bluuebunny/crossref_metadata_2025 huggingface dataset:
Biomarkers of oxidatively induced DNA damage in dreissenid mussels: A genotoxicity assessment tool for the Laurentian Great Lakes
Authors: Jaruga Pawel , Coskun Erdem , Kimbrough Kimani , Jacob Annie , Johnson W. Edward , Dizdaroglu Miral
Published: June 2017

Activities of fast growing human population are altering freshwater ecosystems, endangering their inhabitants and public health. Organic and trace compounds have a high potential for adverse impacts on aquatic organisms in some Great Lakes tributaries. Toxic compounds in tissues of organisms living in contaminated environments change their metabolism and alter cellular components. We measured oxidatively induced DNA damage in the soft tissues of dreissenid mussels to check on the possible contaminant‐induced impact on their DNA. The animals were obtained from archived samples of the National Oceanic and Atmospheric Administration (NOAA) Mussel Watch Program. Mussels were collected from the harbor of Ashtabula River in Ohio, and a reference area located at the Lake Erie shore. Using gas chromatography‐tandem mass spectrometry with isotope dilution, we identified and quantified numerous oxidatively modified DNA bases and 8,5′‐cyclopurine‐2′‐deoxynucleosides. We found significant differences in the concentrations of these potentially mutagenic and/or lethal lesions in the DNA of mussels from the harbor as compared to the animals collected at the reference site. These results align NOAA's data showing that elevated concentrations of polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), and heavy metals were found in mussels within the harbor as compared to mussels collected in the reference site. The measured DNA lesions can be used as biomarkers for identifying DNA damage in mussels from polluted and reference sites. Such biomarkers are needed to identify the bioeffects of contaminants in affected organisms, as well as whether remedial actions have proven successful in reducing observed toxic effects.
High-fidelity PCR enzyme with DNA-binding domain facilitates de novo gene synthesis
Authors: Dolgova A. S. , Stukolova O. A.
Published: June 2017

Nowadays enzymatic synthesis of genes is the most powerful tool for fast resolution of the various tasks in the field of basic and applied biological research. PCR-based gene assembly from overlapping oligonucleotides has become a widely used strategy. However, all the methods described in the literature are not perfect and need an extra processing step. In this study we are verifying Phusion high-fidelity polymerase as a tool to reduce nucleotide mismatches in de novo gene synthesis, thus facilitating subsequent cloning. To test the efficiency of the polymerase, we selected Fel d 4 gene, which is a 581 bp DNA sequence encoding the lipocalin allergen protein, one of the major cat allergens. The approach described here, therefore, would be useful in DNA sequences creation.
Development of PR genes panel for screening aphid-tolerant cultivars in Brassica juncea
Authors: Sandeep Raj R. , Thakur Sonal V. , Hussen Vora Shebhan , Joshi Madhvi N. , Tyagi Shradha Nand , Bagatharia Snehal B.
Published: June 2017

The exorbitant yield loss incurred by Indian farmers every year (10–90%) in rapeseed–mustard (Brassica juncea) is chiefly attributed to the progressive infestation of mustard fields by Lipaphis erysimi (Kalt.), a major insect pest belonging to the family of Homoptera. Currently there are no successful tolerant cultivars developed by conventional means in Brassica juncea with systemic plant responses in the form of direct or indirect defenses against aphid attack. Lack of specific methods for screening large numbers of genotypes required in breeding for selection of tolerant cultivars in mustard is one of the main causes of slow progress in developing resistant varieties of Brassica juncea. Traditional phenotype-based breeding has to be augmented with recent molecular approaches for potential genotype selection and cultivar development in Brassica juncea. In current study a pathogen-responsive gene panel was developed which could be used for expression-assisted breeding program in mustard for selection of tolerant types against aphid infestation, minimizing the huge crop losses suffered by farmers every year.
Improved fat transplantation survival by using the conditioned medium of vascular endothelial growth factor transfected human adipose‐derived stem cells
Authors: Zhang Yang , Xiao Li‐Ling , Li Jiang‐Xuan , Liu Hong‐Wei , Li Sheng‐Hong , Wu Yan‐Yun , Liao Xuan , Rao Cong‐Qiang
Published: June 2017

Autologous fat transplantation has been applied widely in clinic. However, the low survival rate is still a problem to be solved. Studies shows that the human adipose‐derived stem cells (ADSCs) transfected by vascular endothelial growth factor (VEGF) can improve the survival rate of autologous fat transplantation. Our study is to evaluate the effects of the conditioned medium of VEGF‐transfected human adipose‐derived stem cells (VEGF‐ADSCs‐CM) on fat transplantation. ADSCs were isolated and transfected with MOI = 40. The study was divided into three groups, VEGF‐ADSCs‐CM group, normal‐ADSCs‐CM group and control group. The conditioned media for VEGF‐ADSCs‐CM group and normal‐ADSCs‐CM group were collected, and then mixed with fat, with the mixtures being injected into the back of nude mice. On 4, 7, 15, 30, 60 days after transplantation, the grafts were evaluated on the wet weight, histology, ELISA and western blot. As the results revealed, the survival rate of VEGF‐ADSCs‐CM group was highest with the best fat cell morphology, and the VEGF secretion of VEGF‐ADSCs‐CM group was also highest. Therefore, our study demonstrates that VEGF‐ADSCs‐CM can improve the survival rate of fat transplantation effectively, and VEGF‐ADSCs‐CM can be regarded as an effective assisted method for fat transplantation.
Spanwise turbulence structure over permeable walls
Authors: Suga Kazuhiko , Nakagawa Yuka , Kaneda Masayuki
Published: June 2017

Spanwise flow field measurements are carried out for turbulent flows in channels with permeable bottom walls by particle image velocimetry (PIV) to understand the effects of the wall permeability on turbulence structure near porous walls. The porous media used are three kinds of foamed ceramics which have the same porosities (0.8) but different permeabilities. The turbulent flow fields in spanwise planes are discussed using instantaneous and statistical measurement data. At a small permeability Reynolds number ($Re_{K}$), low-speed and high-speed streaks, which are similar to those of solid-wall turbulence, are observed near the walls while at a large$Re_{K}$the observed structure is very different from that of the solid-wall turbulence. It is found that the obtained spanwise scales of the structure can be reasonably correlated with the wall normal distance plus the zero-plane displacement which is estimated from the mean velocity profile. With the distribution profiles of the spanwise streak spacing and integral length scales, the transitional change of the turbulence structure over permeable walls is discussed.
Flow control of weakly non-parallel flows: application to trailing vortices
Authors: Viola F. , Pezzica E. , Iungo G. V. , Gallaire F. , Camarri S.
Published: June 2017

A general formulation is proposed to control the integral amplification factor of harmonic disturbances in weakly non-parallel amplifier flows. The sensitivity of the local spatial stability spectrum to a base-flow modification is first determined, generalizing the results of Bottaro et al. (J. Fluid Mech., vol. 476, 2003, pp. 293–302). This result is then used to evaluate the sensitivity of the overall spatial growth to a modification of the inlet flow condition. This formalism is applied to a non-parallel Batchelor vortex, which is a well-known model for trailing vortices generated by a lifting wing. The resulting sensitivity map indicates the optimal modification of the inlet flow condition enabling the stabilization of the helical modes. It is shown that the control, formulated using a single linearization of the flow dynamics carried out on the uncontrolled configuration, successfully reduces the total spatial amplification of all convectively unstable disturbances.
Critical transitions in thin layer turbulence
Authors: Benavides Santiago Jose , Alexakis Alexandros
Published: June 2017

We investigate a model of thin layer turbulence that follows the evolution of the two-dimensional motions $\boldsymbol{u}_{2D}(x,y)$ along the horizontal directions $(x,y)$ coupled to a single Fourier mode along the vertical direction ($z$) of the form $\boldsymbol{u}_{q}(x,y,z)=[v_{x}(x,y)\sin (qz),v_{y}(x,y)\sin (qz),v_{z}(x,y)\cos (qz)]$, reducing thus the system to two coupled, two-dimensional equations. The model, despite its simplicity and ad hoc construction, displays a rich behaviour. Its reduced dimensionality allows a thorough investigation of the transition from a forward to an inverse cascade of energy as the thickness of the layer $H=\unicode[STIX]{x03C0}/q$ is varied. Starting from a thick layer and reducing its thickness it is shown that two critical heights are met: (i) one for which the forward unidirectional cascade (similar to three-dimensional turbulence) transitions to a bidirectional cascade transferring energy to both small and large scales and (ii) one for which the bidirectional cascade transitions to a unidirectional inverse cascade when the layer becomes very thin (similar to two-dimensional turbulence). The two critical heights are shown to have different properties close to criticality that we are able to analyse with numerical simulations for a wide range of Reynolds numbers and aspect ratios.
Cultural Heritage Challenges in Investment Arbitration: Review of Valentina Vadi'sCultural Heritage in International Investment Law and Arbitration
Authors: Green Martínez Sebastián
Published: June 2017

International investment law is usually oriented to protect investors while cultural heritage law focuses on the protection of unique items and activities of cultural value. These two subsystems coexist and increasingly intersect within the international legal system, mainly in the context of investment arbitration proceedings, where domestic cultural policies are balanced against the interests and rights of foreign investors. The interplay between these subsystems entails legal complexities and challenges and, as a result of the increasing number of cultural heritage disputes, demands new approaches in the fields of cultural governance, international relations and dispute settlement. These issues are thoroughly addressed by Valentina Vadi in her bookCultural Heritage in International Investment Law and Arbitration(Cambridge University Press 2014).
“As Usual, I'll Have to Take an IOU”: W. E. B. Du Bois, the Gift of Black Music and the Cultural Politics of Obligation
Authors: HEFFERNAN NICK
Published: June 2017

In The Souls of Black Folk (1903) W. E. B. Du Bois described African American music as a “gift” to America, contesting the tendency to regard white interest in black culture as appropriation or theft. Yet this metaphor invoked the complex circuits of indebtedness and obligation that are intrinsic to gift exchange in anthropological accounts of the practice, challenging white recipients of the gift to make adequate response. This challenge is most systematically addressed in a sequence of films that tell stories about white enthusiasm for the blues. The Blues Brothers (1980), Crossroads (1986), Blues Brothers 2000 (1998) and Black Snake Moan (2006) depict the blues as a gift and explore how whites might appropriately acknowledge and reciprocate for receiving it in a culture distorted by racial inequalities. The films develop a distinct set of narrative conventions for handling the politics of racial obligation, vacillating between seeing black music as a transracial cultural resource on the one hand and as a racially defined, inalienable possession of African Americans on the other. Using these same conventions, Honeydripper (2007) invites us to see the process of cultural exchange from a different perspective in which the problematic status of the blues as racialized property is diminished.
Integrating disparate occurrence reports to map data-poor species ranges and occupancy: a case study of the Vulnerable bearded pigSus barbatus
Authors: Ke Alison , Luskin Matthew Scott
Published: June 2017

Monitoring species ranges and suitable and occupied habitat are core components of biogeography, ecology and conservation biology, but it is difficult to do for rare, cryptic, wide-ranging, migratory or nomadic species. We present a transparent and objective process to combine multiple types of locality data (peer-reviewed and grey literature, museum collections, camera-trap inventories, and citizen science reports). We illustrate the advantages of this pooled approach by assessing change in range and patch occupancy for a data-poor and threatened nomadic keystone species, the bearded pigSus barbatus, in Borneo, Sumatra and Peninsular Malaysia. We used a collated set of all occurrence observations (n = 240) to create minimum convex polygons for forested habitats for two time periods. We evaluated confidence that a patch was truly occupied by the overlap among data types. We found that 62% of the forest habitat of the Sumatran bearded pigS. barbatus oiwas lost during 1990–2010 and that its range contracted by 76%; the Bornean bearded pigS.barbatus barbatuslost 23 and 24% of its forest habitat and range, respectively, and in Peninsular Malaysia the 93% range collapse of this subspecies during 1985–2010 is more severe than the 33% habitat loss alone would suggest. We conclude that integrating data types can improve mapping of the ranges of many data-poor species.
Attention and Regional Gray Matter Development in Very Preterm Children at Age 12 Years
Authors: Lean Rachel E. , Melzer Tracy R. , Bora Samudragupta , Watts Richard , Woodward Lianne J.
Published: June 2017

Objectives: This study examines the selective, sustained, and executive attention abilities of very preterm (VPT) born children in relation to concurrent structural magnetic resonance imaging (MRI) measures of regional gray matter development at age 12 years. Methods: A regional cohort of 110 VPT (≤32 weeks gestation) and 113 full term (FT) born children were assessed at corrected age 12 years on the Test of Everyday Attention-Children. They also had a structural MRI scan that was subsequently analyzed using voxel-based morphometry to quantify regional between-group differences in cerebral gray matter development, which were then related to attention measures using multivariate methods. Results: VPT children obtained similar selective (p=.85), but poorer sustained (p=.02) and executive attention (p=.01) scores than FT children. VPT children were also characterized by reduced gray matter in the bilateral parietal, temporal, prefrontal and posterior cingulate cortices, bilateral thalami, and left hippocampus; and increased gray matter in the occipital and anterior cingulate cortices (family-wise error–corrected p<.05). Poorer sustained auditory attention was associated with increased gray matter in the anterior cingulate cortex (p=.04). Poor executive shifting attention was associated with reduced gray matter in the right superior temporal cortex (p=.04) and bilateral thalami (p=.05). Poorer executive divided attention was associated with reduced gray matter in the occipital (p=.001), posterior cingulate (p=.02), and left temporal (p=.01) cortices; and increased gray matter in the anterior cingulate cortex (p=.001). Conclusions: Disturbances in regional gray matter development appear to contribute, at least in part, to the poorer attentional performance of VPT children at school age. (JINS, 2017, 23, 539–550)
In Appreciation of AGU’s Outstanding Reviewers of 2016
Authors: Hanson Brooks , Tauxe Lisa
Published: June 2017

Reviewers may receive subscription benefits, discounts on books, and other acknowledgments of their contributions, such as the public citations below from AGU journal editors.
Brg1-mediated Nrf2/HO-1 pathway activation alleviates hepatic ischemia–reperfusion injury
Authors: Ge Mian , Yao Weifeng , Yuan Dongdong , Zhou Shaoli , Chen Xi , Zhang Yihan , Li Haobo , Xia Zhengyuan , Hei Ziqing
Published: June 2017

Cytoprotective gene heme oxygenase 1 (HO-1) could be induced by nuclear factor E2-related factor 2 (Nrf2) nuclear translocation. The purpose of this study was to determine the role of Brahma-related gene 1 (Brg1), a catalytic subunit of SWI2/SNF2-like chromatin remodeling complexes, in Nrf2/HO-1 pathway activation during hepatic ischemia–reperfusion (HIR). Our results showed that hepatic Brg1 was inhibited during early HIR while Brg1 overexpression reduced oxidative injury in CMV-Brg1 mice subjected to HIR. Moreover, promoter-driven luciferase assay showed that overexpression of Brg1 by adenovirus transfection in AML12 cells selectively enhanced HO-1 gene expression after hypoxia/reoxygenation (H/R) treatment but did not affect the other Nrf2 target gene NQO1. Furthermore, inhibition of HO-1 by the selective HO-1 inhibitor zinc protoporphyria could partly reverse the hepatic protective effects of Brg1 overexpression while HO-1-Adv attenuated AML12 cells H/R damage. Further, chromatin immunoprecipitation analysis revealed that Brg1 overexpression, which could significantly increase the recruitment of Brg1 protein to HO-1 but not NQO1 promoter, was recruited by Nrf2 to the HO-1 regulatory regions in AML12 hepatocytes subjected to H/R. In conclusion, our results demonstrated that restoration of Brg1 during reperfusion could enhance Nrf2-mediated inducible expression of HO-1 during HIR to effectively increase antioxidant ability to combat against hepatocytes damage.
P7C3 inhibits GSK3β activation to protect dopaminergic neurons against neurotoxin-induced cell death in vitro and in vivo
Authors: Gu Chao , Zhang Yan , Hu Qingsong , Wu Jiayuan , Ren Haigang , Liu Chun-Feng , Wang Guanghui
Published: June 2017

Parkinson’s disease (PD) is the second most prevalent neurodegenerative disease. Although its pathogenesis remains unclear, mitochondrial dysfunction plays a vital role in the pathology of PD. P7C3, an aminopropyl carbazole, possesses a significant neuroprotective ability in several neurodegenerative disorders, including PD. Here, we showed that P7C3 stabilized mitochondrial membrane potential, reduced reactive oxygen species production, and inhibited cytochromecrelease in MES23.5 cells (a dopaminergic (DA) cell line) exposed to 1-methyl-4-phenylpyridinium (MPP+). In MES23.5 cells, P7C3 inhibited glycogen synthase kinase-3 beta (GSK3β) activation induced by MPP+. P7C3 also inhibited p53 activity and repressed Bax upregulation to protect cells from MPP+toxicity. In addition, the activation of p53 was significantly attenuated with the inhibition of GSK3βactivity by P7C3. Furthermore, P7C3 blocked GSK3βand p53 activation in the midbrain, and prevented DA neuronal loss in the substantia nigra in 1-methyl-4-phenyl-1,2,3,4-tetrahydropyridine mice. Thus, our study demonstrates that P7C3 protects DA neurons from neurotoxin-induced cell death by repressing the GSK3β-p53-Bax pathway bothin vitroandin vivo, thus providing a theoretical basis for P7C3 in the potential clinical treatment of PD.
Biogenic non-crystalline U(IV) revealed as major component in uranium ore deposits
Authors: Bhattacharyya Amrita , Campbell Kate M. , Kelly Shelly D. , Roebbert Yvonne , Weyer Stefan , Bernier-Latmani Rizlan , Borch Thomas
Published: June 2017

Historically, it is believed that crystalline uraninite, produced via the abiotic reduction of hexavalent uranium (U(VI)) is the dominant reduced U species formed in low-temperature uranium roll-front ore deposits. Here we show that non-crystalline U(IV) generated through biologically mediated U(VI) reduction is the predominant U(IV) species in an undisturbed U roll-front ore deposit in Wyoming, USA. Characterization of U species revealed that the majority (∼58-89%) of U is bound as U(IV) to C-containing organic functional groups or inorganic carbonate, while uraninite and U(VI) represent only minor components. The uranium deposit exhibited mostly 238U-enriched isotope signatures, consistent with largely biotic reduction of U(VI) to U(IV). This finding implies that biogenic processes are more important to uranium ore genesis than previously understood. The predominance of a relatively labile form of U(IV) also provides an opportunity for a more economical and environmentally benign mining process, as well as the design of more effective post-mining restoration strategies and human health-risk assessment.
Ultrafast terahertz snapshots of excitonic Rydberg states and electronic coherence in an organometal halide perovskite
Authors: Luo Liang , Men Long , Liu Zhaoyu , Mudryk Yaroslav , Zhao Xin , Yao Yongxin , Park Joong M. , Shinar Ruth , Shinar Joseph , Ho Kai-Ming , Perakis Ilias E. , Vela Javier , Wang Jigang
Published: June 2017

How photoexcitations evolve into Coulomb-bound electron and hole pairs, called excitons, and unbound charge carriers is a key cross-cutting issue in photovoltaics and optoelectronics. Until now, the initial quantum dynamics following photoexcitation remains elusive in the hybrid perovskite system. Here we reveal excitonic Rydberg states with distinct formation pathways by observing the multiple resonant, internal quantum transitions using ultrafast terahertz quasi-particle transport. Nonequilibrium emergent states evolve with a complex co-existence of excitons, carriers and phonons, where a delayed buildup of excitons under on- and off-resonant pumping conditions allows us to distinguish between the loss of electronic coherence and hot state cooling processes. The nearly ∼1 ps dephasing time, efficient electron scattering with discrete terahertz phonons and intermediate binding energy of ∼13.5 meV in perovskites are distinct from conventional photovoltaic semiconductors. In addition to providing implications for coherent energy conversion, these are potentially relevant to the development of light-harvesting and electron-transport devices.
Polymorphism in a high-entropy alloy
Authors: Zhang Fei , Wu Yuan , Lou Hongbo , Zeng Zhidan , Prakapenka Vitali B. , Greenberg Eran , Ren Yang , Yan Jinyuan , Okasinski John S. , Liu Xiongjun , Liu Yong , Zeng Qiaoshi , Lu Zhaoping
Published: June 2017

Polymorphism, which describes the occurrence of different lattice structures in a crystalline material, is a critical phenomenon in materials science and condensed matter physics. Recently, configuration disorder was compositionally engineered into single lattices, leading to the discovery of high-entropy alloys and high-entropy oxides. For these novel entropy-stabilized forms of crystalline matter with extremely high structural stability, is polymorphism still possible? Here by employing in situ high-pressure synchrotron radiation X-ray diffraction, we reveal a polymorphic transition from face-centred-cubic (fcc) structure to hexagonal-close-packing (hcp) structure in the prototype CoCrFeMnNi high-entropy alloy. The transition is irreversible, and our in situ high-temperature synchrotron radiation X-ray diffraction experiments at different pressures of the retained hcp high-entropy alloy reveal that the fcc phase is a stable polymorph at high temperatures, while the hcp structure is more thermodynamically favourable at lower temperatures. As pressure is increased, the critical temperature for the hcp-to-fcc transformation also rises.
Strength of Neisseria meningitidis binding to endothelial cells requires highly-ordered CD147/β2-adrenoceptor clusters assembled by alpha-actinin-4
Authors: Maïssa Nawal , Covarelli Valentina , Janel Sébastien , Durel Beatrice , Simpson Nandi , Bernard Sandra C. , Pardo-Lopez Liliana , Bouzinba-Ségard Haniaa , Faure Camille , Scott Mark G.H. , Coureuil Mathieu , Morand Philippe C. , Lafont Frank , Nassif Xavier , Marullo Stefano , Bourdoulous Sandrine
Published: June 2017

Neisseria meningitidis (meningococcus) is an invasive bacterial pathogen that colonizes human vessels, causing thrombotic lesions and meningitis. Establishment of tight interactions with endothelial cells is crucial for meningococci to resist haemodynamic forces. Two endothelial receptors, CD147 and the β2-adrenergic receptor (β2AR), are sequentially engaged by meningococci to adhere and promote signalling events leading to vascular colonization, but their spatiotemporal coordination is unknown. Here we report that CD147 and β2AR form constitutive hetero-oligomeric complexes. The scaffolding protein α-actinin-4 directly binds to the cytosolic tail of CD147 and governs the assembly of CD147–β2AR complexes in highly ordered clusters at bacterial adhesion sites. This multimolecular assembly process increases the binding strength of meningococci to endothelial cells under shear stress, and creates molecular platforms for the elongation of membrane protrusions surrounding adherent bacteria. Thus, the specific organization of cellular receptors has major impacts on host–pathogen interaction.
Correction: Corrigendum: Small genomic insertions form enhancers that misregulate oncogenes
Authors: Abraham Brian J. , Hnisz Denes , Weintraub Abraham S. , Kwiatkowski Nicholas , Li Charles H. , Li Zhaodong , Weichert-Leahey Nina , Rahman Sunniyat , Liu Yu , Etchin Julia , Li Benshang , Shen Shuhong , Lee Tong Ihn , Zhang Jinghui , Look A. Thomas , Mansour Marc R. , Young Richard A.
Published: June 2017

Nature Communications 8: Article number:14385 (2017); Published: 9 February 2017; Updated: 1 June 2017 In the original version of Supplementary Data 1 associated with this Article, the list of predicted enhancer-associated insertions was inadvertently truncated. The HTML has now been updated to include the correct version of the Supplementary Data 1.
Influence of a patient transfer network of US inpatient facilities on the incidence of nosocomial infections
Authors: Fernández-Gracia Juan , Onnela Jukka-Pekka , Barnett Michael L. , Eguíluz Víctor M. , Christakis Nicholas A.
Published: June 2017

Antibiotic-resistant bacterial infections are a substantial source of morbidity and mortality and have a common reservoir in inpatient settings. Transferring patients between facilities could be a mechanism for the spread of these infections. We wanted to assess whether a network of hospitals, linked by inpatient transfers, contributes to the spread of nosocomial infections and investigate how network structure may be leveraged to design efficient surveillance systems. We construct a network defined by the transfer of Medicare patients across US inpatient facilities using a 100% sample of inpatient discharge claims from 2006–2007. We show the association between network structure and C. difficile incidence, with a 1% increase in a facility’s C. difficile incidence being associated with a 0.53% increase in C. difficile incidence of neighboring facilities. Finally, we used network science methods to determine the facilities to monitor to maximize surveillance efficiency. An optimal surveillance strategy for selecting “sensor” hospitals, based on their network position, detects 80% of the C. difficile infections using only 2% of hospitals as sensors. Selecting a small fraction of facilities as “sensors” could be a cost-effective mechanism to monitor emerging nosocomial infections.
Impact of naturally leaking carbon dioxide on soil properties and ecosystems in the Qinghai-Tibet plateau
Authors: Zhao Xiaohong , Deng Hongzhang , Wang Wenke , Han Feng , Li Chunrong , Zhang Hui , Dai Zhenxue
Published: June 2017

One of the major concerns for CO2 capture and storage (CCS) is the potential risk of CO2 leakage from storage reservoirs on the shallow soil property and vegetation. This study utilizes a naturally occurring CO2 leaking site in the Qinghai-Tibet Plateau to analog a “leaking CCS site”. Our observations from this site indicates that long-term CO2 invasion in the vadose zone results in variations of soil properties, such as pH fluctuation, slight drop of total organic carbon, reduction of nitrogen and phosphorus, and concentration changes of soluble ions. Simultaneously, XRD patterns of the soil suggest that crystallization of soil is enhanced and mineral contents of calcite and anorthite in soil are increased substantially. Parts of the whole ecosystem such as natural wild plants, soil dwelling animals and microorganisms in shallow soil are affected as well. Under a moderate CO2 concentration (less than 110000 ppm), wild plant growth and development are improved, while an intensive CO2 flux over 112000 ppm causes adverse effects on the plant growth, physiological and biochemical system of plants, and crop quality of wheat. Results of this study provide valuable insight for understanding the possible environmental impacts associated with potential CO2 leakage into shallow sediments at carbon sequestration sites.
A comprehensive characterisation of the metabolic profile of varicose veins; implications in elaborating plausible cellular pathways for disease pathogenesis
Authors: Anwar Muzaffar A. , Adesina-Georgiadis Kyrillos N. , Spagou K. , Vorkas P. A. , Li J. V. , Shalhoub Joseph , Holmes Elaine , Davies Alun H.
Published: June 2017

Metabolic phenotypes reflect both the genetic and environmental factors which contribute to the development of varicose veins (VV). This study utilises analytical techniques to provide a comprehensive metabolic picture of VV disease, with the aim of identifying putative cellular pathways of disease pathogenesis. VV (n = 80) and non-VV (n = 35) aqueous and lipid metabolite extracts were analysed using 600 MHz 1H Nuclear Magnetic Resonance spectroscopy and Ultra-Performance Liquid Chromatography Mass Spectrometry. A subset of tissue samples (8 subjects and 8 controls) were analysed for microRNA expression and the data analysed with mirBase (www.mirbase.org). Using Multivariate statistical analysis, Ingenuity pathway analysis software, DIANALAB database and published literature, the association of significant metabolites with relevant cellular pathways were understood. Higher concentrations of glutamate, taurine, myo-inositol, creatine and inosine were present in aqueous extracts and phosphatidylcholine, phosphatidylethanolamine and sphingomyelin in lipid extracts in the VV group compared with non-VV group. Out of 7 differentially expressed miRNAs, spearman correlation testing highlighted correlation of hsa-miR-642a-3p, hsa-miR-4459 and hsa-miR-135a-3p expression with inosine in the vein tissue, while miR-216a-5p, conversely, was correlated with phosphatidylcholine and phosphatidylethanolamine. Pathway analysis revealed an association of phosphatidylcholine and sphingomyelin with inflammation and myo-inositol with cellular proliferation.
Expression and Transcriptional Regulation of Human ATP6V1A Gene in Gastric Cancers
Authors: Wang Pin , Wang Lei , Sha Jie , Lou Guochun , Lu Nannan , Hang Bo , Mao Jian-Hua , Zou Xiaoping
Published: June 2017

Recent studies demonstrate that the invasion and metastasis of gastric cancer (GC) is closely associated with a multi-subunit vacuolar H+-ATPase (V-ATPase). Here we investigated the expression and role of the human ATP6V1A gene that encodes the catalytic subunit A of V-ATPase in GC. We found that ATP6V1A expression level is significantly elevated in GCs compared to normals, but GC patients with higher expression levels of ATP6V1A have a better prognosis. Genomic analysis revealed that APT6V1A copy number is gained in a small fraction of GC patients and lost in a minimum number. Moreover, the ATP6V1A copy number was positively correlated with its mRNA level. To explore additional mechanisms by which ATP6V1A overexpressed in GCs, we investigated the relationship between transcription factor YY1 and ATP6V1A, and found that mRNA expression of YY1 had significant correlation with that of ATP6V1A. To validate that YY1 transcriptionally regulates ATP6V1A, we discovered that the ATP6V1A core promoter region contains three YY1 binding sites. Moreover, RNAi-mediated knockdown of YY1 in GC cells significantly decreased ATP6V1A mRNA and protein expression, while YY1 overexpression increased ATP6V1A expression level. In conclusion, YY1 may play an important regulatory role in ATP6V1A expression with potential mechanistic and clinical implications in GC.
Metal biogeochemistry in constructed wetlands based on fluviatile sand and zeolite- and clinopyroxene-dominated lava sand
Authors: Huang Jen-How , Paul Sonja , Mayer Silke , Moradpour Eloise , Hasselbach Ralf , Gieré Reto , Alewell Christine
Published: June 2017

For the first time, speciation of Fe, Mn, Zn, Ni, Cu and Pb was determined along the profiles of 8 constructed wetlands (CWs) consisting of fluviatile sand (Fluv), clinopyroxene-dominated lava sand (Cl-LS) and zeolite-dominated lava sand (Ze-LS), aiming at quantifying metal behaviour in CWs and the impact caused by different filter materials. With the exception of Mn, which underwent reductive dissolution, CWs were sinks for the studied metals. Metal accumulation rates differed in the following order: Ze-LS ≥ Cl-LS > Fluv CWs, reflecting the highest metal adsorption capacity and the lowest hydraulic conductivity of Ze-LS. Sequential extraction data indicated the highest metal mobility (readily mobilised and adsorbed fractions summing up to ~60%) in Fluv CWs, implying a higher risk of metal release into adjacent environments if Fluv from CWs will be improperly disposed after usage. Zinc and Ni were transported into the deeper CW layers to a larger extent than Cu and Pb, reflecting adsorption affinity to all filter materials in the order of Pb > Cu > Zn > Ni. Therefore, understanding metal speciation and mobility in such materials is crucial when they are considered for application as filters in CWs.
Left ventricular hemodynamic forces as a marker of mechanical dyssynchrony in heart failure patients with left bundle branch block
Authors: Eriksson Jonatan , Zajac Jakub , Alehagen Urban , Bolger Ann F. , Ebbers Tino , Carlhäll Carl-Johan
Published: June 2017

Left bundle branch block (LBBB) causes left ventricular (LV) dyssynchrony which is often associated with heart failure. A significant proportion of heart failure patients do not demonstrate clinical improvement despite cardiac resynchronization therapy (CRT). How LBBB-related effects on LV diastolic function may contribute to those therapeutic failures has not been clarified. We hypothesized that LV hemodynamic forces calculated from 4D flow MRI could serve as a marker of diastolic mechanical dyssynchrony in LBBB hearts. MRI data were acquired in heart failure patients with LBBB or matched patients without LBBB. LV pressure gradients were calculated from the Navier-Stokes equations. Integration of the pressure gradients over the LV volume rendered the hemodynamic forces. The findings demonstrate that the LV filling forces are more orthogonal to the main LV flow direction in heart failure patients with LBBB compared to those without LBBB during early but not late diastole. The greater the conduction abnormality the greater the discordance of LV filling force with the predominant LV flow direction (r2 = 0.49). Such unique flow-specific measures of mechanical dyssynchrony may serve as an additional tool for considering the risks imposed by conduction abnormalities in heart failure patients and prove to be useful in predicting response to CRT.
Quaternary history, population genetic structure and diversity of the cold-adapted Alpine newt Ichthyosaura alpestris in peninsular Italy
Authors: Chiocchio Andrea , Bisconti Roberta , Zampiglia Mauro , Nascetti Giuseppe , Canestrelli Daniele
Published: June 2017

Mediterranean peninsulas are major biodiversity hotspots, and cold-adapted species are an important component of this biodiversity. However, cold-adapted species contributed surprisingly little to our knowledge of the intimate links between Quaternary environmental changes, species’ responses to these changes, and current patterns of intraspecific biodiversity. Here, we investigated the genetic structure and evolutionary history of a cold-adapted amphibian, the Alpine newt Ichthyosaura alpestris, within the Italian peninsula. Nuclear and mitochondrial markers consistently identified three distinct genetic lineages, whose divergence dates to the Early Pleistocene (1.9 and 0.8 million years ago). Our results show that the Italian peninsula provided multiple Pleistocene refugia to this cold-adapted species, and suggest that allopatric fragmentation followed by secondary admixture have been key events in the formation of its current pattern of genetic diversity. Indeed, estimates of population genetic diversity clearly identified contact populations as those achieving the highest levels of diversity. Such concordance among cold-adapted and temperate species in terms of processes triggering the formation of regional patterns of genetic diversity provides strong support for the hypothesis that gene exchange between divergent lineages, rather than long-term stability of refugial populations, has been the main step toward the formation of hotspots of intraspecific biodiversity.
Infectious DNAs derived from insect-specific flavivirus genomes enable identification of pre- and post-entry host restrictions in vertebrate cells
Authors: Piyasena Thisun B. H. , Setoh Yin X. , Hobson-Peters Jody , Newton Natalee D. , Bielefeldt-Ohmann Helle , McLean Breeanna J. , Vet Laura J. , Khromykh Alexander A. , Hall Roy A.
Published: June 2017

Flaviviruses such as West Nile virus (WNV), dengue virus and Zika virus are mosquito-borne pathogens that cause significant human diseases. A novel group of insect-specific flaviviruses (ISFs), which only replicate in mosquitoes, have also been identified. However, little is known about the mechanisms of ISF host restriction. We report the generation of infectious cDNA from two Australian ISFs, Parramatta River virus (PaRV) and Palm Creek virus (PCV). Using circular polymerase extension cloning (CPEC) with a modified OpIE2 insect promoter, infectious cDNA was generated and transfected directly into mosquito cells to produce infectious virus indistinguishable from wild-type virus. When infectious PaRV cDNA under transcriptional control of a mammalian promoter was used to transfect mouse embryo fibroblasts, the virus failed to initiate replication even when cell entry steps were by-passed and the type I interferon response was lacking. We also used CPEC to generate viable chimeric viruses between PCV and WNV. Analysis of these hybrid viruses revealed that ISFs are also restricted from replication in vertebrate cells at the point of entry. The approaches described here to generate infectious ISF DNAs and chimeric viruses provide unique tools to further dissect the mechanisms of their host restriction.
Speckle Tracking Stress Echocardiography Uncovers Early Subclinical Cardiac Involvement in Pediatric Patients with Inflammatory Bowel Diseases
Authors: Hensel Kai O. , Abellan Schneyder Francisca E. , Wilke Lucia , Heusch Andreas , Wirth Stefan , Jenke Andreas C.
Published: June 2017

Inflammatory bowel disease (IBD) is an established risk factor for cardiovascular disease (CVD). However, whether cardiac consequences present early in IBD is unknown. This is the first study in children aiming to unmask altered myocardial mechanics in IBD. We enrolled 50 consecutive normotensive children with Crohn’s disease (CD) (n = 28) or ulcerative colitis (UC) (n = 22). The study groups consisted of 18 patients with active inflammatory disease (mean age 14.6 ± 2.5 years) and 32 children with IBD in remission (14.3 ± 2.3 years). 60 age- and gender-matched children served as healthy controls. Speckle tracking stress echocardiography (STE) was used to assess left ventricular (LV) myocardial strain and strain rate. Circumferential strain rate was significantly decreased in children with active IBD (−1.55 ± 0.26 s−1) and IBD in remission (−1.49 ± 0.26 s−1) versus healthy controls (1.8 ± 0.4 s−1) both at rest (p < 0.001) and during exercise (p = 0.021). Moreover, longitudinal strain rate, circumferential strain and E/E′ ratio were significantly impaired in IBD. Pediatric patients with IBD feature subclinical signs of LV systolic and diastolic myocardial impairment early in the course of CD and UC. This may not be reversible even when IBD is clinically controlled. Patients with IBD should be regularly screened for signs of CVD.
NOD1 deficiency impairs CD44a/Lck as well as PI3K/Akt pathway
Authors: Hu Yi Wei , Wu Xiao Man , Ren Shi Si , Cao Lu , Nie Pin , Chang Ming Xian
Published: June 2017

Pattern recognition receptors (PRRs) are crucial for host defense and tissue homeostasis against infecting pathogens. PRRs are highly conserved cross species, suggesting their key roles in fundamental biological processes. Though much have been learned for NOD1 receptor in the innate and adaptive immune responses, the roles of NOD1 during embryonic and larval stages remain poorly understood. Here, we report that NOD1 is necessary for the modulation of PI3K-Akt pathway and larval survival in zebrafish. Transcriptome analysis revealed that the significantly enriched pathways in NOD1−/− zebrafish larvae were mainly involved in metabolism and immune system processes. Biochemical analysis demonstrated that NOD1 was required for the expression of CD44a that, in turn, activated the PI3K-Akt pathway during larval development. Conversely, over-expression of CD44a in NOD1-deficient zebrafish restored the modulation of the PI3K-Akt pathway and improved larval survival. Collectively, our work indicates that NOD1 plays a previously undetected protective role in larval survival through CD44a-mediated activation of the PI3K-Akt signaling.
Correction: Corrigendum: Asymmetric parental genome engineering by Cas9 during mouse meiotic exit
Authors: Suzuki Toru , Asami Maki , Perry Anthony C. F.
Published: June 2017

Scientific Reports 4: Article number: 7621; published online: 23 December 2014; updated: 01 June 2017. This article was originally published under a CC BY-NC-SA 4.0 license, but has now been made available under a CC BY 4.0 license. The PDF and HTML versions of the paper have been modified accordingly.
Correction: Corrigendum: 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 , Wang Guangzhi , Ji Anlong , Tian Xiaofeng
Published: June 2017

Scientific Reports 6: Article number: 38480; published online: 02 December 2016; updated: 31 May 2017 Guangzhi Wang, Anlong Ji and Xiaofeng Tian were omitted from the author list in the original version of this Article. In addition, an additional affiliation for Guo Zu was omitted. The correct affiliation is listed below:
Optogenetic neuronal stimulation of the lateral cerebellar nucleus promotes persistent functional recovery after stroke
Authors: Shah Aatman M. , Ishizaka Shunsuke , Cheng Michelle Y. , Wang Eric H. , Bautista Alex R. , Levy Sabrina , Smerin Daniel , Sun Guohua , Steinberg Gary K.
Published: June 2017

Stroke induces network-wide changes in the brain, affecting the excitability in both nearby and remotely connected regions. Brain stimulation is a promising neurorestorative technique that has been shown to improve stroke recovery by altering neuronal activity of the target area. However, it is unclear whether the beneficial effect of stimulation is a result of neuronal or non-neuronal activation, as existing stimulation techniques nonspecifically activate/inhibit all cell types (neurons, glia, endothelial cells, oligodendrocytes) in the stimulated area. Furthermore, which brain circuit is efficacious for brain stimulation is unknown. Here we use the optogenetics approach to selectively stimulate neurons in the lateral cerebellar nucleus (LCN), a deep cerebellar nucleus that sends major excitatory output to multiple motor and sensory areas in the forebrain. Repeated LCN stimulations resulted in a robust and persistent recovery on the rotating beam test, even after cessation of stimulations for 2 weeks. Furthermore, western blot analysis demonstrated that LCN stimulations significantly increased the axonal growth protein GAP43 in the ipsilesional somatosensory cortex. Our results demonstrate that pan-neuronal stimulations of the LCN is sufficient to promote robust and persistent recovery after stroke, and thus is a promising target for brain stimulation.
Ultra-high loading of sinoporphyrin sodium in ferritin for single-wave motivated photothermal and photodynamic co-therapy
Authors: Huang Chao , Chu Chengchao , Wang Xiaoyong , Lin Huirong , Wang Junqing , Zeng Yun , Zhu Wenzhen , Wang Yi-Xiang J. , Liu Gang
Published: June 2017

In this work, sinoporphyrin sodium was loaded into RGD-modified ferritin (R-Fn) nanocages by a rapid, scalable and versatile approach for imaging guided photodynamic and photothermal co-therapy.
A novel banded structure ceramic phosphor for high-power white LEDs
Authors: Zhang Ji-Yun , Luo Zhao-Hua , Jiang Hao-Chuan , Jiang Jun , Chen Chun-Hua , Zhang Jing-Xian , Gui Zhen-Zhen
Published: June 2017

We report a novel ceramic phosphor with a banded structure, which consists of two components (with yellow and red light emissions, respectively) arranged alternately on the parallel surface of an LED chip.
Effect of SiO2 support properties on the performance of Cu–SiO2 catalysts for the hydrogenation of levulinic acid to gamma valerolactone using formic acid as a hydrogen source
Authors: Lomate Samadhan , Sultana Asima , Fujitani Tadahiro
Published: June 2017

Vapor phase catalytic transfer hydrogenation of levulinic acid with formic acid was carried out over Cu–SiO2 catalysts having different physicochemical properties.
Selective synthesis of dimethoxyethane via directly catalytic etherification of crude ethylene glycol
Authors: Yu Weiqiang , Lu Fang , Huang Qianqian , Lu Rui , Chen Shuai , Xu Jie
Published: June 2017

A potential diesel fuel additive, dimethoxyethane, was highly selectively produced via etherification of crude ethylene glycol over SAPO-34.
Phosphorylation of a full length amyloid-β peptide modulates its amyloid aggregation, cell binding and neurotoxic properties
Authors: Jamasbi Elaheh , Separovic Frances , Hossain Mohammed Akhter , Ciccotosto Giuseppe Donato
Published: June 2017

Phosphorylation of Aβ42 promotes the formation of amyloid plaques in the brain, which lack the neurotoxic properties associated with oligomeric species causing pathogenesis in Alzheimer's disease.
Structures of dimetallocenes M2(C5H5)2 (M = Zn, Cu, Ni, Co, Fe) and their perfluorinated derivatives
Authors: Li Jing , Li Guoliang , Xie Yaoming , King R. Bruce , Schaefer Henry F.
Published: June 2017

Density functional theory shows that the dizincocenes Zn2(C5X5)2 (X = H, F) have singlet coaxial structures with two (η5-C5X5)Zn units linked by a Zn–Zn single bond. However, the low-energy M2(C5H5)2 (M = Cu–Fe) structures have perpendicular configurations with bridging C5H5 ligands.
A 3D cadmium–vanadium bimetallic framework with luminescence properties
Authors: Li Ning , Zhao Jianguo , Xu Li , Zhang Zhong , Hung Liping , Liu Yiwei , Lu Ying , Liu Shuxia
Published: June 2017

Luminescent properties of a novel cadmium–vanadium bimetallic 3D framework possessing a pillared-layer.
Graphite exfoliation in cellulose solutions
Authors: Ferreira E. S. , da Silva D. S. , Burgo T. A. L. , Batista B. C. , Galembeck F.
Published: June 2017

Shaking graphite powder dispersed in an aqueous alkaline cellulose solution produces stable dispersions of hydrophilic, thin graphite sheets with lateral dimensions reaching many micrometers.
Capacitive performance of amino acid ionic liquid electrolyte-based supercapacitors by molecular dynamics simulation
Authors: Wu Mingbing , Li Wei , Li Song , Feng Guang
Published: June 2017

Capacitance–electric potential curves of amino acid ionic liquid electrolyte-based supercapacitors.
Recent advances in pharmacokinetics approach for herbal medicine
Authors: Zhang Kunming , Yan Guangli , Zhang Aihua , Sun Hui , Wang Xijun
Published: June 2017

Traditional Chinese Medicine (TCM), an indispensable part of herbal medicine, has been used for treating many diseases and/or symptoms for thousands of years.