bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive Geophysical Study at Wabar Crater, Rub Al‐Khali Desert, Saudi Arabia
Authors: Hanafy Sherif M. , Soupios Pantelis , Stampolidis Alexandros , Koch Christian Bender , Al‐Ramadan Khalid , Al‐Shuhail Abdullatif , Solling Theis , Argadestya Ignatius 
Published: September 2021

AbstractInterest in impact craters on the earth's surface has increased worldwide and is being investigated by using remote sensing, geological, boreholes, geophysical, and laboratory measurements. These measurements are used to build dynamic models to study crater formation. In this work, the near‐crater sediments at the young Wabar crater field in Saudi Arabia have been investigated using magnetic, transient electromagnetic (TEM), seismic, and ground‐penetrating radar (GPR) methods. The main objectives of this research were to (a) explore the possibility of any remnant major pieces of the meteorite, (b) investigate the meteoroid direction, and (c) map the deformational structures associated with the meteorite impact. Our results show five different magnetic anomaly types and three layers in the subsurface. The maximum depth of deformation due to the impact of the meteorite is about 25 m as shown by the seismic travel time tomogram, the quasi‐2D TEM, and the 3D GPR model. TEM survey confirmed the geometrical characteristics of the major crater and located another small crater (known as Philby‐A). The magnetic survey shows no evidence of any remnant major pieces of the meteorite; however, it was used to trace ejecta material containing highly dilute magnetic material. The magnetic carrier is most likely spheres of metal incorporated in the black/green glasses. During the expedition, many small pieces of the meteoroid were found and collected for further geochemical analysis. Based on the geophysical findings, the meteorite direction was found to be from north to south.
High‐Resolution Land Surface Modeling of the Effect of Long‐Term Urbanization on Hydrothermal Changes Over Beijing Metropolitan Area
Authors: Ji Peng , Yuan Xing , Liang Xin‐Zhong , Jiao Yang , Zhou Yuyu , Liu Zan 
Published: September 2021

AbstractThe impacts of urbanization on terrestrial thermal and hydrological changes should be considered for sustainable development of urban environment and economy. However, previous studies mainly focused on the impacts at short time scales, which is insufficient to provide the needed information. This study augmented the high‐resolution Conjunctive Surface‐Subsurface Process version 2 (CSSPv2) land model with an urban canopy model that incorporates domestic wastewater recharge (DWWR) and dynamical impervious surface area (ISA) to develop a new CSSPv2_Urban model and conducted 38‐year simulations over the Beijing metropolitan area at 1 km resolution to quantify the urbanization impacts. Compared with CSSPv2, CSSPv2_Urban decreases the root‐mean‐square errors in surface latent/sensible heat fluxes, near‐surface air temperature and land surface temperature by 15%–66%, increases Kling‐Gupta efficiency for streamflow by 27%–34%, and reproduces the observed long‐term trends of land surface temperature and streamflow. It also reduces the corresponding errors in the modern reanalysis products by up to 70%. The model sensitivity analyses showed that the urbanization over Beijing area contributed to 31% of the surface warming during 1979–2017 and kept the warming trend over the new development zone during 2000–2013 when global warming slowed down. Although the large fraction of ISA in the city center increased streamflow by generating more surface runoff, 39%–62% of the increasing trend of streamflow was caused by the increased DWWR. Our study highlights the importance of the urban heat island effect from a climatological perspective and suggests that the influences of urbanization on streamflow may be underestimated if ignoring DWWR.
Evolution and dispersal of snakes across the Cretaceous-Paleogene mass extinction
Authors: Klein Catherine G. , Pisani Davide , Field Daniel J. , Lakin Rebecca , Wills Matthew A. , Longrich Nicholas R. 
Published: September 2021

AbstractMass extinctions have repeatedly shaped global biodiversity. The Cretaceous-Paleogene (K-Pg) mass extinction caused the demise of numerous vertebrate groups, and its aftermath saw the rapid diversification of surviving mammals, birds, frogs, and teleost fishes. However, the effects of the K-Pg extinction on the evolution of snakes—a major clade of predators comprising over 3,700 living species—remains poorly understood. Here, we combine an extensive molecular dataset with phylogenetically and stratigraphically constrained fossil calibrations to infer an evolutionary timescale for Serpentes. We reveal a potential diversification among crown snakes associated with the K-Pg mass extinction, led by the successful colonisation of Asia by the major extant clade Afrophidia. Vertebral morphometrics suggest increasing morphological specialisation among marine snakes through the Paleogene. The dispersal patterns of snakes following the K-Pg underscore the importance of this mass extinction event in shaping Earth’s extant vertebrate faunas.
Near 100% ethene selectivity achieved by tailoring dual active sites to isolate dehydrogenation and oxidation
Authors: Wang Chaojie , Yang Bing , Gu Qingqing , Han Yujia , Tian Ming , Su Yang , Pan Xiaoli , Kang Yu , Huang Chuande , Liu Hua , Liu Xiaoyan , Li Lin , Wang Xiaodong 
Published: September 2021

AbstractProhibiting deep oxidation remains a challenging task in oxidative dehydrogenation of light alkane since the targeted alkene is more reactive than parent substrate. Here we tailor dual active sites to isolate dehydrogenation and oxidation instead of homogeneously active sites responsible for these two steps leading to consecutive oxidation of alkene. The introduction of HY zeolite with acid sites, three-dimensional pore structure and supercages gives rise to Ni2+ Lewis acid sites (LAS) and NiO nanoclusters confined in framework wherein catalytic dehydrogenation of ethane occurs on Ni2+ LAS resulting in the formation of ethene and hydrogen while NiO nanoclusters with decreased oxygen reactivity are responsible for selective oxidation of hydrogen rather than over-oxidizing ethene. Such tailored strategy achieves near 100% ethene selectivity and constitutes a promising basis for highly selective oxidation catalysis beyond oxidative dehydrogenation of light alkane.
Multi-region exome sequencing reveals the intratumoral heterogeneity of surgically resected small cell lung cancer
Authors: Zhou Huaqiang , Hu Yi , Luo Rongzhen , Zhao Yuanyuan , Pan Hui , Ji Liyan , Zhou Ting , Zhang Lanjun , Long Hao , Fu Jianhua , Wen Zhesheng , Wang Siyu , Wang Xin , Lin Peng , Yang Haoxian , Wang Junye , Song Mengmeng , Yi Xin , Yang Ling , Xia Xuefang , Guan Yanfang , Fang Wenfeng , Yang Yunpeng , Hong Shaodong , Huang Yan , Li Pansong , Zhang Yaxiong , Zhou Ningning 
Published: September 2021

AbstractSmall cell lung cancer (SCLC) is a highly malignant tumor which is eventually refractory to any treatment. Intratumoral heterogeneity (ITH) may contribute to treatment failure. However, the extent of ITH in SCLC is still largely unknown. Here, we subject 120 tumor samples from 40 stage I-III SCLC patients to multi-regional whole-exome sequencing. The most common mutant genes are TP53 (88%) and RB1 (72%). We observe a medium level of mutational heterogeneity (0.30, range 0.0~0.98) and tumor mutational burden (TMB, 10.2 mutations/Mb, range 1.1~51.7). Our SCLC samples also exhibit somatic copy number variation (CNV) across all patients, with an average CNV ITH of 0.49 (range 0.02~0.99). In terms of mutation distribution, ITH, TMB, mutation clusters, and gene signatures, patients with combined SCLC behave roughly the same way as patients with pure SCLC. This condition also exists in smoking patients and patients with EGFR mutations. A higher TMB per cluster is associated with better disease-free survival while single-nucleotide variant ITH is linked to worse overall survival, and therefore these features may be used as prognostic biomarkers for SCLC. Together, these findings demonstrate the intratumoral genetic heterogeneity of surgically resected SCLC and provide insights into resistance to treatment.
A common goal to CARE: Cancer Advocates, Researchers, and Clinicians Explore current treatments and clinical trials for breast cancer brain metastases
Authors: Joe Natalie S. , Hodgdon Christine , Kraemer Lianne , Redmond Kristin J. , Stearns Vered , Gilkes Daniele M. 
Published: September 2021

AbstractBreast cancer is the most commonly diagnosed cancer in women worldwide. Approximately one-tenth of all patients with advanced breast cancer develop brain metastases resulting in an overall survival rate of fewer than 2 years. The challenges lie in developing new approaches to treat, monitor, and prevent breast cancer brain metastasis (BCBM). This review will provide an overview of BCBM from the integrated perspective of clinicians, researchers, and patient advocates. We will summarize the current management of BCBM, including diagnosis, treatment, and monitoring. We will highlight ongoing translational research for BCBM, including clinical trials and improved detection methods that can become the mainstay for BCBM treatment if they demonstrate efficacy. We will discuss preclinical BCBM research that focuses on the intrinsic properties of breast cancer cells and the influence of the brain microenvironment. Finally, we will spotlight emerging studies and future research needs to improve survival outcomes and preserve the quality of life for patients with BCBM.
Cellular and humoral immune responses following SARS-CoV-2 mRNA vaccination in patients with multiple sclerosis on anti-CD20 therapy
Authors: Apostolidis Sokratis A. , Kakara Mihir , Painter Mark M. , Goel Rishi R. , Mathew Divij , Lenzi Kerry , Rezk Ayman , Patterson Kristina R. , Espinoza Diego A. , Kadri Jessy C. , Markowitz Daniel M. , E. Markowitz Clyde , Mexhitaj Ina , Jacobs Dina , Babb Allison , Betts Michael R. , Prak Eline T. Luning , Weiskopf Daniela , Grifoni Alba , Lundgreen Kendall A. , Gouma Sigrid , Sette Alessandro , Bates Paul , Hensley Scott E. , Greenplate Allison R. , Wherry E. John , Li Rui , Bar-Or Amit 
Published: September 2021

AbstractSARS-CoV-2 messenger RNA vaccination in healthy individuals generates immune protection against COVID-19. However, little is known about SARS-CoV-2 mRNA vaccine-induced responses in immunosuppressed patients. We investigated induction of antigen-specific antibody, B cell and T cell responses longitudinally in patients with multiple sclerosis (MS) on anti-CD20 antibody monotherapy (n = 20) compared with healthy controls (n = 10) after BNT162b2 or mRNA-1273 mRNA vaccination. Treatment with anti-CD20 monoclonal antibody (aCD20) significantly reduced spike-specific and receptor-binding domain (RBD)-specific antibody and memory B cell responses in most patients, an effect ameliorated with longer duration from last aCD20 treatment and extent of B cell reconstitution. By contrast, all patients with MS treated with aCD20 generated antigen-specific CD4 and CD8 T cell responses after vaccination. Treatment with aCD20 skewed responses, compromising circulating follicular helper T (TFH) cell responses and augmenting CD8 T cell induction, while preserving type 1 helper T (TH1) cell priming. Patients with MS treated with aCD20 lacking anti-RBD IgG had the most severe defect in circulating TFH responses and more robust CD8 T cell responses. These data define the nature of the SARS-CoV-2 vaccine-induced immune landscape in aCD20-treated patients and provide insights into coordinated mRNA vaccine-induced immune responses in humans. Our findings have implications for clinical decision-making and public health policy for immunosuppressed patients including those treated with aCD20.
Immunoregulatory mechanism studies of ginseng leaves on lung cancer based on network pharmacology and molecular docking
Authors: Li Zao-Hui , Yu Dan , Huang Nan-Nan , Wu Jun-Kai , Du Xiao-Wei , Wang Xi-Jun 
Published: September 2021

AbstractPanax ginseng is one of the oldest and most generally prescribed herbs in Eastern traditional medicine to treat diseases. Several studies had documented that ginseng leaves have anti-oxidative, anti-inflammatory, and anticancer properties similar to those of ginseng root. The aim of this research was to forecast of the molecular mechanism of ginseng leaves on lung cancer by molecular docking and network pharmacology so as to decipher ginseng leaves' entire mechanism. The compounds associated with ginseng leaves were searched by TCMSP. TCMSP and Swiss Target Prediction databases were used to sort out the potential targets of the main chemical components. Targets were collected from OMIM, PharmGKB, TTD, DrugBank and GeneCards which related to immunity and lung cancer. Ginseng leaves exert its lung cancer suppressive function by regulating the several signaling proteins, such as JUN, STAT3, AKT1, TNF, MAPK1, TP53. GO and KEGG analyses indicated that the immunoreaction against lung cancer by ginseng leaves might be related to response to lipopolysaccharide, response to oxidative stress, PI3K-Akt, MAPK and TNF pathway. Molecular docking analysis demonstrated that hydrogen bonding was interaction's core forms. The results of CCK8 test and qRT-PCR showed that ginseng leaves inhibit cell proliferation and regulates AKT1 and P53 expression in A549. The present study clarifies the mechanism of Ginseng leaves against lung cancer and provides evidence to support its clinical use.
Development of an efficient gene-targeting system for elucidating infection mechanisms of the fungal pathogen Trichosporon asahii
Authors: Matsumoto Yasuhiko , Nagamachi Tae , Yoshikawa Asami , Yamazaki Hideki , Yamasaki Yusuke , Yamada Tsuyoshi , Sugita Takashi 
Published: September 2021

AbstractTrichosporon asahii is a pathogenic fungus that causes severe, deep-seated fungal infections in neutropenic patients. Elucidating the infection mechanisms of T. asahii based on genetic studies requires a specific gene-targeting system. Here, we established an efficient gene-targeting system in a highly pathogenic T. asahii strain identified using the silkworm infection model. By comparing the pathogenicity of T. asahii clinical isolates in a silkworm infection model, T. asahii MPU129 was identified as a highly pathogenic strain. Using an Agrobacterium tumefaciens-mediated gene transfer system, we obtained a T. asahii MPU129 mutant lacking the ku70 gene, which encodes the Ku70 protein involved in the non-homologous end-joining repair of DNA double-strand breaks. The ku70 gene-deficient mutant showed higher gene-targeting efficiency than the wild-type strain for constructing a mutant lacking the cnb1 gene, which encodes the beta-subunit of calcineurin. The cnb1 gene-deficient mutant showed reduced pathogenicity against silkworms compared with the parental strain. These results suggest that an efficient gene-targeting system in a highly pathogenic T. asahii strain is a useful tool for elucidating the molecular mechanisms of T. asahii infection.
ECG data dependency for atrial fibrillation detection based on residual networks
Authors: Seo Hyo-Chang , Oh Seok , Kim Hyunbin , Joo Segyeong 
Published: September 2021

AbstractAtrial fibrillation (AF) is an arrhythmia that can cause blood clot and may lead to stroke and heart failure. To detect AF, deep learning-based detection algorithms have recently been developed. However, deep learning models were often trained with limited datasets and were evaluated within the same datasets, which makes their performance generally drops on the external datasets, known as data dependency. For this study, three different databases from PhysioNet were used to investigate the data dependency of deep learning-based AF detection algorithm using the residual neural network (Resnet). Resnet 18, 34, 50 and 152 model were trained with raw electrocardiogram (ECG) signal extracted from independent database. The highest accuracy was about 98–99% which is evaluation results of test dataset from the own database. On the other hand, the lowest accuracy was about 53–92% which was evaluation results of the external dataset extracted from different source. There are data dependency according to the train dataset and the test dataset. However, the data dependency decreased as a large amount of train data.
Confining Trypanosoma brucei in emulsion droplets reveals population variabilities in division rates and improves in vitro cultivation
Authors: Oldenburg Simone H. , Buisson Lionel , Beneyton Thomas , Pekin Deniz , Thonnus Magali , Bringaud Frédéric , Rivière Loïc , Baret Jean-Christophe 
Published: September 2021

AbstractTrypanosome parasites are infecting mammals in Sub-Saharan Africa and are transmitted between hosts through bites of the tsetse fly. The transmission from the insect vector to the mammal host causes a number of metabolic and physiological changes. A fraction of the population continuously adapt to the immune system of the host, indicating heterogeneity at the population level. Yet, the cell to cell variability in populations is mostly unknown. We develop here an analytical method for quantitative measurements at the single cell level based on encapsulation and cultivation of single-cell Trypanosoma brucei in emulsion droplets. We first show that mammalian stage trypanosomes survive for several hours to days in droplets, with an influence of droplet size on both survival and growth. We unravel various growth patterns within a population and find that droplet cultivation of trypanosomes results in 10-fold higher cell densities of the highest dividing cell variants compared to standard cultivation techniques. Some variants reach final cell titers in droplets closer to what is observed in nature than standard culture, of practical interest for cell production. Droplet microfluidics is therefore a promising tool for trypanosome cultivation and analysis with further potential for high-throughput single cell trypanosome analysis.
Meta-analysis of gene expression disease signatures in colonic biopsy tissue from patients with ulcerative colitis
Authors: Linggi Bryan , Jairath Vipul , Zou Guangyong , Shackelton Lisa M. , McGovern Dermot P. B. , Salas Azucena , Verstockt Bram , Silverberg Mark S. , Nayeri Shadi , Feagan Brian G. , Vande Casteele Niels 
Published: September 2021

AbstractPublicly available ulcerative colitis (UC) gene expression datasets from observational studies and clinical trials include inherently heterogeneous disease characteristics and methodology. We used meta-analysis to identify a robust UC gene signature from inflamed biopsies. Eight gene expression datasets derived from biopsy tissue samples from noninflammatory bowel disease (IBD) controls and areas of active inflammation from patients with UC were publicly available. Expression- and meta-data were downloaded with GEOquery. Differentially expressed genes (DEG) in individual datasets were defined as those with fold change > 1.5 and a Benjamini–Hochberg adjusted P value < .05. Meta-analysis of all DEG used a random effects model. Reactome pathway enrichment analysis was conducted. Meta-analysis identified 946 up- and 543 down-regulated genes in patients with UC compared to non-IBD controls (1.2 and 1.7 times fewer up- and down-regulated genes than the median of the individual datasets). Top-ranked up- and down-regulated DEG were LCN2 and AQP8. Multiple immune-related pathways (e.g., ‘Chemokine receptors bind chemokine’ and ‘Interleukin-10 signaling’) were significantly up-regulated in UC, while ‘Biological oxidations’ and ‘Fatty acid metabolism’ were downregulated. A web-based data-mining tool with the meta-analysis results was made available (https://premedibd.com/genes.html). A UC inflamed biopsy disease gene signature was derived. This signature may be an unbiased reference for comparison and improve the efficiency of UC biomarker studies by increasing confidence for identification of disease-related genes and pathways.
First report of Borrelia burgdorferi sensu stricto detection in a commune genospecies in Apodemus agrarius in Gwangju, South Korea
Authors: Kim Choon Mee , Park So Young , Kim Dong-Min , Park Jung Wook , Chung Jae Keun 
Published: September 2021

AbstractLyme disease is a tick-borne infectious disease caused by theBorrelia burgdorferisensu lato complex. However, the distribution ofBorreliagenospecies and the tissue detection rate ofBorreliain wild rodents have rarely been investigated. Here, we studied 27 wild rodents (Apodemus agrarius) captured in October and November 2016 in Gwangju, South Korea, and performed nested polymerase chain reaction targetingpyrGandospAto confirmBorreliainfection. Eight rodents (29.6%) tested positive forBorreliainfection. The heart showed the highest infection rate (7/27; 25.9%), followed by the spleen (4/27; 14.8%), kidney (2/27; 7.4%), and lungs (1/27; 3.7%). TheB. afzeliiinfection rate was 25.9%, with the highest rate observed in the heart (7/27; 25.9%), followed by that in the kidney and spleen (both 2/27; 7.4%).B. gariniiandB. burgdorferisensu stricto were detected only in the spleen (1/27; 3.7%). This is the first report ofB. burgdorferisensu stricto infection in wild rodents in South Korea. The rodent hearts showed a highB. afzeliiinfection rate, whereas the rodent spleens showed highB. gariniiandB. burgdorferisensu stricto infection rates. BesidesB. gariniiandB. afzelii,B. burgdorferisensu stricto may cause Lyme disease in South Korea.
Molecular underpinnings of division of labour among workers in a socially complex termite
Authors: Elsner Daniel , Hartfelder Klaus , Korb Judith 
Published: September 2021

AbstractDivision of labour characterizes all major evolutionary transitions, such as the evolution of eukaryotic cells or multicellular organisms. Social insects are characterized by reproductive division of labour, with one or a few reproducing individuals (queens) and many non-reproducing nestmates (workers) forming a colony. Among the workers, further division of labour can occur with different individuals performing different tasks such as foraging, brood care or building. While mechanisms underlying task division are intensively studied in social Hymenoptera, less is known for termites, which independently evolved eusociality. We investigated molecular mechanisms underlying task division in termite workers to test for communality with social Hymenoptera. We compared similar-aged foraging workers with builders of the fungus-growing termiteMacrotermes bellicosususing transcriptomes, endocrine measures and estimators of physiological condition. Based on results for social Hymenoptera and theory, we tested the hypotheses that (i) foragers are in worse physiological conditions than builders, (ii) builders are more similar in their gene expression profile to queens than foragers are, and (iii) builders invest more in anti-ageing mechanism than foragers. Our results support all three hypotheses. We found storage proteins to underlie task division of these similar-aged termite workers and these genes also characterize reproductive division of labour between queens and workers. This implies a co-option of nutrient-based pathways to regulate division of labour across lineages of termites and social Hymenoptera, which are separated by more than 133 million years.