bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of Self-Directed Learning Activities at King Abdulaziz University: A Qualitative Study of Faculty Perceptions
Authors: Balkheyour Ammar , Tombs Michal 
Published: October 2024

AbstractPurposeDoctors are expected to be lifelong learners and engage in continuous professional development throughout their careers. Learning to be a self-directed learner as early as possible is therefore likely to lay the foundation for future learning and development. For this reason, Self-Directed Learning (SDL) has recently been incorporated into the internal medicine curriculum at the Faculty of Medicine in Rabigh at King Abdulaziz University, Saudi Arabia. The purpose of this study was to evaluate faculty perceptions of the effectiveness of these SDL activities.MethodsThe evaluation framework for this study was underpinned by Stufflebeam’s Context, Input, Process and Product (CIPP) evaluation model. Seven faculty members took part in semi-structured interviews that explored their understandings of SDL objectives (Context), their perceptions of the methods and resources used (Input), the implementation of SDL activities (Process) and whether they meet their intended educational goals (Product). Interviews were transcribed and analysed using the thematic analysis method.ResultsFour themes emerged from data and were mapped against the elements of CIPP model: these themes are as follows: faculty perception of SDL (context), content and resources (input), facilitation and scheduling (process) and student engagement and assessment (product).ConclusionsThe faculty had different opinions about the objectives and content of SDL sessions; however, they agreed that these are aligned with internal medicine objectives and clinical content. Faculty perceived SDL activities as a reading task for students to complete prior to group discussion. The data revealed the necessity for faculty training to conduct such sessions. Challenges in the learning environment were reported, including issues in the library access and scheduling of the academic activities. Participants reported poor engagement from students to be a particular challenge and have made suggestions on how this could be addressed. In addition, they emphasized the need for assessment for these sessions.
Early Diagnosis of Vascular Ehlers-Danlos Syndrome Through AI-Powered Facial Analysis: Results from the Montalcino Aortic Consortium
Authors: Murdock David R. , Suresh Adarsh , Martinez Ernesto Calderon , Marin Isabella , Marin Frances , Braverman Alan C. , Yetman Angela T. , Morris Shaine A. , Milewicz Dianna M. 
Published: October 2024

AbstractPurposeVascular Ehlers-Danlos syndrome (vEDS), caused byCOL3A1pathogenic variants, is a rare heritable aortic and arterial disorder associated with early mortality, mainly due to spontaneous vascular dissections and ruptures. Improved methods for diagnosing vEDS are needed so that guideline-based management can be initiated to prevent deadly complications and differentiate vEDS from overlapping conditions like hypermobile EDS (hEDS).MethodsWe implemented an AI facial recognition model based on the PhenoScore framework using a support vector machine (SVM) trained on facial images of thirty individuals, aged 6-65 years, with vEDS from the Montalcino Aortic Consortium (MAC), control images from the Chicago Face Database (CFD), and publicly available images of individuals with hEDS. Cross- validation was used to train the SVM, and statistical measures to evaluate the model performance were calculated. Local Interpretable Model-agnostic Explanations (LIME) was used to generate facial heatmaps highlighting the features driving the model’s predictions.ResultsThe AI classifier showed excellent performance with as few as thirteen vEDS training images and distinguished vEDS from both controls and individuals with hEDS with high accuracy, achieving an area under the receiver operating characteristic curve (AUC) ≥ 0.97. LIME highlighted facial regions already established to characterize the facial features of vEDS patients (e.g., prominent eyes).ConclusionOur results demonstrate the potential of AI-based facial analysis for diagnosing vEDS. This method democratizes the early diagnosis of vEDS by reducing dependence on genetic testing, enabling optimal management and improved outcomes, particularly in resource-limited areas.
PSKH1 kinase activity is differentially modulated via allosteric binding of Ca2+sensor proteins
Authors: Horne Christopher R. , Dite Toby A. , Young Samuel N. , Mather Lucy J. , Dagley Laura F. , Johnson Jared L. , Yaron-Barir Tomer M. , Huntsman Emily M. , Daly Leonard A. , Byrne Dominic P. , Cadell Antonia L. , Ng Boaz H. , Yousef Jumana , Multari Dylan H. , Shen Lianju , McAloon Luke M. , Manning Gerard , Febbraio Mark A. , Means Anthony R. , Cantley Lewis C. , Tanzer Maria C. , Croucher David R. , Eyers Claire E. , Eyers Patrick A. , Scott John W. , Murphy James M. 
Published: October 2024

AbstractProtein Serine Kinase H1 (PSKH1) was recently identified as a crucial factor in kidney development and is overexpressed in prostate, lung and kidney cancers. However, little is known about PSKH1 regulatory mechanisms, leading to its classification as a “dark” kinase. Here, we used biochemistry and mass spectrometry to define PSKH1’s consensus substrate motif, protein interactors, and how interactors, including Ca2+sensor proteins, promote or suppress activity. Intriguingly, despite the absence of a canonical Calmodulin binding motif, Ca2+-Calmodulin activated PSKH1 while, in contrast, the ER-resident Ca2+sensor of the CREC family, Reticulocalbin-3, suppressed PSKH1 catalytic activity. In addition to antagonistic regulation of the PSKH1 kinase domain by Ca2+sensing proteins, we identified UNC119B as a protein interactor that activates PSKH1 via direct engagement of the kinase domain. Our findings identify complementary allosteric mechanisms by which regulatory proteins tune PSKH1’s catalytic activity, and raise the possibility that different Ca2+sensors may act more broadly to tune kinase activities by detecting and decoding extremes of intracellular Ca2+concentrations.
Modeling Glioma Intratumoral Heterogeneity with Primary Human Neural Stem and Progenitor Cells
Authors: Gao Daniel , Liu Daniel Dan , Eastman Anna E. , Womack Nicole L. , Ohene-Gambill Benjamin F. , Baez Michelle , Weissman Irving L. 
Published: October 2024

ABSTRACTGlioblastoma multiforme (GBM) is a deadly form of glioma notable for its significant intratumoral heterogeneity, which is believed to drive therapy resistance. GBM has been observed to mimic a neural stem cell hierarchy reminiscent of normal brain development. However, it is still unclear how cell-of-origin shapes intratumoral heterogeneity. Here, we develop a model of glioma initiation using neural stem and progenitor cells (NSPCs) purified from fetal human brain tissue. We previously described a method to prospectively isolate and culture tripotent neural stem cells (NSCs), bipotent glial progenitor cells (GPCs), and unipotent oligodendrocyte precursor cells (OPCs). We transduced these isogenic lines with dominant-negative TP53R175Hand NF1 knockdown, a commonly-used genetic model of GBM in mice. These reprogrammed lines robustly engrafted when transplanted into the brains of immunodeficient mice, and showed significant expansion over time. Engrafted cells were reextracted from the mouse brain for single cell RNA sequencing (scRNA-seq), in order to quantify how the cell-of-origin modulates the cellular subtypes found in the resulting tumor. This result revealed the strong influence the cell-of-origin plays in glioma heterogeneity. Our platform is highly adaptable and allows for modular and systematic interrogation of how cell-of-origin shape the tumor landscape.
Multifunctional Systems in Synthetic Biology: Single-Stranded DNA Signaling for Precise Control of Gene Activation
Authors: Ng Brian , Ding Yuying , Cornall Matthew , Kumar Ravinash Krishna , Qing Yujia , Bayley Hagan 
Published: October 2024

ABSTRACTControllable gene circuits that respond to defined inputs are essential tools in synthetic biology. By leveraging regulatory mechanisms at either transcriptional or translational levels, synthetic responsive systems have been engineered to recognize diverse signals, such as small molecules (e.g., tetracycline) or physical stimuli (e.g., light). However, these approaches have limitations: small-molecule signals often require high concentrations to be effective, and sophisticated engineering is needed to generate responsive effectors. Here, we establish a simple, versatile gene activation system in which short single-stranded DNAs trigger RNA or protein production by complementing defective single-stranded promoters upstream of target genes. We demonstrate selective gene activation with orthogonal promoters, and logic-gate operations with signal pairs. The signaling system operates in compartmentalized nanoliter droplets scaffolded by bilayers. Signal delivery is controlled by selectively disrupting bilayers or applying transmembrane potential to move signals through protein pores, thereby activating genes within the receiver compartments. This work expands the toolset for engineering multifunctional, responsive materials to meet biotechnological and medical needs, enabling gene activation in response to specific cues.
Medicinal chemistry of benzo[d]isoxazole-4,7-dione analogues identifies the ribosomal small subunit as a target for specific mycobacterial translational fidelity
Authors: Wu Jie , Chaudhuri Swarnava , Feid Sarah Caldwell , Pan Miaomiao , Kawaji Qingwen , Liu Gang , Javid Babak 
Published: October 2024

AbstractMycobacteria have high rates of error in the translation of glutamine and asparagine codons due to a two-step indirect tRNA aminoacylation pathway involving the essential amidotransferase GatCAB. This specific mycobacterial mistranslation is both necessary and sufficient for tolerance to the antibiotic rifampicin. Furthermore, we identified the natural product kasugamycin as a small molecule that could decrease this type of translational error, and potentiate rifampicin-mediated killing of mycobacteria, but whether other small molecules can decrease this specific type of mistranslation is unknown. We screened a library of synthetic small molecules using a pathway-specific whole-cell screen in a reporter strain ofMycobacterium smegmatisfor their ability to decrease specific mycobacterial mistranslation. We synthesized 110 analogs of a parent hit compound and analyzed their bioactivity. To identify the cellular target of the compounds, we biotinylated active and inactive analogs and performed pull-down and mass-spectrometry of bound cellular proteins. We identified benzo[d]isoxazole-4,7-diones as a class of small molecules able to decrease mycobacterial mistranslation. Of the 110 analogs synthesized, we identified 10 with superior potency to the parent compound and analyzed the compounds to infer structure-activity relationships. Pull-down and mass spectrometry of bound cellular proteins identified RpS5 as a potential target of active compounds. Our study identified synthetic small molecules able to decrease mycobacterial mistranslation and confirmed that the small ribosomal subunit can be targeted to decrease mistranslation rates arising from physiologically mischarged tRNAs. Targeting mistranslation may be a potentially attractive means of targeting antibiotic-tolerant bacteria.
THRESHOLD: A Comprehensive Transcriptomic Analysis Tool for Evaluating Gene Saturation and Impact in Disease Progression
Authors: Gammell Finán , Li Jennifer , Elco Christopher , Plavicki Jessica , Uzun Alper 
Published: October 2024

AbstractGene expression studies serve as a foundational tool in molecular biology, providing insights into developmental, physiological, and pathological processes. Variations in gene expression can indicate disease states, which are vital in understanding disease progression, subtype manifestations, and identifying therapeutic targets based on detailed expression patterns. To effectively investigate gene expression patterns, especially in large datasets, a robust and precise analysis tool is crucial. In response to this critical analytical need, we developed THRESHOLD, a novel tool that goes beyond traditional gene expression analysis by introducing the concept of gene saturation. Unlike conventional methods that focus on absolute expression levels or binary differential expression, THRESHOLD quantifies the consistency of gene expression across patients, revealing co-regulation patterns that may otherwise be overlooked. This novel metric offers a unique perspective on gene expression patterns by highlighting consistent trends across patient samples, which are critical for understanding disease mechanisms and stratifying patients based on molecular signatures. The tool offers several features, including user-defined parameters, statistical comparisons, and interactive data visualization. THRESHOLD has uncovered compelling insights into disease progression using TCGA Cancer Datasets. For instance, bladder urothelial carcinoma demonstrated increasing upregulated gene saturation in progressive cancer stages (p < 0.00001). Moreover, THRESHOLD identified heightened gene saturation in patients with earlier onset of prostate adenocarcinoma (p < 0.0001) and revealed a critical fusion transcript, SLC45A2-AMACR, implicated in prostate adenocarcinoma progression, recurrence, and metastasis. Additionally, novel biomarkers and potential candidates for drug therapies were identified through protein-protein interaction networks and functional analyses of saturation data in colon adenocarcinoma and breast invasive carcinoma. Collectively, THRESHOLD advances our understanding of patient stratification and molecular signatures by offering a more detailed view of gene expression dynamics. The THRESHOLD tool is publicly available at:https://github.com/alperuzun/THRESHOLD.
Loss of Cdc42 causes abnormal optic cup morphogenesis and microphthalmia in mouse
Authors: Hofstetter Katrina S. , Haas Paula M. , Kuntz Jonathon P. , Zheng Yi , Fuhrmann Sabine 
Published: October 2024

AbstractCongenital ocular malformations originate from defective morphogenesis during early eye development and cause 25% of childhood blindness. Formation of the eye is a multi-step, dynamic process; it involves evagination of the optic vesicle, followed by distal and ventral invagination, leading to the formation of a two-layered optic cup with a transient optic fissure. These tissue folding events require extensive changes in cell shape and tissue growth mediated by cytoskeleton mechanics and intercellular adhesion. We hypothesized that the Rho GTPase Cdc42 may be an essential, convergent effector downstream of key regulatory factors required for ocular morphogenesis. CDC42 controls actin remodeling, apicobasal polarity, and junction assembly. Here we identify a novel essential function for Cdc42 during eye morphogenesis in mouse; inCdc42mutant eyes expansion of the ventral optic cup is arrested, resulting in microphthalmia and a wide coloboma. Our analyses show that Cdc42 is required for expression of the polarity effector proteins PRKCZ and PARD6, intercellular junction protein tight junction protein 1, β-catenin, actin cytoskeleton F-actin, and contractile protein phospho myosin light chain 2. Expression of RPE fate determinants OTX2 and MITF, and formation of the RPE layer are severely affected in the temporal domain of the proximal optic cup. EdU incorporation is significantly downregulated. In addition, mitotic retinal progenitor cells mis-localized deeper, basal regions, likely contributing to decreased proliferation. We propose that morphogenesis of the ventral optic cup requires Cdc42 function for coordinated optic cup expansion and establishment of subretinal space, tissue tension, and differentiation of the ventral RPE layer.
Serum PFAS and Lipid Concentrations in Ecuadorian Adolescents
Authors: Guerra Michelle , Kayser Georgia , Checkoway Harvey , Suarez-Torres Jose , Lopez Dolores , Martinez Danilo , Huset Carin A. , Peterson Lisa A. , Suarez-Lopez Jose Ricardo 
Published: October 2024

AbstractThere is growing evidence that per- and polyfluoroalkyl substances (PFAS) may alter serum lipid concentrations; however, this topic is understudied in adolescents and Latin American populations. We aimed to characterize these associations among adolescents in Ecuador’s main floricultural region.This cross-sectional study included 97 adolescents ages 11-17 years from Pedro Moncayo County, Ecuador. Generalized estimating equation models were applied to estimate the associations of serum perfluorooctane sulfonic acid (PFOS), perfluorooctanoic acid (PFOA), and perfluorononanoic acid (PFNA) concentrations with serum lipids. Models were adjusted for age, gender, height, body mass index (BMI), acetylcholinesterase (AChE) activity, and hemoglobin concentrations.We observed statistically significant sex-specific associations of all PFAS with triglycerides. Significant inverse relationships between PFAS and triglycerides were observed in females (% lipid difference per 50% increase in: PFOS= −15.0% [95%CI: −24.72, −4.06], PFNA= −25.49% [−36.93, −12.00], and PFOA= −16.55% [−28.16, −3.07]) but not in males. No associations were observed between total cholesterol, high-density lipoprotein (HDL), or low-density lipoprotein (LDL) cholesterol and any PFAS.PFOS, PFOA, and PFNA were inversely associated with triglycerides in adolescent females but not males. Further characterization of sex-specific associations of PFAS and blood lipids in adolescents is warranted.
Mapping the Cellular Etiology of Schizophrenia and Diverse Brain Phenotypes
Authors: Duncan Laramie E , Li Tayden , Salem Madeleine , Li Will , Mortazavi Leili , Senturk Hazal , Shargh Naghmeh , Vesuna Sam , Shen Hanyang , Yoon Jong , Wang Gordon , Ballon Jacob , Tan Longzhi , Pruett Brandon Scott , Knutson Brian , Deisseroth Karl , Giardino William J 
Published: October 2024

Summary paragraphPsychiatric disorders account for a substantial fraction of the world’s disease burden1, and yet the development of novel therapeutics has been notoriously slow2. Likely contributing factors include the complexity of the human brain and the high polygenicity of psychiatric disorders3–5, meaning that thousands of genetic factors contribute to disease risk. Fortunately, technological advances have enabled comprehensive surveys of human brain cell types using transcriptomes from single nuclei (snRNAseq)6–8. Additionally, genome-wide association studies (GWAS) have linked thousands of risk loci to psychiatric disorders9–11. Here, we combined these two landmark data resources to infer the cell types involved in the etiology of schizophrenia and comparison phenotypes. This work demonstrated: 1) cell types that are concordant with prior findings about schizophrenia, 2) novel cell type associations for schizophrenia, 3) greater molecular specificity regarding schizophrenia-associated cell types than was previously available, 4) evidence that well powered genome-wide and brain-wide datasets are required for these analyses, 5) distinct cellular profiles for five brain-related phenotypes, 6) a prototype for a cell-type based classification system for psychiatric and other brain disorders, and 7) a roadmap toward drug repurposing, novel drug development, and personalized treatment recommendations. Thus, this work formalizes a data-driven, cellular and molecular model of complex brain disorders.
TRAUMATIC MICROHEMORHAGES ARE NOT SYNONYMOUS WITH AXONAL INJURY
Authors: Mittenzwei Rhonda , Maioli Heather , Sytsma Karinn , Kirkland Amanda , Keene C. Dirk , Diaz-Arrastia Ramon , Mac Donald Christine , Maffei Chiara , Edlow Brian L. , Nolan Amber L. 
Published: October 2024

SUMMARYDiffuse axonal injury (DAI) is caused by acceleration-deceleration forces during trauma that shear white matter tracts. Susceptibility-weighted MRI (SWI) identifies microbleeds that are considered the radiologic hallmark of DAI and are used in clinical prognostication. However, this assumption is limited by a lack of systematic radiologic-pathologic correlation studies. Here, we performedex vivoSWI on three brains from patients who died after severe TBI and assessed axonal injury around SWI microbleeds using immunohistochemistry to the amyloid beta precursor protein. Axonal injury was present in 28/44 microbleeds (64%), undermining the assumed pathophysiologic 1:1 link between traumatic vascular and axonal injury.
IRAK2 deficiency causes a new immune dysregulation disorder
Authors: Fei Yudie , Liu Lin , Ma Shuangyue , Wang Shihao , Lu Meiping , Xue Jing , Jin Ying , Wang Yusha , Sun Xiangwei , Chen Xiang , Han Xu , Zhang Changming , Guo Li , Zhang Jiahui , Zhong Hua , Wen Lihong , Yu Xiaomin , Zhou Qing , Liu Zhihong 
Published: October 2024

AbstractInterleukin 1 receptor-associated kinase 2 (IRAK2) plays a critical role in immune response by participating in the formation of the Myddosome complex in Toll-like receptor (TLR) signaling pathways. Here, we identified a loss-of-function mutation (IRAK2-Δex2) in theIRAK2gene in three patients, presenting with immune dysregulation, including systemic lupus erythematosus (SLE) and autoinflammatory disease. This mutation leads to the skipping of exon 2 inIRAK2, disrupting its interaction with IRAK4 and impairing the activation of nuclear factor kappa B (NF-κB) and mitogen-activated protein kinase (MAPK) signaling pathways via Myddosome. The patients exhibited aberrantly upregulated type I interferon (IFN) response following LPS stimulation, which was further confirmed in bone marrow-derived macrophages (BMDMs) in mice. Our study suggests that IRAK2 deficiency results in immune dysregulation due to compromised TLR signaling and activated IFN signaling primarily in monocyte-macrophage lineage.One Sentence SummaryA new immune dysregulation disorder caused by a loss-of-function mutation in theIRAK2gene, which disrupts TLR signaling via Myddosome, results in impaired NF-κB activation and upregulated type I interferon responses.
Identification and molecular characterization of missense mutations in orphan GPCR GPR61 occurring in severe obesity
Authors: Tsang Choi Har , Rosa Alexander De , Kozielewicz Paweł 
Published: October 2024

AbstractObesity is a disease defined as “abnormal or excessive fat accumulation that presents a health risk, with a body mass index (BMI) over 30” (World Health Organization). Signalling mediated by hypothalamus-expressed membrane proteins from the GPCR family regulates food intake and metabolism. The orphan GPCR GPR61 was linked to regulation of metabolism and, here, we identify 34 mutations in the GPR61 gene which are present with much higher frequency in severe obesity samples from UK10K obesity screen than in the normal population. The cumulative sum of mutations was higher for the GPR61 gene compared to the highly mutated and well-established target, melanocortin 4 receptor (MC4R). The majority of the GPR61 mutations reduced cell surface expression of overexpressed HiBiT-GPR61 in HEK293A cells. Additionally, the mutations T92P, R236C and R262C reduced ligand-independent GPR61-induced cAMP production, and R236C compromised Gsprotein activation. Therefore, we suggest that GPR61 indeed represents a Gs-coupled receptor with a potential role in the regulation of metabolism. Our data warrant further studies to assess role of this orphan GPCR in metabolism in greater detail.