bluuebunny/crossref_metadata_2025_split huggingface dataset:
The genome of Vicia sativa ssp. amphicarpa provides insights into the role of terpenoids in antimicrobial resistance within subterranean fruits
Authors: Li Mingyu , Pu Jun , Jia Chenglin , Luo Dong , Zhou Qiang , Fang Xiangling , Nie Bin , Liu Wenxian , Nan Zhibiao , Searle Iain Robert , Fang Longfa , Liu Zhipeng 
Published: July 2024

SUMMARYVicia sativa ssp. amphicarpa is a unique forage crop capable of simultaneously producing fruits above and below ground, representing a typical amphicarpic plant. In this study, we sequenced and assembled seven pseudo‐chromosomes of the genome of V. sativa ssp. amphicarpa (n = 7) yielding a genome size of 1.59 Gb, with a total annotation of 48 932 protein‐coding genes. Long terminal repeat (LTR) elements constituted 62.28% of the genome, significantly contributing to the expansion of genome size. Phylogenetic analysis revealed that the divergence between V. sativa ssp. amphicarpa and V. sativa was around 0.88 million years ago (MYA). Comparative transcriptomic and metabolomic analysis of aerial and subterranean pod shells showed biosynthesis of terpenoids in the subterranean pod shells indicating a correlation between the antimicrobial activity of subterranean pod shells and the biosynthesis of terpenoids. Furthermore, functional validation indicates that overexpression of VsTPS5 and VsTPS16 enhances terpenoid biosynthesis for antibacterial activity. Metabolomic analysis suggests the involvement of terpenoids in the antimicrobial properties of subterranean pod shells. Deciphering the genome of V. sativa ssp. amphicarpa elucidated the molecular mechanisms behind the antimicrobial properties of subterranean fruits in amphicarpic plants, providing valuable insights for the study of amphicarpic plant biology.
Blowup algebras of determinantal ideals in prime characteristic
Authors: De Stefani Alessandro , Montaño Jonathan , Núñez‐Betancourt Luis 
Published: July 2024

AbstractWe study when blowup algebras are ‐split or strongly ‐regular. Our main focus is on algebras given by symbolic and ordinary powers of ideals of minors of a generic matrix, a symmetric matrix, and a Hankel matrix. We also study ideals of Pfaffians of a skew‐symmetric matrix. We use these results to obtain bounds on the degrees of the defining equations for these algebras. We also prove that the limit of the normalized regularity of the symbolic powers of these ideals exists and that their depth stabilizes. Finally, we show that, for determinantal ideals, there exists a monomial order for which taking initial ideals commutes with taking symbolic powers. To obtain these results, we develop the notion of ‐split filtrations and symbolic ‐split ideals.
Experiences of parents of teenagers with life-threatening food allergies: a qualitative systematic review protocol
Authors: Dobbin-Williams Karen , Crossman Renee , Swab Michelle 
Published: July 2024

Objective:
The objective of this review is to synthesize the experiences of parents of teenagers with life-threatening food allergies.

Introduction:
Life-threatening food allergies are increasing globally, with a significant effect on families, particularly parents. The teenage years are a time of increasing autonomy for young people; however, for parents living with and caring for a teenager with a life-threatening food allergy, this responsibility can have a considerable impact.

Inclusion criteria:
This review will include qualitative studies on the experiences of parents of teenagers with life-threatening food allergies, including, but not limited to, caregiving, parenting, and psychosocial experiences; any day-to-day activities, happenings, thoughts, or feelings related to parenting a teenager with life-threatening food allergies; and the handing over of responsibility for the allergy to the teenager. The review will include studies on participants in the community and in health care settings such as inpatient hospitalizations, outpatient visits, school and sports events, family dinners, restaurants, and travel. Participants from all cultural backgrounds, socio-economic backgrounds, and countries will be included.

Methods:
The review will follow the JBI methodology for systematic reviews of qualitative evidence. The search for published studies will include CINAHL, MEDLINE, and PsycINFO (EBSCOhost); Embase (Ovid); LILACS, IBSS, and Sociological Abstracts (ProQuest). The search for unpublished studies will include ProQuest Dissertations and Theses, Open Access Theses and Dissertations (OATD), Bielefeld Academic Search Engine (BASE), Google, and Google Scholar. Databases will be searched from inception until the present. JBI tools and guidelines will be used to conduct critical appraisal, data extraction, data synthesis, and assessment of confidence in the findings.

Review registration:
PROSPERO CRD42024503698
Association analysis of indel variants and gene expression identifies MDM4 as a novel locus for skeletal muscle hypertrophy and power athlete status
Authors: Kazan Hasan H. , Kasakolu Anıl , Koncagul Seyrani , Ergun Mehmet A. , John George , Sultanov Rinat I. , Zhelankin Andrey V. , Semenova Ekaterina A. , Yusupov Rinat A. , Kulemin Nikolay A. , Larin Andrey K. , Generozov Edward V. , Bulgay Celal , Ahmetov Ildus I. 
Published: July 2024

AbstractInsertions and deletions (indels) are the second most common type of variation in the human genome. However, limited data on their associations with exercise‐related phenotypes have been documented. The aim of the present study was to examine the association between 18,370 indel variants and power athlete status, followed by additional studies in 357,246 individuals. In the discovery phase, the D allele of the MDM4 gene rs35493922 I/D polymorphism was over‐represented in power athletes compared with control subjects (P = 7.8 × 10−9) and endurance athletes (P = 0.0012). These findings were replicated in independent cohorts, showing a higher D allele frequency in power athletes compared with control subjects (P = 0.016) and endurance athletes (P = 0.031). Furthermore, the D allele was positively associated (P = 0.0013) with greater fat‐free mass in the UK Biobank. MDM4 encodes a protein that inhibits the activity of p53, which induces muscle fibre atrophy. Accordingly, we found that MDM4 expression was significantly higher in the vastus lateralis of power athletes compared with endurance athletes (P = 0.0009) and was positively correlated with the percentage of fast‐twitch muscle fibres (P = 0.0062) and the relative area occupied by fast‐twitch muscle fibres (P = 0.0086). The association between MDM4 gene expression and an increased proportion of fast‐twitch muscle fibres was confirmed in two additional cohorts. Finally, we found that the MDM4 DD genotype was associated with increased MDM4 gene expression in vastus lateralis and greater cross‐sectional area of fast‐twitch muscle fibres. In conclusion, MDM4 is suggested to be a potential regulator of muscle fibre specification and size, with its indel variant being associated with power athlete status.
Development and Analysis of a Novel Bio-Syncretic Parallel Hip Exoskeleton Based on Torque Requirements
Authors: Xu Jilong , Niu Yunzhan , Liu Fucai 
Published: July 2024

Abstract
This study has developed a bio-syncretic parallel hip exoskeleton (BsPH-Exo) to address the misalignment between the rotational center of the hip joint and that of the mechanical joint. BsPH-Exo uses the hip joint as its sole motion constraint to ensure precise alignment with the hip joint center (HJC). To tackle the high costs and technical limitations of traditional methods for measuring HJC coordinates, we propose a new solution: using sensors embedded in BsPH-Exo to gather motion data from both the motors and the human leg, then processing this data through a formula to calculate the exact HJC coordinates. This approach not only simplifies the measurement process but also significantly reduces costs. Through analysis of the workspace, singularity, and maximum torque index, it was found that BsPH-Exo provides a wide range of leg motion while avoiding singularities within the rehabilitation scope. Additionally, the torque law from BsPH-Exo aligns with the torque requirements for human leg movement. In a series of wearable experiments, BsPH-Exo demonstrated its ability to meet rehabilitation training needs and showed excellent controllability in flexion/extension and adduction/abduction directions.
Kinetics, Kinematics, and Muscle Activity Patterns During Back Squat With Different Contributions of Elastic Resistance
Authors: Shi Lin , Lyons Mark , Duncan Michael , Chen Sitong , Han Dong , Yang Chengbo 
Published: July 2024

Purpose: Performing back squats with elastic bands has been widely used in resistance training. Although research demonstrated greater training effects obtained from adding elastic bands to the back squat, little is known regarding the optimal elastic resistance and how it affects neuromuscular performance. This study aimed to compare the force, velocity, power, and muscle activity during back squats with different contributions of elastic resistance. Methods: Thirteen basketball players performed 3 repetitions of the back squat at 85% of 1-repetition maximum across 4 conditions: (1) total load from free weight and (2) 20%, (3) 30%, and (4) 40% of the total load from elastic band and the remaining load from free weight. The eccentric and concentric phases of the back squat were divided into upper, middle, and bottom phases. Results: In the eccentric phase, mean velocity progressively increased with increasing elastic resistance, and muscle activity of the vastus medialis and rectus femoris significantly increased with the largest elastic resistance in the upper phase (P ≤ .036). In the concentric phase, mean power (P ≤ .021) and rate of force development (P ≤ .002) significantly increased with increasing elastic resistance. Furthermore, muscle activity of the vastus lateralis and vastus medialis significantly improved with the largest elastic resistance in the upper phases (P ≤ .021). Conclusion: Velocity, power, rate of force development, and selective muscle activity increased as the elastic resistance increased in different phases during the back-squat exercise.
How to Equalize High- and Low-Intensity Endurance Exercise Dose
Authors: Matomäki Pekka , Nuuttila Olli-Pekka , Heinonen Olli J. , Kyröläinen Heikki , Nummela Ari 
Published: July 2024

Purpose: Without appropriate standardization of exercise doses, comparing high- (HI) and low-intensity (LI) training outcomes might become a matter of speculation. In athletic preparation, proper quantification ensures an optimized stress-to-recovery ratio. This review aims to compare HI and LI doses by estimating theoretically the conversion ratio, 1:x, between HI and LI: How many minutes, x, of LI are equivalent to 1 minute of HI using various quantification methods? A scrutinized analysis on how the dose increases in relation to duration and intensity was also made. Analysis: An estimation was conducted across 4 categories encompassing 10 different approaches: (1) “arbitrary” methods, (2) physiological and perceptual measurements during exercise, (3) postexercise measurements, and comparison to (4a) acute and (4b) chronic intensity-related maximum dose. The first 2 categories provide the most conservative estimation for the HI:LI ratio (1:1.5–1:10), and the third, slightly higher (1:4–1:11). The category (4a) provides the highest estimation (1:52+) and (4b) suggests 1:10 to 1:20. The exercise dose in the majority of the approaches increase linearly in relation to duration and exponentially in relation to intensity. Conclusions: As dose estimations provide divergent evaluations of the HI:LI ratio, the choice of metric will have a large impact on the research designs, results, and interpretations. Therefore, researchers should familiarize themselves with the foundations and weaknesses of their metrics and justify their choice. Last, the linear relationship between duration and exercise dose is in many cases assumed rather than thoroughly tested, and its use should be subjected to closer scrutiny.
Neisserial adhesin A (NadA) binds human Siglec-5 and Siglec-14 with high affinity and promotes bacterial adhesion/invasion
Authors: Benucci Barbara , Spinello Zaira , Calvaresi Valeria , Viviani Viola , Perrotta Andrea , Faleri Agnese , Utrio Lanfaloni Sabrina , Pansegrau Werner , d’Alterio Liana , Bartolini Erika , Pinzuti Irene , Sampieri Katia , Giordano Anna , Rappuoli Rino , Pizza Mariagrazia , Masignani Vega , Norais Nathalie , Maione Domenico , Merola Marcello 
Published: July 2024

ABSTRACT

Neisserial adhesin A (NadA) is a meningococcal surface protein included as recombinant antigen in 4CMenB, a protein-based vaccine able to induce protective immune responses against
Neisseria meningitidis
serogroup B (MenB). Although NadA is involved in the adhesion/invasion of epithelial cells and human myeloid cells, its function in meningococcal physiology is still poorly understood. To clarify the role played by NadA in the host-pathogen interaction, we sought to identify its cellular receptors. We screened a protein microarray encompassing 2,846 human and 297 mouse surface/secreted recombinant proteins using recombinant NadA as probe. Efficient NadA binding was revealed on the paired sialic acid-binding immunoglobulin-type lectins receptors 5 and 14 (Siglec-5 and Siglec-14), but not on Siglec-9 therein used as control. The interaction was confirmed by biochemical tools with the determination of the
K

D

value in the order of nanomolar and the identification of the NadA binding site by hydrogen-deuterium exchange coupled to mass spectrometry. The N-terminal domain of the Siglec-5 that recognizes the sialic acid was identified as the NadA binding domain. Intriguingly, exogenously added recombinant soluble Siglecs, including Siglec-9, were found to decorate
N. meningitidis
surface in a NadA-dependent manner. However, Siglec-5 and Siglec-14 transiently expressed in CHO-K1 cells endorsed NadA binding and increased
N. meningitidis
adhesion/invasion while Siglec-9 did not. Taken together, Siglec-5 and Siglec-14 satisfy all features of NadA receptors suggesting a possible role of NadA in the acute meningococcal infection.

IMPORTANCE

Bacteria have developed several strategies for cell colonization and immune evasion. Knowledge of the host and pathogen factors involved in these mechanisms is crucial to build efficacious countermoves. Neisserial adhesin A (NadA) is a meningococcal surface protein included in the anti-meningococcus B vaccine 4CMenB, which mediates adhesion to and invasion of epithelial cells. Although NadA has been shown to bind to other cell types, like myeloid and endothelial cells, it still remains orphan of a defined host receptor. We have identified two strong NadA interactors, Siglec-5 and Siglec-14, which are mainly expressed on myeloid cells. This showcases that NadA is an additional and key player among the
Neisseria meningitidis
factors targeting immune cells. We thus provide novel insights on the strategies exploited by
N. meningitidis
during the infection process, which can progress to a severe illness and death.
Chlamydia
-containing spheres are a novel and predominant form of egress by the pathogen
Chlamydia psittaci
Authors: Scholz Jana , Holland Gudrun , Laue Michael , Banhart Sebastian , Heuer Dagmar 
Published: July 2024

ABSTRACT

The egress of intracellular bacteria from host cells and cellular tissues is a critical process during the infection cycle. This process is essential for bacteria to spread inside the host and can influence the outcome of an infection. For the obligate intracellular Gram-negative zoonotic bacterium
Chlamydia psittaci,
little is known about the mechanisms resulting in bacterial egress from the infected epithelium. Here, we describe and characterize
Chlamydia
-containing spheres (CCSs), a novel and predominant type of non-lytic egress utilized by
Chlamydia
spp. CCSs are spherical, low-phase contrast structures surrounded by a phosphatidylserine-exposing membrane with specific barrier functions. They contain infectious progeny and morphologically impaired cellular organelles. CCS formation is a sequential process starting with the proteolytic cleavage of a DEVD tetrapeptide-containing substrate that can be detected inside the chlamydial inclusions, followed by an increase in the intracellular calcium concentration of the infected cell. Subsequently, blebbing of the plasma membrane begins, the inclusion membrane destabilizes, and the proteolytic cleavage of a DEVD-containing substrate increases rapidly within the whole infected cell. Finally, infected, blebbing cells detach and leave the monolayer, thereby forming CCS. This sequence of events is unique for chlamydial CCS formation and fundamentally different from previously described
Chlamydia
egress pathways. Thus, CCS formation represents a major, previously uncharacterized egress pathway for intracellular pathogens that could be linked to
Chlamydia
biology in general and might influence the infection outcome
in vivo
.

IMPORTANCE

Host cell egress is essential for intracellular pathogens to spread within an organism and for host-to-host transmission. Here, we characterize
Chlamydia
-containing sphere (CCS) formation as a novel and predominant non-lytic egress pathway of the intracellular pathogens
Chlamydia psittaci
and
Chlamydia trachomatis
. CCS formation is fundamentally different from extrusion formation, the previously described non-lytic egress pathway of
C. trachomatis
. CCS formation is a unique sequential process, including proteolytic activity, followed by an increase in intracellular calcium concentration, inclusion membrane destabilization, plasma membrane blebbing, and the final detachment of a whole phosphatidylserine-exposing former host cell. Thus, CCS formation represents an important and previously uncharacterized egress pathway for intracellular pathogens that could possibly be linked to
Chlamydia
biology, including host tropism, protection from host cell defense mechanisms, or bacterial pathogenicity.
Membrane potential dynamics unveil the promise of bioelectrical antimicrobial susceptibility Testing (BeAST) for anti-fungal screening
Authors: de Souza-Guerreiro Tailise Carolina , Huan Bacellar Letícia , da Costa Thyerre Santana , Edwards Conor L. A. , Tasic Ljubica , Asally Munehiro 
Published: July 2024

ABSTRACT

Membrane potential is a useful marker for antimicrobial susceptibility testing (AST) due to its fundamental roles in cell function. However, the difficulties associated with measuring the membrane potential in microbes restrict its broad application. In this study, we present bioelectrical AST (BeAST) using the model fungus
Saccharomyces cerevisiae
. Using fluorescent indicators [DiBAC4(3), ThT, and TMRM], we measured plasma and mitochondrial membrane-potential dynamics upon electric stimulation. We find that a 2.5 second electric stimulation induces hyperpolarization of plasma membrane lasting 20 minutes in vital
S. cerevisiae
, but depolarization in inhibited cells. The numerical simulation of FitzHugh-Nagumo model successfully recapitulates vitality-dependent dynamics. The model also suggests that the magnitude of plasma-membrane potential dynamics (PMD) correlates with the degree of inhibition. To test this prediction and to examine if BeAST can be used for assessing novel anti-fungal compounds, we treat cells with biogenic silver nanoparticles (bioAgNPs) synthesized using orange fruit flavonoids and Fusarium oxysporum. Comparing BeAST with optical density assay alongside various stressors, we show that PMD correlates with the magnitude of growth inhibitions. These results suggest that BeAST holds promise for screening anti-fungal compounds, offering a valuable approach to tackling antimicrobial resistance.

IMPORTANCE
Rapid assessment of the efficacy of antimicrobials is important for optimizing treatments, avoiding misuse and facilitating the screening of new antimicrobials. The need for rapid antimicrobial susceptibility testing (AST) is growing with the rise of antimicrobial resistance. Here, we present bioelectrical AST (BeAST). Combining time-lapse microscopy and mathematical modeling, we show that electrically induced membrane potential dynamics of yeast cells correspond to the strength of growth inhibition. Furthermore, we demonstrate the utility of BeAST for assessing antimicrobial activities of novel compounds using biogenic silver nanoparticles.
Role of the antiparallel double-stranded filament form of FtsA in activating the
Escherichia coli
divisome
Authors: Perkins Abbigale , Mounange-Badimi Mwidy Sava , Margolin William 
Published: July 2024

ABSTRACT

The actin-like FtsA protein is essential for function of the cell division machinery, or divisome, in many bacteria including
Escherichia coli
. Previous
in vitro
studies demonstrated that purified wild-type FtsA assembles into closed mini-rings on lipid membranes, but oligomeric variants of FtsA such as FtsA
R286W
and FtsA
G50E
can bypass certain divisome defects and form arc and double-stranded (DS) oligomeric states, respectively, which may reflect conversion of an inactive to an active form of FtsA. However, it remains unproven which oligomeric forms of FtsA are responsible for assembling and activating the divisome. Here, we used an
in vivo
crosslinking assay for FtsA DS filaments to show that they largely depend on proper divisome assembly and are prevalent at later stages of cell division. We also used a previously reported variant that fails to assemble DS filaments, FtsA
M96E R153D
, to investigate the roles of FtsA oligomeric states in divisome assembly and activation. We show that FtsA
M96E R153D
cannot form DS filaments
in vivo
, fails to replace native FtsA, and confers a dominant negative phenotype, underscoring the importance of the DS filament stage for FtsA function. Surprisingly, however, activation of the divisome through the
ftsL
* or
ftsW
* superfission alleles suppressed the dominant negative phenotype and rescued the functionality of FtsA
M96E R153D
. Our results suggest that FtsA DS filaments are needed for divisome activation once it is assembled, but they are not essential for divisome assembly or guiding septum synthesis.

IMPORTANCE

Cell division is fundamental for cellular duplication. In simple cells like
Escherichia coli
bacteria, the actin homolog FtsA is essential for cell division and assembles into a variety of protein filaments at the cytoplasmic membrane. These filaments not only help tether polymers of the tubulin-like FtsZ to the membrane at early stages of cell division but also play crucial roles in recruiting other cell division proteins to a complex called the divisome. Once assembled, the
E. coli
divisome subsequently activates synthesis of the division septum that splits the cell in two. One recently discovered oligomeric conformation of FtsA is an antiparallel double-stranded filament. Using a combination of
in vivo
crosslinking and genetics, we provide evidence suggesting that these FtsA double filaments have a crucial role in activating the septum synthesis enzymes.