bluuebunny/crossref_metadata_2025_split huggingface dataset:
LRRK2 mediates haloperidol-induced changes in indirect pathway striatal projection neurons
Authors: Chen Chuyu , Masotti Meghan , Shepard Nathaniel , Promes Vanessa , Tombesi Giulia , Arango Daniel , Manzoni Claudia , Greggio Elisa , Hilfiker Sabine , Kozorovitskiy Yevgenia , Parisiadou Loukia 
Published: June 2024

AbstractHaloperidol is used to manage psychotic symptoms in several neurological disorders through mechanisms that involve antagonism of dopamine D2 receptors that are highly expressed in the striatum. Significant side effects of haloperidol, known as extrapyramidal symptoms, lead to motor deficits similar to those seen in Parkinson’s disease and present a major challenge in clinical settings. The underlying molecular mechanisms responsible for these side effects remain poorly understood. Parkinson’s disease-associated LRRK2 kinase has an important role in striatal physiology and a known link to dopamine D2 receptor signaling. Here, we systematically explore convergent signaling of haloperidol and LRRK2 through pharmacological or genetic inhibition of LRRK2 kinase, as well as knock-in mouse models expressing pathogenic mutant LRRK2 with increased kinase activity. Behavioral assays show that LRRK2 kinase inhibition ameliorates haloperidol-induced motor changes in mice. A combination of electrophysiological and anatomical approaches reveals that LRRK2 kinase inhibition interferes with haloperidol-induced changes, specifically in striatal neurons of the indirect pathway. Proteomic studies and targeted intracellular pathway analyses demonstrate that haloperidol induces a similar pattern of intracellular signaling as increased LRRK2 kinase activity. Our study suggests that LRRK2 kinase plays a key role in striatal dopamine D2 receptor signaling underlying the undesirable motor side effects of haloperidol. This work opens up new therapeutic avenues for dopamine-related disorders, such as psychosis, also furthering our understanding of Parkinson’s disease pathophysiology.SummaryChen et al. demonstrate that haloperidol mediated changes in the striatal indirect pathway neurons and circuits are linked to Parkinson’s disease associated LRRK2. Inhibiting LRRK2 kinase activity ameliorates the motoric side effects of haloperidol, suggesting a potential approach to alleviating the unwanted side effects of antipsychotics.
A Nanobody Interaction with SARS-CoV-2 Spike Allows the Versatile Targeting of Lentivirus Vectors
Authors: Alfadhli Ayna , Bates Timothy A. , Barklis Robin Lid , Romanaggi CeAnn , Tafesse Fikadu G. , Barklis Eric 
Published: June 2024

ABSTRACTWhile investigating methods to target gene delivery vectors to specific cell types, we examined the potential of using a nanobody against the SARS-CoV-2 Spike protein receptor binding domain to direct lentivirus infection of Spike-expressing cells. Using three different approaches, we found that lentiviruses with surface-exposed nanobody domains selectively infect Spike-expressing cells. The targeting is dependent on the fusion function of Spike, and conforms to a model in which nanobody binding to the Spike protein triggers the Spike fusion machinery. The nanobody-Spike interaction also is capable of directing cell-cell fusion, and the selective infection of nanobody-expressing cells by Spike-pseudotyped lentivirus vectors. Significantly, cells infected with SARS-CoV-2 are efficiently and selectively infected by lentivirus vectors pseudotyped with a chimeric nanobody protein. Our results suggest that cells infected by any virus that forms syncytia may be targeted for gene delivery using an appropriate nanobody or virus receptor mimic. Vectors modified in this fashion may prove useful in the delivery of immunomodulators to infected foci to mitigate the effects of viral infections.IMPORTANCEWe have discovered that lentiviruses decorated on their surfaces with a nanobody against the SARS-CoV-2 Spike protein selectively infect Spike-expressing cells. Infection is dependent on the specificity of the nanobody and the fusion function of the Spike protein, and conforms to a reverse fusion model, in which nanobody binding to Spike triggers the Spike fusion machinery. The nanobody-Spike interaction also can drive cell-cell fusion, and infection of nanobody-expressing cells with viruses carrying the Spike protein. Importantly, cells infected with SARS-CoV-2 are selectively infected with nanobody-decorated lentiviruses. These results suggest that cells infected by any virus that expresses an active receptor-binding fusion protein may be targeted by vectors for delivery of cargoes to mitigate infections.
Molecular and spatial transcriptomic classification of midbrain dopamine neurons and their alterations in a LRRK2G2019Smodel of Parkinson’s disease
Authors: Gaertner Zachary , Oram Cameron , Schneeweis Amanda , Schonfeld Elan , Bolduc Cyril , Chen Chuyu , Dombeck Daniel , Parisiadou Loukia , Poulin Jean-Francois , Awatramani Rajeshwar 
Published: June 2024

AbstractSeveral studies have revealed that midbrain dopamine (DA) neurons, even within a single neuroanatomical area, display heterogeneous properties. In parallel, studies using single cell profiling techniques have begun to cluster DA neurons into subtypes based on their molecular signatures. Recent work has shown that molecularly defined DA subtypes within the substantia nigra (SNc) display distinctive anatomic and functional properties, and differential vulnerability in Parkinson’s disease (PD). Based on these provocative results, a granular understanding of these putative subtypes and their alterations in PD models, is imperative. We developed an optimized pipeline for single-nuclear RNA sequencing (snRNA-seq) and generated a high-resolution hierarchically organized map revealing 20 molecularly distinct DA neuron subtypes belonging to three main families. We integrated this data with spatial MERFISH technology to map, with high definition, the location of these subtypes in the mouse midbrain, revealing heterogeneity even within neuroanatomical sub-structures. Finally, we demonstrate that in the preclinical LRRK2G2019Sknock-in mouse model of PD, subtype organization and proportions are preserved. Transcriptional alterations occur in many subtypes including those localized to the ventral tier SNc, where differential expression is observed in synaptic pathways, which might account for previously described DA release deficits in this model. Our work provides an advancement of current taxonomic schemes of the mouse midbrain DA neuron subtypes, a high-resolution view of their spatial locations, and their alterations in a prodromal mouse model of PD.Teaser: Using snRNASeq and MERFISH we identified midbrain DA subtypes, mapped their spatial location, and identified alterations in a LRRK2 model
Optimizing in vitro spherulation cues in the fungal pathogenCoccidioides
Authors: Homer Christina , Ochoa Elena , Voorhies Mark , Sil Anita 
Published: June 2024

AbstractCoccidioides spp. are part of a group of thermally dimorphic fungal pathogens, which grow as filamentous cells (hyphae) in the soil and transform to a different morphology upon inhalation into the host. TheCoccidioideshost form, the spherule, is unique and highly under characterized due to both technical and biocontainment challenges. Each spherule arises from an environmental spore (arthroconidium), matures, and develops hundreds of internal endospores, which are released from the spherule upon rupture. Each endospore can then go on to form another spherule in a cycle called spherulation. One of the foremost technical challenges has been reliably growing spherules in culture without the formation of contaminating hyphae, and consistently inducing endospore release from spherules. Here, we present optimization of in vitro spherule growth and endospore release, by closely controlling starting cell density in the culture, using freshly-harvested arthroconidia, and decreasing the concentration of multiple salts in spherulation media. We developed a minimal media to test spherule growth on various carbon and nitrogen sources. We defined a critical role for the dispersant Tamol in both early spherule formation and prevention of the accumulation of a visible film around spherules. Finally, we examined how the conditions under which arthroconidia are generated influence their transcriptome and subsequent development into spherules, demonstrating that this is an important variable to control when designing spherulation experiments. Together, our data reveal multiple strategies to optimize in vitro spherulation growth, enabling characterization of this virulence-relevant morphology.
Uncovering social states in healthy and clinical populations using digital phenotyping and Hidden Markov Models
Authors: Leaning Imogen E. , Costanzo Andrea , Jagesar Raj , Reus Lianne M. , Visser Pieter Jelle , Kas Martien J.H. , Beckmann Christian , Ruhé Henricus G. , Marquand Andre F. 
Published: June 2024

AbstractBrain related disorders are characterised by observable behavioural symptoms. Smartphones can passively collect objective behavioural data, avoiding recall bias. Despite promising clinical utility, analysing smartphone data is challenging as datasets often include a range of missingness-prone temporal features. Hidden Markov Models (HMMs) provide interpretable, lower-dimensional temporal representations of data, allowing missingness. We applied an HMM to an aggregate dataset of smartphone measures designed to assess social functioning in healthy controls (HCs) (n=247), participants with schizophrenia (n=18), Alzheimer’s disease (AD) (n=26) and memory complaints (n=57). We selected a model with socially “active” and “inactive” states, generated hidden state sequences per participant and calculated their “dwell time”, i.e. the percentage of time spent in the socially active state. We identified lower dwell times in AD versus HCs and higher dwell times related to increased social functioning questionnaire scores in HCs, finding the HMM to be a practical method for digital phenotyping analysis.
Assessing the impact of a mandatory calorie labelling policy in out-of-home food outlets in England on consumer behaviour: a natural experimental study
Authors: Essman Michael , Burgoine Thomas , Jones Andrew , Polden Megan , Robinson Eric , Sacks Gary , Sharp Stephen J. , Smith Richard , Vanderlee Lana , White Christine M. , White Martin , Hammond David , Adams Jean 
Published: June 2024

AbstractBackgroundOut-of-home (OOH) food tends to be energy-dense and nutrient-poor. In response, England implemented a mandatory calorie labelling policy in the OOH sector. We evaluated changes in consumer behaviours after the policy was implemented in April 2022.MethodsWe employed a natural experimental design to assess pre-post changes in noticing and using nutrition information, and behaviours associated with menu labelling. We compared changes in England to comparator jurisdictions without similar policies. Data included four consecutive years (2019-2022) from the International Food Policy Study; participants were adults aged 18 years or older. Mixed effects logistic regression models assessed pre-post changes in binary outcomes, and mixed effects negative binomial regression assessed changes in frequency of OOH eating.ResultsIn England, noticing nutrition information increased from 16.0% (15.6 to 16.4) in 2020 to 19.7% (19.1 to 20.2) in 2021 and to 25.8% (25.5 to 26.1) in 2022. This increase was 4.8 percentage points (95% CI 2.5 to 7.1) higher in England versus the comparator group. Using nutrition information increased in England from 8.0% (7.5% to 8.4%) in 2020 to 11.8% (10.9% to 12.6%) in 2021 and to 13.5% (13.1% to 13.9%) in 2022. There was a 2.7 percentage point (95% CI 2.0 to 3.4) greater increase in England versus the comparator group from 2020 to 2021. Ordering something different was the only behaviour associated with menu labelling that increased after the policy in England: from 12.6% (12.4 to 12.7) in 2020 to 15.2% (14.7 to 15.6) in 2021 and to 17.7% (17.6 to 17.8) in 2022. There was a 2.8 percentage points (95% CI 1.8 to 3.9) greater increase in England versus the comparator group from 2021 to 2022. Frequency of OOH eating did not change after policy implementation.ConclusionsThe introduction of mandatory calorie labelling in England led to increases in self-reported noticing and using, with the key behavioural impact on ordering something different. This suggests that while calorie labelling can enhance awareness, translating this into behaviour change remains limited to shifting orders. Additional strategies may be required to maximize the public health benefits of calorie labelling.
AI-Enhanced Subtyping of Thymic Tumors: Attention-based MIL with Pathology-Specific Feature Extraction
Authors: Kussaibi Haitham 
Published: June 2024

ABSTRACTPurposeThe precise classification of thymic tumors using whole slide images (WSIs) is essential for accurate diagnosis and treatment. While traditional Convolutional Neural Networks (CNNs) are commonly used for this purpose, emerging models tailored to pathology, such as Phikon and HistoEncoder, present promising alternatives as feature extractors. Additionally, the limited availability of annotated WSIs has driven the development of weakly-supervised classifiers like multiple-instance learning (MIL) models. In this study, we evaluate nine different combinations of extractor-classifier pairs for thymic tumor subtyping, including a novel, self-developed attention-based MIL classifier, AttenMIL.MethodsThe process began with curating a dataset of thymic tumor Whole Slide Images (WSIs) from the TCGA platform. Using the Yottixel method, patches were derived from these WSIs, and features were extracted from the patches using three different pathology-specific models: Phikon, HistoEncoder, and a pathology-fine-tuned ResNet50. The extracted features were then organized into small bags of instances through a chunking technique. Subsequently, three MIL classifiers AttenMIL, TransMIL, and Chowder were trained. Finally, the efficacy and generalizability of nine different combinations of extractor-classifier pairs were evaluated on unseen test images. Confusion matrices for each pair were utilized to provide insights into misclassification patterns and potential error sources.ResultsThe Phikon feature extractor consistently delivered the highest classification accuracies, particularly when paired with the AttenMIL and Chowder classifiers, achieving up to 99% accuracy. This combination significantly outperformed other feature extractor-classifier pairs. Confusion matrices revealed that the AB and B3 subtypes were the most commonly confused classes across the different models.ConclusionsThe study demonstrates the potential of domain-specific feature extractors like Phikon, when coupled with robust MIL classifiers such as the novel AttenMIL and Chowder, in enhancing the accuracy and reliability of thymic tumor classification. The chunking-based augmentation method proved effective for thymic tumors, which are relatively homogeneous, but its applicability to heterogeneous tumors remains to be explored. Future research should address class imbalances and improve generalizability to different datasets.Statements and DeclarationsCompeting InterestsThe author has declared no competing interest.No funding was received for conducting this study.Declaration of generative AI and AI-assisted technologies in the writing processWhile preparing this work, the author used ChatGPT to improve language and readability. After using this tool/service, the author reviewed and edited the content as needed and took full responsibility for the publication’s content.
Pathogenic diversification of the gut commensalProvidencia alcalifaciensvia acquisition of a second type III secretion system
Authors: Klein Jessica A. , Predeus Alexander V. , Greissl Aimee R. , Clark-Herrera Mattie M. , Cruz Eddy , Cundiff Jennifer A. , Haeberle Amanda L. , Howell Maya , Lele Aaditi , Robinson Donna J. , Westerman Trina L. , Wrande Marie , Wright Sarah J. , Green Nicole M. , Vallance Bruce A. , McClelland Michael , Mejia Andres , Goodman Alan G. , Elfenbein Johanna R. , Knodler Leigh A. 
Published: June 2024

AbstractProvidencia alcalifaciensis a Gram-negative bacterium found in a wide variety of water and land environments and organisms. It has been isolated as part of the gut microbiome of animals and insects, as well as from stool samples of patients with diarrhea. SpecificP. alcalifaciensstrains encode gene homologs of virulence factors found in other pathogenic members of the same Enterobacterales order, such asSalmonella entericaserovar Typhimurium andShigella flexneri.Whether these genes are also pathogenic determinants inP. alcalifaciensis not known. Here we have usedP. alcalifaciens205/92, a clinical isolate, within vitroandin vivoinfection models to investigateP. alcalifaciens-host interactions at the cellular level. Our particular focus was the role of two type III secretion systems (T3SS) belonging to the Inv-Mxi/Spa family. T3SS1bis widespread inProvidenciaspp. and encoded on the chromosome. T3SS1ais encoded on a large plasmid that is present in a subset ofP. alcalifaciensstrains, which are primarily isolates from diarrheal patients. Using a combination of electron and fluorescence microscopy and gentamicin protection assays we show thatP. alcalifaciens205/92 is internalized into eukaryotic cells, rapidly lyses its internalization vacuole and proliferates in the cytosol. This triggers caspase-4 dependent inflammasome responses in gut epithelial cells. The requirement for the T3SS1ain entry, vacuole lysis and cytosolic proliferation is host-cell type specific, playing a more prominent role in human intestinal epithelial cells as compared to macrophages. In a bovine ligated intestinal loop model,P. alcalifacienscolonizes the intestinal mucosa, inducing mild epithelial damage with negligible fluid accumulation. No overt role for T3SS1aor T3SS1bwas seen in the calf infection model. However, T3SS1bwas required for the rapid killing ofDrosophila melanogaster. We propose that the acquisition of two T3SS by horizontal gene transfer has allowedP. alcalifaciensto diversify its host range, from a highly virulent pathogen of insects to an opportunistic gastrointestinal pathogen of animals.
CLCC1 Governs Bilayer Equilibration at the Endoplasmic Reticulum to Maintain Cellular and Systemic Lipid Homeostasis
Authors: Wu Lingzhi , Wang Jianqin , Wang Yawei , Yang Junhan , Yao Yuanhang , Huang Dong , Hu Yating , Xu Xinxuan , Wang Renqian , Du Wenjing , Shi Yiting , Li Quan , Liu Lu , Zhu Yuangang , Wang Xiao , Guo Qiang , Xu Li , Li Peng , Chen Xiao-Wei 
Published: June 2024

AbstractThe intricate orchestration of lipid production, storage, and mobilization is vital for cellular and systemic homeostasis1,2. Dysfunctional plasma lipid control represents the major risk factor for cardio-metabolic diseases, the leading cause of human mortality3,4. Within the cellular landscape, the endoplasmic reticulum (ER) is the central hub of lipid synthesis and secretion, particularly in metabolically active hepatocytes in the liver or enterocytes in the gut5,6. Initially assembled in the ER lumen, lipid-ferrying lipoproteins necessitate the cross-membrane transfer of both neutral and phospho-lipids onto the lumenal apolipoprotein B (APOB), in a poorly-defined process7–10. Here we show that trans-bilayer equilibration of phospholipids, regulated by the ER protein CLCC1, determines lipid partition across the ER membrane and consequently systemic lipid homeostasis. CLCC1 partners with the phospholipid scramblase TMEM41B11,12to recognize imbalanced bilayers and promote lipid scrambling, thereby licensing lipoprotein biogenesis and the subsequent bulk lipid transport. Strikingly, loss of CLCC1 or TMEM41B leads to the emergence of giant lumenal lipid droplets enclosed by extensively imbalanced ER bilayers, and consequently drastically accelerated pathogenesis of metabolic-dysfunction-associated liver steatohepatitis (MASH). The above results establish phospholipid scrambling at the ER as the lynchpin to maintain a dynamic equilibrium. Considering the requirement of trans-bilayer phospholipid equilibration in numerous biological processes, ranging from catabolic autophagy to viral infection13–16, our study may enable further elucidation of a previously under-appreciated homeostatic control mechanism intrinsic to the ER function in lipid biogenesis and distribution.
Lower motor performance is linked with poor sleep quality, depressive symptoms, and grey matter volume alterations
Authors: Küppers Vincent , Bi Hanwen , Nicolaisen-Sobesky Eliana , Hoffstaedter Felix , Yeo B.T. Thomas , Drzezga Alexander , Eickhoff Simon B. , Tahmasian Masoud 
Published: June 2024

AbstractMotor performance (MP) is essential for functional independence and well-being, particularly in later life. However, the relationship between behavioural aspects such as sleep quality and depressive symptoms, which contribute to MP, and the underlying structural brain substrates of their interplay remains unclear. This study used three population-based cohorts of younger and older adults (n=1,950) from the Human Connectome Project-Young Adult (HCP-YA), HCP-Aging (HCP-A), and enhanced Nathan Kline Institute-Rockland sample (eNKI-RS). Several canonical correlation analyses were computed within a machine learning framework to assess the associations between each of the three domains (sleep quality, depressive symptoms, grey matter volume (GMV)) and MP. The HCP-YA analyses showed progressively stronger associations between MP and each domain: depressive symptoms (unexpectedly positive, r=0.13, SD=0.06), sleep quality (r=0.17, SD=0.05), and GMV (r=0.19, SD=0.06). Combining sleep and depressive symptoms significantly improved the canonical correlations (r=0.25, SD=0.05), while the addition of GMV exhibited no further increase (r=0.23, SD=0.06). In young adults, better sleep quality, mild depressive symptoms, and GMV of several brain regions were associated with better MP. This was conceptually replicated in young adults from the eNKI-RS cohort. In HCP-Aging, better sleep quality, fewer depressive symptoms, and increased GMV were associated with MP. Robust multivariate associations were observed between sleep quality, depressive symptoms and GMV with MP, as well as age-related variations in these factors. Future studies should further explore these associations and consider interventions targeting sleep and mental health to test the potential effects on MP across the lifespan.