bluuebunny/crossref_metadata_2025_split huggingface dataset:
CircRNA-5692 inhibits the progression of hepatocellular carcinoma by sponging miR-328-5p to enhance DAB2IP expression
Authors: Liu Zhenguo , Yu Yaqun , Huang Zebing , Kong Yi , Hu Xingwang , Xiao Wei , Quan Jun , Fan Xuegong 
Published: November 2019

AbstractCircular RNAs (circRNAs), one kind of noncoding RNAs, can interact with miRNA and transcription factors to regulate gene expression. However, little is known on which circRNA is crucial for the pathogenesis of hepatocellular carcinoma (HCC). CircRNA expression profile was analyzed by a microarray. Regulatory gene targets were predicted by bioinformatics analysis and validated by luciferase assay. Their expression was determined by qRT-PCR and Western blotting. DNA methylation was determined by methylation-specific PCR. Gene knockdown and overexpression were mediated by lentivirus-mediated shRNA and transfection with plasmids for cDNA expression, respectively. MTT assay, wound-healing assay, transwell invasion assay, and flow cytometry were used to determine malignant behaviors of HCC cells. HCC xenograft mouse model was used to determine the in vivo effects of circRNA-5692. CircRNA-5692 expression was downregulated in HCC tissues, and circRNA-5692 overexpression attenuated the malignant behaviors of HCC cells. Bioinformatics predicted that circRNA-5692 interacted with miR-328-5p, which targeted the DAB2IP mRNA. Actually, miR-328-5p promoted the malignant behaviors of HCC cells, while DAB2IP had opposite effects. Moreover, circRNA-5692 overexpression inhibited the growth of xenograft HCC tumors in vivo by decreasing miR-328-5p expression to enhance DAB2IP expression. In conclusion, the circRNA-5692–miR-328-5p–DAB2IP regulatory pathway inhibits the progression of HCC. Our findings may provide potential new targets for the diagnosis and therapy of HCC.
MKL1 promotes endothelial-to-mesenchymal transition and liver fibrosis by activating TWIST1 transcription
Authors: Li Zilong , Chen Baoyu , Dong Wenhui , Kong Ming , Fan Zhiwen , Yu Liming , Wu Dongmei , Lu Jun , Xu Yong 
Published: November 2019

AbstractExcessive fibrogenic response in the liver disrupts normal hepatic anatomy and function heralding such end-stage liver diseases as hepatocellular carcinoma and cirrhosis. Sinusoidal endothelial cells contribute to myofibroblast activation and liver fibrosis by undergoing endothelial-mesenchymal transition (EndMT). The underlying mechanism remains poorly defined. Here we report that inhibition or endothelial-specific deletion of MKL1, a transcriptional modulator, attenuated liver fibrosis in mice. MKL1 inhibition or deletion suppressed EndMT induced by TGF-β. Mechanistically, MKL1 was recruited to the promoter region of TWIST1, a master regulator of EndMT, and activated TWIST1 transcription in a STAT3-dependent manner. A small-molecule STAT3 inhibitor (C188-9) alleviated EndMT in cultured cells and bile duct ligation (BDL) induced liver fibrosis in mice. Finally, direct inhibition of TWIST1 by a small-molecule compound harmine was paralleled by blockade of EndMT in cultured cells and liver fibrosis in mice. In conclusion, our data unveil a novel mechanism underlying EndMT and liver fibrosis and highlight the possibility of targeting the STAT3-MKL1-TWIST1 axis in the intervention of aberrant liver fibrogenesis.
GraphTyper2 enables population-scale genotyping of structural variation using pangenome graphs
Authors: Eggertsson Hannes P. , Kristmundsdottir Snaedis , Beyter Doruk , Jonsson Hakon , Skuladottir Astros , Hardarson Marteinn T. , Gudbjartsson Daniel F. , Stefansson Kari , Halldorsson Bjarni V. , Melsted Pall 
Published: November 2019

AbstractAnalysis of sequence diversity in the human genome is fundamental for genetic studies. Structural variants (SVs) are frequently omitted in sequence analysis studies, although each has a relatively large impact on the genome. Here, we present GraphTyper2, which uses pangenome graphs to genotype SVs and small variants using short-reads. Comparison to the syndip benchmark dataset shows that our SV genotyping is sensitive and variant segregation in families demonstrates the accuracy of our approach. We demonstrate that incorporating public assembly data into our pipeline greatly improves sensitivity, particularly for large insertions. We validate 6,812 SVs on average per genome using long-read data of 41 Icelanders. We show that GraphTyper2 can simultaneously genotype tens of thousands of whole-genomes by characterizing 60 million small variants and half a million SVs in 49,962 Icelanders, including 80 thousand SVs with high-confidence.
Solid-to-liquid phase transitions of sub-nanometer clusters enhance chemical transformation
Authors: Sun Juan-Juan , Cheng Jun 
Published: November 2019

AbstractUnderstanding the nature of active sites is crucial in heterogeneous catalysis, and dynamic changes of catalyst structures during reaction turnover have brought into focus the dynamic nature of active sites. However, much less is known on how the structural dynamics couples with elementary reactions. Here we report an anomalous decrease in reaction free energies and barriers on dynamical sub-nanometer Au clusters. We calculate temperature dependence of free energies using ab initio molecular dynamics, and find significant entropic effects due to solid-to-liquid phase transitions of the Au clusters induced by adsorption of different states along the reaction coordinate. This finding demonstrates that catalyst dynamics can play an important role in catalyst activity.
An oceanic perspective on Greenland’s recent freshwater discharge since 1850
Authors: Perner Kerstin , Moros Matthias , Otterå Odd Helge , Blanz Thomas , Schneider Ralph R. , Jansen Eystein 
Published: November 2019

AbstractInstrumental data evidence an accelerating freshwater release from Arctic sea ice export and the Greenland Ice Sheet over the past three decades causing cooling and freshening in the subpolar North Atlantic region. However, evaluating the observed acceleration on a historical oceanic and climatic perspective remains challenging given the short available instrumental time series. Here we provide a marine perspective on the freshwater releases to the ocean since 1850 as reflected in the northern limb of the Subpolar Gyre. Our reconstructions suggest that the recent acceleration tracks back to the 1940s/50s and is unprecedented since 1850. The melting, initiated by the 1920s natural rise in solar irradiance, accelerated in response to a combined effect of natural and anthropogenic forcing factors. We find that Greenland’s freshwater discharge has contributed to a nutrient-driven fertilization of the upper ocean and consequently increased the marine primary productivity since the 1940s/50s.
Disassociation of Vitamin D’s Calcemic Activity and Non-calcemic Genomic Activity and Individual Responsiveness: A Randomized Controlled Double-Blind Clinical Trial
Authors: Shirvani Arash , Kalajian Tyler Arek , Song Anjeli , Holick Michael F. 
Published: November 2019

AbstractThe aims of this randomized controlled double-blind clinical trial were to assess the impact of vitamin D supplementation on calcium metabolism and non-calcemic broad gene expression by relating them to the individual’s responsiveness to varying doses of vitamin D3. Thirty healthy adults were randomized to receive 600, 4,000 or 10,000 IU/d of vitamin D3 for 6 months. Circulating parathyroid hormone (PTH), 25(OH)D, calcium and peripheral white blood cells broad gene expression were evaluated. We observed a dose-dependent increase in 25(OH)D concentrations, decreased PTH and no change in serum calcium. A plateau in PTH levels was achieved at 16 weeks in the 4000 and 10,000 IU/d groups. There was a dose-dependent 25(OH)D alteration in broad gene expression with 162, 320 and 1289 genes up- or down-regulated in their white blood cells, respectively. Our results clearly indicated that there is an individual’s responsiveness on broad gene expression to varying doses of vitamin D3. Vitamin D3 supplementation at 10,000 IU/d produced genomic alterations several fold higher than 4,000 IU/d even without further changes in PTH levels. Our findings may help explain why there are some inconsistency in the results of different vitamin D’s clinical trials.
Machine learning-based dynamic mortality prediction after traumatic brain injury
Authors: Raj Rahul , Luostarinen Teemu , Pursiainen Eetu , Posti Jussi P. , Takala Riikka S. K. , Bendel Stepani , Konttila Teijo , Korja Miikka 
Published: November 2019

AbstractOur aim was to create simple and largely scalable machine learning-based algorithms that could predict mortality in a real-time fashion during intensive care after traumatic brain injury. We performed an observational multicenter study including adult TBI patients that were monitored for intracranial pressure (ICP) for at least 24 h in three ICUs. We used machine learning-based logistic regression modeling to create two algorithms (based on ICP, mean arterial pressure [MAP], cerebral perfusion pressure [CPP] and Glasgow Coma Scale [GCS]) to predict 30-day mortality. We used a stratified cross-validation technique for internal validation. Of 472 included patients, 92 patients (19%) died within 30 days. Following cross-validation, the ICP-MAP-CPP algorithm’s area under the receiver operating characteristic curve (AUC) increased from 0.67 (95% confidence interval [CI] 0.60–0.74) on day 1 to 0.81 (95% CI 0.75–0.87) on day 5. The ICP-MAP-CPP-GCS algorithm’s AUC increased from 0.72 (95% CI 0.64–0.78) on day 1 to 0.84 (95% CI 0.78–0.90) on day 5. Algorithm misclassification was seen among patients undergoing decompressive craniectomy. In conclusion, we present a new concept of dynamic prognostication for patients with TBI treated in the ICU. Our simple algorithms, based on only three and four main variables, discriminated between survivors and non-survivors with accuracies up to 81% and 84%. These open-sourced simple algorithms can likely be further developed, also in low and middle-income countries.
Surface Chemistry Dependence on Aluminum Doping in Ni-rich LiNi0.8Co0.2−yAlyO2 Cathodes
Authors: Lebens-Higgins Zachary W. , Halat David M. , Faenza Nicholas V. , Wahila Matthew J. , Mascheck Manfred , Wiell Tomas , Eriksson Susanna K. , Palmgren Paul , Rodriguez Jose , Badway Fadwa , Pereira Nathalie , Amatucci Glenn G. , Lee Tien-Lin , Grey Clare P. , Piper Louis F. J. 
Published: November 2019

AbstractAluminum is a common dopant across oxide cathodes for improving the bulk and cathode-electrolyte interface (CEI) stability. Aluminum in the bulk is known to enhance structural and thermal stability, yet the exact influence of aluminum at the CEI remains unclear. To address this, we utilized a combination of X-ray photoelectron and absorption spectroscopy to identify aluminum surface environments and extent of transition metal reduction for Ni-rich LiNi0.8Co0.2−yAlyO2 (0%, 5%, or 20% Al) layered oxide cathodes tested at 4.75 V under thermal stress (60 °C). For these tests, we compared the conventional LiPF6 salt with the more thermally stable LiBF4 salt. The CEI layers are inherently different between these two electrolyte salts, particularly for the highest level of Al-doping (20%) where a thicker (thinner) CEI layer is found for LiPF6 (LiBF4). Focusing on the aluminum environment, we reveal the type of surface aluminum species are dependent on the electrolyte salt, as Al-O-F- and Al-F-like species form when using LiPF6 and LiBF4, respectively. In both cases, we find cathode-electrolyte reactions drive the formation of a protective Al-F-like barrier at the CEI in Al-doped oxide cathodes.
Spatial light modulator aided noninvasive imaging through scattering layers
Authors: Mukherjee Saswata , Vijayakumar A. , Rosen Joseph 
Published: November 2019

AbstractWe propose and demonstrate a new imaging technique to noninvasively see through scattering layers with the aid of a spatial light modulator (SLM). A relay system projects the incoherent light pattern emitting from the scattering layer onto the SLM. Two coded phase masks are displayed, one after another, on the SLM to modulate the projected scattered field and the two corresponding intensity patterns are recorded by a digital camera. The above procedure helps to achieve two goals. Firstly, since the coded phase masks are digitally synthesized, the point spread function of the imaging system can be engineered such that the image retrieval becomes more reliable. Secondly, the two recorded intensity patterns are subtracted one from the other and by that the background noise of the recovered image is minimized. The above two advantages along with a modified phase retrieval algorithm enable a relatively easier and accurate convergence to the image of the covered object.
Gas-Source CVD Growth of Atomic Layered WS2 from WF6 and H2S Precursors with High Grain Size Uniformity
Authors: Okada Mitsuhiro , Okada Naoya , Chang Wen-Hsin , Endo Takahiko , Ando Atsushi , Shimizu Tetsuo , Kubo Toshitaka , Miyata Yasumitsu , Irisawa Toshifumi 
Published: November 2019

AbstractTwo-dimensional (2D) transition-metal dichalcogenides have attracted a considerable amount of attention because of their potential for post-silicon device applications, as well as for exploring fundamental physics in an ideal 2D system. We tested the chemical vapour deposition (CVD) of WS2 using the gaseous precursors WF6 and H2S, augmented by the Na-assistance method. When Na was present during growth, the process created triangle-shaped WS2 crystals that were 10 μm in size and exhibited semiconducting characteristics. By contrast, the Na-free growth of WS2 resulted in a continuous film with metallic behaviour. These results clearly demonstrate that alkali-metal assistance is valid even in applications of gas-source CVD without oxygen-containing species, where intermediates comprising Na, W, and S can play an important role. We observed that the WS2 crystals grown by gas-source CVD exhibited a narrow size distribution when compared with crystals grown by conventional solid-source CVD, indicating that the crystal nucleation occurred almost simultaneously across the substrate, and that uniform lateral growth was dominant afterwards. This phenomenon was attributed to the suppression of inhomogeneous nucleation through the fast and uniform diffusion of the gas-phase precursors, supported by the Na-assisted suppression of the fast reactions between WF6 and H2S.
Scaling behaviour in music and cortical dynamics interplay to mediate music listening pleasure
Authors: Teixeira Borges Ana Filipa , Irrmischer Mona , Brockmeier Thomas , Smit Dirk J. A. , Mansvelder Huibert D. , Linkenkaer-Hansen Klaus 
Published: November 2019

AbstractThe pleasure of music listening regulates daily behaviour and promotes rehabilitation in healthcare. Human behaviour emerges from the modulation of spontaneous timely coordinated neuronal networks. Too little is known about the physical properties and neurophysiological underpinnings of music to understand its perception, its health benefit and to deploy personalized or standardized music-therapy. Prior studies revealed how macroscopic neuronal and music patterns scale with frequency according to a 1/fαrelationship, where a is the scaling exponent. Here, we examine how this hallmark in music and neuronal dynamics relate to pleasure. Using electroencephalography, electrocardiography and behavioural data in healthy subjects, we show that music listening decreases the scaling exponent of neuronal activity and—in temporal areas—this change is linked to pleasure. Default-state scaling exponents of the most pleased individuals were higher and approached those found in music loudness fluctuations. Furthermore, the scaling in selective regions and timescales and the average heart rate were largely proportional to the scaling of the melody. The scaling behaviour of heartbeat and neuronal fluctuations were associated during music listening. Our results point to a 1/fresonancebetween brain and music and a temporal rescaling of neuronal activity in the temporal cortex as mechanisms underlying music appreciation.
Evolutionary patterns of chimeric retrogenes in Oryza species
Authors: Zhou Yanli , Zhang Chengjun 
Published: November 2019

AbstractChimeric retroposition is a process by which RNA is reverse transcribed and the resulting cDNA is integrated into the genome along with flanking sequences. This process plays essential roles and drives genome evolution. Although the origination rates of chimeric retrogenes are high in plant genomes, the evolutionary patterns of the retrogenes and their parental genes are relatively uncharacterised in the rice genome. In this study, we evaluated the substitution ratio of 24 retrogenes and their parental genes to clarify their evolutionary patterns. The results indicated that seven gene pairs were under positive selection. Additionally, soon after new chimeric retrogenes were formed, they rapidly evolved. However, an unexpected pattern was also revealed. Specifically, after an undefined period following the formation of new chimeric retrogenes, the parental genes, rather than the new chimeric retrogenes, rapidly evolved under positive selection. We also observed that one retro chimeric gene (RCG3) was highly expressed in infected calli, whereas its parental gene was not. Finally, a comparison of our Ka/Ks analysis with that of other species indicated that the proportion of genes under positive selection is greater for chimeric retrogenes than for non-chimeric retrogenes in the rice genome.
Novel patient risk factors and validation of a difficulty scoring system in laparoscopic repeat hepatectomy
Authors: Okamura Yukiyasu , Yamamoto Yusuke , Sugiura Teiichi , Ito Takaaki , Ashida Ryo , Ohgi Katsuhisa , Uesaka Katsuhiko 
Published: November 2019

AbstractThe indications for laparoscopic liver resection have expanded; however, the safety and benefits of laparoscopic repeat hepatectomy (LRH) remain unclear. We retrospectively reviewed data from 137 patients who underwent partial hepatectomy or left lateral sectionectomy without thoracotomy. We compared patients’ clinical factors using a difficulty scoring system for LRH. We defined factors associated with blood loss volumes in the 75th percentile or above as risk factors for bleeding in open repeat hepatectomy, and determined whether these factors were useful for LRH risk assessment. Open repeat hepatectomy and LRH was performed in 96 and 41 patients, respectively. Four of 41 (9.8%) patients undergoing LRH were converted to laparotomy. Blood loss volume was significantly greater in the intermediate-risk group than in the low-risk group (P = 0.046). Multivariate analysis revealed that the presence of tumours located adjacent and caudal or dorsal to the primary tumour site was an independent risk factor for bleeding in LRH (odds ratio 3.21, 95% confidence interval 1.16–8.88, P = 0.024). Our study validated the usefulness of a difficulty scoring system, identified patient factors that predicted the difficulty of LRH, and presented a novel difficulty scoring system for LRH based on an existing difficulty scoring system.
Changes in and significance of platelet function and parameters in Kawasaki disease
Authors: Zheng Xiaolan , Wu Wenchao , Zhang Yi , Wu Gang 
Published: November 2019

AbstractKawasaki disease (KD) is a systemic febrile, inflammatory vascular disease of unknown etiology. The coronary artery abnormality (CAA) caused by KD has become the most commonly acquired heart disease in children. Initial treatment of intravenous immunoglobulin (IVIG) can reduce the incidence of CAA. Thrombocytosis is common during the course of KD, but changes in and significances of platelet function and parameters are unclear. In this study, we enrolled 120 patients, including 40 patients with KD, 40 febrile controls, and 40 afebrile controls. The platelet function was assessed using the platelet function analyzer (PFA)-200. Platelet parameters, including platelet count (PLT), mean platelet volume (MPV), platelet distribution width (PDW), and platelet hematocrit (PCT) were measured. In the febrile period, the PDW and MPV were lower in KD patients (P < 0.05). The platelet function did not change significantly during the febrile period of KD but weakened in the defervescence phase. No significant differences between the CAA and normal groups, and between IVIG resistance and response groups. The diagnostic cutoff value of the PDW level for predicting KD was 10.85 fL with a sensitivity of 55% and a specificity of 77.5% (area under curve (AUC) = 0.690, 95% confidence interval (CI): 0.574–0.806, P < 0.01). Besides, the MPV level was 9.55 fL with sensitivity of 75% and specificity of 70% (AUC = 0.733, 95%CI: 0.620–0.846, P < 0.001). This is the first longitudinal study of platelet function changes in KD patients using PFA-200. Besides, lower PDW and MPV may be available markers for early diagnosis of KD.
TH17 cells expressing CD146 are significantly increased in patients with Systemic sclerosis
Authors: Gabsi Amira , Heim Xavier , Dlala Akram , Gati Asma , Sakhri Haifa , Abidi Ahmed , Amri Sonia , Neili Bilel , Leroyer Aurelie S. , Bertaud Alexandrine , Smiti Khanfir Monia , Said Fatma , Houman Mohamed Habib , Granel Brigitte , Blot-Chabaud Marcel , Bardin Nathalie , Marrakchi Raja 
Published: November 2019

AbstractSystemic sclerosis (SSc) is an autoimmune disorder characterized by vascular damage, excessive fibrosis and abnormal T cells immune-regulation. CD146 is an adhesion molecule essentially expressed in the vascular system, but also on TH17 lymphocytes. In view of the recently described role of CD146 in SSc, we hypothesized an involvement of CD146 positive TH17 cells in this disease. Compared to healthy controls, we showed that both soluble form of CD146 (sCD146), and IL17A levels were increased in patients with SSc with a positive correlation between both factors. A significant increase in TH17 cells attested by an increase of RORγT, IL17A mRNA and CD4+ IL17A+ cell was observed in patients with SSc. Interestingly, the percentage of TH17 cells expressing CD146 was higher in patients with SSc and inversely correlated with pulmonary fibrosis. In vitro experiments showed an augmentation of the percentage of TH17 cells expressing CD146 after cell treatment with sCD146, suggesting that, in patients the increase of this sub-population could be the consequence of the sCD146 increase in serum. In conclusion, TH17 cells expressing CD146 could represent a new component of the adaptive immune response, opening the way for the generation of new tools for the management of SSc.
Extraction of polyphenols and synthesis of new activated carbon from spent coffee grounds
Authors: Ramón-Gonçalves Marina , Alcaraz Lorena , Pérez-Ferreras Susana , León-González María Eugenia , Rosales-Conrado Noelia , López Félix A. 
Published: November 2019

AbstractA valorization process of spent coffee grounds (SCG) was studied. Thus, a two-stage process, the first stage of polyphenols extraction and synthesis of a carbonaceous precursor and a subsequent stage of obtaining activated carbon (AC) by means of a carbonization process from the precursor of the previous stage, was performed. The extraction was carried out with a hydro-alcoholic solution in a pressure reactor, modifying time, temperature and different mixtures EtOH:H2O. To optimize the polyphenols extraction, a two-level factorial experimental design with three replicates at the central point was used. The best results were obtained by using a temperature of 80 °C during 30 min with a mixture of EtOH:H2O 50:50 (v/v). Caffeine and chlorogenic acid were the most abundant compounds in the analysed extracts, ranging from 0.09 to 4.8 mg∙g−1 and 0.06 to 9.7 mg∙g−1, respectively. Similarly, an experimental design was realized in order to analyze the influence of different variables in the AC obtained process (reaction time, temperature and KOH:precursor ratio). The best results were 1 h, 850 °C, and a mixture of 2.5:1. The obtained activated carbons exhibit a great specific surface (between 1600 m2∙g−1 and 2330 m2∙g−1) with a microporous surface. Finally, the adsorption capacity of the activated carbons was evaluated by methylene blue adsorption.