bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying Patients with Cognitive Motor Dissociation Using Resting-state Temporal Stability
Authors: Wu Hang , Xie Qiuyou , Pan Jiahui , Liang Qimei , Lan Yue , Guo Yequn , Han Junrong , Xie Musi , Liu Yueyao , Jiang Liubei , Wu Xuehai , Li Yuanqing , Qin Pengmin 
Published: October 2022

AbstractBackgroundUsing task-dependent neuroimaging techniques, recent studies discovered a fraction of patients with disorders of consciousness (DOC) who had no command-following behaviors but showed a clear sign of awareness, which was defined as cognitive motor dissociation (CMD). Although many efforts were made to identify the CMD, existing task-dependent approaches might fail when patients had multiple cognitive function (e.g., attention, memory) impairments, and thus lead to false-negative findings. However, recent advances in resting-state fMRI (rs-fMRI) analysis allow investigation of the dynamic change of spontaneous brain activity, which might be a powerful tool to test the patient’s cognitive functions, while its capacity in identifying CMD was unclear.MethodsThe rs-fMRI study included 119 participants from three independent research sites. A sliding-window approach was used to investigate the dynamic functional connectivity of the brain in two aspects: the global and regional temporal stability, which measures how stable the brain functional architecture is across time. The temporal stability was compared in the first dataset (36/16 DOC/controls), and then a Support Vector Machine (SVM) classifier was built to discriminate DOC patients from controls. Furthermore, the generalizability of the SVM classifier was tested in the second independent dataset (35/21 DOC/controls). Finally, the SVM classifier was applied to the third independent dataset where patients underwent an rs-fMRI and brain-computer interface assessment (4/7 CMD/potential non-CMD), to test its performance in identifying CMD.ResultsOur results showed that the global and regional temporal stability were impaired in DOC patients, especially in regions from the cingulo-opercular task control, default mode, fronto-parietal task control, and salience network. Using the temporal stability as features, the SVM model not only showed a good performance in the first dataset (accuracy = 90 %), but a good generalizability in the second dataset (accuracy = 82 %). Most importantly, the SVM model generalized well in identifying CMD in the third dataset (accuracy = 91 %).ConclusionThe current findings suggested that rs-fMRI could be a potential tool to assist in diagnosing CMD. Furthermore, the temporal stability investigated in this study also contributed to a deeper understanding of the neural mechanism of the consciousness.
An armored marine reptile from the Early Triassic of South China
Authors: Wolniewicz Andrzej S. , Shen Yuefeng , Li Qiang , Sun Yuanyuan , Qiao Yu , Chen Yajie , Liu Jun 
Published: October 2022

AbstractSauropterygia was a taxonomically and ecomorphologically diverse clade of Mesozoic marine reptiles spanning the Early Triassic to the Late Cretaceous. Sauropterygians are traditionally divided into two groups representing two markedly different body plans – the short-necked, durophagous Placodontia and the long-necked Eosauropterygia – whereas Saurosphargidae, a small clade of marine reptiles possessing a dorsal ‘rib-basket’, is considered as the sauropterygian sister-group. However, the early evolutionary history of sauropterygians and their phylogenetic relationships with other groups within Diapsida are still incompletely understood. Here, we report a new saurosphargid from the Early Triassic of South China –Prosaurosphargis yingzishanensisgen. et sp. nov. – representing the earliest known occurrence of the clade. An updated phylogenetic analysis focussing on the interrelationships within diapsid reptiles recovers saurosphargids as nested within sauropterygians, forming a clade with eosauropterygians to the exclusion of placodonts. Furthermore, a clade comprisingEusaurosphargisandPalatodontais recovered as the sauropterygian sister-group within Sauropterygomorpha tax. nov. The phylogenetic position of several Early and Middle Triassic sauropterygians of previously uncertain phylogenetic affinity, such asAtopodentatus, Hanosaurus, MajiashanosaurusandCorosaurus, is also clarified, elucidating the early evolutionary assembly of the sauropterygian body plan. Finally, our phylogenetic analysis recovers Testudinata and Archosauromorpha within Archelosauria, a result strongly supported by molecular data, but until now not recovered by any phylogenetic analysis using a morphology-only data set. Our study provides evidence for the rapid diversification of sauropterygians in the aftermath of the Permo-Triassic mass extinction event and emphasises the importance of broad taxonomic sampling in reconstructing phylogenetic relationships among extinct taxa.
Distinct beta frequencies reflect categorical decisions
Authors: Rassi Elie , Zhang Yi , Mendoza German , Mendez Juan Carlos , Merchant Hugo , Haegens Saskia 
Published: October 2022

AbstractBeta oscillations are involved in a variety of cognitive functions beyond their traditional sensorimotor role. Based on prior findings of content-specific beta synchronization during working memory and decision making, we hypothesized that beta activity supports the activation and reactivation of cortical representations by mediating neural ensemble formation within and between brain regions. We here found that beta activity in monkey dorsolateral prefrontal cortex (dlPFC) and in pre-supplementary motor area (preSMA) reflects the content of a stimulus in relation to the task context, regardless of its objective properties. In multiple versions of a categorization task, we changed the boundary between categories from one block of trials to the next, such that a stimulus which belonged to one of two categories during one block could belong to the other category during the next one. During a delay in which monkeys had to hold their categorical decision in mind, we found that two distinct beta-band frequencies were consistently associated with the same two relative categories, and that activity in these respective bands predicted the animals’ responses. We characterized beta at these frequencies as transient bursts with distinct temporal profiles. We further showed that dlPFC and preSMA are connected via these distinct frequency channels, with dlPFC driving the frequency separation, a result supported by Granger causality and spike-field coherence analyses. In sum, these results provide support for the role of beta in forming neural ensembles, and further show that such ensembles synchronize at different beta frequencies.
Performance evaluation of mesoscopic photoacoustic imaging
Authors: Hacker Lina , Brown Emma L. , Lefebvre Thierry L. , Sweeney Paul W. , Bohndiek Sarah E 
Published: October 2022

AbstractPhotoacoustic mesoscopy visualises vascular architecture and associated tissue structures at high resolution at up to 3 mm depth. The technique has shown promise in both preclinical and clinical imaging studies, with possible applications in oncology and dermatology, however, the accuracy and precision of photoacoustic mesoscopy has not been well established. Here, we present a performance evaluation of a commercial photoacoustic mesoscopy system for imaging vascular structures. Typical artefact types are first highlighted and limitations due to non-isotropic illumination and detection are evaluated with respect to rotation, angularity, and depth of the target. Then, using tailored phantoms and mouse models we demonstrate high system precision, with acceptable coefficients of variation (COV) between repeated scans (short term (1h): COV=1.2%; long term (25 days): COV=9.6%), from target repositioning (without: COV=1.2%, with: COV=4.1%), or from varyingin vivouser experience (experienced: COV=15.9%, unexperienced: COV=20.2%). While our findings support the robustness of the technique, they also underscore the general challenges of limited field-of-view photoacoustic systems in accurately imaging vessel-like structures, thereby guiding users to correctly interpret biologically-relevant information.
Mapping a mutation causing pale yellow petals inBrassica rapa
Authors: Chow Hiu Tung , Mosher Rebecca A. 
Published: October 2022

AbstractPetal color is an important trait for both ornamental purposes and also for attracting pollinators. Here, we report a mutation ofBrassica rapaR-o-18 with pale yellow petals that we retrieved from an EMS population and namedwhiter shade of pale(wsp). Phenotypic segregation ratio of an F2 mapping population indicates the phenotype is controlled by a single recessive gene. Mapping data from the whole genome sequencing coupled with allele frequency analysis suggests the mutation is located in a ∼2 Mbp interval on chromosome 2. The interval contains a putative esterase/lipase/thioesterase protein previously demonstrated to account for floral color inB. rapa. We demonstrate thatwspcarries a G to A missense mutation causing an aspartate to asparagine substitution within the putative lysophospholipid acyltransferase domain.
Targeting the Immune-Fibrosis Axis in Myocardial Infarction and Heart Failure
Authors: Amrute Junedh M. , Luo Xin , Penna Vinay , Bredemeyer Andrea , Yamawaki Tracy , Heo Gyu Seong , Shi Sally , Koenig Andrew , Yang Steven , Kadyrov Farid , Jones Cameran , Kuppe Christoph , Kopecky Benjamin , Hayat Sikander , Ma Pan , Feng Guoshai , Terada Yuriko , Fu Angela , Furtado Milena , Kreisel Daniel , Stitziel Nathan O. , Li Chi-Ming , Kramann Rafael , Liu Yongjian , Ason Brandon , Lavine Kory J. 
Published: October 2022

AbstractCardiac fibrosis is causally linked to heart failure pathogenesis and adverse clinical outcomes. However, the precise fibroblast populations that drive fibrosis in the human heart and the mechanisms that govern their emergence remain incompletely defined. Here, we performed Cellular Indexing of Transcriptomes and Epitomes by sequencing (CITE-seq) in 22 explanted human hearts from healthy donors, acute myocardial infarction (MI), and chronic ischemic and non-ischemic cardiomyopathy patients. We identified a fibroblast trajectory marked by fibroblast activator protein (FAP) and periostin (POSTN) expression that was independent of myofibroblasts, peaked early after MI, remained elevated in chronic heart failure, and displayed a transcriptional signature consistent with fibrotic activity. We assessed the applicability of cardiac fibrosis models and demonstrated that mouse MI, angiotensin II/phenylephrine infusion, and pressure overload models were superior compared to cultured human heart and dermal fibroblasts in recapitulating cardiac fibroblast diversity including pathogenic cell states. Ligand-receptor analysis and spatial transcriptomics predicted interactions between macrophages, T cells, and fibroblasts within spatially defined niches. CCR2+monocyte and macrophage states were the dominant source of ligands targeting fibroblasts. Inhibition of IL-1β signaling to cardiac fibroblasts was sufficient to suppress fibrosis, emergence, and maturation of FAP+POSTN+fibroblasts. Herein, we identify a human fibroblast trajectory marked by FAP and POSTN expression that is associated with cardiac fibrosis and identify macrophage-fibroblast crosstalk mediated by IL-1β signaling as a key regulator of pathologic fibroblast differentiation and fibrosis.
Encoding object-location memories along the proximodistal axis of CA1
Authors: Teratani-Ota Yusuke , Wiltgen Brian J. 
Published: October 2022

AbstractThe hippocampus is thought to combine “what” and “where” information from the cortex so that objects and events can be represented within the spatial context in which they occur. Surprisingly then, these distinct types of information remain partially segregated in the output region of the hippocampus, area CA1. In this region, objects preferentially activate neurons in the distal segment (adjacent to the subiculum) while spatial locations are precisely represented by neurons in the proximal segment (adjacent to CA2). This difference likely results from distinct anatomical connections; proximal CA1 receives direct input from the medial entorhinal cortex (which encodes spatial context) whereas distal CA1 has reciprocal connections with the lateral entorhinal cortex (which encodes objects and events). Based on these findings, it has been proposed that CA1 contains two distinct representations; one that encodes the animal’s spatial location and another that encodes objects that are present in the environment. The current study aimed to determine the role of distal CA1 in learning the location of objects in an environment. To do this, we first examined c-Fos expression in proximal and distal CA1 to see if we could replicate previous findings and confirm that neurons in these distinct segment are responsive to different stimuli. As previous studies indicate that catecholamines can regulate the activity of segments of CA1, we then investigate the role of catecholamines on learning object locations using 6-OHDA or SCH23390 to lesion catecholaminergic input and block D1/D5 receptors, respectively. Finally, we monitored calcium activity with fiber photometry while animals performed a hippocampal-dependent object location memory task.
Critically endangered franciscana dolphins in an estuarine area: fine-scale habitat use and distribution from acoustic monitoring in Babitonga Bay, southern Brazil
Authors: Paitach Renan L. , Bortolotto Guilherme A. , Amundin Mats , Cremer Marta J. 
Published: October 2022

AbstractFranciscana dolphins in Babitonga Bay represent the only population of that critically endangered species which is confined to an estuary. Surrounded by large cities and harbors, that environment presents intense human activities and potential impacts that may threaten the dolphins. Understanding their habitat use and distribution can inform mitigation of such impacts. Here we used acoustic data from sixty fixed passive acoustic monitoring stations, implemented between June and December 2018. The relationship between the occurrence of franciscanas and environmental variables was investigated with generalized additive mixed models. The selected model presented 51% of explained deviance and included “time of day”, “intensity of presence of Guiana dolphins”, “maximum slope”, and “bottom sediment”, among other less statistically significant variables. A daily distribution pattern was identified, with franciscanas remaining in the areas of greatest occurrence especially in the morning and seemed to prefer sandy bottom and flatter areas. Areas intensively used by Guyana dolphins were avoided. Additionally, we mapped their distribution using “Empirical Bayesian Kriging” to identify the main areas of occurrence and for foraging. Franciscanas are consistently predominant in the innermost region of the estuary, without expressive use of the entrance channel, but with a wider range in winter than in the spring. The area around the islands, between the north and south banks, represents an important foraging area, a behavior more frequent during dawn and night. This study provides important insights into critical habitat and behavioral patterns of franciscanas, especially this critically endangered population.
Patterns of community science data use in peer-reviewed research on biodiversity
Authors: Binley A.D. , Vincent J.G. , Rytwinski T. , Proctor C.A. , Urness E.S. , Davis S.A. , Soroye P. , Bennett J.R. 
Published: October 2022

AbstractCommunity science (“citizen science”) represent a potentially abundant and inexpensive source of information for biodiversity research. However, analyzing such data has inherent challenges. To explore where and how community science data are translated into scientific knowledge, we conducted a literature review in a sample of 334 peer-reviewed scientific articles. Specifically, we investigated how the use of community science data varied among taxonomic groups and geographic regions, and what threats to biodiversity, if any, were examined. Community science data were used mostly for research on birds and invertebrates, and the data used were mainly from the United States and the United Kingdom. Literature in certain countries used a wider breadth of projects, while others made repeated use of comparably fewer datasets. Community science efforts were largely used to measure abundance, trends, distributions, and range shifts. However, few articles linked these metrics to any particular threats to biodiversity. Furthermore, community science data were used infrequently for research on threatened species and limited mostly to count data rather than collecting more specific information such as life history, phenological or genetic data, suggesting that community science may be underutilized for these key aspects of biodiversity conservation. We conclude that even with the rise of community science data use in research, there remains tremendous potential to better use these existing datasets for biodiversity research.
Long-term spatially-replicated data show no physical cost to a benefactor species in a facilitative plant-plant interaction
Authors: Raath-Krüger Morgan J. , Schöb Christian , McGeoch Melodie A. , Burger Divan A. , Strydom Tanya , le Roux Peter C. 
Published: October 2022

AbstractFacilitation is an interaction where one species (the benefactor) positively impacts another (the beneficiary). However, the reciprocal effects of beneficiaries on their benefactors are typically only documented using short-term datasets. We useAzorella selago, a cushion plant species and benefactor, and a co-occurring grass species,Agrostis magellanica, on sub-Antarctic Marion Island, comparing cushion plants and the grasses growing on them over a 13-year period using a correlative approach. We additionally compare the feedback effect ofA. magellanicaonA. selagoidentified using our long-term dataset with data collected from a single time period. We hypothesized thatA. selagosize and vitality would be negatively affected byA. magellanicacover and that the effect ofA. magellanicaonA. selagowould become more negative with increasing beneficiary cover and abiotic-severity, due to, e.g., more intense competition for resources. We additionally hypothesized thatA. magellanicacover would increase more on cushion plants with greater dead stem cover, since dead stems do not inhibit grass colonization or growth. The relationship betweenA. magellanicacover andA. selagosize and vitality was not significant in the long-term dataset, and the feedback effect ofA. magellanicaonA. selagodid not vary significantly with altitude or aspect; however, data from a single time period did not consistently identify this same lack of correlation. Moreover,A. selagodead stem cover was not significantly related to an increase inA. magellanicacover over the long term; however, we observed contrasting results from short-term datasets. Long-term datasets may, therefore, be more robust (and practical) for assessing beneficiary feedback effects than conventional approaches, particularly when benefactors are slow-growing. For the first time using a long-term dataset, we show a lack of physical cost to a benefactor species in a facilitative interaction, in contrast to the majority of short-term studies.
Development of Loop-mediated Isothermal Amplification (LAMP) Assays Using Five Primers Reduces the False-positive Rate in COVID-19 Diagnosis
Authors: Alhamid Galyah , Tombuloglu Huseyin , Al-Suhaimi Ebtesam 
Published: October 2022

AbstractThe reverse-transcription loop-mediated isothermal amplification (RT-LAMP) is a cheaper and faster testing alternative for detecting SARS-CoV-2. However, high false-positive rate due to misamplification is one of the major limitations. To overcome misamplifications, we developed colorimetric and fluorometric RT-LAMP assays. The assay performances was verified by the gold-standard RT-qPCR technique on 150 clinical samples. Compared to other primer sets with six primers (N, S, andRdRp), E-ID1 primer set, including five primers, performed superbly on both colorimetric and fluorometric assays, yielding sensitivities of 89.5% and 100%, respectively, with a limit of detection of 20 copies/µL. The colorimetric RT-LAMP had a specificity of 97.2% and an accuracy of 94.5%, while the fluorometric RT-LAMP obtained 96.9% and 98%, respectively. No misamplification was evident even after 120 minutes, which is crucial for the success of this technique. These findings are important to support the use of RT-LAMP in the healthcare systems in fighting COVID-19.
Selection on visual opsin genes in diurnal Neotropical frogs and loss of theSWS2opsin in poison frogs
Authors: Wan YC , Navarrete MJ , O’Connell LA , Uricchio LH , Roland AB , Maan ME , Ron SR , Betancourth-Cundar M , Pie MR , Howell KA , Richards-Zawacki CL , Cummings ME , Cannatella DC , Santos JC , Tarvin RD 
Published: October 2022

AbstractAmphibians are ideal for studying visual system evolution because their biphasic (aquatic and terrestrial) life history and ecological diversity expose them to a broad range of visual conditions. Here we evaluate signatures of selection on visual opsin genes across Neotropical anurans and focus on three diurnal clades that are well-known for the concurrence of conspicuous colors and chemical defense (i.e., aposematism): poison frogs (Dendrobatidae), Harlequin toads (Bufonidae:Atelopus), and pumpkin toadlets (Brachycephalidae:Brachycephalus). We found evidence of positive selection on 44 amino acid sites inLWS, SWS1, SWS2,andRH1opsin genes, of which one inLWSand two inRH1have been previously identified as spectral tuning sites in other vertebrates. Given that anurans have mostly nocturnal habits, the patterns of selection revealed new sites that might be important in spectral tuning for frogs, potentially for adaptation to diurnal habits and for color-based intraspecific communication. Furthermore, we provide evidence thatSWS2, normally expressed in rod cells in amphibians, has likely been lost in the ancestor of Dendrobatidae, suggesting that under low-light levels, dendrobatids have inferior wavelength discrimination compared to other frogs. This loss might follow the origin of diurnal activity in dendrobatids and could have implications for their chemical ecology, biodiversity, and behavior. Our analyses show that assessments of opsin diversification in understudied groups could expand our understanding of the role of sensory system evolution in ecological adaptation.