bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative analysis of genome‐wide lncRNA and mRNA expression in newly synthesized Brassica hexaploids
Authors: Wang Ruihua , Zou Jun , Meng Jinling , Wang Jianbo 
Published: May 2018

AbstractPolyploidization, as a significant evolution force, has been considered to facilitate plant diversity. The expression levels of lncRNAs and how they control the expression of protein‐coding genes in allopolyploids remain largely unknown. In this study, lncRNA expression profiles were compared between Brassica hexaploid and its parents using a high‐throughput sequencing approach. A total of 2,725, 1,672, and 2,810 lncRNAs were discovered in Brassica rapa, Brassica carinata, and Brassica hexaploid, respectively. It was also discovered that 725 lncRNAs were differentially expressed between Brassica hexaploid and its parents, and 379 lncRNAs were nonadditively expressed in this hexaploid. LncRNAs have multiple expression patterns between Brassica hexaploid and its parents and show paternal parent‐biased expression. These lncRNAs were found to implement regulatory functions directly in the long‐chain form, and acted as precursors or targets of miRNAs. According to the prediction of the targets of differentially expressed lncRNAs, 109 lncRNAs were annotated, and their target genes were involved in the metabolic process, pigmentation, reproduction, exposure to stimulus, biological regulation, and so on. Compared with the paternal parent, differentially expressed lncRNAs between Brassica hexaploid and its maternal parent participated in more regulation pathways. Additionally, 61 lncRNAs were identified as putative targets of known miRNAs, and 15 other lncRNAs worked as precursors of miRNAs. Some conservative motifs of lncRNAs from different groups were detected, which indicated that these motifs could be responsible for their regulatory roles. Our findings may provide a reference for the further study of the function and action mechanisms of lncRNAs during plant evolution.
T cells and ILC2s are major effector cells in influenza‐induced exacerbation of allergic airway inflammation in mice
Authors: Li Bobby W. S. , de Bruijn Marjolein J. W. , Lukkes Melanie , van Nimwegen Menno , Bergen Ingrid M. , KleinJan Alex , GeurtsvanKessel Corine H. , Andeweg Arno , Rimmelzwaan Guus F. , Hendriks Rudi W. 
Published: May 2018

AbstractInfluenza virus infection is an important cause of severe asthma exacerbations, but it remains unclear how a Th1‐mediated antiviral response triggers a prototypical Th2 disease. We investigated CD4+ T cells and group 2 innate lymphoid cells (ILC2s) in influenza virus‐infected mice. We found that ILC2s accumulated in the lung rapidly after influenza virus infection, but the induction of IL‐5 and IL‐13 secretion was delayed and concomitant with T cell activation. In an influenza‐induced exacerbation of allergic airway inflammation model we noticed an initial reduction of ILC2 numbers and cytokine production in broncho‐alveolar lavage compared to chronic house dust mite (HDM)‐mediated airway inflammation alone. ILC2s phenotype was characterized by low T1/ST2, ICOS, KLRG1, and CD25 expression, resembling naïve ILC2s. The contribution of ILC2s to type 2 cytokine production in the early stage of the influenza‐induced exacerbation was limited. In contrast, T cells showed increased IL‐4 and IL‐5 production when exposed to both HDM and influenza virus. Upon virus clearance, ILC2s regained an activated T1/ST2highICOShighKLRG1highCD25high phenotype paired with cytokine production and were major contributors to the type 2 cytokine milieu. Collectively, our data indicate that both T cells and ILC2s contribute to influenza‐induced exacerbation of allergic airway inflammation, but with different kinetics.
Atomic Layer Electrodeposition of Pt on Nanoporous Au and its Application in pH Sensing
Authors: Lee Euna , Sung Moonchang , Wang Yumi , Kim Jongwon 
Published: May 2018

AbstractThe preparation of nanoporous metal structures has received a substantial amount of attention because of the unique properties and various applications of these structures. In this work, the preparation of nanoporous Pt structures by modification of nanoporous gold (NPG) surfaces with Pt was achieved. An atomic layer electrodeposition (ALED) technique previously reported for the modification of flat Au surfaces with Pt was applied to the NPG surfaces to produce Pt‐modified NPG structures. The optimal ALED parameters, such as deposition potential, time, and number of cycles, for the preparation of Pt‐modified NPG structures were investigated. Scanning electron microscopy and energy‐dispersive X‐ray analysis confirmed the successful preparation of nanoporous Pt structures by ALED techniques. The Pt‐modified NPG performed well as a pH sensor with a Nernstian slope and negligible hysteresis. The method of preparing the nanoporous Pt structures reported in this work could be utilized in various applications such as electrocatalysis and electroanalysis.
Proteinase pattern of honeybee prepupae from healthy and American Foulbrood infected bees investigated by zymography
Authors: Felicioli Antonio , Turchi Barbara , Fratini Filippo , Giusti Matteo , Nuvoloni Roberta , Dani Francesca Romana , Sagona Simona 
Published: May 2018

AbstractAmerican foulbrood disease (AFB) is the main devastating disease that affects honeybees’ brood, caused by Paenibacillus larvae. The trend of the research on AFB has addressed the mechanisms by which P. larvae bacteria kill honeybee larvae. Since prepupae could react to the infection of AFB by increasing protease synthesis, the aim of this work was to compare protease activity in worker prepupae belonging to healthy colonies and to colonies affected by AFB. This investigation was performed by zymography. In gel, proteolytic activity was observed in prepupae extracts belonging only to the healthy colonies. In the prepupae extracts, 2D zimography followed by protein identification by MS allowed to detect Trypsin‐1 and Chymotrypsin‐1, which were not observed in diseased specimens. Further investigations are needed to clarify the involvement of these proteinases in the immune response of honeybee larvae and the mechanisms by which P. larvae inhibits protease production in its host.
Method to estimate the approximate samples size that yield a certain number of significant GWAS signals in polygenic traits
Authors: Bacanu Silviu‐Alin , Kendler Kenneth S. 
Published: May 2018

ABSTRACTTo argue for increased sample collection for disorders without significant findings, researchers resorted to plotting, for multiple traits, the number of significant findings as a function of the sample size. However, for polygenic traits, the prevalence of the disorder confounds the relationship between the number of significant findings and the sample size. To adjust the number of significant findings for prevalence, we develop a method that uses the expected noncentrality of the contrast between liabilities of cases and controls. We empirically find that, when compared to the sample size, this measure is a better predictor of number of significant findings. Even more, we show that the sample size effect on the number of signals is explained by the noncentrality measure. Finally, we provide an R script to estimate the required sample size (noncentrality) needed to yield a prespecified number of significant findings, along with the converse.
Interfacial tension and contact angle in CO2‐water/nanofluid‐quartz system
Authors: Zheng Xianglei , Barrios Ana C. , Perreault François , Yun Tae Sup , Jang Jaewon 
Published: May 2018

AbstractNanoparticles can modify the interface properties that are critical for fluid flow in porous media. The interfacial tension (IFT) between CO2 and water and the contact angle (CA) of a water droplet on a mineral surface under high CO2 pressure are critical parameters for CO2‐related applications such as CO2 geological sequestration and CO2‐enhanced resource recovery. This study investigated the IFT and CA in a water‐CO2‐quartz system and a nanofluid (water including either Al2O3 or TiO2 nanoparticles)‐CO2‐quartz system. The values of the IFT and CA were obtained by axisymmetric drop shape analysis (ADSA) for a droplet on a quartz surface in a chamber pressurized with CO2. The effect of nanoparticles on the IFT and CA was explored by comparing the values for the pure water‐CO2‐quartz system. In addition, the effect of CO2 adsorption onto the substrate on the wettability was investigated. The results show that the values of the IFT decrease with increasing CO2 pressure, and the addition of nanoparticles to pure water lowers the IFT further (∼up to a 40% reduction in the liquid CO2 pressure range). The de‐wetting phenomenon was observed for both gaseous and liquid CO2 conditions. © 2018 Society of Chemical Industry and John Wiley & Sons, Ltd.
Extracellular interleukin‐17F has a protective effect in oral tongue squamous cell carcinoma
Authors: Almahmoudi Rabeia , Salem Abdelhakim , Sieviläinen Meri , Sundquist Elias , Almangush Alhadi , Toppila‐Salmi Sanna , Paavonen Timo , Salo Tuula , Al‐Samadi Ahmed 
Published: May 2018

AbstractBackgroundOral tongue squamous cell carcinoma (SCC) is characterized by early metastasis and poor prognosis. Interleukin‐17F (IL‐17F) plays a protective role in many tumors. However, IL‐17F expression in oral tongue SCC tissue has not been investigated.MethodsImmunostaining of 83 oral tongue SCC specimens and blinded‐scoring were used to map IL‐17F expression, location, and distribution. Survival curves were constructed according to Kaplan‐Meier method. The Cox proportional hazard model was applied for univariate and multivariate survival analyses.ResultsMast cells are the major source of IL‐17F in oral tongue SCC. In multivariate analysis, only the extracellular mast cell‐derived IL‐17F at the tumor invasion front was associated with better disease‐specific survival in patients with all‐stages and early‐stages of oral tongue SCC.ConclusionExtracellular mast cell‐derived IL‐17F is antitumorigenic in oral tongue SCC. It separates patients with early‐stage disease who are at high risk from patients who are at low risk. Furthermore, when analyzing tentative prognostic molecules, we conclude that in addition to the staining intensity, attention must be paid to the cellular source, distribution, and location of the molecule.
Data assimilation in groundwater modelling: ensemble Kalman filter versus ensemble smoothers
Authors: Li Liangping , Puzel Ryan , Davis Arden 
Published: May 2018

AbstractGroundwater modelling calls for an effective and robust data integrating method to fill the gap between the model and observation data. The ensemble Kalman filter (EnKF), a real‐time data assimilation method, has been increasingly applied in multiple disciplines such as petroleum engineering and hydrogeology. In this approach, a groundwater model is updated sequentially with measured data such as hydraulic head and concentration. As an alternative to the EnKF, the ensemble smoother (ES) has been proposed for updating groundwater models using all the data together, with much less computational cost. To further improve the performance of the ES, an iterative ES has been proposed for continuously updating the model by assimilating measurements together. In this work, we compare the performance of the EnKF, the ES, and the iterative ES using a synthetic example in groundwater modelling. Hydraulic head data modelled on the basis of the reference conductivity field are used to inversely estimate conductivities at unsampled locations. Results are evaluated in terms of the characterization of conductivity and groundwater flow predictions. It is concluded that (a) the iterative ES works better than the standard ES because of its continuous updating and (b) the iterative ES could achieve results comparable with those of the EnKF, with less computational cost. These findings show that the iterative ES should be paid much more attention for data assimilation in groundwater modelling.
The isotopic signature of monsoon conditions, cloud modes, and rainfall type
Authors: Zwart Costijn , Munksgaard Niels C. , Protat Alain , Kurita Naoyuki , Lambrinidis Dionisia , Bird Michael I. 
Published: May 2018

AbstractThis work provides a comprehensive physically based framework for the interpretation of the north Australian rainfall stable isotope record (δ18O and δ2H). Until now, interpretations mainly relied on statistical relationships between rainfall amount and isotopic values on monthly timescales. Here, we use multiseason daily rainfall stable isotope and high resolution (10 min) ground‐based C‐band polarimetric radar data and show that the five weather types (monsoon regimes) that constitute the Australian wet season each have a characteristic isotope ratio. The data suggest that this is not only due to changes in regional rainfall amount during these regimes but, more importantly, is due to different rain and cloud types that are associated with the large scale circulation regimes. Negative (positive) isotope anomalies occurred when stratiform rainfall fractions were large (small) and the horizontal extent of raining areas were largest (smallest). Intense, yet isolated, convective conditions were associated with enriched isotope values whereas more depleted isotope values were observed when convection was widespread but less intense. This means that isotopic proxy records may record the frequency of which these typical wet season regimes occur. Positive anomalies in paleoclimatic records are most likely associated with periods where continental convection dominates and convection is sea‐breeze forced. Negative anomalies may be interpreted as periods when the monsoon trough is active, convection is of the oceanic type, less electric, and stratiform areas are wide spread. This connection between variability of rainfall isotope anomalies and the intrinsic properties of convection and its large‐scale environment has important implications for all fields of research that use rainfall stable isotopes.
Soil moisture response to rainfall on the Chinese Loess Plateau after a long‐term vegetation rehabilitation
Authors: Jin Zhao , Guo Li , Lin Henry , Wang Yunqiang , Yu Yunlong , Chu Guangcheng , Zhang Jing 
Published: May 2018

AbstractThe Chinese Loess Plateau (CLP) is a unique Critical Zone with deep loess deposits, where soil moisture is primarily replenished by seasonal monsoon rainfall. However, the role of vegetation, coupled with complex topography, on rainwater infiltration on the CLP, especially after long‐term revegetation for controlling erosion, is inadequately quantified. Over the growing season of 2016, we monitored soil moisture at the 30‐min interval at 5 depths (10, 20, 40, 60, and 100 cm) in an afforested catchment and a nearby catchment with natural regrowth of grasses. Two monitoring sites were established in each catchment, one in the downhill gully and the other in the uphill slope. We found that vegetation, topography, and rainfall attributes together determined rainwater infiltration and soil moisture replenishment. An accumulated rainfall amount of 9 mm was required to trigger soil moisture response at 10‐cm depth at the 2 grassland sites and the forestland uphill‐slope site whereas 14 mm of rainfall was required for the forestland gully site covered by dense undergrowth and trees. Rainfall events with larger sums and higher peak intensities permitted rainwater infiltration to deeper soil depths. However, no rain recharged soil moisture to 100‐cm depth during the monitoring period. The forestland uphill‐slope site showed the deepest wetting depth (up to 60‐cm depth), fastest wetting‐front velocity (up to 4 cm/hr below 10‐cm depth), and the most significant soil moisture increase (up to 15% cm 3 cm−3 increase at 10‐cm depth) after rainfall in the growing season. The grassland gully site had the highest soil water storage, whereas soil moisture was depleted the most at the forestland gully site. Findings of this study reveal the transient dynamics of soil moisture after rainfall on the CLP, which signifies the role of revegetation on rainwater infiltration in the loess Critical Zone.
Influence of collagen‐based integrin α1 and α2 mediated signaling on human mesenchymal stem cell osteogenesis in three dimensional contexts
Authors: Becerra‐Bayona Silvia M. , Guiza‐Arguello Viviana R. , Russell Brooke , Höök Magnus , Hahn Mariah S. 
Published: May 2018

AbstractCollagen I interactions with integrins α1 and α2 are known to support human mesenchymal stem cell (hMSC) osteogenesis. Nonetheless, elucidating the relative impact of specific integrin interactions has proven challenging, in part due to the complexity of native collagen. In the present work, we employed two collagen‐mimetic proteins—Scl2‐2 and Scl2‐3— to compare the osteogenic effects of integrin α1 versus α2 signaling. Scl2‐2 and Scl2‐3 were both derived from Scl2‐1, a triple helical protein lacking known cell adhesion, cytokine binding, and matrix metalloproteinase sites. However, Scl2‐2 and Scl2‐3 were each engineered to display distinct collagen‐based cell adhesion motifs: GFPGER (binding integrins α1 and α2) or GFPGEN (binding only integrin α1), respectively. hMSCs were cultured within poly(ethylene glycol) (PEG) hydrogels containing either Scl2‐2 or Scl2‐3 for 2 weeks. PEG‐Scl2‐2 gels were associated with increased hMSC osterix expression, osteopontin production, and calcium deposition relative to PEG‐Scl2‐3 gels. These data indicate that integrin α2 signaling may have an increased osteogenic effect relative to integrin α1. Since p38 is activated by integrin α2 but not by integrin α1, hMSCs were further cultured in PEG‐Scl2‐2 hydrogels in the presence of a p38 inhibitor. Results suggest that p38 activity may play a key role in collagen‐supported hMSC osteogenesis. This knowledge can be used toward the rational design of scaffolds which intrinsically promote hMSC osteogenesis. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 106A: 2594–2604, 2018.
microRNA‐665 promotes the proliferation and matrix degradation of nucleus pulposus through targeting GDF5 in intervertebral disc degeneration
Authors: Tan Hongyu , Zhao Liang , Song Ruipeng , Liu Yilin , Wang Limin 
Published: May 2018

AbstractGrowing evidences suggested that microRNAs (miRNAs) played important roles in the development of intervertebral disc degeneration (IDD). However, the expression level and function of miR‐665 in IDD remain unknown. In this study, we showed that the expression level of miR‐665 was upregulated in degenerative human NP samples. In addition, miR‐665 expression level gradually increased with the exacerbation of disc degeneration grade. Moreover, miR‐665 expression level was positively associated with the Pfirrmann grade. Ectopic expression of miR‐665 promoted NP cell growth. Furthermore, miR‐665 overexpression decreased aggrecan and Col II expression and ectopic expression of miR‐665 increased MMP‐3 and MMP‐13 expression in NP cell. We identified growth differentiation factor 5 (GDF5) was a direct target gene of miR‐665 in NP cell and enforced expression of miR‐665 decreased GDF5 expression. Elevated expression of miR‐665 enhanced NP cell proliferation and decreased aggrecan and Col II expression. In addition, ectopic expression of miR‐665 increased MMP‐3 and MMP‐13 expression through inhibiting GDF5 expression in NP cells. These results suggested that dysregulated miR‐665 expression might act an important role in the development of IDD.
Proliferation and invasion of colon cancer cells are suppressed by knockdown of TOP2A
Authors: Zhang Rui , Xu Jian , Zhao Jian , Bai Jing H. 
Published: May 2018

AbstractRecent research has shown that TOP2A plays an important role in the tumorigenesis of many malignancies, such as breast cancer, ovarian cancer, and prostate cancer. However, few studies have been conducted on TOP2A expression and functions in colon cancer. In the present study, we found that TOP2A expression was obviously elevated in colon cancer tissues compared to adjacent non‐cancerous tissues. Depletion of TOP2A in HCT116 and SW480 colon cancer cells by transfection of specific small interfering RNA significantly suppressed proliferation and inhibited invasion of cells, even induced apoptosis as indicated by both MTT assay, Annexin V/propidium iodide staining, and Transwell assay. Furthermore, we explored the underlying mechanisms. Knockdown of TOP2A not only affects the expression of cell apoptosis‐related (Bcl‐2 and Bax) and invasion‐related proteins (MMP‐2 and MMP‐9), but also reduced the phosphorylation levels of ERK and AKT. In conclusion, we showed that TOP2A was upregulated in colon cancer tissue samples and that TOP2A may serve as an oncogene in colon cancer.
Computational discovery of potent drugs to improve the treatment of pyrazinamide resistant Mycobacterium tuberculosis mutants
Authors: Jagadeb Manaswini , Rath Surya N. , Sonawane Avinash 
Published: May 2018

AbstractEmergence of multi‐drug resistance tuberculosis has become a serious health problem globally. Accumulation of mutations in the drug target led to the development of multi‐drug resistant mycobacterial strains that have made most of the conventional drugs ineffective. Hence, there is desperate need for the development of new therapeutic strategies. Here, we focused on the analysis of mutations in Mycobacterium tuberculosis (Mtb) PncA (pyrazinamidase) that is responsible for resistance against first‐line anti‐tuberculosis pyrazinamide (PZA) drug. First, PZA and its two isoforms were analyzed for their binding affinity toward ligand binding cavity of Mtb wild‐type and mutant PncA proteins. The observations suggested that some drug resistant mutations cause strong binding of PncA with the active form of PZA and impair its release, which is required to inhibit the growth of Mtb. To improve the treatment of PZA resistant Mtb, high throughput virtual drug screening was performed to identify potent drug molecules from a library of compounds derived from ChEMBL database. From this library, we predicted a lead molecule (terta‐butyl(2S,4S)‐4‐amino‐2‐cyclopropyl‐6‐(trifluoromethyl)‐3,4‐dihydro‐2H‐quinoline‐1‐carboxylate) to be more effective against PZA resistant Mtb strains in comparison to PZA. The lead molecule showed better drug‐like properties such as high affinity and atomic interactions with wild‐type and drug‐resistant mutations in Mtb PncA proteins. Further, molecular dynamic simulation studies showed that this lead molecule has better conformational stability and compatibility with drug‐resistant PncA proteins in comparison to PZA drug. We hypothesized that the predicted lead compound could be more effective, and thus may improve the treatment of PZA resistant tuberculosis.