bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole Genome based Insights into the Phylogeny and Evolution of the Juglandaceae
Authors: Zhou Huijuan , Hu Yiheng , Ebrahimi Aziz , Liu Peiliang , Woeste Keith , Zhang Shuoxin , Zhao Peng 
Published: May 2021

Abstract
Background: The walnut family (Juglandaceae) contains commercially important woody trees commonly called walnut, wingnut, pecan and hickory. Phylogenetic relationships in the Juglandaceae are problematic, and their historical diversification has not been clarified, in part because of low phylogenetic resolution and/or insufficient marker variability. Results: We reconstructed the backbone phylogenetic relationships of Juglandaceae using organelle and nuclear genome data from 27 species. The divergence time of Juglandaceae was estimated to be 78.7 Mya. The major lineages diversified in warm and dry habitats during the mid-Paleocene and early Eocene. The plastid, mitochondrial, and nuclear phylogenetic analyses all revealed three subfamilies, i.e., Juglandoideae, Engelhardioideae, Rhoipteleoideae. Five genera of Juglandoideae were strongly supported. Juglandaceae were estimated to have originated during the late Cretaceous, while Juglandoideae were estimated to have originated during the Paleocene, with evidence for rapid diversification events during several glacial and geological periods. The phylogenetic analyses of organelle sequences and nuclear genome yielded highly supported incongruence positions for J. cinerea, J. hopeiensis, and Platycarya strobilacea. Winged fruit were the ancestral condition in the Juglandoideae, but adaptation to novel regeneration regimes after the Creaceous-Paleogene boundary led to the independent evolution of zoochory among several genera of the Juglandaceae. Conclusions: A fully resolved, strongly supported, time-calibrated phylogenetic tree of Juglandaceae can provide an important framework for studying classification, diversification, biogeography, and comparative genomics of plant lineages.
Signature Identification and User Activity Analysis on Whatsapp Web through Network Data
Authors: S Ramraj , G Usha 
Published: May 2021

Abstract
WhatsApp messenger is a popular instant messaging application that employs end-to-end encryption for communication. WhatsApp Web is the browser-based implementation of WhatsApp messenger. Users of WhatsApp communicate securely using SSL protocol. Encryption and use of common port for communication by multiple applications poses challenge in traffic classification for application identification. It is highly needed to analyze the network traffic for the purpose of QoS, Intrusion Detection and application specific traffic classification. In this paper, we have done traffic analysis on the network packets captured through data transfer in whatsapp web. In the result, we have explored the user activities such as message texting, contact sharing, voice message, location sharing, media transfer and status viewing. Packet level traffic analysis of user activities reveal patterns in the encrypted SSL communication. This pattern is identified across SSL packet lengths for WhatsApp media transfer and voice message communication. Other important features WhatsApp is the ability to view the status of the message being sent. We have identified the read and unread message status in these data packets by exposing signatures in the network layer. These signatures are identified with the help of the SSL lengths in the TLS header information of WhatsApp Web network traffic traces. Various other information on WhatsApp traffic presented in our study is relevant to the version of WhatsApp Web v0.3.2386.
MAPK Signaling Pathway was Dysregulated in Acute Myeloid Leukemia with RUNX1 Mutations
Authors: he Mingmin , Cai Xiongwei , Zeng Yuanyuan 
Published: May 2021

Abstract
The purpose of this study was to investigate the relationship between RUNX1 mutations and MAPK signaling pathway in acute myeloid leukemia (AML). In this study, we analyzed miRNA expression with 5 mutant RUNX1 and 9 wild-type RUNX1 cases from TCGA database of AML. Six miRNAs were differently expressed with significance, and three of them were related to overall survival. Predicted target genes of these 3 miRNAs were highly enriched in MAPK signaling pathway by functional enrichment with miRWalk3.0. Besides, genes among RUNX1 associated genes directly regulated by RUNX1 were involved in MAPK signaling pathway, too. Taken together, we demonstrate three DEmiRNAs and three genes correlated to RUNX1 were correlated with prognosis in AML, and RUNX1 modulated MAPK signaling pathway in AML.
Surface Charge-Dependent Mitochondrial Response to Similar Intracellular Nanoparticle Contents at Sublethal Dosages
Authors: Jin Xiaoting , Yu Haiyi , Zhang Ze , Cui Tenglong , Wu Qi , Liu Xiaolei , Gao Jie , Zhao Xingchen , Shi Jianbo , Qu Guangbo , Jiang Guibin 
Published: May 2021

Abstract
Background: Considering the inevitability for humans to be frequently exposed to nanoparticles (NPs), understanding the biosafety of NPs is important for rational usage. As an important part of the innate immune system, macrophages are widely distributed in vital tissues and are also a dominant cell type that engulfs particles. Mitochondria are one of the most sensitive organelles when macrophages are exposed to NPs. However, previous studies have mainly reported the mitochondrial response upon high-dose NP treatment. Herein, with gold nanoparticles (AuNPs) as a model, we investigated the mitochondrial alterations induced by NPs at a sublethal concentration.Results: At a similar internal exposure dose, different AuNPs showed distinct degrees of effects on mitochondrial alterations, including reduced tubular mitochondria, damaged mitochondria, increased reactive oxygen species (ROS), and decreased adenosine triphosphate (ATP). Cluster analysis, two-way ANOVA, and multiple linear regression suggested that the surface properties of AuNPs were the dominant determinants of the mitochondrial response. Based on the correlation analysis, the mitochondrial response was increased with the change in zeta potential from negative to positive. The alterations in mitochondrial respiratory chain proteins indicated that complex V was an indicator of the mitochondrial response to low-dose NPs.Conclusion: Our current study suggests potential hazards of modified AuNPs on mitochondria even under sublethal dose, indicates the possibility of surface modification in biocompatibility improvement, and provides a new way to better evaluation of nanomaterials biosafety.
Environmental Enrichment Protects Offspring of Preeclamptic-Like Rat Model From Cognitive Decline
Authors: Lu Huiqing , Gong Lili , Xu Huangfang , Zhou Qiongjie , Zhao Huanqiang , Wu Suwen , Hu Rong , Li Xiaotian 
Published: May 2021

Abstract
Background: Preeclampsia affects 5-8% of all pregnancies and contributes to adverse pregnancy and birth outcome. In addition to short-term effects of preeclampsia, it can exert long-term adverse effects on offspring. Numerous studies has demonstrated that offspring of preeclamptic women exhibited cognitive deficit from childhood to old age. However, effective ways to improving their cognitive ability remains to be investigated. The aim of this study was to explore whether Environmental Enrichment in early life could restore cognitive ability of offspring of preeclampsia rat model, as well as cellular and molecular mechanism by which EE improve cognitive ability.Methods: L-NAME was used to establish preeclampsia rat model. The spatial learning and memory ability of 56-day-old offspring was evaluated by Morris Water Maze. Immunofluorescence was performed to evaluate cell proliferation and apoptosis in the DG region of hippocampus. qRT-PCR was performed to examine the expression level of neurogenesis-associated genes and inflammatory cytokines. Enzyme-linked immune absorbent assay was performed to evaluate the concentration of Vascular endothelial growth factor (VEGF) and inflammatory cytokines in the hippocampus.Results: The administration of L-NAME led to increased systolic blood pressure and urine protein level of pregnant rat. Offspring in L-NAME group exhibited impaired spatial learning ability and memory. The hippocampus neurogenesis and synaptic plasticity was impaired in offspring of L-NAME group. Furthermore, the cell apoptosis in hippocampus was increased in L-NAME group. The hippocampus was skewed to a pro-inflammatory profile, reflected by increased inflammatory cytokines level. While EE improved cognitive ability of offspring in L-NAME group and resulted in increased hippocampal neurogenesis and synaptic proteins expression level, decreased apoptosis level and inflammatory cytokines.Conclusions: Environment Enrichment resolves cognitive impairment in offspring of preeclampsia rat model by improving hippocampal neurogenesis and synaptic plasticity, normalizing the apoptosis level and the inflammation balance.
Metagenomics Revealing Molecular Profiling of Microbial Community Structure and Metabolic Capacity In Bamucuo, Tibet
Authors: Wei Cai , Sun Dan , Yuan Wenliang , Li Lei , Dai Chaoxu , Chen Zuozhou , Zeng Xiaomin , Wang Shihang , Tang Yifan , Jiang Shouwen , Wu Zhichao , Peng Xiaoning , Jiang Linhua , peng Sihua 
Published: May 2021

Abstract
Background: The Qinghai-Tibet Plateau (QTP) is the highest plateau in the world, and the microorganisms there play vital ecological roles in the global biogeochemical cycle; however, detailed information on the microbial communities in QTP is still lacking. Results: Here, we performed a landscape survey of the microorganisms in Bamucuo, Tibet, resulting in 160,212 (soil) and 135,994 (water) contigs by shotgun metagenomic methods, and generated 75 nearly complete metagenome-assembled genomes (MAGs). Proteobacteria, Actinobacteria and Firmicutes were found to be the three most dominant bacterial phyla, while Euryarchaeota was the most dominant archaeal phylum. Surprisingly, Pandoravirus salinus was found in the soil microbial community. The KEGG annotations showed that the genes related to metabolism accounted for 62.9% (soil) and 58.4% (water), respectively. Of the 75 MAGs, 63 were found to contain the genes related to all the six carbon fixation pathways, and the heavy metal resistance genes, the pressure response subsystem, and the secondary metabolite biosynthesis gene clusters (BGCs) were discovered to be abundant. Conclusions: We concluded that the microorganisms in Bamucuo fix carbon mainly through the 3-hydroxypropionic bi-cycle pathway; this study, for the first time, characterized the microbial community composition and metabolic capacity in QTP high-altitude areas (with an altitude of 4,555 meters), confirmed that QTP is a huge and valuable resource bank in which more new non-resistant antibiotics and many other bioactive substances could be developed, and provided the expanded information for further microbial community studies in QTP.
Improved Catalytic Performance of Carrier-Free Immobilized Lipase by Advanced Cross-Linked Enzyme Aggregates Technology
Authors: Jiaojiao Xia , Yan Yan , Zou Bin , Onyinye Adesanya Idowu 
Published: May 2021

Abstract
The cross-linked enzyme aggregates (CLEAs) are one of the technologies that quickly immobilize the enzyme without a carrier. This carrier-free immobilization method has the advantages of simple operation, high reusability and low cost. In this study, ionic liquid with amino group (1-aminopropyl-3-methylimidazole bromide，IL) was used as the novel functional surface molecule to modify industrialized lipase (Candida rugosa lipase, CRL). The enzymatic properties of the prepared CRL-FIL-CLEAs were investigated. The activity of CRL-FIL-CLEAs (5.51 U/mg protein) was 1.9 times higher than that of CRL-CLEAs without surface modification (2.86 U/mg protein). After incubation at 60℃ for 50 min, CRL-FIL-CLEAs still maintained 61% of its initial activity, while the value for CRL-CLEAs was only 22%. After repeated use for five times, compared with the 22% residual activity of CRL-CLEAs, the value of CRL-FIL-CLEAs was 51%. Further kinetic analysis indicated that the Km values for CRL-FIL-CLEAs and CRL-CLEAs were 4.80 mM and 8.06 mM, respectively, which was inferred that the affinity to substrate was increased after modification. Based on the above results, it was indicated that this method provided a new idea for the effective synthesis of immobilized enzyme.
Comparing Infant and Toddler Sleep Patterns Prior to and During the First Wave of Home Confinement Due to COVID-19 in Spain
Authors: Cassanello Pia , Irene Ruiz-Botia , Pere Sala-Castellvi , Carlos Martin Juan , Martínez-Sanchez Jose , Albert Balaguer 
Published: May 2021

Abstract
IntroductionRecent literature has shown that sleep patterns are shaped during the first years of life, playing a relevant role in children’s functioning. We focused on comparing sleep patterns in infants and toddlers in Spain before and during COVID-19 home confinement to assess the immediate impact on sleep patterns. Methodse compared data from two cross-sectional surveys from parents of 1,658 children three to 36 months of age from Spain. One conducted before COVID-19 (2017-2018, n=1,380) and another during COVID-19 pandemic (March-May of 2020, n=254). We used an internet self-administrated questionnaire using the Brief Infant Sleep Questionnaire (BISQ) criteria in both surveys.ResultsDuring confinement infants and toddlers went to sleep later (median bedtime 21.5 before confinement vs. 21.6 during confinement p=0.004). We found a statistically significant increase in infants’ and toddlers’ sleep latency by >30 minutes during confinement (p<0.001). Based on the recommended BISQ criteria for classifying inadequate sleep patterns, we observed a statistically significant increase in poor sleepers meeting at least one criterion during confinement (p<0.001). ConclusionsParents during COVID-19 home confinement reported several factors affecting the quality of their children’s sleep. Follow-up studies can help understand the potential long-term effects of the COVID-19 pandemic on sleep patterns.
Spatial Modeling of Relationship Between Soil Erosion Factors and Land-use Changes at Sub-Watershed Scale for the Talar Watershed, Iran
Authors: Mircholli Fahimeh , Khanghah Maziar Mohammadi , Sadeghi Seyed Hamidreza 
Published: May 2021

Abstract
Soil erosion is one of the most common types of land degradation. To provide useful information for proper management, quantitative soil erosion evaluation and identification of effective factors are needed. However, rare studies have been reported on spatial modeling of soil erosion in connection with affective factors to prioritize the locality and the type of erosion control measures Hence, the aim of this study was to (1) assess erosion-prone areas in the Talar Watershed, Iran, using the Revised Universal Soil Loss Equation (RUSLE) model, and (2) investigate the relationship between soil erosion variability and land-use changes. Toward that, the ordinary least squares (OLS), geographically weighted regression (GWR) models, and Principal Component Analysis (PCA) were used to analyze spatial relationships between soil erosion, and land-use, and the RUSLE factors. The results of the OLS and GWR models indicated these relationships are spatially non-stationary and GWR models had a good predictive performance rather than OLS with lower Akaike's Information Criterion (from 254.31 to 276.81 in OLS, and from 247.87 to 269.42 in GWR) and higher adjusted R2 values (from 0.12 to 0.54 in OLS, and from 0.36 to 0.66 in GWR). Among the aforementioned variables, LS factor, P factor, forest, and irrigated land were the most effective variables in GWR models. The results of PCA showed PC1 and PC2 explained 66.2 % of the variation in soil erosion concerning land-use and the RUSLE factors. These results provided appropriate references for managers and experts in the proper planning of the study watershed.
Microscopic Nuclei Classification, Segmentation, and Detection with improved Deep Convolutional Neural Networks (DCNN)
Authors: Alom Md Zahangir , Asari Vijayan K. , Parwani Anil , Taha Tarek M. 
Published: May 2021

Abstract
BackgroundNuclei classification, segmentation, and detection from pathological images are challenging tasks due to cellular heterogeneity in the Whole Slide Images (WSI).MethodsIn this work, we propose advanced DCNN models for nuclei classification, segmentation, and detection tasks. The Densely Connected Neural Network (DCNN) and Densely Connected Recurrent Convolutional Network(DCRN) models are applied for the nuclei classification tasks. The Recurrent Residual U-Net (R2U-Net) and the R2UNet-based regression model named as the University of Dayton Net (UD-Net) are applied for nuclei segmentation and detection tasks respectively.The experiments are conducted on publicly available datasets including Routine Colon Cancer (RCC) classification and detection and the Nuclei Segmentation Challenge 2018 datasets for segmentation task. The performance of the proposed methods is compared against the existing approaches in terms of precision, recall, Dice Coefficient (DC), Mean Squared Error (MSE), F1-score, and overall testing accuracy by performing pixels and cell-level analysis.ResultsThe experimental results demonstrate around 2.2% and 4.5% higher performance in terms of F1-score for nuclei classification and detection tasks when compared to the recently published DCNN based method. Also, for nuclei segmentation, the R2U-Net shows around 91.63% testing accuracy in terms of DC which is around 0.76% higher compared to the U-Net model.ConclusionThe proposed methods demonstrate robustness with better quantitative and qualitative results in three different tasks for analyzing the WSI.
The Effect of Preserving Pregnancy in Cervical Cancer Diagnosed During Pregnancy: A Retrospective Study
Authors: He Zuoxi , Xie Chuan , Qi Xiaorong , Hu Zhengjun , He Yuedong 
Published: May 2021

Abstract
ObjectiveCervical cancer diagnosed during pregnancy is a rare event, and data regarding efficacy of cancer treatment during pregnancy is limited. This study aimed to assess the safety of continuation of the pregnancy for mother and fetus when concomitantly diagnosed with cervical cancer.MethodsThis study retrospectively analyzed all cervical cancer patients diagnosed while pregnant or immediately postpartum, inclusive from Jan 2010 to June 2019 at our institute. Patient clinical details and follow-up were obtained from hospital records. ResultsThe study comprised 40 patients with clinical cancer stages of ⅠA1 (1/40, 2.5%); ⅠB1 (15/40, 37.5%); IB2 (10/40, 25%); ⅡA (12/40, 30%); and ⅡB (2/40, 5%). There were 38 patients diagnosed during pregnancy, and 2 diagnosed in the postpartum period. Of the 38 patients, 17 were diagnosed in the first trimester, 13 in the second trimester, and 8 in the third trimester. Ten of 38 patients (26.3%) continued their pregnancy after learning of their diagnosis; 7 (70%) in the third trimester and 3 (30%) in the second trimester. The mean time from diagnosis to surgery in the patients who continued their pregnancy was 52.7 days, which was statistically significantly greater than the termination of pregnancy group (52.7 vs 16.3 days, P < 0.01). Notably, there was no survival difference between the 2 groups (100% vs 90.91%, P =0.54), and none of the pregnant women who ultimately died had delayed treatment due to pregnancy. Similarly, the surgical estimated blood loss and operative duration comparing the 2 groups were not significantly different. ConclusionsIn the present study, the gestational age of pregnancy at the time of initial diagnosis of cervical cancer was an important determinant in the disease management. Continuation of the pregnancy when diagnosed with cervical cancer did not affect the oncologic outcome of the mother nor increase either surgical or obstetric complications. Additionally, the use of neoadjuvant chemotherapy did not threaten the health of the fetus. These results may be useful in counseling patients facing the diagnosis of cervical cancer during pregnancy.
MMP-14-targeted Nanoprobe for in vivo Fluorescence Imaging of Rupture-prone Carotid Plaques
Authors: Han Mengtao , Liu Kaining , Xiao Hongqiu , Sun Tao , Wang Fei , He Yiming , Wang Donghai 
Published: May 2021

Abstract
Background: The identification of rupture-prone carotid plaques for preventing stroke remains a clinical challenge. Macrophage matrix metalloproteinase (MMP)-14, which contributes to plaque progression and destabilisation, could be a promising biomarker for plaque imaging. This study aimed to design and synthesise an MMP-14-targeted nanoprobe to noninvasively visualise the behaviour of M1 macrophages in atherosclerotic plaques.Methods: A fluorescence molecular imaging probe (AuNPs@PEG-Peptide-Cy5.5) was constructed by covalently attaching the fluorescent dye cyanine (Cy) 5.5, an MMP-14 substrate, and polyethylene glycol (PEG) 5000-wrapped gold nanoparticles (AuNPs), and then administered via tail vein injection to carotid atherosclerosis models for in vivo fluorescence imaging. Additionally, carotid tissues and cultured macrophages were analysed for nanoprobe binding, and MMP-14 and inflammation-related marker expression was evaluated by polymerase chain reaction, western blotting, and immunohistochemistry.Results: MMP-14 expression significantly increased with plaque progression, along with the upregulation of MMP-2 and inflammatory M1 markers, CD68 and F4/80, and significant downregulation of the M2 marker CD206. All of cell, tissue and in vivo fluorescence imaging exhibited a favourable targeting efficacy of AuNPs@PEG-Peptide-Cy5.5 for MMP-14.Conclusions: MMP-14, a cell membrane-anchoring enzyme, can serve as a biomarker of vulnerable plaques, and MMP-14 substrate-based AuNPs@PEG-Peptide-Cy5.5, with an intense fluorescence signal after activation and good biocompatibility, can be applied to screen for and monitor plaque progression in vivo.