bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ligand-Coupled Conformational Changes in a Cyclic Nucleotide-Gated Ion Channel Revealed by Time-Resolved Transition Metal Ion FRET
Authors: Eggan Pierce , Gordon Sharona E. , Zagotta William N. 
Published: April 2024

AbstractCyclic nucleotide-binding domain (CNBD) ion channels play crucial roles in cellular-signaling and excitability and are regulated by the direct binding of cyclic adenosine- or guanosine-monophosphate (cAMP, cGMP). However, the precise allosteric mechanism governing channel activation upon ligand binding, particularly the energetic changes within domains, remains poorly understood. The prokaryotic CNBD channel SthK offers a valuable model for investigating this allosteric mechanism. In this study, we investigated the conformational dynamics and energetics of the SthK C-terminal region using a combination of steady-state and time-resolved transition metal ion Förster resonance energy transfer (tmFRET) experiments. We engineered donor-acceptor pairs at specific sites within a SthK C-terminal fragment by incorporating a fluorescent noncanonical amino acid donor and metal ion acceptors. Measuring tmFRET with fluorescence lifetimes, we determined intramolecular distance distributions in the absence and presence of cAMP or cGMP. The probability distributions between conformational states without and with ligand were used to calculate the changes in free energy (ΔG) and differences in free energy change (ΔΔG) in the context of a simple four-state model. Our findings reveal that cAMP binding produces large structural changes, with a very favorable ΔΔG. In contrast to cAMP, cGMP behaved as a partial agonist and only weakly promoted the active state. Furthermore, we assessed the impact of protein oligomerization and ionic strength on the structure and energetics of the conformational states. This study demonstrates the effectiveness of time-resolved tmFRET in determining the conformational states and the ligand-dependent energetics of the SthK C-terminal region.Significance StatementAllosteric regulation is pivotal for the function of most proteins, especially ion channels like the cyclic nucleotide-binding domain (CNBD) channels. This study examines the allosteric mechanism of ligand binding in the C-terminal region of the prokaryotic CNBD ion channel SthK using steady-state and time-resolved tmFRET. We uncovered significant structural and energetic changes induced by ligand binding with the full-agonist cAMP and the weak partial agonist cGMP. Our approach also highlights the effectiveness of using fluorescence lifetimes to reveal conformational heterogeneity and free energy changes in proteins. These findings deepen our understanding of CNBD channel activation overall and lay the groundwork for a more comprehensive characterization of the effects of mutations and pharmacological agents in these channels.
Engineering PEG10 assembled endogenous virus-like particles with genetically encoded neoantigen peptides for cancer vaccination
Authors: Tang Ruijing , Guo Luobin , Wei Tingyu , Chen Tingting , Yang Huan , Ye Honghao , Lin Fangzhou , Zeng Yongyi , Yu Haijun , Cai Zhixiong , Liu Xiaolong 
Published: April 2024

AbstractTumor neoantigen peptide vaccines hold potential for boosting cancer immunotherapy, yet efficiently co-delivering peptides and adjuvants to antigen-presenting cells in vivo remains challenging. Virus-like particle (VLP), which is a kind of multiprotein structure organized as virus, can deliver therapeutic substances into cells and stimulate immune response. However, the weak targeted delivery of VLP in vivo and its susceptibility to neutralization by antibodies hinder their clinical applications. Here, we firstly designed a novel protein carrier using the mammalian-derived capsid protein PEG10, which can self-assemble into endogenous VLP (eVLP) with high protein loading and transfection efficiency. Then, an engineered tumor vaccine, named ePAC, was developed by packaging genetically encoded neoantigen into eVLP with further modification of CpG-ODN on its surface to serve as an adjuvant and targeting unit to dendritic cells (DCs). Significantly, ePAC can efficiently target and transport neoantigens to DCs, and promote DCs maturation to induce neoantigen-specific T cells. Moreover, in mouse orthotopic liver cancer and humanized mouse tumor models, ePAC combined with anti-TIM-3 exhibited remarkable antitumor efficacy. Overall, these results support that ePAC could be safely utilized as cancer vaccines for antitumor therapy, showing significant potential for clinical translation.
Results from Integrating Gender-Based Violence Services into HIV Care – a Case Study of Lighthouse Trust ART Clinic in Malawi
Authors: Kiruthu-Kamamia Christine , Kumwenda Tapiwa , Lungu Joseph , Sande Odala , Diele Joseph , MacLachlan Ellen , Thawani Agnes 
Published: April 2024

AbstractIntroductionGender-based violence (GBV) not only poses significant public health and human rights challenges but is also closely associated with HIV. GBV acts as a barrier to HIV prevention, testing, and treatment adherence, and fear of GBV inhibits disclosure of HIV status to sexual partners. In Malawi, where both GBV and HIV prevalence is high, integrating GBV services into HIV care is crucial. We describe the integration of GBV services into Lighthouse Trust’s ART clinics in Malawi, including screening, documentation, program implementation, and outcomes.MethodsWe conducted a retrospective analysis from January 2020 to September 2023. Data on cases identified, post-GBV services, and perpetrator demographics were collected from the GBV register. We used descriptive statistics to describe the program outcomes.ResultsWe documented 7148 reported GBV cases from January 2020 to September 2023. Young women, particularly those aged 10-19, constituted a significant proportion of survivors. Psycho-social services were the most common type of service that was offered to GBV survivors (25%), followed by HIV testing (19%) and STI screening(18%). Perpetrators were mostly known to survivors or intimate partners of the survivor.ConclusionWe successfully integrated GBV services into the Lighthouse Trust ART clinic, in close collaboration with the one-stop centers. Training healthcare providers enhanced support for GBV survivors, with a focus on increasing awareness, especially for minors. Recommended actions include improving access to services, confidentiality, and multi-sectoral collaboration to ensure comprehensive care aimed to create a safer, more dignified healthcare environment for all, particularly GBV survivors.Key MessagesKey Findings Teaser Key MessageWe successfully integrated GBV services into HIV care via adequate training, screening and identification procedures, and documentation.Integrating GBV screening into ART care identified over 7000 cases with most cases of sexual violence in women aged 10 to 19 years.There is still a need for public awareness of GBV and access to support services.Key Messages and Implications to policy, program managers, donors etcWe provide a replicable model for healthcare providers and facility administrators, demonstrating the effectiveness of standardized screening, care, and referral processes in improving the support and outcomes for GBV survivors in low-resource settings.Our findings can inform the development of more inclusive health policies and support services that address the needs of all GBV survivors.
Chikungunya Seroprevalence among Patients Presenting with Febrile illnesses in selected health facilities in Mt. Elgon region, Kenya
Authors: Kageha Sheila , Ngoi Joyce M. , Kubo Toru , Morita Kouichi , Mwau Matilu 
Published: April 2024

AbstractBackgroundChikungunya is an emerging epidemic-prone vector-borne disease of considerable significance globally. Infection with chikungunya virus induces an acute illness characterized by fever and painful arthralgia, which can evolve to chronic arthritis and rheumatism especially in elderly patients. Whereas febrile illness and arthralgia are common clinical presentations amongst residents of Mt. Elgon, the role of chikungunya virus as a causative agent is undocumented. This study was carried out to determine the prevalence of IgA, IgM and IgG antibodies against Chikungunya Virus (CHIKV) antigens in patients presenting with acute febrile illnesses in Mt. Elgon region, Kenya.MethodsThis was a cross-sectional seroprevalence study on febrile patients visiting Endebes, Andersen and Kitale County Referal Hospitals. Sociodemographic data was collected whenever possible. Serum samples were collected and screened using Indirect ELISA for 1gG+IgM+IgA antibodies. Sera that tested positive by ELISA were subjected to standard plaque reduction neutralization assays (PRNT) performed on monolayer cultures of Vero E6 cells for confirmation.ResultsBy ELISA, a total of 317/1359 (23.33%) sera were positive for CHIKV antibodies. Of the 317 positive sera, 305 (96.21%) were of sufficient quantity and were subjected to PRNT. Ultimately, 127 (9.3%) samples tested positive for CHIKV neutralising antibodies by PRNT.ConclusionThese findings suggest active circulation of CHIKV in Mt. Elgon, even though it has previously been considered a non-endemic region for the virus. There is need to closely monitor and continuously put in place surveillance strategies to prevent probable potential outbreaks in the future.
Impact of exposure frequency on disease burden of the common cold - a mathematical modeling perspective
Authors: Gerdes Sebastian , Rank Michael , Glauche Ingmar , Roeder Ingo 
Published: April 2024

ABSTRACTThe common cold is a frequent disease in humans and can be caused by a multitude of different viruses. Despite its typically mild nature, the high prevalence of the common cold causes significant human suffering and economic costs. Oftentimes, strategies to reduce contacts are used in order to prevent infection. To better understand the dynamics of this ubiquitous ailment, we develop two novel mathematical models: the common cold ordinary differential equation (CC-ODE) model at the population level, and the common cold individual-based (CC-IB) model at the individual level. Our study aims to investigate whether the frequency of population / individual exposure to an exemplary common cold pathogen influences the average disease burden associated with this virus.On the one hand, the CC-ODE model captures the dynamics of the common cold within a population, considering factors such as infectivity and contact rates, as well as development of specific immunity in the population. On the other hand, the CC-IB model provides a granular perspective by simulating individual-level interactions and infection dynamics, incorporating heterogeneity in contact rates.By employing these models, we explore the impact of exposure frequencies upon the net disease burden of common cold infections in theoretical settings. In both modeling approaches, we show that under specific parameter configurations (i.e., characteristics of the virus and the population), increased exposure can result in a lower average disease burden. While increasing contact rates may be ethically justifiable for low-mortality common cold pathogens, we explicitly do not advocate for such measures in severe illnesses. The mathematical approaches we introduce are simple yet powerful and can be taken as a starting point for the investigation of specific common cold pathogens and scenarios.
Associations between IL-6 and trajectories of depressive symptoms across the life course: Evidence from ALSPAC and UK Biobank cohorts
Authors: Edmondson-Stait A. J. , Davyson E. , Shen X. , Adams M. J. , Khandaker G. M. , Miron V. E. , McIntosh A. M. , Lawrie S. M. , Kwong A. S. F. , Whalley H. C. 
Published: April 2024

AbstractPeripheral inflammatory markers, including serum IL-6, are associated with depression, but less is known about how these markers associate with depression at different stages of the life-course. We examined associations between serum IL-6 levels at baseline and subsequent depression symptom trajectories in two longitudinal cohorts: ALSPAC (age 10-28y;N=4,835) and UK Biobank (39- 86y;N=39,613) using multi-level growth curve modelling. Models were adjusted for sex, BMI and socioeconomic factors. Depressive symptoms were measured using the Short Moods and Feelings Questionnaire (SMFQ) in ALSPAC (max timepoints=11) and the Patient Health Questionnaire-2 (PHQ-2) in UK Biobank (max timepoints=8). Higher baseline IL-6 was associated with worse depression symptom trajectories in both cohorts (largest effect size: 0.046 (ALSPAC, age 16y)). These associations were stronger in the younger ALSPAC cohort, where additionally higher IL-6 at age 9 years was associated with worse depression symptoms trajectories in females compared to males. Weaker sex differences were observed in the older cohort, UK Biobank. These findings suggest that systemic inflammation may influence the severity and course of depressive symptoms across the life course, which is apparent regardless of age and differences in measures and number of time points between these large, population-based cohorts.
Bad company? The pericardium microbiome in people investigated for tuberculosis pericarditis in an HIV-prevalent setting
Authors: Nyawo Georgina , Naidoo Charissa , Wu Benjamin G. , Kwok Benjamin , Clemente Jose C. , Li Yonghua , Minnies Stephanie , Reeve Byron , Moodley Suventha , John Thadathilankal-Jess , Karamchand Sumanth , Singh Shivani , Pecararo Alfonso , Doubell Anton , Kyriakakis Charles , Warren Robin , Segal Leopoldo N. , Theron Grant 
Published: April 2024

AbstractBackgroundThe microbiome likely plays a role in tuberculosis (TB) pathogenesis. We evaluated the site-of-disease microbiome and predicted metagenome in people with presumptive tuberculous pericarditis, a major cause of mortality, and explored for the first time, the interaction between its association with C-reactive protein (CRP), a potential diagnostic biomarker and the site-of-disease microbiome in extrapulmonary TB.MethodsPeople with effusions requiring diagnostic pericardiocentesis (n=139) provided background sampling controls and pericardial fluid (PF) for 16S rRNA gene sequencing analysed using QIIME2 and PICRUSt2. Blood was collected to measure CRP.ResultsPF from people with definite (dTB, n=91), probable (pTB, n=25), and non- (nTB, n=23) tuberculous pericarditis differed in β-diversity. dTBs were, vs. nTBs,Mycobacterium-, Lacticigenium-,andKocuria-enriched. Within dTBs, HIV-positives wereMycobacterium-, Bifidobacterium-,Methylobacterium-, andLeptothrix-enriched vs. HIV-negatives and HIV-positive dTBs on ART wereMycobacterium- andBifidobacterium-depleted vs. those not on ART. Compared to nTBs, dTBs exhibited short-chain fatty acid (SCFA) and mycobacterial metabolism microbial pathway enrichment. People with additional non-pericardial involvement had differentially PF taxa (e.g.,Mycobacterium-enrichment andStreptococcus-depletion associated with pulmonary infiltrates).Mycobacteriumreads were in 34% (31/91), 8% (2/25) and 17% (4/23) of dTBs, pTBs, and nTBs, respectively. β-diversity differed between patients with CRP above vs. below the median value (Pseudomonas-depleted). There was no correlation between enriched taxa in dTBs and CRP.ConclusionsPF is compositionally distinct based on TB status, HIV (and ART) status and dTBs are enriched in SCFA-associated taxa. The clinical significance of these findings, including mycobacterial reads in nTBs and pTBs, requires evaluation.
Evidence of Gender Disparities in Citations and Altmetric Attention Score in Oncology
Authors: Campbell Rebecca A. , Helstrom Emma , Chew Lauren , Eapen Renu , Plimack Elizabeth , Correa Andres , Albersen Maarten , Kutikov Alexander , Abbosh Philip , Calaway Adam , Nizam Amanda , Gupta Shilpa , Psutka Sarah , Barata Pedro , Dizman Nazli , Sindhani Mohit , Weight Christopher , Haber Georges , Bukavina Laura 
Published: April 2024

AbstractIn this study, we assess gender disparities in both citation rates and Altmetric Attention Scores (AAS) within oncology, utilizing a dataset comprising over 600,000 articles from the past 15 years. The analysis focuses on the differential impact of gender on citation metrics and AAS, the latter of which expands the evaluation of research impact beyond traditional citation analysis to include digital engagement metrics such as social media mentions, news coverage, and policy discussions.Methodologically, the study taps into the Altmetric database, using gender identification tools like the Gender Guesser API to classify articles by the gender composition of their first and last authors. Findings reveal a systemic over-citation of male-first and male-last author pairs (MM), with a mean citation difference (MCD) of +4.7. In stark contrast, female-first and female-last author pairs (WW) experience under-citation, with an MCD of -3.5.A detailed examination of the Altmetric Attention Score shows that female-first authors receive a 7.19% lower AAS compared to male-first authors, indicating significant gender biases in the broader academic and public engagement. Delving deeper into the components of AAS, specifically news media coverage, reveals that female-first authors are covered 10.9% less in news media, 20.4% less patent references and 33.4% in Weibo mentions than their male counterparts. This disparity is significant and suggests a broader trend of underrepresentation and undervaluation of female-led research in more public-facing and influential media outlets.These results underscore the persistent influence of gender on the recognition and valuation of scientific contributions within the field of oncology. They highlight the need for academia and publishing entities to implement more equitable practices to mitigate these disparities and ensure a balanced representation and recognition of scholarly work across genders.
A posterior approach to correct for focal plane offsets in lattice light sheet structured illumination microscopy
Authors: Shi Yu , Daugird Tim A. , Legant Wesley R. 
Published: April 2024

AbstractSignificanceLattice light sheet structured illumination microscopy (latticeSIM) has proven highly effective in producing 3D images with super resolution rapidly and with minimal photobleaching. However, due to the use of two separate objectives, sample-induced aberrations can result in an offset between the planes of excitation and detection, causing artifacts in the reconstructed images.AimWe introduce a posterior approach to detect and correct for the axial offset between the excitation and detection focal planes in latticeSIM and provide a method to minimize artifacts in the reconstructed images.ApproachWe utilized the residual phase information within the overlap regions of the laterally shifted structured illumination microscopy (SIM) information components in frequency space to retrieve the axial offset between the excitation and the detection focal planes in latticeSIM.ResultsWe validated our technique through simulations and experiments, encompassing a range of samples from fluorescent beads to subcellular structures of adherent cells. We also show utilizing transfer functions with the same axial offset as that which was present during the data acquisition results in reconstructed images with minimal artifacts and salvages otherwise unusable data.ConclusionWe envision that our method will be a valuable addition to restore image quality in latticeSIM datasets even for those acquired under non-ideal experimental conditions.
Centromeric chromatin clearings demarcate the site of kinetochore formation
Authors: Kixmoeller Kathryn , Chang Yi-Wei , Black Ben E. 
Published: April 2024

AbstractThe centromere is the chromosomal locus that recruits the kinetochore, directing faithful propagation of the genome during cell division. The kinetochore has been interrogated by electron microscopy since the middle of the last century, but with methodologies that compromised fine structure. Using cryo-ET on human mitotic chromosomes, we reveal a distinctive architecture at the centromere: clustered 20-25 nm nucleosome-associated complexes within chromatin clearings that delineate them from surrounding chromatin. Centromere components CENP-C and CENP-N are each required for the integrity of the complexes, while CENP-C is also required to maintain the chromatin clearing. We further visualize the scaffold of the fibrous corona, a structure amplified at unattached kinetochores, revealing crescent-shaped parallel arrays of fibrils that extend >1 μm. Thus, we reveal how the organization of centromeric chromatin creates a clearing at the site of kinetochore formation as well as the nature of kinetochore amplification mediated by corona fibrils.
A Cell-Permeable Nanobody to Restore F508del Cystic Fibrosis Transmembrane Conductance Regulator Activity
Authors: Franz Luise , Rubil Tihomir , Balázs Anita , Overtus Marie , Kemnitz-Hassanin Kristin , Govaerts Cedric , Mall Marcus A. , Hackenberger Christian P.R. 
Published: April 2024

AbstractNanobodies have gained considerable attention as particularly promising biopharmaceuticals. However, nanobody-based modalities are currently limited to extracellular targets due to a lack of efficient delivery methods required to reach targets inside cells. In this study, we introduce cell-permeable nanobodies for targeting a disease-relevant intracellular protein, namely the cystic fibrosis transmembrane conductance regulator (CFTR) chloride channel with the most common cystic fibrosis (CF)-causing mutation F508del. We employ cell-penetrating peptides (CPPs) to deliver a CFTR-binding nanobody (NB1) that stabilizes misfolded F508del-CFTR and prevents its degradation to restore its function. Our data show that conjugation of a disulfide-linked CPP in combination with a cell-surface anchored CPP-additive enables intracellular delivery of NB1 into CF bronchial epithelial cells, which promotes maturation and trafficking of F508del-CFTR protein to the apical cell membrane. Furthermore, we demonstrate that the cell-permeable nanobody restores CFTR chloride channel function, which can be further enhanced by the clinically approved small molecule CFTR potentiator ivacaftor. This study highlights the use of cell-permeable nanobodies for modulation of protein function and illustrates their therapeutic potential as next-generation biopharmaceuticals for intracellular delivery and targeting.Abstract Figure
Serotype switching inPseudomonas aeruginosaST111 enhances adhesion and virulence
Authors: Anbo Mikkel , Lubna Mahbuba Akter , Moustafa Dina A. , Paiva Telmo O. , Serioli Laura , Zor Kinga , Sternberg Claus , Jeannot Katy , Dufrêne Yves F. , Goldberg Joanna B. , Jelsbak Lars 
Published: April 2024

AbstractEvolution of the highly successful and multidrug resistant clone ST111 inPseudomonas aeruginosainvolves serotype switching from O-antigen O4 to O12. How expression of a different O-antigen serotype alters pathogen physiology to enable global dissemination of this high-risk clone-type is not understood. Here, we engineered isogenic laboratory and clinicalP. aeruginosastrains that express the different O-antigen gene clusters to assess the correlation of structural differences of O4 and O12 O-antigens to pathogen-relevant phenotypic traits. We show that serotype O12 is associated with enhanced adhesion, type IV pili dependent twitching motility, and tolerance to host defense molecules and serum. Moreover, we find that serotype O4 is less virulent compared to O12 in an acute murine pneumonia infection in terms of both colonization and survival rate. Finally, we find that these O-antigen effects may be explained by specific biophysical properties of the serotype repeat unit found in O4 and O12, and by differences in membrane stability between O4 and O12 expressing cells. The results demonstrate that differences in O-antigen sugar composition can directly affectP. aeruginosapathogenicity traits, and provide a better understanding of the potential selective advantages that underlie serotype switching and emergence of serotype O12 ST111.