bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Milan system for reporting salivary gland cytopathology: A study of inter‐observer reproducibility
Authors: Layfield Lester J. , Esebua Magda , Yang Zhongbo , Vatzmitsel Maryna , Giorgadze Tamara , Schmidt Robert 
Published: May 2019

AbstractBackgroundIn 2018, the Milan System for Reporting Salivary Gland Cytopathology was published defining a diagnostic categorization scheme with known malignancy risks and clinical follow up recommendations. Inter‐observer reproducibility of the categories was not defined.MethodsSalivary gland fine‐needle aspirations (FNA) were reviewed over a 5 year period and classified by three independent observers. Inter‐observer reproducibility was estimated using observed agreement and chance corrected agreement (Cohen's kappa).ResultsFour hundred and eight cases were reviewed with chance corrected agreement of 0.42 for the original Milan System and 0.48 for a modified system using “similar follow up” categories. Categories 4A and 6B showed substantial agreement (kappa =0.71 and 0.72).ConclusionThe Milan System shows moderate over all agreement between observers. Strongest inter‐observer agreement was seen for categories 4A and 6B.
The use of The Bethesda System for Reporting Thyroid Cytopathology in a Chinese population: An analysis of 13 351 specimens
Authors: Ke Jiang , Jianyong Lei , Ying Liu , Genpeng Li , Linlin Song , Zhihui Li , Jinnan Li , Xueying Su , Yong Jiang , Jingqiang Zhu 
Published: May 2019

AbstractAimsThe Bethesda System for Reporting Thyroid Cytopathology (TBSRTC) has been widely adopted since its introduction. In this study, we aimed to report our experience using this reporting system at a College of American Pathologists (CAP)‐accredited hospital laboratory in a large series of Chinese patients.MethodsAll patients who underwent preoperative ultrasound‐guided thyroid fine‐needle aspiration (FNA) from January 2011 to August 2016 were retrospectively analyzed. Thyroid FNAs were classified according to the Bethesda System. For patients who underwent subsequent surgery at our institution, the diagnostic performance of the preoperative FNA was further analyzed according to four different calculation criteria. All of the follicular variants of papillary thyroid carcinoma specimens were reviewed to exclude NIFTP (noninvasive follicular thyroid neoplasm with papillary‐like nuclear features).ResultsA total of 13 351 thyroid FNAs were included in this analysis. Of the 12 530 sampled patients, 3594 (28.7%) underwent thyroidectomy, and the malignancy rates for each cytological category were as follows: 66.7% unsatisfactory, 14.2% benign, 53.5% undetermined significance, 30.2% follicular neoplasm, 82.0% suspicious, and 99.1% malignant. Only 12 (0.36% of all PTC) patients were reclassified as having NIFTP. The sensitivities of the preoperative FNAs were all above 95.0% and were as high as 99.0%. The specificities ranged from 50.3% to 63.9%, depending on which criteria were used. The positive predictive value was 95.4% for criteria 1 and 2 and was 94.2% for criteria 3 and 4. The negative predictive values ranged from 64.5% to 85.8%. The diagnostic accuracies all exceeded 90.0%, with the highest being 94.8%.ConclusionThis study revealed the great efficacy and accuracy of TBSRTC in a large Chinese population for the first time.
Staging and normal table of postembryonic development of the clownfish (Amphiprion ocellaris)
Authors: Roux Natacha , Salis Pauline , Lambert Anne , Logeux Valentin , Soulat Olivier , Romans Pascal , Frédérich Bruno , Lecchini David , Laudet Vincent 
Published: May 2019

AbstractBackgroundThe clownfish Amphiprion ocellaris is one of the rare coral reef fish species that can be reared in aquaria. With relatively short embryonic and larval development, it could be used as a model species to study the impact of global changes such as temperature rise or anthropogenic threats (eg, pollution) on the postembryonic development at molecular and endocrinological levels. Establishing a developmental table allows us to standardize sampling for the scientific community willing to conduct experiments on this species on different areas: ecology, evolution, and developmental biology.ResultsHere, we describe the postembryonic developmental stages for the clownfish A. ocellaris from hatching to juvenile stages (30 days posthatching). We quantitatively followed the postembryonic growth and described qualitative traits: head, paired and unpaired fins, notochord flexion, and pigmentation changes. The occurrence of these changes over time allowed us to define seven stages, for which we provide precise descriptions.ConclusionsOur work gives an easy system to determine A. ocellaris postembryonic stages allowing, thus, to develop this species as a model species for coral reef fishes. In light of global warming, the access to the full postembryonic development stages of coral reef fish is important to determine stressors that can affect such processes.
Patterns of univariate and multivariate plasticity to elevated carbon dioxide in six European populations ofArabidopsis thaliana
Authors: Jonas Mark , Cioce Brandon 
Published: May 2019

AbstractThe impact of elevated carbon dioxide on plants is a growing concern in evolutionary ecology and global change biology. Characterizing patterns of phenotypic integration and multivariate plasticity to elevated carbon dioxide can provide insights into ecological and evolutionary dynamics in future human‐altered environments. Here, we examined univariate and multivariate responses to carbon enrichment in six functional traits among six European accessions ofArabidopsis thaliana. We detected phenotypic plasticity in both univariate and multivariate phenotypes, but did not find significant variation in plasticity (genotype by environment interactions) within or among accessions. Eigenvector, eigenvalue variance, and common principal components analyses showed that elevated carbon dioxide altered patterns of trait covariance, reduced the strength of phenotypic integration, and decreased population‐level differentiation in the multivariate phenotype. Our data suggest that future carbon dioxide conditions may influence evolutionary dynamics in natural populations ofA. thaliana.
Evidence of stress imprinting with population‐level differences in two moss species
Authors: Liu Weiqiu , Xu Jianqu , Fu Wei , Wang Xiangyuan , Lei Chunyi , Chen Yunfeng 
Published: May 2019

AbstractPlants are often repeatedly exposed to stresses during their lives and have a mechanism called stress imprinting that provides “memories” of stresses they experience and increases their ability to cope with later stresses. To test hypotheses that primed bryophytes can preserve their stress imprinting after 6 days of recovery and induce higher levels of osmolytes and ROS‐scavenging activities upon later stress exposure, and there exist population‐level differentiation in their desiccation defenses, we transplanted samples of two populations of each of two moss species, Hypnum plumaeforme and Pogonatum cirratum, in a nature reserve in southern China. After 16 months of acclimation, sets of each population were subjected to control, one‐time desiccation stress, duplicated desiccation stress and cross‐stress (low temperature stress followed by desiccation stress) treatments. Levels of oxidant enzymes, osmolytes, and phytohormones in the samples were then determined. The desiccation stress generally led to increases in activities or contents of superoxide dismutase, guaiacol peroxidase, catalase, proline, soluble sugars, soluble proteins, and stress hormones including abscisic acid (ABA), jasmonates (JA), and salicylic acid (SA), with differences between both species and populations. After a 6‐day recovery period, contents of phytohormones (including ABA, JA, SA, and cytokinins) in stressed H. plumaeforme had substantially fallen toward control levels. The duplicated and cross‐stress treatments generally led to further accumulation of proline, soluble sugars, and soluble proteins, with further increases in activities of antioxidant enzymes in some cases. Furthermore, significant differences between allochthonous and native populations were found in contents of malondialdehyde and osmolytes, as well as antioxidant enzyme activities. Our results confirm the hypotheses and highlight the importance of osmolytes in mosses' stress responses.
Cascading Ecological Impacts of Fullerenes in Freshwater Ecosystems
Authors: Moore Elizabeth A. , Babbitt Callie W. , Connelly Sandra J. , Tyler Anna Christina , Rogalskyj George 
Published: May 2019

Abstract
Carbonaceous nanomaterials, such as fullerenes (C60, C70) and the derivative phenyl-C61-butyric acid methyl ester (PCBM), have promising application in solar energy technologies. Although the acute ecotoxicity of C60 has been reported widely in the literature, ecotoxicity assays for different fullerene forms and broader ecosystem impact studies remain scarce. To address these knowledge gaps, acute, chronic, and life stage exposure studies with freshwater zooplankton, Daphnia magna and Daphnia pulex, were performed for each material. Experimental results indicated that C60 and PCBM are not acutely toxic at estimated environmentally relevant concentrations; however, C70 had significant acute effects. All forms of fullerene caused a gradual elevation in heart rate over time and visual darkening of the Daphnia spp. carapace. The impact of fullerenes on susceptibility to predation was then assessed experimentally by presenting D. pulex to the visual predator Lepomis macrochirus (bluegill). Predation risk was significantly increased in fullerene-exposed D. pulex. The present study underscores the need to broaden the scope of traditional ecotoxicity for emerging materials: studies are required that evaluate portfolios of related nanomaterials and that capture chronic and cascading ecosystem-level effects. Environ Toxicol Chem 2019;38:1714‒1723. © 2019 SETAC
Abstract
Fullerene exposure can create cascading ecological impacts that are not captured through acute toxicity assays alone. PC61BM = phenyl-C61-butyric acid methyl ester.
An optimal multitier resource allocation of cloud RAN in 5G using machine learning
Authors: Bashir Ali Kashif , Arul Rajakumar , Basheer Shakila , Raja Gunasekaran , Jayaraman Ramkumar , Qureshi Nawab Muhammad Faseeh 
Published: May 2019

AbstractThe networks are evolving drastically since last few years in order to meet user requirements. For example, the 5G is offering most of the available spectrum under one umbrella. In this work, we will address the resource allocation problem in fifth‐generation (5G) networks, to be exact in the Cloud Radio Access Networks (C‐RANs). The radio access network mechanisms involve multiple network topologies that are isolated based on the spectrum bands and it should be enhanced with numerous access technology in the deployment of 5G network. The C‐RAN is one of the optimal technique to combine all the available spectral bands. However, existing C‐RAN mechanisms lacks the intelligence perspective on choosing the spectral bands. Thus, C‐RAN mechanism requires an advanced tool to identify network topology to allocate the network resources for substantial traffic volumes. Therefore, there is a need to propose a framework that handles spectral resources based on user requirements and network behavior. In this work, we introduced a new C‐RAN architecture modified as multitier Heterogeneous Cloud Radio Access Networks in a 5G environment. This architecture handles spectral resources efficiently. Based on the simulation analysis, the proposed multitier H‐CRAN architecture with improved control unit in network management perspective enables augmented granularity, end‐to‐end optimization, and guaranteed quality of service by 15 percentages over the existing system.
A community‐based, cross‐sectional study of hrHPV DNA self‐sampling‐based cervical cancer screening in rural Karnataka, India
Authors: Adsul Prajakta , Srinivas Vijaya , Gowda Savitha , Nayaka Shivamma , Pramathesh Rashmi , Chandrappa Kavitha , Khan Anisa , Jayakrishna Poornima , Madhivanan Purnima 
Published: May 2019

AbstractObjectiveTo examine the feasibility of implementing a high‐risk HPV (hrHPV) DNA‐based screening program for cervical cancer and the prevalence of hrHPV DNA‐positive women in a community setting in rural India.MethodsA cross‐sectional study was conducted at the community level in the Hunsur taluk of the Mysore district from January to August 2016. Cervical cancer screening was conducted with self‐collected vaginal samples that were analyzed using the Hybrid Capture 2 (HC2) assay (Qiagen, USA).ResultsThe majority of participants were aged 30–39 years, with no formal schooling, from a lower caste, and lived below an annual household income of US$1499. After group health education and one‐on‐one counseling, a total of 473 women underwent self‐sampling. Of these, 36 (7.6%) were positive for hrHPV and only 24 (66.6%) underwent follow‐up diagnostic triaging. Cancer was detected in two women, who were referred to appropriate healthcare facilities for further treatment.ConclusionImplementation of hrHPV DNA‐based screening tests using self‐sampling can be feasible in rural settings in India. However, substantial resources are required for providing health education and one‐on‐one counseling to inform asymptomatic women about the benefits of testing and, more importantly, to improve compliance with follow‐up.
Biological nascent evolution of snail bone and collagen revealed by nonlinear optical microscopy
Authors: Li Rui , Wang Lei , Mu Xijiao , Chen Maodu , Sun Mengtao 
Published: May 2019

AbstractUsing nonlinear optical microscopy of coherent antistokes Raman scattering (CARS), second harmonic generation (SHG) and two‐photo excitation fluorescence, we in situ observed how the collagen and the bone grow synergistically and competitively during nascent biological evolution. The and ions were first observed to be dispersed in the liquid environment, and the collagen was observed 2 days later. With the help of the collagen, the and ions gradually moved closer to the collagen, and then the bone was produced in the forms of CaCO3 and CaPO3. When the bone was completed with the help of the collagen, the collagen gradually disappeared. The biological evolution of snail bone and collagen can be well revealed by CARS and SHG, and in addition, the biological evolution of structure and morphology can be clearly observed day by day.
Enhancing expression level and stability of transgene mediated by episomal vector via buffering DNA methyltransferase in transfected CHO cells
Authors: Wang Xiao‐Yin , Yi Dan‐Dan , Wang Tian‐Yun , Wu Yan‐Fang , Chai Yu‐Rong , Xu Dan‐Hua , Zhao Chun‐Peng , Song Chao 
Published: May 2019

AbstractNonviral episomal vectors present attractive alternative vehicles for gene therapy applications. Previously, we have established a new type of nonviral episomal vector‐mediated by the characteristic motifs of matrix attachment regions (MARs), which is driven by the cytomegalovirus (CMV) promoter. However, the CMV promoter is intrinsically susceptible to silencing, resulting in declined productivity during long‐term culture. In this study, Chinese hamster ovary (CHO) cells and DNA methyltransferase‐deficient (Dnmt3a‐deficient) CHO cells were transfected with plasmid‐mediated by MAR, or CHO cells were treated with the DNA methylation inhibitor 5‐Aza‐2′‐deoxycytidine. Flow cytometry, plasmid rescue experiments, fluorescence in‐situ hybridization (FISH), and bisulfite sequencing were performed to observe transgene expression, its state of existence, and the CpG methylation level of the CMV promoter. The results indicated that all DNA methylation inhibitor and methyltransferase deficient cells could increase transgene expression levels and stability in the presence or absence of selection pressure after a 60‐generation culture. Plasmid rescue assay and FISH analysis showed that the vector still existed episomally after long‐time culture. Moreover, a relatively lower CMV promoter methylation level was observed in Dnmt3a‐deficient cell lines and CHO cells treated with 5‐Aza‐2′‐deoxycytidine. In addition, Dnmt3a‐deficient cells were superior to the DNA methylation inhibitor treatment regarding the transgene expression and long‐term stability. Our study provides the first evidence that lower DNA methyltransferase can enhance expression level and stability of transgenes mediated by episomal vectors in transfected CHO cells.
V617F‐independent upregulation of JAK2 gene expression in patients with inflammatory bowel disease
Authors: Asadzadeh‐Aghdaei Hamid , Mashayekhi Kazem , Koushki Khadijeh , Azimzadeh Pedram , Rostami‐Nejad Mohammad , Amani Davar , Chaleshi Vahid , Haftcheshmeh Saeed Mohammadian , Sahebkar Amirhossein , Zali Mohammad Reza 
Published: May 2019

AbstractBackgroundInflammatory bowel disease (IBD) is one of the most important immune‐mediated disorders of the gastrointestinal tract. Besides, IBD is associated with numerous extraintestinal complications such as venous thromboembolism (VTE), an important risk factor for vascular complications, which results in the increased morbidity and mortality. The JAK2 (Janus kinase 2) V617F mutation is a well‐known point mutation which is involved in the pathogenesis of IBD, and VTE. Therefore, the aims of this study were to evaluate expression of JAK2 and association of V617F mutation in JAK2 of Iranian patients with IBD.MethodsTwo hundred and forty‐six patients with IBD (209 UC and 37 CD) and 206 healthy controls were enrolled in this study. The genomic DNA and total RNA were extracted from peripheral blood mononuclear cells (PBMCs). Then, the JAK2 V617F mutation detection was performed using the restriction fragment length polymorphism (RFLP) method. In addition, the JAK2 mRNA expression was evaluated using a quantitative polymerase chain reaction (q‐PCR) using the SYBR Green assay.ResultsThere was no association of V61F mutation in patients with IBD with or without thrombosis compared with healthy control. However, the relative mRNA expression of JAK2 was significantly upregulated in patients with IBD in comparison with healthy control (P < 0.0001). In addition, the JAK2 mRNA expression was significantly decreased in patients with IBD having thrombosis compared with those without thrombosis (
P < 0.0001).ConclusionsTaken together our findings suggested that JAK2 V61F‐independent upregulation of JAK2 mRNA expression in patients with IBD. Moreover, despite the absence of JAK2 V617F mutation in patients with IBD, the increased gene expression of JAK2 can be explained by another molecular mechanism such as regulation of gene expression at the transcriptional level which may play crucial roles in the pathogenesis of IBD.
Plasma metabolite biomarkers related to secondary hyperparathyroidism and parathyroid hormone
Authors: Shen Qixia , Xiang Wenyu , Ye Sen , Lei Xin , Wang Lefeng , Jia Sha , Shao Xue , Weng Chunhua , Shen Xiujin , Wang Yucheng , Feng Shi , Qu Lihui , Wang Cuili , Chen Jianghua , Zhang Ping , Jiang Hong 
Published: May 2019

AbstractBackgroundHyperphosphatemia, hypocalcemia, and elevation of parathyroid hormone (PTH) are typical abnormalities of uremic patients with Secondary hyperparathyroidism (SHPT). However, metabolic imbalance associated with SHPT is not well understood.MethodsA total of 15 SHPT patients with an intact parathyroid hormone (iPTH) level > 600 pg/mL were set as preoperative (PR) group, 15 age‐ and gender‐matched controls who had undergone parathyroidectomy plus forearm transplantation because of hyperparathyroidism and achieved an iPTH level <150 pg/mL were set as postoperative (PO) group. Metabolite profiling of these 30 uremic patients and five healthy controls (HC) was performed using ultra performance liquid chromatography‐mass spectrometry.ResultsFive differential metabolites, including allyl isothiocyanate, L‐phenylalanine, D‐Aspartic acid, indoleacetaldehyde, and D‐galactose correlated with PTH were identified in this study. Taking them as a biomarker signature, PR group can be distinguished from HC group with an area under the curve (AUC) of 0.947 (95% CI, 0.76‐1) and PO group with an AUC of 0.6 (95% CI, 0.38‐0.807).ConclusionsThe serum metabolome correlated with PTH is successfully demonstrated for a better understanding of the pathogenesis of SHPT.
Modulation of cancer cell signaling by long noncoding RNAs
Authors: Mirhosseini Seyed Ali , Sarfi Mohammad , Samavarchi Tehrani Sadra , Mirazakhani Mohammad , Maniati Mahmood , Amani Jafar 
Published: May 2019

AbstractCellular signaling pathways play a very important role in almost all molecular processes in the cell, and are generally composed of a complex set of cascades in which enzymes and proteins play a key role. These signaling pathways include different types of cellular signaling classified based on their receptors and effector proteins such as enzyme‐linked receptors, cytokine receptors, and G‐protein‐coupled receptors each of which is subdivided into different classes. Signaling pathways are tightly controlled by different mechanisms mostly thorough inhibiting/activating their receptors or effector proteins. In the last two decades, our knowledge of molecular biology has changed dramatically and today we know that more than 85% of the human genome expresses noncoding RNAs most of which are crucial in the cellular and molecular mechanisms of cells. One of these noncoding RNAs are long noncoding RNAs (lncRNA) containing more than 200 nucleotides. LncRNAs participate in the progression of cancer growth through several mechanism including signaling pathways. In this review, we summarize some of the most important of lncRNAs and their effect on important signaling pathways.
Identification of circular RNA‐associated competing endogenous RNA network in the development of cleft palate
Authors: Shu Xuan , Cheng Liuhanghang , Dong Zejun , Shu Shenyou 
Published: May 2019

AbstractCircular RNAs (circRNAs) serve as competing endogenous RNAs (ceRNAs) and indirectly regulate gene expression through shared microRNAs (miRNAs). However, the regulatory mechanisms of circRNA as ceRNA associated with the fusion of palatal shelves in palatogenesis are yet unclear. This study aimed to explore the potential mechanism underlying the role of circRNA as ceRNA in cleft palate (CP). First, we systematically analyzed RNA‐seq and miRNA‐seq data after high‐throughput sequencing for embryonic palatal shelf tissues from a mouse CP model induced by maternal exposure to all‐trans retinoic acid on embryonic gestation day 14.5 (E14.5). Thirty‐nine circRNAs, 18 miRNAs, and 936 messenger RNAs (mRNAs) were significantly dysregulated (log2 [fold change {FC}] > 1; P < 0.05). Thereafter, we constructed a circRNA‐associated ceRNA network. Finally, we determined the circRNA_0954–miRNA‐881‐3p‐PRKAR1α ceRNA network as a hub involved in palatogenesis. Gene Ontology analysis revealed that ceRNA‐related genes were associated with facial morphogenesis and developmental gene silencing. Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated that ceRNA‐related genes are involved in apoptosis (P < 0.05, fold enrichment >1). Quantitative reverse transcription polymerase chain reaction was performed to verify the results of ceRNA analysis. We found that the circRNA‐miRNA‐mRNA ceRNA network is involved in palatogenesis. The present results imply that circRNA_0954‐miRNA‐881‐3p‐PRKAR1α ceRNA network may cause dysfunctional palatal fusion and might facilitate the development of novel epigenetic biomarkers to treat CP in the future.