Considered the “Holy Grail” for Sustainable Production of Finfish Aquafeeds?
Authors: Panteli Nikolas , Kousoulaki Katerina , Antonopoulou Efthimia , Carter Chris G. , Nengas Ioannis , Henry Morgane , Karapanagiotidis Ioannis T. , Mente Elena
Published: September 2024

The immense production of fishmeal and fish oil is dramatically intensifying the severe state of pelagic fisheries overexploitation. The latter in conjunction with the increasing demand for low‐cost protein‐rich food supply prompt aquaculture to employ new practice. Several novel dietary ingredients are currently under evaluation for potential incorporation in aquafeeds in an effort to shift the aquaculture sector toward a more sustainable and economic production. The present review aims to summarize the existing findings regarding the effects of studied alternatives to fishmeal and fish oil on the most valuable and commercially produced marine (Sparus aurata and Dicentrarchus labrax) and freshwater (Salmo salar and Oncorhynchus mykiss) finfish species in European aquaculture. Alternative protein sources, including macroalage (marine plants), krill (marine fishery), insects (terrestrial), terrestrial animal by‐products (processed/rendered), and single cell ingredient (biotechnology), are discussed for their efficiency in promoting the growth and the welfare of both fry and adult cultured finfish species. Applicability of these ingredients is reviewed in terms of nutrient composition, dietary inclusion level, performance output, digestibility, and health benefits. In addition, a meta‐analysis was conducted based on data from peer‐reviewed scientific publications in order to assess whether novel ingredients meet the dietary protein (amino acid) and lipid requirements of finfishes. Aquafeed reformulation strategies should ensure the recommended daily nutritional requirements and additionally indicate the meta‐analysis alternatives, such as microalgae, which are deficient in essential amino acids. The sustainable expansion of aquaculture is on the horizon, but which novel ingredients may be regarded as the key drivers to its establishment?
Ambiguous and Complex – Rural Revival in a Peripheral Mountain Region (SW Poland)
Authors: Latocha‐Wites Agnieszka , Kajdanek Katarzyna , Sikorski Dominik , Szmytkie Robert , Tomczak Przemysław
Published: September 2024

The general development conditions of rural areas have been addressed by many authors; however, the conditions and factors that allow the depopulated problem rural areas to re‐enter the development path are an understudied phenomenon. This article examines the types and drivers of rural revival, evaluates the transformations of rural areas and forecasts their future development. It focuses on a representative region for the key transformations of mountainous rural areas in the Polish‐Czech borderland. This study offers a complex, interdisciplinary approach using quantitative and qualitative methods to examine the in‐depth mechanisms of rural transformation and to vocalise local knowledge and inhabitants' perceptions. The results demonstrate that the depopulated and marginalised peripheral rural regions have the potential to return to the development path, but the symptoms, drivers and perceptions of rural transformations vary greatly across the region. The study highlights the complexity and ambiguity of assessing, evaluating and forecasting rural transformations.
Survey of pediatric massive transfusion protocol practice at United States level I trauma centers: An AABB Pediatric Transfusion Medicine Subsection study
Authors: Adkins Brian D. , Noland Daniel K. , Jacobs Jeremy W. , Booth Garrett S. , Malicki Denise , Helander Louise , Jacquot Cyril , Buscema Gina , Goel Ruchika , Andrews Jennifer , Lieberman Lani
Published: September 2024

Background

Trauma remains the leading cause of pediatric mortality in the United States. Although use of massive transfusion protocols (MTPs) in this population is widespread, optimal pediatric resuscitation is not well established. We sought to assess contemporary pediatric MTP practice in the United States.

Study Design and Methods

A web‐based survey was designed by the Association for the Advancement of Blood & Biotherapies (AABB) Pediatric Transfusion Medicine Subsection and distributed to select American College of Surgeons (ACS) Level I Verified pediatric trauma centers. The survey assessed current MTP policy, implementation, and recent changes in practice.

Results

Response rate was 55% (22/40). Almost half of the respondents were from the South. The median RBC:plasma ratio was 1 (interquartile range 1–1.5). Protocolized fibrinogen supplementation was common while integration of antifibrinolytic therapy into MTPs was infrequent. Viscoelastic testing (VET) was available at most sites, 71% (15/21, one site did not respond), and was generally utilized on an ad‐hoc basis. Roughly, a third of sites had changed their MTP in the past 3 years due to blood supply issues, and about a third reported having group O Whole Blood on‐site.

Conclusion

MTP practice is similar throughout the United States. Though fibrinogen supplementation is common—other emerging interventions such as antifibrinolytic therapy or utilization of routine viscoelastic testing—are not widespread. Pediatric transfusion medicine experts must continue to follow practice change, as contemporary large trials begin to characterize new supportive modalities to optimize resuscitation in pediatric trauma patients.
Characterization of blood bank and transfusion medicine practices for pregnant individuals with fetuses at risk of hemolytic disease in the United States
Authors: Jacobs Jeremy W. , Booth Garrett S. , Moise Kenneth J. , Adkins Brian D. , Bakhtary Sara , Fasano Ross M. , Goel Ruchika , Hinton Hannah D. , Laghari Sadia A. , Stephens Laura D. , Tormey Christopher A. , Crowe Elizabeth P. , Bloch Evan M. , Abels Elizabeth A.
Published: September 2024

Background

Hemolytic disease of the fetus and newborn (HDFN) is caused by maternal alloantibody‐mediated destruction of fetal/neonatal red blood cells (RBCs). While the pathophysiology has been well‐characterized, the clinical and laboratory monitoring practices are inconsistent.

Methods

We surveyed 103 US institutions to characterize laboratory testing practices for individuals with fetuses at risk of HDFN. Questions included antibody testing and titration methodologies, the use of critical titers, paternal and cell‐free fetal DNA testing, and result reporting and documentation practices.

Results

The response rate was 44% (45/103). Most respondents (96%, 43/45) assess maternal antibody titers, primarily using conventional tube‐based methods only (79%, 34/43). Among respondents, 51% (23/45) rescreen all individuals for antibodies in the third trimester, and 60% (27/45) perform paternal RBC antigen testing. A minority (27%, 12/45) utilize cell‐free fetal DNA (cffDNA) testing to predict fetal antigen status. Maternal antibody titers are performed even when the fetus is not considered to be at risk of HDFN based on cffDNA or paternal RBC antigen testing at 23% (10/43) of sites that assess titers.

Discussion

There is heterogeneity across US institutions regarding the testing, monitoring, and reporting practices for pregnant individuals with fetuses at risk of HDFN, including the use of antibody titers in screening and monitoring programs, the use of paternal RBC antigen testing and cffDNA, and documentation of fetal antigen results. Standardization of laboratory testing protocols and closer collaboration between the blood bank and transfusion medicine service and the obstetric/maternal‐fetal medicine service are needed.
Optimal Control of a Roll-to-Roll Dry Transfer Process With Bounded Dynamics Convexification
Authors: Martin Christopher , Zhao Qishen , Bakshi Soovadeep , Velasquez Enrique , Li Wei , Chen Dongmei
Published: September 2024

For efficient roll-to-roll (R2R) production of flexible electronic components, a precise R2R transfer peeling process is essential, requiring accurate modeling and control. This paper introduces a novel approach to confining the dynamics of a nonlinear R2R mechanical peeling system within a convex set known as a norm-bounded linear differential inclusion (NLDI). This method utilizes constraints on uncertain system variables to create a tighter NLDI representation compared to other convexification techniques. Moreover, it offers drastically reduced computational cost compared to previous methods applied to convexify the R2R peeling system. The NLDI is employed to generate an H∞-optimal controller for the R2R peeling system, and both simulations and experiments demonstrate better dynamic performance compared to other controllers for R2R transfer.
Design, Modeling, and Control of a Hardware-in-the-Loop Testbed for Off-Road Vehicles
Authors: Zhao Gaonan , Yao Jie , Edson Connor P. , Sun Zongxuan
Published: September 2024

This paper presents the design, modeling, and control of a hardware-in-the-loop (HIL) testbed for off-road vehicles. The proposed HIL testbed employs a transient hydrostatic dynamometer to load a diesel engine to emulate any loading cycles of a wheel loader, which is a representative off-road vehicle. A fully validated wheel loader model is used to calculate the engine load, including both the drive and work functions. Besides, iterative learning control (ILC) has been designed for the loading torque tracking of the hydrostatic dynamometer to ensure accurate emulation of real-world operation scenarios. The developed HIL testbed is used to demonstrate more than 26% energy benefits of automated wheel loaders through systematic optimization compared with human-operated wheel loaders. This HIL testbed serves as a robust platform for advancing research and development across various off-road vehicles, including excavators, tractors, and harvesters.
Comprehensive Analysis of Critical Heat Flux and Heat Transfers in a Confined Jet Impingement Boiling Cooling System
Authors: Guerfi Djamel Eddine , Roux Stéphane , Allanic Nadine , Sarda Alain , Lecointe Damien
Published: September 2024

This study deepens the understanding of the heterogeneity of thermal exchanges in a cylindrical channel cooled by impinging water jets, considering the influence of transverse air flow and gravity. The results reveal distinct cooling zones, with higher intensity near the stagnation points, where the Critical Heat Flux (CHF) recorded of 4.29 MW/m2 corresponds to a heat transfer coefficient of 19.46 KW/(m2 · K). This CHF value decreases by 50% in the jet overlap points and ranges between 39% to 43% of CHF in the upper and lower zones of the channel, perfectly aligning with bibliographic references and thereby enhancing the credibility of the model. This three-dimensional model based on the inverse method, used to calculate thermal parameters, demonstrates remarkable efficiency with an average relative error of 3%, considering the difference in cooled mass between each side of the channel and the heterogeneity of cooling between the inlet and outlet of the channel.

The detailed analysis of local and zonal parameters highlights the importance of the precise position of the jets. This study provides a comprehensive view of the challenges related to cooling cylindrical surfaces. These results enrich the field of thermal management, paving the way for enhanced applications of this technique in critical industrial environments.
Numerical Estimation of Heat Transfer Parameters: A Study on Inverse Methods in Combustion Chambers
Authors: Tahan Meryem , Özkökdemir Emir
Published: September 2024

Inverse heat transfer problems have consistently remained a crucial focal point in research and improvement efforts. These problems typically provide an opportunity to approximate the determination of a property or condition, in cases where it is not possible to measure a boundary condition or a thermophysical property of a material, using various methods based on measured values. The unknown heat transfer can be estimated by using a parameter or function estimation approach with the inverse heat transfer method. If the functional form of the unknown parameters is known, the inverse problem can be solved to determine several parameters within the function. Conversely, if there is no information regarding the functional form of the problem, function estimation can be performed to find the solution. In the thermal design of systems with complex heat flows, such as combustion chambers, it is important to clearly know the thermal loads to which the inner surface of the structure is subjected. It is not possible to obtain these loads by direct measurements. On the other hand, heat transfer parameters at the inner surface can be estimated by inverse methods using measurements taken from the outer surface. With the inverse method mentioned in this study, the heat transfer parameters at the inner surface of a combustion chamber are numerically estimated using temperature measurements taken from the outer surface. A generic combustion chamber is modelled by conduction based finite element method. The unknown heat transfer parameters of the model are iteratively obtained by an optimization algorithm. Subsequently, a variety of optimization methods are utilized to minimize predictive errors, thereby evaluating the uniqueness of the resulting solution.
Examining the Symmetry of a Turbulent Wake Arising From Asymmetric Turbulent Shear Layers: An Experimental and Analytical Study
Authors: Momayez Ladan , Dghim Marouen , Ferchichi Mohsen , Daneshmand Farhang
Published: September 2024

This study examines the wake of a plate subject to asymmetric boundary layers at the trailing edge. In contrast to previous studies, this work varies shear layer asymmetry using tripping wires while keeping the Reynolds number and pressure constant. Six distinct conditions are considered, encompassing the natural wake and asymmetric wakes for five different values of θ/θo where θ is the boundary layer momentum thickness of the disturbed upper plate side, while θo is momentum thickness of the natural boundary on the lower plate side. Both boundary layers are turbulent, and the wake flow statistics were measured at downstream position, x/h. These conditions were studied to gain deeper insight into wake evolution and self-similarity. Significant changes in velocity profiles were observed with increasing momentum thickness ratio. The asymmetric wake showed distinct differences, including a velocity defect (Ud = Ue – Ū) where Ue is edge velocity of the wake and Ū is mean velocity and higher shear stress compared to the symmetric case. The study suggests the presence of long memory in wakes due to self-preserving states established by initial conditions.

Developing analytic methods in conjunction with Reynolds stress profile and Reynolds stress shape functions, we were able to formulate a self-similarity equation for the wake.
Thermoelectric Waste Heat Recovery in a Concentric Tube Silencer for Automotive System
Authors: Lucidi Michael , Farouk Bakhtier
Published: September 2024

In this work, a concentric tube silencer is modeled and studied for its thermodynamic properties using time-dependent compressible computational fluid dynamics. The silencer is simultaneously studied for its capabilities to transfer heat to thermoelectric devices surrounding the silencer, as well as its ability to reduce noise. Two silencer geometries, one with round and the other with square cross-sections, are considered. Efforts have been conducted to recapture the heat from the exhaust for reuse within the automotive system. One such effort involved the ’modified silencing heat exchanger’ recently proposed to replace the muffler of automobiles with a passive device that simultaneously silences the outgoing exhaust while collecting heat. As the muffler is intrinsically involved in treating the loud exhaust produced by an automotive engine, it serves as an ideal location for recapturing the heat generated by said engines and overall improving the efficiency of the system that it is tied into. Previous work has found that the heat transfer to the walls of a concentric tube silencer has a noticeable effect on the frequency bands of the silencer’s overall transmission loss characteristics.
Examination of nonideal film growth in batch atomic layer deposition for plasma-resistant coatings
Authors: Guo Lanxin , Wang Yixian , Pang Zifan , Han Xin , Wang Yafeng , Peng Lipei , Gao Xin , Pei Chunlei , Wang Tuo , Gong Jinlong
Published: September 2024

Atomic layer deposition (ALD) can be used to fabricate protective coatings including moisture barrier layers for organic light emitting diodes, anticorrosion layers for photoelectrodes, and plasma-resistant coating for semiconductor manufacturing equipment, which necessitates the deposition of large and thick ALD films via batch ALD. However, batch ALD for the fabrication of large-area and thick coatings exhibits nonideal film growth, a phenomenon that cannot solely be explained by transient concentration distribution within the deposition chamber. This paper describes the application of precursor “exposure” (in the unit of Langmuir, or Pa s), defined as the integral of concentration over time, as a metric to assess the growth per cycle (GPC) distribution under nonideal ALD conditions, demonstrating that the local GPC correlates well with the cumulative precursor exposure at that site. Consequently, this measure can effectively predict the nonuniformity (NU) distribution of film thickness and facilitate the determination of optimal operating conditions that ensure maximal uniformity of exposure. Under this condition, the intrafilm NU of ALD-grown Al2O3 film (nominal thickness 300 nm) was reduced to 1.2%, and the interfilm NU is diminished to as low as 3.3%. These values represent reductions of 40% and 45%, respectively, compared to the NU levels observed under nonideal conditions (insufficient trimethylaluminum, TMA exposure downstream). The plasma etch rate of ALD-deposited films is merely 4.3 nm/min, representing a reduction of one-half compared to films deposited under nonideal conditions (9.8 nm/min) with overload TMA exposure downstream leading to chemical vapor deposition-like reactions.
Challenges and Future Directions for Promoting Intersectional Quantitative Studies in Physical Activity Research
Authors: Sone Mari , Altenburg Teatske M. , ChinAPaw Mai J.M.
Published: September 2024

Understanding health inequalities is essential for improving social justice. Intersectionality refers to a theoretical framework for studying the intersection of multiple social categorizations that create unique experiences and related social inequalities. Currently, the majority of the intersectional studies in the physical activity field have a qualitative design; thus, there is a need for quantitative intersectional studies. This commentary aims to explore primary obstacles impeding intersectional quantitative research and provide recommendations for overcoming these obstacles in physical activity research. In the commentary, we discuss that the lack of accessibility of large-scale and diverse data sets, and suboptimal social categorizations and intersectionality-related questions may contribute to the scarcity of intersectional quantitative research in the field. To facilitate intersectional quantitative analyses, we advocate for making large-scale data sets accessible for intersectional secondary analyses, diverse sampling, standardizing questions and categories related to intersectionality, promoting inclusive research designs and methods, and using the appropriate questions and social categorization that reflect the distinct experiences of each subgroup. By addressing these challenges, researchers may gain new insights into health disparities, making physical activity research more inclusive and contributing to more equitable health outcomes.
Profiling sorghum-microbe interactions with a specialized photoaffinity probe identifies key sorgoleone binders in
Acinetobacter pittii
Authors: Van Fossen Elise M. , Kroll Jared O. , Anderson Lindsey N. , McNaughton Andrew D. , Herrera Daisy , Oda Yasuhiro , Wilson Andrew J. , Nelson William C. , Kumar Neeraj , Frank Andrew R. , Elmore Joshua R. , Handakumbura Pubudu , Lin Vivian S. , Egbert Robert G.
Published: September 2024

Interactions between plants and soil microbial communities that benefit plant growth and enhance nutrient acquisition are driven by the selective release of metabolites from plant roots, or root exudation. To investigate these plant-microbe interactions, we developed a photoaffinity probe based on sorgoleone (
so
rgoleone
d
iazirine
a
lkyne for
p
hoto
a
ffinity
l
abeling, SoDA-PAL), a hydrophobic secondary metabolite and allelochemical produced in
Sorghum bicolor
root exudates. We applied SoDA-PAL to the identification of sorgoleone-binding proteins in
Acinetobacter pittii
SO1, a potential plant growth-promoting microbe isolated from sorghum rhizosphere soil. Competitive photoaffinity labeling of
A. pittii
whole cell lysates with SoDA-PAL identified 137 statistically enriched proteins, including putative transporters, transcriptional regulators, and a subset of proteins with predicted enzymatic functions. We performed computational protein modeling and docking with sorgoleone to prioritize candidates for experimental validation and then confirmed binding of sorgoleone to four of these proteins
in vitro
: the α/β fold hydrolase SrgB (OH685_09420), a fumarylacetoacetase (OH685_02300), a lysophospholipase (OH685_14215), and an unannotated hypothetical protein (OH685_18625). Our application of this specialized sorgoleone-based probe coupled with structural bioinformatics streamlines the identification of microbial proteins involved in metabolite recognition, metabolism, and toxicity, widening our understanding of the range of cellular pathways that can be affected by a plant secondary metabolite.

IMPORTANCE

Here, we demonstrate that a photoaffinity-based chemical probe modeled after sorgoleone, an important secondary metabolite released by sorghum roots, can be used to identify microbial proteins that directly interact with sorgoleone. We applied this probe to the sorghum-associated bacterium
Acinetobacter pittii
and showed that probe labeling is dose-dependent and sensitive to competition with purified sorgoleone. Coupling the probe with proteomics and computational analysis facilitated the identification of putative sorgoleone binders, including a protein implicated in a conserved pathway essential for sorgoleone catabolism. We anticipate that discoveries seeded by this workflow will expand our understanding of the molecular mechanisms by which specific metabolites in root exudates shape the sorghum rhizosphere microbiome.
Identification of a chlorosalicylic acid decarboxylase (CsaD) involved in decarboxylation of 3,6-DCSA from an anaerobic dicamba-degrading sludge
Authors: Zhang Xuan , Wu Ningning , Geng Keke , Yuan Cansheng , Wang Baozhan , Shi Junyu , Qiu Jiguo , He Jian
Published: September 2024

3,6-Dichlorosalicylic acid (3,6-DCSA) is the demethylation metabolite of herbicide 3,6-dichloro-2-methoxy benzoic acid (dicamba). Previous studies have shown that anaerobic sludge further transformed 3,6-DCSA through decarboxylation and dechlorination. However, the anaerobe, enzyme, and gene involved in the anaerobic degradation of 3,6-DCSA are still unknown. In this study, an anaerobic sludge that efficiently degraded dicamba was enriched, and a 3,6-DCSA decarboxylase, designated chlorosalicylic acid decarboxylase (CsaD), was partially purified and identified from the anaerobic sludge. Metagenomic analysis showed that the
csaD
gene was located in a gene cluster of metagenome-assembled genome 8 (MAG8). MAG8 belonged to an uncultured order, OPB41, in the class
Coriobacteriia
of the phylum
Actinobacteria
, and its abundance increased approximately once during the enrichment process. CsaD was a non-oxidative decarboxylase in the amidohydrolase 2 family catalyzing the decarboxylation of 3,6-DCSA and 6-chlorosalicylic acid (6-CSA). Its affinity and catalytic efficiency for 3,6-DCSA were significantly higher than those for 6-CSA. This study provides new insights into the anaerobic catabolism of herbicide dicamba.

IMPORTANCE

Dicamba, an important hormone herbicide, easily migrates to anoxic habitats such as sediment, ground water, and deep soil. Thus, the anaerobic catabolism of dicamba is of importance. Anaerobic bacteria or sludge demethylated dicamba to 3,6-DCSA, and in a previous study, based on metabolite identification, it was proposed that 3,6-DCSA be further degraded via two pathways: decarboxylation to 2,5-dichlorophenol, then dechlorination to 3-chlorophenol (3-CP); or dechlorination to 6-CSA, then decarboxylation to 3-CP. However, there was no physiological and genetic validation for the pathway. In this study, CsaD catalyzed the decarboxylation of both 3,6-DCSA and 6-CSA, providing enzyme-level evidence for the anaerobic catabolism of 3,6-DCSA through the two pathways. CsaD was located in MAG8, which belonged to an uncultured anaerobic actinomycetes order, OPB41, indicating that anaerobic actinomycetes in OPB41 was involved in the decarboxylation of 3,6-DCSA. This study provides a basis for understanding the anaerobic catabolism of dicamba and the demethylation product, 3,6-DCSA.
Flagellar point mutation causes social aggregation in laboratory-adapted
Bacillus subtilis
under conditions that promote swimming
Authors: Alvi Safiya , Mondelo V. Denise , Boyle Jacqueline , Buck Amanda , Gejo Justin , Mason Molly , Matta Shriya , Sheridan Abigail , Kreutzberger Mark A. B. , Egelman Edward H. , McLoon Anna
Published: September 2024

Motility allows microbes to explore and maximize success in their environment; however, many laboratory bacterial strains have a reduced or altered capacity for motility. Swimming motility in
Bacillus subtilis
depends on peritrichous flagella and is carried out individually as cells move by biased random walks toward attractants. Previously, we adapted
Bacillus subtilis
strain 3610 to the laboratory for 300 generations in lysogeny broth (LB) batch culture and isolated lab-adapted strains. Strain SH2 is motility-defective and in broth culture forms large, frequently spherical aggregates of cells. A single point mutation in the flagellin gene
hag
that causes amino acid 259 to switch from A to T is necessary and sufficient to cause these social cell aggregates, and aggregation occurs between flagellated cells bearing this point mutation regardless of the strain background. Cells associate when bearing this mutation, but flagellar rotation is needed to pull associating cells into spherical aggregates. Using electron microscopy, we are able to show that the SH2 flagellar filament has limited polymorphism when compared to other flagellar structures. This limited polymorphism hinders the flagellum’s ability to function as a motility apparatus but appears to alter its function to that of cell aggregation/adhesion. We speculate that the genotype-specific aggregation of cells producing Hag
A259T
flagella could have increased representation in a batch-culture experiment by allowing similar cells to go through a transfer together and also that this mutation could serve as an early step to evolve sociality in the natural world.

IMPORTANCE

The first life forms on this planet were prokaryotic, and the earliest environments were aquatic, and from these relatively simple starting conditions, complex communities of microbes and ultimately multicellular organisms were able to evolve. Usually, motile cells in aqueous environments swim as individuals but become social by giving up motility and secreting extracellular substances to become a biofilm. Here, we identify a single point mutation in the flagellum that is sufficient to allow cells containing this mutation to specifically form large, suspended groups of cells. The specific change in the flagellar filament protein subunits causes a unique change in the flagellar structure. This could represent a distinct way for closely related cells to associate as an early precursor to sociality.
The combination of three CD4-induced antibodies targeting highly conserved Env regions with a small CD4-mimetic achieves potent ADCC activity
Authors: Marchitto Lorie , Richard Jonathan , Prévost Jérémie , Tauzin Alexandra , Yang Derek , Chiu Ta-Jung , Chen Hung-Ching , Díaz-Salinas Marco A. , Nayrac Manon , Benlarbi Mehdi , Beaudoin-Bussières Guillaume , Anand Sai Priya , Dionne Katrina , Bélanger Étienne , Chatterjee Debashree , Medjahed Halima , Bourassa Catherine , Tolbert William D. , Hahn Beatrice H. , Munro James B. , Pazgier Marzena , Smith Amos B. , Finzi Andrés
Published: September 2024

The majority of naturally elicited antibodies against the HIV-1 envelope glycoproteins (Env) are non-neutralizing (nnAbs) because they are unable to recognize the Env trimer in its native “closed” conformation. Nevertheless, it has been shown that nnAbs have the potential to eliminate HIV-1-infected cells by antibody-dependent cellular cytotoxicity (ADCC) provided that Env is present on the cell surface in its “open” conformation. This is because most nnAbs recognize epitopes that become accessible only after Env interaction with CD4 and the exposure of epitopes that are normally occluded in the closed trimer. HIV-1 limits this vulnerability by downregulating CD4 from the surface of infected cells, thus preventing a premature encounter of Env with CD4. Small CD4-mimetics (CD4mc) sensitize HIV-1-infected cells to ADCC by opening the Env glycoprotein and exposing CD4-induced (CD4i) epitopes. There are two families of CD4i nnAbs, termed anti-cluster A and anti-CoRBS Abs, which are known to mediate ADCC in the presence of CD4mc. Here, we performed Fab competition experiments and found that anti-gp41 cluster I antibodies comprise a major fraction of the plasma ADCC activity in people living with HIV (PLWH). Moreover, addition of gp41 cluster I antibodies to cluster A and CoRBS antibodies greatly enhanced ADCC-mediated cell killing in the presence of a potent indoline CD4mc, CJF-III-288. This cocktail outperformed broadly neutralizing antibodies and even showed activity against HIV-1-infected monocyte-derived macrophages. Thus, combining CD4i antibodies with different specificities achieves maximal ADCC activity, which may be of utility in HIV cure strategies.

IMPORTANCE

The elimination of HIV-1-infected cells remains an important medical goal. Although current antiretroviral therapy decreases viral loads below detection levels, it does not eliminate latently infected cells that form the viral reservoir. Here, we developed a cocktail of non-neutralizing antibodies targeting highly conserved Env regions and combined it with a potent indoline CD4mc. This combination exhibited potent ADCC activity against HIV-1-infected primary CD4 + T cells as well as monocyte-derived macrophages, suggesting its potential utility in decreasing the size of the viral reservoir.
The complete mitochondrial genome of the banana pathogen
Fusarium oxysporum
f. sp.
cubense
M5
Authors: Maldonado-Bonilla Luis David , Caballero-Pérez Juan , Ángeles-Argáiz Rodolfo Enrique
Published: September 2024

We report the complete mitochondrial genome of a causal agent of banana fusarium wilt isolated in Mexico. The whole set of genes encoding proteins related to respiration and ATP synthesis, rRNAs, tRNAs are enlisted. Two open reading frames of unknown function conserved in
Fusarium oxysporum
were also identified.
Complete genome sequence of
Synechocystis
sp. LKSZ1 isolated from a pond in the Suzukakedai campus of Tokyo Institute of Technology
Authors: Okumura Leonardo Ken , Masuda Shinji
Published: September 2024

Cyanobacteria belonging to the
Synechocystis
genus have been isolated from diverse aquatic environments. This announcement reports the complete genome sequence of
Synechocystis
sp. LKSZ1 newly isolated from a pond in a university campus in Yokohama, Japan. The genome sequencing was performed using the PacBio Revio HiFi long-read technology.
Complete genome sequence of
E. coli
lytic bacteriophage BAU.Micro_ELP-22, isolated from sewage water, Bangladesh
Authors: Kallol Md. Arefin , Nazir K.H.M. Nazmul Hussain , Alam Jahangir , Rahman Md. Bahanur , Rahman Marzia
Published: September 2024

Escherichia coli
lytic bacteriophage BAU.Micro_ELP-22 was isolated from sewage wastewater as a therapeutic agent alternative to antibiotics. The phage genome is 373,488 bp in length, encoding 744 protein-coding sequences and 7 tRNAs, and contains no antibiotic resistance, virulence, or temperate marker genes, which specifies its potentiality as a compatible phage therapy candidate.
Complete genome sequences of four lytic bacteriophages against multidrug-resistant
Enterococcus faecium
Authors: Soro Oumarou , Kigen Collins , Nyerere Andrew , Gachoya Moses , Wachira James , Onyonyi Vanessa , Georges Martin , Wataka Allan , Ondolo Stephen , Cherono Karen , Odoyo Erick , Musila Lillian
Published: September 2024

We report the genome sequences of four
Enterococcus faecium
phages isolated from environmental wastewater in Kenya. They are double-stranded DNA phages with genomes varying in length from 42,231 to 43,348 bp, with G+C contents ranging from 34.96% to 35.2%. The genomes contain 78–82 coding sequences.
First draft genome sequence of a
Pectobacterium polaris
strain isolated in South Africa from potato tuber affected by soft rot
Authors: Dapuliga Christiana C. , Claussen Maike , Schmidt Stefan
Published: September 2024

A phytopathogenic strain of
Pectobacterium polaris
(designated SRB2) was isolated for the first time in South Africa from a potato tuber affected by soft rot. The draft genome of strain SRB2 encodes various plant cell wall-degrading enzymes and genes associated with biofilm formation and virulence. Antibiotic resistance genes were not detected.
Supplemental Material: Exploring the relationship between sedimentary transport systems and basin dynamics: A case study from the Levant Basin (Eastern Mediterranean Sea) before, during, and after the Messinian
Authors: Moneron Jimmy , al. et
Published: September 2024

This supplemental material provides an additional methodology for estimating widths of subduction-related flexure using theoretical calculations.
Diagnosis and management of hidradenitis suppurativa: a review for the emergency clinician
Authors: Klufas Daniel M , Ojute Feyisayo , Shochat Guy , Naik Haley B
Published: September 2024

Hidradenitis suppurativa (HS) is a complex, chronic skin disease characterised by painful inflammatory nodules, abscesses, dermal tunnels, sinus tracts and fistulae with a predilection for intertriginous skin. HS carries a substantial disease burden due to its prevalence, associated comorbidities and quality of life impacts and is associated with high healthcare resource utilisation. Clarity regarding the prevalence and pathogenesis of HS has led to improved therapies and more patients seeking care in both outpatient and acute care settings, including the emergency department. Emergency medicine providers play a critical role in HS diagnosis, management of acute flares and connection of HS patients with long-term dermatologic care, which can in turn help manage utilisation of acute care resources.
Risk of hepatic events associated with use of sodium-glucose cotransporter-2 inhibitors versus glucagon-like peptide-1 receptor agonists, and thiazolidinediones among patients with metabolic dysfunction-associated steatotic liver disease
Authors: Bea Sungho , Ko Hwa Yeon , Bae Jae Hyun , Cho Young Min , Chang Yoosoo , Ryu Seungho , Byrne Christopher D , Shin Ju-Young
Published: September 2024

Objective

To examine the hepatic effectiveness of sodium-glucose cotransporter-2 inhibitors (SGLT-2i) through a head-to-head comparison with glucagon-like peptide-1 receptor agonists (GLP-1RA) or thiazolidinediones (TZD) in patients with metabolic dysfunction-associated steatotic liver disease (MASLD).

Design

This population-based cohort study was conducted using a nationwide healthcare claims database (2014–2022) of Korea. We included individuals with MASLD (aged ≥40 years) who initiated SGLT-2i or comparator drugs (GLP-1RA or TZD). Primary outcome was a composite of hepatic decompensation events, including ascites, oesophageal varices with bleeding, hepatic failure or liver transplant. Liver-cause death and all-cause death were also assessed as secondary outcomes. Cox proportional hazards models were used to estimated HRs with 95% CIs.

Results

After 1:1 propensity score matching, we included 22 550 patients who initiated SGLT-2i and GLP-1RA (median age=57 years, 60% male), and 191 628 patients who initiated SGLT-2i and TZD (median age=57 years, 72% male). Compared with GLP-1RA, SGLT-2i showed a similar risk of hepatic decompensation events (HR 0.93, 95% CI 0.76 to 1.14). Compared with TZD, SGLT-2i demonstrated a reduced risk of hepatic decompensation events (HR 0.77, 95% CI 0.72 to 0.82). As compared with TZD, the results of secondary analyses showed significantly lower hepatic decompensation event risks with SGLT-2i when stratified by sex (male: HR 0.87 (95% CI 0.80–0.94); female: HR 0.62 (95% CI 0.55–0.69)).

Conclusions

In this nationwide cohort study, SGLT-2i was associated with a lower risk of hepatic decompensation events in patients with MASLD compared with TZD, while demonstrating similar effectiveness to GLP-1RA.
Whether mTICI 3 or mTICI 2b is better in patients with vertebrobasilar artery occlusion undergoing endovascular treatment depends on pc-ASPECTS
Authors: Zhang Pan , Chen Ping , Xu Yingjie , Hu Miaomiao , Wang Ruyue , Li Zhanglin , Alexandre Andrea M , Pedicelli Alessandro , Broccolini Aldobrando , Scarcia Luca , Liu Xinfeng , Sun Wen
Published: September 2024

Background

The clinical relevance of differentiating between mTICI (modified Thrombolysis In Cerebral Infarction) 2b and mTICI 3 in patients with vertebrobasilar artery occlusion (VBAO) remains unclear. This study aimed to investigate whether mTICI 3 improves functional outcomes compared with mTICI 2b in patients with VBAO and whether this improvement differs according to extent of ischemic damage.

Methods

This retrospective study enrolled patients with VBAO within 24 hours of the estimated occlusion time at 65 stroke centers in a nationwide registration in China. The primary outcome was favorable functional outcome (modified Rankin scale score 0–3) at 90 days. Patients were matched by final mTICI grade using propensity score matching (PSM) and inverse probability of treatment weighting (IPTW). Logistic regression and ordinal regression models were used to assess the impact of mTICI 2b versus mTICI 3 grading on prognosis, based on different extent of ischemia damage (posterior circulation Alberta Stroke Program Early CT Score—pc-ASPECTS of 9–10, 7–8, and 3–6) and treatment strategies (bridging therapy and direct endovascular therapy (EVT)).

Results

A total of 2075 patients with VBAO and successful reperfusion were included, 652 patients (31.4%) achieved mTICI 2b and 1423 patients (68.6%) achieved mTICI 3. After adjustment for confounders, achieving mTICI 3 following EVT in patients with VBAO and pc-ASPECTS 9–10 (OR 1.54, 95% CI 1.16 to 2.03) and pc-ASPECTS 7–8 (OR 1.80, 95% CI (1.26 to 2.56) were associated with favorable functional outcome compared with mTICI 2b, especially in those receiving direct EVT. However, in patients with pc-ASPECTS≤6, functional outcomes at 90 days did not differ between mTICI 3 and mTICI 2b (OR 1.12, 95% CI 0.67 to 1.88), irrespective of using bridging therapy or direct EVT.

Conclusion

In patients with VBAO undergoing EVT with pc-ASPECTS>6, achieving mTICI 3 favors better outcomes compared with mTICI 2b, especially in those receiving direct EVT. However, in patients with pc-ASPECTS≤6, mTICI 3 did not improve functional outcomes compared with mTICI 2b. Interventionalists should carefully assess the risk-benefit of additional maneuvers once mTICI 2b reperfusion is restored in EVT for patients with VBAO and pc-ASPECTS≤6. Further studies are needed to guide treatment decisions in these cases.
Associations between work-related factors and sickness presenteeism: a prospective study using the national French working conditions survey
Authors: Niedhammer Isabelle , Pineau Elodie , Bertrais Sandrine
Published: September 2024

Objectives

The objectives were to assess the prospective associations between work-related factors, including psychosocial and physical work factors and working time/hours factors, and sickness presenteeism alone or combined with sickness absence.

Methods

The study relied on prospective data of a national representative sample of 16 129 employees followed up from 2013 to 2016 in France. Work-related factors were assessed in 2013 and included 20 psychosocial work factors, 4 working time/hours factors and 4 physical work factors. Sickness presenteeism was studied using two items in 2016: the presence and duration of sickness presenteeism within the last 12 months. Weighted Hurdle and multinomial logistic regression models were performed to study the prospective associations between work-related factors at baseline and sickness presenteeism (both presence and duration) and sickness absence at follow-up. Models were adjusted for covariates.

Results

Almost all psychosocial and physical work factors were predictive of sickness presenteeism (ORs ranging from 1.30 to 2.07 for men, and from 1.16 to 2.30 for women) but only some of them predicted its duration. Dose–response associations were observed between multiple exposures to these factors and sickness presenteeism. These factors predicted more sickness presenteeism alone or combined with sickness absence than sickness absence alone. Gender differences were observed in these associations, as some associations were found to be stronger among women than among men.

Conclusions

There is a need to study sickness presenteeism and sickness absence combined. Prevention oriented towards the psychosocial and physical work environment may contribute to reduce sickness presenteeism and sickness absence.
Large eddy simulations of a Francis turbine operating at ultra-low load to overload conditions
Authors: Altimemy Muhannad , Caspar Justin , Shkarah Ahmed , Oztekin Alparslan
Published: September 2024

Due to the increasing global power demand, hydropower plants face the challenge of operating at flow rates far from their best efficiency point to comply with the electrical grid. Consequently, turbine units experience unstable high swirling flows under different load conditions, reducing the life of system components. Understanding the mechanisms behind the onset and sustenance of these instabilities in the swirling flow leaving the turbine runner is crucial for improving turbine performance. To achieve this, large eddy simulations were conducted to characterize the unsteady flow inside an industrial-sized Francis turbine. The turbine was studied under a wide range of flow rates, 100%, 80%, 60%, 40%, and 120% of the design flow rate. A high swirl velocity was introduced as the flow rate deviated from 100% load, causing significant changes in the flow structure. An organized structure of vortex filaments in a helical pattern is seen inside the draft tube at 80% and 60% load, and the 40% load case showed an unorganized collection of small-scale vortices. A straight vortex cavity is seen in the draft tube center at 120% excess load. At the best design point, the magnitude of the swirl velocity was 0.1 times the tip speed. However, as the flow rate dropped to 40% of the design flow rate, the magnitude increased to 0.4 times the tip speed near the wall. In addition, the 40% load case had the highest magnitude of pressure fluctuations, over 25 times the peak design case near the runner. This showed that a very unsteady flow field could damage the system or cause unstable operation at ultra-low partial loads. Generated power dropped dramatically as the flow rate decreased, and more noise was present in the power signal.