bluuebunny/crossref_metadata_2025_split huggingface dataset:
Germline copy number variations are associated with breast cancer risk and prognosis
Authors: Kumaran Mahalakshmi , Cass Carol E. , Graham Kathryn , Mackey John R. , Hubaux Roland , Lam Wan , Yasui Yutaka , Damaraju Sambasivarao 
Published: November 2017

AbstractBreast cancer is one of the most common cancers among women, and susceptibility is explained by genetic, lifestyle and environmental components. Copy Number Variants (CNVs) are structural DNA variations that contribute to diverse phenotypes via gene-dosage effects or cis-regulation. In this study, we aimed to identify germline CNVs associated with breast cancer susceptibility and their relevance to prognosis. We performed whole genome CNV genotyping in 422 cases and 348 controls using Human Affymetrix SNP 6 array. Principal component analysis for population stratification revealed 84 outliers leaving 366 cases and 320 controls of Caucasian ancestry for association analysis; CNVs with frequency > 10% and overlapping with protein coding genes were considered for breast cancer risk and prognostic relevance. Coding genes within the CNVs identified were interrogated for gene- dosage effects by correlating copy number status with gene expression profiles in breast tumor tissue. We identified 200 CNVs associated with breast cancer (q-value < 0.05). Of these, 21 CNV regions (overlapping with 22 genes) also showed association with prognosis. We validated representative CNVs overlapping with APOBEC3B and GSTM1 genes using the TaqMan assay. Germline CNVs conferred dosage effects on gene expression in breast tissue. The candidate CNVs identified in this study warrant independent replication.
The depleted mineralization of the fungicide chlorothalonil derived from loss in soil microbial diversity
Authors: de Souza Adijailton Jose , de Andrade Pedro Avelino Maia , de Araújo Pereira Arthur Prudêncio , Andreote Fernando Dini , Tornisielo Valdemar Luiz , Regitano Jussara Borges 
Published: November 2017

AbstractThere are lack of studies regarding the effects of microbial diversity on specific soil functions, such as pesticides degradation. This study evaluated the role of bacterial community diversity and biochar on chlorothalonil (CTN) degradation, using ‘dilution to extinction’ approach, PCR-DGGE/16S rRNA gene technique, and radiorespirometry (14C-CTN). Biochar and microbial community dilution affected structure of the microbial community. In spite of that, CTN mineralization was slow, but dissipation was very fast (D50 < 1.0 d) due to immediate chemical degradation and formation of non-extractable (bound) residues. However, any depletion on soil microbial diversity strongly affected CTN mineralization, suggesting that this function is related to less abundant but specific microbial groups (CTN degraders) or to soil microbial diversity. The extent of these effects will strongly depend on the compound nature (recalcitrance) and soil matrix/substrate (bioavailability). It can be corroborated by the fact that biochar affected CTN sorption, its bioavailability, and subsequently its mineralization rate in the NS. These data indicate a strong relationship between soil microbial diversity and pesticide degradation, which is an acting form to mitigate xenobiotics accumulation in the environment.
Graphene-Insulator-Semiconductor Junction for Hybrid Photodetection Modalities
Authors: Howell Stephen W. , Ruiz Isaac , Davids Paul S. , Harrison Richard K. , Smith Sean W. , Goldflam Michael D. , Martin Jeffrey B. , Martinez Nicholas J. , Beechem Thomas E. 
Published: November 2017

AbstractA sensitive optical detector is presented based on a deeply depleted graphene-insulator-semiconducting (D2GIS) junction, which offers the possibility of simultaneously leveraging the advantages of both charge integration and localized amplification. Direct read-out and built-in amplification are accomplished via photogating of a graphene field-effect transistor (GFET) by carriers generated within a deeply depleted low-doped silicon substrate. Analogous to a depleted metal-oxide-semiconducting junction, photo-generated charge collects in the potential well that forms at the semiconductor/insulator interface and induces charges of opposite polarity within the graphene film modifying its conductivity. This device enables simultaneous photo-induced charge integration with continuous “on detector” readout through use of graphene. The resulting devices exhibit responsivities as high as 2,500 A/W (25,000 S/W) for visible wavelengths and a dynamic range of 30 dB. As both the graphene and device principles are transferrable to arbitrary semiconductor absorbers, D2GIS devices offer a high-performance paradigm for imaging across the electromagnetic spectrum.
Tunable Dirac points and high spin polarization in ferromagnetic-strain graphene superlattices
Authors: Wu Qing-Ping , Liu Zheng-Fang , Chen Ai-Xi , Xiao Xian-Bo , Miao Guo-Xing 
Published: November 2017

AbstractSpin-dependent energy bands and transport properties of ferromagnetic-strain graphene superlattices are studied. The high spin polarization appears at the Dirac points due to the presence of spin-dependent Dirac points in the energy band structure. A gap can be induced in the vicinity of Dirac points by strain and the width of the gap is enlarged with increasing strain strength, which is beneficial for enhancing spin polarization. Moreover, a full spin polarization can be achieved at large strain strength. The position and number of the Dirac points corresponding to high spin polarization can be effectively manipulated with barrier width, well width and effective exchange field, which reveals a remarkable tunability on the wavevector filtering behavior.
MicroRNAs regulating superoxide dismutase 2 are new circulating biomarkers of heart failure
Authors: Dubois-Deruy Emilie , Cuvelliez Marie , Fiedler Jan , Charrier Henri , Mulder Paul , Hebbar Eleonore , Pfanne Angelika , Beseme Olivia , Chwastyniak Maggy , Amouyel Philippe , Richard Vincent , Bauters Christophe , Thum Thomas , Pinet Florence 
Published: November 2017

AbstractAlthough several risk factors such as infarct size have been identified, the progression of heart failure (HF) remains difficult to predict in clinical practice. Using an experimental rat model of post-myocardial infarction (MI), we previously identified 45 proteins differentially modulated during HF by proteomic analysis. This study sought to identify microRNAs (miRNAs) able to regulate these proteins and to test their relevance as biomarkers for HF. In silico bioinformatical analysis selected 13 miRNAs related to the 45 proteins previously identified. These miRNAs were analyzed in the rat and in cohorts of patients phenotyped for left ventricular remodeling (LVR). We identified that 3 miRNAs, miR-21-5p, miR-23a-3p and miR-222-3p, and their target Mn superoxide dismutase (SOD2) were significantly increased in LV and plasma of HF-rats. We found by luciferase activity a direct interaction of miR-222-3p with 3′UTR of SOD2. Transfection of human cardiomyocytes with miR-222-3p mimic or inhibitor induced respectively a decrease and an increase of SOD2 expression. Circulating levels of the 3 miRNAs and their target SOD2 were associated with high LVR post-MI in REVE-2 patients. We demonstrated for the first time the potential of microRNAs regulating SOD2 as new circulating biomarkers of HF.
Interplay between Exciton and Free Carriers in Organolead Perovskite Films
Authors: Wang Wei , Li Yu , Wang Xiangyuan , Liu Yang , Lv Yanping , Wang Shufeng , Wang Kai , Shi Yantao , Xiao Lixin , Chen Zhijian , Gong Qihuang 
Published: November 2017

AbstractFor highly interested organolead perovskite based solar cells, the exciton and free carriers are the photoproducts in the working layers. In this study, we revealed their two forms of relations depending on heat-annealing condition. In non-annealed films and single crystal, they are in density-dependent dynamical balance (co-existing). For the sufficiently heat-annealed films, they present a significant emissive exciton-carrier collision (ECC). The two relations indicate the emergence of a subgrain morphology within the tetragonal phase of crystal grain, induced by heat annealing process. Such subgrain structure could be assigned to a ferroelastic twinning structure recently found inside the crystal grain of the films. Since the heat annealing is a general procedure in preparing perovskite working layers, we propose that the ECC and subgrain morphology widely exist in real devices. We suggest that the subgrain structure provides another level of morphological basis for in depth understanding high performance of organolead perovskite working layers.
CXCL10/CXCR3 axis is associated with disease activity and the development of mucocutaneous lesions in patients with Behçet’s disease
Authors: Lee Sang Jin , Kang Shin Eui , Kang Eun Ha , Choi Byoong Yong , Masek-Hammerman Katherine , Syed Jameel , Zhan Yutian , Neff-Phillips Kathleen , Park Jin Kyun , Lee Eun Young , Lee Eun Bong , Song Yeong Wook 
Published: November 2017

AbstractThe objective of this study was to investigate CXC chemokines and its receptor in patients with Behcet’s disease (BD) and their associations with disease activity. Blood samples were collected from 109 BD patients and 36 age- and sex-matched healthy controls (HCs). Twenty-two follow-up blood samples were collected in BD patients. Serum CXC chemokines (CXCL1, CXCL8, CXCL9, CXCL10, CXCL12, CXCL13 and CXCL16) and cell surface marker expression (CD3, CD4 and CXCR3) in peripheral blood mononuclear cells (PBMCs) were assayed. Clinical features including disease activity were evaluated at the time of blood collection. CXCR3 expression in skin and intestinal lesions from BD patients and HCs was assessed via immunohistochemistry. Serum CXCL10 levels were correlated with disease activity in terms of Behçet’s Disease Current Activity Form (BDCAF) (p < 0.001). In follow-up BD patients, changes in serum CXCL10 levels tended to be correlated with those of BDCAF. The percentage of CXCR3 expression in CD3-positive cells in PBMCs was inversely correlated with serum CXCL10 levels in BD patients (p = 0.022). By immunohistochemistry, the number of CXCR3-positive mononuclear cells was higher in skin and intestinal lesions of BD patients than in those of HCs. These results suggest that the CXCL10/CXCR3 axis may contribute to the pathogenesis of BD.
Flux-tunable phase shifter for microwaves
Authors: Kokkoniemi Roope , Ollikainen Tuomas , Lake Russell E. , Saarenpää Sakari , Tan Kuan Y. , Kokkala Janne I. , Dağ Ceren B. , Govenius Joonas , Möttönen Mikko 
Published: November 2017

AbstractWe introduce a magnetic-flux-tunable phase shifter for propagating microwave photons, based on three equidistant superconducting quantum interference devices (SQUIDs) on a transmission line. We experimentally implement the phase shifter and demonstrate that it produces a broad range of phase shifts and full transmission within the experimental uncertainty. Together with previously demonstrated beam splitters, this phase shifter can be utilized to implement arbitrary single-qubit gates for qubits based on propagating microwave photons. These results complement previous demonstrations of on-demand single-photon sources and detectors, and hence assist in the pursuit of an all-microwave quantum computer based on propagating photons.
Human stem cell-derived retinal epithelial cells activate complement via collectin 11 in response to stress
Authors: Fanelli Giorgia , Gonzalez-Cordero Anai , Gardner Peter J. , Peng Qi , Fernando Milan , Kloc Magdalena , Farrar Conrad A. , Naeem Arifa , Garred Peter , Ali Robin R. , Sacks Steven H. 
Published: November 2017

AbstractAge-related macular degeneration (AMD) is a major cause of blindness and is associated with complement dysregulation. The disease is a potential target for stem cell therapy but success is likely to be limited by the inflammatory response. We investigated the innate immune properties of human induced-pluripotent stem cell (iPSC)-derived RPE cells, particularly with regard to the complement pathway. We focused on collectin-11 (CL-11), a pattern recognition molecule that can trigger complement activation in renal epithelial tissue. We found evidence of constitutive and hypoxia-induced expression of CL-11 in iPS-RPE cells, and in the extracellular fluid. Complement activation on the cell surface occurred in conjunction with CL-11 binding. CL-11 has been shown to activate inflammatory responses through recognition of L-fucose, which we confirmed by showing that fucosidase-treated cells, largely, failed to activate complement. The presence of CL-11 in healthy murine and human retinal tissues confirmed the biological relevance of CL-11. Our data describe a new trigger mechanism of complement activation that could be important in disease pathogenesis and therapeutic interventions.
Targeted Metabolomics Reveals Abnormal Hepatic Energy Metabolism by Depletion of β-Carotene Oxygenase 2 in Mice
Authors: Wu Lei , Guo Xin , Lyu Yi , Clarke Stephen L. , Lucas Edralin A. , Smith Brenda J. , Hildebrand Deana , Wang Weiqun , Medeiros Denis M. , Shen Xinchun , Lin Dingbo 
Published: November 2017

Abstractβ-carotene oxygenase 2 (BCO2) is a carotenoid cleavage enzyme located in the inner mitochondrial membrane. Ablation of BCO2 impairs mitochondrial function leading to oxidative stress. Herein, we performed a targeted metabolomics study using ultrahigh performance liquid chromatography-tandem mass spectroscopy and gas chromatography-mass spectroscopy to discriminate global metabolites profiles in liver samples from six-week-old male BCO2 systemic knockout (KO), heterozygous (Het), and wild type (WT) mice fed a chow diet. Principal components analysis revealed distinct differences in metabolites in the livers of KO mice, compared to WT and Het mice. However, no marked difference was found in the metabolites of the Het mouse liver compared to the WT. We then conducted random forest analysis to classify the potential biomarkers to further elucidate the different metabolomics profiles. We found that systemic ablation of BCO2 led to perturbations in mitochondrial function and metabolism in the TCA cycle, amino acids, carnitine, lipids, and bile acids. In conclusion, BCO2 is essential to macronutrient and mitochondrial metabolism in the livers of mice. The ablation of BCO2 causes dysfunctional mitochondria and altered energy metabolism, which further leads to systemic oxidative stress and inflammation. A single functional copy of BCO2 largely rescues the hepatic metabolic homeostasis in mice.
Efficient production and characterization of the novel and highly active antifungal protein AfpB from Penicillium digitatum
Authors: Garrigues Sandra , Gandía Mónica , Popa Crina , Borics Attila , Marx Florentine , Coca María , Marcos Jose F. , Manzanares Paloma 
Published: November 2017

AbstractFilamentous fungi encode distinct antifungal proteins (AFPs) that offer great potential to develop new antifungals. Fungi are considered immune to their own AFPs as occurs in Penicillium chrysogenum, the producer of the well-known PAF. The Penicillium digitatum genome encodes only one afp gene (afpB), and the corresponding protein (AfpB) belongs to the class B phylogenetic cluster. Previous attempts to detect AfpB were not successful. In this work, immunodetection confirmed the absence of AfpB accumulation in wild type and previous recombinant constitutive P. digitatum strains. Biotechnological production and secretion of AfpB were achieved in P. digitatum with the use of a P. chrysogenum-based expression cassette and in the yeast Pichia pastoris with the α-factor signal peptide. Both strategies allowed proper protein folding, efficient production and single-step purification of AfpB from culture supernatants. AfpB showed antifungal activity higher than the P. chrysogenum PAF against the majority of the fungi tested, especially against Penicillium species and including P. digitatum, which was highly sensitive to the self-AfpB. Spectroscopic data suggest that native folding is not required for activity. AfpB also showed notable ability to withstand protease and thermal degradation and no haemolytic activity, making AfpB a promising candidate for the control of pathogenic fungi.
Ilex latifolia Thunb protects mice from HFD-induced body weight gain
Authors: Wu Hailan , Chen Yue-Lei , Yu Yueyuan , Zang Jin , Wu Yikuan , He Zhao 
Published: November 2017

AbstractKuding tea is implicated in alleviating metabolic disorders in traditional Chinese medicine. However, the role of Ilex latifolia Thunb (kuding tea), one of the large leaf kuding tea species, in the prevention of the development of obesity remains to be determined. We show here that 7-week-old male mice treated with an Ilex latifolia Thunb supplement for 14 weeks were resistant to HFD-induced body weight gain and hepatic steatosis, accompanied by improved insulin sensitivity. Ilex latifolia Thunb supplementation dramatically reduced the systemic and tissue inflammation levels of mice via reducing pro-inflammatory cytokine levels, increasing anti-inflammatory cytokine levels in the circulation and inhibiting p38 MAPK and p65 NF-κB signaling in adipose tissue. Together, these results indicate that Ilex latifolia Thunb protects mice from the development of obesity and is a potential compound pool for the development of novel anti-obesity drugs.
Pathway Towards High-Efficiency Eu-doped GaN Light-Emitting Diodes
Authors: Fragkos Ioannis E. , Tan Chee-Keong , Dierolf Volkmar , Fujiwara Yasufumi , Tansu Nelson 
Published: November 2017

AbstractA physically intuitive current injection efficiency model for a GaN:Eu quantum well (QW) has been developed to clarify the necessary means to achieve device quantum efficiency higher than the state-of-the-art GaN:Eu system for red light emission. The identification and analysis of limiting factors for high internal quantum efficiencies (IQE) are accomplished through the current injection efficiency model. In addition, the issue of the significantly lower IQE in the electrically-driven GaN:Eu devices in comparison to the optically-pumped GaN:Eu devices is clarified in the framework of this injection efficiency model. The improved understanding of the quantum efficiency issue through current injection efficiency model provides a pathway to address the limiting factors in electrically-driven devices. Based on our developed injection efficiency model, several experimental approaches have been suggested to address the limitations in achieving high IQE GaN:Eu QW based devices in red spectral regime.
Advantages of a technique using two 50 degree arcs in simultaneous integrated boost radiotherapy for left-sidebreast cancer
Authors: Xi Dan , Ding Yun , Hu Rui , Gu Wendong , Mu Jinming , Li Qilin 
Published: November 2017

AbstractThis study evaluated radiotherapy techniques with 15 cases for simultaneous integrated boost to treat whole left breast and tumor bed following breast conserving surgery. Treatment plans were generated using three techniques: volumetric modulated arc therapy (VMAT) with a partial arc of 190° (1ARC), VMAT with two tangential mini-arcs of 50° each (2TARC) and intensity modulated radiation therapy with four fixed angle fields (4IMRT). Dosimetric parameters for the whole breast (Target), the boost tumor bed (Boost), and surrounding normal organs were compared. Chair Index (CHI) was introduced to evaluate the dose homogeneity in Target given the two levels of prescription dose. The dose coverage in Target was better in 1ARC and 2TARC than that in 4IMRT. The mean CHI in 1ARC (2.47) and 2TARC (2.62) were higher than that in 4IMRT (1.71, p < 0.05), and this indicated the dose homogeneity of Target was better in 1ARC and 2TARC than that in 4IMRT. The mean doses to right lung, and contralateral breast in 4IMRT were lower than those in 2TARC but the differences between them were small. 2TARC was better than 4IMRT with respect to the dose to ipsilateral lung and heart. Overall, 2TARC was optimal among three techniques.
Spaceborne Synthetic Aperture Radar Survey of Subsidence in Hampton Roads, Virginia (USA)
Authors: Bekaert D. P. S. , Hamlington B. D. , Buzzanga B. , Jones C. E. 
Published: November 2017

AbstractOver the past century, the Hampton Roads area of the Chesapeake Bay region has experienced one of the highest rates of relative sea level rise on the Atlantic coast of the United States. This rate of relative sea level rise results from a combination of land subsidence, which has long been known to be present in the region, and rising seas associated with global warming on long timescales and exacerbated by shifts in ocean dynamics on shorter timescales. An understanding of the current-day magnitude of each component is needed to create accurate projections of future relative sea level rise upon which to base planning efforts. The objective of this study is to estimate the land component of relative sea level rise using interferometric synthetic aperture radar (InSAR) analysis applied to ALOS-1 synthetic aperture radar data acquired during 2007–2011 to generate high-spatial resolution (20–30 m) estimates of vertical land motion. Although these results are limited by the uncertainty associated with the small set of available historical SAR data, they highlight both localized rates of high subsidence and a significant spatial variability in subsidence, emphasizing the need for further measurement, which could be done with Sentinel-1 and NASA’s upcoming NISAR mission.
Impacts of elevated CO2 on exogenous Bacillus thuringiensis toxins and transgene expression in transgenic rice under different levels of nitrogen
Authors: Jiang Shoulin , Lu Yongqing , Dai Yang , Qian Lei , Muhammad Adnan Bodlah , Li Teng , Wan Guijun , Parajulee Megha N. , Chen Fajun 
Published: November 2017

AbstractRecent studies have highlighted great challenges of transgene silencing for transgenic plants facing climate change. In order to understand the impacts of elevated CO2 on exogenous Bacillus thuringiensis (Bt) toxins and transgene expression in transgenic rice under different levels of N-fertilizer supply, we investigated the biomass, exogenous Bt toxins, Bt-transgene expression and methylation status in Bt rice exposed to two levels of CO2 concentrations and nitrogen (N) supply (1/8, 1/4, 1/2, 1 and 2 N). It is elucidated that the increased levels of global atmospheric CO2 concentration will trigger up-regulation of Bt toxin expression in transgenic rice, especially with appropriate increase of N fertilizer supply, while, to some extent, the exogenous Bt-transgene expression is reduced at sub-N levels (1/4 and 1/2N), even though the total protein of plant tissues is reduced and the plant growth is restricted. The unpredictable and stochastic occurrence of transgene silencing and epigenetic alternations remains unresolved for most transgenic plants. It is expected that N fertilization supply may promote the expression of transgenic Bt toxin in transgenic Bt rice, particularly under elevated CO2.