bluuebunny/crossref_metadata_2025 huggingface dataset:
Specific protein-RNA interactions are mostly preserved in biomolecular condensates
Authors: de Vries Tebbe , Novakovic Mihajlo , Ni Yinan , Smok Izabela , Inghelram Clara , Bikaki Maria , Sarnowski Chris P. , Han Yaning , Emmanouilidis Leonidas , Padroni Giacomo , Leitner Alexander , Allain Frédéric H.-T.
Published: March 2024

Many biomolecular condensates are enriched in and depend on RNAs and RNA binding proteins (RBPs). So far, only a few studies have addressed the characterization of the intermolecular interactions responsible for liquid-liquid phase separation (LLPS) and the impact of condensation on RBPs and RNAs. Here, we present an approach to study protein-RNA interactions inside biomolecular condensates by applying cross-linking of isotope labeled RNA and tandem mass spectrometry to phase-separating systems (LLPS-CLIR-MS). LLPS-CLIR-MS enables the characterization of intermolecular interactions present within biomolecular condensates at residue-specific resolution and allows a comparison with the same complexes in the dispersed phase. We observe that sequence-specific RBP-RNA interactions present in the dispersed phase are generally maintained inside condensates. In addition, LLPS-CLIR-MS identifies structural alterations at the protein-RNA interfaces, including additional unspecific contacts in the condensed phase. Our approach offers a procedure to derive structural information of protein-RNA complexes within biomolecular condensates that could be critical for integrative structural modeling of ribonucleoproteins (RNPs) in this form.
B cell depletion with anti-CD20 promotes neuroprotection in a BAFF-dependent manner in mice and humans
Authors: Wang Angela A. , Luessi Felix , Neziraj Tradite , Pössnecker Elisabeth , Zuo Michelle , Engel Sinah , Hanuscheck Nicholas , Florescu Alexandra , Bugbee Eryn , Ma Xianjie I. , Rana Fatima , Lee Dennis , Ward Lesley A. , Kuhle Jens , Himbert Johannes , Schraad Muriel , van Puijenbroek Erwin , Klein Christian , Urich Eduard , Ramaglia Valeria , Pröbstel Anne-Katrin , Zipp Frauke , Gommerman Jennifer L.
Published: March 2024

Anti-CD20 therapy to deplete B cells is highly efficacious in preventing new white matter lesions in patients with relapsing-remitting multiple sclerosis (RRMS), but its protective capacity against gray matter injury and axonal damage is unclear. In a passive experimental autoimmune encephalomyelitis (EAE) model whereby T
H
17 cells promote brain leptomeningeal immune cell aggregates, we found that anti-CD20 treatment effectively spared myelin content and prevented myeloid cell activation, oxidative damage, and mitochondrial stress in the subpial gray matter. Anti-CD20 treatment increased B cell survival factor (BAFF) in the serum, cerebrospinal fluid, and leptomeninges of mice with EAE. Although anti-CD20 prevented gray matter demyelination, axonal loss, and neuronal atrophy, co-treatment with anti-BAFF abrogated these benefits. Consistent with the murine studies, we observed that elevated BAFF concentrations after anti-CD20 treatment in patients with RRMS were associated with better clinical outcomes. Moreover, BAFF promoted survival of human neurons in vitro. Together, our data demonstrate that BAFF exerts beneficial functions in MS and EAE in the context of anti-CD20 treatment.
Multitasking functions of bacterial extracellular DNA in biofilms
Authors: Sharma Dhirendra Kumar , Rajpurohit Yogendra Singh
Published: March 2024

Bacterial biofilms are intricate ecosystems of microbial communities that adhere to various surfaces and are enveloped by an extracellular matrix composed of polymeric substances. Within the context of bacterial biofilms, extracellular DNA (eDNA) originates from cell lysis or is actively secreted, where it exerts a significant influence on the formation, stability, and resistance of biofilms to environmental stressors. The exploration of eDNA within bacterial biofilms holds paramount importance in research, with far-reaching implications for both human health and the environment. An enhanced understanding of the functions of eDNA in biofilm formation and antibiotic resistance could inspire the development of strategies to combat biofilm-related infections and improve the management of antibiotic resistance. This comprehensive review encapsulates the latest discoveries concerning eDNA, encompassing its origins, functions within bacterial biofilms, and significance in bacterial pathogenesis.
HtrA, fatty acids, and membrane protein interplay in
Chlamydia trachomatis
to impact stress response and trigger early cellular exit
Authors: Strange Natalie , Luu Laurence , Ong Vanissa , Wee Bryan A. , Phillips Matthew J. A. , McCaughey Laura , Steele Joel R. , Barlow Christopher K. , Cranfield Charles G. , Myers Garry , Mazraani Rami , Rock Charles , Timms Peter , Huston Wilhelmina M.
Published: March 2024

Chlamydia trachomatis
is an intracellular bacterial pathogen that undergoes a biphasic developmental cycle, consisting of intracellular reticulate bodies and extracellular infectious elementary bodies. A conserved bacterial protease, HtrA, was shown previously to be essential for
Chlamydia
during the reticulate body phase, using a novel inhibitor (JO146). In this study, isolates selected for the survival of JO146 treatment were found to have polymorphisms in the acyl-acyl carrier protein synthetase gene (
aasC
)
. AasC
encodes the enzyme responsible for activating fatty acids from the host cell or synthesis to be incorporated into lipid bilayers. The isolates had distinct lipidomes with varied fatty acid compositions. A reduction in the lipid compositions that HtrA prefers to bind to was detected, yet HtrA and MOMP (a key outer membrane protein) were present at higher levels in the variants. Reduced progeny production and an earlier cellular exit were observed. Transcriptome analysis identified that multiple genes were downregulated in the variants especially stress and DNA processing factors. Here, we have shown that the fatty acid composition of chlamydial lipids, HtrA, and membrane proteins interplay and, when disrupted, impact chlamydial stress response that could trigger early cellular exit.

IMPORTANCE

Chlamydia trachomatis
is an important obligate intracellular pathogen that has a unique biphasic developmental cycle. HtrA is an essential stress or virulence protease in many bacteria, with many different functions. Previously, we demonstrated that HtrA is critical for
Chlamydia
using a novel inhibitor. In the present study, we characterized genetic variants of
Chlamydia trachomatis
with reduced susceptibility to the HtrA inhibitor. The variants were changed in membrane fatty acid composition, outer membrane proteins, and transcription of stress genes. Earlier and more synchronous cellular exit was observed. Combined, this links stress response to fatty acids, membrane proteins, and HtrA interplay with the outcome of disrupted timing of chlamydial cellular exit.
The PKA-CREB1 axis regulates coronavirus proliferation by viral helicase nsp13 association
Authors: Zheng Tong , Shen Beilei , Bai Yu , Li Entao , Zhang Xun , Hu Yong , Gao Ting , Dong Qincai , Zhu Lin , Jin Rui , Shi Hui , Liu Hainan , Gao Yuwei , Liu Xuan , Cao Cheng
Published: March 2024

The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed a worldwide threat in the past 3 years. Although it has been widely and intensively investigated, the mechanism underlying the coronavirus-host interaction requires further elucidation, which may contribute to the development of new antiviral strategies. Here, we demonstrated that the host cAMP-responsive element-binding protein (CREB1) interacts with the non-structural protein 13 (nsp13) of SARS-CoV-2, a conserved helicase for coronavirus replication, both in cells and in lung tissues subjected to SARS-CoV-2 infection. The ATPase and helicase activity of viral nsp13 were shown to be potentiated by CREB1 association, as well as by Protein kinase A (PKA)-mediated CREB1 activation. SARS-CoV-2 replication is significantly suppressed by PKA Cα, cAMP-activated protein kinase catalytic subunit alpha (PRKACA), and CREB1 knockdown or inhibition. Consistently, the CREB1 inhibitor 666-15 has shown significant antiviral effects against both the WIV04 strain and the Omicron strain of the SARS-CoV-2. Our findings indicate that the PKA-CREB1 signaling axis may serve as a novel therapeutic target against coronavirus infection.

IMPORTANCE

In this study, we provide solid evidence that host transcription factor cAMP-responsive element-binding protein (CREB1) interacts directly with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) helicase non-structural protein 13 (nsp13) and potentiate its ATPase and helicase activity. And by live SARS-CoV-2 virus infection, the inhibition of CREB1 dramatically impairs SARS-CoV-2 replication
in vivo
. Notably, the IC50 of CREB1 inhibitor 666-15 is comparable to that of remdesivir. These results may extend to all highly pathogenic coronaviruses due to the conserved nsp13 sequences in the virus.
Reanalysis of single-cell RNA sequencing data does not support herpes simplex virus 1 latency in non-neuronal ganglionic cells in mice
Authors: Ouwendijk Werner J. D. , Roychoudhury Pavitra , Cunningham Anthony L. , Jerome Keith R. , Koelle David M. , Kinchington Paul R. , Mohr Ian , Wilson Angus C. , Verjans Georges G. M. G. M. , Depledge Daniel P.
Published: March 2024

Most individuals are latently infected with herpes simplex virus type 1 (HSV-1), and it is well-established that HSV-1 establishes latency in sensory neurons of peripheral ganglia. However, it was recently proposed that latent HSV-1 is also present in immune cells recovered from the ganglia of experimentally infected mice. Here, we reanalyzed the single-cell RNA sequencing (scRNA-Seq) data that formed the basis for that conclusion. Unexpectedly, off-target priming in 3’ scRNA-Seq experiments enabled the detection of non-polyadenylated HSV-1
latency-associated transcript
(
LAT
) intronic RNAs. However,
LAT
reads were near-exclusively detected in mixed populations of cells undergoing cell death. Specific loss of HSV-1
LAT
and neuronal transcripts during quality control filtering indicated widespread destruction of neurons, supporting the presence of contaminating cell-free RNA in other cells following tissue processing. In conclusion, the reported detection of latent HSV-1 in non-neuronal cells is best explained using compromised scRNA-Seq datasets.

IMPORTANCE

Most people are infected with herpes simplex virus type 1 (HSV-1) during their life. Once infected, the virus generally remains in a latent (silent) state, hiding within the neurons of peripheral ganglia. Periodic reactivation (reawakening) of the virus may cause fresh diseases such as cold sores. A recent study using single-cell RNA sequencing (scRNA-Seq) proposed that HSV-1 can also establish latency in the immune cells of mice, challenging existing dogma. We reanalyzed the data from that study and identified several flaws in the methodologies and analyses performed that invalidate the published conclusions. Specifically, we showed that the methodologies used resulted in widespread destruction of neurons which resulted in the presence of contaminants that confound the data analysis. We thus conclude that there remains little to no evidence for HSV-1 latency in immune cells.
Rickettsia rickettsii
virulence determinants RARP2 and RapL mitigate IFN-
β
signaling in primary human dermal microvascular endothelial cells
Authors: Fitzsimmons Liam , Bublitz DeAnna , Clark Tina , Hackstadt Ted
Published: March 2024

We compared the growth characteristics of a virulent
Rickettsia rickettsii
strain (Sheila Smith) to an attenuated
R. rickettsii
stain (Iowa) and a non-pathogenic species (
R. montanensis
) in primary human dermal microvascular endothelial cells (HDMEC). All replicated in Vero cells, however, only the Sheila Smith strain productively replicated in HDMECs. The Iowa strain showed minimal replication over a 24-h period, while
R. montanensis
lost viability and induced lysis of the HDMECs via a rapid programmed cell death response. Both the virulent and attenuated
R. rickettsii
strains, but not
R. montanensis
, induced an interferon-1 response, although the response was of lesser magnitude and delayed in the Sheila Smith strain. IFN-β secretion correlated with increased host cell lysis, and treatment with anti-IFNAR2 antibody decreased lysis from Iowa-infected but not Sheila Smith-infected cells. Both Sheila Smith- and Iowa-infected cells eventually lysed, although the response from Sheila Smith was delayed and showed characteristics of apoptosis. We, therefore, examined whether reconstitution of the Iowa strain with two recently described putative virulence determinants might enhance survival of Iowa within HDMECs. Reconstitution with RARP2, which is inhibitory to anterograde trafficking through the Golgi apparatus, reduced IFN-β secretion but had no effect on cell lysis. RapL, which proteolytically processes surface exposed autotransporters and enhances replication of Iowa in Guinea pigs, suppressed both IFN-β production and host cell lysis. These findings suggest distinct mechanisms by which virulent spotted fever group rickettsiae may enhance intracellular survival and replication.

IMPORTANCE

We examined a naturally occurring non-pathogenic rickettsial species,
R. montanensis
, a laboratory-attenuated
R. rickettsii
strain (Iowa), and a fully virulent
R. rickettsii
strain (Sheila Smith) for growth in human dermal microvascular endothelial cells. The two avirulent strains replicated poorly or not at all. Only the virulent Sheila Smith strain replicated. IFN-β production correlated with the inhibition of
R. rickettsii
Iowa. Reconstitution of Iowa with either of two recently described putative virulence determinants altered the IFN-β response. A rickettsial ankyrin repeat protein, RARP2, disrupts the
trans-
Golgi network and inhibits IFN-β secretion. An autotransporter peptidase, RapL, restores proteolytic maturation of outer membrane autotransporters and diminishes the IFN-β response to enhance cell survival and permit replication of the recombinant strain. These studies point the way toward discovery of mechanisms for innate immune response avoidance by virulent rickettsia.
Inhibition of multiple staphylococcal growth states by a small molecule that disrupts membrane fluidity and voltage
Authors: Dombach Jamie L. , Christensen Grace L. , Allgood Samual C. , Quintana Joaquin L. J. , Detweiler Corrella S.
Published: March 2024

New molecular approaches to disrupting bacterial infections are needed. The bacterial cell membrane is an essential structure with diverse potential lipid and protein targets for antimicrobials. While rapid lysis of the bacterial cell membrane kills bacteria, lytic compounds are generally toxic to whole animals. In contrast, compounds that subtly damage the bacterial cell membrane could disable a microbe, facilitating pathogen clearance by the immune system with limited compound toxicity. A previously described small molecule, D66, terminates
Salmonella enterica
serotype Typhimurium (
S
. Typhimurium) infection of macrophages and reduces tissue colonization in mice. The compound dissipates bacterial inner membrane voltage without rapid cell lysis under broth conditions that permeabilize the outer membrane or disable efflux pumps. In standard media, the cell envelope protects Gram-negative bacteria from D66. We evaluated the activity of D66 in Gram-positive bacteria because their distinct envelope structure, specifically the absence of an outer membrane, could facilitate mechanism of action studies. We observed that D66 inhibited Gram-positive bacterial cell growth, rapidly increased
Staphylococcus aureus
membrane fluidity, and disrupted membrane voltage while barrier function remained intact. The compound also prevented planktonic staphylococcus from forming biofilms and a disturbed three-dimensional structure in 1-day-old biofilms. D66 furthermore reduced the survival of staphylococcal persister cells and of intracellular
S. aureus
. These data indicate that staphylococcal cells in multiple growth states germane to infection are susceptible to changes in lipid packing and membrane conductivity. Thus, agents that subtly damage bacterial cell membranes could have utility in preventing or treating disease.

IMPORTANCE

An underutilized potential antibacterial target is the cell membrane, which supports or associates with approximately half of bacterial proteins and has a phospholipid makeup distinct from mammalian cell membranes. Previously, an experimental small molecule, D66, was shown to subtly damage Gram-negative bacterial cell membranes and to disrupt infection of mammalian cells. Here, we show that D66 increases the fluidity of Gram-positive bacterial cell membranes, dissipates membrane voltage, and inhibits the human pathogen
Staphylococcus aureus
in several infection-relevant growth states. Thus, compounds that cause membrane damage without lysing cells could be useful for mitigating infections caused by
S. aureus
.
The host transcriptional response to superinfection by influenza A virus and
Streptococcus pneumoniae
Authors: Cohn Ofir , Yankovitz Gal , Mandelboim Michal , Peshes-Yaloz Naama , Brandes Rachel , Bacharach Eran , Gat-Viks Irit
Published: March 2024

Secondary bacterial challenges during influenza virus infection “superinfection”) cause excessive mortality and hospitalization. Here, we present a longitudinal study of bulk gene expression changes in murine lungs during superinfection, with an initial influenza A virus infection and a subsequent
Streptococcus pneumoniae
infection. In addition to the well-characterized impairment of the host response, we identified superinfection-specific alterations in the global transcriptional program that are linked to the host’s ability to resist the pathogens. Particularly, whereas superinfected mice manifested an excessive rapid induction of the resistance-to-infection program, there was a substantial tissue-level rewiring of this program: upon superinfection, interferon-regulated genes were switched from positive to negative correlations with the host’s resistance state, whereas genes of fatty acid metabolism switched from negative to positive correlations with resistance states. Thus, the transcriptional resistance state in superinfection is reprogrammed toward repressed interferon signaling and induced fatty acid metabolism. Our findings suggest new insights into a tissue-level remodeling of the host defense upon superinfection, providing promising targets for future therapeutic interventions.

IMPORTANCE

Secondary bacterial infections are the most frequent complications during influenza A virus (IAV) pandemic outbreaks, contributing to excessive morbidity and mortality in the human population. Most IAV-related deaths are attributed to
Streptococcus pneumoniae
(SP) infections, which usually begin within the first week of IAV infection in the respiratory tracts. Here, we focused on longitudinal transcriptional responses during a superinfection model consisting of an SP infection that follows an initial IAV infection, comparing superinfection to an IAV-only infection, an SP-only infection, and control treatments. Our longitudinal data allowed a fine analysis of gene expression changes during superinfection. For instance, we found that superinfected mice exhibited rapid gene expression induction or reduction within the first 12 h after encountering the second pathogen. Cell proliferation and immune response activation processes were upregulated, while endothelial processes, vasculogenesis, and angiogenesis were downregulated, providing promising targets for future therapeutic interventions. We further analyzed the longitudinal transcriptional responses in the context of a previously defined spectrum of the host’s resistance state, revealing superinfection-specific reprogramming of resistance states, such as reprogramming of fatty acid metabolism and interferon signaling. The reprogrammed functions are compelling new targets for switching the pathogenic superinfection state into a single-infection state.
Carbapenemase-producing Enterobacterales strains causing infections in companion animals—Portugal
Authors: Moreira da Silva Joana , Menezes Juliana , Fernandes Laura , Santos Costa Sofia , Amaral Andreia , Pomba Constança
Published: March 2024

An increase in
Klebsiella pneumoniae
carbapenem-resistant human nosocomial strains is occurring in Europe, namely with the
bla
OXA-48-like
and
bla
KPC-like
genes. We determined the prevalence of carbapenemase-producing Enterobacterales clinical strains in companion animals in Portugal and characterized their mobile genetic elements. Susceptibility data of a consecutive collection of 977 Enterobacterales clinical strains from a Portuguese private veterinary diagnostic laboratory were evaluated (January–December 2020). Additional phenotypical and genotypical assays were performed in a subset of 261 strains with a resistant phenotype. Whole-genome sequencing was performed for carbapenemase-producing strains. The frequency of carbapenemase-producing Enterobacterales clinical strains in companion animals in Portugal was 0.51% (
n
= 5/977). Thus, five strains were characterized: (i) one OXA-181-producing
K. pneumoniae
ST273, (ii) two KPC-3-producing
K. pneumoniae
ST147; (iii) one KPC-3-producing
K. pneumoniae
ST392; and (iv) one OXA-48-producing
E. coli
ST127. The
bla
KPC-3
gene was located on transposon Tn
4401d
on IncFIA type plasmid for the
K. pneumoniae
ST147 strains and on a IncN-type plasmid for the
K. pneumoniae
ST392 strain, while
bla
OXA-181
gene was located on an IncX3 plasmid. All
de novo
assembled plasmids and plasmid-encoded transposons harboring carbapenemase genes were homologous to those previously described in the human healthcare. No plasmid replicons were detected on the OXA-48-producing
E. coli
ST127. The dissemination of carbapenem resistance is occurring horizontally
via
plasmid spreading from the human high burden carbapenem resistance setting to the companion animal sector. Furthermore, companion animals may act as reservoirs of carbapenem resistance. Implementation of carbapenemase detection methods in routine clinical veterinary microbiology is urgently needed.

IMPORTANCE

This is the first study on the prevalence of carbapenemase-producing Enterobacterales (CPE) clinical strains from companion animals in Portugal. Despite the generally low prevalence of CPE in companion animals, it is imperative for veterinary diagnostic laboratories to employ diagnostic methods for carbapenemase detection. The resemblance found in the mobile genetic elements transporting carbapenemase genes between veterinary medicine and human medicine implies a potential circulation within a One Health framework.
Prevalence and determinants of antibiotics self-medication among indigenous people of Bangladesh: a cross-sectional study
Authors: Mannan Adnan , Chakma Kallyan , Dewan Gourab , Saha Ayan , Chy Naim Uddin Hasan A , Mehedi H M Hamidullah , Hossain Amzad , Wnaiza Jannatun , Ahsan Md Tanveer , Rana Md Mashud , Alam Nazmul
Published: March 2024

Objectives

Self-medication with antibiotics (SMA) contributes significantly to the emergence of antimicrobial resistance (AMR), especially in low-income countries including Bangladesh. This study aimed to generate evidence on the self-reported prevalence of antibiotic self-medication and its determinants among indigenous people residing in Bangladesh’s Chittagong Hill Tracts (CHT) districts.

Design

This study used a cross-sectional design with data collected through a survey using a semi-structured questionnaire.

Setting

This study was conducted from late January to early July 2021; among different indigenous group populations aged 18 years or more olders residing in the three districts of CHT.

Participants

A total of 1336 indigenous people residing in Bangladesh’s CHT districts were included.

Primary outcome and explanatory variables

The primary outcome measure was SMA while explanatory variables were socio-demographic characteristics, health status of participants, and knowledge of antibiotics usage and its side effects.

Results

Among the study participants, more males (60.54%) than females (51.57%) reported using antibiotics. The SMA rate was high among individuals with education levels below secondary (over 50%) and those in the low-income group (55.19%). The most common diseases reported were cough, cold and fever, with azithromycin being the most frequently used antibiotic. Levels of education, family income, having a chronic illness and place of residence were found to be the significant predictors of having good knowledge of antibiotic use as found in the ordered logit model. Findings from a logistic regression model revealed that men had 1.6 times higher odds (adjusted OR (AOR) 1.57; 95% CI 1.12 to 2.19) of SMA than women. Participants with ≥US$893 per month family income had lowest odds (AOR 0.14; 95% CI 0.03 to 0.64) of SMA than those who earned <US$417. Participants living in Rangamati districts had a lower risk of SMA (…) than those in Bandarban district. rate of SMA (AOR 0.52; 95% CI 0.30 to 0.90) than those in Bandarban district.

Conclusion

Male gender, family income, place of residence and knowledge of antibiotics were the significant predictors of antibiotic self-medication. Hence, it is important to streamline awareness-raising campaigns at the community level to mitigate the practice of SMA in indigenous people and ultimately address the devastating effects of Antimicrobial resistance (AMR) in Bangladesh.
Barriers and facilitators to use of digital health tools by healthcare practitioners and their patients, before and during the COVID-19 pandemic: a multimethods study
Authors: Turnbull Sophie Louise , Dack Charlotte , Lei Jiedi , Aksu Irem , Grant Sabrina , Lasseter Gemma , Silarova Barbora , Ainsworth Ben
Published: March 2024

Objectives

To explore how healthcare practitioners (HCPs) made decisions about the implementation of digital health technologies (DHTs) in their clinical practice before and during the COVID-19 pandemic.

Design

A multimethods study, comprising semistructured interviews conducted prior to the COVID-19 pandemic, supplemented with an online survey that was conducted during the pandemic with a different sample, to ensure the qualitative findings remained relevant within the rapidly changing healthcare context. Participants were recruited through HCP networks, snowballing and social media. Data were analysed thematically.

Setting

Phone interviews and online survey.

Participants

HCPs represented a range of professions from primary and secondary care across England, with varied socioeconomic deprivation.

Results

24 HCPs were interviewed, and 16 HCPs responded to the survey. In the interviews, HCPs described three levels where decisions were made, which determined who would have access to what DHTs: health organisation, HCP and patient levels. These decisions resulted in the unequal implementation of DHTs across health services, created barriers for HCPs using DHTs in their practice and influenced HCPs’ decisions on which patients to supply DHTs with. In the survey, HCPs described being provided support to overcome some of the barriers at the organisation and HCP level during the pandemic. However, they cited similar concerns to pre-pandemic about barriers patients faced using DHTs (eg, digital literacy). In the absence of centralised guidance on how to manage these barriers, health services made their own decisions about how to adapt their services for those who struggled with DHTs.

Conclusions

Decision-making at the health organisation, HCP and patient levels influences inequalities in access to DHTs for HCPs and patients. The mobilisation of centralised information and resources during the pandemic can be viewed as good practice for reducing barriers to use of DHTs for HCPs. However, attention must also be paid to reducing barriers to accessing DHTs for patients.
Characteristics, treatment patterns and burden of illness in US patients with asthma newly initiating multiple-inhaler triple therapy
Authors: Numbere Beade , Liu Yunhao , Zhang Shiyuan , Czira Alexandrosz , Lu Yifei
Published: March 2024

Introduction

For patients with asthma who remain symptomatic on medium-dose inhaled corticosteroid/long-acting β2-agonist, add-on long-acting muscarinic antagonist is a treatment option, which can be administered as multiple-inhaler triple therapy (MITT). A high proportion of patients (61.5%–88.2%) discontinue MITT use within 1 year postinitiation; however, which patients discontinue and their treatment patterns at initiation are unknown. This study aimed to understand the demographic, clinical and treatment-related characteristics of patients with asthma who newly initiated MITT, by discontinuation status.

Methods

This retrospective cohort study used administrative data from IBM Truven MarketScan Commercial Claims and Encounters Database with Medicare supplement between 1 January 2016 and 31 December 2019. Adult patients with asthma who initiated MITT between 1 January 2017 and 31 March 2019 were included and were classified based on their discontinuation status. ‘Continuous users’ had continuous use of MITT and ‘discontinuers’ discontinued treatment within the 6-month period postinitiation. Demographics and clinical characteristics, asthma treatment use prior to MITT initiation (12-month baseline period), mode of MITT initiation and complexity of regimen were described.

Results

Of 4132 patients (mean age: 49.0 years, 67.9% female), 78.0% (n=3224) were discontinuers; 22.0% (n=908) were continuous users. Demographic and other clinical and treatment-related characteristics during baseline were broadly similar between cohorts. A significantly higher proportion of continuous users versus discontinuers had ≥6 dispensed claims for short-acting β2-agonist canisters (16.0% vs 12.5%; p=0.006) during baseline and initiated a once-daily MITT regimen (35.2% vs 26.2%; p<0.001). Fewer continuous MITT users used a mix of once-daily and twice-daily regimens than those who discontinued MITT (64.3% vs 72.3%; p<0.001).

Conclusions

Most patients with asthma discontinued MITT within 6 months. Results indicate that patients with a history of uncontrolled, symptomatic asthma and those using less complex triple therapy regimens at initiation are less likely to discontinue MITT than patients with controlled asthma and those using a complex MITT regimen.
Novel superficial temporal artery access route for middle meningeal artery embolization and treatment of chronic subdural hematoma
Authors: Eccles Alan , Charalambides Constantinos , Bartlett Andrew , Lim Carys , Mortimer Alex
Published: March 2024

We describe the use of direct superficial temporal artery puncture to access the left middle meningeal artery for embolization of a recurrent chronic subdural hematoma in a patient with a type A aortic dissection, involving the origin of the left common carotid artery which precluded conventional access from a radial or femoral approach.
Anunnaki: A Modular Framework for Developing Trusted Artificial Intelligence
Authors: Langford Michael Austin , Zilberman Sol , Cheng Betty
Published: March 2024

Trustworthy artificial intelligence (Trusted AI) is of utmost importance when learning-enabled components (LECs) are used in autonomous, safety-critical systems. When reliant on deep learning, these systems need to address the reliability, robustness, and interpretability of learning models. In addition to developing strategies to address these concerns, appropriate software architectures are needed to coordinate LECs and ensure they deliver acceptable behavior even under uncertain conditions. This work describes Anunnaki, a model-driven framework comprising loosely-coupled modular services designed to monitor and manage LECs with respect to Trusted AI assurance concerns when faced with different sources of uncertainty. More specifically, the Anunnaki framework supports the composition of independent, modular services to assess and improve the resilience and robustness of AI systems. The design of Annunaki was guided by several key software engineering principles (e.g., modularity, composability, and reusability) in order to facilitate its use and maintenance to support different aggregate monitoring and assurance analysis tools for LESs and their respective data sets. We demonstrate Anunnaki on two autonomous platforms, a terrestrial rover, and an unmanned aerial vehicle. Our studies show how Anunnaki can be used to manage the operations of different autonomous learning-enabled systems with vision-based LECs while exposed to uncertain environmental conditions.
A Quality of Experience and Visual Attention Evaluation for 360° Videos with Non-spatial and Spatial Audio
Authors: Hirway Amit , Qiao Yuansong , Murray Niall
Published: March 2024

This article presents the results of an empirical study that aimed to investigate the influence of various types of audio (spatial and non-spatial) on the user quality of experience (QoE) of and visual attention in 360° videos. The study compared the head pose, eye gaze, pupil dilations, heart rate, and subjective responses of 73 users who watched ten 360° videos with different sound configurations. The configurations evaluated were no sound; non-spatial (stereo) audio; and two spatial sound conditions (first- and third-order ambisonics). The videos covered various categories and presented both indoor and outdoor scenarios. The subjective responses were analyzed using an ANOVA (Analysis of Variance) to assess mean differences between sound conditions. Data visualization was also employed to enhance the interpretability of the results. The findings reveal diverse viewing patterns, physiological responses, and subjective experiences among users watching 360° videos with different sound conditions. Spatial audio, in particular third-order ambisonics, garnered heightened attention. This is evident in increased pupil dilation and heart rate. Furthermore, the presence of spatial audio led to more diverse head poses when sound sources were distributed across the scene. These findings have important implications for the development of effective techniques for optimizing processing, encoding, distributing, and rendering content in virtual reality (VR) and 360° videos with spatialized audio. These insights are also relevant in the creative realms of content design and enhancement. They provide valuable guidance on how spatial audio influences user attention, physiological responses, and overall subjective experiences. Understanding these dynamics can assist content creators and designers in crafting immersive experiences that leverage spatialized audio to captivate users, enhance engagement, and optimize the overall quality of VR and 360° video content. The dataset, scripts used for data collection, ffmpeg commands used for processing the videos, and the subjective questionnaire and its statistical analysis are publicly available.
Electrochemical Removal of HF from Carbonate-based LiPF6-containing Li-ion Battery Electrolytes
Authors: Ge Xiaokun , Huck Marten , Kuhlmann Andreas , Tiemann Michael , Weinberger Christian , Xu Xiaodan , Zhao Zhenyu , Steinrück Hans-Georg
Published: March 2024

Due to the hydrolytic instability of LiPF6 in carbonate-based solvents, HF is a typical impurity in Li-ion battery electrolytes. HF significantly influences the performance of Li-ion batteries, for example by impacting the formation of the solid electrolyte interphase at the anode and by affecting transition metal dissolution at the cathode. Additionally, HF complicates studying fundamental interfacial electrochemistry of Li-ion battery electrolytes, such as direct anion reduction, because it is electrocatalytically relatively unstable, resulting in a LiF passivation layer. Methods to selectively remove ppm levels of HF from LiPF6-containing carbonate-based electrolytes are limited. We introduce and benchmark a simple yet efficient electrochemical method to selectively remove ppm amounts of HF from LiPF6-containing carbonate-based electrolytes. The basic idea is the application of a suitable potential to a high surface-area metallic electrode upon which only HF reacts (electrocatalytically) while all other electrolyte components are unaffected under the respective conditions.
A New Battery SOC/SOH/eSOH Estimation Method Using a PBM and Interconnected SPKFs: Part II. SOH and eSOH Estimation
Authors: Lopetegi Iker , Plett Gregory L. , Trimboli M. Scott , Oca Laura , Miguel Eduardo , Iraola Unai
Published: March 2024

Battery management systems (BMSs) are required to estimate many non-measurable values that describe the actual operating condition of batteries; such as state of charge (SOC) or state of health (SOH). In order to improve accuracy, many physical states and parameters can be estimated using physics-based models (PBMs). These estimates could be used to improve the control and prognosis of batteries. In a series of papers, we propose a new method to estimate internal physical states, SOC, SOH and other electrode-specific state of health (eSOH) parameters of a lithium-ion battery, using interconnected sigma-point Kalman filters (SPKFs) and a single-particle model with electrolyte dynamics (SPMe). This second paper focuses on the estimation of the eSOH parameter. Simulation results show that the method is capable of estimating the eSOH parameters and key degradation modes that can occur inside a lithium-ion battery cell using only cell voltage and current measurements.
Three-Layer Electrorefining of Molten Zinc Held on Porous Carbon or Silica Sheets in Molten LiCl–KCl–ZnCl2
Authors: Yasuda Kouji , Yamada Shoya , Uda Tetsuya
Published: March 2024

We investigated a three-layer electrolysis process utilizing porous holding materials with poor wettability to molten metal, which enables to establish a three-layer configuration of metal(l)/electrolyte(l)/metal(l) by holding metals above the electrolyte regardless of their densities. In this study, porous carbon or silica sheets were used as the holding materials for electrorefining experiments of Zn metal in molten LiCl–KCl–ZnCl2 at 723 K. Three types of experiments were carried out focusing on anodic polarization, electrorefining with cathodic carbon, and three-layer electrolysis using liquid Zn as cathode. The concentration of impurity elements in the Zn was reduced by a factor of 8 to 200 in this experimental condition, highlighting the purification effectiveness of the method. From the results obtained, we have identified certain challenges associated with the three-layer electrolysis process. Furthermore, we discuss potential prospects for industrialization.
Optimization of Si-containing and SiO based Anodes with Single-Walled Carbon Nanotubes for High Energy Density Applications
Authors: Dressler R. A. , Dahn J. R.
Published: March 2024

Lithium-ion batteries require a high energy density when being used in applications such as electric vehicles or portable electronics. This can be achieved on a large scale by improving packaging and implementation, or on a material scale by selecting more energy dense electrode active material. Silicon can be used as a replacement for graphite in negative electrodes if the detrimental volume expansions can be contained. These volume expansions cause continuous mechanical degradation capacity loss leading to short lifetimes that do not meet industry standards. These high-capacity high volume expansion materials such as silicon and SiO must be used in conjunction with more stable electrode materials like graphite to reduce the mechanical degradation caused by volume change. Single-walled carbon nanotubes are shown to be a simple yet effective drop in addition to improve electrical connectivity and increase capacity retention in these silicon-based composite negative electrodes. This added particle interconnectivity from the high tensile strength carbon nanotubes allows for the use of simple binders such as CMC/SBR to create composite electrodes with competitive performance without the use of expensive polymers or complex nanostructures.
Comparison of an oral mixed meal plus arginine and intravenous glucose, GLP-1 plus arginine to unmask residual islet function in longstanding type 1 diabetes
Authors: Uitbeijerse Bas S. , Nijhoff Michiel F. , de Koning Eelco J. P.
Published: March 2024

If beta cell function is detectable, the beta cells react relatively normal to the different stimuli except for the first phase response to intravenous glucose. An oral mixed meal followed by an intravenous arginine bolus can identify residual beta cell function/mass as well as the more commonly used glucose potentiated arginine-induced insulin secretion during a hyperglycemic clamp.
Fear of Progression and Resilience as Mediators of the Association between Family Function and Quality of Life among Patients with Cervical Cancer
Authors: Wang Chuntao , Wang Yaling , Wu Fan , Qu Jiling , Wang Qiuyi , Hengudomsub Pornpat , Wacharasin Chintana , Zhou Lanshu
Published: March 2024

Objective. To explore the impact of family function on quality of life (QoL) and investigate the mediating effects of fear of progression (FoP) and resilience in the pathway from family function to QoL among patients with cervical cancer (CC). Methods. A multicenter cross-sectional survey with convenience sampling was conducted from December 2021 to December 2022. A total of 252 patients with cervical cancer were recruited from five tertiary hospitals in Jiangsu Province, China. Patients completed the 5-item self-administered Family Adaptation, Partnership, Growth, Affection, Resolve (APGAR) scale, the Fear of Progress Questionnaire short-form, the 14-item Resilience Scale, and the 12-item Short-Form Health Survey. Structural equation modeling (SEM) was performed to explore the mediation effect of FoP and resilience between family function and QoL for CC patients. Bootstrapping procedures were used to verify the significance of the indirect effects of the mediating variables. Results. The mean score of family function was 7.97 ± 2.41 (scale range: 0–10), FoP was 29.58 ± 10.14 (scale range: 12–60), and resilience was 69.37 ± 14.36 (scale range: 14–98). The mean score for physical component summary (PCS) was 41.87 ± 10.00 (scale range: 0–100), and the mean score for mental component summary (MCS) was 46.68 ± 11.78 (scale range: 0–100). Family function positively predicted patients’ resilience and negatively predicted their FoP, while FoP negatively predicted CC patients’ resilience and QoL, and resilience positively predicted patients’ QoL. Patients’ family function was associated with their QoL directly and indirectly through the mediation of FoP and resilience, and the model explained 7% of the variation in FoP, 24% of the variation in resilience, and 42% of the variation in QoL. Conclusions. Chinese CC patients expressed poor QoL. FoP and resilience could mediate the association between patients’ family function and QoL. Healthcare professionals could improve QoL of patients with cervical cancer through reducing FoP and enhancing resilience.
Synergistic Effect of B-Type Lotus Seedpod Oligomeric Procyanidin and Probiotics against Adhesion of Enterotoxigenic Escherichia coli In Vitro
Authors: Tang Cuie , Li Donghui , Xie Bijun , Li Yan , Sun Zhida
Published: March 2024

Enterotoxigenic Escherichia coli (ETEC) adhesion to gut epithelial cells is a prerequisite for diarrhea. Here, we studied the synergistic effect and potential mechanism of B-type lotus seedpod oligomeric procyanidin (LSPC) combined with probiotics against adhesion of ETEC. The results indicated that LSPC exhibited an effective anti-ETEC adhesion effect. LSPC showed signally synergistic effects with probiotics, e.g., Streptococcus thermophilus (ST) and Lactobacillus rhamnosus (LGG) in response to ETEC adhesion, with the combination of LSPC and LGG being the most efficacious. This may be attributed to the restoration of transmembrane resistance of cells, the increased expression of anti-inflammatory factors (IL-10, 1.89-fold), and the reduction of cellular inflammatory factor levels (TNF-α and IL-8), regulated by LGG-LSPC, resulting in a better enhancement of cellular immune defense and barrier function. In addition, the results of gas chromatography showed that LSPC, as a prebiotic, could significantly increase the total amount of short-chain fatty acids (especially, butyric acid) produced by probiotics (e.g., LGG), thus better maintaining intestinal health against ETEC infection. In conclusion, the synergistic effect of LSPC and probiotics (represented by LGG) against ETEC adhesion in epithelial cells may be achieved through the enhancement of cellular immune defense, cellular barrier function, and maintenance of homeostasis in the gut.
Single-Cell Chromatin Accessibility Analysis Reveals the Epigenetic Basis and Signature Transcription Factors for the Molecular Subtypes of Colorectal Cancers
Authors: Liu Zhenyu , Hu Yuqiong , Xie Haoling , Chen Kexuan , Wen Lu , Fu Wei , Zhou Xin , Tang Fuchou
Published: March 2024

Colorectal cancer is a highly heterogeneous disease, with well-characterized subtypes based on genome, DNA methylome, and transcriptome signatures. To chart the epigenetic landscape of colorectal cancers, we generated a high-quality single-cell chromatin accessibility atlas of epithelial cells for 29 patients. Abnormal chromatin states acquired in adenomas were largely retained in colorectal cancers, which were tightly accompanied by opposite changes of DNA methylation. Unsupervised analysis on malignant cells revealed two epigenetic subtypes, exactly matching the iCMS classification, and key iCMS-specific transcription factors (TFs) were identified, including HNF4A and PPARA for iCMS2 tumors and FOXA3 and MAFK for iCMS3 tumors. Notably, subtype-specific TFs bind to distinct target gene sets and contribute to both interpatient similarities and diversities for both chromatin accessibilities and RNA expressions. Moreover, we identified CpG-island methylator phenotypes and pinpointed chromatin state signatures and TF regulators for the CIMP-high subtype. Our work systematically revealed the epigenetic basis of the well-known iCMS and CIMP classifications of colorectal cancers.

Significance:

Our work revealed the epigenetic basis of the well-known iCMS and CIMP classifications of colorectal cancers. Moreover, interpatient minor similarities and major diversities of chromatin accessibility signatures of TF target genes can faithfully explain the corresponding interpatient minor similarities and major diversities of RNA expression signatures of colorectal cancers, respectively.

This article is featured in Selected Articles from This Issue, p. 897