bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recurring adaptive introgression of a supergene variant that determines social organization
Authors: Stolle Eckart , Pracana Rodrigo , López-Osorio Federico , Priebe Marian K. , Hernández Gabriel Luis , Castillo-Carrillo Claudia , Arias Maria Cristina , Paris Carolina Ivon , Bollazzi Martin , Priyam Anurag , Wurm Yannick 
Published: March 2022

AbstractIntrogression has been proposed as an essential source of adaptive genetic variation. However, a key barrier to adaptive introgression is that recombination can break down combinations of alleles that underpin many traits. This barrier might be overcome in supergene regions, where suppressed recombination leads to joint inheritance across many loci. Here, we study the evolution of a large supergene region that determines a major social and ecological trait in Solenopsis fire ants: whether colonies have one queen or multiple queens. Using coalescent-based phylogenies built from the genomes of 365 haploid fire ant males, we show that the supergene variant responsible for multiple-queen colonies evolved in one species and repeatedly spread to other species through introgressive hybridization. This finding highlights how supergene architecture can enable a complex adaptive phenotype to recurrently permeate species boundaries.
Past terrestrial hydroclimate sensitivity controlled by Earth system feedbacks
Authors: Feng Ran , Bhattacharya Tripti , Otto-Bliesner Bette L. , Brady Esther C. , Haywood Alan M. , Tindall Julia C. , Hunter Stephen J. , Abe-Ouchi Ayako , Chan Wing-Le , Kageyama Masa , Contoux Camille , Guo Chuncheng , Li Xiangyu , Lohmann Gerrit , Stepanek Christian , Tan Ning , Zhang Qiong , Zhang Zhongshi , Han Zixuan , Williams Charles J. R. , Lunt Daniel J. , Dowsett Harry J. , Chandan Deepak , Peltier W. Richard 
Published: March 2022

AbstractDespite tectonic conditions and atmospheric CO2 levels (pCO2) similar to those of present-day, geological reconstructions from the mid-Pliocene (3.3-3.0 Ma) document high lake levels in the Sahel and mesic conditions in subtropical Eurasia, suggesting drastic reorganizations of subtropical terrestrial hydroclimate during this interval. Here, using a compilation of proxy data and multi-model paleoclimate simulations, we show that the mid-Pliocene hydroclimate state is not driven by direct CO2 radiative forcing but by a loss of northern high-latitude ice sheets and continental greening. These ice sheet and vegetation changes are long-term Earth system feedbacks to elevated pCO2. Further, the moist conditions in the Sahel and subtropical Eurasia during the mid-Pliocene are a product of enhanced tropospheric humidity and a stationary wave response to the surface warming pattern, which varies strongly with land cover changes. These findings highlight the potential for amplified terrestrial hydroclimate responses over long timescales to a sustained CO2 forcing.
Malfunction of airway basal stem cells plays a crucial role in pathophysiology of tracheobronchopathia osteoplastica
Authors: Hong Yue , Shan Shan , Gu Ye , Huang Haidong , Zhang Quncheng , Han Yang , Dong Yongpin , Liu Zeyu , Huang Moli , Ren Tao 
Published: March 2022

AbstractUnderstanding disease-associated stem cell abnormality has major clinical implications for prevention and treatment of human disorders, as well as for regenerative medicine. Here we report a multifaceted study on airway epithelial stem cells in Tracheobronchopathia Osteochondroplastica (TO), an under-detected tracheobronchial disorder of unknown etiology and lack of specific treatment. Epithelial squamous metaplasia and heterotopic bone formation with abnormal cartilage proliferation and calcium deposits are key pathological hallmarks of this disorder, but it is unknown whether they are coincident or share certain pathogenic mechanisms in common. By functional evaluation and genome-wide profiling at both transcriptional and epigenetic levels, we reveal a role of airway basal cells in TO progression by acting as a repository of inflammatory and TGFβ-BMP signals, which contributes to both epithelial metaplasia and mesenchymal osteo-chondrogenesis via extracellular signaling and matrix remodeling. Restoration of microenvironment by cell correction or local pathway intervention may provide therapeutic benefits.
Enhanced jet stream waviness induced by suppressed tropical Pacific convection during boreal summer
Authors: Sun Xiaoting , Ding Qinghua , Wang Shih-Yu Simon , Topál Dániel , Li Qingquan , Castro Christopher , Teng Haiyan , Luo Rui , Ding Yihui 
Published: March 2022

AbstractConsensus on the cause of recent midlatitude circulation changes toward a wavier manner in the Northern Hemisphere has not been reached, albeit a number of studies collectively suggest that this phenomenon is driven by global warming and associated Arctic amplification. Here, through a fingerprint analysis of various global simulations and a tropical heating-imposed experiment, we suggest that the suppression of tropical convection along the Inter Tropical Convergence Zone induced by sea surface temperature (SST) cooling trends over the tropical Eastern Pacific contributed to the increased summertime midlatitude waviness in the past 40 years through the generation of a Rossby-wave-train propagating within the jet waveguide and the reduced north-south temperature gradient. This perspective indicates less of an influence from the Arctic amplification on the observed mid-latitude wave amplification than what was previously estimated. This study also emphasizes the need to better predict the tropical Pacific SST variability in order to project the summer jet waviness and consequent weather extremes.
Structure-based design of prefusion-stabilized human metapneumovirus fusion proteins
Authors: Hsieh Ching-Lin , Rush Scott A. , Palomo Concepcion , Chou Chia-Wei , Pickens Whitney , Más Vicente , McLellan Jason S. 
Published: March 2022

AbstractThe human metapneumovirus (hMPV) fusion (F) protein is essential for viral entry and is a key target of neutralizing antibodies and vaccine development. The prefusion conformation is thought to be the optimal vaccine antigen, but previously described prefusion F proteins expressed poorly and were not well stabilized. Here, we use structures of hMPV F to guide the design of 42 variants containing stabilizing substitutions. Through combinatorial addition of disulfide bonds, cavity-filling substitutions, and improved electrostatic interactions, we describe a prefusion-stabilized F protein (DS-CavEs2) that expresses at 15 mg/L and has a melting temperature of 71.9 °C. Crystal structures of two prefusion-stabilized hMPV F variants reveal that antigenic surfaces are largely unperturbed. Importantly, immunization of mice with DS-CavEs2 elicits significantly higher neutralizing antibody titers against hMPV A1 and B1 viruses than postfusion F. The improved properties of DS-CavEs2 will advance the development of hMPV vaccines and the isolation of therapeutic antibodies.
Little-Parks like oscillations in lightly doped cuprate superconductors
Authors: Liao Menghan , Zhu Yuying , Hu Shuxu , Zhong Ruidan , Schneeloch John , Gu Genda , Zhang Ding , Xue Qi-Kun 
Published: March 2022

AbstractUnderstanding the rich and competing electronic orders in cuprate superconductors may provide important insight into the mechanism of high-temperature superconductivity. Here, by measuring Bi2Sr2CaCu2O8+x in the extremely underdoped regime, we obtain evidence for a distinct type of ordering, which manifests itself as resistance oscillations at low magnetic fields (≤10 T) and at temperatures around the superconducting transition. By tuning the doping level p continuously, we reveal that these low-field oscillations occur only when p < 0.1. The oscillation amplitude increases with decreasing p but the oscillation period stays almost constant. We show that these low-field oscillations can be well described by assuming a periodic superconducting structure with a mesh size of about 50 nm. Such a charge order, which is distinctly different from the well-established charge density wave and pair density wave, seems to be an unexpected piece of the puzzle on the correlated physics in cuprates.
Functional genomics of RAP proteins and their role in mitoribosome regulation in Plasmodium falciparum
Authors: Hollin Thomas , Abel Steven , Falla Alejandra , Pasaje Charisse Flerida A. , Bhatia Anil , Hur Manhoi , Kirkwood Jay S. , Saraf Anita , Prudhomme Jacques , De Souza Amancio , Florens Laurence , Niles Jacquin C. , Le Roch Karine G. 
Published: March 2022

AbstractThe RAP (RNA-binding domain abundant in Apicomplexans) protein family has been identified in various organisms. Despite expansion of this protein family in apicomplexan parasites, their main biological functions remain unknown. In this study, we use inducible knockdown studies in the human malaria parasite, Plasmodium falciparum, to show that two RAP proteins, PF3D7_0105200 (PfRAP01) and PF3D7_1470600 (PfRAP21), are essential for parasite survival and localize to the mitochondrion. Using transcriptomics, metabolomics, and proteomics profiling experiments, we further demonstrate that these RAP proteins are involved in mitochondrial RNA metabolism. Using high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (eCLIP-seq), we validate that PfRAP01 and PfRAP21 are true RNA-binding proteins and interact specifically with mitochondrial rRNAs. Finally, mitochondrial enrichment experiments followed by deep sequencing of small RNAs demonstrate that PfRAP21 controls mitochondrial rRNA expression. Collectively, our results establish the role of these RAP proteins in mitoribosome activity and contribute to further understanding this protein family in malaria parasites.
Loss of the Bardet-Biedl protein Bbs1 alters photoreceptor outer segment protein and lipid composition
Authors: Masek Markus , Etard Christelle , Hofmann Claudia , Hülsmeier Andreas J. , Zang Jingjing , Takamiya Masanari , Gesemann Matthias , Neuhauss Stephan C. F. , Hornemann Thorsten , Strähle Uwe , Bachmann-Gagescu Ruxandra 
Published: March 2022

AbstractPrimary cilia are key sensory organelles whose dysfunction leads to ciliopathy disorders such as Bardet-Biedl syndrome (BBS). Retinal degeneration is common in ciliopathies, since the outer segments (OSs) of photoreceptors are highly specialized primary cilia. BBS1, encoded by the most commonly mutated BBS-associated gene, is part of the BBSome protein complex. Using a bbs1 zebrafish mutant, we show that retinal development and photoreceptor differentiation are unaffected by Bbs1-loss, supported by an initially unaffected transcriptome. Quantitative proteomics and lipidomics on samples enriched for isolated OSs show that Bbs1 is required for BBSome-complex stability and that Bbs1-loss leads to accumulation of membrane-associated proteins in OSs, with enrichment in proteins involved in lipid homeostasis. Disruption of the tightly regulated OS lipid composition with increased OS cholesterol content are paralleled by early functional visual deficits, which precede progressive OS morphological anomalies. Our findings identify a role for Bbs1/BBSome in OS lipid homeostasis, suggesting a pathomechanism underlying retinal degeneration in BBS.
Long-range transport of 2D excitons with acoustic waves
Authors: Peng Ruoming , Ripin Adina , Ye Yusen , Zhu Jiayi , Wu Changming , Lee Seokhyeong , Li Huan , Taniguchi Takashi , Watanabe Kenji , Cao Ting , Xu Xiaodong , Li Mo 
Published: March 2022

AbstractExcitons are elementary optical excitation in semiconductors. The ability to manipulate and transport these quasiparticles would enable excitonic circuits and devices for quantum photonic technologies. Recently, interlayer excitons in 2D semiconductors have emerged as a promising candidate for engineering excitonic devices due to their long lifetime, large exciton binding energy, and gate tunability. However, the charge-neutral nature of the excitons leads to weak response to the in-plane electric field and thus inhibits transport beyond the diffusion length. Here, we demonstrate the directional transport of interlayer excitons in bilayer WSe2 driven by the propagating potential traps induced by surface acoustic waves (SAW). We show that at 100 K, the SAW-driven excitonic transport is activated above a threshold acoustic power and reaches 20 μm, a distance at least ten times longer than the diffusion length and only limited by the device size. Temperature-dependent measurement reveals the transition from the diffusion-limited regime at low temperature to the acoustic field-driven regime at elevated temperature. Our work shows that acoustic waves are an effective, contact-free means to control exciton dynamics and transport, promising for realizing 2D materials-based excitonic devices such as exciton transistors, switches, and transducers up to room temperature.
Alternative trastuzumab dosing strategies in HER2-positive early breast cancer are associated with patient out-of-pocket savings
Authors: Hsieh Po-Hung , Kacew Alec J. , Dreyer Marie , Serritella Anthony V. , Knoebel Randall W. , Strohbehn Garth W. , Ratain Mark J. 
Published: March 2022

AbstractPatients with breast cancer frequently experience financial hardship, often due to the high costs of anti-cancer drugs. We sought to develop alternative trastuzumab dosing strategies, compare their pharmacokinetic effectiveness to standard dosing, and assess the expected financial implications of transitioning to them. We extracted clinical data from the records of 135 retrospectively identified patients with HER2-positive early breast cancer at a single, urban comprehensive cancer center who were treated with trastuzumab between 2017 and 2019. We performed pharmacokinetic simulations on a range of trastuzumab dose levels and frequencies, assessing efficacy by trough trastuzumab concentration (Ctrough) and population and individual likelihoods of Ctrough exceeding trastuzumab minimum effective concentration (MEC). We performed deterministic financial modeling to estimate the treatment-associated financial savings from alternative dosing strategies. Trastuzumab maintenance doses of 4 mg/kg every 3 weeks (Q3W) and 6 mg/kg every 4 weeks (Q4W) had nearly identical probabilities of Ctrough being above MEC as standard of care 6 mg/kg every 3 weeks. In the primary financial analysis, both trastuzumab 4 mg/kg Q3W and 6 mg/kg Q4W were associated with significant drug- and administration-related out-of-pocket cost savings over the duration of therapy, ranging from $765 (neoadjuvant, Q4W) to $2791 (adjuvant, Q4W). In particular, Q4W trastuzumab increased savings related to lost wages and travel cost avoidance. Low-dose and reduced frequency trastuzumab in appropriately selected patients may significantly reduce total drug utilization and meaningfully reduce patient financial toxicity. Prospective clinical trials evaluating low-dose or reduced-frequency administration of therapeutic monoclonal antibodies are warranted and needed.
A pan-tissue DNA methylation atlas enables in silico decomposition of human tissue methylomes at cell-type resolution
Authors: Zhu Tianyu , Liu Jacklyn , Beck Stephan , Pan Sun , Capper David , Lechner Matt , Thirlwell Chrissie , Breeze Charles E. , Teschendorff Andrew E. 
Published: March 2022

AbstractBulk-tissue DNA methylomes represent an average over many different cell types, hampering our understanding of cell-type-specific contributions to disease development. As single-cell methylomics is not scalable to large cohorts of individuals, cost-effective computational solutions are needed, yet current methods are limited to tissues such as blood. Here we leverage the high-resolution nature of tissue-specific single-cell RNA-sequencing datasets to construct a DNA methylation atlas defined for 13 solid tissue types and 40 cell types. We comprehensively validate this atlas in independent bulk and single-nucleus DNA methylation datasets. We demonstrate that it correctly predicts the cell of origin of diverse cancer types and discovers new prognostic associations in olfactory neuroblastoma and stage 2 melanoma. In brain, the atlas predicts a neuronal origin for schizophrenia, with neuron-specific differential DNA methylation enriched for corresponding genome-wide association study risk loci. In summary, the DNA methylation atlas enables the decomposition of 13 different human tissue types at a high cellular resolution, paving the way for an improved interpretation of epigenetic data.
A long-term dataset of topography and nearshore bathymetry at the macrotidal pocket beach of Porsmilin, France
Authors: Bertin Stéphane , Floc’h France , Le Dantec Nicolas , Jaud Marion , Cancouët Romain , Franzetti Marcaurélio , Cuq Véronique , Prunier Christophe , Ammann Jérôme , Augereau Emmanuel , Lamarche Stevenn , Belleney Déborah , Rouan Mathias , David Laurence , Deschamps Anne , Delacourt Christophe , Suanez Serge 
Published: March 2022

AbstractLong-term datasets documenting the evolution of coastal forms and processes, through the provision of recurring beach as well as shoreface morphological observations and accompanying time-series of environmental controls, remain difficult to collect and are rarely made available. However, they are increasingly needed to further our understanding of coastal change and to improve the models that will help planning what our future coast will be. This data descriptor presents the results of topographic and bathymetric surveys at Porsmilin, a macrotidal embayed beach situated in Brittany, northwest France. The Porsmilin beach survey program was launched in January 2003 by the Institut Universitaire Européen de la Mer (IUEM/Univ. Brest) and is continuing today in the framework of the French coastal observation service SNO-DYNALIT. The dataset contains over 16 years of monthly beach profile surveys and a large collection of repeated high-resolution subtidal and subaerial digital elevation models (DEMs). The dataset is accompanied by time-series of inshore waves and water levels, and enriched metadata, that will facilitate its future reuse in coastal research.
Housing unit and urbanization estimates for the continental U.S. in consistent tract boundaries, 1940–2019
Authors: Markley Scott N. , Holloway Steven R. , Hafley Taylor J. , Hauer Mathew E. 
Published: March 2022

AbstractSubcounty housing unit counts are important for studying geo-historical patterns of (sub)urbanization, land-use change, and residential loss and gain. The most commonly used subcounty geographical unit for social research in the United States is the census tract. However, the changing geometries and historically incomplete coverage of tracts present significant obstacles for longitudinal analysis that existing datasets do not sufficiently address. Overcoming these barriers, we provide housing unit estimates in consistent 2010 tract boundaries for every census year from 1940 to 2010 plus 2019 for the entire continental US. Moreover, we develop an “urbanization year” indicator that denotes if and when tracts became “urbanized” during this timeframe. We produce these data by blending existing interpolation techniques with a novel procedure we call “maximum reabsorption.” Conducting out-of-sample validation, we find that our hybrid approach generally produces more reliable estimates than existing alternatives. The final dataset, Historical Housing Unit and Urbanization Database 2010 (HHUUD10), has myriad potential uses for research involving housing, population, and land-use change, as well as (sub)urbanization.
Global seasonal Sentinel-1 interferometric coherence and backscatter data set
Authors: Kellndorfer Josef , Cartus Oliver , Lavalle Marco , Magnard Christophe , Milillo Pietro , Oveisgharan Shadi , Osmanoglu Batu , Rosen Paul A. , Wegmüller Urs 
Published: March 2022

AbstractThis data set is the first-of-its-kind spatial representation of multi-seasonal, global C-band Synthetic Aperture Radar (SAR) interferometric repeat-pass coherence and backscatter signatures. Coverage comprises land masses and ice sheets from 82° Northern to 79° Southern latitudes. The data set is derived from multi-temporal repeat-pass interferometric processing of about 205,000 Sentinel-1 C-band SAR images acquired in Interferometric Wide-Swath Mode from 1-Dec-2019 to 30-Nov-2020. The data set encompasses three sets of seasonal (December-February, March-May, June-August, September-November) metrics produced with a pixel spacing of three arcseconds: 1) Median 6-, 12-, 18-, 24-, 36-, and 48-days repeat-pass coherence at VV or HH polarizations, 2) Mean radiometrically terrain corrected backscatter (γ0) at VV and VH, or HH and HV polarizations, and 3) Estimated parameters of an exponential coherence decay model. The data set has been produced to obtain global, spatially detailed information on how decorrelation affects interferometric measurements of surface displacement and is rich in spatial and temporal information for a variety of mapping applications.
A comprehensive catalogue of plant-pollinator interactions for Chile
Authors: Muschett Giselle , Fontúrbel Francisco E. 
Published: March 2022

AbstractPollinators and pollination services provide invaluable ecosystem services to agriculture and contribute to the maintenance of biodiversity. In Chile, pollination contributes greatly to the diversity of native ecosystems and provides ecosystem services to crops, but local pollinator abundance and diversity, as well as plant-animal interactions, remain poorly understood. We compiled all available information from the published scientific literature on pollinators, flower visitors, and plant-pollinator interactions in Chile and found 120 publications from which we extracted 2619 records. Those records contain locality, habit type, and establishment means of 357 plant species from 83 families. Thus, we built a database compiling information on their pollinators and flower visitors, including information on 492 pollinator species from 97 families and 13 orders. Our database provides the first systematisation of information about pollinators and pollination in Chile. This country relies heavily on pollinators both for its agricultural industry and its unique and highly endemic biodiversity. This information can be reused in future studies and would contribute significantly to pollinator conservation strategies.
A hybrid machine learning/deep learning COVID-19 severity predictive model from CT images and clinical data
Authors: Chieregato Matteo , Frangiamore Fabio , Morassi Mauro , Baresi Claudia , Nici Stefania , Bassetti Chiara , Bnà Claudio , Galelli Marco 
Published: March 2022

AbstractCOVID-19 clinical presentation and prognosis are highly variable, ranging from asymptomatic and paucisymptomatic cases to acute respiratory distress syndrome and multi-organ involvement. We developed a hybrid machine learning/deep learning model to classify patients in two outcome categories, non-ICU and ICU (intensive care admission or death), using 558 patients admitted in a northern Italy hospital in February/May of 2020. A fully 3D patient-level CNN classifier on baseline CT images is used as feature extractor. Features extracted, alongside with laboratory and clinical data, are fed for selection in a Boruta algorithm with SHAP game theoretical values. A classifier is built on the reduced feature space using CatBoost gradient boosting algorithm and reaching a probabilistic AUC of 0.949 on holdout test set. The model aims to provide clinical decision support to medical doctors, with the probability score of belonging to an outcome class and with case-based SHAP interpretation of features importance.