bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reply to Li et al. “IsOculudentavisa bird or even archosaur?”
Authors: O’Connor Jingmai , Xing Lida , Chiappe Luis , Schmitz Lars , Li Gang , Yi Qiru 
Published: June 2020

AbstractWe welcome any new interpretation or alternative hypothesis regarding the taxonomic affinity of the enigmaticOculudentavis khaungraae. However, here we demonstrate that Li et al. have failed to provide conclusive evidence for the reidentification of HPG-15-3 as a squamate. We analyse this specimen in a matrix that includes a broad sample of diapsid reptiles and resolve support for this identification only when no avian taxa are included. Regardless of whether this peculiar skull belongs to a tiny bird or to a bizarre new group of lizards, the holotype ofOculudentavis khaungraaeis a very interesting and unusual specimen, the discovery of which represents an important contribution to palaeontology. Its discovery documents a potential new case of convergent evolution in reptiles, while highlighting the importance of amber deposits for documenting taxa not recorded in sedimentary deposits.
LayNii: A software suite for layer-fMRI
Authors: Huber Laurentius (Renzo) , Poser Benedikt A. , Bandettini Peter A. , Arora Kabir , Wagstyl Konrad , Cho Shinho , Goense Jozien , Nothnagel Nils , Morgan Andrew Tyler , van den Hurk Job , Müller Anna K , Reynolds Richard C. , Glen Daniel R. , Goebel Rainer , Gulban Omer Faruk 
Published: June 2020

AbstractHigh-resolution fMRI in the sub-millimeter regime allows researchers to resolve brain activity across cortical layers and columns non-invasively. While these high-resolution data make it possible to address novel questions of directional information flow within and across brain circuits, the corresponding data analyses are challenged by MRI artifacts, including image blurring, image distortions, low SNR, and restricted coverage. These challenges often result in insufficient spatial accuracy of conventional analysis pipelines. Here we introduce a new software suite that is specifically designed for layer-specific functional MRI: LayNii. This toolbox is a collection of command-line executable programs written in C/C++ and is distributed open-source and as pre-compiled binaries for Linux, Windows, and macOS. LayNii is designed for layer-fMRI data that suffer from SNR and coverage constraints and thus cannot be straightforwardly analyzed in alternative software packages. Some of the most popular programs of LayNii contain ‘layerification’ and columnarization in the native voxel space of functional data as well as many other layer-fMRI specific analysis tasks: layer-specific smoothing, model-based vein mitigation of GE-BOLD data, quality assessment of artifact dominated sub-millimeter fMRI, as well as analyses of VASO data.HighlightsA new software toolbox is introduced for layer-specific functional MRI: LayNii.LayNii is a suite of command-line executable C++ programs for Linux, Windows, and macOS.LayNii is designed for layer-fMRI data that suffer from SNR and coverage constraints.LayNii performs layerification in the native voxel space of functional data.LayNii performs layer-smoothing, GE-BOLD deveining, QA, and VASO analysis.Abstract FigureGraphical abstract
Identification of the Molecular Basis of Anti-fibrotic Effects of Soluble Guanylate Cyclase Activator Using the Human Lung Fibroblast Phosphoproteome
Authors: Kim Sunhwa , Saigal Ashmita , Zhao Weilong , Amini Peyvand , Tamburino Alex M. , Raghavan Subharekha , Hoek Maarten 
Published: June 2020

AbstractIdiopathic pulmonary fibrosis (IPF) is an irreversible and progressive fibrotic lung disease. Advanced IPF patients often demonstrate pulmonary hypertension, which severely impairs patients’ quality of life. The critical physiological roles of soluble guanylate cyclase (sGC)-cyclic guanosine monophosphate (cGMP) pathway have been well characterized in vasodilation and the corresponding therapies and pathway agonists have shown clinical benefits in treating hypertension. In recent years, many preclinical studies have demonstrated anti-fibrotic efficacy of sGC-cGMP activation in various experimental fibrosis models but the molecular basis of the efficacy in these models are not well understood. Also, sGC pathway agonism has demonstrated encouraging clinical benefits in advanced IPF patients (NCT00517933). Here, we have revealed the novel phosphorylation events downstream of sGC activation in human lung fibroblasts using phosphoproteomics. sGCact A, a potent and selective sGC activator, significantly attenuated more than 2,000 phosphorylation sites. About 20% of phosphorylation events, attenuated by transforming growth factor β (TGFβ), a master regulator of fibrosis, were further dysregulated in the sGCact A co-treated lung fibroblasts. The overall magnitude and diversity of the sGCact A phosphoproteome was extensive. Further investigation would be required to understand how these newly identified changes facilitate human pulmonary fibrosis.
Predicting targets and costs for feral-cat reduction on large islands using stochastic population models
Authors: Venning Kathryn R. W. , Saltré Frédérik , Bradshaw Corey J. A. 
Published: June 2020

AbstractFeral cats are some of the most destructive invasive predators worldwide, particularly in insular environments; hence, density-reduction campaigns are often applied to alleviate the predation mortality they add to native fauna. Density-reduction and eradication efforts are costly procedures with important outcomes for native fauna recovery, so they require adequate planning to be successful. These plans need to include empirical density-reduction models that can guide yearly culling quotas, and resource roll-out for the duration of the culling period. This ensures densities are reduced over the long term and that no resources are wasted. We constructed a stochastic population model with cost estimates to test the relative effectiveness and cost-efficiency of two main culling scenarios for a 10-year eradication campaign of cats on Kangaroo Island, Australia: (1) constant proportional annual cull (one-phase), and (2) high initial culling followed by a constant proportional maintenance cull (two-phase). A one-phase cull of at least 0.35 of the annual population size would reduce the final population to 0.1 of its original size, while a two-phase cull with an initial cull of minimum 0.6 and minimum 0.5 maintenance cull would reduce the final population to 0.01 of its initial size by 2030. Cost estimates varied widely depending on the methods applied (shooting, trapping, aerial poison baits,Felixer™ poison-delivery system), but using baiting, trapping andFelixerswith additional shooting to meet culling quotas was the most cost-effective combination (minimum cost: AU$19.56 million; range: AU$16.87 million–AU$20.69 million). Our model provides an adaptable and general assessment tool for cat reductions in Australia and potentially elsewhere, and provides relative culling costs for the Kangaroo Island programme specifically.
Brief Report: Test-Retest Reliability of Explicit Auditory Processing Measures
Authors: Saito Kazuya , Sun Hui , Tierney Adam 
Published: June 2020

AbstractIn this brief report, we examined the test-retest reliability of our in-house explicit auditory processing measures in the context of 30 L1 and L2 English users. The participants took the same test battery which consisted of a total of four discrimination tasks (encoding acoustic details of formant, pitch, duration, and rise time) and two reproduction tasks (repeating novel melodic and rhythmic patterns) at Days 1 and 2. According to the results, the participants’ initial and second test scores demonstrated medium-to-large associations (r= .562-.907). The results suggest that the tests can tap into various dimensions of individuals’ auditory acuity and integration abilities.
How to better communicate exponential growth of infectious diseases
Authors: Schonger Martin , Sele Daniela 
Published: June 2020

AbstractExponential growth bias is the phenomenon that humans underestimate exponential growth. In the context of infectious diseases, this bias may lead to failure to understand the effectiveness of non-pharmaceutical interventions (NPIs). Communicating the same scenario in different ways (framing) has been found to have a large impact on people’s evaluations and behavior in the contexts of social behavior, risk taking and health care. We find that framing matters for people’s assessment of the benefits of NPIs. In two commonly used frames, most subjects in our experiment drastically underestimate the number of cases NPIs avoid. Framing growth in terms of doubling times, rather than growth rates, reduces bias. When the scenario is framed in terms of time gained, rather than cases avoided, the median subject assesses the benefit of NPIs correctly. These findings suggest changes that public health authorities can adopt to better communicate the exponential spread of infectious diseases.
Synchronised inflations generate greater gravity dependent lung ventilation in neonates
Authors: Dowse G , Perkins E , Thomson J , Schinckel N , Pereira-Fantini PM , Tingay DG 
Published: June 2020

ABSTRACTObjectiveSynchronising positive pressure inflations with an infant’s own breathing is considered lung protective, but the ventilation patterns within the infant lung during synchronous and asynchronous inflations are unknown. The aim of this study was to describe the regional distribution patterns of tidal ventilation within the lung during mechanical ventilation that is synchronous or asynchronous with an infant’s own breathing effort.MethodsIntubated infants receiving synchronised mechanical ventilation at The Royal Children’s Hospital NICU were studied. During four 10-minute periods of routine care, regional distribution of tidal volume (VT; Electrical Impedance Tomography), delivered pressure and airway flow (Florian Respiratory Monitor) were measured for every inflation. Post hoc, each inflation was then classified as synchronous or asynchronous from video data of the ventilator screen, and the distribution of absolute VT and delivered ventilation characteristics determined.Results2749 inflations (2462 synchronous) were analysed in 19 infants; mean (SD) age 28 (30) day, GA 35 (5) weeks. Synchronous inflations were associated with a shorter respiratory cycle (p=0.004) and more homogenous VT (centre of ventilation) along the right (0%) to left (100%) lung plane; 45.3 (8.6)% vs 48.8 (9.4)% (uniform ventilation 46%). The gravity dependent centre of ventilation was a mean (95% CI) 2.1 (−0.5, 4.6)% more towards the dependent lung during synchronous inflations. Tidal ventilation relative to anatomical lung size was more homogenous during synchronised inflations in the dependent lung.ConclusionSynchronous mechanical ventilator lung inflations generate more gravity dependent lung ventilation and more uniform right to left ventilation than asynchronous inflations.
A discrete-time-evolution model to forecast progress of Covid-19 outbreak
Authors: Curado Evaldo M. F. , Curado Marco R. 
Published: June 2020

AbstractBased on well-known infection models, we constructed a new model to forecast the propagation of the Covid-19 pandemic which yields a discrete-time evolution with one day interval. The proposed model can be easily implemented with daily updated data sets of the pandemic publicly available by many sources. It has only two adjustable parameters and is able to predict the evolution of the total number of infected people in a country for the next 14 days, if parameters do not change during this time. The model incorporates the main aspects of the disease such as the the fact that there are asymptomatic and symptomatic phases (both capable of propagating the virus), and that these phases take almost two weeks before the infected person status evolves to the next (asymptomatic becomes symptomatic or symptomatic becomes either recovered or dead). One advantage of the model is that it gives directly the number of total infected people in each day (in thousands, tens of thousands or hundred of thousands). The model was tested with data from Brazil, UK and South Korea, it predicts quite well the evolution of the disease and therefore may be a useful tool to estimate the propagation of the disease.
Combining segmental bulk- and single-cell RNA-sequencing to define the chondrocyte gene expression signature in the murine knee joint
Authors: Sunkara Vikram , Heinz Gitta A. , Heinrich Frederik F. , Durek Pawel , Mobasheri Ali , Mashreghi Mir-Farzin , Lang Annemarie 
Published: June 2020

AbstractObjectiveDue to the small size of the murine knee joint, extracting the chondrocyte transcriptome from articular cartilage (AC) is a major technical challenge. In this study, we demonstrate a new and pragmatic approach of combining bulk RNA-sequencing (RNA-seq) and single cell (sc)RNA-seq to address this problem.DesignWe propose a new cutting strategy of the murine femur which produces three segments with a predictable mixed cell populations, where one segment contains AC and growth plate (GP) chondrocytes, another contains GP chondrocytes, and the last segment contains only bone and bone marrow. We analysed the bulk RNA-seq of the different segments to find common and distinct genes between the segments. Then, the segment containing AC chondrocytes was digested and analysed via scRNA-seq.ResultsDifferential expression analysis using bulk RNA-seq identified 350 candidate chondrocyte gene in the AC segment. Gene set enrichment analysis of these genes revealed biological processes related- and non-related to chondrocytes, including, cartilage development (adj. p-value: 3.45E-17) and endochondral bone growth (adj. p-value 1.22E-4), respectively. ScRNA-seq of the AC segment found a cluster of 131 cells containing mainly chondrocytes. This cluster had 759 differentially expressed genes which enriched for extracellular matrix organisation (adj. p-value 7.76E-40) and other joint development processes. The intersection of the gene sets of bulk- and scRNA-seq contained 75 genes, where all but ten genes were previously implicated in cartilage homeostasis or osteoarthritis (OA) progression.ConclusionsOur approach has the potential to detect the scarce disease phenotypes of chondrocytes in murine OA models.
Protein Profiles: Biases and Protocols
Authors: Urban Gregor , Torrisi Mirko , Magnan Christophe N. , Pollastri Gianluca , Baldi Pierre 
Published: June 2020

AbstractThe use of evolutionary profiles to predict protein secondary structure, as well as other protein structural features, has been standard practice since the 1990s. Using profiles in the input of such predictors, in place or in addition to the sequence itself, leads to significantly more accurate predictors. While profiles can enhance structural signals, their role remains somewhat surprising as proteins do not use profiles when folding in vivo. Furthermore, the same sequence-based redundancy reduction protocols initially derived to train and evaluate sequence-based predictors, have been applied to train and evaluate profile-based predictors. This can lead to unfair comparisons since profile may facilitate the bleeding of information between training and test sets. Here we use the extensively studied problem of secondary structure prediction to better evaluate the role of profiles and show that: (1) high levels of profile similarity between training and test proteins are observed when using standard sequence-based redundancy protocols; (2) the gain in accuracy for profile-based predictors, over sequence-based predictors, strongly relies on these high levels of profile similarity between training and test proteins; and (3) the overall accuracy of a profile-based predictor on a given protein dataset provides abiasedmeasure when trying to estimate the actual accuracy of the predictor, or when comparing it to other predictors. We show, however, that this bias can be avoided by implementing a new protocol (EVALpro) which evaluates the accuracy of profile-based predictors as a function of the profile similarity between training and test proteins. Such a protocol not only allows for a fair comparison of the predictors on equally hard or easy examples, but also completely removes the need for selecting arbitrary similarity cutoffs when selecting test proteins. The EVALpro program is available for download from the SCRATCH suite (http://scratch.proteomics.ics.uci.edu).
MAGI1 inhibits the AMOTL2/p38 stress pathway and prevents luminal breast tumorigenesis
Authors: Kantar Diala , Mur Emilie Bousquet , Mancini Maicol , Slaninova Vera , Salah Yezza Ben , Costa Luca , Forest Elodie , Lassus Patrice , Géminard Charles , Boissière-Michot Florence , Orsetti Béatrice , Theillet Charles , Colinge Jacques , Benistant Christine , Maraver Antonio , Heron-Milhavet Lisa , Djiane Alexandre 
Published: June 2020

ABSTRACTAlterations to cell polarization or to intercellular junctions are often associated with epithelial cancer progression, including breast cancers (BCa). We show here that the loss of the junctional scaffold protein MAGI1 is associated with bad prognosis in luminal BCa, and promotes tumorigenesis. E-cadherin and the actin binding scaffold AMOTL2 accumulate inMAGI1deficient cells which are subjected to increased stiffness. These alterations are associated with low YAP activity, the terminal Hippo-pathway effector, but with an elevated ROCK and p38 Stress Activated Protein Kinase activities. Blocking ROCK prevented p38 activation, suggesting that MAGI1 limits p38 activity in part through releasing actin strength. Importantly, the increased tumorigenicity ofMAGI1deficient cells is rescued in the absence of AMOTL2 or after inhibition of p38, demonstrating that MAGI1 acts as a tumor-suppressor in luminal BCa by inhibiting an AMOTL2/p38 stress pathway.
Managing mixed stands can mitigate severe climate change impacts on ecosystem functioning
Authors: Jourdan M. , Cordonnier T. , Dreyfus P. , Riond C. , de Coligny F. , Morin X. 
Published: June 2020

AbstractClimate change affects forest ecosystem processes and related services due to increasing temperature and increasing extreme drought event frequency. This effect can be direct through the alteration of the physiological responses of trees, but also indirect, by modifying interactions between trees and thus changing communities’ composition. Such changes might affect species richness with high impacts on ecosystem functioning, especially productivity.Regarding management issues, mixed stands are usually considered a good option to maintain forest cover and ecosystem services under climate change. However, the possibility to maintain these mixed stands with management actions with positive effects on forest functioning under climate change remains uncertain and deserves further investigations. Relying on a simulation-based study with a forest gap model, we thus addressed the following questions: (1) Are monospecific stands vulnerable to climate change? (2) Would mixed stands significantly mitigate climate change effects on forest productivity and wood production under climate change? (3) Would conversion to mixed stand management affect significantly forest productivity and wood production under climate change compare to monospecific management?With a 150 years simulation approach, we quantified potential climate change effect (using RCP 8.5) compared to present climate and managements effect in the French Alps, focusing on five tree species. The gap-model we used included a management module, which allowed testing six silvicultural scenarios on different stands, with various composition, structure or environmental conditions, under climate change.These simulations showed that monospecific stands currently growing in stressful conditions would be too vulnerable to climate change to be maintained. Managing mixed stands or conversion from pure to mixed stands would make it possible to maintain higher productivity in the long-term than monospecific stands, even under severe climate change. This pattern depends to species and sites considered. Our results will feed into discussion on forest management in the context of climate change.
AC. elegansmodel ofC9orf72-associated ALS/FTD uncovers a conserved role for eIF2D in RAN translation
Authors: Sonobe Yoshifumi , Aburas Jihad , Islam Priota , Gendron Tania F. , Brown André E.X. , Roos Raymond P. , Kratsios Paschalis 
Published: June 2020

ABSTRACTA hexanucleotide repeat expansion GGGGCC in the noncoding region ofC9orf72is the most common cause of inherited amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Potentially toxic dipeptide repeats (DPRs) are synthesized from the GGGGCC sequence via repeat associated non-AUG (RAN) translation. We developedC. elegansmodels that express, either ubiquitously or exclusively in neurons, a transgene with 75 GGGGCC repeats flanked by intronicC9orf72sequence. The worms generate DPRs (poly-glycine-alanine [poly-GA], poly-glycine-proline [poly-GP]) and display neurodegeneration, locomotor and lifespan defects. Mutation of a non-canonical translation-initiating codon (CUG) upstream of the repeats blocked poly-GA production and ameliorated disease, suggesting poly-GA is pathogenic. Importantly, eukaryotic translation initiation factor 2D (eif-2D/eIF2D) was necessary for RAN translation. Genetic removal ofeif-2Dincreased lifespan in bothC. elegansmodels.In vitrofindings in human cells demonstrated a conserved role foreif-2D/eIF2Din RAN translation that could be exploited for ALS and FTD therapy.
Contextual experience modifies functional connectome indices of topological strength and organization
Authors: Pompilus Marjory , Colon-Perez Luis M. , Grudny Matteo M. , Febo Marcelo 
Published: June 2020

ABSTRACTStimuli presented at short temporal delays before functional magnetic resonance imaging (fMRI) can have a robust impact on the organization of synchronous activity in resting state networks. This presents an opportunity to investigate how sensory, affective and cognitive stimuli alter functional connectivity in rodent models. In the present study, we assessed the effect of a familiar contextual stimulus presented 10 minutes prior to sedation for imaging on functional connectivity. A subset of animals were co-presented with an unfamiliar social stimulus in the same environment to further investigate the effect of familiarity on network topology. Female and male rats were imaged at 11.1 Tesla and graph theory analysis was applied to matrices generated from seed-based functional connectivity data sets with 144 brain regions (nodes) and 10,152 pairwise correlations (edges). Our results show an unconventional network topology in response to the familiar (context) but not the unfamiliar (social) stimulus. The familiar stimulus strongly reduced network strength, global efficiency, and altered the location of the highest eigenvector centrality nodes from cortex to the hypothalamus. We did not observe changes in modular organization, nodal cartographic assignments, assortative mixing, rich club organization, and network resilience. The results suggest that experiential factors, perhaps involving associative or episodic memory, can exert a dramatic effect on functional network strength and efficiency when presented at a short temporal delay before imaging.