bluuebunny/crossref_metadata_2025_split huggingface dataset:
The TLX-miR-219 cascade regulates neural stem cell proliferation in neurodevelopment and schizophrenia iPSC model
Authors: Murai Kiyohito , Sun Guoqiang , Ye Peng , Tian E. , Yang Su , Cui Qi , Sun Guihua , Trinh Daniel , Sun Olivia , Hong Teresa , Wen Zhexing , Kalkum Markus , Riggs Arthur D. , Song Hongjun , Ming Guo-li , Shi Yanhong 
Published: March 2016

AbstractDysregulated expression of miR-219, a brain-specific microRNA, has been observed in neurodevelopmental disorders, such as schizophrenia (SCZ). However, its role in normal mammalian neural stem cells (NSCs) and in SCZ pathogenesis remains unknown. We show here that the nuclear receptor TLX, an essential regulator of NSC proliferation and self-renewal, inhibits miR-219 processing. miR-219 suppresses mouse NSC proliferation downstream of TLX. Moreover, we demonstrate upregulation of miR-219 and downregulation of TLX expression in NSCs derived from SCZ patient iPSCs and DISC1-mutant isogenic iPSCs. SCZ NSCs exhibit reduced cell proliferation. Overexpression of TLX or inhibition of miR-219 action rescues the proliferative defect in SCZ NSCs. Therefore, this study uncovers an important role for TLX and miR-219 in both normal neurodevelopment and in SCZ patient iPSC-derived NSCs. Moreover, this study reveals an unexpected role for TLX in regulating microRNA processing, independent of its well-characterized role in transcriptional regulation.
Propagation phasor approach for holographic image reconstruction
Authors: Luo Wei , Zhang Yibo , Göröcs Zoltán , Feizi Alborz , Ozcan Aydogan 
Published: March 2016

AbstractTo achieve high-resolution and wide field-of-view, digital holographic imaging techniques need to tackle two major challenges: phase recovery and spatial undersampling. Previously, these challenges were separately addressed using phase retrieval and pixel super-resolution algorithms, which utilize the diversity of different imaging parameters. Although existing holographic imaging methods can achieve large space-bandwidth-products by performing pixel super-resolution and phase retrieval sequentially, they require large amounts of data, which might be a limitation in high-speed or cost-effective imaging applications. Here we report a propagation phasor approach, which for the first time combines phase retrieval and pixel super-resolution into a unified mathematical framework and enables the synthesis of new holographic image reconstruction methods with significantly improved data efficiency. In this approach, twin image and spatial aliasing signals, along with other digital artifacts, are interpreted as noise terms that are modulated by phasors that analytically depend on the lateral displacement between hologram and sensor planes, sample-to-sensor distance, wavelength, and the illumination angle. Compared to previous holographic reconstruction techniques, this new framework results in five- to seven-fold reduced number of raw measurements, while still achieving a competitive resolution and space-bandwidth-product. We also demonstrated the success of this approach by imaging biological specimens including Papanicolaou and blood smears.
Ecosystem services provided by a complex coastal region: challenges of classification and mapping
Authors: Sousa Lisa P. , Sousa Ana I. , Alves Fátima L. , Lillebø Ana I. 
Published: March 2016

AbstractA variety of ecosystem services classification systems and mapping approaches are available in the scientific and technical literature, which needs to be selected and adapted when applied to complex territories (e.g. in the interface between water and land, estuary and sea). This paper provides a framework for addressing ecosystem services in complex coastal regions. The roadmap comprises the definition of the exact geographic boundaries of the study area; the use of CICES (Common International Classification of Ecosystem Services) for ecosystem services identification and classification; and the definition of qualitative indicators that will serve as basis to map the ecosystem services. Due to its complexity, the Ria de Aveiro coastal region was selected as case study, presenting an opportunity to explore the application of such approaches at a regional scale. The main challenges of implementing the proposed roadmap, together with its advantages are discussed in this research. The results highlight the importance of considering both the connectivity of natural systems and the complexity of the governance framework; the flexibility and robustness, but also the challenges when applying CICES at regional scale; and the challenges regarding ecosystem services mapping.
Dynamic channel adjustments in the Jingjiang Reach of the Middle Yangtze River
Authors: Xia Junqiang , Deng Shanshan , Lu Jinyou , Xu Quanxi , Zong Quanli , Tan Guangming 
Published: March 2016

AbstractSignificant channel adjustments have occurred in the Jingjiang Reach of the Middle Yangtze River, because of the operation of the Three Gorges Project (TGP). The Jingjiang Reach is selected as the study area, covering the Upper Jingjiang Reach (UJR) and Lower Jingjiang Reach (LJR). The reach-scale bankfull channel dimensions in the study reach were calculated annually from 2002 to 2013 by means of a reach-averaged approach and surveyed post-flood profiles at 171 sections. We find from the calculated results that: the reach-scale bankfull widths changed slightly in the UJR and LJR, with the corresponding depths increasing by 1.6 m and 1.0 m; the channel adjustments occurred mainly with respect to bankfull depth because of the construction of large-scale bank revetment works, although there were significant bank erosion processes in local regions without the bank protection engineering. The reach-scale bankfull dimensions in the UJR and LJR generally responded to the previous five-year average fluvial erosion intensity during flood seasons, with higher correlations being obtained for the depth and cross-sectional area. It is concluded that these dynamic adjustments of the channel geometry are a direct result of recent human activities such as the TGP operation.
Structure-Based Virtual Ligand Screening on the XRCC4/DNA Ligase IV Interface
Authors: Menchon Grégory , Bombarde Oriane , Trivedi Mansi , Négrel Aurélie , Inard Cyril , Giudetti Brigitte , Baltas Michel , Milon Alain , Modesti Mauro , Czaplicki Georges , Calsou Patrick 
Published: March 2016

AbstractThe association of DNA Ligase IV (Lig4) with XRCC4 is essential for repair of DNA double-strand breaks (DSBs) by Non-homologous end-joining (NHEJ) in humans. DSBs cytotoxicity is largely exploited in anticancer therapy. Thus, NHEJ is an attractive target for strategies aimed at increasing the sensitivity of tumors to clastogenic anticancer treatments. However the high affinity of the XRCC4/Lig4 interaction and the extended protein-protein interface make drug screening on this target particularly challenging. Here, we conducted a pioneering study aimed at interfering with XRCC4/Lig4 assembly. By Molecular Dynamics simulation using the crystal structure of the complex, we first delineated the Lig4 clamp domain as a limited suitable target. Then, we performedin silicoscreening of ~95,000 filtered molecules on this Lig4 subdomain. Hits were evaluated by Differential Scanning Fluorimetry, Saturation Transfer Difference - NMR spectroscopy and interaction assays with purified recombinant proteins. In this way we identified the first molecule able to prevent Lig4 binding to XRCC4in vitro. This compound has a unique tripartite interaction with the Lig4 clamp domain that suggests a starting chemotype for rational design of analogous molecules with improved affinity.
Identification of OCTN2 variants and their association with phenotypes of Crohn’s disease in a Korean population
Authors: Park Hyo Jin , Jung Eun Suk , Kong Kyoung Ae , Park Eun-Mi , Cheon Jae Hee , Choi Ji Ha 
Published: March 2016

AbstractCrohn’s disease (CD) is a chronic inflammatory bowel disease and a genetic variant in the OCTN2, g.-207G > C is significantly associated with CD susceptibility. This study was aimed to identify novel OCTN2 functional promoter variants and their roles in transcriptional regulation using various in vitro assays. In addition, we investigated the association between OCTN2 genotypes and CD through genetic analysis using DNA samples from 193 patients with CD and 281 healthy controls. Among the three major promoter haplotypes of OCTN2 identified, one haplotype, H3, showed a significant decrease in promoter activity: two polymorphisms in H3 were associated with a significant reduction in promoter activity. In particular, we found that the reduced transcriptional activity of those two polymorphisms results from a reduction in the binding affinity of the activators, NF-E2 and YY1, to the OCTN2 promoter. The functional haplotype of the OCTN2 promoter was associated with clinical course of CD such as the disease behavior and need for surgery. However, genetic variants or haplotypes of OCTN2 did not affect the susceptibility to CD. Our results suggest that a common promoter haplotype of OCTN2 regulates the transcriptional rate of OCTN2 and influences the clinical course of CD.
A New Acyl-homoserine Lactone Molecule Generated by Nitrobacter winogradskyi
Authors: Shen Qiuxuan , Gao Jie , Liu Jun , Liu Shuangjiang , Liu Zijun , Wang Yinghuan , Guo Baoyuan , Zhuang Xuliang , Zhuang Guoqiang 
Published: March 2016

AbstractIt is crucial to reveal the regulatory mechanism of nitrification to understand nitrogen conversion in agricultural systems and wastewater treatment. In this study, the nwiI gene of Nitrobacter winogradskyi was confirmed to be a homoserine lactone synthase by heterologous expression in Escherichia coli that synthesized several acyl-homoserine lactone signals with 7 to 11 carbon acyl groups. A novel signal, 7, 8-trans-N-(decanoyl) homoserine lactone (C10:1-HSL), was identified in both N. winogradskyi and the recombined E. coli. Furthermore, this novel signal also triggered variances in the nitrification rate and the level of transcripts for the genes involved in the nitrification process. These results indicate that quorum sensing may have a potential role in regulating nitrogen metabolism.
Localized surface plasmon resonances dominated giant lateral photovoltaic effect observed in ZnO/Ag/Si nanostructure
Authors: Zhang Ke , Wang Hui , Gan Zhikai , Zhou Peiqi , Mei Chunlian , Huang Xu , Xia Yuxing 
Published: March 2016

AbstractWe report substantially enlarged lateral photovoltaic effect (LPE) in the ZnO/Ag/Si nanostructures. The maximum LPE sensitivity (55.05 mv/mm) obtained in this structure is about seven times larger than that observed in the control sample (7.88 mv/mm) of ZnO/Si. We attribute this phenomenon to the strong localized surface plasmon resonances (LSPRs) induced by nano Ag semicontinuous films. Quite different from the traditional LPE in PN junction type structures, in which light-generated carriers contributed to LPE merely depends on direct excitation of light in semiconductor, this work firstly demonstrates that, by introducing a super thin metal Ag in the interface between two different kinds of semiconductors, the nanoscale Ag embedded in the interface will produce strong resonance of localized field, causing extra intraband excitation, interband excitation and an enhanced direct excitation. As a consequence, these LSPRs dominated contributions harvest much more carriers, giving rise to a greatly enhanced LPE. In particular, this LSPRs-driven mechanism constitutes a sharp contrast to the traditional LPE operation mechanism. This work suggests a brand new LSPRs approach for tailoring LPE-based devices and also opens avenues of research within current photoelectric sensors area.
Peltaster fructicola genome reveals evolution from an invasive phytopathogen to an ectophytic parasite
Authors: Xu Chao , Chen Huan , Gleason Mark L. , Xu Jin-Rong , Liu Huiquan , Zhang Rong , Sun Guangyu 
Published: March 2016

AbstractSooty blotch and flyspeck (SBFS) fungi are unconventional plant pathogens that cause economic losses by blemishing the surface appearance of infected fruit. Here, we introduce the 18.14-Mb genome of Peltaster fructicola, one of the most prevalent SBFS species on apple. This undersized assembly contains only 8,334 predicted protein-coding genes and a very small repertoire of repetitive elements. Phylogenomics and comparative genomics revealed that P. fructicola had undergone a reductive evolution, during which the numbers of orphan genes and genes involved in plant cell wall degradation, secondary metabolism, and secreted peptidases and effectors were drastically reduced. In contrast, the genes controlling 1,8-dihydroxynaphthalene (DHN)-melanin biosynthesis and appressorium-mediated penetration were retained substantially. Additionally, microscopic examination of the surfaces of infected apple indicated for the first time that P. fructicola can not only dissolve epicuticular waxes but also partially penetrate the cuticle proper. Our findings indicate that genome contraction, characterized mainly by the massive loss of pathogenicity-related genes, has played an important role in the evolution of P. fructicola (and by implication other SBFS species) from a plant-penetrating ancestor to a non-invasive ectophyte, displaying a novel form of trophic interaction between plants and fungi.
Preservation of ancestral Cretaceous microflora recovered from a hypersaline oil reservoir
Authors: Gales Grégoire , Tsesmetzis Nicolas , Neria Isabel , Alazard Didier , Coulon Stéphanie , Lomans Bart P. , Morin Dominique , Ollivier Bernard , Borgomano Jean , Joulian Catherine 
Published: March 2016

AbstractMicrobiology of a hypersaline oil reservoir located in Central Africa was investigated with molecular and culture methods applied to preserved core samples. Here we show that the community structure was partially acquired during sedimentation, as many prokaryotic 16S rRNA gene sequences retrieved from the extracted DNA are phylogenetically related to actual Archaea inhabiting surface evaporitic environments, similar to the Cretaceous sediment paleoenvironment. Results are discussed in term of microorganisms and/or DNA preservation in such hypersaline and Mg-rich solutions. High salt concentrations together with anaerobic conditions could have preserved microbial/molecular diversity originating from the ancient sediment basin wherein organic matter was deposited.
A high-throughput peptidomic strategy to decipher the molecular diversity of cyclic cysteine-rich peptides
Authors: Serra Aida , Hemu Xinya , Nguyen Giang K. T. , Nguyen Ngan T. K. , Sze Siu Kwan , Tam James P. 
Published: March 2016

AbstractCyclotides are plant cyclic cysteine-rich peptides (CRPs). The cyclic nature is reported to be gene-determined with a precursor containing a cyclization-competent domain which contains an essential C-terminal Asn/Asp (Asx) processing signal recognized by a cyclase. Linear forms of cyclotides are rare and are likely uncyclizable because they lack this essential C-terminal Asx signal (uncyclotide). Here we show that in the cyclotide-producing plantClitoria ternatea, both cyclic and acyclic products, collectively named cliotides, can be bioprocessed from the same cyclization-competent precursor. Using an improved peptidomic strategy coupled with the novel Asx-specific endopeptidase butelase 2 to linearize cliotides at a biosynthetic ligation site for transcriptomic analysis, we characterized 272 cliotides derived from 38 genes. Several types of post-translational modifications of the processed cyclotides were observed, including deamidation, oxidation, hydroxylation, dehydration, glycosylation, methylation, and truncation. Taken together, our results suggest that cyclotide biosynthesis involves ‘fuzzy’ processing of precursors into both cyclic and linear forms as well as post-translational modifications to achieve molecular diversity, which is a commonly found trait of natural product biosynthesis.
Antioxidants inhibit advanced glycosylation end-product-induced apoptosis by downregulation of miR-223 in human adipose tissue-derived stem cells
Authors: Wang Zhe , Li Hongqiu , Guo Ran , Wang Qiushi , Zhang Dianbao 
Published: March 2016

AbstractAdvanced glycosylation end products (AGEs) are endogenous inflammatory mediators that induce apoptosis of mesenchymal stem cells. A potential mechanism includes increased generation of reactive oxygen species (ROS). MicroRNA-223 (miR-223) is implicated in the regulation of cell growth and apoptosis in several cell types. Here, we tested the hypothesis that antioxidants N-acetylcysteine (NAC) and ascorbic acid 2-phosphate (AAP) inhibit AGE-induced apoptosis via a microRNA-dependent mechanism in human adipose tissue-derived stem cells (ADSCs). Results showed that AGE-HSA enhanced apoptosis and caspase-3 activity in ADSCs. AGE-HSA also increased ROS generation and upregulated the expression of miR-223. Interestingly, reductions in ROS generation and apoptosis and upregulation of miR-223 were found in ADSCs treated with antioxidants NAC and AAP. Furthermore, miR-223 mimics blocked antioxidant inhibition of AGE-induced apoptosis and ROS generation. Knockdown of miR-223 amplified the protective effects of antioxidants on apoptosis induced by AGE-HSA. miR-223 acted by targeting fibroblast growth factor receptor 2. These results indicate that NAC and AAP suppress AGE-HSA-induced apoptosis of ADSCs, possibly through downregulation of miR-223.
YiXin-Shu, a ShengMai-San-based traditional Chinese medicine formula, attenuates myocardial ischemia/reperfusion injury by suppressing mitochondrial mediated apoptosis and upregulating liver-X-receptor α
Authors: Zhao Yichao , Xu Longwei , Qiao Zhiqing , Gao Lingchen , Ding Song , Ying Xiaoying , Su Yuanyuan , Lin Nan , He Ben , Pu Jun 
Published: March 2016

AbstractPositive evidence from clinical trials has fueled growing acceptance of traditional Chinese medicine (TCM) for the treatment of cardiac diseases; however, little is known about the underlying mechanisms. Here, we investigated the nature and underlying mechanisms of the effects of YiXin-Shu (YXS), an antioxidant-enriched TCM formula, on myocardial ischemia/reperfusion (MI/R) injury. YXS pretreatment significantly reduced infarct size and improved viable myocardium metabolism and cardiac function in hypercholesterolemic mice. Mechanistically, YXS attenuated myocardial apoptosis by inhibiting the mitochondrial mediated apoptosis pathway (as reflected by inhibition of mitochondrial swelling, cytochromecrelease and caspase-9 activity and normalization of Bcl-2 and Bax levels) without altering the death receptor and endoplasmic reticulum-stress death pathways. Moreover, YXS reduced oxidative/nitrative stress (as reflected by decreased superoxide and nitrotyrosine content and normalized pro- and anti-oxidant enzyme levels). Interestingly, YXS upregulated endogenous nuclear receptors including LXRα, PPARα, PPARβ and ERα andin-vivoknockdown of cardiac-specific LXRα significantly blunted the cardio-protective effects of YXS. Collectively, these data show that YXS is effective in mitigating MI/R injury by suppressing mitochondrial mediated apoptosis and oxidative stress and by upregulating LXRα, thereby providing a rationale for future clinical trials and clinical applications.
Diet of dingoes and other wild dogs in peri-urban areas of north-eastern Australia
Authors: Allen Benjamin L. , Carmelito Erin , Amos Matt , Goullet Mark S. , Allen Lee R. , Speed James , Gentle Matt , Leung Luke K.-P. 
Published: March 2016

AbstractKnowledge of the resource requirements of urban predators can improve our understanding of their ecology and assist town planners and wildlife management agencies in developing management approaches that alleviate human-wildlife conflicts. Here we examine food and dietary items identified in scats of dingoes in peri-urban areas of north-eastern Australia to better understand their resource requirements and the potential for dingoes to threaten locally fragmented populations of native fauna. Our primary aim was to determine what peri-urban dingoes eat and whether or not this differs between regions. We identified over 40 different food items in dingo scats, almost all of which were mammals. Individual species commonly observed in dingo scats included agile wallabies, northern brown bandicoots and swamp wallabies. Birds were relatively common in some areas but not others, as were invertebrates. Dingoes were identified as a significant potential threat to fragmented populations of koalas. Dietary overlap was typically very high or near-identical between regions, indicating that peri-urban dingoes ate the same types or sizes of prey in different areas. Future studies should seek to quantify actual and perceived impacts of and human attitudes towards, peri-urban dingoes and to develop management strategies with a greater chance of reducing human-wildlife conflicts.
High speed direct imaging of thin metal film ablation by movie-mode dynamic transmission electron microscopy
Authors: Hihath Sahar , Santala Melissa K. , Cen Xi , Campbell Geoffrey , van Benthem Klaus 
Published: March 2016

AbstractObliteration of matter by pulsed laser beams is not only prevalent in science fiction movies, but finds numerous technological applications ranging from additive manufacturing over machining of micro- and nanostructured features to health care. Pulse lengths ranging from femtoseconds to nanoseconds are utilized at varying laser beam energies and pulse lengths and enable the removal of nanometric volumes of material. While the mechanisms for removal of material by laser irradiation, i.e., laser ablation, are well understood on the micrometer length scale, it was previously impossible to directly observe obliteration processes on smaller scales due to experimental limitations for the combination of nanometer spatial and nanosecond temporal resolution. Here, we report the direct observation of metal thin film ablation from a solid substrate through dynamic transmission electron microscopy. Quantitative analysis reveals liquid-phase dewetting of the thin-film, followed by hydrodynamic sputtering of nano- to submicron sized metal droplets. We discovered unexpected fracturing of the substrate due to evolving thermal stresses. This study confirms that hydrodynamic sputtering remains a valid mechanism for droplet expulsion on the nanoscale, while irradiation induced stress fields represent limit laser processing of nanostructured materials. Our results allow for improved safety during laser ablation in manufacturing and medical applications.
Three-dimensional printing of continuous-fiber composites by in-nozzle impregnation
Authors: Matsuzaki Ryosuke , Ueda Masahito , Namiki Masaki , Jeong Tae-Kun , Asahara Hirosuke , Horiguchi Keisuke , Nakamura Taishi , Todoroki Akira , Hirano Yoshiyasu 
Published: March 2016

AbstractWe have developed a method for the three-dimensional (3D) printing of continuous fiber-reinforced thermoplastics based on fused-deposition modeling. The technique enables direct 3D fabrication without the use of molds and may become the standard next-generation composite fabrication methodology. A thermoplastic filament and continuous fibers were separately supplied to the 3D printer and the fibers were impregnated with the filament within the heated nozzle of the printer immediately before printing. Polylactic acid was used as the matrix while carbon fibers, or twisted yarns of natural jute fibers, were used as the reinforcements. The thermoplastics reinforced with unidirectional jute fibers were examples of plant-sourced composites; those reinforced with unidirectional carbon fiber showed mechanical properties superior to those of both the jute-reinforced and unreinforced thermoplastics. Continuous fiber reinforcement improved the tensile strength of the printed composites relative to the values shown by conventional 3D-printed polymer-based composites.