bluuebunny/crossref_metadata_2025_split huggingface dataset:
GMOL: An Interactive Tool for 3D Genome Structure Visualization
Authors: Nowotny Jackson , Wells Avery , Oluwadare Oluwatosin , Xu Lingfei , Cao Renzhi , Trieu Tuan , He Chenfeng , Cheng Jianlin 
Published: February 2016

AbstractIt has been shown that genome spatial structures largely affect both genome activity and DNA function. Knowing this, many researchers are currently attempting to accurately model genome structures. Despite these increased efforts there still exists a shortage of tools dedicated to visualizing the genome. Creating a tool that can accurately visualize the genome can aid researchers by highlighting structural relationships that may not be obvious when examining the sequence information alone. Here we present a desktop application, known as GMOL, designed to effectively visualize genome structures so that researchers may better analyze genomic data. GMOL was developed based upon our multi-scale approach that allows a user to scale between six separate levels within the genome. With GMOL, a user can choose any unit at any scale and scale it up or down to visualize its structure and retrieve corresponding genome sequences. Users can also interactively manipulate and measure the whole genome structure and extract static images and machine-readable data files in PDB format from the multi-scale structure. By using GMOL researchers will be able to better understand and analyze genome structure models and the impact their structural relations have on genome activity and DNA function.
Heme Oxygenase-1 and 2 Common Genetic Variants and Risk for Multiple Sclerosis
Authors: Agúndez José A. G. , García-Martín Elena , Martínez Carmen , Benito-León Julián , Millán-Pascual Jorge , Díaz-Sánchez María , Calleja Patricia , Pisa Diana , Turpín-Fenoll Laura , Alonso-Navarro Hortensia , Pastor Pau , Ortega-Cubero Sara , Ayuso-Peralta Lucía , Torrecillas Dolores , García-Albea Esteban , Plaza-Nieto José Francisco , Jiménez-Jiménez Félix Javier 
Published: February 2016

AbstractSeveral neurochemical, neuropathological and experimental data suggest a possible role of oxidative stress in the ethiopathogenesis of multiple sclerosis(MS). Heme-oxygenases(HMOX) are an important defensive mechanism against oxidative stress and HMOX1 is overexpressed in the brain and spinal cord of MS patients and in experimental autoimmune encephalomyelitis(EAE). We analyzed whether common polymorphisms affecting theHMOX1andHMOX2genes are related with the risk to develop MS. We analyzed the distribution of genotypes and allelic frequencies of theHMOX1rs2071746,HMOX1rs2071747,HMOX2rs2270363 andHMOX2rs1051308 SNPs, as well as the presence of Copy number variations(CNVs) of these genes in 292 subjects MS and 533 healthy controls, using TaqMan assays. The frequencies ofHMOX2 rs1051308AA genotype andHMOX2 rs1051308AandHMOX1 rs2071746Aalleles were higher in MS patients than in controls, although only that of the SNPHMOX2rs1051308 in men remained as significant after correction for multiple comparisons. None of the studied polymorphisms was related to the age at disease onset or with the MS phenotype. The present study suggests a weak association betweenHMOX2rs1051308 polymorphism and the risk to develop MS in Spanish Caucasian men and a trend towards association between theHMOX1 rs2071746Aand MS risk.
An Investigation of the Behavior of Solvent based Polycaprolactone ink for Material Jetting
Authors: He Yinfeng , Wildman Ricky D. , Tuck Chris J. , Christie Steven D. R. , Edmondson Steven 
Published: February 2016

AbstractAn initial study of processing bioresorbable polycaprolactone (PCL) through material jetting was conducted using a Fujifilm Dimatix DMP-2830 material printer. The aim of this work was to investigate a potential solvent based method of jetting polycaprolactone. Several solvents were used to prepare a PCL solvent based ink and 1, 4-dioxane was chosen with the consideration of both solubility and safety. The morphology of PCL formed under different substrate temperatures, droplet spacings were investigated. Multi-layer PCL structures were printed and characterized. This work shows that biodegradable polycaprolactone can be processed through material jetting.
Prostaglandin I2 Attenuates Prostaglandin E2-Stimulated Expression of Interferon γ in a β-Amyloid Protein- and NF-κB-Dependent Mechanism
Authors: Wang Pu , Guan Pei-Pei , Yu Xin , Zhang Li-Chao , Su Ya-Nan , Wang Zhan-You 
Published: February 2016

AbstractCyclooxygenase-2 (COX-2) has been recently identified as being involved in the pathogenesis of Alzheimer’s disease (AD). However, the role of an important COX-2 metabolic product, prostaglandin (PG) I2, in AD development remains unknown. Using mouse-derived astrocytes as well as APP/PS1 transgenic mice as model systems, we firstly elucidated the mechanisms of interferon γ (IFNγ) regulation by PGE2 and PGI2. Specifically, PGE2 accumulation in astrocytes activated the ERK1/2 and NF-κB signaling pathways by phosphorylation, which resulted in IFNγ expression. In contrast, the administration of PGI2 attenuated the effects of PGE2 on stimulating the production of IFNγ via inhibiting the translocation of NF-κB from the cytosol to the nucleus. Due to these observations, we further studied these prostaglandins and found that both PGE2 and PGI2 increased Aβ1–42 levels. In detail, PGE2 induced IFNγ expression in an Aβ1–42-dependent manner, whereas PGI2-induced Aβ1–42 production did not alleviate cells from IFNγ inhibition by PGI2 treatment. More importantly, our data also revealed that not only Aβ1–42 oligomer but also fibrillar have the ability to induce the expression of IFNγ via stimulation of NF-κB nuclear translocation in astrocytes of APP/PS1 mice. The production of IFNγ finally accelerated the deposition of Aβ1–42 in β-amyloid plaques.
Overexpression of RNF2 Is an Independent Predictor of Outcome in Patients with Urothelial Carcinoma of the Bladder Undergoing Radical Cystectomy
Authors: Li Xiang-Dong , Chen Si-Liang , Dong Pei , Chen Jie-Wei , Wang Feng-Wei , Guo Sheng-Jie , Jiang Li-Juan , Zhou Fang-Jian , Xie Dan , Liu Zhuo-Wei 
Published: February 2016

AbstractRNF2 (ring finger protein 2) is frequently overexpressed in several types of human cancer, but the status of RNF2 amplification and expression in urothelial carcinoma of the bladder (UCB) and its clinical/prognostic significance is unclear. In this study, immunohistochemical analysis and fluorescence in situ hybridization (FISH) were used to examine the expression and amplification of RNF2 in 184 UCB patients after radical cystectomy. Overexpression of RNF2 was observed in 44.0% of UCBs and was found to significantly associate with shortened overall and cancer-specific survival (P < 0.001). In different subsets of UCBs, RNF2 overexpression was also identified as a prognostic indicator in patients with pT1, pT2, pN(−), and/or negative surgical margins (P < 0.05). Importantly, RNF2 overexpression together with pT status and surgical margin status provided significant independent prognostic parameters in multivariate analysis (P < 0.01). FISH results showed amplification of RNF2 in 8/79 (10.1%) of informative UCB cases. Additionally, RNF2 overexpression was significantly associated with RNF2 gene amplification (P = 0.004) and cell proliferation (P = 0.003). These findings suggested that overexpression of RNF2, as examined by immunohistochemical analysis, might serve as a novel prognostic biomarker and potential therapeutic target for UCB patients who undergo radical cystectomy.
cJun N-terminal kinase (JNK) phosphorylation of serine 36 is critical for p66Shc activation
Authors: Khalid Sana , Drasche Astrid , Thurner Marco , Hermann Martin , Ashraf Muhammad Imtiaz , Fresser Friedrich , Baier Gottfried , Kremser Leopold , Lindner Herbert , Troppmair Jakob 
Published: February 2016

Abstractp66Shc-dependent ROS production contributes to many pathologies including ischemia/reperfusion injury (IRI) during solid organ transplantation. Inhibiting p66Shc activation may provide a novel therapeutic approach to prevent damage, which is poorly managed by antioxidants in vivo. Previous work suggested that pro-oxidant and a pro-apoptotic function of p66Shc required mitochondrial import, which depended on serine 36 phosphorylation. PKCß has been proposed as S36 kinase but cJun N-terminal kinases (JNKs) may also phosphorylate this residue. To simulate the early stages of ischemia/reperfusion (IR) we either used H2O2 treatment or hypoxia/reoxygenation (HR). As during reperfusion in vivo, we observed increased JNK and p38 activity in mouse embryonic fibroblasts (MEFs) and HL-1 cardiomyocytes along with significantly increased p66ShcS36 phosphorylation, ROS production and cell damage. Application of specific inhibitors caused a pronounced decrease in p66ShcS36 phosphorylation only in the case of JNK1/2. Moreover, S36 phosphorylation of recombinant p66Shc by JNK1 but not PKCß was demonstrated. We further confirmed JNK1/2-dependent regulation of p66ShcS36 phosphorylation, ROS production and cell death using JNK1/2 deficient MEFs. Finally, the low ROS phenotype of JNK1/2 knockout MEFs was reversed by the phosphomimetic p66ShcS36E mutant. Inhibiting JNK1/2-regulated p66Shc activation may thus provide a therapeutic approach for the prevention of oxidative damage.
13C Pathway Analysis for the Role of Formate in Electricity Generation by Shewanella Oneidensis MR-1 Using Lactate in Microbial Fuel Cells
Authors: Luo Shuai , Guo Weihua , H. Nealson Kenneth , Feng Xueyang , He Zhen 
Published: February 2016

AbstractMicrobial fuel cell (MFC) is a promising technology for direct electricity generation from organics by microorganisms. The type of electron donors fed into MFCs affects the electrical performance and mechanistic understanding of such effects is important to optimize the MFC performance. In this study, we used a model organism in MFCs, Shewanella oneidensis MR-1 and 13C pathway analysis to investigate the role of formate in electricity generation and the related microbial metabolism. Our results indicated a synergistic effect of formate and lactate on electricity generation and extra formate addition on the original lactate resulted in more electrical output than using formate or lactate as a sole electron donor. Based on the 13C tracer analysis, we discovered decoupled cell growth and electricity generation in S. oneidensis MR-1 during co-utilization of lactate and formate (i.e., while the lactate was mainly metabolized to support the cell growth, the formate was oxidized to release electrons for higher electricity generation). To our best knowledge, this is the first time that 13C tracer analysis was applied to study microbial metabolism in MFCs and it was demonstrated to be a valuable tool to understand the metabolic pathways affected by electron donors in the selected electrochemically-active microorganisms.
Genetic diversity at the Dhn3 locus in Turkish Hordeum spontaneum populations with comparative structural analyses
Authors: Uçarlı Cüneyt , McGuffin Liam J. , Çaputlu Süleyman , Aravena Andres , Gürel Filiz 
Published: February 2016

AbstractWe analysed Hordeum spontaneum accessions from 21 different locations to understand the genetic diversity of HsDhn3 alleles and effects of single base mutations on the intrinsically disordered structure of the resulting polypeptide (HsDHN3). HsDHN3 was found to be YSK2-type with a low-frequency 6-aa deletion in the beginning of Exon 1. There is relatively high diversity in the intron region of HsDhn3 compared to the two exon regions. We have found subtle differences in K segments led to changes in amino acids chemical properties. Predictions for protein interaction profiles suggest the presence of a protein-binding site in HsDHN3 that coincides with the K1 segment. Comparison of DHN3 to closely related cereals showed that all of them contain a nuclear localization signal sequence flanking to the K1 segment and a novel conserved region located between the S and K1 segments [E(D/T)DGMGGR]. We found that H. vulgare, H. spontaneum, and Triticum urartu DHN3s have a greater number of phosphorylation sites for protein kinase C than other cereal species, which may be related to stress adaptation. Our results show that the nature and extent of mutations in the conserved segments of K1 and K2 are likely to be key factors in protection of cells.
Pilocarpine-induced seizures trigger differential regulation of microRNA-stability related genes in rat hippocampal neurons
Authors: Kinjo Erika R. , Higa Guilherme S. V. , Santos Bianca A. , de Sousa Erica , Damico Marcio V. , Walter Lais T. , Morya Edgard , Valle Angela C. , Britto Luiz R. G. , Kihara Alexandre H. 
Published: February 2016

AbstractEpileptogenesis in the temporal lobe elicits regulation of gene expression and protein translation, leading to reorganization of neuronal networks. In this process, miRNAs were described as being regulated in a cell-specific manner, although mechanistics of miRNAs activity are poorly understood. The specificity of miRNAs on their target genes depends on their intracellular concentration, reflecting the balance of biosynthesis and degradation. Herein, we confirmed that pilocarpine application promptly (<30 min) induces status epilepticus (SE) as revealed by changes in rat electrocorticogram particularly in fast-beta range (21–30 Hz). SE simultaneously upregulated XRN2 and downregulated PAPD4 gene expression in the hippocampus, two genes related to miRNA degradation and stability, respectively. Moreover, SE decreased the number of XRN2-positive cells in the hilus, while reduced the number of PAPD4-positive cells in CA1. XRN2 and PAPD4 levels did not change in calretinin- and CamKII-positive cells, although it was possible to determine that PAPD4, but not XRN2, was upregulated in parvalbumin-positive cells, revealing that SE induction unbalances the accumulation of these functional-opposed proteins in inhibitory interneurons that directly innervate distinct domains of pyramidal cells. Therefore, we were able to disclose a possible mechanism underlying the differential regulation of miRNAs in specific neurons during epileptogenesis.
Activation and Connectivity within the Default Mode Network Contribute Independently to Future-Oriented Thought
Authors: Xu Xiaoxiao , Yuan Hong , Lei Xu 
Published: February 2016

AbstractFuture-oriented thought, a projection of the self into the future to pre-experience an event, has been linked to default mode network (DMN). Previous studies showed that the DMN was generally divided into two subsystems: anterior part (aDMN) and posterior part (pDMN). The former is mostly related to self-referential mental thought and latter engages in episodic memory retrieval and scene construction. However, functional contribution of these two subsystems and functional connectivity between them during future-oriented thought has rarely been reported. Here, we investigated these issues by using an experimental paradigm that allowed prospective, episodic decisions concerning one’s future (Future Self) to be compared with self-referential decisions about one’s immediate present state (Present Self). Additionally, two parallel control conditions that relied on non-personal semantic knowledge (Future Non-Self Control and Present Non-Self Control) were conducted. Our results revealed that the aDMN was preferentially activated when participants reflected on their present states, whereas the pDMN exhibited preferentially activation when participants reflected on their personal future. Intriguingly, significantly decreased aDMN-pDMN connectivity was observed when thinking about their future relative to other conditions. These results support the notion that activation within these subsystems and connectivity between them contribute differently to future-oriented thought.
β-elemene sensitizes hepatocellular carcinoma cells to oxaliplatin by preventing oxaliplatin-induced degradation of copper transporter 1
Authors: Li Xiaoqiang , Lin Zhenhai , Zhang Bo , Guo Lei , Liu Shuang , Li Hui , Zhang Jubo , Ye Qinghai 
Published: February 2016

Abstractβ-elemene, a Curcuma wenyujin plant extract, has been used widely as a tumor adjuvant therapeutic agent. However, how to obtain optimum therapeutic effects by combining this compound with other agents remain unclear. In this study, we found that β-elemene, which alone had little effect on hepatocellular carcinoma (HCC) cell proliferation, exerted a synergistic anti-proliferative effect in HCC cells when dosed in combination with oxaliplatin, which increased the amounts of platinum accumulation and platinum-DNA adduct significantly and augmented the oxaliplatin-induced apoptosis. Western blot and laser scanning confocal microscopy studies indicated that β-elemene enhanced the sensitivity of HCC cells to oxaliplatin by upregulating copper transporter 1 (CTR1), a major controller of intracellular platinum accumulation. In an orthotopic transplantation HCC model in nude mice, HCC tumor growth was inhibited significantly by oxaliplatin combined with β-elemene, as compared with oxaliplatin alone. Notably, CTR1 protein expression in xenograft HCC was upregulated in mice who received β-elemene treatment. Taken together, our findings show that β-elemene can block the reduction of CTR1 resulting from oxaliplatin treatment, and therefore has a synergistic anti-HCC effect with oxaliplatin by enhancing cellular uptake of oxaliplatin. The synergistic effects of β-elemene and oxaliplatin deserve further evaluation in clinical settings.
Peptide mini-scaffold facilitates JNK3 activation in cells
Authors: Zhan Xuanzhi , Stoy Henriette , Kaoud Tamer S. , Perry Nicole A. , Chen Qiuyan , Perez Alejandro , Els-Heindl Sylvia , Slagis Jack V. , Iverson Tina M. , Beck-Sickinger Annette G. , Gurevich Eugenia V. , Dalby Kevin N. , Gurevich Vsevolod V. 
Published: February 2016

AbstractThree-kinase mitogen-activated protein kinase (MAPK) signaling cascades are present in virtually all eukaryotic cells. MAPK cascades are organized by scaffold proteins, which assemble cognate kinases into productive signaling complexes. Arrestin-3 facilitates JNK activation in cells, and a short 25-residue arrestin-3 peptide was identified as the critical JNK3-binding element. Here we demonstrate that this peptide also binds MKK4, MKK7, and ASK1, which are upstream JNK3-activating kinases. This peptide is sufficient to enhance JNK3 activity in cells. A homologous arrestin-2 peptide, which differs only in four positions, binds MKK4, but not MKK7 or JNK3, and is ineffective in cells at enhancing activation of JNK3. The arrestin-3 peptide is the smallest MAPK scaffold known. This peptide or its mimics can regulate MAPKs, affecting cellular decisions to live or die.
Prediction Methods in Solar Sunspots Cycles
Authors: Ng Kim Kwee 
Published: February 2016

AbstractAn understanding of the Ohl’s Precursor Method, which is used to predict the upcoming sunspots activity, is presented by employing a simplified movable divided-blocks diagram. Using a new approach, the total number of sunspots in a solar cycle and the maximum averaged monthly sunspots number Rz(max) are both shown to be statistically related to the geomagnetic activity index in the prior solar cycle. The correlation factors are significant and they are respectively found to be 0.91 ± 0.13 and 0.85 ± 0.17. The projected result is consistent with the current observation of solar cycle 24 which appears to have attained at least Rz(max) at 78.7 ± 11.7 in March 2014. Moreover, in a statistical study of the time-delayed solar events, the average time between the peak in the monthly geomagnetic index and the peak in the monthly sunspots numbers in the succeeding ascending phase of the sunspot activity is found to be 57.6 ± 3.1 months. The statistically determined time-delayed interval confirms earlier observational results by others that the Sun’s electromagnetic dipole is moving toward the Sun’s Equator during a solar cycle.
Empirical evidence for large X-effects in animals with undifferentiated sex chromosomes
Authors: Dufresnes Christophe , Majtyka Tomasz , Baird Stuart J. E. , Gerchen Jörn F. , Borzée Amaël , Savary Romain , Ogielska Maria , Perrin Nicolas , Stöck Matthias 
Published: February 2016

AbstractReproductive isolation is crucial for the process of speciation to progress. Sex chromosomes have been assigned a key role in driving reproductive isolation but empirical evidence from natural population processes has been restricted to organisms with degenerated sex chromosomes such as mammals and birds. Here we report restricted introgression at sex-linked compared to autosomal markers in a hybrid zone between two incipient species of European tree frog,Hyla arboreaandH. orientalis, whose homologous X and Y sex chromosomes are undifferentiated. This large X-effect cannot result from the dominance or faster-X aspects of Haldane’s rule, which are specific to degenerated sex chromosomes, but rather supports a role for faster-heterogametic-sex or faster-male evolutionary processes. Our data suggest a prominent contribution of undifferentiated sex chromosomes to speciation.
Dislocation-enhanced experimental-scale vacancy loop formation in hcp Zirconium in one single collision cascade
Authors: Zhou Wei , Tian Jiting , Zheng Jian , Xue Jianming , Peng Shuming 
Published: February 2016

AbstractLarge defects are the main factor leading to the degradation of material properties under irradiation environments. It is commonly assumed that the large defects are mainly formed through cluster growth under continuous irradiations. Besides this mechanism, recent experiments and simulations show that sometimes an individual ion can also directly create a large defect. Here we report a novel mechanism for the formation of the large defects, as discovered by our Molecular Dynamics (MD) simulations of the collision cascades in hcp Zirconium (Zr): a pre-existing edge dislocation (ED) can significantly promote the nucleation of the vacancy clusters and even facilitate the direct formation of an experimental-scale large vacancy loop (about 3 nm) in only one single displacement cascade. This dislocation-related mechanism may be the key for understanding the experimental results in the low-dose irradiated Zr where the high-density large dislocation loops are observed but difficult to be explained by the two mechanisms mentioned above. Considering that intrinsic dislocations exist in nearly all crystalline materials, our results provide a significant concept: pre-existing dislocations have a strong influence on the primary damage production and taking them into account is indispensable for assessing and improving the material’s irradiation-resistance.
Prevalence of HPV infection among 28,457 Chinese women in Yunnan Province, southwest China
Authors: Li Zheng , Liu Feng , Cheng Si , Shi Lei , Yan Zhiling , Yang Jie , Shi Li , Yao Yufeng , Ma Yanbing 
Published: February 2016

AbstractHuman papillomavirus (HPV) infection plays a key role in the development of cervical cancer. The aim of the current study was to investigate the HPV type distribution in Chinese women from Yunnan Province, southwest China. A total of 28,457 individuals ranging in age from 17–84 years were recruited from 13 clinical hospitals located in 10 different regions of Yunnan Province. Cervicovaginal swabs were collected from each participant and HPV screening was performed using Luminex xMAP technology. Our results showed that the HPV prevalence was 12.9% in Yunnan Province. Overall, 10.6% of the individuals were positive for a single HPV type and 2.3% were positive for multiple types. Among the individuals who tested positive for a single HPV type and multiple HPV types, the three most prevalent high-risk types were 52, 16 and 58. Age subgroup analysis showed two peaks for the frequencies of single and multiple HPV infections, one for the group of women under 25 years old and the other for the group over 56 years old. Here, we present data regarding the prevalence and type distribution of HPV infection, which will aid in the estimation of the potential clinical benefit and cost-effectiveness of HPV screening and vaccination in China.