bluuebunny/crossref_metadata_2025_split huggingface dataset:
Non‐Local Triggering in Rock Fracture
Authors: Xiong Qiquan , Hampton Jesse C. 
Published: September 2020

AbstractCombining multiphysics observations in the laboratory, we present novel phenomena for the analogue between rock fracture and seismicity. We show, for the first time in a laboratory setting, how a large‐scale flaw in rock can facilitate “non‐local triggering”—remotely triggered damage in rock mass. Results prove analogues of rock fracture evolution to natural seismicity including several lab‐analogues on seismicity model predictions beyond power law. We observe under specimen‐scale criticality a relatively small AE perturbation occurring at a seemingly random location can trigger cascading events whose spatial span can traverse the entire rock fracture system. The inclination angle of the non‐local triggering pairs shows dependence on the large‐scale flaw, and the subsequent generations of triggered AEs by these non‐local triggers decline significantly slower than that of the general triggers. The rock fracture system evolves to a state where the resistance to non‐local triggering continuously reduces, bridging the gap between an idealized lab setting and a natural fault. The non‐locally triggered events can also be reactivated as the rock fracture system evolves towards increased complexity. These lab‐observations as well as the understanding on the analogue relationship between rock fracture and seismicity may shed new light on the insight of the periodical, dynamic, and unpredictable nature of the multiscale rock fracture process.
Characterization of Surface Heterogeneity‐Induced Convection Using Cluster Analysis
Authors: Chen Jingyi , Hagos Samson , Xiao Heng , Fast Jerome D. , Feng Zhe 
Published: September 2020

AbstractLand‐atmosphere interactions and boundary layer processes often control the formation of shallow clouds and subsequently deep convective precipitation over the U.S. Southern Great Plains. In this study, we examine the impacts of large‐scale advection on the cloud populations and land‐atmospheric coupling observed during the Holistic Interactions of Shallow Clouds, Aerosols, and Land‐Ecosystems field campaign in 2016. We performed two large eddy simulations using the Weather Research and Forecasting Model for a day in which the transition from clear‐sky to shallow precipitating clouds and isolated deep convection was observed. The control simulation reproduced the overall distribution of cloud populations by using realistic soil conditions with an interactive land model. In the sensitivity simulation where large‐scale advection is removed, a strong relationship between the land and boundary layer is found. To study the timing, location, and intensity of convective initiation and the relationship of clouds with land surface properties, a cluster analysis of equivalent potential temperature is performed for the simulation without large‐scale advection. That analysis shows that convective clouds first form over regions with higher surface sensible heat flux. Precipitation from those convective clouds likely triggers new updrafts nearby about 2 hr later through the lifting associated with cold pools. The cluster analysis also shows that in addition to the spatial pattern of soil moisture, land use and soil texture in western Oklahoma also influence the location of convective initiation.
The cross-talk between methylation and phosphorylation in lymphoid-specific helicase drives cancer stem-like properties
Authors: Liu Na , Yang Rui , Shi Ying , Chen Ling , Liu Yating , Wang Zuli , Liu Shouping , Ouyang Lianlian , Wang Haiyan , Lai Weiwei , Mao Chao , Wang Min , Cheng Yan , Liu Shuang , Wang Xiang , Zhou Hu , Cao Ya , Xiao Desheng , Tao Yongguang 
Published: September 2020

AbstractPosttranslational modifications (PTMs) of proteins, including chromatin modifiers, play crucial roles in the dynamic alteration of various protein properties and functions including stem-cell properties. However, the roles of Lymphoid-specific helicase (LSH), a DNA methylation modifier, in modulating stem-like properties in cancer are still not clearly clarified. Therefore, exploring PTMs modulation of LSH activity will be of great significance to further understand the function and activity of LSH. Here, we demonstrate that LSH is capable to undergo PTMs, including methylation and phosphorylation. The arginine methyltransferase PRMT5 can methylate LSH at R309 residue, meanwhile, LSH could as well be phosphorylated by MAPK1 kinase at S503 residue. We further show that the accumulation of phosphorylation of LSH at S503 site exhibits downregulation of LSH methylation at R309 residue, which eventually promoting stem-like properties in lung cancer. Whereas, phosphorylation-deficient LSH S503A mutant promotes the accumulation of LSH methylation at R309 residue and attenuates stem-like properties, indicating the critical roles of LSH PTMs in modulating stem-like properties. Thus, our study highlights the importance of the crosstalk between LSH PTMs in determining its activity and function in lung cancer stem-cell maintenance.
Direct interactions with commensal streptococci modify intercellular communication behaviors of Streptococcus mutans
Authors: Kaspar Justin R , Lee Kyulim , Richard Brook , Walker Alejandro R , Burne Robert A 
Published: September 2020

Abstract
The formation of dental caries is a complex process that ultimately leads to damage of the tooth enamel from acids produced by microbes in attached biofilms. The bacterial interactions occurring within these biofilms between cariogenic bacteria, such as the mutans streptococci, and health-associated commensal streptococci, are thought to be critical determinants of health and disease. To better understand these interactions, a Streptococcus mutans reporter strain that actively monitors cell–cell communication via peptide signaling was cocultured with different commensal streptococci. Signaling by S. mutans, normally highly active in monoculture, was completely inhibited by several species of commensals, but only when the bacteria were in direct contact with S. mutans. We identified a novel gene expression pattern that occurred in S. mutans when cultured directly with these commensals. Finally, mutant derivatives of commensals lacking previously shown antagonistic gene products displayed wild-type levels of signal inhibition in cocultures. Collectively, these results reveal a novel pathway(s) in multiple health-associated commensal streptococci that blocks peptide signaling and induces a common contact-dependent pattern of differential gene expression in S. mutans. Understanding the molecular basis for this inhibition will assist in the rational design of new risk assessments, diagnostics, and treatments for the most pervasive oral infectious diseases.
Gene loss through pseudogenization contributes to the ecological diversification of a generalist Roseobacter lineage
Authors: Chu Xiao , Li Siyao , Wang Sishuo , Luo Danli , Luo Haiwei 
Published: September 2020

Abstract
Ecologically relevant genes generally show patchy distributions among related bacterial genomes. This is commonly attributed to lateral gene transfer, whereas the opposite mechanism—gene loss—has rarely been explored. Pseudogenization is a major mechanism underlying gene loss, and pseudogenes are best characterized by comparing closely related genomes because of their short life spans. To explore the role of pseudogenization in microbial ecological diversification, we apply rigorous methods to characterize pseudogenes in the 279 newly sequenced Ruegeria isolates of the globally abundant Roseobacter group collected from two typical coastal habitats in Hong Kong, the coral Platygyra acuta and the macroalga Sargassum hemiphyllum. Pseudogenes contribute to ~16% of the accessory genomes of these strains. Ancestral state reconstruction reveals that many pseudogenization events are correlated with ancestral niche shifts. Specifically, genes related to resource scavenging and energy acquisition were often pseudogenized when roseobacters inhabiting carbon-limited and energy-poor coral skeleton switched to other resource-richer niches. For roseobacters inhabiting the macroalgal niches, genes for nitrogen regulation and carbohydrate utilization were important but became dispensable upon shift to coral skeleton where nitrate is abundant but carbohydrates are less available. Whereas low-energy-demanding secondary transporters are more favorable in coral skeleton, ATP-driven primary transporters are preferentially kept in the energy-replete macroalgal niches. Moreover, a large proportion of these families mediate organismal interactions, suggesting their rapid losses by pseudogenization as a potential response to host and niche shift. These findings illustrate an important role of pseudogenization in shaping genome content and driving ecological diversification of marine roseobacters.
Fluoxetine-induced recovery of serotonin and norepinephrine projections in a mouse model of post-stroke depression
Authors: Zahrai Amin , Vahid-Ansari Faranak , Daigle Mireille , Albert Paul R. 
Published: September 2020

AbstractChronic treatment with fluoxetine (FLX) is required for its antidepressant effects, but the role of serotonin (5-HT) axonal plasticity in FLX action is unknown. To address this, we examined mice with a stroke in the left medial prefrontal cortex (mPFC) resulting in persistent anxiety-like and depression-like behaviors and memory deficits as a model of post-stroke depression. Chronic treatment with FLX (but not exercise) completely reversed the behavioral phenotype and partially reversed changes in FosB-labeled cells in the mPFC, nucleus accumbens, septum, hippocampus, basolateral amygdala (BLA), and dorsal raphe. In these regions, 5-HT or norepinephrine (NE) innervation was quantified by staining for 5-HT or NE transporters, respectively. 5-HT synapses and synaptic triads were identified as synaptophysin-stained sites on 5-HT axons located proximal to gephyrin-stained or PSD95-stained spines. A week after stroke, 5-HT innervation was greatly reduced at the stroke site (left cingulate gyrus (CG) of the mPFC) and the left BLA. Chronically, 5-HT and NE innervation was reduced at the left CG, nucleus accumbens, and BLA, with no changes in other regions. In these areas, pre-synaptic and post-synaptic 5-HT synapses and triads to inhibitory (gephyrin+) sites were reduced, while 5-HT contacts at excitatory (PSD95+) sites were reduced in the CG and prelimbic mPFC. Chronic FLX, but not exercise, reversed these reductions in 5-HT innervation but incompletely restored NE projections. Changes in 5-HT innervation were verified using YFP staining in mice expressing YFP-tagged channelrhodopsin in 5-HT neurons. Thus, FLX-induced 5-HT axonal neuroplasticity of forebrain projections may help mediate recovery from brain injury.
STING regulates BCR signaling in normal and malignant B cells
Authors: Tang Chih-Hang Anthony , Lee Avery C. , Chang Shiun , Xu Qin , Shao Andong , Lo Yun , Spalek Walker T. , Pinilla-Ibarz Javier A. , Del Valle Juan R. , Hu Chih-Chi Andrew 
Published: September 2020

AbstractSTING is an endoplasmic reticulum (ER)-resident protein critical for sensing cytoplasmic DNA and promoting the production of type I interferons; however, the role of STING in B cell receptor (BCR) signaling remains unclear. We generated STING V154M knock-in mice and showed that B cells carrying constitutively activated STING specifically degraded membrane-bound IgM, Igα, and Igβ via SEL1L/HRD1-mediated ER-associated degradation (ERAD). B cells with activated STING were thus less capable of responding to BCR activation by phosphorylating Igα and Syk than those without activated STING. When immunized with T-independent antigens, STING V154M mice produced significantly fewer antigen-specific plasma cells and antibodies than immunized wild-type (WT) mice. We further generated B cell-specific STINGKO mice and showed that STINGKO B cells indeed responded to activation by transducing stronger BCR signals than their STING-proficient counterparts. When B cell-specific STINGKO mice were T-independently immunized, they produced significantly more antigen-specific plasma cells and antibodies than immunized STINGWT mice. Since both human and mouse IGHV-unmutated malignant chronic lymphocytic leukemia (CLL) cells downregulated the expression of STING, we explored whether STING downregulation could contribute to the well-established robust BCR signaling phenotype in malignant CLL cells. We generated a STING-deficient CLL mouse model and showed that STING-deficient CLL cells were indeed more responsive to BCR activation than their STING-proficient counterparts. These results revealed a novel B cell-intrinsic role of STING in negatively regulating BCR signaling in both normal and malignant B cells.
Clinical development of CAR T cell therapy in China: 2020 update
Authors: Wei Jianshu , Guo Yelei , Wang Yao , Wu Zhiqiang , Bo Jian , Zhang Bin , Zhu Jun , Han Weidong 
Published: September 2020

AbstractChimeric antigen receptor (CAR) T-cell therapy has achieved significant success in the treatment of hematological malignancies. In recent years, fast-growing CAR T clinical trials have actively explored their potential application scenarios. According to the data from the clinicaltrials.gov website, China became the country with the most registered CAR T trials in September 2017. As of June 30, 2020, the number of registered CAR T trials in China has reached 357. In addition, as many as 150 other CAR T trials have been registered on ChiCTR. Although CAR T therapy is flourishing in China, there are still some problems that cannot be ignored. In this review, we aim to systematically summarize the clinical practice of CAR T-cell therapy in China. This review will provide an informative reference for colleagues in the field, and a better understanding of the history and current situation will help us more reasonably conduct research and promote cooperation.
The use of mobile phone data to inform analysis of COVID-19 pandemic epidemiology
Authors: Grantz Kyra H. , Meredith Hannah R. , Cummings Derek A. T. , Metcalf C. Jessica E. , Grenfell Bryan T. , Giles John R. , Mehta Shruti , Solomon Sunil , Labrique Alain , Kishore Nishant , Buckee Caroline O. , Wesolowski Amy 
Published: September 2020

AbstractThe ongoing coronavirus disease 2019 (COVID-19) pandemic has heightened discussion of the use of mobile phone data in outbreak response. Mobile phone data have been proposed to monitor effectiveness of non-pharmaceutical interventions, to assess potential drivers of spatiotemporal spread, and to support contact tracing efforts. While these data may be an important part of COVID-19 response, their use must be considered alongside a careful understanding of the behaviors and populations they capture. Here, we review the different applications for mobile phone data in guiding and evaluating COVID-19 response, the relevance of these applications for infectious disease transmission and control, and potential sources and implications of selection bias in mobile phone data. We also discuss best practices and potential pitfalls for directly integrating the collection, analysis, and interpretation of these data into public health decision making.
Genetic variant effects on gene expression in human pancreatic islets and their implications for T2D
Authors: Viñuela Ana , Varshney Arushi , van de Bunt Martijn , Prasad Rashmi B. , Asplund Olof , Bennett Amanda , Boehnke Michael , Brown Andrew A. , Erdos Michael R. , Fadista João , Hansson Ola , Hatem Gad , Howald Cédric , Iyengar Apoorva K. , Johnson Paul , Krus Ulrika , MacDonald Patrick E. , Mahajan Anubha , Manning Fox Jocelyn E. , Narisu Narisu , Nylander Vibe , Orchard Peter , Oskolkov Nikolay , Panousis Nikolaos I. , Payne Anthony , Stitzel Michael L. , Vadlamudi Swarooparani , Welch Ryan , Collins Francis S. , Mohlke Karen L. , Gloyn Anna L. , Scott Laura J. , Dermitzakis Emmanouil T. , Groop Leif , Parker Stephen C. J. , McCarthy Mark I. 
Published: September 2020

AbstractMost signals detected by genome-wide association studies map to non-coding sequence and their tissue-specific effects influence transcriptional regulation. However, key tissues and cell-types required for functional inference are absent from large-scale resources. Here we explore the relationship between genetic variants influencing predisposition to type 2 diabetes (T2D) and related glycemic traits, and human pancreatic islet transcription using data from 420 donors. We find: (a) 7741 cis-eQTLs in islets with a replication rate across 44 GTEx tissues between 40% and 73%; (b) marked overlap between islet cis-eQTL signals and active regulatory sequences in islets, with reduced eQTL effect size observed in the stretch enhancers most strongly implicated in GWAS signal location; (c) enrichment of islet cis-eQTL signals with T2D risk variants identified in genome-wide association studies; and (d) colocalization between 47 islet cis-eQTLs and variants influencing T2D or glycemic traits, including DGKB and TCF7L2. Our findings illustrate the advantages of performing functional and regulatory studies in disease relevant tissues.
Evidence corroborates identity of isolated fossil feather as a wing covert of Archaeopteryx
Authors: Carney Ryan M. , Tischlinger Helmut , Shawkey Matthew D. 
Published: September 2020

AbstractThe historic fossil feather from the Jurassic Solnhofen has played a pivotal but controversial role in our evolutionary understanding of dinosaurs and birds. Recently, a study confirmed the diagnostic morphology of the feather’s original calamus, but nonetheless challenged the proposed identity as an Archaeopteryx covert. However, there are errors in the results and interpretations presented. Here we show that the feather is most likely an upper major primary covert, based on its long calamus (23.3% total length) and eight other anatomical attributes. Critically, this hypothesis is independently supported by evidence of similar primary coverts in multiple specimens of Archaeopteryx–including from the same fossil site and horizon as the isolated feather. We also provide additional insights, such as an updated colour reconstruction of the entire feather as matte black, with 90% probability. Given the isolated nature of the fossil feather, we can never know the anatomical and taxonomic provenance with 100% certainty. However, based on all available evidence, the most empirical and parsimonious conclusion is that this feather represents a primary covert from the ancient wing of Archaeopteryx.
Contact lenses, the reverse Pulfrich effect, and anti-Pulfrich monovision corrections
Authors: Rodriguez-Lopez Victor , Dorronsoro Carlos , Burge Johannes 
Published: September 2020

AbstractInterocular differences in image blur can cause processing speed differences that lead to dramatic misperceptions of the distance and three-dimensional direction of moving objects. This recently discovered illusion—the reverse Pulfrich effect—is caused by optical conditions induced by monovision, a common correction for presbyopia. Fortunately, anti-Pulfrich monovision corrections, which darken the blurring lens, can eliminate the illusion for many viewing conditions. However, the reverse Pulfrich effect and the efficacy of anti-Pulfrich corrections have been demonstrated only with trial lenses. This situation should be addressed, for clinical and scientific reasons. First, it is important to replicate these effects with contact lenses, the most common method for delivering monovision. Second, trial lenses of different powers, unlike contacts, can cause large magnification differences between the eyes. To confidently attribute the reverse Pulfrich effect to interocular optical blur differences, and to ensure that previously reported effect sizes are reliable, one must control for magnification. Here, in a within-observer study with five separate experiments, we demonstrate that (1) contact lenses and trial lenses induce indistinguishable reverse Pulfrich effects, (2) anti-Pulfrich corrections are equally effective when induced by contact and trial lenses, and (3) magnification differences do not cause or impact the Pulfrich effect.
A non-lethal method for detection of Bonamia ostreae in flat oyster (Ostrea edulis) using environmental DNA
Authors: Jørgensen Louise von Gersdorff , Nielsen Johan Wedel , Villadsen Mikkel Kehler , Vismann Bent , Dalvin Sussie , Mathiessen Heidi , Madsen Lone , Kania Per Walter , Buchmann Kurt 
Published: September 2020

AbstractSurveillance and diagnosis of parasitic Bonamia ostreae infections in flat oysters (Ostrea edulis) are prerequisites for protection and management of wild populations. In addition, reliable and non-lethal detection methods are required for selection of healthy brood oysters in aquaculture productions. Here we present a non-lethal diagnostic technique based on environmental DNA (eDNA) from water samples and demonstrate applications in laboratory trials. Forty oysters originating from Limfjorden, Denmark were kept in 30 ppt sea water in individual tanks. Water was sampled 6 days later, after which all oysters were euthanized and examined for infection, applying PCR. Four oysters (10%) were found to be infected with B. ostreae in gill and mantle tissue. eDNA purified from the water surrounding these oysters contained parasite DNA. A subsequent sampling from the field encompassed 20 oysters and 15 water samples from 5 different locations. Only one oyster turned out positive and all water samples proved negative for B. ostreae eDNA. With this new method B. ostreae may be detected by only sampling water from the environment of isolated oysters or isolated oyster populations. This non-lethal diagnostic eDNA method could have potential for future surveys and oyster breeding programs aiming at producing disease-free oysters.
Identification of the dog orthologue of human MAS-related G protein coupled receptor X2 (MRGPRX2) essential for drug-induced pseudo-allergic reactions
Authors: Hamamura-Yasuno Eri , Iguchi Takuma , Kumagai Kazuyoshi , Tsuchiya Yoshimi , Mori Kazuhiko 
Published: September 2020

AbstractMAS-related G protein coupled receptor-X2 (MRGPRX2), expressed in human mast cells, is associated with drug-induced pseudo-allergic reactions. Dogs are highly susceptible to drug-induced anaphylactoid reactions caused by various drugs; however, the distribution and physiological function of canine MRGPR family genes, including MRGPRX2, remain largely unknown. In the present study, we clarified the distribution of dog MRGPR family genes by real-time quantitative PCR and in situ hybridisation. We also investigated the stimulatory effects of various histamine-releasing agents, including fluoroquinolones, on HEK293 cells transiently transfected with dog MRGPR family genes to identify their physiological function. Dog MRGPRX2 and MRGPRG were distributed in a limited number of tissues, including the skin (from the eyelid, abdomen, and cheek), whereas MRGPRD and MRGPRF were extensively expressed in almost all tissues examined. Histochemical and in situ hybridisation analyses revealed that MRGPRX2 was expressed in dog connective tissue-type mast cells in the skin. Intracellular Ca2+ mobilisation assay revealed that HEK293 cells, expressing dog MRGPRX2 or human MRGPRX2, but not dog MRGPRD, MRGPRF, and MRGPRG, responded to histamine-releasing agents. Our results suggest that dog MRGPRX2 is the functional orthologue of human MRGPRX2 and plays an essential role in drug-induced anaphylactoid reactions in dogs.