bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-dimensionality of tree communities structure host-parasitoid networks and their phylogenetic composition
Authors: Wang Ming-Qiang , Guo Shi-Kun , Guo Peng-Fei , Yang Juan-Juan , Chen Guo-Ai , Chesters Douglas , Orr Michael , Niu Ze-Qing , Staab Michael , Chen Jing-Ting , Li Yi , Zhou Qing-Song , Fornoff Felix , Shi Xiaoyu , Li Shan , Martini Massimo , Klein Alexandra-Maria , Schuldt Andreas , Liu Xiaojuan , Ma Keping , Bruelheide Helge , Luo Arong , Zhu Chao-Dong 
Published: June 2024

AbstractEnvironmental factors can influence ecological networks, but these effects are poorly understood in the realm of the phylogeny of host-parasitoid interactions. Especially, we lack a comprehensive understanding of the ways that biotic factors, including plant species richness, overall community phylogenetic and functional composition of consumers, and abiotic factors such as microclimate, determining host–parasitoid network structure and host–parasitoid community dynamics. To address this, we leveraged a five-year dataset of trap-nesting bees and wasps and their parasitoids collected in a highly-controlled, large-scale subtropical tree biodiversity experiment. We tested for effects of tree species richness, tree phylogenetic and functional diversity, and species and phylogenetic composition on species and phylogenetic diversity of both host and parasitoid communities and the composition of their interaction networks. We show that multiple components of tree diversity and canopy cover impacted both, species and phylogenetic composition of hosts and parasitoids. Generally, phylogenetic associations between hosts and parasitoids reflected non-randomly structured interactions between phylogenetic trees of hosts and parasitoids. Further, host-parasitoid network structure was influenced by tree species richness, tree phylogenetic diversity, and canopy cover. Our study indicates that the composition of higher trophic levels and corresponding interaction networks are determined by plant diversity and canopy cover especially via trophic links in species-rich ecosystems.
Cerebrospinal Fluid Dynamics: Uncovering Alternative Blood Vessel Clearance Mechanisms
Authors: Yuan Qiuju , Satyanarayanan Senthil Kumaran , Lee Suki Man-Yan , Yan Lingli , Wang Yaofeng , Xian Yan-Fang , He Liumin , Zhou Yingying , Wu Wutian , Song You-Qiang , Su Huanxing , Lin Zhi-Xiu , Qin Dajiang 
Published: June 2024

AbstractThe pathways that run along the olfactory nerves crossing the cribriform plate and connecting to lymphatic vessels in the nasal cavity, have been identified as a crucial route for cerebrospinal fluid (CSF) outflow. However, the presence of a CSF efflux pathway through blood vessels in this region has yet to be clarified. This study aimed to elucidate the anatomical connections between the subarachnoid space and the bloodstream at the nasal epithelium and the venous drainage routes of the nasal epithelium in mice. Our findings demonstrated that CSF tracers could be drained not only through lymphatic vessels in the nasal cavity and cervical lymph nodes (CLNs), but also through the blood vessels in this area that extend to its venous drainage routes, including the facial and jugular veins. Additionally, we showed that ligation of CLNs neither impeded the influx and efflux of CSF tracers nor exacerbated Alzheimer’s disease (AD)-related pathology in AD mice. Our work reveals a previously unrecognized pathway for CSF drainage through blood vessels within the nasal mucosa. These findings provide insight into the efficient removal of waste products, facilitating optimal functioning of neural tissue within the susceptible tissue of our brains.
Neuromodulation with Ultrasound: Hypotheses on the Directionality of Effects and Community Resource
Authors: Caffaratti Hugo , Slater Ben , Shaheen Nour , Rhone Ariane , Calmus Ryan , Kritikos Michael , Kumar Sukhbinder , Dlouhy Brian , Oya Hiroyuki , Griffiths Tim , Boes Aaron D. , Trapp Nicholas , Kaiser Marcus , Sallet Jérôme , Banks Matthew I. , Howard Matthew A. , Zanaty Mario , Petkov Christopher I. 
Published: June 2024

ABSTRACTLow-intensity Transcranial Ultrasound Stimulation is a promising non-invasive technique for brain stimulation and focal neuromodulation. Research with humans and animal models has raised the possibility that TUS can be biased towards enhancing or suppressing neural function. Here, we first collate a set of hypotheses on the directionality of TUS effects and conduct an initial meta-analysis on the availablehealthy human participantTUS studies reporting stimulation parameters and outcomes (n =47 studies, 52 experiments). In these initial exploratory analyses, we find that parameters such as the intensity and continuity of stimulation (duty cycle) with univariate tests show only statistical trends towards likely enhancement or suppressed of function with TUS. Multivariate machine learning analyses are currently limited by the small sample size. Given that human TUS sample sizes will continue to increase, predictability on the directionality of TUS effects could improve if this database can continue to grow as TUS studies more systematically explore the TUS stimulation parameter space and report outcomes. Therefore, we establish aninTUSdatabase and resource for the systematic reporting of TUS parameters and outcomes to assist in greater precision in TUS use for brain stimulation and neuromodulation. The paper concludes with a selective review ofhuman clinical TUSstudies illustrating how hypotheses on the directionality of TUS effects could be developed for empirical testing in the intended clinical application, not limited to the examples provided.HighlightsCollated set of hypotheses on using TUS to bias towards enhancement or suppressionMeta-analysis results identify parameters that may bias directionality of TUS effectsinTUSresource established for systematic reporting of TUS parameters and outcomesSelective review of patient TUS studies for enhancing or suppressing neural function
Functional dysconnectivity of visual and somatomotor networks yields a simple and robust biomarker for psychosis
Authors: Keane Brian P. , Abrham Yonatan , Cole Michael W. , Johnson Brent A. , Hu Boyang , Cocuzza Carrisa V. 
Published: June 2024

AbstractPeople with psychosis exhibit thalamo-cortical hyperconnectivity and cortico-cortical hypoconnectivity with sensory networks, however, it remains unclear if this applies to all sensory networks, whether it arises from other illness factors, or whether such differences could form the basis of a viable biomarker. To address the foregoing, we harnessed data from the Human Connectome Early Psychosis Project and computed resting-state functional connectivity (RSFC) matrices for 54 healthy controls and 105 psychosis patients. Primary visual, secondary visual (“visual2”), auditory, and somatomotor networks were defined via a recent brain network partition. RSFC was determined for 718 regions via regularized partial correlation. Psychosis patients— both affective and non-affective—exhibited cortico-cortical hypoconnectivity and thalamo-cortical hyperconnectivity in somatomotor and visual2 networks but not in auditory or primary visual networks. When we averaged and normalized the visual2 and somatomotor network connections, and subtracted the thalamo-cortical and cortico-cortical connectivity values, a robust psychosis biomarker emerged (p=2e-10, Hedges’ g=1.05). This “somato-visual” biomarker was present in antipsychotic-naive patients and did not depend on confounds such as psychiatric comorbidities, substance/nicotine use, stress, anxiety, or demographics. It had moderate test-retest reliability (ICC=.61) and could be recovered in five-minute scans. The marker could discriminate groups in leave-one-site-out cross-validation (AUC=.79) and improve group classification upon being added to a well-known neurocognition task. Finally, it could differentiate later-stage psychosis patients from healthy or ADHD controls in two independent data sets. These results introduce a simple and robust RSFC biomarker that can distinguish psychosis patients from controls by the early illness stages.
Developing Consensus for an Upper and Lower Limb Athlete Pain Assessment Framework – A Real-time Delphi Study with International Sports Physiotherapists
Authors: Purcell Ciarán , Fullen Brona M , Ward Tomás , Caulfield Brian M 
Published: June 2024

AbstractObjectivesThere is no current consensus on the key items sports physiotherapists should consider when completing a comprehensive biopsychosocial upper or lower limb pain assessment with athletes. We sought to develop recommendations to inform a framework for the assessment of upper and lower limb pain in athletes.DesignReal-time DelphiMethodsWe recruited sports physiotherapists currently working with athletes through the International Society of Sports Physical Therapists and Irish Society of Chartered Physiotherapists. Participants voted on 86 pain assessment items chosen using best available evidence. The real-time Delphi method facilitated independent anonymous voting, commenting and immediate review of consensus. Participants indicated level of agreement for inclusion in an upper and lower limb athlete pain assessment framework on a 6-point Likert scale from Strongly Disagree to Strongly Agree, and how often they are/will be required in practice on a 5-point scale fromNevertoAlways.Criteria for consensus agreement and inclusion were i) >70% sports physiotherapists voting agree/strongly agree AND ii) median vote selected by physiotherapists was Agree or Strongly Agree.Results41 sports physiotherapists (female n=20, male n=21), visited the survey an average of 5.3 times (±5), resulting in a completion rate of 98%. 64 assessment items (neurophysiological n=20, biomechanical n=15, affective n=8, cognitive n=3, socioenvironmental n=10, general assessment aspects of assessment n=8) met the criteria for consensus. Frequency of use in practice wasAlwaysfor 28 itemsOftenfor 32 items andSometimesfor 4 items.ConclusionWe have presented stakeholder-generated recommendations and priorities for athlete pain assessment.
A Longitudinal Exploration ofCACNA1A-related Hemiplegic Migraine in Children
Authors: Schaare Donna , Lusk Laina , Karlin Alexis , Kaufman Michael C. , Magielski Jan , Sarasua Sara M. , Allison Kendra , Boccuto Luigi , Helbig Ingo 
Published: June 2024

AbstractIntroductionSince the initial description ofCACNA1A-related hemiplegic migraine (HM), the phenotypic spectrum has expanded from mild episodes in neurotypical individuals to potentially life-threatening events frequently seen in individuals with developmental and epileptic encephalopathies. However, the overall longitudinal course throughout childhood remains unknown.MethodsWe analyzed HM and seizure history in individuals withCACNA1A-related HM, delineating frequency and severity of events in monthly increments through a standardized approach. Combining these data with medication prescription information, we assessed the response of HM to different agents.ResultsOur cohort involved 15 individuals between 3 and 29 years (163 patient years) and included 11 unique and two recurrent variants (p.R1349Q and p.V1393M; bothn=2). The age of first confirmed HM ranged from 14 months to 13 years (average 3 years). 25% of all HM events were severe (lasting >3 days) and 73% of individuals had at least 1 severe occurrence. Spacing of HM events ranged from 1 month to 14 years and changes in HM severity over time of showed increases or decreases of >2 severity levels in 12/122 events. Eight individuals had epilepsy, but severity of epilepsy did not correlate with frequency and severity of HM events. While levetiracetam (n=6) and acetazolamide (n=5) were the most frequently used medications, they did not show efficacy in HM prevention or HM severity reduction. However, verapamil (n=3) showed efficacy in preventing HM episodes (OR 2.68, CI 1.39-5.67).SignificanceThe longitudinal course ofCACNA1A-related HM lacks recognizable patterns for timing and severity of HM events or correlation with seizure patterns. Our data underscores the unpredictability ofCACNA1A-related HM, highlighting the need for close surveillance for reoccurring HM events even in individuals with symptom-free periods.Key points24% of hemiplegic migraines (HM) inCACNA1A-related disorders are severe, involving cerebral edema and greater than 4 days to recoverTiming and severity of HM are unpredictable, with large changes in severity between events, and age of onset ranging from 1-13 yearsEpilepsy occurred in 53% of individuals, with neither the timing nor severity of seizures correlated with HM
The impact of heterogeneous spatial autocorrelation on comparisons of brain maps
Authors: Leech R , Smallwood JS , Moran R , Jones EJH , Vowles N , Leech D , Viegas EM , Turkheimer FE , Alberti F , Margulies D , Jefferies E , Bernhardt B , Váša F 
Published: June 2024

AbstractIt is increasingly common to statistically compare macroscopic brain maps to assess how spatially similar they are. Due to the presence of spatial autocorrelation, statistical inference can be challenging; to address this, random permutation approaches based on null models are widely used. Here, we show how that the presence of heterogeneity in the spatial autocorrelation across brain maps may affect statistical inference in common approaches for spatially correlated maps. In response, we highlight the need to explicitly model spatial processes, including non-stationarity, for more accurate statistical inference. We illustrate how a Bayesian spatial regression approach can be applied to compare functional and structural cortical brain maps, even in the presence of heterogeneity. By explicitly modelling spatial processes underlying the data, a much wider and more sophisticated range of neurobiological questions can be answered about the relationship between brain maps than with current approaches.
Deep learning uncovers histological patterns of YAP1/TEAD activity related to disease aggressiveness in cancer patients
Authors: Schmauch Benoit , Cabeli Vincent , Domingues Omar Darwiche , Douget Jean-Eudes Le , Hardy Alexandra , Belbahri Reda , Maussion Charles , Romagnoni Alberto , Eckstein Markus , Fuchs Florian , Swalduz Aurélie , Lantuejoul Sylvie , Crochet Hugo , Ghiringhelli François , Derangere Valentin , Truntzer Caroline , Pass Harvey , Moreira Andre L. , Chiriboga Luis , Zheng Yuanning , Ozawa Michael , Howitt Brooke E. , Gevaert Olivier , Girard Nicolas , Rexhepaj Elton , Valtingojer Iris , Debussche Laurent , de Rinaldis Emanuele , Nestle Frank , Spanakis Emmanuel , Fantin Valeria R. , Durand Eric Y. , Classe Marion , Loga Katharina Von , Pronier Elodie , Cesaroni Matteo 
Published: June 2024

SummaryOver the last decade, Hippo signaling has emerged as a major tumor-suppressing pathway. Its dysregulation is associated with abnormal expression ofYAP1andTEAD-family genes. Recent works have highlighted the role of YAP1/TEAD activity in several cancers and its potential therapeutic implications. Therefore, identifying patients with a dysregulated Hippo pathway is key to enhancing treatment impact. Although recent studies have derived RNAseq-based signatures, there remains a need for a reproducible and cost-effective method to measure the pathway activation. In recent years, deep learning applied to histology slides have emerged as an effective way to predict molecular information from a data modality available in clinical routine. Here, we trained models to predict YAP1/TEAD activity from H&E-stained histology slides in multiple cancers. The robustness of our approach was assessed in seven independent validation cohorts. Finally, we showed that histological markers of disease aggressiveness were associated with dysfunctional Hippo signaling.
uORF-targeting steric block antisense oligonucleotides do not reproducibly activate RNASEH1 expression
Authors: Ahlskog Nina , Svrzikapa Nenad , Abuhamdah Rushdie , Kye Mahnseok , Jad Yahya , Feng Ning , Hanson Britt , Wood Matthew J.A. , Roberts Thomas C. 
Published: June 2024

AbstractUpstream open reading frames (uORFs) arecis-regulatory motifs that are predicted to occur in the 5ʹ untranslated region (UTR) of the majority of human protein-coding transcripts. uORFs are typically associated with repression of the downstream primary open reading frame (pORF) at either the level of translation, or by promoting mRNA turnover via the nonsense-mediated decay pathway. Interference with uORF activity provides a potential mechanism for targeted upregulation of the expression of specific transcripts. It was recently reported that steric block antisense oligonucleotides (ASOs) can bind to and mask uORF start codons in order to inhibit translation initiation, and thereby disrupt uORF-mediated gene regulation. Given the relative maturity of the oligonucleotide field, such a uORF blocking mechanism might have widespread therapeutic utility. Here, we re-synthesised three of the most potent ASOs targeting theRNASEH1uORF described in the study by Lianget al. and investigated their potential for RNASEH1 protein upregulation. No upregulation (of endogenous or reporter protein expression) was observed with any of the oligonucleotides tested at doses ranging from 25 nM to 300 nM. Conversely, we observed downregulation of expression in some instances, consistent with well-established mechanisms of blocking ribosome procession. Experiments were performed using multiple transfection protocol setups, with care taken to replicate the conditions of the original study. Transfection efficiency was confirmed using aMALAT1-targeting gapmer ASO as a positive control. We conclude that previously-describedRNASEH1uORF-targeting steric block ASOs are incapable of upregulating pORF protein expression in our hands.
Three-dimensional body reconstruction enables quantification of liquid consumption in small invertebrates
Authors: Galante Henrique , Czaczkes Tomer J. , De Agrò Massimo 
Published: June 2024

AbstractQuantifying feeding patterns provides valuable insights into animal behaviour. However, small invertebrates often consume incredibly small amounts of food. This renders traditional methods, such as weighing individuals before and after food acquisition, either inaccurate or prohibitively expensive. Here, we present a non-invasive method to quantify food consumption of small invertebrates whose body expands during feeding. Using the markerless pose estimation software DeepLabCut, we three-dimensionally track the body of Argentine ants,Linepithema humile. Using these extracted markers, we developed an algorithm which computationally reconstructs the ant’s body, directly measuring volumetric change over time. Moreover, we provide measures of accuracy and quantify the ant’s feeding response to a range of sucrose concentrations, as well as a gradient of caffeine-laced sucrose solutions. Small invertebrates are often prolific invasive species and disease vectors, causing significant ecological and economical damage. Understanding their feeding behaviour could be an important step towards effective control strategies.
Profiling endogenous airway proteases and antiproteases and measuring proteolytic activation of Influenza HA usingin vitroandex vivohuman airway surface liquid samples
Authors: Brocke Stephanie A , Reidel Boris , Ehre Camille , Rebuli Meghan E , Robinette Carole , Schichlein Kevin D , Brooks Christian A , Jaspers Ilona 
Published: June 2024

AbstractImbalance of airway proteases and antiproteases has been implicated in diseases such as COPD and environmental exposures including cigarette smoke and ozone. To initiate infection, endogenous proteases are commandeered by respiratory viruses upon encountering the airway epithelium. The airway proteolytic environment likely contains redundant antiproteases and proteases with diverse catalytic mechanisms, however a proteomic profile of these enzymes and inhibitors in airway samples has not been reported. The objective of this study was to first profile extracellular proteases and antiproteases using human airway epithelial cell cultures andex vivonasal epithelial lining fluid (NELF) samples. Secondly, we present an optimized method for probing the proteolytic environment of airway surface liquid samples (in vitroandex vivo) using fluorogenic peptides modeling the cleavage sites of respiratory viruses. We detected 48 proteases in the apical wash of cultured human nasal epithelial cells (HNECs) (n=6) and 57 in NELF (n=13) samples from healthy human subjects using mass-spectrometry based proteomics. Additionally, we detected 29 and 48 antiproteases in the HNEC apical washes and NELF, respectively. We observed large interindividual variability in rate of cleavage of an Influenza H1 peptide in theex vivoclinical samples. Since protease and antiprotease levels have been found to be altered in the airways of smokers, we compared proteolytic cleavage inex vivonasal lavage samples from male/female smokers and non-smokers. There was a statistically significant increase in proteolysis of Influenza H1 in NLF from male smokers compared to female smokers. Furthermore, we measured cleavage of the S1/S2 site of SARS-CoV, SARS-CoV-2, and SARS-CoV-2 Delta peptides in various airway samples, suggesting the method could be used for other viruses of public health relevance. This assay presents a direct and efficient method of evaluating the proteolytic environment of human airway samples in assessment of therapeutic treatment, exposure, or underlying disease.
Membrane binding properties of the cytoskeletal protein bactofilin
Authors: Liu Ying , Karmakar Rajani , Steinchen Wieland , Mukherjee Saumyak , Bange Gert , Schäfer Lars V. , Thanbichler Martin 
Published: June 2024

AbstractBactofilins are a widespread family of cytoskeletal proteins with important roles in bacterial morphogenesis, chromosome organization and motility. They polymerize in a nucleotide-independent manner, forming non-polar filaments that are typically associated with the cytoplasmic membrane. Membrane binding was suggested to be mediated by a short N-terminal peptide, but the underlying mechanism and the conservation of this interaction determinant among bacteria remain unclear. Here, we use the bactofilin homolog BacA of the stalked bacteriumCaulobacter crescentusas a model to analyze the membranebinding behavior of bactofilins. Based on site-directed mutagenesis of the N-terminal region, we identify the full membrane-targeting sequence of BacA (MFSKQAKS) and identify amino acid residues that are critical for its functionin vivoandin vitro. Molecular dynamics simulations then provide detailed insight into the molecular mechanism underlying the membrane affinity of this peptide. Collectively these analyses reveal a delicate interplay between the water exclusion of hydrophobic N-terminal residues, the arrangement of the peptide within the membrane and the electrostatic attraction between positively charged groups in the peptide and negative charges in the phospholipid molecules. A comprehensive bioinformatic analysis shows that the composition and properties of the membrane-targeting sequence of BacA are conserved in numerous bactofilin homologs from diverse bacterial phyla. Notably, our findings reveal a mutual interdependence between the membrane binding and polymerization activities of BacA. Moreover, we demonstrate that both of these activities have a pivotal role in the recruitment of the BacA client protein PbpC, a membrane-bound cell wall synthase involved in stalk formation whose N-terminal region turns out to associate with the core polymerization domain of BacA. Together, these results unravel the mechanistic underpinnings of membrane binding by bactofilin homologs, thereby illuminating a previously obscure but important aspect in the biology of this cytoskeletal protein family.