bluuebunny/crossref_metadata_2025_split huggingface dataset:
WRN regulates pathway choice between classical and alternative non-homologous end joining
Authors: Shamanna Raghavendra A. , Lu Huiming , de Freitas Jessica K. , Tian Jane , Croteau Deborah L. , Bohr Vilhelm A. 
Published: December 2016

AbstractWerner syndrome (WS) is an accelerated ageing disorder with genomic instability caused by WRN protein deficiency. Many features seen in WS can be explained by the diverse functions of WRN in DNA metabolism. However, the origin of the large genomic deletions and telomere fusions are not yet understood. Here, we report that WRN regulates the pathway choice between classical (c)- and alternative (alt)-nonhomologous end joining (NHEJ) during DNA double-strand break (DSB) repair. It promotes c-NHEJ via helicase and exonuclease activities and inhibits alt-NHEJ using non-enzymatic functions. When WRN is recruited to the DSBs it suppresses the recruitment of MRE11 and CtIP, and protects the DSBs from 5′ end resection. Moreover, knockdown of Wrn, alone or in combination with Trf2 in mouse embryonic fibroblasts results in increased telomere fusions, which were ablated by Ctip knockdown. We show that WRN regulates alt-NHEJ and shields DSBs from MRE11/CtIP-mediated resection to prevent large deletions and telomere fusions.
Profilometry of thin films on rough substrates by Raman spectroscopy
Authors: Ledinský Martin , Paviet-Salomon Bertrand , Vetushka Aliaksei , Geissbühler Jonas , Tomasi Andrea , Despeisse Matthieu , De Wolf Stefaan , Ballif Christophe , Fejfar Antonín 
Published: December 2016

AbstractThin, light-absorbing films attenuate the Raman signal of underlying substrates. In this article, we exploit this phenomenon to develop a contactless thickness profiling method for thin films deposited on rough substrates. We demonstrate this technique by probing profiles of thin amorphous silicon stripes deposited on rough crystalline silicon surfaces, which is a structure exploited in high-efficiency silicon heterojunction solar cells. Our spatially-resolved Raman measurements enable the thickness mapping of amorphous silicon over the whole active area of test solar cells with very high precision; the thickness detection limit is well below 1 nm and the spatial resolution is down to 500 nm, limited only by the optical resolution. We also discuss the wider applicability of this technique for the characterization of thin layers prepared on Raman/photoluminescence-active substrates, as well as its use for single-layer counting in multilayer 2D materials such as graphene, MoS2 and WS2.
Protein self-assembly onto nanodots leads to formation of conductive bio-based hybrids
Authors: Hu Xiao , Dong Chenbo , Su Rigu , Xu Quan , Dinu Cerasela Zoica 
Published: December 2016

AbstractThe next generation of nanowires that could advance the integration of functional nanosystems into synthetic applications from photocatalysis to optical devices need to demonstrate increased ability to promote electron transfer at their interfaces while ensuring optimum quantum confinement. Herein we used the biological recognition and the self-assembly properties of tubulin, a protein involved in building the filaments of cellular microtubules, to create stable, free standing and conductive sulfur-doped carbon nanodots-based conductive bio-hybrids. The physical and chemical properties (e.g., composition, morphology, diameter etc.) of such user-synthesized hybrids were investigated using atomic and spectroscopic techniques, while the electron transfer rate was estimated using peak currents formed during voltammetry scanning. Our results demonstrate the ability to create individually hybrid nanowires capable to reduce energy losses; such hybrids could possibly be used in the future for the advancement and implementation into nanometer-scale functional devices.
Identification and Structural Characterization of the N-terminal Amyloid Core of Orb2 isoform A
Authors: Cervantes Silvia A. , Bajakian Thalia H. , Soria Maria A. , Falk Alexander S. , Service Rachel J. , Langen Ralf , Siemer Ansgar B. 
Published: December 2016

AbstractOrb2 is a functional amyloid that plays a key role in Drosophila long-term memory formation. Orb2 has two isoforms that differ in their N-termini. The N-terminus of the A isoform (Orb2A) that precedes its Q-rich prion-like domain has been shown to be important for Orb2 aggregation and long-term memory. However, besides the fact that it forms fibrillar aggregates, structural information of Orb2 is largely absent. To understand the importance of the N-terminus of Orb2A and its relation to the fibril core, we recorded solid-state NMR and EPR data on fibrils formed by the first 88 residues of Orb2A (Orb2A88). These data show that the N-terminus of Orb2A not only promotes the formation of fibrils, but also forms the fibril core of Orb2A88. This fibril core has an in-register parallel β-sheet structure and does not include the Q-rich, prion-like domain of Orb2. The Q-rich domain is part of the unstructured region, which becomes increasingly dynamic towards the C-terminus.
Identification of KIAA1199 as a Biomarker for Pancreatic Intraepithelial Neoplasia
Authors: Suh Han Na , Jun Sohee , Oh Ah-Young , Srivastava Mrinal , Lee Sunhye , Taniguchi Cullen M. , Zhang Songlin , Lee Won Sup , Chen Junjie , Park Bum-Joon , Park Jae-Il 
Published: December 2016

AbstractPancreatic cancer is one of the most aggressive cancers and has an extremely poor prognosis. Despite recent progress in both basic and clinical research, most pancreatic cancers are detected at an incurable stage owing to the absence of disease-specific symptoms. Thus, developing novel approaches for detecting pancreatic cancer at an early stage is imperative. Our in silico and immunohistochemical analyses showed that KIAA1199 is specifically expressed in human pancreatic cancer cells and pancreatic intraepithelial neoplasia, the early lesion of pancreatic cancer, in a genetically engineered mouse model and in human patient samples. We also detected secreted KIAA1199 protein in blood samples obtained from pancreatic cancer mouse models, but not in normal mice. Furthermore, we found that assessing KIAA1199 autoantibody increased the sensitivity of detecting pancreatic cancer. These results indicate the potential benefits of using KIAA1199 as a biomarker for early-stage pancreatic cancer.
Non-small cell lung cancer: quantitative phenotypic analysis of CT images as a potential marker of prognosis
Authors: Song Jiangdian , Liu Zaiyi , Zhong Wenzhao , Huang Yanqi , Ma Zelan , Dong Di , Liang Changhong , Tian Jie 
Published: December 2016

AbstractThis was a retrospective study to investigate the predictive and prognostic ability of quantitative computed tomography phenotypic features in patients with non-small cell lung cancer (NSCLC). 661 patients with pathological confirmed as NSCLC were enrolled between 2007 and 2014. 592 phenotypic descriptors was automatically extracted on the pre-therapy CT images. Firstly, support vector machine (SVM) was used to evaluate the predictive value of each feature for pathology and TNM clinical stage. Secondly, Cox proportional hazards model was used to evaluate the prognostic value of these imaging signatures selected by SVM which subjected to a primary cohort of 138 patients, and an external independent validation of 61 patients. The results indicated that predictive accuracy for histopathology, N staging, and overall clinical stage was 75.16%, 79.40% and 80.33%, respectively. Besides, Cox models indicated the signatures selected by SVM: “correlation of co-occurrence after wavelet transform” was significantly associated with overall survival in the two datasets (hazard ratio [HR]: 1.65, 95% confidence interval [CI]: 1.41–2.75, p = 0.010; and HR: 2.74, 95%CI: 1.10–6.85, p = 0.027, respectively). Our study indicates that the phenotypic features might provide some insight in metastatic potential or aggressiveness for NSCLC, which potentially offer clinical value in directing personalized therapeutic regimen selection for NSCLC.
Antiproliferative activities of Amaryllidaceae alkaloids from Lycoris radiata targeting DNA topoisomerase I
Authors: Chen Gui-Lin , Tian Yong-Qiang , Wu Jian-Lin , Li Na , Guo Ming-Quan 
Published: December 2016

AbstractCrude Amaryllidaceae alkaloids (AAs) extracted from Lycoris radiata are reported to exhibit significant anti-cancer activity. However, the specific alkaloids responsible for the pharmacodynamic activity and their targets still remain elusive. In this context, we strived to combine affinity ultrafiltration with topoisomerase I (Top I) as a target enzyme aiming to fish out specific bioactive AAs from Lycoris radiata. 11 AAs from Lycoris radiata were thus screened out, among which hippeastrine (peak 5) with the highest Enrichment factor (EF) against Top I exhibited good dose-dependent inhibition with IC50 at 7.25 ± 0.20 μg/mL comparable to camptothecin (positive control) at 6.72 ± 0.23 μg/mL. The molecular docking simulation further indicated the inhibitory mechanism between Top I and hippeastrine. The in vitro antiproliferation assays finally revealed that hippeastrine strongly inhibited the proliferation of HT-29 and Hep G2 cells in an intuitive dose-dependent manner with the IC50 values at 3.98 ± 0.29 μg/mL and 11.85 ± 0.20 μg/mL, respectively, and also induced significant cellular morphological changes, which further validated our screening method and the potent antineoplastic effects. Collectively, these results suggested that hippeastrine could be a very promising anticancer candidate for the therapy of cancer in the near future.
A carotenogenic mini-pathway introduced into white corn does not affect development or agronomic performance
Authors: Zanga Daniela , Capell Teresa , Slafer Gustavo A. , Christou Paul , Savin Roxana 
Published: December 2016

AbstractHigh-carotenoid corn (Carolight®) has been developed as a vehicle to deliver pro-vitamin A in the diet and thus address vitamin A deficiency in at-risk populations in developing countries. Like any other novel crop, the performance of Carolight® must be tested in different environments to ensure that optimal yields and productivity are maintained, particularly in this case to ensure that the engineered metabolic pathway does not attract a yield penalty. Here we compared the performance of Carolight® with its near isogenic white corn inbred parental line under greenhouse and field conditions, and monitored the stability of the introduced trait. We found that Carolight® was indistinguishable from its near isogenic line in terms of agronomic performance, particularly grain yield and its main components. We also established experimentally that the functionality of the introduced trait was indistinguishable when plants were grown in a controlled environment or in the field. Such thorough characterization under different agronomic conditions is rarely performed even for first-generation traits such as herbicide tolerance and pest resistance, and certainly not for complex second-generation traits such as the metabolic remodeling in the Carolight® variety. Our results therefore indicate that Carolight® can now be incorporated into breeding lines to generate hybrids with locally adapted varieties for further product development and assessment.
Deep sequencing of the 16S ribosomal RNA of the neonatal oral microbiome: a comparison of breast-fed and formula-fed infants
Authors: Al-Shehri S. S. , Sweeney E. L. , Cowley D. M. , Liley H. G. , Ranasinghe P. D. , Charles B. G. , Shaw P. N. , Vagenas D. , Duley J. A. , Knox C. L. 
Published: December 2016

AbstractIn utero and upon delivery, neonates are exposed to a wide array of microorganisms from various sources, including maternal bacteria. Prior studies have proposed that the mode of feeding shapes the gut microbiota and, subsequently the child’s health. However, the effect of the mode of feeding and its influence on the development of the neonatal oral microbiota in early infancy has not yet been reported. The aim of this study was to compare the oral microbiota of healthy infants that were exclusively breast-fed or formula-fed using 16S-rRNA gene sequencing. We demonstrated that the oral bacterial communities were dominated by the phylum Firmicutes, in both groups. There was a higher prevalence of the phylum Bacteroidetes in the mouths of formula-fed infants than in breast-fed infants (p = 0.01), but in contrast Actinobacteria were more prevalent in breast-fed babies; Proteobacteria was more prevalent in saliva of breast-fed babies than in formula-fed neonates (p = 0.04). We also found evidence suggesting that the oral microbiota composition changed over time, particularly Streptococcus species, which had an increasing trend between 4–8 weeks in both groups. This study findings confirmed that the mode of feeding influences the development of oral microbiota, and this may have implications for long-term human health.
Different responses of alpine plants to nitrogen addition: effects on plant-plant interactions
Authors: Wang Jun , Luo Peng , Yang Hao , Mou Chengxiang , Mo Li 
Published: December 2016

AbstractThe different responses of plant species to resource stress are keys to understand the dynamics of plant community in a changing environment. To test the hypothesis that nitrogen (N) increase would benefit N competitive species, rather than N stress-tolerant species, to compete with neighbours, we conducted an experiment with neighbour removal, N addition and soil moisture as treatments in an alpine grassland on the southeastern Tibetan Plateau. Both growths and competitive-response abilities (CRA, the ability to tolerate the inhibitory effects of neighbors) of Kobresia macrantha, Polygonum viviparum and Potentilla anserine in wet site were facilitated by N addition, conversely, both growths and CRA of Taraxacum mongolicum and Ligularia virgaurea were suppressed by N addition, indicating that the responses of CRA of target species under N addition were consistent with the N utilization strategies of them. Moreover, the facilitative effects of N addition on competitive-response abilities of Kobresia macrantha and Polygonum viviparum were not found at the dry site, illustrating that soil moisture can alter the changes of neighbour effects caused by N addition. Life strategy of dominant species in plant community on the undisturbed southeastern Tibetan Plateau may shift from N stress-tolerant to N competitive, if the N increases continuously.
Source apportionment of chlorinated polycyclic aromatic hydrocarbons associated with ambient particles in a Japanese megacity
Authors: Kamiya Yuta , Iijima Akihiro , Ikemori Fumikazu , Okuda Tomoaki , Ohura Takeshi 
Published: December 2016

AbstractChlorinated polycyclic aromatic hydrocarbons (ClPAHs) are novel species of environmental contaminants whose possible sources remain unclear. The occurrence of ClPAHs within total suspended particles (TSP) is compared with weekly air samples at two sites of differing characteristics (industrial and residential) in the megacity of Nagoya, Japan. Samples were collected over 12 months during 2011–2012. All 24 species of targeted ClPAHs were detected at both industrial and residential sites, where mean concentrations of total ClPAHs in TSP were 20.7 and 14.1 pg/m3, respectively. High concentrations at the industrial site were frequently observed during winter, suggesting potent seasonal ClPAH sources there. Positive matrix factorization modeling of particulate ClPAH source identification and apportioning were conducted for datasets including ClPAHs, PAHs, elements and ions, plus elemental carbons in TSP. Eight factors were identified as possible ClPAH sources, with estimates that the dominant one was a specific source of ClPAH emission (31%), followed by traffic (23%), photodegradable and semi-volatile species (18%), long-range transport (11%), and industry and oil combustion (10%). Source contributions of ClPAHs differed substantially from those of PAHs. This suggests specific and/or potent ClPAH sources in the local area, and that the production mechanisms between ClPAHs and PAHs are substantially different.
Authentication of Chinese vintage liquors using bomb-pulse 14C
Authors: Cheng Peng , Zhou Weijian , Burr G. S. , Fu Yunchong , Fan Yukun , Wu Shugang 
Published: December 2016

AbstractThe older a bottle of Chinese vintage liquor is, the higher the price it commands. Driven by the potential for higher profits, some newly-founded distilleries openly sell liquor whose storage ages are exaggerated. In China, the market for vintage liquor has become fraught with uncertainty and a pressing need has arisen to establish an effective method to authenticate the age of vintage liquors. A radiocarbon (14C) dating method is described here that can verify cellar-stored years of Chinese liquors distilled within the last fifty years. Two different flavored Chinese liquors produced in “the golden triangular region” in the Upper Yangtze River region in southwest China, with known cellar-stored years, were analyzed to benchmark the technique. Strong flavored liquors are found to be consistent with local atmospheric Δ14C values. A small offset of 2–3 years between predicted vintage years of soy-sauce flavored liquors and strong flavored liquors is found to be associated with the fermentation cycle of certain varieties. The technique can measure cellar-stored years of a wide range of liquors including those with fundamentally different aromas. This demonstrates the strength of our method in identifying suspect Chinese vintage liquors.
Foldable and Disposable Memory on Paper
Authors: Lee Byung-Hyun , Lee Dong-Il , Bae Hagyoul , Seong Hyejeong , Jeon Seung-Bae , Seol Myung-Lok , Han Jin-Woo , Meyyappan M. , Im Sung-Gap , Choi Yang-Kyu 
Published: December 2016

AbstractFoldable organic memory on cellulose nanofibril paper with bendable and rollable characteristics is demonstrated by employing initiated chemical vapor deposition (iCVD) for polymerization of the resistive switching layer and inkjet printing of the electrode, where iCVD based on all-dry and room temperature process is very suitable for paper electronics. This memory exhibits a low operation voltage of 1.5 V enabling battery operation compared to previous reports and wide memory window. The memory performance is maintained after folding tests, showing high endurance. Furthermore, the quick and complete disposable nature demonstrated here is attractive for security applications. This work provides an effective platform for green, foldable and disposable electronics based on low cost and versatile materials.
Warming Trends and Bleaching Stress of the World’s Coral Reefs 1985–2012
Authors: Heron Scott F. , Maynard Jeffrey A. , van Hooidonk Ruben , Eakin C. Mark 
Published: December 2016

AbstractCoral reefs across the world’s oceans are in the midst of the longest bleaching event on record (from 2014 to at least 2016). As many of the world’s reefs are remote, there is limited information on how past thermal conditions have influenced reef composition and current stress responses. Using satellite temperature data for 1985–2012, the analysis we present is the first to quantify, for global reef locations, spatial variations in warming trends, thermal stress events and temperature variability at reef-scale (~4 km). Among over 60,000 reef pixels globally, 97% show positive SST trends during the study period with 60% warming significantly. Annual trends exceeded summertime trends at most locations. This indicates that the period of summer-like temperatures has become longer through the record, with a corresponding shortening of the ‘winter’ reprieve from warm temperatures. The frequency of bleaching-level thermal stress increased three-fold between 1985–91 and 2006–12 – a trend climate model projections suggest will continue. The thermal history data products developed enable needed studies relating thermal history to bleaching resistance and community composition. Such analyses can help identify reefs more resilient to thermal stress.
Co-expression network analyses identify functional modules associated with development and stress response in Gossypium arboreum
Authors: You Qi , Zhang Liwei , Yi Xin , Zhang Kang , Yao Dongxia , Zhang Xueyan , Wang Qianhua , Zhao Xinhua , Ling Yi , Xu Wenying , Li Fuguang , Su Zhen 
Published: December 2016

AbstractCotton is an economically important crop, essential for the agriculture and textile industries. Through integrating transcriptomic data, we discovered that multi-dimensional co-expression network analysis was powerful for predicting cotton gene functions and functional modules. Here, the recently available transcriptomic data on Gossypium arboreum, including data on multiple growth stages of tissues and stress treatment samples were applied to construct a co-expression network exploring multi-dimensional expression (development and stress) through multi-layered approaches. Based on differential gene expression and network analysis, a fibre development regulatory module of the gene GaKNL1 was found to regulate the second cell wall through repressing the activity of REVOLUTA, and a tissue-selective module of GaJAZ1a was examined in response to water stress. Moreover, comparative genomics analysis of the JAZ1-related regulatory module revealed high conservation across plant species. In addition, 1155 functional modules were identified through integrating the co-expression network, module classification and function enrichment tools, which cover functions such as metabolism, stress responses, and transcriptional regulation. In the end, an online platform was built for network analysis (http://structuralbiology.cau.edu.cn/arboreum), which could help to refine the annotation of cotton gene function and establish a data mining system to identify functional genes or modules with important agronomic traits.
Optimized invisibility cloaks from the Logarithm conformal mapping
Authors: Zhu Chunhui , Liu Lijun , Song Zhengyong , Liu Qing Huo 
Published: December 2016

AbstractInvisibility cloaks designed from the coordinate transformation method have attracted increasing interest recently. Conformal transformation optics scheme leads to cloaks that possess isotopic media, thus provides a prospective way to facilitate easier realization. Reducing the maximum value of the refractive index required by the cloaks is very important in practical imple- mentation. This letter studies on how the parameters in the logarithm conformal mapping control the cloaking effect. The optimized invisibility cloaks are designed. The maximum values of the refractive index required from the first kind and the second kind of logarithm conformal mappings are reduced to 9.779 and 12.936, respectively.
Wideband helicity dependent spoof surface plasmon polaritons coupling metasurface based on dispersion design
Authors: Dong Guoxiang , Shi Hongyu , He Yuchen , Zhang Anxue , Wei Xiaoyong , Zhuang Yongyong , Du Bai , Xia Song , Xu Zhuo 
Published: December 2016

AbstractThe surface plasmon polaritons (SPPs) have many potential application due to their local field enhancement and sub-wavelength characteristics. Recently, the gradient metasurface is introduced to couple the spoof SPPs in microwave frequency band. One of the most important issue which should be solved is the narrowband of spoof SPPs coupling on the gradient metasurface. Here, the metasurface is proposed to achieve the wideband helicity dependent directional spoof SPPs coupling for circular polarized light. Our research show that the coupling frequency of spoof SPPs on the gradient metasurface is determined by the dispersion of the metasurface, so the coupling frequency can be controlled by dispersion design. The careful design of each cell geometric parameters has provided many appropriate dispersion relations possessed by just one metasurface. The wave vector matching between the propagating wave and the spoof SPPs has been achieved at several frequencies for certain wave vector provided by the metasurface, which leads to wideband spoof SPPs coupling. This work has shown that wideband helicity dependent directional spoof SPPs coupling has been achieved with a high efficiency. Hence, the proposed wideband spoof SPPs coupling presents the improvement in practice applications.