bluuebunny/crossref_metadata_2025 huggingface dataset:
The Safety, Acceptability and Efficacy ofAlena, a Modularized CBT-based Mobile App Intervention for Social Anxiety: a Randomised Controlled Trial
Authors: Garvert Mona M. , Linke Stuart , McCloud Tayla , Meyer Sofie S. , Sobanska Sandra , Long Alexander , Huys Quentin J. M. , Ahmadi Mandana
Published: June 2023

Social anxiety disorder is a debilitating mental health condition characterized by intense fear of social situations that can significantly impair daily life if left untreated. Cognitive behavioral therapy (CBT) is an effective treatment, but many patients experience slow progress, possibly due to the heterogeneity of cognitive dysfunction contributing to the maintenance of the disease that is not adequately reflected in a typical one-size-fits-all CBT approach. In addition, many patients only seek treatment late, because human therapists can themselves constitute phobic stimuli. To address these challenges, we developedAlena,a digital CBT program based on the Clark and Wells model of social anxiety (Clark and Wells, 1995) that was reorganized to target the four key cognitive functions associated with the maintenance of social anxiety disorder in separate therapy modules: negative beliefs, self-directed attention, rumination, and avoidance behaviors. Here, we tested the safety, acceptability and efficacy of this therapy program. In a randomized controlled trial, primary outcomes showed the app to be safe and acceptable. Secondary endpoint analyses showed that SPIN scores were significantly reduced in the treatment compared to the control group, and a larger number of participants who completed the four-week digital CBT program showed a reliable reduction in their social anxiety scores compared to a waitlist control group. Our findings suggest that targeted digital CBT without therapist involvement was safe, acceptable and showed promising signs of rapid efficacy in the treatment of social anxiety disorder.
Towards Longitudinal Glioma Segmentation: Evaluating combined pre- and post-treatment MRI training data for automated tumor segmentation using nnU-Net
Authors: Ranjbar Sara , Singleton Kyle W. , Curtin Lee , Paulson Lisa , Clark-Swanson Kamala , Hawkins-Daarud Andrea , Mitchell J. Ross , Jackson Pamela R. , Swanson Kristin R.
Published: June 2023

Identification of key phenotypic regions such as necrosis, contrast enhancement, and edema on magnetic resonance imaging (MRI) is important for understanding disease evolution and treatment response in patients with glioma. Manual delineation is time intensive and not feasible for a clinical workflow. Automating phenotypic region segmentation overcomes many issues with manual segmentation, however, current glioma segmentation datasets focus on pre-treatment, diagnostic scans, where treatment effects and surgical cavities are not present. Thus, existing automatic segmentation models are not applicable to post-treatment imaging that is used for longitudinal evaluation of care. Here, we present a comparison of three-dimensional convolutional neural networks (nnU-Net architecture) trained on large temporally defined pre-treatment, post-treatment, and mixed cohorts. We used a total of 1563 imaging timepoints from 854 patients curated from 13 different institutions as well as diverse public data sets to understand the capabilities and limitations of automatic segmentation on glioma images with different phenotypic and treatment appearance. We assessed the performance of models using Dice coefficients on test cases from each group comparing predictions with manual segmentations generated by trained technicians. We demonstrate that training a combined model can be as effective as models trained on just one temporal group. The results highlight the importance of a diverse training set, that includes images from the course of disease and with effects from treatment, in the creation of a model that can accurately segment glioma MRIs at multiple treatment time points.
Gamma spectral event power is elevated in Fragile X Syndrome and associated with single trial gamma power during auditory chirp
Authors: Liu Yanchen , Liu Rui , Horn Paul S. , Westerkamp Grace , Blank Elizabeth , Erickson Craig , Pedapati Ernest V.
Published: June 2023

Background

Fragile X syndrome (FXS) is a neurodevelopmental disorder resulting from silencing of the FMR1 gene. One of the most common and debilitating symptoms of FXS is sensory hyperarousal, especially in the auditory domain. Although the neural mechanisms of auditory hyperarousal in FXS are not well understood, electroencephalography (EEG) studies demonstrate increases in background gamma power during auditory paradigms, which are associated with more severe behavior and impairments in auditory synchronization.

Methods

High-frequency neural responses to the auditory chirp stimulus were studied in 36 individuals with FXS and 39 controls. Gamma Non-continuous high power events (spectral events) were quantified and compared from source localized EEG recordings. Correlation testing of spectral event properties was performed to averaged EEG features and clinical measures.

Results

Our results show that gamma event peak power was increased in the temporal source of male subjects with FXS (p<0.001, adj. p=0.008) as well as correlated with background average gamma power, while event number, event duration, and frequency span did not differ between groups. Further, absolute event power was positively correlated with clinical measures of obsessive behavior (R=0.63, adj. p=0.011) and stereotypic behavior (R=0.57, adj. p=0.031).

Conclusions

Our results indicate that gamma event peak absolute power likely underlies the increased background single trial gamma power observed during auditory processing in FXS, and that the temporal dynamics of gamma activity do not differ.
Social genomics, cognition, and well-being during the COVID-19 pandemic
Authors: Bateman James R. , Krishnamurthy Sudarshan , Quillen Ellen E. , Waugh Christian E. , Kershaw Kiarri N. , Lockhart Samuel N. , Hughes Timothy M. , Seeman Teresa E. , Cole Steve W. , Craft Suzanne
Published: June 2023

INTRODUCTION

Adverse psychosocial exposure is associated with increased proinflammatory gene expression and reduced type-1 interferon gene expression, a profile known as the conserved transcriptional response to adversity (CTRA). Little is known about CTRA activity in the context of cognitive impairment, although chronic inflammatory activation has been posited as one mechanism contributing to late-life cognitive decline.

METHODS

We studied 171 community-dwelling older adults from the Wake Forest Alzheimer’s Disease Research Center who answered questions via a telephone questionnaire battery about their perceived stress, loneliness, well-being, and impact of COVID-19 on their life, and who provided a self-collected dried blood spot sample. Of those, 148 had adequate samples for mRNA analysis, and 143 were included in the final analysis, which including participants adjudicated as having normal cognition (NC,n= 91) or mild cognitive impairment (MCI,n= 52) were included in the analysis. Mixed effect linear models were used to quantify associations between psychosocial variables and CTRA gene expression.

RESULTS

In both NC and MCI groups, eudaimonic well-being (typically associated with a sense of purpose) was inversely associated with CTRA gene expression whereas hedonic well-being (typically associated with pleasure seeking) was positively associated. In participants with NC, coping through social support was associated with lower CTRA gene expression, whereas coping by distraction and reframing was associated with higher CTRA gene expression. CTRA gene expression was not related to coping strategies for participants with MCI, or to either loneliness or perceived stress in either group.

DISCUSSION

Eudaimonic and hedonic well-being remain important correlates of molecular markers of stress, even in people with MCI. However, prodromal cognitive decline appears to moderate the significance of coping strategies as a correlate of CTRA gene expression. These results suggest that MCI can selectively alter biobehavioral interactions in ways that could potentially affect the rate of future cognitive decline and may serve as targets for future intervention efforts.
Evaluating ChatGPT’s Performance in Responding to Questions About Endoscopic Procedures for Patients
Authors: Ali Hassam , Patel Pratik , Obaitan Itegbemie , Mohan Babu P. , Sohail Amir Humza , Smith-Martinez Lucia , Lambert Karrisa , Gangwani Manesh Kumar , Easler Jeffrey J. , Adler Douglas G.
Published: June 2023

Background and aims

We aimed to assess the accuracy, completeness, and consistency of ChatGPT’s responses to frequently asked questions concerning the management and care of patients receiving endoscopic procedures and to compare its performance to Generative Pre-trained Transformer 4 (GPT-4) in providing emotional support.

Methods

Frequently asked questions (N = 117) about esophagogastroduodenoscopy (EGD), colonoscopy, endoscopic ultrasound (EUS), and endoscopic retrograde cholangiopancreatography (ERCP) were collected from professional societies, institutions, and social media. ChatGPT’s responses were generated and graded by board-certified gastroenterologists and advanced endoscopists. Emotional support questions were assessed by a psychiatrist.

Results

ChatGPT demonstrated high accuracy in answering questions about EGD (94.8% comprehensive or correct but insufficient), colonoscopy (100% comprehensive or correct but insufficient), ERCP (91% comprehensive or correct but insufficient), and EUS (87% comprehensive or correct but insufficient). No answers were deemed entirely incorrect (0%). Reproducibility was significant across all categories. ChatGPT’s emotional support performance was inferior to the newer GPT-4 model.

Conclusion

ChatGPT provides accurate and consistent responses to patient questions about common endoscopic procedures and demonstrates potential as a supplementary information resource for patients and healthcare providers.
Albumin-binding RNAi Conjugate for Carrier Free Treatment of Arthritis
Authors: Colazo Juan M. , Hoogenboezem Ella N. , Keech Megan C. , Francini Nora , Shah Veeraj , Yu Fang , Lo Justin H. , Sorets Alexander G. , McCune Joshua T. , Cho Hongsik , DeJulius Carlisle R. , Michell Danielle L. , Maerz Tristan , Vickers Kacey C. , Gibson-Corley Katherine N. , Hasty Karen A. , Crofford Leslie , Cook Rebecca S. , Duvall Craig L.
Published: June 2023

Osteoarthritis (OA) and rheumatoid arthritis (RA) are joint diseases that are associated with pain and lost quality of life. No disease modifying OA drugs are currently available. RA treatments are better established but are not always effective and can cause immune suppression. Here, an MMP13-selective siRNA conjugate was developed that, when delivered intravenously, docks onto endogenous albumin and promotes preferential accumulation in articular cartilage and synovia of OA and RA joints. MMP13 expression was diminished upon intravenous delivery of MMP13 siRNA conjugates, consequently decreasing multiple histological and molecular markers of disease severity, while also reducing clinical manifestations such as swelling (RA) and joint pressure sensitivity (RA and OA). Importantly, MMP13 silencing provided more comprehensive OA treatment efficacy than standard of care (steroids) or experimental MMP inhibitors. These data demonstrate the utility of albumin ‘hitchhiking’ for drug delivery to arthritic joints, and establish the therapeutic utility of systemically delivered anti-MMP13 siRNA conjugates in OA and RA.

Editorial summary

Lipophilic siRNA conjugates optimized for albumin binding and “hitchhiking” can be leveraged to achieve preferential delivery to and gene silencing activity within arthritic joints. Chemical stabilization of the lipophilic siRNA enables intravenous siRNA delivery without lipid or polymer encapsulation. Using siRNA sequences targeting MMP13, a key driver of arthritis-related inflammation, albumin hitchhiking siRNA diminished MMP13, inflammation, and manifestations of osteoarthritis and rheumatoid arthritis at molecular, histological, and clinical levels, consistently outperforming clinical standards of care and small molecule MMP antagonists.
Signal Improved ultra-Fast Light-sheet Microscope (SIFT) for large tissue imaging
Authors: Prince Md Nasful Huda , Garcia Benjamin , Henn Cory , Yi Yating , Susaki Etsuo A. , Watakabe Yuki , Nemoto Tomomi , Lidke Keith A , Zhao Hu , Remiro Irene Salinas , Liu Sheng , Chakraborty Tonmoy
Published: June 2023

Light-sheet fluorescence microscopy (LSFM) in conjunction with tissue clearing techniques enables morphological investigation of large tissues faster and with excellent optical sectioning. Recently, cleared tissue axially swept light-sheet microscope (ctASLM) demonstrated three-dimensional isotropic resolution in millimeter-scaled tissues. But ASLM based microscopes suffer from low detection signal and slow imaging speed. Here we report a simple and efficient imaging platform that employs precise control of two fixed distant light-sheet foci to carry out ASLM. This allowed us to carry out full field of view (FOV) imaging at 40 frames per second (fps) which is a four-fold improvement compared to the current state-of-the-art. In addition, in a particular frame rate, our method doubles the signal compared to the current ASLM technique. To augment the overall imaging performance, we also developed a deep learning based tissue information classifier that enables faster determination of tissue boundary. We demonstrated the performance of our imaging platform on various cleared tissue samples and demonstrated its robustness over a wide range of clearing protocols.
Graph Laplacian Spectrum, topological properties, and high-order interactions of Structural Brain Networks are Subject-Specific, Repeatable but Highly Dependent on Graph Construction Scheme
Authors: Dimitriadis Stavros I
Published: June 2023

It has been proposed that the estimation of the normalized graph Laplacian over a brain network’s spectral decomposition can reveal the connectome harmonics (eigenvectors) corresponding to certain frequencies (eigenvalues). Here, I used test-retest dMRI data from the Human Connectome Project to explore the repeatability, and the influence of graph construction schemes on a) graph Laplacian spectrum, b) topological properties, c) high-order interactions, and d) their associations on from structural brain network (SBN). Additionally, I investigated the performance of subject’s identification accuracy (brain fingerprinting) of the graph Laplacian spectrum, the topological properties, and the high-order interactions. Normalized Laplacian eigenvalues were found to be subject-specific and repeatable across the five graph construction schemes. The repeatability of connectome harmonics is lower than that of the Laplacian eigenvalues and shows a heavy dependency on the graph construction scheme. A repeatable relationship between specific topological properties of the SBN with the Laplacian spectrum was also revealed. The identification accuracy of normalized Laplacian eigenvalues was absolute (100%) across the graph construction schemes, while a similar performance was observed for a combination of topological properties of SBN (communities,3,4-motifs) only for the 9m-OMST. Collectively, Laplacian spectrum, topological properties, and high-order interactions characterized uniquely SBN.
The phenological response of European vegetation to urbanisation is mediated by macrobioclimatic factors
Authors: Galán Díaz Javier , Gutiérrez-Bustillo Adela Montserrat , Rojo Jesús
Published: June 2023

Plant phenology is a crucial component of ecosystem functioning and is affected by multiple elements of global change; we therefore need to quantify the current phenological changes associated to human activities and understand their impacts on ecosystems. Urbanisation and the intensification of anthropogenic activities alter meteorological conditions and cause phenological changes in urban vegetation worldwide. We used remote sensing data to evaluate the phenological response (start of season date SOS, length of season LOS and end of season date EOS) to urbanisation in the 69 most populated pan-European metropolitan areas (i.e., those that include cities with a population over 450,000 inhabitants) for the period 2002-2021, taking into account the main vegetation types (evergreen forests, deciduous forests, mixed forests, sparse woody vegetation and grasslands). We found that macrobioclimatic factors strongly determined the strength and direction of the phenological response to urbanisation intensity. In general, SOS advanced and LOS increased with urbanisation intensity across Europe. However, the greatest advances in SOS were registered in metropolitan areas in the Mediterranean region, where there was also more uncertainty in the relationship between SOS and urbanisation. The EOS advanced with urbanisation in metropolitan areas in the Mediterranean macrobioclimate (except for deciduous forests), whereas the opposite trend was observed in metropolitan areas from the Temperate macrobioclimate. Our results suggest that macrobioclimatic constraints operating at the continental scale mediate the relationship between plant phenology and urbanisation intensity.
Assessing the dynamics ofMycobacterium bovisinfection in three French badger populations
Authors: Calenge Clément , Payne Ariane , Réveillaud Édouard , Richomme Céline , Girard Sébastien , Desvaux Stéphanie
Published: June 2023

The Sylvatub system is a national surveillance program established in 2011 in France to monitor infections caused byMycobacterium bovis, the main etiologic agent of bovine tuberculosis, in wild species. This participatory program, involving both national and local stakeholders, allowed us to monitor the progression of the infection in three badger populations in clusters covering between 3222 km2and 7698 km2from 2013 to 2019. In each cluster, badgers were trapped and tested forM. bovis. Our first aim was to describe the dynamics of the infection in these clusters. We developed a Bayesian model of prevalence accounting for the spatial structure of the cases, the imperfect and variable sensitivity of the diagnostic tests, and the correlation of the infection status of badgers in the same commune caused by local factors (e.g., social structure and proximity to infected farms). This model revealed that the prevalence increased with time in one cluster (Dordogne/Charentes), decreased in the second cluster (Burgundy), and remained stable in the third cluster (Bearn). In all the clusters, the infection was strongly spatially structured, whereas the mean correlation between the infection status of the animals trapped in the same commune was negligible. Our second aim was to develop indicators for monitoringM. bovisinfection by stakeholders of the program. We used the model to estimate, in each cluster, (i) the mean prevalence level at mid-period, and (ii) the proportion of the badger population that became infected in one year. We then derived two indicators of these two key quantities from a much simpler regression model, and we showed how these two indicators could be easily used to monitor the infection in the three clusters. We showed with simulations that these two simpler indicators were good approximations of these key quantities.
Ribosome clustering and surface layer reorganization in the microsporidian host-invasion apparatus
Authors: Sharma Himanshu , Jespersen Nathan , Ehrenbolger Kai , Carlson Lars-Anders , Barandun Jonas
Published: June 2023

During host cell invasion, microsporidian spores translocate their entire cytoplasmic content through a thin, hollow superstructure known as the polar tube. To achieve this, the polar tube transitions from a compact spring-like state inside the environmental spore to a long needle-like tube capable of long-range sporoplasm delivery. The unique mechanical properties of the building blocks of the polar tube allow for an explosive transition from compact to extended state and support the rapid cargo translocation process. The molecular and structural factors enabling this ultrafast process and the structural changes during cargo delivery are unknown. Here, we employ light microscopy and in situ cryo-electron tomography to visualize multiple ultrastructural states of the polar tube, allowing us to evaluate the kinetics of its germination and characterize the underlying morphological transitions. We describe a cargo-filled state with a unique ordered arrangement of microsporidian ribosomes, which cluster along the thin tube wall, and an empty post-translocation state with a reduced diameter but a thicker wall. Together with a proteomic analysis of endogenously affinity-purified polar tubes, our work provides comprehensive data on the infection apparatus of microsporidia and demonstrates that ribosomes are efficiently transported through polar tubes in a spiral-like parallel arrangement.
Non-genetic differences underlie variability in proliferation among esophageal epithelial clones
Authors: Reyes Hueros Raúl A. , Gier Rodrigo A. , Shaffer Sydney M.
Published: June 2023

The growth potential of individual epithelial cells is a key determinant of tissue development, homeostasis, and disease progression. Although it is known that epithelial progenitor cells vary in their proliferative capacity, the cell states underlying these differences are yet to be uncovered. Here we performed clonal tracing through imaging and cellular barcoding of an in vitro model of esophageal epithelial cells (EPC2-hTERT). We found that individual clones possess unique growth and differentiation capacities, with a subset of clones growing exponentially. Further, we discovered that this proliferative potential for a clone is heritable through cell division and can be influenced by extrinsic cues from neighboring cells. Combining barcoding with single-cell RNA-sequencing (scRNA-seq), we identified the cellular states associated with the highly proliferative clones, which include genes in the WNT and PI3K pathways. Importantly, we also identified a subset of cells resembling the highly proliferative cell state in the healthy human esophageal epithelium and, to a greater extent, in esophageal squamous cell carcinoma (ESCC). These findings highlight the physiological relevance of our cell line model, providing insights into the behavior of esophageal epithelial cells during homeostasis and disease.
conn2res: A toolbox for connectome-based reservoir computing
Authors: Suárez Laura E. , Mihalik Agoston , Milisav Filip , Marshall Kenji , Li Mingze , Vértes Petra E. , Lajoie Guillaume , Misic Bratislav
Published: June 2023

The connection patterns of neural circuits form a complex network. How signaling in these circuits manifests as complex cognition and adaptive behaviour remains the central question in neuroscience. Concomitant advances in connectomics and artificial intelligence open fundamentally new opportunities to understand how connection patterns shape computational capacity in biological brain networks. Reservoir computing is a versatile paradigm that uses nonlinear dynamics of high-dimensional dynamical systems to perform computations and approximate cognitive functions. Here we presentconn2res: an open-source Python toolbox for implementing biological neural networks as artificial neural networks.conn2resis modular, allowing arbitrary architectures and arbitrary dynamics to be imposed. The toolbox allows researchers to input connectomes reconstructed using multiple techniques, from tract tracing to noninvasive diffusion imaging, and to impose multiple dynamical systems, from simple spiking neurons to memristive dynamics. The versatility of theconn2restoolbox allows us to ask new questions at the confluence of neuroscience and artificial intelligence. By reconceptualizing function as computation,conn2ressets the stage for a more mechanistic understanding of structure-function relationships in brain networks.
A NanoDam toolkit for tissue-specific transcription factor profiling inC. elegans
Authors: Yee Callista , Xiao Yutong , Katsanos Dimitris , Medwig-Kinney Taylor N. , Zhang Wan , Shen Kang , Matus David Q. , Barkoulas Michalis
Published: June 2023

During development of multicellular organisms, cells must execute precise molecular decisions to achieve cell fate specification and differentiation. These decisions are orchestrated by networks of transcription factors (TFs) which act to regulate gene expression of specific cohorts of genes to ultimately confer identity. Depending on the cellular context, TF expression can vary dramatically both spatially and temporally. These differences in expression patterns can result in tissue-specific differences in TF binding to downstream targets. To identify targets on a tissue-specific basis, Targeted DamID (TaDa) has been recently introduced to generate TF binding profiles in various models includingC. elegans. However, TaDa suffers from portability such that a new promoter-TF fusion transgene must be constructed for every new experimental condition of interest. Here, we adapt NanoDam for usage inC. elegans, which relies on endogenous TF-GFP knock-ins, a plethora of which have already been generated by the community. We report that NanoDam single copy transgenes consisting of lowly expressed, tissue-specific GFP nanobody-Dam fusions, when combined with endogenous GFP-tagged alleles of TFs, results in robust, tissue-specific profiling. Using an endogenous GFP-tagged allele of EGL-43/EVI1, we performed NanoDam profiling of two disparate tissue types, the anchor cell (AC) and dopaminergic neurons, and identify targets unique to each and shared by both cell types. We also identify two GATA TFs, ELT-6 and EGL-18, as novel regulators of AC invasion. Together, we demonstrate that NanoDam is capable of profiling endogenous GFP-tagged TFs to identify novel downstream targets in specific cell types ofC. elegans.
Behavioral control through the direct, focal silencing of neuronal activity
Authors: Elleman Anna V. , Milicic Nikola , Williams Damian J. , Liu Christine J. , Haynes Allison L. , Simko Jane , Ehrlich David E. , Makinson Christopher D. , Bois J. Du
Published: June 2023

Voltage-gated sodium channel (NaV) activity underlies electrical signaling, synaptic release, circuit function, and, ultimately, behavior. Molecular tools that enable precise control of NaVsubpopulations make possible temporal regulation of neuronal activity and cellular communication. To rapidly modulate NaVcurrents, we have rendered a potent NaVinhibitor, saxitoxin, transiently inert through chemical protection with a novel nitrobenzyl-derived photocleavable group. Light-induced uncaging of the photocaged toxin, STX-bpc, effects rapid inhibitor release and focal NaVblock. We demonstrate the efficacy of this reagent for manipulating action potentials in mammalian neurons and brain slice and for altering locomotor behavior in larval zebrafish. Photo-uncaging of STX-bpc is a non-invasive, effective method for reversible, spatiotemporally precise tuning of NaVcurrents, application of which requires no genetic manipulation of the biological sample.
Atg8-LC3 controls systemic nutrient surplus signaling from flies to humans
Authors: Madan Aditi , Kelly Kevin P. , Sullivan Camille E. , Poling Michelle E. , Brent Ava E. , Alassaf Mroj , Dubrulle Julien , Rajan Akhila
Published: June 2023

Organisms experience constant nutritional flux, and homeostatic mechanisms evolved to operate at the nexus of extreme nutritional states - scarcity and surplus. Thus, we surmised that decoding bidirectional molecular switches that operate at the interface of scarcity response and surplus signaling will enable the development of strategies to treat disorders that arise from nutrient imbalance states. Adipocytes secrete leptin, an interleukin protein, which signals nutrient surplus to the central brain to regulate feeding and energy expenditure. We report that Atg8-LC3-family proteins, best known for their role in autophagy, are required for leptin secretion inDrosophilaand human adipocytes. Atg8-LC3 genetic knockdown and point mutations to the Atg8-LC3 interaction motif (AIM/LIR) of leptin, and its functional ortholog inDrosophila, Upd2, disrupt adipokine secretion and increase adipokine retention in human and fly cells. At an organismal level, Atg8-driven Upd2 retention increases organismal resilience to nutrient extremes by rewiring the transcriptome, organismal feeding behavior, and hunger response. Comparative proteomic analyses reveal that LC3 directs leptin to an exosome secretory pathway. We use genetic knockdown in primary human adipocytes to establish that LC3 is required for leptin secretion in a physiologically relevant mammalian system. Hence, we uncover a previously unknown and evolutionarily conserved role for Atg8-LC3 in promoting adipocyte-brain nutrient surplus signaling. We propose that Atg8-LC3’s bidirectional role in nutrient sensing-conveying nutrient surplus and responding to nutrient deprivation-enables organisms to manage nutrient flux effectively.
Offline Two-dimensional Liquid Chromatography-Mass Spectrometry for Deep Annotation of the Fecal Metabolome
Authors: Anderson Brady G. , Raskind Alexander , Hissong Rylan , Dougherty Michael K. , McGill Sarah K. , Gulati Ajay , Theriot Casey M. , Kennedy Robert T. , Evans Charles R.
Published: June 2023

Compound identification is an essential task in the workflow of untargeted metabolomics since the interpretation of the data in a biological context depends on the correct assignment of chemical identities to the features it contains. Current techniques fall short of identifying all or even most observable features in untargeted metabolomics data, even after rigorous data cleaning approaches to remove degenerate features are applied. Hence, new strategies are required to annotate the metabolome more deeply and accurately. The human fecal metabolome, which is the focus of substantial biomedical interest, is a more complex, more variable, yet lesser-investigated sample matrix compared to widely studied sample types like human plasma. This manuscript describes a novel experimental strategy using multidimensional chromatography to facilitate compound identification in untargeted metabolomics. Pooled fecal metabolite extract samples were fractionated using offline semi-preparative liquid chromatography. The resulting fractions were analyzed by an orthogonal LC-MS/MS method, and the data were searched against commercial, public, and local spectral libraries. Multidimensional chromatography yielded more than a 3-fold improvement in identified compounds compared to the typical single-dimensional LC-MS/MS approach and successfully identified several rare and novel compounds, including atypical conjugated bile acid species. Most features identified by the new approach could be matched to features that were detectable but not identifiable in the original single-dimension LC-MS data. Overall, our approach represents a powerful strategy for deeper annotation of the metabolome that can be implemented with commercially-available instrumentation, and should apply to any dataset requiring deeper annotation of the metabolome.
Functional ultrasound imaging of stroke in awake rats
Authors: Brunner Clément , Montaldo Gabriel , Urban Alan
Published: June 2023

Anesthesia is a major confounding factor in preclinical stroke research as stroke rarely occurs in sedated patients. Moreover, anesthesia affects both brain functions and the stroke outcome acting as neurotoxic or protective agent. So far, no approaches were well suited to induce stroke while imaging hemodynamics along with simultaneous large-scale recording of brain functions in awake animals. For this reason, the first critical hours following the stroke insult and associated functional alteration remain poorly understood. Here, we present a strategy to investigate both stroke hemodynamics and stroke-induced functional alterations without the confounding effect of anesthesia, i.e., under awake condition. Functional ultrasound (fUS) imaging was used to continuously monitor variations in cerebral blood volume (CBV) in +65 brain regions/hemisphere for up to 3hrs after stroke onset. The focal cortical ischemia was induced using a chemo-thrombotic agent suited for permanent middle cerebral artery occlusion in awake rats, and followed by ipsi- and contralesional whiskers stimulation to investigate on the dynamic of the thalamo-cortical functions. Early (0-3hrs) and delayed (day 5) fUS recording enabled to characterize the features of the ischemia (location, CBV loss), spreading depolarizations (occurrence, amplitude) and functional alteration of the somatosensory thalamo-cortical circuits. Post-stroke thalamo-cortical functions were affected not only early after the stroke onset but were also altered secondarly and remotely from the initial insult. Overall, our procedure enables early, continuous, and chronic evaluations of hemodynamics and brain functions which, combined to stroke or other pathologies, aims to better understand physiopathologies toward the development of clinically relevant therapeutic strategies.
Gap junctions arbitrate binocular course control in flies
Authors: Pokusaeva Victoria O. , Satapathy Roshan , Symonova Olga , Jösch Maximilian
Published: June 2023

Animals utilize visual motion cues to maintain stability and navigate accurately. The optomotor response, a reflexive behavior for visual stabilization, has been used to study this visuomotor transformation. However, there is a disparity between the simplicity of this behavior and the intricate circuit components believed to govern it. Here we bridge this divide by exploring the course control repertoire inDrosophilaand establishing a direct link between behavior and the underlying circuit motifs. Specifically, we demonstrate that visual motion information from both eyes plays a crucial role in movement control through bilateral interactions facilitated by gap junctions. These electrical interactions augment the classic stabilization behavior by inverting the response direction and the behavioral strategy. Our findings reveal how animals combine monocular motion cues to generate a variety of behaviors, determine the functional role of the circuit components, and show that gap junctions can mediate non-linear operations with a decisive role in animal behavior.
Proteostatic tuning underpins the evolution of novel multicellular traits
Authors: Montrose Kristopher , Lac Dung T. , Burnetti Anthony J. , Tong Kai , Bozdag G. Ozan , Hukkanen Mikaela , Ratcliff William C. , Saarikangas Juha
Published: June 2023

The evolution of multicellularity paved the way for the origin of complex life on Earth, but little is known about the mechanistic basis of early multicellular evolution. Here, we examine the molecular basis of multicellular adaptation in the Multicellularity Long Term Evolution Experiment (MuLTEE). We demonstrate that cellular elongation, a key adaptation underpinning increased biophysical toughness and organismal size, is convergently driven by downregulation of the chaperone Hsp90. Mechanistically, Hsp90-mediated morphogenesis operates by destabilizing the cyclin-dependent kinase Cdc28, resulting in delayed mitosis and prolonged polarized growth. Reinstatement of Hsp90 or Cdc28 expression resulted in shortened cells that formed smaller groups with reduced multicellular fitness. Together, our results show how ancient protein folding systems can be tuned to drive rapid evolution at a new level of biological individuality by revealing novel developmental phenotypes.

Teaser

Downregulation of Hsp90 decouples cell cycle progression and growth to drive the evolution of macroscopic multicellularity.
SARS-CoV-2 human challenge reveals single-gene blood transcriptional biomarkers that discriminate early and late phases of acute respiratory viral infections
Authors: Rosenheim Joshua , Gupta Rishi K , Thakker Clare , Mann Tiffeney , Bell Lucy CK , Broderick Claire M , Madon Kieran , Papargyris Loukas , Dayananda Pete , Kwok Andrew J , Greenan-Barrett James , Wagstaffe Helen R , Conibear Emily , Fenn Joe , Hakki Seran , Lindeboom Rik GH , Dratva Lisa M , Lemetais Briac , Weight Caroline M , Venturini Cristina , Kaforou Myrsini , Levin Michael , Kalinova Mariya , Mann Alex , Catchpole Andrew , Knight Julian C , Nikolić Marko Z. , Teichmann Sarah A. , Killingley Ben , Barclay Wendy , Chain Benjamin M , Lalvani Ajit , Heyderman Robert S , Chiu Christopher , Noursadeghi Mahdad
Published: June 2023

Evaluation of host-response blood transcriptional signatures of viral infection have so far failed to test whether these biomarkers reflect different biological processes that may be leveraged for distinct translational applications. We addressed this question in the SARS-CoV-2 human challenge model. We found differential time profiles for interferon (IFN) stimulated blood transcriptional responses represented by measurement of single genes. MX1 transcripts correlated with a rapid and transient wave of type 1 IFN stimulated genes (ISG) across all cell types, which may precede PCR detection of replicative infection. Another ISG, IFI27, showed a delayed but sustained response restricted to myeloid peripheral blood mononuclear cells, attributable to gene and cell-specific epigenetic regulation. These findings were reproducible in diverse respiratory virus challenges, and in natural infection with SARS-CoV-2 or unselected respiratory viruses. The MX1 response achieved superior diagnostic accuracy in early infection, correlation with viral load and identification of virus culture positivity, with potential to stratify patients for time sensitive antiviral treatment. IFI27 achieved superior diagnostic accuracy across the time course of symptomatic infection. Compared to blood, measurement of these responses in nasal mucosal samples was less sensitive and did not discriminate between early and late phases of infection.
Flexibly encoded GWAS identifies novel nonadditive SNPs in individuals of African and European ancestry
Authors: Zhou Jiayan , Guare Lindsay , Garao Rico Andre Luis , Zarzar Tomas Gonzalez , Palmiero Nicole , Assimes Themistocles L. , Verma Shefali Setia , Hall Molly Ann
Published: June 2023

Most genome-wide association studies (GWASs) assume an additive inheritance model, where heterozygous genotypes (HET) are coded with half the risk of homozygous alternate genotypes (HA), leading to less explained nonadditive genetic effects for complex diseases. Yet, growing evidence indicates that with flexible modeling, many single-nucleotide polymorphisms (SNPs) show nonadditive effects, including dominant and recessive, which will be missed using only the additive model. We developed Elastic Data-Driven Encoding (EDGE) to determine the HET to HA ratio of risk. Simulation results demonstrated that EDGE outperformed traditional methods across all simulated models for power while maintaining a conserved false positive rate. This research lays the necessary groundwork for integrating nonadditive genetic effects into GWAS workflows to identify novel disease-risk SNPs, which may ultimately improve polygenic risk prediction in diverse populations and springboard future applications to thousands of disease phenotypes and other omic domains to improve disease-prediction capability.
Lower nerve growth factor levels in major depression and suicidal behaviors: effects of adverse childhood experiences and recurrence of illness
Authors: Maes Michael , Rachayon Muanpetch , Jirakran Ketsupar , Sodsai Pimpayao , Sughondhabirom Atapol
Published: June 2023

Background

Major depressive disorder (MDD) and its severe subtype, major dysmood disorder (MDMD), are distinguished by activation of inflammatory and growth factor subnetworks, which are associated with recurrence of illness (ROI) and adverse childhood experiences (ACE). Nerve growth factor (NGF) plays a crucial role in facilitating neuro-immune communications and may regulate the inflammatory response.

Methods

The present study examined the effects of ACE and ROI on culture supernatant NGF, stem cell factor (SCF), stem cell GF (SCGF), hepatocyte GF (HGF), and macrophage colony stimulating factor (M-CSF), in relation to a neurotoxicity (NT) cytokine profile.

Results

NGF levels are lower in MDD (p=0.003), particularly MDMD (p<0.001), as compared with normal controls. ROI and ACE were significantly and inversely associated with NGF (≤0.003) and the NGF/NT ratio (≤0.001), whereas there are no effects of ACE and ROI on SCF, SCGF, HGF, or M-CSF. Lowered NGF (p=0.003) and the NGF/NT ratio (p<0.001) are highly significantly and inversely associated with the severity of the current depression phenome, conceptualized as a latent vector extracted from the current severity of depression, anxiety, and suicidal behaviors. We found that one validated and replicable latent vector could be extracted from NGF, ROI, and the depression phenome, which therefore constitutes a novel ROI-NGF-pathway-phenotype. ACE explained 59.5% of the variance in the latter pathway phenotype (p<0.001).

Conclusions

The imbalance between decreased NGF and increased neurotoxic cytokines during the acute phase of severe depression may contribute to decreased neuroprotection, increased neuro-affective toxicity, and chronic mild inflammation.
T:B cell cooperation in ectopic lymphoid follicles propagates CNS autoimmunity
Authors: Kolz Anna , Bauer Isabel Julia , de la Rosa Clara , Kavaka Vladyslav , Thomann Anna Sophie , Schmitz Rosa , Kerschensteiner Martin , Beltran Eduardo , Kawakami Naoto , Peters Anneli
Published: June 2023

Meningeal ectopic lymphoid follicle-like structures (eLFs) have been described in multiple sclerosis (MS) and its animal model experimental autoimmune encephalomyelitis (EAE), but their role in CNS autoimmunity is unclear. To analyze the cellular phenotypes and interactions within these structures, we employed a Th17 adoptive transfer EAE model featuring formation of large, numerous eLFs. Single-cell transcriptomic analysis revealed that clusters of activated B cells and B1/Marginal Zone-like B cells are overrepresented in the CNS and identified B cells poised for undergoing antigen-driven germinal center (GC) reactions and clonal expansion in the CNS. Furthermore, CNS B cells showed enhanced capacity for antigen presentation and immunological synapse formation compared to peripheral B cells. To directly visualize Th17:B cell cooperation in eLFs, we labeled Th17 cells with a ratiometric calcium sensor, and tracked their interactions with tdTomato-labeled B cells in real-time. Thereby, we demonstrated for the first time that T and B cells form long-lasting antigen-specific contacts in meningeal eLFs that result in reactivation of autoreactive T cells. Consistent with these findings, autoreactive T cells depended on CNS B cells to maintain a pro-inflammatory cytokine profile in the CNS. Collectively, our study reveals that extensive T:B cell cooperation occurs in meningeal eLFs in our model promoting differentiation and clonal expansion of B cells, as well as reactivation of CNS T cells and thereby supporting smoldering inflammatory processes within the CNS compartment. Our results provide valuable insights into the function of eLFs and may provide a direction for future research in MS.
Decoding Arbitrary and Informed Decisions from Intracranial Recordings in Humans
Authors: Marras Laura , Verwoert Maxime , Ottenhoff Maarten C. , Goulis Sophocles , van Dijk Johannes P. , Tousseyn Simon , Wagner Louis , Colon Albert J. , Kubben Pieter L. , Janssen Marcus L.F. , Herff Steffen A. , Herff Christian
Published: June 2023

Ideally, decisions are made based on prior knowledge, which allows for informed choices. Real life, however, often requires us to make decisions arbitrarily, without sufficient information. Decoding decision making processes from neural activity could allow for cognitive neuroprostheses and Brain-Computer Interfaces (BCIs) to support decision processes in rapid human-machine interactions, weigh decision-making confidence, and further enable neuromodulation protocols for the treatment of reward-related dysfunctions. To understand the differences between the decision-making processes in arbitrary and informed decisions, we recorded intracranial electroencephalography in a large number of cortical and subcortical areas from 5 patients during a categorization task. We demonstrate that individual decisions can be decoded from Local Field Potentials (LFPs) before motor response, in both arbitrary and informed conditions. Our analysis revealed dissimilar spatio-temporal patterns between arbitrary and informed decision-making, with arbitrary decisions being decodable in fewer brain regions and earlier in time compared to informed decisions.
241,000 to 335,000 Years Old Rock Engravings Made byHomo nalediin the Rising Star Cave system, South Africa
Authors: Berger Lee R. , Hawks John , Fuentes Agustin , van Rooyen Dirk , Tsikoane Mathabela , Ramalepa Maropeng , Nkwe Samuel , Molopyane Keneiloe
Published: June 2023

The production of painted, etched or engraved designs on cave walls or other surfaces is recognized as a major cognitive step in human evolution. Such intentional designs, which are widely interpreted as signifying, recording, and transmitting information in a durable manner were once considered exclusive to Late PleistoceneHomo sapiens. Recent work has demonstrated that other hominin groups also made such marks, including Neanderthals (Rodríguez-Vidal et al., 2014; Hoffmann et al., 2018), and possibly Middle-PleistoceneHomo erectus(Joordens et al., 2015). Such durable signs indicate an intentionality characteristic of meaning-making (Kissel and Fuentes 2018) which has been argued to require significant levels of cognitive abilities not found in species with smaller brain sizes (Parkington, 2010). In fact, the evolution of such meaning-making symbols is thought to be a core aspect of what it means to be “human” (Henshilwood, 2009). Here we present the first known example of abstract patterns and shapes engraved within the Dinaledi subsystem of the Rising Star Cave in South Africa. We identified markings incised into the dolomitic limestone walls of the cave. The engravings described here are deeply impressed cross-hatchings and other geometric shapes. The surfaces bearing these engravings appear to have been prepared and smoothed. In some areas there is residue that creates a sheen on the surface possibly indicating repeated handling or rubbing of the rock, and there is evidence of the application of dirt or sand to the surface by non-natural processes.Homo naledientered this part of the cave system and buried bodies within the both the Dinaledi Chamber and adjacent Hill Antechamber between 241 and 335 ka (Dirks et al., 2017; Robbins et al., 2021, Berger et al, 2023a). The engravings described here are found on a pillar in the Hill Antechamber that extends into the natural fissure corridor that links the two chambers and we associate them withH. naledi.