bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Comprehensive Review of Indentation of Gels and Soft Biological Materials
Authors: He Dongjing , Malu Deep , Hu Yuhang 
Published: April 2024

Abstract
Indentation measurement has emerged as a widely adapted technique for elucidating the mechanical properties of soft hydrated materials. These materials, encompassing gels, cells, and biological tissues, possess pivotal mechanical characteristics crucial for a myriad of applications across engineering and biological realms. From engineering endeavors to biological processes linked to both normal physiological activity and pathological conditions, understanding the mechanical behavior of soft hydrated materials is paramount. The indentation method is particularly suitable for accessing the mechanical properties of these materials as it offers the ability to conduct assessments in liquid environment across diverse length and time scales with minimal sample preparation. Nonetheless, understanding the physical principles underpinning indentation testing and the corresponding contact mechanics theories, making judicious choices regarding indentation testing methods and associated experimental parameters, and accurately interpreting the experimental results are challenging tasks. In this review, we delve into the methodology and applications of indentation in assessing the mechanical properties of soft hydrated materials, spanning elastic, viscoelastic, poroelastic, coupled viscoporoelastic, and adhesion properties, as well as fracture toughness. Each category is accomplished by the theoretical models elucidating underlying physics, followed by ensuring discussions on experimental setup requirements. Furthermore, we consolidate recent advancements in indentation measurements for soft hydrated materials highlighting its multifaceted applications. Looking forward, we offer insights into the future trajectory of the indentation method on soft hydrated materials and the potential applications. This comprehensive review aims to furnish readers with a profound understanding of indentation techniques and a pragmatic roadmap of characterizing the mechanical properties of soft hydrated materials.
HssS activation by membrane heme defines a paradigm for two-component system signaling in
Staphylococcus aureus
Authors: Saillant Vincent , Morey Léo , Lipuma Damien , Boëton Pierre , Siponen Marina , Arnoux Pascal , Lechardeur Delphine 
Published: April 2024

ABSTRACT

Strict management of intracellular heme pools, which are both toxic and beneficial, is crucial for bacterial survival during infection. The human pathogen
Staphylococcus aureus
uses a two-component heme sensing system (HssRS), which counteracts environmental heme toxicity by triggering expression of the efflux transporter HrtBA. The HssS heme sensor is a HisKA-type histidine kinase, characterized as a membrane-bound homodimer containing an extracellular sensor and a cytoplasmic conserved catalytic domain. To elucidate HssS heme-sensing mechanism, a structural simulation of the HssS dimer based on Alphafold2 was docked with heme. In this model, a heme-binding site is present in the HssS dimer between the membrane and extracellular domains. Heme is embedded in the membrane bilayer with its two protruding porphyrin propionates interacting with two conserved Arg94 and Arg163 that are located extracellularly. Single substitutions of these arginines and two highly conserved phenylalanines, Phe25 and Phe128, in the predicted hydrophobic pocket limited the ability of HssS to induce HrtBA synthesis. Combination of the four substitutions abolished HssS activation. Wild-type (WT) HssS copurified with heme from
Escherichia coli,
whereas heme binding was strongly attenuated in the variants. This study gives evidence that exogenous heme interacts with HssS at the membrane/extracellular interface to initiate HssS activation and induce HrtBA-mediated heme extrusion from the membrane. This “gatekeeper” mechanism could limit intracellular diffusion of exogenous heme in
S. aureus
and may serve as a paradigm for how efflux transporters control detoxification of exogenous hydrophobic stressors.

IMPORTANCE

In the host blood, pathogenic bacteria are exposed to the red pigment heme that concentrates in their lipid membranes, generating cytotoxicity. To overcome heme toxicity,
Staphylococcus aureus
expresses a membrane sensor protein, HssS. Activation of HssS by heme triggers a phosphotransfer mechanism leading to the expression of a heme efflux system, HrtBA. This detoxification system prevents intracellular accumulation of heme. Our structural and functional data reveal a heme-binding hydrophobic cavity in HssS within the transmembrane domains (TM) helices at the interface with the extracellular domain. This structural pocket is important for the function of HssS as a heme sensor. Our findings provide a new basis for the elucidation of pathogen-sensing mechanisms as a prerequisite to the discovery of inhibitors.
Experimental evolution of
Staphylococcus aureus
in macrophages: dissection of a conditional adaptive trait promoting intracellular survival
Authors: Alves Joana , Vrieling Manouk , Ring Natalie , Yebra Gonzalo , Pickering Amy , Prajsnar Tomasz K. , Renshaw Stephen A. , Fitzgerald J. Ross 
Published: April 2024

ABSTRACT

Staphylococcus aureus
is a major pathogen associated with important diseases in humans and animals. Macrophages are a key component of the innate immune response to
S. aureus
infection and play a major role in disease outcomes. To investigate the adaptive evolution of
S. aureus
in response to macrophages, we developed an experimental infection assay.
S. aureus
strains representing major human epidemic clones were passaged many times in a macrophage cell line, accumulating mutations in an array of genomic loci. Phenotypic analysis revealed the emergence of a lineage exhibiting increased survival in macrophages and human blood, and resistance to vancomycin. The evolved lineage exhibited a previously undescribed small colony variant (SCV) phenotype characterized by hyper-pigmentation, which resulted from a missense mutation in
rsbW
. Notably, the novel SCV was a conditional adaptive trait that was unstable in nutrient-replete conditions
in vitro
, rapidly converting from hyper-pigmented SCV to a non-pigmented large colony variant via spontaneous
sigB
deletion events. Importantly, we identified similar deletions in the genome sequences of a limited number of clinical
S. aureus
isolates from public databases, indicating that related events may occur during clinical infection. Experimental infection of zebrafish did not reveal a difference in virulence between parent and novel SCV but demonstrated an
in vivo
fitness cost for the compensatory
sigB
deletion events. Taken together, we report an experimental evolutionary approach for investigating bacterial innate immune cell interactions, revealing a conditional adaptation that promotes
S. aureus
survival in macrophages and resistance to vancomycin.

IMPORTANCE

Staphylococcus aureus
is an important human bacterial pathogen. The host response to
S. aureus
involves the production of innate immune cells such as macrophages which are important for fighting infection. Here we report a new model of experimental evolution for studying how
S. aureus
can evade killing by macrophages. We identified a novel adaptive phenotype that promotes survival in macrophages and blood and resistance to antibiotics. The phenotype is lost rapidly upon growth in nutrient-rich conditions via disruption of the alternative sigma factor sigB, revealing a conditional niche-specific fitness advantage. Genomic analysis of clinical isolates suggests similar adaptations may occur during human infections. Our model may be used broadly to identify adaptations of
S. aureus
to the innate immune response.
ESBL-producing
Atlantibacter hermannii
harboring a plasmid encoding IS
26
up and down stream of
bla
CTX-M-27
,
bla
LAP-2
, and
qnrS1
isolated from an edible river
Anabas testudineus
fish
Authors: Jinnai Michio , Yamaguchi Takahiro , Minh Doan Tran Nguyen , Hoang Oanh Nguyen , Thi Hien Le , Thanh Phong Ngo , Hoai Phuong Hoang , Do Phuc Nguyen , Van Chinh Dang , Kumeda Yuko , Hase Astushi , Nakayama Tatsuya 
Published: April 2024

ABSTRACT

Extended-spectrum β-lactamase-producing
Atlantibacter hermannii
was isolated from an edible river fish,
Anabas testudineus
, which was sold in a market located in Vietnam. The genome sequence was obtained by using next-generation sequencing, which involved Oxford Nanopore and Illumina technologies. The 92 kb plasmid encodes the gene
bla
CTX-M-27
.
Metagenome-assembled genome of withering syndrome causative agent, “
Candidatus
Xenohaliotis californiensis,“ from endangered white abalone (
Haliotis sorenseni
)
Authors: Kunselman Emily , Allard Sarah , Burge Colleen , Marshman Blythe , Frederick Alyssa , Gilbert Jack 
Published: April 2024

ABSTRACT

The genome of “
Candidatus
Xenohaliotis californiensis” was assembled from shotgun metagenomic sequencing of experimentally infected white abalone. Ninety-one percent genome completeness was achieved with low contamination. Sequencing this genome provides the opportunity to track pathogen evolution over time, conduct gene expression experiments, and study dynamics between this pathogen and its phage.
Complete genome sequences of two avian pathogenic
Escherichia coli
strains isolated from broilers exhibiting colibacillosis in Mississippi
Authors: Jia Linan , Arick II Mark A. , Hsu Chuan-Yu , Peterson Daniel G. , Evans Jeffrey D. , Robinson Kelsy , Adhikari Pratima , Zhang Li 
Published: April 2024

ABSTRACT

We report the whole-genome sequences of
Escherichia coli
strains APEC-O2-MS1266 and APEC-O2-MS1657 isolated from the liver and heart of infected broilers in Mississippi State, US. The genomic information of these two causative strains may provide a valuable reference for comparative studies of avian pathogenic
E. coli
.
Complete genome sequence of
Chlamydia psittaci
NRM_5 strain isolated from the fecal samples of a wild Indian ring-necked parakeet (
Psittacula krameri manillens
is) in Japan
Authors: Sassa-O'Brien Yukiko , Wu Chien-Fu , Matsushita Yasuhiko , Ohya Kenji , Moriyama Hiromitsu , Fukushi Hideto 
Published: April 2024

ABSTRACT

We report here the whole-genome sequence of the
Chlamydia psittaci
NRM_5 strain isolated from the fecal samples of wild Indian ring-necked parakeet (
Psittacula krameri manillensis
) in Japan. The sequence type is ST35, which is known to be associated with pigeons and doves, indicating the potential for transmission among bird species.
Complete genome sequence of
Bacillus cereus
A01
Authors: Li Jiahao , Wu Xiuyun , Meng Jing 
Published: April 2024

ABSTRACT

Bacillus cereus,
a class of facultative aerobic gram-positive bacteria, is frequently isolated from soil, growing plants, and the intestinal tract of insects and mammals. Here, we report the complete genome sequence of
B. cereus
A01, whose total genome length is 6,097,808 bp, with a GC content of 34.92%.
Investigating the air quality surrounding new schools in England: polluted playgrounds and school buildings are a source of avoidable harm
Authors: Mahfouz Yasmin , Tydeman Florence , Robertson Meredith 
Published: April 2024

Objective
To assess levels of pollutants at the sites of new schools and whether pupils are likely to be protected from associated risks.

Setting
Air pollution causes damage to children’s health by increasing respiratory tract infection rates, asthma exacerbations, allergies and childhood cancers. Further effects include poorer neurocognitive outcomes and multisystemic illness in adulthood.

Design
We obtained a list of all 187 proposed new schools in England from 2017 to 2025 and found locations for 147 of them. We assessed air quality against WHO air quality targets and the air quality percentile of the location relative to pollution levels across the UK. We review relevant legislation and guidance.

Results
Our analysis found 86% of new schools (126/147) exceeded all three WHO targets, and every location exceeded at least one. Nationally, 76% (112/147) of sites were in the 60th or greater pollution percentile. Within London, the median pollution percentile was the 90th, with a minimum of 76th and maximum of 99th (IQR=83 rd to 94th).

Conclusion
The guidance for school proposals does not include any requirement to assess air quality at the identified site. Building regulations also fail to consider how widespread poor air quality is, and significantly underestimates the levels of major air pollutants surrounding schools. Therefore it is unlikely that adequate action to reduce pupil and staff exposure is undertaken.
We argue that air quality assessment should be mandatory at the proposal and planning stage of any new school building and that national guidance and legislation urgently needs to be updated.
Varicella mimicking complications of acute rhinosinusitis in an infant
Authors: Kunz Seraina , Bergsma Patrick , Brand Yves 
Published: April 2024

Varicella is the manifestation of primary infection with the varicella-zoster virus, mainly affecting preschool and school-aged children. The children suffer from a generalised, vesicular rash and fever. Despite the infection’s typically non-threatening course, a variety of severe complications have been described.The authors present the case of a female infant suffering from varicella and developing preseptal cellulitis with a frontal abscess while being treated with intravenous antibiotics. Otorhinolaryngology consultation was sought since the clinical image was highly suggestive for sinusitis complications, namely orbital cellulitis and frontal bone osteomyelitis (Pott’s puffy tumour). However, the child was below the age of frontal sinus development and there was no other apparent sign of sinonasal involvement. Ultrasonography revealed a mid-frontal collection without signs of abscess formation preseptally or postseptally, leading to the diagnosis of cutaneous superinfection of varicella lesions. The frontal abscess was drained, and the child fully recovered under antibiotic treatment.
Best practices for the dissemination and implementation of neuromuscular training injury prevention warm-ups in youth team sport: a systematic review
Authors: Lutz Destiny , van den Berg Carla , Räisänen Anu M , Shill Isla J , Kim Jemma , Vaandering Kenzie , Hayden Alix , Pasanen Kati , Schneider Kathryn J , Emery Carolyn A , Owoeye Oluwatoyosi B A 
Published: April 2024

ObjectiveTo evaluate best practices for neuromuscular training (NMT) injury prevention warm-up programme dissemination and implementation (D&I) in youth team sports, including characteristics, contextual predictors and D&I strategy effectiveness.DesignSystematic review.Data sourcesSeven databases were searched.EligibilityThe literature search followed Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Inclusion criteria: participation in a team sport, ≥70% youth participants (<19 years), D&I outcomes with/without NMT-related D&I strategies. The risk of bias was assessed using the Downs & Black checklist.ResultsOf 8334 identified papers, 68 were included. Sport participants included boys, girls and coaches. Top sports were soccer, basketball and rugby. Study designs included randomised controlled trials (RCTs) (29.4%), cross-sectional (23.5%) and quasi-experimental studies (13.2%). The median Downs & Black score was 14/33. Injury prevention effectiveness (vs efficacy) was rarely (8.3%) prioritised across the RCTs evaluating NMT programmes. Two RCTs (2.9%) used Type 2/3 hybrid approaches to investigate D&I strategies. 19 studies (31.6%) used D&I frameworks/models. Top barriers were time restrictions, lack of buy-in/support and limited benefit awareness. Top facilitators were comprehensive workshops and resource accessibility. Common D&I strategies included Workshops with supplementary Resources (WR; n=24) and Workshops with Resources plus in-season Personnel support (WRP; n=14). WR (70%) and WRP (64%) were similar in potential D&I effect. WR and WRP had similar injury reduction (36–72%) with higher adherence showing greater effectiveness.ConclusionsWorkshops including supplementary resources supported the success of NMT programme implementation, however, few studies examined effectiveness. High-quality D&I studies are needed to optimise the translation of NMT programmes into routine practice in youth sport.
Sepsis screening protocol implementation: a clinician-validated rapid realist review
Authors: Melville Jonathan , Carr Tracey , Goodridge Donna , Muhajarine Nazeem , Groot Gary 
Published: April 2024

IntroductionThe failed or partial implementation of clinical practices negatively impacts patient safety and increases systemic inefficiencies. Implementation of sepsis screening guidelines has been undertaken in many settings with mixed results. Without a theoretical understanding of what leads to successful implementation, improving implementation will continue to be ad hoc or intuitive. This study proposes a programme theory for how and why the successful implementation of sepsis screening guidelines can occur.MethodsA rapid realist review was conducted to develop a focused programme theory for the implementation of sepsis screening guidelines. An independent two-reviewer approach was used to iteratively extract and synthesise context and mechanism data. Theoretical context-mechanism-outcome propositions were refined and validated by clinicians using a focus group and individual realist interviews. Implementation resources and clinical reasoning were differentiated in articulating mechanisms.ResultsEighteen articles were included in the rapid review. The theoretical domains framework was identified as the salient substantive theory informing the programme theory. The theory consisted of five main middle-range propositions. Three promoting mechanisms included positive belief about the benefits of the protocol, belief in the legitimacy of using the protocol and trust within the clinical team. Two inhibiting mechanisms included pessimism about the protocol being beneficial and pessimism about the team. Successful implementation was defined as achieving fidelity and sustained use of the intervention. Two intermediate outcomes, acceptability and feasibility of the intervention, and adoption, were necessary to achieve before successful implementation.ConclusionThis rapid realist review synthesised key information from the literature and clinician feedback to develop a theory-based approach to clinical implementation of sepsis screening. The programme theory presents knowledge users with an outline of how and why clinical interventions lead to successful implementation and could be applied in other clinical areas to improve quality and safety.
Occupational injuries caused by fire and smoke in Victoria, Australia, 2003–2021: a descriptive study
Authors: Berecki-Gisolf Janneke , Wah Win , Walker-Bone Karen 
Published: April 2024

ObjectivesHospital attendance related to fire, flame or smoke exposure is commonly associated with work. The aim of this study was to examine time trends and risk factors for work-related fire/flame/smoke injuries in Victoria, Australia.MethodsThis study was based on emergency department (ED) presentation records from the Victorian Emergency Minimum Dataset, 2003–2021. Cases were people aged 15–74 years with injury-related ED presentations, if cause of injury was recorded as fire/flame/smoke, based on coded data and/or narratives. Work-related rates were calculated per employed persons; non-work rates were calculated per population. Work-related and non-work-related cases were compared using logistic regression modelling.ResultsThere were 11 838 ED presentations related to fire/flame/smoke: 1864 (15.7%) were work-related. Non-work-related rates were 12.3 ED presentations per 100 000population, and work-related rates were 3.43 per 100 000employed personsannually. Over the study period, work-related rates decreased annually by 2.0% (p<0.0001), while non-work rates increased by 1.1% (p<0.0001). Work-related cases (vs non-work) were associated with summer (vs winter), but the association with extreme bushfire periods (Victorian ‘Black Saturday’ and ‘Black Summer’) was not statistically significant. Work-related cases were less severe than non-work-related cases, evidenced by triage status and subsequent admission.ConclusionsRates of occupational fire/flame/smoke-related injury presentations decreased over the past two decades in Victoria, while non-work-related rates increased. This could reflect improved safety in the workplace. Hospital data, however, cannot be used to distinguish occupation or industry therefore, employment data linkage studies are recommended to further inform workplace preventive measures.
Characteristics analysis and nonlinear control of a digital hydraulic pressure tracking system for high-speed helicopter wet friction clutch
Authors: Gao Qiang , Liu Huayi , Niu Mingyang 
Published: April 2024

The reliability and control precision of the engagement and disengagement of wet friction clutch are crucial to the transmission of high-speed helicopters. In contrast to the traditional proportional hydraulic system, the digital hydraulic system provides a viable solution due to the use of several fast switching valves (FSVs). In this research, a digital hydraulic pressure tracking system using two fast switching valve arrays (DHPTS-FSVA) is proposed and its nonlinear model is established. First, the static and dynamic characteristics of the DHPTS-FSVA are deeply analyzed by virtue of the half-bridge resistance theory. Moreover, a novel pressure control strategy is proposed, which consists of nonlinear adaptive control method, differential pulse width modulation (PWM) with pressure compensation, and logic allocation strategy of PWM duty ratio. Finally, comparative simulation and experimental results indicate that the maximum, average, and standard deviation of the errors are reduced by at least 16.1%, 45.1%, and 39.5%, respectively, at the tracking frequencies of 1 and 2 Hz, which proves that the proposed controller exhibits better tracking performance at low frequencies.
$$\bar{B}_s^0 \rightarrow D_{s1}(2460)^+ K^-, D_{s1}(2536)^+ K^-$$ and the nature of the two $$D_{s1}$$ resonances
Authors: Lin Jia-Xin , Chen Hua-Xing , Liang Wei-Hong , Xiao Chu-Wen , Oset Eulogio 
Published: April 2024

AbstractStarting from the molecular picture for the $$D_{s1}(2460)$$

D

s
1

(
2460
)

and $$D_{s1}(2536)$$

D

s
1

(
2536
)

resonances, which are dynamically generated by the interaction of coupled channels, the most important of which are the $$D^*K$$

D
∗

K

for the $$D_{s1}(2460)$$

D

s
1

(
2460
)

and $$DK^*$$

D

K
∗

for the $$D_{s1}(2536)$$

D

s
1

(
2536
)

, we evaluate the ratio of decay widths for the $$\bar{B}_s^0 \rightarrow D_{s1}(2460)^+ K^-$$

B

¯

s
0

→

D

s
1

(
2460
)

+

K
-

and $$\bar{B}_s^0 \rightarrow D_{s1}(2536)^+ K^-$$

B

¯

s
0

→

D

s
1

(
2536
)

+

K
-

decays, the latter of which has been recently investigated by the LHCb collaboration, and we obtain a ratio of the order of unity. The present results should provide an incentive for the related decay into the $$D_{s1}(2460)$$

D

s
1

(
2460
)

resonance to be performed, which would provide valuable information on the nature of these two resonances.