bluuebunny/crossref_metadata_2025_split huggingface dataset:
The c-Jun N-terminal kinase (JNK) pathway is activated in human interstitial cystitis (IC) and rat protamine sulfate induced cystitis
Authors: Zhao Jiang , Wang Liang , Dong Xingyou , Hu Xiaoyan , Zhou Long , Liu Qina , Song Bo , Wu Qingjian , Li Longkun 
Published: February 2016

AbstractThe pathogenesis of bladder pain syndrome/interstitial cystitis (BPS/IC) is currently unclear. However, inflammation has been suggested to play an important role in BPS/IC. JNK downstream signaling plays an important role in numerous chronic inflammatory diseases. However, studies of the JNK pathway in BPS/IC are limited. In this study, we investigated the role of the JNK pathway in human BPS/IC and rat protamine sulfate (PS)-induced cystitis and examined the effect of the selective JNK inhibitor SP600125 on rat bladder cystitis. In our study, we demonstrated that the JNK signaling pathway was activated (the expression of JNK, c-Jun, p-JNK, p-c-Jun, IL-6 and TNF-α were significantly increasing in BPS/IC compared to the non-BPS/IC patients) and resulted in inflammation in human BPS/IC. Further animal models showed that the JNK pathway played an important role in the pathogenesis of cystitis. JNK inhibitors, SP600125, effectively inhibited the expression of p-JNK, p-c-Jun, IL-6 and TNF-α. The inhibition of these pathways had a protective effect on PS-induced rat cystitis by significantly decreasing histological score and mast cell count and improving bladder micturition function (micturition frequency significantly decreasing and bladder capacity significantly increasing). Therefore, JNK inhibition could be used as a potential treatment for BPS/IC.
Electro-thermal control of aluminum-doped zinc oxide/vanadium dioxide multilayered thin films for smart-device applications
Authors: Skuza J. R. , Scott D. W. , Mundle R. M. , Pradhan A. K. 
Published: February 2016

AbstractWe demonstrate the electro-thermal control of aluminum-doped zinc oxide (Al:ZnO) /vanadium dioxide (VO2) multilayered thin films, where the application of a small electric field enables precise control of the applied heat to the VO2 thin film to induce its semiconductor-metal transition (SMT). The transparent conducting oxide nature of the top Al:ZnO film can be tuned to facilitate the fine control of the SMT of the VO2 thin film and its associated properties. In addition, the Al:ZnO film provides a capping layer to the VO2 thin film, which inhibits oxidation to a more energetically favorable and stable V2O5 phase. It also decreases the SMT of the VO2 thin film by approximately 5–10 °C because of an additional stress induced on the VO2 thin film and/or an alteration of the oxygen vacancy concentration in the VO2 thin film. These results have significant impacts on technological applications for both passive and active devices by exploiting this near-room-temperature SMT.
Plasmon Excitations of Multi-layer Graphene on a Conducting Substrate
Authors: Gumbs Godfrey , Iurov Andrii , Wu Jhao-Ying , Lin M. F. , Fekete Paula 
Published: February 2016

AbstractWe predict the existence of low-frequency nonlocal plasmons at the vacuum-surface interface of a superlattice of N graphene layers interacting with conducting substrate. We derive a dispersion function that incorporates the polarization function of both the graphene monolayers and the semi-infinite electron liquid at whose surface the electrons scatter specularly. We find a surface plasmon-polariton that is not damped by particle-hole excitations or the bulk modes and which separates below the continuum mini-band of bulk plasmon modes. The surface plasmon frequency of the hybrid structure always lies below "Equation missing", the surface plasmon frequency of the conducting substrate. The intensity of this mode depends on the distance of the graphene layers from the conductor’s surface, the energy band gap between valence and conduction bands of graphene monolayer and, most importantly, on the number of two-dimensional layers. For a sufficiently large number of layers "Equation missing" the hybrid structure has no surface plasmon. The existence of plasmons with different dispersion relations indicates that quasiparticles with different group velocity may coexist for various ranges of wavelengths determined by the number of layers in the superlattice.
Activation of EGFR by small compounds through coupling the generation of hydrogen peroxide to stable dimerization of Cu/Zn SOD1
Authors: Sakanyan Vehary , Hulin Philippe , Alves de Sousa Rodolphe , Silva Viviane A. O. , Hambardzumyan Artur , Nedellec Steven , Tomasoni Christophe , Logé Cédric , Pineau Charles , Roussakis Christos , Fleury Fabrice , Artaud Isabelle 
Published: February 2016

AbstractActivation of cell signaling by reactive chemicals and pollutants is an important issue for human health. It has been shown that lipophilic nitro-benzoxadiazole (NBD) compounds rapidly move across the plasma membrane and enhance Epidermal Growth Factor Receptor (EGFR) tyrosine phosphorylation in cancer cells. Unlike ligand-dependent activation, the mechanism of this induction relies on the generation of hydrogen peroxide, which is involved in the activation of the catalytic site of the receptor and the inactivation of protein tyrosine phosphatase PTP-1B. Production of H2O2during redox transformation of NBD compounds is associated with the transition of a monomeric form of Cu/Zn superoxide dismutase 1 (SOD1) to stable dimers. The highly stable and functionally active SOD1 dimer, in the absence of adequate activities in downstream reactions, promotes the disproportionate production and accumulation of intracellular hydrogen peroxide shortly after exposure to NBD compounds. The intrinsic fluorescence of small compounds was used to demonstrate their binding to SOD1. Our data indicate that H2O2and concomitantly generated electrophilic intermediates behave as independent entities, but all contribute to the biological reactivity of NBD compounds. This study opens a promising path to identify new biomarkers of oxidative/electrophilic stress in the progression of cancer and other diseases.
ECM microenvironment unlocks brown adipogenic potential of adult human bone marrow-derived MSCs
Authors: Lee Michelle H. , Goralczyk Anna G. , Kriszt Rókus , Ang Xiu Min , Badowski Cedric , Li Ying , Summers Scott A. , Toh Sue-Anne , Yassin M. Shabeer , Shabbir Asim , Sheppard Allan , Raghunath Michael 
Published: February 2016

AbstractKey to realizing the diagnostic and therapeutic potential of human brown/brite adipocytes is the identification of a renewable, easily accessible and safe tissue source of progenitor cells and an efficacious in vitro differentiation protocol. We show that macromolecular crowding (MMC) facilitates brown adipocyte differentiation in adult human bone marrow mesenchymal stem cells (bmMSCs), as evidenced by substantially upregulating uncoupling protein 1 (UCP1) and uncoupled respiration. Moreover, MMC also induced ‘browning’ in bmMSC-derived white adipocytes. Mechanistically, MMC creates a 3D extracellular matrix architecture enshrouding maturing adipocytes in a collagen IV cocoon that is engaged by paxillin-positive focal adhesions also at the apical side of cells, without contact to the stiff support structure. This leads to an enhanced matrix-cell signaling, reflected by increased phosphorylation of ATF2, a key transcription factor in UCP1 regulation. Thus, tuning the dimensionality of the microenvironment in vitro can unlock a strong brown potential dormant in bone marrow.
The roles and impacts of human hunter-gatherers in North Pacific marine food webs
Authors: Dunne Jennifer A. , Maschner Herbert , Betts Matthew W. , Huntly Nancy , Russell Roly , Williams Richard J. , Wood Spencer A. 
Published: February 2016

AbstractThere is a nearly 10,000-year history of human presence in the western Gulf of Alaska, but little understanding of how human foragers integrated into and impacted ecosystems through their roles as hunter-gatherers. We present two highly resolved intertidal and nearshore food webs for the Sanak Archipelago in the eastern Aleutian Islands and use them to compare trophic roles of prehistoric humans to other species. We find that the native Aleut people played distinctive roles as super-generalist and highly-omnivorous consumers closely connected to other species. Although the human population was positioned to have strong effects, arrival and presence of Aleut people in the Sanak Archipelago does not appear associated with long-term extinctions. We simulated food web dynamics to explore to what degree introducing a species with trophic roles like those of an Aleut forager, and allowing for variable strong feeding to reflect use of hunting technology, is likely to trigger extinctions. Potential extinctions decreased when an invading omnivorous super-generalist consumer focused strong feeding on decreasing fractions of its possible resources. This study presents the first assessment of the structural roles of humans as consumers within complex ecological networks, and potential impacts of those roles and feeding behavior on associated extinctions.
Effects of High Hydrostatic Pressure on Expression Profiles of In Vitro Produced Vitrified Bovine Blastocysts
Authors: Jiang Zongliang , Harrington Patrick , Zhang Ming , Marjani Sadie L. , Park Joonghoon , Kuo Lynn , Pribenszky Csaba , Tian Xiuchun 
Published: February 2016

AbstractHigh hydrostatic pressure (HHP) has been used to pre-condition embryos before essential, yet potentially detrimental procedures such as cryopreservation. However, the mechanisms for HHP are poorly understood. We treated bovine blastocysts with three different HHP (40, 60 and 80 MPa) in combination with three recovery periods (0, 1 h, 2 h post HHP). Re-expansion rates were significantly higher at 40 and 60 but lower at 80 MPa after vitrification-warming in the treated groups than controls. Microarray analysis revealed 399 differentially expressed transcripts, representing 254 unique genes, among different groups. Gene ontology analysis indicated that HHP at 40 and 60 MPa promoted embryo competence through down-regulation of genes in cell death and apoptosis, and up-regulation of genes in RNA processing, cellular growth and proliferation. In contrast, 80 MPa up-regulated genes in apoptosis, and down-regulated protein folding and cell cycle-related genes. Moreover, gene expression was also influenced by the length of the recovery time after HHP. The significantly over-represented categories were apoptosis and cell death in the 1 h group, and protein folding, response to unfolded protein and cell cycle in the 2 h group compared to 0 h. Taken together, HHP promotes competence of vitrified bovine blastocysts through modest transcriptional changes.
Abdominal obesity is strongly associated with Cardiovascular Disease and its Risk Factors in Elderly and very Elderly Community-dwelling Chinese
Authors: Fan Huimin , Li Xiaolin , Zheng Liang , Chen Xiaoli , lan Qin , Wu Hong , Ding Xugang , Qian Dingguang , Shen Yixin , Yu Zuoren , Fan Lieying , Chen Ming , Tomlinson Brian , Chan Paul , Zhang Yuzhen , Liu Zhongmin 
Published: February 2016

AbstractObesity is usually considered to predispose to atherosclerotic cardiovascular disease (ASCVD) but milder degrees of obesity or overweight may be protective in some elderly populations. We examined the relationships between general and abdominal obesity indices with ASCVD and its risk factors in elderly (aged ≥65 years) Shanghai community residents Among the 3950 participants, 21.5% had ASCVD, 56.2% had body mass index (BMI) ≥24 kg/m2, 50.1% had high waist circumference (WC) and 77.1% had waist-to-height ratio (WHtR) ≥0.50. WHtR increased with age in both men and women whereas WC increased with age only in women and BMI decreased with age only in men. The optimal WHtR cut-off value to predict the risk of ASCVD determined by receiver operating characteristic analysis was WHtR ≥0.53 with a prevalence of 55.8%. Having abdominal obesity was significantly associated with prevalent ASCVD with WHtR ≥0.53 having a higher value for the odds ratio than high WC, whereas high BMI was not associated. All three indices predicted high glucose, triglycerides and hsCRP levels but only the WHtR ≥0.53 showed a significant association with physical activity. Abdominal obesity indices, but not BMI, predicted prevalent ASCVD and its risk factors in this elderly Chinese population.
MIA PaCa-2 and PANC-1 – pancreas ductal adenocarcinoma cell lines with neuroendocrine differentiation and somatostatin receptors
Authors: Gradiz Rui , Silva Henriqueta C. , Carvalho Lina , Botelho Maria Filomena , Mota-Pinto Anabela 
Published: February 2016

AbstractStudies using cell lines should always characterize these cells to ensure that the results are not distorted by unexpected morphological or genetic changes possibly due to culture time or passage number. Thus, the aim of this study was to describe those MIA PaCa-2 and PANC-1 cell line phenotype and genotype characteristics that may play a crucial role in pancreatic cancer therapeutic assays, namely neuroendocrine chemotherapy and peptide receptor radionuclide therapy. Epithelial, mesenchymal, endocrine and stem cell marker characterization was performed by immunohistochemistry and flow cytometry and genotyping by PCR, gene sequencing and capillary electrophoresis. MIA PaCa-2 (polymorphism) expresses CK5.6, AE1/AE3, E-cadherin, vimentin, chromogranin A, synaptophysin, SSTR2 and NTR1 but not CD56. PANC-1 (pleomorphism) expresses CK5.6, MNF-116, vimentin, chromogranin A, CD56 and SSTR2 but not E-cadherin, synaptophysin or NTR1. MIA PaCA-1 is CD24−, CD44+/++, CD326−/+ and CD133/1−, while PANC-1 is CD24−/+, CD44+, CD326−/+ and CD133/1−. Both cell lines have KRAS and TP53 mutations and homozygous deletions including the first 3 exons of CDKN2A/p16INK4A, but no SMAD4/DPC4 mutations or microsatellite instability. Both have neuroendocrine differentiation and SSTR2 receptors, precisely the features making them suitable for the therapies we propose to assay in future studies.
Ecological-network models link diversity, structure and function in the plankton food-web
Authors: D’Alelio Domenico , Libralato Simone , Wyatt Timothy , Ribera d’Alcalà Maurizio 
Published: February 2016

AbstractA planktonic food-web model including sixty-three functional nodes (representing auto- mixo- and heterotrophs) was developed to integrate most trophic diversity present in the plankton. The model was implemented in two variants - which we named ‘green’ and ‘blue’ - characterized by opposite amounts of phytoplankton biomass and representing, respectively, bloom and non-bloom states of the system. Taxonomically disaggregated food-webs described herein allowed to shed light on how components of the plankton community changed their trophic behavior in the two different conditions and modified the overall functioning of the plankton food web. The green and blue food-webs showed distinct organizations in terms of trophic roles of the nodes and carbon fluxes between them. Such re-organization stemmed from switches in selective grazing by both metazoan and protozoan consumers. Switches in food-web structure resulted in relatively small differences in the efficiency of material transfer towards higher trophic levels. For instance, from green to blue states, a seven-fold decrease in phytoplankton biomass translated into only a two-fold decrease in potential planktivorous fish biomass. By linking diversity, structure and function in the plankton food-web, we discuss the role of internal mechanisms, relying on species-specific functionalities, in driving the ‘adaptive’ responses of plankton communities to perturbations.
Proteomics of HCV virions reveals an essential role for the nucleoporin Nup98 in virus morphogenesis
Authors: Lussignol Marion , Kopp Martina , Molloy Kelly , Vizcay-Barrena Gema , Fleck Roland A. , Dorner Marcus , Bell Kierstin L. , Chait Brian T. , Rice Charles M. , Catanese Maria Teresa 
Published: February 2016

Significance
Virion proteomics represents a powerful and unbiased approach to gain insights into the process of virus assembly and the host factors important for infection. For hepatitis C virus (HCV), it is known that infectious virions are assembled alongside endogenous lipoproteins to give rise to a chimeric lipoviral particle. Host-derived apolipoproteins coat the exterior of circulating particles, making for a veiled pathogen. The protein composition of HCV remains, however, undefined. Here, using MS, we identified novel viral and cellular proteins specifically associated with HCV virions and discovered an essential interaction between the capsid protein and the nucleoporin Nup98 that is required for virion biogenesis.
Bi-induced acceptor level responsible for partial compensation of native free electron density in InP1−xBix dilute bismide alloys
Authors: Gelczuk Łukasz , Stokowski Hubert , Kopaczek Jan , Zhang Liyao , Li Yaoyao , Wang Kai , Wang Peng , Wang Shumin , Kudrawiec Robert 
Published: February 2016

Abstract
Deep level transient spectroscopy (DLTS) has been applied to study electron and hole traps in InPBi alloys with 2.2 and 2.4% Bi grown by molecular beam epitaxy. One donor-like trap with the activation energy of 0.45–0.47 eV and one acceptor-like trap with activation energy of 0.08 eV have been identified in DLTS measurements. For the reference sample (InP grown at the same temperature), the deep donor trap has also been observed, while the acceptor trap was not detected. According to the literature, the deep donor level found in InP(Bi) at 0.45–0.47 eV below the conduction band has been attributed to the isolated PIn defect, while the second trap, which is observed only for Bi containing samples at 0.08 eV above the valence band can be attributed to Bi clusters in InPBi. This acceptor level was proposed to be responsible for the observed partial compensation of native free electron density in InPBi layers. It is also shown that the deep donor traps are active in photoluminescence (PL). A strong radiative recombination between donor traps and the valence band are observed in PL spectra at energy 0.6–0.8 eV, i.e. ~0.47 eV below the energy gap of InPBi, which is determined by contactless electroreflectance.
Modified pulse growth and misfit strain release of an AlN heteroepilayer with a Mg–Si codoping pair by MOCVD
Authors: Soomro Abdul Majid , Wu Chenping , Lin Na , Zheng Tongchang , Wang Huachun , Chen Hangyang , Li Jinchai , Li Shuping , Cai Duanjun , Kang Junyong 
Published: February 2016

Abstract
We report the modified pulse growth method together with an alternating introduction of larger-radius impurity (Mg) for the quality improvement and misfit strain release of an AlN epitaxial layer by the metal–organic chemical vapour deposition (MOCVD) method. Various pulse growth methods were employed to control the migration of Al atoms on the substrate surface. The results showed that the pulse time and overlapping of V/III flux is closely related with the enhancement of the 2D and 3D growth mode. In order to reduce the misfit strain between AlN and sapphire, an impurity of larger atomic radius (e.g. Mg) was doped into the AlN lattice to minimize the rigidity of the AlN epilayer. It was found that the codoping of Mg–Si ultrathin layers could significantly minimize the residual strain as well as the density of threading dislocations.
MgSe/CdSe coupled quantum wells with optimized MgSe coupling layer thickness and near infrared intersubband absorption around 1.55 μm
Authors: Chen Guopeng , Tamargo Maria C , Shen Aidong 
Published: February 2016

Abstract
The authors report the optimization of MgSe coupling layer thickness in MgSe/CdSe coupled quantum well (QW) structures and its effect on structural and optical quality as well as electron energy levels in the QWs. The structures were grown by molecular beam epitaxy with MgSe coupling layer thickness varying from 2 mono-layers (MLs), to 4 MLs. X-ray diffraction measurements showed that the thinner the MgSe coupling layer thickness the better the structural quality of the samples. Photoluminescence showed red shift of QW emissions with the decrease of MgSe coupling layer thickness, as a result of stronger coupling of electron states in samples with thinner coupling layers. While in the structures with thinner (2 MLs) coupling layers, the electron energy levels broadening may weaken the intersubband (ISB) transitions, the weak ISB absorption in samples with thicker (4 MLs) coupling layers are likely due to the poorer overall sample quality. Optimized MgSe coupling layer thickness is found to be around 3 MLs, with which a clear coupling effect is observed with ISB absorption around 1.55 μm.
Computationally expanding infinium HumanMethylation450 BeadChip array data to reveal distinct DNA methylation patterns of rheumatoid arthritis
Authors: Fan Shicai , Li Chengzhe , Ai Rizi , Wang Mengchi , Firestein Gary S. , Wang Wei 
Published: February 2016

Abstract
Motivation: DNA methylation signatures in rheumatoid arthritis (RA) have been identified in fibroblast-like synoviocytes (FLS) with Illumina HumanMethylation450 array. Since &lt;2% of CpG sites are covered by the Illumina 450K array and whole genome bisulfite sequencing is still too expensive for many samples, computationally predicting DNA methylation levels based on 450K data would be valuable to discover more RA-related genes.
Results: We developed a computational model that is trained on 14 tissues with both whole genome bisulfite sequencing and 450K array data. This model integrates information derived from the similarity of local methylation pattern between tissues, the methylation information of flanking CpG sites and the methylation tendency of flanking DNA sequences. The predicted and measured methylation values were highly correlated with a Pearson correlation coefficient of 0.9 in leave-one-tissue-out cross-validations. Importantly, the majority (76%) of the top 10% differentially methylated loci among the 14 tissues was correctly detected using the predicted methylation values. Applying this model to 450K data of RA, osteoarthritis and normal FLS, we successfully expanded the coverage of CpG sites 18.5-fold and accounts for about 30% of all the CpGs in the human genome. By integrative omics study, we identified genes and pathways tightly related to RA pathogenesis, among which 12 genes were supported by triple evidences, including 6 genes already known to perform specific roles in RA and 6 genes as new potential therapeutic targets.
Availability and implementation: The source code, required data for prediction, and demo data for test are freely available at: http://wanglab.ucsd.edu/star/LR450K/.
Contact: wei-wang@ucsd.edu or gfirestein@ucsd.edu
Supplementary information: Supplementary data are available at Bioinformatics online.