bluuebunny/crossref_metadata_2025_split huggingface dataset:
Online psychometric performance of the Athens Insomnia Scale among Colombian people
Authors: Campo-Arias Adalberto , Caballero-Domínguez Carmen Cecilia , Pedrozo-Pupo John Carlos 
Published: March 2024

AbstractObjectiveThe study aimed to perform confirmatory factor, internal consistency, and differential item functioning analyses of AIS in two Colombian online samples.MethodsTwo samples were recruited online at different times. A secondary validation study was conducted with the participation of adults. The first sample was adults from the general population (n = 700, between 18 and 76 years, M = 37.05, SD = 12.70, and 68% were female adults). The second sample included patients with asthma or chronic obstructive pulmonary disease (n = 292, between 18 and 96 years (M = 60.44, SD = 17.57, and 64.73% were female). Separated confirmatory factor analyses and Cronbach’s alpha and McDonald’s omega were computed for each factor. Moreover, gender DIF was calculated using Kendall’s tau.ResultsThe data adjusted better for the AIS two-dimensional model in the general population sample (chi-squared of 111.25 [df of 19, p < .001], RMSEA of .08, CFI of .96, TLI of .95, and SRMR of .04) and the clinical sample (chi-squared of 96.83 [df of 19, p < .001], RMSEA of .12, CFI of .94, TLI of .91, and SRMR of .05). The internal consistency was high, both Cronbach alpha and McDonald’s omega of .88 in the general population sample, and Cronbach’s alpha of .85 and McDonald’s omega of .88 in the clinical sample. Gender non-differential item functioning was not found among any sample.ConclusionsAIS shows a two-dimensional structure, high internal consistency, and gender non-differential item functioning in two online samples in Colombia. It is necessary to corroborate these findings in other samples.
The antioxidants esculetin and quercetin modulate differently redox balance in human NB4 leukemia cells
Authors: Rubio Virginia , García-Pérez Ana Isabel , Herráez Angel , Puebla Lilian , Diez José C. 
Published: March 2024

AbstractThe aim is to study the involvement of reactive oxygen species on redox homeostasis of acute promyelocytic leukemia cells using two antioxidants as models for tentative leukemia therapies. The NB4 leukemia cell line has increased reactive oxygen species (ROS) levels. Esculetin and quercetin are antioxidants that alter redox equilibrium, diminishing cell viability and inducing cell death in some cancer cells. The analysis of the role of reactive oxygen species on redox balance and apoptosis in NB4 leukemia cells was addressed by modulating redox balance with oxidants hydrogen peroxide (H2O2) andtert-butylhydroperoxide (t-BHP) and antioxidant compounds (esculetin and quercetin). Cell viability of NB4 cells was measured by flow cytometry using propidium iodide (PI). Colorimetric MTT (3-(4, 5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) gave an index of cell metabolism. Apoptosis was measured using Annexin V-FITC (fluorescein isothiocyanate coupled to annexin V). Intracellular ROS levels were detected using the fluorescent probes H2DCFDA (2’, 7’-dichloro-dihydrofluorescein diacetate) and DHE (dihydro-ethidine). Pre-treatment with quercetin prevented early loss of cell viability induced by either H2O2ort-BHP. It reduced apoptosis produced by H2O2and prevented that induced byt-BHP. Pre-treatment with esculetin, in contrast, increased apoptosis induced by H2O2but reduced that produced byt-BHP. The superoxide anion content increased after incubation with either H2O2ort-BHP, mainly in esculetin pretreatment. Esculetin, but not quercetin, prevented peroxide production by either H2O2ort-BHP. Therefore, esculetin and quercetin regulate differentially redox balance in human NB4 human leukemia cells, presumably via different redox mechanisms, which opens up potential applications in antileukemia therapy.
A differential requirement for ciliary transition zone proteins in human and mouse neural progenitor fate specification
Authors: Wiegering Antonia , Anselme Isabelle , Brunetti Ludovica , Metayer-Derout Laura , Calderon Damelys , Thomas Sophie , Nedelec Stéphane , Eschstruth Alexis , Serpieri Valentina , Catala Martin , Antoniewski Christophe , Schneider-Maunoury Sylvie , Stedman Aline 
Published: March 2024

AbstractStudying developmental processes in the context of the human central nervous system is essential to understand neurodevelopmental diseases. In this paper we perform a comparative functional study of the ciliopathy geneRPGRIP1Lin human and mouse spinal development usingin vitro3D differentiation of pluripotent stem cells.RPGRIP1L, a causal gene of severe neurodevelopmental ciliopathies such as Joubert and Meckel syndromes, encodes a scaffolding protein of the ciliary transition zone involved in ciliary gating. Previous work has identified a major role forRpgrip1lin mouse brain and spinal cord development, via controlling the Sonic Hedgehog (SHH)/GLI pathway. We show that spinal organoids derived fromRpgrip1lmutant mouse embryonic stem cells faithfully recapitulate the loss of motoneurons and the strong reduction of SHH signaling observed in the mutant mice. In contrast, human induced pluripotent stem cells mutant forRPGRIP1Lproduce motoneurons and activate the SHH pathway at levels similar to wild types, a property shared by human iPSCs mutant for another ciliopathy geneTMEM67. Moreover, we show that, in humanRPGRIP1Lmutant organoids, motoneurons acquire a more anterior identity, expressingHOXgenes and other proteins normally present in the hindbrain and cervical spinal cord while motoneurons from wild type organoids strictly display a caudal brachial identity. By performing a temporal transcriptome analysis throughout the differentiation process, we find that the antero-posterior specification defect arises in early axial progenitors and correlates with the loss of cilia in these cells. Thus, this study uncovers distinct functions in humans and mice for ciliopathy proteins and a novel role for RPGRIP1L in human spinal antero-posterior patterning. These findings have important implications for understanding the role of cilia in human spinal cord development and the pathogenic mechanisms of neurodevelopmental ciliopathies.
Disordered proteins interact with the chemical environment to tune their protective function during drying
Authors: KC Shraddha , Nguyen Kenny , Nicholson Vincent , Walgren Annie , Trent Tony , Gollub Edith , Romero Sofia , Holehouse Alex S. , Sukenik Shahar , Boothby Thomas C. 
Published: March 2024

AbstractThe conformational ensemble and function of intrinsically disordered proteins (IDPs) are sensitive to their solution environment. The inherent malleability of disordered proteins combined with the exposure of their residues accounts for this sensitivity. One context in which IDPs play important roles that is concomitant with massive changes to the intracellular environment is during desiccation (extreme drying). The ability of organisms to survive desiccation has long been linked to the accumulation of high levels of cosolutes such as trehalose or sucrose as well as the enrichment of IDPs, such as late embryogenesis abundant (LEA) proteins or cytoplasmic abundant heat soluble (CAHS) proteins. Despite knowing that IDPs play important roles and are co-enriched alongside endogenous, species-specific cosolutes during desiccation, little is known mechanistically about how IDP-cosolute interactions influence desiccation tolerance. Here, we test the notion that the protective function of desiccation-related IDPs is enhanced through conformational changes induced by endogenous cosolutes. We find that desiccation-related IDPs derived from four different organisms spanning two LEA protein families and the CAHS protein family, synergize best with endogenous cosolutes during drying to promote desiccation protection. Yet the structural parameters of protective IDPs do not correlate with synergy for either CAHS or LEA proteins. We further demonstrate that for CAHS, but not LEA proteins, synergy is related to self-assembly and the formation of a gel. Our results suggest that functional synergy between IDPs and endogenous cosolutes is a convergent desiccation protection strategy seen among different IDP families and organisms, yet, the mechanisms underlying this synergy differ between IDP families.
PIKfyve controls dendritic cell function and tumor immunity
Authors: Choi Jae Eun , Qiao Yuanyuan , Kryczek Ilona , Yu Jiali , Gurkan Jonathan , Bao Yi , Gondal Mahnoor , Tien Jean Ching-Yi , Maj Tomasz , Yazdani Sahr , Parolia Abhijit , Xia Houjun , Zhou JiaJia , Wei Shuang , Grove Sara , Vatan Linda , Lin Heng , Li Gaopeng , Zheng Yang , Zhang Yuping , Cao Xuhong , Su Fengyun , Wang Rui , He Tongchen , Cieslik Marcin , Green Michael D. , Zou Weiping , Chinnaiyan Arul M. 
Published: March 2024

AbstractThe modern armamentarium for cancer treatment includes immunotherapy and targeted therapy, such as protein kinase inhibitors. However, the mechanisms that allow cancer-targeting drugs to effectively mobilize dendritic cells (DCs) and affect immunotherapy are poorly understood. Here, we report that among shared gene targets of clinically relevant protein kinase inhibitors, highPIKFYVEexpression was least predictive of complete response in patients who received immune checkpoint blockade (ICB). In immune cells, highPIKFYVEexpression in DCs was associated with worse response to ICB. Genetic and pharmacological studies demonstrated that PIKfyve ablation enhanced DC function via selectively altering the alternate/non-canonical NF-κB pathway. Both loss ofPikfyvein DCs and treatment with apilimod, a potent and specific PIKfyve inhibitor, restrained tumor growth, enhanced DC-dependent T cell immunity, and potentiated ICB efficacy in tumor-bearing mouse models. Furthermore, the combination of a vaccine adjuvant and apilimod reduced tumor progressionin vivo. Thus, PIKfyve negatively controls DCs, and PIKfyve inhibition has promise for cancer immunotherapy and vaccine treatment strategies.
Designed fluorescent protein cages as fiducial markers for targeted cell imaging
Authors: Gee Morgan , Atai Kaiser , Coller Hilary A. , Yeates Todd O. , Castells-Graells Roger 
Published: March 2024

ABSTRACTUnderstanding how proteins function within their cellular environments is essential for cellular biology and biomedical research. However, current imaging techniques exhibit limitations, particularly in the study of small complexes and individual proteins within cells. Previously, protein cages have been employed as imaging scaffolds to study purified small proteins using cryo-electron microscopy (cryo-EM). Here we demonstrate an approach to deliver designed protein cages – endowed with fluorescence and targeted binding properties – into cells, thereby serving as fiducial markers for cellular imaging. We used protein cages with anti-GFP DARPin domains to target a mitochondrial protein (MFN1) expressed in mammalian cells, which was genetically fused to GFP. We demonstrate that the protein cages can penetrate cells, are directed to specific subcellular locations, and are detectable with confocal microscopy. This innovation represents a milestone in developing tools for in-depth cellular exploration, especially in conjunction with methods such as cryo-correlative light and electron microscopy (cryo-CLEM).
Autism-associated PTCHD1 missense variants bind to the SNARE-associated protein, SNAPIN, but exhibit impaired subcellular trafficking
Authors: Pastore Stephen F. , Xie Connie T.Y. , RoyaDerwish  , Muhammad Tahir , Blahova Tereza , El-masri Sierra C. , Frankland Paul W. , Hamel Paul A. , Vincent John B. 
Published: March 2024

AbstractBackgroundPatched domain-containing 1 (PTCHD1) is a susceptibility gene for autism spectrum disorder and intellectual disability. Its function in brain development and neurotransmission remains elusive. Studies have sought to characterize PTCHD1 function by elucidating its neural network of interacting proteins. However, given the current paucity of functional information, many PTCHD1 missense variants in clinical databases are classified as variants of uncertain significance (VUSs), severely limiting the healthcare resources available to patients and families.MethodsA yeast two-hybrid assay was used to identify synaptic PTCHD1-interacting proteins. Candidate binding partners were validated by cloning; transient over-expression in HEK293T cells, followed by co-immunoprecipitation and immunoblotting; and immunocytochemistry in differentiated P19 cells. To evaluate the pathogenicity of clinical missense variants, site-directed mutagenesis was employed, followed by transient over-expression and immunocytochemistry in non-neuronal (HEK293T) and neuronal (Neuro-2A cells) systems.ResultsA novel interaction was identified between the first lumenal loop of PTCHD1 and the SNARE-associated protein SNAPIN, which is implicated in synaptic vesicle exocytosis. Clinically associated missense variants within this region did not disrupt SNAPIN binding, indicating that the pathoetiology of these variants is unrelated to this interaction. However, six of the 12 missense variants tested exhibited pronounced retention within the endoplasmic reticulum, and impaired neuronal and non-neuronal trafficking to the plasma membrane.ConclusionsThese data yield insights regarding the role of PTCHD1 in neurodevelopment and neurotransmission, and suggest a neuropathological mechanism for missense variants. These findings provide a platform for diagnostic assay and VUS interpretation, allowing for clinical re-classification of these variants.
The diversity of clinicalMycobacterium abscessusisolates in morphology, glycopeptidolipids and infection rates in a macrophage model
Authors: Pichler Virginia , Dalkilic Lara , Shoaib Ghazaleh , Shapira Tirosh , Rankine-Wilson Leah , Boudehen Yves-Marie , Chao Joseph , Sexton Danielle , Prieto Miguel , Quon Bradley , Tocheva Elitza , Kremer Laurent , Hsiao William , Av-Gay Yossef 
Published: March 2024

AbstractMycobacterium abscessus(Mab) colonies adopt smooth (S) or rough (R) morphotypes, which are linked to the presence or absence of glycopeptidolipids (GPL), respectively. Though clinically relevant, the association between GPL levels, morphotype and pathogenesis are poorly understood. To investigate the degree of correlation between Mab morphology, GPL levels, and infectivity, we generated isolates from Mab-positive sputum samples from cystic fibrosis patients. Isolated strains were categorised based on their morphology, GPL profile, and replication rate in macrophages. Our findings revealed that around 50% of isolates displayed mixed morphologies and GPL analysis confirmed a consistent relationship between GPL content and morphotype was only found in smooth isolates. Across morphotype groups, no differences were observedin vitro, yet using a high-content THP-1 cellex vivoinfection model, clinical R strains were observed to replicate at higher levels. Moreover, the proportion of infected macrophages was notably higher among clinical R strains compared to their S counterparts at 72 hours post-infection. Clinical variants also infected at significantly higher rates compared to laboratory strains, highlighting the limited translatability of lab strain infection data to clinical contexts. Our study confirmed the general correlation between morphotype and GPL levels in smooth strains yet unveiled more variability within morphotype groups than previously recognised, particularly during intracellular infection. As the rough morphotype is of highest clinical concern, these findings contribute to the expanding knowledge base surrounding Mab infections, offering insights that can steer diagnostic methodologies, and treatment approaches.
A gnotobiotic mouse model with divergent equol-producing phenotype: potential for determining microbial-driven health impacts of soy isoflavone daidzein
Authors: Leonard Lindsay M. , Simpson Abigayle M. R. , Li Shiyu , Reddivari Lavanya , Cross Tzu-Wen L. 
Published: March 2024

AbstractThe implications of soy consumption on human health have been a subject of debate, largely due to the mixed evidence regarding its benefits and potential risks. The variability in responses to soy has been partly attributed to differences in the metabolism of soy isoflavones, compounds with structural similarities to estrogen. Approximately one-third of humans possess gut bacteria capable of converting soy isoflavone daidzein into equol, a metabolite produced exclusively by gut microbiota with significant estrogenic potency. In contrast, lab-raised rodents are efficient equol producers, except for those raised germ-free. This discrepancy raises concerns about the applicability of traditional rodent models to humans. Herein, we designed a gnotobiotic mouse model to differentiate between equol producers and non-producers by introducing synthetic bacterial communities with and without the capacity into female and male germ-free mice. These gnotobiotic mice display equol-producing phenotypes consistent with the capacity of the gut microbiota received. Our findings confirm the model’s efficacy in mimicking human equol production capacity, offering a promising tool for future studies to explore the relationship between endogenous equol production and health outcomes like cardiometabolic and fertility. This approach aims to refine dietary guidelines by considering individual microbiome differences.
Orderly specification and precise laminar deployment of cortical glutamatergic projection neuron types through intermediate progenitors
Authors: Huilgol Dhananjay , Levine Jesse M , Galbavy William , Wang Bor-Shuen , Josh Huang Z. 
Published: March 2024

SUMMARYThe cerebral cortex comprises diverse types of glutamatergic projection neurons (PNs) generated from radial glial progenitors (RGs) through either direct neurogenesis or indirect neurogenesis (iNG) via intermediate progenitors (IPs). A foundational concept in corticogenesis is the “inside-out” model whereby successive generations of PNs sequentially migrate to deep then progressively more superficial layers, but its biological significance remains unclear; and the role of iNG in this process is unknown. Using genetic strategies linking PN birth-dating to projection mapping in mice, we found that the laminar deployment of IP-derived PNs substantially deviate from an inside-out rule: PNs destined to non-consecutive layers are generated at the same time, and different PN types of the same layer are generated at non-contiguous times. The overarching scheme of iNG is the sequential specification and precise laminar deployment of projection-defined PN types, which may contribute to the orderly assembly of cortical output channels and processing streams.HIGHLIGHTS-Each IP is fate-restricted to generate a pair of near-identical PNs-Corticogenesis involves the orderly generation of fate-restricted IP temporal cohorts-IP temporal cohorts sequentially as well as concurrently specify multiple PN types-The deployment of PN types to specific layers does not follow an inside-out order
Release of P-TEFb from the Super Elongation Complex promotes HIV-1 latency reversal
Authors: Cisneros William J. , Walter Miriam , Soliman Shimaa H.A. , Simons Lacy M. , Cornish Daphne , Halle Ariel W. , Kim Eun-Young , Wolinsky Steven M. , Shilatifard Ali , Hultquist Judd F. 
Published: March 2024

ABSTRACTThe persistence of HIV-1 in long-lived latent reservoirs during suppressive antiretroviral therapy (ART) remains one of the principal barriers to a functional cure. Blocks to transcriptional elongation play a central role in maintaining the latent state, and several latency reversal strategies focus on the release of positive transcription elongation factor b (P-TEFb) from sequestration by negative regulatory complexes, such as the 7SK complex and BRD4. Another major cellular reservoir of P-TEFb is in Super Elongation Complexes (SECs), which play broad regulatory roles in host gene expression. Still, it is unknown if the release of P-TEFb from SECs is a viable latency reversal strategy. Here, we demonstrate that the SEC is not required for HIV-1 replication in primary CD4+ T cells and that a small molecular inhibitor of the P-TEFb/SEC interaction (termed KL-2) increases viral transcription. KL-2 acts synergistically with other latency reversing agents (LRAs) to reactivate viral transcription in several cell line models of latency in a manner that is, at least in part, dependent on the viral Tat protein. Finally, we demonstrate that KL-2 enhances viral reactivation in peripheral blood mononuclear cells (PBMCs) from people living with HIV on suppressive ART, most notably in combination with inhibitor of apoptosis protein antagonists (IAPi). Taken together, these results suggest that the release of P-TEFb from cellular SECs may be a novel route for HIV-1 latency reactivation.AUTHOR SUMMARYSince the start of the HIV pandemic, it is estimated that nearly 86 million people have been infected with the virus, and about 40 million people have died. Modern antiretroviral therapies potently restrict viral replication and prevent the onset of AIDS, saving millions of lives. However, these therapies are not curative due to the persistence of the virus in a silenced or ‘latent’ state in long-lived cells of the body. One proposed strategy to clear this latent reservoir, termed “shock and kill”, is to activate these silenced viruses such that the infected cells can be cleared from the body by the immune system. While several drugs have been developed that can activate latent viruses, none have proven effective at reducing the size of the latent reservoir in patients in clinical trials. Here, we describe a new method for latency reactivation using a small molecule inhibitor of a human protein complex called the Super Elongation Complex (SEC). Inhibiting the SEC enhances viral transcription during active infection and triggers the reactivation of latent viruses, especially when in combination with other latency reversing agents. These results pave the way for developing more effective strategies to reactivate latent viruses towards a functional cure.
A platform for the recombinant production of Group A Streptococcus glycoconjugate vaccines
Authors: Castro Sowmya Ajay , Passmore Ian J. , Ndeh Didier , Shaw Helen Alexandra , Ruda Alessandro , Burns Keira , Thomson Sarah , Nagar Rupa , Alagesan Kathirvel , Lucas Kieron , Abouelhadid Sherif , Reglinski Mark , Schwarz-Linek Ulrich , Mawas Fatme , Widmalm Göran , Wren Brendan W. , Dorfmueller Helge C. 
Published: March 2024

ABSTRACTStrep A is a human-exclusive bacterial pathogen killing annually more than 500,000 patients, and no current licensed vaccine exists. Strep A bacteria are highly diverse, but all produce an essential, abundant, and conserved surface carbohydrate, the Group A Carbohydrate, which contains a rhamnose polysaccharide (RhaPS) backbone. RhaPS is a validated universal vaccine candidate in a glycoconjugate prepared by chemical conjugation of the native carbohydrate to a carrier protein. We engineered the Group A Carbohydratte biosynthesis pathway to enable recombinant production using the industry standard route to couple RhaPS to selected carrier proteins withinE. colicells. The structural integrity of the produced recombinant glycoconjugate vaccines was confirmed by NMR spectroscopy and mass spectrometry. Purified RhaPS glycoconjugates elicited carbohydrate-specific antibodies in mice and rabbits and bound to the surface of multiple Strep A strains of diverse M-types, confirming the recombinantly produced RhaPS glycoconjugates as valuable vaccine candidates.