bluuebunny/crossref_metadata_2025_split huggingface dataset:
Associations Between Resting State Functional Brain Connectivity and Childhood Anhedonia: A Reproduction and Replication Study
Authors: Zhou Yi , Pat Narun , Neale Michael C. 
Published: October 2022

AbstractBackgroundPreviously, a study using a sample of the Adolescent Brain Cognitive Development (ABCD)® study from the earlier 1.0 release found differences in several resting state functional MRI (rsfMRI) brain connectivity measures associated with children reporting anhedonia. Here, we aim to reproduce, replicate, and extend the previous findings using data from the later ABCD study 4.0 release, which includes a significantly larger sample.MethodsTo reproduce and replicate the previous authors’ findings, we analyzed data from the ABCD 1.0 release (n = 2437), in an independent subsample from the newer ABCD 4.0 release (n = 6456), and in the full ABCD 4.0 release sample (n = 8866). Additionally, we assessed whether using a multiple linear regression approach could improve replicability by controlling for the effects of comorbid psychiatric conditions and socio-demographic covariates.ResultsWe could only replicate the significant association between anhedonia and theWithin Cingulo-Opercular network connectivitymeasure in an independent subsample of the ABCD 4.0 data release. When using the larger full ABCD 4.0 sample, six out of the eleven previously reported associations remained significant. Accounting for socio-demographic covariates and comorbid conditions using multiple linear regression did not improve replicability but allowed for the identification of specific and independent effects of anhedonia on 16 rsfMRI connectivity measures in the full ABCD 4.0 release sample.ConclusionReplication of previous findings were limited. A multiple linear regression approach helped resolve the specificity of rsfMRI connectivity associations with anhedonia.
Extending the audiogram with loudness growth: revealing complementarity in bimodal aiding
Authors: Lambriks Lars , van Hoof Marc , George Erwin , Devocht Elke 
Published: October 2022

AbstractIntroductionClinically, the audiogram is the most commonly used measure when evaluating hearing loss and fitting hearing aids. As an extension, we present the loudness audiogram, which does not only show auditory thresholds but also visualises the full course of loudness perception.MethodsIn a group of 15 bimodal users, loudness growth was measured with the cochlear implant and hearing aid separately using a loudness scaling procedure. Loudness growth curves were constructed, using a novel loudness function, for each modality and then integrated in a graph plotting frequency, stimulus intensity level, and loudness perception. Bimodal benefit, defined as the difference between wearing a cochlear implant and hearing aid together versus wearing only a cochlear implant, was assessed for multiple speech outcomes.ResultsLoudness growth was related to bimodal benefit for speech understanding in noise and to some aspects of speech quality. No correlations between loudness and speech in quiet were found. Patients who had predominantly unequal loudness input from the hearing aid, gained more bimodal benefit for speech understanding in noise compared to those patients whose hearing aid provided mainly equivalent input.DiscussionFitting the cochlear implant and a contralateral hearing aid to create equal loudness at all frequencies may not always be beneficial for speech understanding.
Determination of insulin secretion from stem cell-derived islet organoids with liquid chromatography-tandem mass spectrometry
Authors: Olsen Christine , Wang Chencheng , Abadpour Shadab , Lundanes Elsa , Hansen Audun Skau , Skottvoll Frøydis Sved , Scholz Hanne , Wilson Steven Ray 
Published: October 2022

AbstractOrganoids are laboratory-grown 3D organ models, mimicking human organs for e.g. drug development and personalized therapy. Islet organoids (typically 100-200 μm), which can be grown from the patient’s own cells, are emerging as prototypes for transplantation-based therapy of diabetes. Selective methods for quantifying insulin production from islet organoids are needed, but sensitivity and carry-over have been major bottlenecks in previous efforts. We have developed a reverse phase liquid chromatography-tandem mass spectrometry (RPLC-MS/MS) method for studying the insulin secretion of islet organoids. In contrast to our previous attempts using nano-scale LC columns, conventional 2.1 mm inner diameter LC column (combined with triple quadrupole mass spectrometry) was well suited for sensitive and selective measurements of insulin secreted from islet organoids with low microliter-scale samples. Insulin is highly prone to carry-over, so standard tubings and injector parts were replaced with shielded fused silica nanoViper™ connectors. As samples were expected to be very limited, an extended Box-Behnken experimental design for the MS settings was conducted to maximize performance. The finale method has excellent sensitivity, accuracy and precision (limit of detection: ≤ 0.2 pg/μL, relative error: ≤ ±10%, relative standard deviation: < 10%), and was well suited for measuring 20 μL amounts of Krebs buffer containing insulin secreted from islet organoids.
Localized APP pathology in the hippocampus is sufficient to result in progressive disorganization of the timing of neuronal firing patterns
Authors: Viana da Silva Silvia , Haberl Matthias G. , Gaur Kshitij , Patel Rina , Narayan Gautam , Ledakis Max , Fu Maylin L. , Koo Edward H. , Leutgeb Jill K. , Leutgeb Stefan 
Published: October 2022

AbstractDeficits in spatial navigation are among the early symptoms in Alzheimer’s disease patients, consistent with the hippocampal formation as the site for spatial computations and disease onset. Although the correspondence between the early symptoms and brain regions that are affected early in the disease has been recognized, it is not clear whether progressive cognitive decline is solely caused by a spreading pathology or whether a focal pathology can by itself cause aberrant neuronal activity in a larger network. These possibilities cannot be distinguished in standard disease models which broadly express APP across brain regions. We therefore generated a mouse model in which the expression of mutant human APP was limited to hippocampal CA3 cells (CA3-APP mice). We first asked whether the limited pathology in CA3 can result in memory deficits and found impaired performance of CA3-APP mice in a hippocampus-dependent memory task. By then recording in the CA1 region, we asked to what extent neuronal activity patterns emerged in a brain region which received projections from APP-expressing CA3 cells, but did itself not show any primary pathology. While the spatial firing patterns of CA1 cells were preserved, we observed a reduced theta oscillation frequency in the local field potential and in a subpopulation of principal cells in CA1. Furthermore, CA1 interneurons showed decreased theta oscillation frequencies, and this effect was even more pronounced in CA3 interneurons, which also do not directly express APP. Pathology that is highly localized and limited to presynaptic cells is thus sufficient to cause aberrant firing patterns in postsynaptic neuronal networks, which indicates that disease progression is not only from a spreading molecular pathology but also mediated by progressive physiological dysfunction.
Fast-exchanging spirocyclic rhodamine probes for aptamer-based super-resolution RNA imaging
Authors: Englert Daniel , Burger Eva-Maria , Lackner Jens , Lampe Marko , Bühler Bastian , Grün Franziska , Schokolowski Janin , Nienhaus G. Ulrich , Jäschke Andres , Sunbul Murat 
Published: October 2022

AbstractLive-cell RNA imaging with high spatial and temporal resolution remains a major challenge. Here we report the development of RhoBAST:SpyRho, a fluorescent light-up aptamer (FLAP) system ideally suited for visualizing RNAs in live or fixed cells with various advanced fluorescence microscopy modalities. Overcoming problems associated with low cell permeability, brightness, fluorogenicity, and signal-to-background ratio of previous fluorophores, we designed a novel probe, SpyRho (Spirocyclic Rhodamine), which tightly binds to the RhoBAST aptamer. High brightness and fluorogenicity is achieved by shifting the equilibrium between spirolactam and quinoid. With its high affinity and fast ligand exchange, RhoBAST:SpyRho is a superb system for both super-resolution SMLM and STED imaging. Its excellent performance in SMLM and the first reported super-resolved STED images of specifically labeled RNA in live mammalian cells represent significant advances over other FLAPs. The versatility of RhoBAST:SpyRho is further demonstrated by imaging endogenous chromosomal loci and proteins.
Identification of the area sampled by traps: a modelling study with tsetse
Authors: Vale Glyn A , Hargrove John W , Torr Steve J 
Published: October 2022

AbstractBackgroundSampling with traps provides the most common means of investigating the abundance, composition and condition of tsetse populations. It is thus important to know the size of the area from which the samples originate, but that topic is poorly understood.Methods and principal findingsThe topic was clarified with the aid of a simple deterministic model of the mobility, births and deaths of tsetse. The model assessed how the sampled area changed according to variations in the numbers, arrangement and catching efficiency of traps deployed for different periods in a large block of homogeneous habitat subject to different levels of fly mortality. The greatest impacts on the size of the sampled area are produced by the flies’ mean daily step length and the duration of trapping. There is little effect of trap type. The daily death rate of adult flies is unimportant unless tsetse control measures increase the mortality several times above the low natural rates. Formulae are suggested for predicting the probability that any given captured fly will have originated from various areas around the trap.ConclusionsFormulae for predicting the probability that any given captured fly originated from various areas around the trap are produced. Using a mean daily step length (d)of 395m, typical of a savannah species of tsetse, then any fly caught by a single trap in a 5-day trapping period could be regarded, with roughly 95% confidence, as originating from within a distance of 1.3km of the trap, that is from an area of 5.5km2.Authors SummaryWe produced a simple, deterministic model to highlight important principles in the neglected matter of the probability that any trapped tsetse will have originated from various sizes of area around the trapping site. The modelling was kept simple by envisaging the use of just one trap, or a group of only five traps, evenly spaced inside a circular area within a large block of homogeneous habitat and operated for no more than 30 days. In deriving formulae for the sampled area, we found it appropriate to consider only the flies’ mean daily step length, and the number of days duration of trapping. The type of trap employed was unimportant. The daily mortality of the adult tsetse population had little effect unless the death rates imposed by control measures were several times greater than the natural rates.
Analysis of an Indian colorectal cancer faecal microbiome collection demonstrates universal colorectal cancer-associated patterns, but closest correlation with other Indian cohorts
Authors: Bose Mayilvahanan , Wood Henry M , Young Caroline ,   International CRC Microbiome Network (AMS/CRUK), Quirke Philip , Seshadri Ramakrishan Ayloor 
Published: October 2022

AbstractIt is increasingly being recognised that changes in the gut microbiome have either a causative or associative relationship with colorectal cancer (CRC). However, most of this research has been carried out in a small number of developed countries with high CRC incidence. It is unknown if lower incidence countries such as India have similar microbial associations.Having previously established protocols to facilitate microbiome research in regions with developing research infrastructure, we have now collected and sequenced microbial samples from a larger cohort study of 46 Indian CRC patients and 43 healthy volunteers. When comparing to previous global collections, these samples resemble other Asian samples, with relatively high levels ofPrevotella. Predicting cancer status between cohorts shows good concordance. When compared to a previous collection of Indian CRC patients, there was similar concordance, despite different sequencing technologies between cohorts. These results show that there does seem to be a global CRC microbiome, and that some inference between studies is reasonable. However, we also demonstrate that there is definite regional variation, with more similarities between location-matched comparisons. This emphasises the importance of developing protocols and advancing infrastructure to allow as many countries as possible to contribute to microbiome studies of their own populations.ImportanceColorectal cancer is increasing in many countries, thought to be partly due to the interaction between gut bacteria and changing diets. While it is known that populations in different parts of the world have very different gut microbiomes, the study of their role in colorectal cancer is almost exclusively based in the USA and Europe. We have previously shown that there is overlap between the colorectal cancer microbiome in multiple different countries, establishing robust protocols in the process. Here we expand that into a new Indian cohort. We show that while there are similarities between countries, by concentrating on one country, we can uncover important local patterns. This shows the value of sharing expertise and ensuring that work of this nature is possible wherever this disease occurs.
Integrative single-cell meta-analysis reveals disease-relevant vascular cell states and markers in human atherosclerosis
Authors: Mosquera Jose Verdezoto , Auguste Gaëlle , Wong Doris , Turner Adam W. , Hodonsky Chani J. , Lino Cardenas Christian L. , Theofilatos Konstantinos , Bos Maxime , Kavousi Maryam , Peyser Patricia A. , Mayr Manuel , Kovacic Jason C. , Björkegren Johan L. M. , Malhotra Rajeev , van der Laan Sander W. , Zang Chongzhi , Sheffield Nathan C. , Miller Clint L. 
Published: October 2022

AbstractCoronary artery disease (CAD) and atherosclerosis are characterized by plaque formation in the arteries wall. CAD progression involves complex interactions and phenotypic plasticity within and between distinct vascular and immune cell lineages. Single-cell RNA-seq (scRNA-seq) studies have highlighted lineage-specific transcriptomic signatures, but the reported cell phenotypes in humans remain controversial. Here, we meta-analyzed four scRNA-seq datasets, creating the first map of human cell diversity in atherosclerosis. We generated an atlas of 118,578 high-quality cells, characterized cell-type diversity and provided insights into smooth muscle cell (SMC) phenotypic modulation, transcription factor activity and cell-cell communication. We integrated genome-wide association study (GWAS) data and uncovered a critical role for modulated SMC phenotypes in CAD and coronary calcification. Finally, we identified candidate markers of fibromyocyte and fibrochondrogenic human SMCs (LTBP1andCRTAC1) that may serve as proxies of atherosclerosis progression. Altogether, we created a unified cellular map of atherosclerosis informing cell state-specific mechanistic and translational studies of cardiovascular diseases.
Modelling the distribution of rare and data-poor diadromous fish at sea for protected area management
Authors: Elliott Sophie A. M. , Acou Anthony , Beaulaton Laurent , Guitton Jérôme , Réveillac Elodie , Rivot Etienne 
Published: October 2022

ABSTRACTAnthropogenic pressures have resulted in declines in diadromous fish. Many diadromous fish which were commercially important are now threatened and protected. Little is known about their marine life history phases, and no observation-based Species Distribution Model exists for this group of species at sea. Yet, fisheries dependent and independent data could provide new insights into the distribution of diadromous fish at sea.We collated a database of 168 904 hauls from fisheries observer bycatch data and scientific fisheries surveys, from eastern Atlantic and Mediterranean waters. The distribution of eleven rare and data-poor diadromous fish (shads, lampreys, salmonids, the European eel, the thinlip mullet, smelt and the European flounder) were modelled. A Bayesian site occupancy model, that incorporates imperfect detection to account for repeat detections and non-detections, the non-random nature of fishing gear type and spatial autocorrelation was used. From the model outputs, we explored bycatch risk and the role of MPAs, required under the Marine Strategy Framework Directive and Habitat Directive and assessed.Diadromous fish were observed within relatively shallow coastal areas. Species specific gear bycatch trends were observed. Core distribution areas corresponded to their known water basin presence, indicating connectivity with their freshwater habitats. Numerous Habitat Directive Marine Protected Areas were found to be of relevance.Given the coastal distribution of these species, they are exposed to higher anthropogenic pressures from both terrestrial and marine environments. Risk of bycatch at sea for most species appears to be low. Nonetheless, for threatened individuals, even a small amount of bycatch may impact their populations, especially since misreporting is likely to be high. Differences in catchability between gears highlight potential benefits of limiting access of certain gears within protected areas to reduce bycatch.
The Molecular Signatures Database Revisited: Extending Support for Mouse Data
Authors: Castanza Anthony S. , Recla Jill M. , Eby David , Thorvaldsdóttir Helga , Bult Carol J. , Mesirov Jill P. 
Published: October 2022

ABSTRACTThe Molecular Signatures Database (MSigDB) serves as the primary repository of biological signature gene sets for performing Gene Set Enrichment Analysis (GSEA). In the more than 15 years since its creation, MSigDB has served over 290,000 users in their use of GSEA to perform statistically rigorous analysis of coordinated patterns of gene expression changes by leveraging the prior knowledge of tens of thousands of deposited signatures. In that time, the sets provided in MSigDB have been offered exclusively in the human gene space and only minimally supporting analysis of mouse model data through mapping to human genes. Here we present two substantial improvements to MSigDB: first, by providing gene sets from widely used resources in the mouse gene space; and second, by offering substantially improved orthology mapping resources for comparative analysis of both mouse and human datasets.
A cross-species proteomic map reveals neoteny of human synapse development
Authors: Wang Li , Pang Kaifang , Zhou Li , Cebrián-Silla Arantxa , González-Granero Susana , Wang Shaohui , Bi Qiuli , White Matthew L. , Ho Brandon , Li Jiani , Li Tao , Perez Yonatan , Huang Eric J. , Winkler Ethan A. , Paredes Mercedes F. , Kovner Rothem , Sestan Nenad , Pollen Alex A. , Liu Pengyuan , Li Jingjing , Piao Xianhua , García-Verdugo José Manuel , Alvarez-Buylla Arturo , Liu Zhandong , Kriegstein Arnold R. 
Published: October 2022

AbstractThe molecular mechanisms and evolutionary changes accompanying synapse development are still poorly understood. Here, we generated a cross-species proteomic map of synapse development in the human, macaque, and mouse neocortex. By tracking the changes of >1,000 postsynaptic density (PSD) proteins from midgestation to young adulthood, we found that PSD maturation in humans separates into three major phases that are dominated by distinct pathways. Cross-species comparisons reveal that the human PSD matures about two to three times slower than other species and contains higher levels of Rho guanine nucleotide exchange factors (RhoGEFs) in the perinatal period. Enhancement of the RhoGEF signaling in human neurons delays the morphological maturation of dendritic spines and the functional maturation of synapses, potentially contributing to the neotenic traits of human brain development. In addition, PSD proteins can be divided into four modules that exert stage- and cell type-specific functions, possibly explaining their differential associations with cognitive functions and diseases. Together, our proteomic map of synapse development provides a blueprint for studying the molecular basis and evolutionary changes of synapse maturation.
Developmental staging and future research directions of the model marine tubewormHydroides elegans
Authors: Nesbit Katherine T. , Shikuma Nicholas J. 
Published: October 2022

ABSTRACTBackgroundThe biofouling marine tube worm,Hydroides elegans, is an indirect developing polychaete with significance as a model organism for questions in developmental biology and the evolution of host-microbe interactions. However, a complete description of the life cycle from fertilization through sexual maturity remains scattered in the literature, and lacks standardization.ResultsHere we present a unified staging scheme detailing the major morphological changes that occur during the entire life cycle of the animal. These data represent a complete record of the life cycle, and serve as a foundation for connecting molecular changes with morphology.ConclusionsThe present descriptions and associated staging scheme are especially timely as this system gains traction within research communities. Characterizing theHydroideslife cycle is essential for investigating the molecular mechanisms that drive major developmental transitions, like metamorphosis, in response to bacteria.
NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange
Authors: Pillich RT , Chen J , Churas C , Fong D , Ideker T , Liu SN , Gyori BM , Karis K , Ono K , Pico A , Pratt D 
Published: October 2022

AbstractMotivationThe investigation of sets of genes using biological pathways is a common task for researchers and is supported by a wide variety of software tools. This type of analysis generates hypotheses about the biological processes active or modulated in a specific experimental context.ResultsThe NDEx Integrated Query (IQuery) is a new tool for network and pathway-based gene set interpretation that complements or extends existing resources. It combines novel sources of pathways, integration with Cytoscape, and the ability to store and share analysis results. The IQuery web application performs multiple gene set analyses based on diverse pathways and networks stored in NDEx. These include curated pathways from WikiPathways and SIGNOR, published pathway figures from the last 27 years, machine-assembled networks using the INDRA system, and the new NCI-PID v2.0, an updated version of the popular NCI Pathway Interaction Database. IQuery’s integration with MSigDB and cBioPortal now provides pathway analysis in the context of these two resources.Availability and ImplementationIQuery is available athttps://www.ndexbio.org/iqueryand is implemented in Javascript and Java.ContactDexter Pratt (depratt@health.ucsd.edu)