bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Illumination of Thunderclouds by Lightning: 3. Retrieving Optical Source Altitude
Authors: Peterson Michael , Light Tracy E. L. , Mach Douglas 
Published: December 2021

AbstractOptical space‐based lightning sensors such as the Geostationary Lightning Mapper (GLM) detect and geolocate lightning by recording rapid changes in cloud top illumination. While lightning locations can be determined to within a pixel on the GLM imaging array, these instruments are not individually able to natively report lightning altitude. It has previously been shown that thunderclouds are illuminated differently based on the altitude of the optical source. In this study, we examine how altitude information can be extracted from the spatial distributions of GLM energy recorded from each optical pulse. We match GLM “groups” with Lightning Mapping Array (LMA) source data that accurately report the 3‐D positions of coincident Radio‐Frequency (RF) emitters. We then use machine learning methods to predict the mean LMA source altitudes matched to GLM groups using metrics from the optical data that describe the amplitude, breadth, and texture of the group spatial energy distribution. The resulting model can predict the LMA mean source altitude from GLM group data with a median absolute error of <1.5 km, which is sufficient to determine the location of the charge layer where the optical energy originated. This model is able to capture changes to the source altitude distribution in response to convective processes in the thunderstorm, and the GLM predictions can reveal the vertical structure of individual flashes ‐ enabling 3‐D flash geolocation with GLM for the first time. Future work will account for differences in thunderstorm charge/precipitation structures and viewing angle across the GLM Field of View.
Full Waveform Ambient Noise Tomography for the Northern Mississippi Embayment
Authors: Yang Y. , Langston C. A. , Powell C. A. , Thomas W. A. 
Published: December 2021

AbstractWe use seismic ambient noise data recorded by broadband stations around the northern Mississippi Embayment to develop a three‐dimensional shear wave velocity model with full waveform inversion. Empirical Green's functions at periods between 8 and 40s are extracted using a data processing flow based on the continuous wavelet transform. Synthetic waveforms are calculated with an isotropic model through a Graphics Processor Unit‐enabled, collocated finite‐difference code. Starting from the Central United States Velocity Model, the shear wave velocity is iteratively updated with sensitivity kernels constructed using the adjoint method. Several mid‐crustal velocity variations are related to major geological features including the Mississippi Valley graben (MVG), the Ouachita thrust belt, and the Missouri batholith. An intrusion is imaged in northwestern Alabama, coincident with a previously unexplained gravity high. A major change in mid‐crustal velocity occurs across the MVG; much higher velocity crust is present southeast of the graben than northwest. The high velocities are attributed to numerous igneous intrusions, possibly related to formation of the Granite‐Rhyolite province. A strength contrast produced by the change in mid‐crustal velocities may have facilitated formation of the younger, shallower MVG, as external stresses became tensional during Iapetus rifting. The rift pillow is interpreted as the deeper expression of the high velocity crust. Low velocity crust is present below southern Missouri starting at a depth of roughly 20 km. The boundary between the low velocity crust and higher velocity crust to the south and east is sharp and coincides with the Nd‐line.
What Contributes to the Inter‐Annual Variability in Tropical Lower Stratospheric Temperatures?
Authors: Ming Alison , Hitchcock Peter 
Published: December 2021

AbstractThe inter‐annual variability in mid and lower stratospheric temperatures for the period 1984–2019 is decomposed into dynamical and radiative contributions using a radiative calculation perturbed with changes in dynamical heating, trace gases and aerosol optical depth. The temperature timeseries obtained is highly correlated with the de‐seasonalized ERA5 temperature (r2 > 0.6 in the region 15 to 70 hPa, 1992 to 2019–after the Pinatubo volcanic eruption). Ozone and dynamical heating contributions are found to be equally important, with water vapor, stratospheric aerosols, and carbon dioxide playing smaller roles. Prominent aspects of the temperature timeseries are closely reproduced, including the 1991 Pinatubo volcanic eruption, the year‐2000 water vapor drop, and the 2016 Quasi‐biennial oscillation (QBO) disruption. Below 20 hPa, ozone is primarily controlled by transport and is positively correlated to the upwelling. This ozone‐transport feedback acts to increase the temperature response to a change in upwelling by providing an additional ozone‐induced radiative temperature change. This can be quantified as an enhancement of the dynamical heating of about 20% at 70 hPa. A Principal Oscillation Pattern (POP) analysis is used to estimate the contribution of the ozone QBO (±1 K at 70 hPa). The non‐QBO ozone variability is also shown to be significant. Using the QBO leading POP timeseries as representative of the regular QBO signal, the QBO 2016 disruption is shown to have an anomalously large radiative impact on temperature due to the ozone change ( at 70 hPa).
Estimates on the Frequency of Volcanic Eruptions on Venus
Authors: Byrne Paul K. , Krishnamoorthy Siddharth 
Published: December 2021

AbstractVenus hosts many thousands of volcanic landforms, including individual edifices, volcanotectonic structures, and vast expanses of effusively emplaced plains lavas. Numerous lines of circumstantial evidence together suggest that the planet is volcanically active today. Although previous studies have calculated volcanic eruptive fluxes on the basis of the volumes of lava needed to bury craters of various diameters on Venus, no estimates of the frequency of volcanic eruptions on the planet yet exist. In this study, we analyzed records for eruptive events on Earth between 1 January 1980 and 21 January 2021 for which data on duration and eruption intensity were available, and classified those events by tectonic setting. We then extrapolated those results to Venus by a simple scaling factor. We estimate that as many as 120 discrete eruptions, from individual volcanic edifices and of any duration and intensity, may occur on Venus per Earth year. Further, within any given 60‐day window—a nominal timeframe over which an aerial platform capable of detecting volcanic activity might operate in the middle Venus atmosphere—we expect about four new eruptions to begin, with that number rising to almost eight when both new events and those ending within 100 days of the main eruption are included, or to as many as 20 when considering activity that lasts for 1,000 days. Several complementary techniques exist with which to search for volcanic eruptions at Venus, either from orbit, within the atmosphere, or on the surface, that can be used to test the estimates we make here.
Circular RNA circPPP6R3 upregulates CD44 to promote the progression of clear cell renal cell carcinoma via sponging miR-1238-3p
Authors: Chen Zhiliang , Zheng Zaosong , Xie Yingwei , Zhong Qiyu , Shangguan Wentai , Zhang Yishan , Zhu Dingjun , Xie Wenlian 
Published: December 2021

AbstractCircular RNAs (circRNAs) are a type of covalently closed circular-formed RNAs and play crucial roles in the oncogenesis and progression of various human cancers. Here we identified a novel circRNA, circPPP6R3, to be highly expressed both in clear cell renal cell carcinoma (ccRCC) tissues and cell lines based on analyzing high-throughput sequencing data and qRT-PCR analysis. Highly expressed circPPP6R3 was positively correlated with higher histological grade, T stage, and M stage as well as advanced clinical stage of ccRCC patients. Functionally, knockdown of circPPP6R3 attenuated the proliferation, migration, and invasion of ccRCC cells whereas overexpression had the reverse effects. Mechanistically, the biotin-labeled pull-down assay and dual-luciferase reporter assay revealed that circPPP6R3 directly interacted with miR-1238-3p. miR-1238-3p inhibitors had a rescue effect on the proliferative and metastatic capacities by knockdown of circPPP6R3. Moreover, RNA-sequencing analysis and dual-luciferase reporter assay indicated that circPPP6R3 upregulated CD44, a cell-surface glycoprotein contributed to the cell adhesion and metastasis, via sponging to miR-1238-3p. Further investigation revealed that MMP9 and Vimentin were regulated by CD44 in ccRCC. Our study thus provided evidence that the regulatory network involving circPPP6R3/miR-1238-3p/CD44 axis might provide promising biomarkers as well as a therapeutic approach for ccRCC.
Single-cell transcriptomic analysis reveals the critical molecular pattern of UV-induced cutaneous squamous cell carcinoma
Authors: Yan Guorong , Li Liang , Zhu Sibo , Wu Yuhao , Liu Yeqiang , Zhu Lude , Zhao Zijun , Wu Fei , Jia Ning , Liao Caihe , Jiang Long , Zeng Qingyu , Wang Peiru , Shi Lei , Zheng Zhe , Fang Shan , Zhang Guolong , Tang Yichen , Wang Xiuli 
Published: December 2021

AbstractCutaneous squamous cell carcinoma (cSCC) is the second most common nonmelanoma skin cancer characterized by high invasiveness, heterogeneity, and mainly occurs in the ultraviolet (UV)-exposed regions of the skin, but its pathogenesis is still unclear. Here, we generated single-cell transcriptome profiles for 350 cells from six primary UV-induced cSCCs, together with matched adjacent skin samples, and three healthy control skin tissues by single-cell RNA-sequencing technology based on Smart-seq2 strategy. A series of bioinformatics analyses and in vitro experiments were used to decipher and validate the critical molecular pattern of cSCC. Results showed that cSCC cells and normal keratinocytes were significantly distinct in gene expression and chromosomal copy number variation. Furthermore, cSCC cells exhibited 18 hallmark pathways of cancer by gene set enrichment analysis. Differential expression analysis demonstrated that many members belonging to S100 gene family, SPRR gene family, and FABP5 were significantly upregulated in cSCC cells. Further experiments confirmed their upregulation and showed that S100A9 or FABP5 knockdown in cSCC cells inhibited their proliferation and migration through NF-κB pathway. Taken together, our data provide a valuable resource for deciphering the molecular pattern in UV-induced cSCC at a single-cell level and suggest that S100A9 and FABP5 may provide novel targets for therapeutic intervention of cSCC in the future.
The long noncoding RNA H19 regulates tumor plasticity in neuroendocrine prostate cancer
Authors: Singh Neha , Ramnarine Varune R. , Song Jin H. , Pandey Ritu , Padi Sathish K. R. , Nouri Mannan , Olive Virginie , Kobelev Maxim , Okumura Koichi , McCarthy David , Hanna Michelle M. , Mukherjee Piali , Sun Belinda , Lee Benjamin R. , Parker J. Brandon , Chakravarti Debabrata , Warfel Noel A. , Zhou Muhan , Bearss Jeremiah J. , Gibb Ewan A. , Alshalalfa Mohammed , Karnes R. Jefferey , Small Eric J. , Aggarwal Rahul , Feng Felix , Wang Yuzhuo , Buttyan Ralph , Zoubeidi Amina , Rubin Mark , Gleave Martin , Slack Frank J. , Davicioni Elai , Beltran Himisha , Collins Colin , Kraft Andrew S. 
Published: December 2021

AbstractNeuroendocrine (NE) prostate cancer (NEPC) is a lethal subtype of castration-resistant prostate cancer (PCa) arising either de novo or from transdifferentiated prostate adenocarcinoma following androgen deprivation therapy (ADT). Extensive computational analysis has identified a high degree of association between the long noncoding RNA (lncRNA) H19 and NEPC, with the longest isoform highly expressed in NEPC. H19 regulates PCa lineage plasticity by driving a bidirectional cell identity of NE phenotype (H19 overexpression) or luminal phenotype (H19 knockdown). It contributes to treatment resistance, with the knockdown of H19 re-sensitizing PCa to ADT. It is also essential for the proliferation and invasion of NEPC. H19 levels are negatively regulated by androgen signaling via androgen receptor (AR). When androgen is absent SOX2 levels increase, driving H19 transcription and facilitating transdifferentiation. H19 facilitates the PRC2 complex in regulating methylation changes at H3K27me3/H3K4me3 histone sites of AR-driven and NEPC-related genes. Additionally, this lncRNA induces alterations in genome-wide DNA methylation on CpG sites, further regulating genes associated with the NEPC phenotype. Our clinical data identify H19 as a candidate diagnostic marker and predictive marker of NEPC with elevated H19 levels associated with an increased probability of biochemical recurrence and metastatic disease in patients receiving ADT. Here we report H19 as an early upstream regulator of cell fate, plasticity, and treatment resistance in NEPC that can reverse/transform cells to a treatable form of PCa once therapeutically deactivated.
The genomes of 204 Vitis vinifera accessions reveal the origin of European wine grapes
Authors: Magris Gabriele , Jurman Irena , Fornasiero Alice , Paparelli Eleonora , Schwope Rachel , Marroni Fabio , Di Gaspero Gabriele , Morgante Michele 
Published: December 2021

AbstractIn order to elucidate the still controversial processes that originated European wine grapes from its wild progenitor, here we analyse 204 genomes of Vitis vinifera and show that all analyses support a single domestication event that occurred in Western Asia and was followed by numerous and pervasive introgressions from European wild populations. This admixture generated the so-called international wine grapes that have diffused from Alpine countries worldwide. Across Europe, marked differences in genomic diversity are observed in local varieties that are traditionally cultivated in different wine producing countries, with Italy and France showing the largest diversity. Three genomic regions of reduced genetic diversity are observed, presumably as a consequence of artificial selection. In the lowest diversity region, two candidate genes that gained berry–specific expression in domesticated varieties may contribute to the change in berry size and morphology that makes the fruit attractive for human consumption and adapted for winemaking.
Subclonal heterogeneity and evolution in breast cancer
Authors: Mavrommati Ioanna , Johnson Flora , Echeverria Gloria V. , Natrajan Rachael 
Published: December 2021

AbstractSubclonal heterogeneity and evolution are characteristics of breast cancer that play a fundamental role in tumour development, progression and resistance to current therapies. In this review, we focus on the recent advances in understanding the epigenetic and transcriptomic changes that occur within breast cancer and their importance in terms of cancer development, progression and therapy resistance with a particular focus on alterations at the single-cell level. Furthermore, we highlight the utility of using single-cell tracing and molecular barcoding methodologies in preclinical models to assess disease evolution and response to therapy. We discuss how the integration of single-cell profiling from patient samples can be used in conjunction with results from preclinical models to untangle the complexities of this disease and identify biomarkers of disease progression, including measures of intra-tumour heterogeneity themselves, and how enhancing this understanding has the potential to uncover new targetable vulnerabilities in breast cancer.
Acute respiratory infections in an adult refugee population: an observational study
Authors: Jablonka Alexandra , Dopfer Christian , Happle Christine , Shalabi Andree , Wetzke Martin , Hummers Eva , Friede Tim , Heinemann Stephanie , Hillermann Nele , Simmenroth Anne , Müller Frank 
Published: December 2021

AbstractThe presence of acute infectious respiratory diseases (ARD) is one of the main reasons why recently arrived refugees seek medical help. This paper investigates the incidence rates of acute respiratory diseases in an adult refugee population as well as associated sociodemographic factors and drug treatments. We conducted a retrospective observational study of deidentified medical records. The data were collected between 2015 and 2019 in the health care centers of two large German initial reception centers for refugees. Multivariable analyses controlling for sociodemographics were carried out using generalized estimating equations. Out of 10,431 eligible residents, 6965 medical encounters of 2840 adult patients were recorded over 30 months. Of all the adult patients, 34.4% sought medical help for a respiratory symptom or diagnosis at least once. Older patients and patients from Sub-Saharan Africa sought help less often. The occurrence of ARD showed a typical distribution over the course of the year. Facility occupancy was not associated with ARD occurrence. Acute respiratory symptoms are a leading cause for adult refugee patients to seek medical care. The doctor contact rates due to ARD were consistently two to three times higher among refugees than among German residents.
Validation of an ecological momentary assessment to measure processing speed and executive function in schizophrenia
Authors: Shvetz Cecelia , Gu Feng , Drodge Jessica , Torous John , Guimond Synthia 
Published: December 2021

AbstractCognitive impairments are a core feature of schizophrenia that have negative impacts on functional outcomes. However, it remains challenging to assess these impairments in clinical settings. Smartphone apps provide the opportunity to measure cognitive impairments in an accessible way; however, more research is needed to validate these cognitive assessments in schizophrenia. We assessed the initial accessibility, validity, and reliability of a smartphone-based cognitive test to measure cognition in schizophrenia. A total of 29 individuals with schizophrenia and 34 controls were included in the analyses. Participants completed the standard pen-and-paper Trail Making Tests (TMT) A and B, and smartphone-based versions, Jewels Trail Tests (JTT) A and B, at the single in-lab visit. Participants were asked to complete the JTT remotely once per week for three months. We also investigated how subjective sleep quality and mood may affect cognitive performance longitudinally. In-lab and remote JTT scores moderately and positively correlated with in-lab TMT scores. Moderate test-retest reliability was observed across the in-lab, first remote, and last remote completion times of the JTT. Additionally, individuals with schizophrenia had significantly lower performance compared to controls on both the in-lab JTT and TMT. Self-reported mood had a significant effect on JTT A performance over time but no other significant relationships were found remotely. Our results support the initial accessibility, validity and reliability of using the JTT to measure cognition in schizophrenia. Future research to develop additional smartphone-based cognitive tests as well as with larger samples and in other psychiatric populations are warranted.
Machine learning prediction of antiviral-HPV protein interactions for anti-HPV pharmacotherapy
Authors: Lin Hui-Heng , Zhang Qian-Ru , Kong Xiangjun , Zhang Liuping , Zhang Yong , Tang Yanyan , Xu Hongyan 
Published: December 2021

AbstractPersistent infection with high-risk types Human Papillomavirus could cause diseases including cervical cancers and oropharyngeal cancers. Nonetheless, so far there is no effective pharmacotherapy for treating the infection from high-risk HPV types, and hence it remains to be a severe threat to the health of female. Based on drug repositioning strategy, we trained and benchmarked multiple machine learning models so as to predict potential effective antiviral drugs for HPV infection in this work. Through optimizing models, measuring models’ predictive performance using 182 pairs of antiviral-target interaction dataset which were all approved by the United States Food and Drug Administration, and benchmarking different models’ predictive performance, we identified the optimized Support Vector Machine and K-Nearest Neighbor classifier with high precision score were the best two predictors (0.80 and 0.85 respectively) amongst classifiers of Support Vector Machine, Random forest, Adaboost, Naïve Bayes, K-Nearest Neighbors, and Logistic regression classifier. We applied these two predictors together and successfully predicted 57 pairs of antiviral-HPV protein interactions from 864 pairs of antiviral-HPV protein associations. Our work provided good drug candidates for anti-HPV drug discovery. So far as we know, we are the first one to conduct such HPV-oriented computational drug repositioning study.
The role of cysteine residues in the allosteric modulation of the chromophore phototransformations of biphotochromic fluorescent protein SAASoti
Authors: Gavshina A. V. , Marynich N. K. , Khrenova M. G. , Solovyev I. D. , Savitsky A. P. 
Published: December 2021

AbstractBiphotochromic fluorescent protein SAASoti contains five cysteine residues in its sequence and a V127T point mutation transforms it to the monomeric form, mSAASoti. These cysteine residues are located far from the chromophore and might control its properties only allosterically. The influence of individual, double and triple cysteine substitutions of mSAASoti on fluorescent parameters and phototransformation reactions (irreversible green-to-red photoconversion and reversible photoswitching) is studied. A set of mSAASoti mutant forms (C21N, C117S, C71V, C105V, C175A, C21N/C71V, C21N/C175A, C21N/C71G/C175A) is obtained by site-directed mutagenesis. We demonstrate that the C21N variant exists in a monomeric form up to high concentrations, the C71V substitution accelerates photoconversion to the red form and the C105V variant has the maximum photoswitching rate. All C175A-containing variants demonstrate different photoswitching kinetics and decreased photostability during subsequent switching cycles compared with other considered systems. Classical molecular dynamic simulations reveal that the F177 side chain located in the vicinity of the chromophore is considerably more flexible in the mSAASoti compared with its C175A variant. This might be the explanation of the experimentally observed slowdown the thermal relaxation rate, i.e., trans–cis isomerization of the chromophore in mSAASoti upon C175A substitution.
Definitions of bronchopulmonary dysplasia and long-term outcomes of extremely preterm infants in Korean Neonatal Network
Authors: Jeon Ga Won , Oh Minkyung , Chang Yun Sil 
Published: December 2021

AbstractNew definitions for bronchopulmonary dysplasia (BPD) have recently been suggested, and an accurate diagnosis, including severity classification with proper definition, is crucial to identify high-risk infants for appropriate interventions. To determine whether recently suggested BPD definitions can better predict long-term outcomes of BPD in extremely preterm infants (EPIs) than the original BPD definition, BPD was classified with severity 1, 2, and 3 using three different definitions: definition A (original), National Institute of Child Health and Human Development (NICHD) definition in 2001; definition B, the modified NICHD 2016 definition (graded by the oxygen concentration and the respiratory support at 36 weeks’ postmenstrual age [PMA]); and definition C, the modified Jensen 2019 definition (graded by the respiratory support at 36 weeks’ PMA). We evaluated 1050 EPIs using a national cohort. Whereas EPIs with grade 2 or 3 BPD as per definition A did not show any increase in the risk, EPIs with BPD diagnosed by definition B and C showed significantly increased risk for poor outcomes, such as respiratory mortality and morbidities, neurodevelopmental delay, and growth restriction at 18–24 months of corrected age. The recently suggested definition and severity grading better reflects long-term childhood morbidities than the original definition in EPIs.