bluuebunny/crossref_metadata_2025_split huggingface dataset:
Data science competition for cross-site delineation and classification of individual trees from airborne remote sensing data
Authors: Graves Sarah Jane , Marconi Sergio , Stewart Dylan , Harmon Ira , Weinstein Ben G. , Kanazawa Yuzi , Scholl Victoria M , Joseph Maxwell B , McClinchy Joseph , Browne Luke , Sullivan Megan K , Estrada-Villegas Sergio , Tusa Eduardo , Wang Daisy Zhe , Singh Aditya , Bohlman Stephanie A , Zare Alina , White Ethan P. 
Published: August 2021

AbstractDelineating and classifying individual trees in remote sensing data is challenging. Many tree crown delineation methods have difficulty in closed-canopy forests and do not leverage multiple datasets. Methods to classify individual species are often accurate for common species, but perform poorly for less common species and when applied to new sites. We ran a data science competition to help identify effective methods for delineation of individual crowns and classification to determine species identity. This competition included data from multiple sites to assess the methods’ ability to generalize learning across multiple sites simultaneously, and transfer learning to novel sites where the methods were not trained. Six teams, representing 4 countries and 9 individual participants, submitted predictions. Methods from a previous competition were also applied and used as the baseline to understand whether the methods are changing and improving over time. The best delineation method was based on an instance segmentation pipeline, closely followed by a Faster R-CNN pipeline, both of which outperformed the baseline method. However, the baseline (based on a growing region algorithm) still performed well as did the Faster R-CNN. All delineation methods generalized well and transferred to novel forests effectively. The best species classification method was based on a two-stage fully connected neural network, which significantly outperformed the baseline (a random forest and Gradient boosting ensemble). The classification methods generalized well, with all teams training their models using multiple sites simultaneously, but the predictions from these trained models generally failed to transfer effectively to a novel site. Classification performance was strongly influenced by the number of field-based species IDs available for training the models, with most methods predicting common species well at the training sites. Classification errors (i.e., species misidentification) were most common between similar species in the same genus and different species that occur in the same habitat. The best methods handled class imbalance well and learned unique spectral features even with limited data. Most methods performed better than baseline in detecting new (untrained) species, especially in the site with no training data. Our experience further shows that data science competitions are useful for comparing different methods through the use of a standardized dataset and set of evaluation criteria, which highlights promising approaches and common challenges, and therefore advances the ecological and remote sensing field as a whole.
A flexible summary-based colocalization method with application to the mucin Cystic Fibrosis lung disease modifier locus
Authors: Wang Fan , Panjwani Naim , Wang Cheng , Sun Lei , Strug Lisa J 
Published: August 2021

AbstractMucus obstruction is a central feature in the Cystic Fibrosis (CF) airways. A genome-wide association study (GWAS) of lung disease by the CF Gene Modifier Consortium (CFGMC) identified a significant locus containing two mucin genes, MUC20 and MUC4. Expression quantitative trait locus (eQTL) analysis using human nasal epithelial (HNE) from 94 CF Canadians in the CFGMC demonstrated MUC4 eQTLs that mirrored the lung association pattern in the region, suggesting that MUC4 expression may mediate CF lung disease. Complications arose, however, with colocalization testing using existing methods: the locus is complex and the associated SNPs span a 0.2Mb region with high linkage disequilibrium and evidence of eQTLs for multiple genes and tissues (heterogeneity). We previously developed the Simple Sum (SS), a powerful colocalization test in regions with heterogeneity, but SS assumed eQTLs to be present to achieve type I error control. Here we propose a two-stage SS (SS2) colocalization test that avoids a prior eQTL assumptions, accounts for multiple hypothesis testing and the composite null hypothesis and enables meta-analysis. We compare SS2 to published approaches through simulation and demonstrate type I error control for all settings with the greatest power in the presence of high LD and heterogeneity. Applying SS2 to the MUC20/MUC4 CF lung disease locus with eQTLs from CF HNE revealed significant colocalization with MUC4 (p = 1.71×10−5) rather than MUC20. The SS2 is a powerful method to inform the responsible gene(s) at a locus and guide future functional studies. SS2 has been implemented in the application LocusFocus (locusfocus.research.sickkids.ca).
SIRPα sequesters SHP-2 to promote IL-4/13 signaling and alternative activation of macrophages
Authors: Shi Lei , Kidder Koby , Bian Zhen , Chiang Samantha Kuon Ting , Ouellette Corbett , Liu Yuan 
Published: August 2021

AbstractThe Th2 cytokines IL-4 and IL-13 through activation of their shared receptor IL-4Rα direct macrophage alternative activation to promote immunosuppression and wound healing. However, the mechanisms that control macrophage responses to IL-4/13 are not fully understood. Apart from driving JAK-STAT and PI3K-Akt pathways to polarize macrophages toward the alternative phenotype, the activated IL-4/13 receptors recruit negative regulators SHP-1 and SHP-2, which dephosphorylate IL-4Rα and decrease its signaling. Here we report that SIRPα spatially restricts SHP-2 and, by such, promotes IL-4/13 signaling and macrophage alternative activation. SIRPα executes this regulation via its cytoplasmic ITIMs/ITSMs that undergo phosphorylation by IL-4/13-induced, Src kinase-activated Bruton’s tyrosine kinase (Btk), resulting in recruitment of SHP-2 and preclusion of SHP-2 from binding to and inhibiting IL-4/13 receptors. Despite that this regulation occurs independent of CD47, extracellular CD47 ligation of SIRPα facilitates its cytoplasmic phosphorylation and SHP-2 sequestration, leading to stronger IL-4/13 signaling and enhanced macrophage expression of IL-10, TGFβ, CD206, arginase-1, etc. Conversely, deficiency of SIRPα allows SHP-2 to freely bind to γC or IL-13Rα1 and through which dephosphorylate IL-4Rα, dampening its signaling. Consistent with these findings, impaired wound healing in Sirpα−/−mice under experimental colitis correlated with a deficit of immunosuppressive macrophages in the colon, a condition that was corrected by transfusion of ex vivo-produced SIRPαhighalternatively activated macrophages.
SARS-CoV-2 vaccine effectiveness in immunosuppressed kidney transplant recipients
Authors: Chemaitelly Hiam , AlMukdad Sawsan , Joy Jobin Paravila , Ayoub Houssein H. , Yassine Hadi M. , Benslimane Fatiha M. , Al Khatib Hebah A. , Tang Patrick , Hasan Mohammad R. , Coyle Peter , Al Kanaani Zaina , Al Kuwari Einas , Jeremijenko Andrew , Kaleeckal Anvar Hassan , Latif Ali Nizar , Shaik Riyazuddin Mohammad , Abdul Rahim Hanan F. , Nasrallah Gheyath K. , Al Kuwari Mohamed Ghaith , Butt Adeel A. , Al Romaihi Hamad Eid , Al-Thani Mohamed H. , Alkadi Mohamad M. , Ali Omar , Al-Maslamani Muna , Bertollini Roberto , Al Malki Hassan , Almaslamani Yousuf , Abu-Raddad Laith J. , Al Khal Abdullatif 
Published: August 2021

AbstractCOVID-19 vaccine protection against infection in immunosuppressed solid organ transplant recipients is unknown but possibly weak with the low proportion of these patients mounting a robust humoral and cellular immune response after vaccination. Using a retrospective cohort study design with cross-over, we assessed vaccine effectiveness among 782 kidney transplant recipients registered at Hamad Medical Corporation, the national public healthcare provider in Qatar, where the BNT162b2 (Pfizer-BioNTech) and mRNA-1273 (Moderna) vaccines have been used in the national immunization campaign. Vaccine effectiveness against any SARS-CoV-2 infection was estimated at 46.6% (95% CI: 0.0-73.7%) ≥14 days after the second dose, 66.0% (95% CI: 21.3-85.3%) ≥42 days after the second dose, and 73.9% (95% CI: 33.0-89.9%) ≥56 days after the second dose. Vaccine effectiveness against any severe, critical, or fatal COVID-19 disease was estimated at 72.3% (95% CI: 0.0-90.9%) ≥14 days after the second dose, 85.0% (95% CI: 35.7-96.5%) ≥42 days after the second dose, and 83.8% (95% CI: 31.3-96.2%) ≥56 days after the second dose. Most vaccine breakthrough infections occurred in the first few weeks after receiving the first and/or second dose. Vaccine effectiveness reached considerable levels in kidney transplant recipients, but vaccine protection mounted slowly and did not reach a high level until several weeks after the second dose.
MAVS expression in alveolar macrophages is essential for host resistance against Aspergillus fumigatus
Authors: Wang Xi , Cunha Cristina , Grau Madeleine S. , Robertson Shelly J. , Lacerda João F. , Campos António , Lagrou Katrien , Maertens Johan , Best Sonja M. , Carvalho Agostinho , Obar Joshua J. 
Published: August 2021

ABSTRACTOur recent data demonstrates a critical role of the RIG-I-like receptor (RLR) family in regulating antifungal immunity against Aspergillus fumigatus in a murine model. However, the importance of this pathway in humans and the cell type(s) which utilize this innate immune receptor to detect A. fumigatus remains unresolved. Here using patients who underwent hematopoietic stem cell transplantation (HSCT), we demonstrate that a polymorphism in human MAVS present in the donor genome was associated with the incidence of invasive pulmonary aspergillosis (IPA). Moreover, in a separate cohort of confirmed IPA patients, polymorphisms in the IFIH1 gene alter the inflammatory response, including interferon-responsive chemokines. Returning to our murine model, we now demonstrate that CD11c+ SiglecF+ alveolar macrophages require Mavs expression to maintain host resistance against A. fumigatus. Our data support the role of MAVS signaling in mediating antifungal immunity in both mice and human at least in part through the role of MAVS-dependent signaling in alveolar macrophages.
Classifying Radiology Abstracts with Deep Learning
Authors: Chen Hongyu , Shih George 
Published: August 2021

AbstractBackgroundThe Radiological Society of North America (RSNA) receives more than 8000 abstracts yearly for scientific presentations, scientific posters, and scientific papers. Each abstract is assigned manually one of 16 top-level categories (e.g. “Breast Imaging”) for workflow purposes. Additionally, each abstract receives a grade from 1-10 based on a variety of subjective factors such as style and perceived writing quality. Using machine learning to automate, at least partially, the categorization of abstract submissions can result in saving many hours of manual labor.MethodsA total of 45527 RSNA abstract submissions from 2014 through 2019 were ingested, tokenized, and pre-processed with a standard natural language programming protocol. A bag-of-words (BOW) model was used as a baseline to evaluate two more sophisticated models, convolutional neural networks and recurrent neural networks, and also evaluate an ensemble model featuring all three neural networks.Resultsensemble model was able to achieve 73% testing accuracy for classifying the 16 top-level categories, outperforming all other models. The top model for classifying abstract grade was also an ensemble model, achieving a mean average error (MAE) of 1.01.ConclusionWhile the baseline BOW model was the highest performing individual classifier, ensemble models that included state-of-the-art neural networks were able to outperform it. Our research shows that machine learning techniques can, to a reasonable degree of accuracy, predict both objective factors such as abstract category as well as subjective factors such as abstract grade. This work builds upon previous research involving using natural language processing on scientific abstracts to make useful inferences that address a meaningful problem.
Speeding and Traffic-Related Injuries and Fatalities during the 2020 COVID-19 Pandemic: The Cases of Seattle and New York City
Authors: Liao Felix Haifeng , Lowry Michael 
Published: August 2021

ABSTRACTDespite fewer cars on roads during the COVID-19 pandemic, deaths associated with motor vehicle collisions in New York City and Seattle remained largely unchanged in 2020. Using police data on weekly counts of collisions, we compared trends in 2020 with those of 2019, while controlling for the reduction of traffic volumes and seasonal weather conditions. Results of difference-in-differences estimation suggest that during the early months of the pandemic, or March-May, the incidence rates of severe or fatal injury crashes related to speeding increased by nearly 8 times in Seattle and more than 4 times in New York City. In the rest of 2020, they were still significantly higher than what would be expected in the absence of the pandemic. This research suggests that in similar situations that depress travel demand (e.g., another pandemic), policymakers should formulate plans to reduce speeding which may prevent an upswing in severe injuries and fatalities.
T cell responses to SARS-CoV-2 in people with and without neurologic symptoms of long COVID
Authors: Visvabharathy Lavanya , Hanson Barbara A. , Orban Zachary S. , Lim Patrick H. , Palacio Nicole M. , Jimenez Millenia , Clark Jeffrey R. , Graham Edith L. , Liotta Eric M. , Tachas George , Penaloza-MacMaster Pablo , Koralnik Igor J. 
Published: August 2021

AbstractMany people experiencing long COVID syndrome, or post-acute sequelae of SARS-CoV-2 infection (PASC), suffer from debilitating neurologic symptoms (Neuro-PASC). However, whether virus-specific adaptive immunity is affected in Neuro-PASC patients remains poorly understood. We report that Neuro-PASC patients exhibit distinct immunological signatures composed of elevated humoral and cellular responses toward SARS-CoV-2 Nucleocapsid protein at an average of 6 months post-infection compared to healthy COVID convalescents. Neuro-PASC patients also had enhanced virus-specific production of IL-6 from and diminished activation of CD8+T cells. Furthermore, the severity of cognitive deficits or quality of life disturbances in Neuro-PASC patients were associated with a reduced diversity of effector molecule expression in T cells but elevated IFN-γ production to the C-terminal domain of Nucleocapsid protein. Proteomics analysis showed enhanced plasma immunoregulatory proteins and reduced pro-inflammatory and antiviral response proteins in Neuro-PASC patients compared with healthy COVID convalescents, which were also correlated with worse neurocognitive dysfunction. These data provide new insight into the pathogenesis of long COVID syndrome and a framework for the rational design of predictive biomarkers and therapeutic interventions.One Sentence SummaryAdaptive immunity is altered in patients with neurologic manifestations of long COVID.
Tankyrase interacts with the allosteric site of glucokinase and inhibits its glucose-sensing function in the beta cell
Authors: Chi Nai-Wen , Eisemann Travis , Yeh Tsung-Yin J. , Roy Swati , Chi Tyler J. , Lu Sunny H. , Pascal John M. , Osborn Olivia 
Published: August 2021

ABSTRACTInsulin secretion in the pancreatic beta cell is rate-limited by glucokinase (GCK), the glucose sensor that catalyzes the first step of glucose metabolism. GCK consists of two lobes connected by a flexible hinge that allows the kinase to exhibit a spectrum of conformations ranging from the active, closed form to several inactive, less-compact forms. Activating GCK mutations can cause hyperinsulinemia and hypoglycemia in infants. A similar phenotype exhibited by tankyrase (TNKS)-deficient mice prompted us to investigate whether TNKS might modulate the glucose-sensing function of GCK. We found that TNKS colocalizes and directly interacts with GCK. Their interaction is mediated by two ankyrin-repeat clusters (ARC-2 and −5) in TNKS and a tankyrase-binding motif (TBM, aa 63-68) in the GCK hinge. This interaction is conformation sensitive, human GCK variants that cause hyperglycemia (V62M) or hypoglycemia (S64Y) enhance or diminish the interaction respectively, even though they have no impact on TNKS interaction in the context of a GCK peptide (V62M) or a peptide library (S64Y). Moreover, the TNKS-GCK interaction is inhibited by high glucose concentrations, which are known to stabilize GCK in the active (closed, glucose-avid) conformation. Conversely, glucose phosphorylation by GCK in vitro is inhibited by TNKS. To study this in vitro inhibitory effect in the MIN6 beta cells, we showed that glucose-stimulated insulin secretion is suppressed upon stabilization of the TNKS protein and is conversely enhanced upon TNKS knockdown. Based on these findings as well as by contrasting with hexokinase-2, we propose that TNKS is a physiological GCK inhibitor in pancreatic beta cells that acts by trapping the kinase in the open (inactive) conformation.
Mechanisms of ecological divergence with gene flow in a reef-building coral on an isolated atoll in Western Australia
Authors: Thomas L , Underwood JN , Rose NH , Fuller ZL , Richards ZT , Dugal L , Grimaldi C , Cooke IR , Palumbi SR , Gilmour JP 
Published: August 2021

AbstractUnderstanding the mechanisms driving phenotypic variation in traits facing intensified selection from climate change is a crucial step in developing effective conservation and restoration initiatives. This is particularly true for reef-building corals, which are among the most vulnerable to climate change and are in dramatic decline globally. At the Rowley Shoals in Western Australia, the prominent reef flat becomes exposed on low tide and the stagnant water in the shallow atoll lagoons heats up, creating a natural laboratory for characterising the mechanisms that control phenotypic responses to different environments. We combined whole genome re-sequencing, common garden heat stress experiments, transcriptome-wide gene expression analyses, and symbiont metabarcoding to explore the mechanisms that facilitate survival in contrasting habitat conditions. Our data show that, despite high gene flow between habitats, spatially varying selection drives subtle shifts in allele frequencies at hundreds of loci. These changes were concentrated into several islands of divergence spanning hundreds of SNPs that showed strong linkage disequilibrium and were associated with a coordinated increase in minor allele frequencies in corals taken from the lagoon habitat, where the range of environmental conditions is greatest. Common garden heat stress assays showed individuals from the lagoon exhibited higher bleaching resistance than colonies from the reef slope, and RNAseq identified pronounced physiological differences between the corals from the two habitats, primarily associated with molecular pathways including cell signalling, ion transport and metabolism. Despite the pronounced physioloigical and environmental differences between habitats, metabarcoding of theSymbiodiniaceaeITS2 region revealed all colonies to be associated exclusively with the genusCladocopium, with no detectable differences between habitats. This study contributes to the growing number of studies documenting the complex mechanisms that facilitate coral survival in extreme environments, and showcases the utility of combining multiple sequencing techniques to unravel complex climate-related traits.
Extent and complexity of RNA processing in the development of honey bee queen and worker castes revealed by Nanopore direct RNA sequencing
Authors: He Xu Jiang , Barron Andrew B. , Yang Liu , Chen Hu , He Yu Zhu , Zhang Li Zhen , Huang Qiang , Wang Zi Long , Wu Xiao Bo , Yan Wei Yu , Zeng Zhi Jiang 
Published: August 2021

AbstractThe distinct honey bee (Apis mellifera) worker and queen castes have become a model for the study of genomic mechanisms of phenotypic plasticity. Prior studies have explored differences in gene expression and methylation during development of the two castes, but thus far no study has performed a genome-wide analysis of differences in RNA processing. To address this here we performed a Nanopore-based direct RNA sequencing with exceptionally long reads to compare the mRNA transcripts between honey bee queen and workers at three points during their larval development. We found thousands of significantly differentially expressed isoforms (DEIs) between queen and worker larvae. Most DEIs contained alternative splicing, and many of them contained at least two types of alternative splicing patterns, indicating complex RNA processing in honey bee caste differentiation. We found a negative correlation between poly(A) length and DEI expression, suggesting that poly(A) tails participate in the regulation of isoform expression. Hundreds of isoforms uniquely expressed in either queens or workers during their larval development, and isoforms were expressed at different points in queen and worker larval development demonstrating a dynamic relationship between isoform expression and developmental mechanisms. These findings show the full complexity of RNA processing and transcript expression in honey bee phenotypic plasticity.
Segregation of neural crest specific lineage trajectories from a heterogeneous neural plate border territory only emerges at neurulation
Authors: Williams Ruth M , Lukoseviciute Martyna , Sauka-Spengler Tatjana , Bronner Marianne E 
Published: August 2021

AbstractThe epiblast of vertebrate embryos is comprised of neural and non-neural ectoderm, with the border territory at their intersection harbouring neural crest and cranial placode progenitors. Here we profile avian epiblast cells as a function of time using single-cell RNA-seq to define transcriptional changes in the emerging ‘neural plate border’. The results reveal gradual establishment of heterogeneous neural plate border signatures, including novel genes that we validate by fluorescent in situ hybridisation. Developmental trajectory analysis shows that segregation of neural plate border lineages only commences at early neurulation, rather than at gastrulation as previously predicted. We find that cells expressing the prospective neural crest marker Pax7 contribute to multiple lineages, and a subset of premigratory neural crest cells shares a transcriptional signature with their border precursors. Together, our results suggest that cells at the neural plate border remain heterogeneous until early neurulation, at which time progenitors become progressively allocated toward defined lineages.