bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human Mesenchymal stem cells program macrophage plasticity by altering their metabolic status via a PGE2-dependent mechanism
Authors: Vasandan Anoop Babu , Jahnavi Sowmya , Shashank Chandanala , Prasad Priya , Kumar Anujith , Prasanna S. Jyothi 
Published: December 2016

AbstractMesenchymal stem cells (MSCs) are speculated to act at macrophage-injury interfaces to mediate efficient repair. To explore this facet in-depth this study evaluates the influence of MSCs on human macrophages existing in distinct functional states. MSCs promoted macrophage differentiation, enhanced respiratory burst and potentiated microbicidal responses in naïve macrophages (Mφ). Functional attenuation of inflammatory M1 macrophages was associated with a concomitant shift towards alternatively activated M2 state in MSC-M1 co-cultures. In contrast, alternate macrophage (M2) activation was enhanced in MSC-M2 co-cultures. Elucidation of key macrophage metabolic programs in Mo/MSC, M1/MSC and M2/MSC co-cultures indicated changes in Glucose transporter1 (GLUT1 expression/glucose uptake, IDO1 protein/activity, SIRTUIN1 and alterations in AMPK and mTOR activity, reflecting MSC-instructed metabolic shifts. Inability of Cox2 knockdown MSCs to attenuate M1 macrophages and their inefficiency in instructing metabolic shifts in polarized macrophages establishes a key role for MSC-secreted PGE2 in manipulating macrophage metabolic status and plasticity. Functional significance of MSC-mediated macrophage activation shifts was further validated on human endothelial cells prone to M1 mediated injury. In conclusion, we propose a novel role for MSC secreted factors induced at the MSC-macrophage interface in re-educating macrophages by manipulating metabolic programs in differentially polarized macrophages.
Mal-Lys: prediction of lysine malonylation sites in proteins integrated sequence-based features with mRMR feature selection
Authors: Xu Yan , Ding Ya-Xin , Ding Jun , Wu Ling-Yun , Xue Yu 
Published: December 2016

AbstractLysine malonylation is an important post-translational modification (PTM) in proteins, and has been characterized to be associated with diseases. However, identifying malonyllysine sites still remains to be a great challenge due to the labor-intensive and time-consuming experiments. In view of this situation, the establishment of a useful computational method and the development of an efficient predictor are highly desired. In this study, a predictor Mal-Lys which incorporated residue sequence order information, position-specific amino acid propensity and physicochemical properties was proposed. A feature selection method of minimum Redundancy Maximum Relevance (mRMR) was used to select optimal ones from the whole features. With the leave-one-out validation, the value of the area under the curve (AUC) was calculated as 0.8143, whereas 6-, 8- and 10-fold cross-validations had similar AUC values which showed the robustness of the predictor Mal-Lys. The predictor also showed satisfying performance in the experimental data from the UniProt database. Meanwhile, a user-friendly web-server for Mal-Lys is accessible at http://app.aporc.org/Mal-Lys/.
Switchable 3D optofluidic Y-branch waveguides tuned by Dean flows
Authors: Li L. , Zhu X.Q. , Liang L. , Zuo Y. F. , Xu Y. S. , Yang Y. , Yuan Y. J. , Huang Q. Q. 
Published: December 2016

AbstractOptical branch waveguides are one of the most important optical elements and have been widely exploited for optical communication systems. However, prevailing devices are typically solid and have limit in tunability. Liquid optical devices have attracted more interest for the advantage of tunability of liquid media, but their signals suffer serious leakage if the refractive index (RI) of liquid is smaller than that of solid channels. This paper demonstrates the tunable three-dimensional (3D) optofluidic Y-branch waveguides in plannar microchannels by simply introducing Dean flow. This device can reconfigure 3D Y-branch profiles and separate the intensity of light as tunable ratio from 0 to 1 by adjusting the flow rates with low loss. Different from the prevailing 2D liquid counterparts, the 3D configuration offer much more freedom in the selection of liquid media as liquid’s RI can be totally independent to the solid channel structure. The transmission loss through the device is estimated to 0.97 db when the splitting angle is 10°, which shows the light is confined better in the 3D liquid structures than traditional 2D liquid counterparts. The Y-branch waveguides show potential in applications of integrated optofluidic devices.
Locating the quantum critical point of the Bose-Hubbard model through singularities of simple observables
Authors: Łącki Mateusz , Damski Bogdan , Zakrzewski Jakub 
Published: December 2016

AbstractWe show that the critical point of the two-dimensional Bose-Hubbard model can be easily found through studies of either on-site atom number fluctuations or the nearest-neighbor two-point correlation function (the expectation value of the tunnelling operator). Our strategy to locate the critical point is based on the observation that the derivatives of these observables with respect to the parameter that drives the superfluid-Mott insulator transition are singular at the critical point in the thermodynamic limit. Performing the quantum Monte Carlo simulations of the two-dimensional Bose-Hubbard model, we show that this technique leads to the accurate determination of the position of its critical point. Our results can be easily extended to the three-dimensional Bose-Hubbard model and different Hubbard-like models. They provide a simple experimentally-relevant way of locating critical points in various cold atomic lattice systems.
Loss of EGFR-ASAP1 signaling in metastatic and unresectable hepatoblastoma
Authors: Ranganathan Sarangarajan , Ningappa Mylarappa , Ashokkumar Chethan , Higgs Brandon W. , Min Jun , Sun Qing , Schmitt Lori , Subramaniam Shankar , Hakonarson Hakon , Sindhi Rakesh 
Published: December 2016

AbstractHepatoblastoma (HBL), the most common childhood liver cancer is cured with surgical resection after chemotherapy or with liver transplantation if local invasion and multifocality preclude resection. However, variable survival rates of 60–80% and debilitating chemotherapy sequelae argue for more informed treatment selection, which is not possible by grading the Wnt-β-catenin over activity present in most HBL tumors. A hypothesis-generating whole transcriptome analysis shows that HBL tumors removed at transplantation are enriched most for cancer signaling pathways which depend predominantly on epidermal growth factor (EGF) signaling, and to a lesser extent, on aberrant Wnt-β-catenin signaling. We therefore evaluated whether EGFR, ASAP1, ERBB2 and ERBB4, which signal downstream after ligation of EGF, and which show aberrant expression in several other invasive cancers, would also predict HBL tumor invasiveness. Immunohistochemistry of HBL tumors (n = 60), which are histologically heterogeneous, shows that compared with well-differentiated fetal cells, less differentiated embryonal and undifferentiated small cells (SCU) progressively lose EGFR and ASAP1 expression. This trend is exaggerated in unresectable, locally invasive or metastatic tumors, in which embryonal tumor cells are EGFR-negative, while SCU cells are EGFR-negative and ASAP1-negative. Loss of EGFR-ASAP1 signaling characterizes undifferentiated and invasive HBL. EGFR-expressing HBL tumors present novel therapeutic targeting opportunities.
Superficial vimentin mediates DENV-2 infection of vascular endothelial cells
Authors: Yang Jie , Zou Lingyun , Yang Yi , Yuan Jizhen , Hu Zhen , Liu Hui , Peng Huagang , Shang Weilong , Zhang Xiaopeng , Zhu Junmin , Rao Xiancai 
Published: December 2016

AbstractDamage to vascular endothelial cells (VECs) is a critical hallmark of hemorrhagic diseases caused by dengue virus (DENV). However, the precise molecular event involved in DENV binding and infection of VECs has yet to be clarified. In this study, vimentin (55 kDa) was identified to be involved in DENV-2 adsorption into VECs. This protein is located on the surface of VECs and interacts with DENV-2 envelope protein domain III (EDIII). The expression level of the superficial vimentin on VECs was not affected by viral infection or siRNA interference, indicating that the protein exists in a particular mode. Furthermore, the rod domain of the vimentin protein mainly functions in DENV-2 adsorption into VECs. Molecular docking results predicted several residues in vimentin rod and DENV EDIII; these residues may be responsible for cell–virus interactions. We propose that the superficial vimentin could be a novel molecule involved in DENV binding and infection of VECs. DENV EDIII directly interacts with the rod domain of vimentin on the VEC surface and thus mediates the infection.
Modulated switching current density and spin-orbit torques in MnGa/Ta films with inserting ferromagnetic layers
Authors: Meng Kangkang , Miao Jun , Xu Xiaoguang , Wu Yong , Xiao Jiaxing , Zhao Jianhua , Jiang Yong 
Published: December 2016

AbstractWe report modulated switching current density and spin-orbit torques (SOT) in MnGa/Ta films with inserting very thin Co2FeAl and Co layers. Ferromagnetic coupling has been found in MnGa/Co2FeAl/Ta, resulting in a decreased effective anisotropy field. On the contrary, in MnGa/Co/Ta, antiferromagnetic coupling plays a dominant role. The switching current density Jc in MnGa/Ta is 8.5 × 107 A/cm2. After inserting 0.8-nm-thick Co2FeAl and Co, theJc becomes 5 × 107 A/cm2 and 9 × 107 A/cm2, respectively. By performing adiabatic harmonic Hall voltage measurements, it is demonstrated that the inserted Co2FeAl layer has mainly enhanced the field-like torques, while in MnGa/Co/Ta the damping-like torques have been enhanced. Finally, the enhanced spin Hall effect (SHE) has also been studied using the spin Hall magnetoresistance measurement. The modulated Jc and SOT are ascribed to the combination of magnetic coupling, Rashba effect and SHE at the interfaces.
Novel chemoimmunotherapeutic strategy for hepatocellular carcinoma based on a genome-wide association study
Authors: Goto Kaku , Annan Dorcas A. , Morita Tomoko , Li Wenwen , Muroyama Ryosuke , Matsubara Yasuo , Ito Sayaka , Nakagawa Ryo , Tanoue Yasushi , Jinushi Masahisa , Kato Naoya 
Published: December 2016

AbstractPharmacotherapeutic options are limited for hepatocellular carcinoma (HCC). Recently, we identified the anti-tumor ligand MHC class I polypeptide-related sequence A (MICA) gene as a susceptibility gene for hepatitis C virus-induced HCC in a genome-wide association study (GWAS). To prove the concept of HCC immunotherapy based on the results of a GWAS, in the present study, we searched for drugs that could restore MICA expression. A screen of the FDA-approved drug library identified the anti-cancer agent vorinostat as the strongest hit, suggesting histone deacetylase inhibitors (HDACis) as potent candidates. Indeed, the HDACi-induced expression of MICA specific to HCC cells enhanced natural killer (NK) cell-mediated cytotoxicity in co-culture, which was further reinforced by treatment with an inhibitor of MICA sheddase. Similarly augmented anti-tumor activity of NK cells via NK group 2D was observed in vivo. Metabolomics analysis revealed HDACi-mediated alterations in energy supply and stresses for MICA induction and HCC inhibition, providing a mechanism for the chemoimmunotherapeutic actions. These data are indicative of promising strategies for selective HCC innate immunotherapy.
Design of a hydroxyapatite-binding antimicrobial peptide with improved retention and antibacterial efficacy for oral pathogen control
Authors: Huang Zhi-bin , Shi Xin , Mao Jing , Gong Shi-qiang 
Published: December 2016

AbstractControlling and reducing the formation of pathogenic biofilm on tooth surface is the key to the prevention and treatment of the biofilm-associated oral diseases. Antimicrobial peptides (AMPs), considered as possible future alternatives for conventional antibiotics, have been extensively studied for the control of bacterial infection. Due to the rapid dilution and degradation by human saliva, AMP preparations designed for oral use with longer retention and higher efficacy are in urgent need. To this end, a hydroxyapatite (HAp)-binding antimicrobial peptide (HBAMP), which is based on the fusion of a specific HAp-binding heptapeptide (HBP7) domain and a broad-spectrum antimicrobial peptide (KSLW) domain, has been developed in our laboratory. HBAMP was supposed to form a contact-active antibacterial interface on tooth surface to inhibit the formation of biofilms. In this study, we investigated its binding behaviour, antibacterial activity against bacteria in both planktonic and sessile states, enzymatic stability in human saliva, and cytocompatibility to human gingival fibroblasts (HGFs). Our findings suggest that HBAMP could adsorb on tooth surface to provide effective antibacterial activity with improved retention. This study provides a proof-of-concept on using conjugated molecules to promote antibacterial efficacy by synergistically actions of HBAMP free in solution and bound on tooth surface.
High-yield fabrication and properties of 1.4 nm nanodiamonds with narrow size distribution
Authors: Stehlik Stepan , Varga Marian , Ledinsky Martin , Miliaieva Daria , Kozak Halyna , Skakalova Viera , Mangler Clemens , Pennycook Timothy J. , Meyer Jannik C. , Kromka Alexander , Rezek Bohuslav 
Published: December 2016

AbstractDetonation nanodiamonds (DNDs) with a typical size of 5 nm have attracted broad interest in science and technology. Further size reduction of DNDs would bring these nanoparticles to the molecular-size level and open new prospects for research and applications in various fields, ranging from quantum physics to biomedicine. Here we show a controllable size reduction of the DND mean size down to 1.4 nm without significant particle loss and with additional disintegration of DND core agglutinates by air annealing, leading to a significantly narrowed size distribution (±0.7 nm). This process is scalable to large quantities. Such molecular-sized DNDs keep their diamond structure and characteristic DND features as shown by Raman spectroscopy, infrared spectroscopy, STEM and EELS. The size of 1 nm is identified as a limit, below which the DNDs become amorphous.
Thrombomodulin regulates monocye differentiation via PKCδ and ERK1/2 pathway in vitro and in atherosclerotic artery
Authors: Tsai Chien-Sung , Lin Yi-Wen , Huang Chun-Yao , Shih Chun-Min , Tsai Yi-Ting , Tsao Nai-Wen , Lin Chin-Sheng , Shih Chun-Che , Jeng Hellen , Lin Feng-Yen 
Published: December 2016

AbstractThrombomodulin (TM) modulates the activation of protein C and coagulation. Additionally, TM regulates monocyte migration and inflammation. However, its role on monocyte differentiation is still unknown. We investigated the effects of TM on monocyte differentiation. First, we found that TM was increased when THP-1 cells were treated with phorbol-12-myristate-13-acetate (PMA). Overexpression of TM enhanced the macrophage markers, CD14 and CD68 expression in PMA-induced THP-1. TM siRNA depressed the PMA-induced increase of p21Cip1/WAF1 via ERK1/2-NF-kB p65 signaling. TM regulated cytoskeletal reorganization via its interaction with paxillin, cofilin, LIMK1, and PYK2. In addition, PMA-induced p21Cip1/WAF1 expression, CD14-positive cell labeling intensity and ERK1/2 phosphorylation were markedly inhibited when protein kinase C-δ (PKCδ) was knocked down. We identified that TM directly interacts with PKCδ. PKCδ was highly expressed in human atherosclerotic arteries and colocalized with TM in CD68-positive infiltrated macrophages of plaques, indicating that the coordination between TM and PKCδ in macrophages participated in atherogenesis. TM may act as a scaffold for PKCδ docking, which keeps PKCδ in the region close to the monocyte membrane to promote the activation of ERK1/2. Taken together, our findings suggest that TM-PKCδ interaction may contribute to cardiovascular disorders by affecting monocye differentiation, which may develop future therapeutic applications.
Novel groups and unique distribution of phage phoH genes in paddy waters in northeast China
Authors: Wang Xinzhen , Liu Junjie , Yu Zhenhua , Jin Jian , Liu Xiaobing , Wang Guanghua 
Published: December 2016

AbstractAlthough bacteriophages are ubiquitous in various environments, their genetic diversity is primarily investigated in pelagic marine environments. Corresponding studies in terrestrial environments are few. In this study, we conducted the first survey of phage diversity in the paddy ecosystem by targeting a new viral biomarker gene, phoH. A total of 424 phoH sequences were obtained from four paddy waters generated from a pot experiment with different soils collected from open paddy fields in northeast China. The majority of phoH sequences in paddy waters were novel, with the highest identity of ≤70% with known phoH sequences. Four unique groups (Group α, Group β, Group γ and Group δ) and seven new subgroups (Group 2b, Group 3d, Group 3e, Group 6a, Group 6b, Group 6c and Group 6d) were formed exclusively with the clones from the paddy waters, suggesting novel phage phoH groups exist in the paddy ecosystem. Additionally, the distribution proportions of phoH clones in different groups varied among paddy water samples, suggesting the phage community in paddy fields is biogeographically distributed. Furthermore, non-metric multidimensional scaling analysis indicated that phage phoH assemblages in paddy waters were distinct from those in marine waters.
OER activity manipulated by IrO6 coordination geometry: an insight from pyrochlore iridates
Authors: Sun Wei , Liu Ji-Yuan , Gong Xue-Qing , Zaman Waqas-Qamar , Cao Li-Mei , Yang Ji 
Published: December 2016

AbstractThe anodic reaction of oxygen evolution reaction (OER), an important point for electrolysis, however, remains the obstacle due to its complicated reaction at electrochemical interfaces. Iridium oxide (IrO2) is the only currently known 5d transition metal oxide possessing admirable OER activity. Tremendous efforts have been carried out to enhance the activity of iridium oxides. Unfortunately there lies a gap in understanding what factors responsible for the activity in doped IrO2 or the novel crystal structure. Based on two metallic pyrochlores (Bi2Ir2O7 and Pb2Ir2O6.5) and IrO2. It has been found that there exists a strong correlation between the specific OER activity and IrO6 coordination geometry. The more distortion in IrO6 geometry ascends the activity of Ir sites, and generates activity order of Pb-Ir > IrO2 > Bi-Ir. Our characterizations reveal that distorted IrO6 in Pb-Ir induces a disappearance of J = 1/2 subbands in valence band, while Bi-Ir and IrO2 resist this nature probe. The performed DFT calculations indicated the distortion in IrO6 geometry can optimize binding strength between Ir-5d and O-2p due to broader d band width. Based on this insight, enhancement in OER activity is obtained by effects that change IrO6 octahedral geometry through doping or utilizing structural manipulation with nature of distorted octahedral coordination.
Protective effects of ginsenoside Rg1 on intestinal ischemia/reperfusion injury-induced oxidative stress and apoptosis via activation of the Wnt/β-catenin pathway
Authors: Zu Guo , Guo Jing , Che Ningwei , Zhou Tingting , Zhang Xiangwen 
Published: December 2016

AbstractGinsenoside Rg1 (Rg1) is one of the major bioactive ingredients in Panax ginseng, and it attenuates inflammation and apoptosis. The aims of our study were to explore the potential of Rg1 for the treatment of intestinal I/R injury and to determine whether the protective effects of Rg1 were exerted through the Wnt/β-catenin signaling pathway. In this study, Rg1 treatment ameliorated inflammatory factors, ROS and apoptosis that were induced by intestinal I/R injury. Cell viability was increased and cell apoptosis was decreased with Rg1 pretreatment following hypoxia/reoxygenation (H/R) in the in vitro study. Rg1 activated the Wnt/β-catenin signaling pathway in both the in vivo and in vitro models, and in the in vitro study, the activation was blocked by DKK1. Our study provides evidence that pretreatment with Rg1 significantly reduces ROS and apoptosis induced by intestinal I/R injury via activation of the Wnt/β-catenin pathway. Taken together, our results suggest that Rg1 could exert its therapeutic effects on intestinal I/R injury through the Wnt/β-catenin signaling pathway and provide a novel treatment modality for intestinal I/R injury.
Experimental Evidence for Olfactory Imprinting by Sockeye Salmon at Embryonic and Smolt Stages
Authors: Havey Michelle A. , Dittman Andrew H. , Quinn Thomas P. , Lema Sean C. , May Darran 
Published: December 2016

AbstractAnadromous salmonids have an extraordinary ability to migrate back to their natal streams to spawn as adults, but the mechanisms underlying this ability are not completely known. Many experiments indicate that salmon imprint on natal odors at the smolt stage prior to seaward migration, but the life history and population genetics of some species, notably Sockeye Salmon Oncorhynchus nerka, suggest that imprinting also occurs during the period between hatching and emergence from the gravel as fry. To test the hypothesis that Sockeye Salmon imprint during this period, we exposed juveniles to a mixture of odorants during either the alevin or smolt stage. The smolt exposure group was further divided into different exposure durations (6 weeks, 1 week, and 1 d) to evaluate the duration of odor exposure needed for imprinting during that stage. Imprinting was assessed by testing fish as mature adults in two‐choice mazes containing unfamiliar water with and without the mixture of odorants. Fish exposed either as alevins or for 6 weeks as smolts both spent significantly more time in the odor‐scented arm than control fish (unexposed to the odors as juveniles). Fish exposed to odors for 1 week or 1 d as smolts showed similar but weaker responses. Concurrent measures of gill Na+/K+‐ATPase activity and plasma thyroxine confirmed that the fish exposed as smolts were undergoing parr–smolt transformation during exposure. We conclude that Sockeye Salmon imprinted as both alevins and smolts and that longer periods of odor exposure yielded greater behavioral responses to odors as adults, though specific times within the parr–smolt transformation period may be more sensitive to imprinting than others.Received June 21, 2016; accepted September 13, 2016 Published online December 2, 2016
Family or friends: what counts more for drinking behaviour of young adults? / Familia o amigos: ¿qué pesa más en los hábitos de consumo de alcohol de los jóvenes?
Authors: Tartaglia Stefano , Fedi Angela , Miglietta Anna 
Published: December 2016

The scientific literature stresses the importance of culture and social environment in determining what people think about alcohol consumption and consequently do. Several pieces of research have proved the influence on young adults’ alcohol use of proximal social contexts of their family and peers. The present study aimed at investigating the influence of family behaviours and norms compared to the peers’ influence in a context where the culture of alcohol is changing between the different generations. Data were collected by means of a self-report questionnaire on a sample of 598 young adults (average age 22.20 years). The variables investigated were socio-demographic characteristics, the alcohol consumption of parents and friends and the parents’ and peers’ approval of alcohol consumption. The results confirmed the role of family and friends in influencing young adults’ consumption of alcohol, stressing a difference between perceived behaviours and norms. The perceived consumption of parents and friends influenced the participants’ consumption. On the contrary, the effects of the approval of drinking were limited. Globally friends had a stronger influence on alcohol consumption in comparison with family.