bluuebunny/crossref_metadata_2025_split huggingface dataset:
‘AND’ logic gates at work: Crystal structure of Rad53 bound to Dbf4 and Cdc7
Authors: Almawi Ahmad W. , Matthews Lindsay A. , Larasati  , Myrox Polina , Boulton Stephen , Lai Christine , Moraes Trevor , Melacini Giuseppe , Ghirlando Rodolfo , Duncker Bernard P. , Guarné Alba 
Published: September 2016

AbstractForkhead-associated (FHA) domains are phosphopeptide recognition modules found in many signaling proteins. The Saccharomyces cerevisiae protein kinase Rad53 is a key regulator of the DNA damage checkpoint and uses its two FHA domains to interact with multiple binding partners during the checkpoint response. One of these binding partners is the Dbf4-dependent kinase (DDK), a heterodimer composed of the Cdc7 kinase and its regulatory subunit Dbf4. Binding of Rad53 to DDK, through its N-terminal FHA (FHA1) domain, ultimately inhibits DDK kinase activity, thereby preventing firing of late origins. We have previously found that the FHA1 domain of Rad53 binds simultaneously to Dbf4 and a phosphoepitope, suggesting that this domain functions as an ‘AND’ logic gate. Here, we present the crystal structures of the FHA1 domain of Rad53 bound to Dbf4, in the presence and absence of a Cdc7 phosphorylated peptide. Our results reveal how the FHA1 uses a canonical binding interface to recognize the Cdc7 phosphopeptide and a non-canonical interface to bind Dbf4. Based on these data we propose a mechanism to explain how Rad53 enhances the specificity of FHA1-mediated transient interactions.
Accumulation of heavy metals and trace elements in fluvial sediments received effluents from traditional and semiconductor industries
Authors: Hsu Liang-Ching , Huang Ching-Yi , Chuang Yen-Hsun , Chen Ho-Wen , Chan Ya-Ting , Teah Heng Yi , Chen Tsan-Yao , Chang Chiung-Fen , Liu Yu-Ting , Tzou Yu-Min 
Published: September 2016

AbstractMetal accumulation in sediments threatens adjacent ecosystems due to the potential of metal mobilization and the subsequent uptake into food webs. Here, contents of heavy metals (Cd, Cr, Cu, Ni, Pb, and Zn) and trace elements (Ga, In, Mo, and Se) were determined for river waters and bed sediments that received sewage discharged from traditional and semiconductor industries. We used principal component analysis (PCA) to determine the metal distribution in relation to environmental factors such as pH, EC, and organic matter (OM) contents in the river basin. While water PCA categorized discharged metals into three groups that implied potential origins of contamination, sediment PCA only indicated a correlation between metal accumulation and OM contents. Such discrepancy in metal distribution between river water and bed sediment highlighted the significance of physical-chemical properties of sediment, especially OM, in metal retention. Moreover, we used Se XANES as an example to test the species transformation during metal transportation from effluent outlets to bed sediments and found a portion of Se inventory shifted from less soluble elemental Se to the high soluble and toxic selenite and selenate. The consideration of environmental factors is required to develop pollution managements and assess environmental risks for bed sediments.
Quantitative lateral flow strip assays as User-Friendly Tools To Detect Biomarker Profiles For Leprosy
Authors: van Hooij Anouk , Tjon Kon Fat Elisa M. , Richardus Renate , van den Eeden Susan J. F. , Wilson Louis , de Dood Claudia J. , Faber Roel , Alam Korshed , Richardus Jan Hendrik , Corstjens Paul L. A. M. , Geluk Annemieke 
Published: September 2016

AbstractLeprosy is a debilitating, infectious disease caused by Mycobacterium leprae. Despite the availability of multidrug therapy, transmission is unremitting. Thus, early identification of M. leprae infection is essential to reduce transmission. The immune response to M. leprae is determined by host genetics, resulting in paucibacillary (PB) and multibacillary (MB) leprosy associated with dominant cellular or humoral immunity, respectively. This spectral pathology of leprosy compels detection of immunity to M. leprae to be based on multiple, diverse biomarkers. In this study we have applied quantitative user friendly lateral flow assays (LFAs) for four immune markers (anti-PGL-I antibodies, IL-10, CCL4 and IP-10) for whole blood samples from a longitudinal BCG vaccination field-trial in Bangladesh. Different biomarker profiles, in contrast to single markers, distinguished M. leprae infected from non-infected test groups, patients from household contacts (HHC) and endemic controls (EC), or MB from PB patients. The test protocol presented in this study merging detection of innate, adaptive cellular as well as humoral immunity, thus provides a convenient tool to measure specific biomarker profiles for M. leprae infection and leprosy utilizing a field-friendly technology.
Temporal efficiency evaluation and small-worldness characterization in temporal networks
Authors: Dai Zhongxiang , Chen Yu , Li Junhua , Fam Johnson , Bezerianos Anastasios , Sun Yu 
Published: September 2016

AbstractNumerous real-world systems can be modeled as networks. To date, most network studies have been conducted assuming stationary network characteristics. Many systems, however, undergo topological changes over time. Temporal networks, which incorporate time into conventional network models, are therefore more accurate representations of such dynamic systems. Here, we introduce a novel generalized analytical framework for temporal networks, which enables 1) robust evaluation of the efficiency of temporal information exchange using two new network metrics and 2) quantitative inspection of the temporal small-worldness. Specifically, we define new robust temporal network efficiency measures by incorporating the time dependency of temporal distance. We propose a temporal regular network model and based on this plus the redefined temporal efficiency metrics and widely used temporal random network models, we introduce a quantitative approach for identifying temporal small-world architectures (featuring high temporal network efficiency both globally and locally). In addition, within this framework, we can uncover network-specific dynamic structures. Applications to brain networks, international trade networks and social networks reveal prominent temporal small-world properties with distinct dynamic network structures. We believe that the framework can provide further insight into dynamic changes in the network topology of various real-world systems and significantly promote research on temporal networks.
Etoposide Induces Apoptosis in Activated Human Hepatic Stellate Cells via ER Stress
Authors: Wang Chen , Zhang Feng , Cao Yu , Zhang Mingming , Wang Aixiu , Xu Mingcui , Su Min , Zhang Ming , Zhuge Yuzheng 
Published: September 2016

AbstractThe activation of hepatic stellate cells (HSCs) plays a vital role in the progression of liver fibrosis and the induction of HSCs apoptosis may attenuate or reverse fibrogenesis. The therapeutic effects of etoposide(VP-16), a widely used anticancer agent, on HSCs apoptosis and liver fibrosis resolution are still unclear. Here, we report that VP-16 reduced the proliferation of LX-2 cells and led to significantly high levels of apoptosis, as indicated by Annexin V staining and the proteolytic cleavage of the executioner caspase-3 and PARP. Additionally, the unfolded protein response regulators CHOP, BIP, caspase-12, p-eIF2α and IRE1α, which are considered endoplasmic reticulum (ER) stress markers, were upregulated by VP-16. The strong inhibitory effect of VP-16 on LX-2 cells was mainly dependent on ER stress, which activated JNK signaling pathway. Remarkably, VP-16 treatment decreased the expression of α-SMA and type I collagen and simultaneously increased the ratio of matrix metalloproteinases (MMPs) to tissue inhibitor of matrix metalloproteinases (TIMPs). In contrast, VP-16 induced significantly more apoptosis in HSCs than in normal hepatocytes. Taken together, our findings demonstrate that VP-16 exerts a proapoptotic effect on LX-2 cells and has an antifibrogenic effect on collagen deposition, suggesting a new strategy for the treatment of liver fibrosis.
Bacteroides intestinalis DSM 17393, a member of the human colonic microbiome, upregulates multiple endoxylanases during growth on xylan
Authors: Wang Kui , Pereira Gabriel V. , Cavalcante Janaina J. V. , Zhang Meiling , Mackie Roderick , Cann Isaac 
Published: September 2016

AbstractMany human diets contain arabinoxylan and the ease of genome sequencing coupled with reduced cost have led to unraveling the arsenal of genes utilized by the colonic Bacteroidetes to depolymerize this polysaccharide. The colonic Bacteroidetes with potential to ferment arabinoxylans include Bacteroides intestinalis. In this study, we analyzed the hydrolytic activities of members of a xylan degradation cluster encoded on the genome of Bacteroides intestinalis DSM 17393. Here, it is demonstrated that a cocktail of the xylanolytic enzymes completely hydrolyze arabinoxylans found in human diets. We show that this bacterium and relatives have evolved and secrete a unique bifunctional endoxylanase/arabinofuranosidase in the same polypeptide. The bifunctional enzyme and other secreted enzymes attack the polysaccharides extracellularly to remove the side-chains, exposing the xylan backbone for cleavage to xylo-oligosaccharides and xylose. These end products are transported into the cell where a β-xylosidase cleaves the oligosaccharides to fermentable sugars. While our experiments focused on B. intestinalis, it is likely that the extracellular enzymes also release nutrients to members of the colonic microbial community that practice cross-feeding. The presence of the genes characterized in this study in other colonic Bacteroidetes suggests a conserved strategy for energy acquisition from arabinoxylan, a component of human diets.
Distribution and characteristics of rodent picornaviruses in China
Authors: Du Jiang , Lu Liang , Liu Feng , Su Haoxiang , Dong Jie , Sun Lilian , Zhu Yafang , Ren Xianwen , Yang Fan , Guo Fei , Liu Qiyong , Wu Zhiqiang , Jin Qi 
Published: September 2016

AbstractRodents are important reservoir hosts of many important zoonotic viruses. The family Picornaviridae contains clinically important pathogens that infect humans and animals, and increasing numbers of rodent picornaviruses have recently been associated with zoonoses. We collected 574 pharyngeal and anal swab specimens from 287 rodents of 10 different species from eight representative regions of China from October 2013 to July 2015. Seven representative sequences identified from six rodent species were amplified as full genomes and classified into four lineages. Three lineage 1 viruses belonged to a novel genus of picornaviruses and was more closely related to Hepatovirus than to others genera of picornaviruses based on aa homology. Lineage 2, lineage 3, and lineage 4 viruses belonged to the genera Rosavirus, Hunnivirus, and Enterovirus, respectively, representing new species. According to both phylogenetic and identity analyses, Lineage 2 viruses had a close relationship with rosavirus 2 which was recovered from the feces of a child in Gambia and Lineage 3 viruses had a close relationship with domestic animal Hunnivirus. Lineage 4 viruses provide the first evidence of these enteroviruses and their evolution in rodent hosts in China.
Quantitative imaging of heterogeneous dynamics in drying and aging paints
Authors: van der Kooij Hanne M. , Fokkink Remco , van der Gucht Jasper , Sprakel Joris 
Published: September 2016

AbstractDrying and aging paint dispersions display a wealth of complex phenomena that make their study fascinating yet challenging. To meet the growing demand for sustainable, high-quality paints, it is essential to unravel the microscopic mechanisms underlying these phenomena. Visualising the governing dynamics is, however, intrinsically difficult because the dynamics are typically heterogeneous and span a wide range of time scales. Moreover, the high turbidity of paints precludes conventional imaging techniques from reaching deep inside the paint. To address these challenges, we apply a scattering technique, Laser Speckle Imaging, as a versatile and quantitative tool to elucidate the internal dynamics, with microscopic resolution and spanning seven decades of time. We present a toolbox of data analysis and image processing methods that allows a tailored investigation of virtually any turbid dispersion, regardless of the geometry and substrate. Using these tools we watch a variety of paints dry and age with unprecedented detail.
Resonantly Enhanced Emission from a Luminescent Nanostructured Waveguide
Authors: Inada Yasuhisa , Hashiya Akira , Nitta Mitsuru , Tomita Shogo , Tsujimoto Akira , Suzuki Masa-aki , Yamaki Takeyuki , Hirasawa Taku 
Published: September 2016

AbstractControlling the characteristics of photon emission represents a significant challenge for both fundamental science and device technologies. Research on microcavities, photonic crystals and plasmonic nanocavities has focused on controlling spontaneous emission by way of designing a resonant structure around the emitter to modify the local density of photonic states. In this work, we demonstrate resonantly enhanced emission using luminescent nanostructured waveguide resonance (LUNAR). Our concept is based on coupling between emitters in the luminescent waveguide and a resonant waveguide mode that interacts with a periodic nanostructure and hence outcouples via diffraction. We show that the enhancement of resonance emission can be controlled by tuning the design parameters. We also demonstrate that the enhanced emission is attributable to the accelerated spontaneous emission rate that increases the probability of photon emission in the resonant mode, accompanied by enhanced the local density of photonic states. This study demonstrates that nanostructured luminescent materials can be designed to exhibit functional and enhanced emission. We anticipate that our concept will be used to improve the performance of a variety of photonic and optical applications ranging from bio/chemical sensors to lighting, displays and projectors.
Nur77 exacerbates PC12 cellular injury in vitro by aggravating mitochondrial impairment and endoplasmic reticulum stress
Authors: Gao Huimin , Chen Zhaoyu , Fu Yongmei , Yang Xiaoyan , Weng Ruihui , Wang Rui , Lu Jianjun , Pan Mengqiu , Jin Kunlin , McElroy Chris , Tang Beisha , Xia Ying , Wang Qing 
Published: September 2016

AbstractThe nuclear orphan receptor, Nur77 plays important roles in neuroimflammation, apoptosis, and dopaminergic neurodegeneration. We conducted a further mechanistic investigation into the association of Nur77 with cell death. Cytosporone B (Csn-B), an agonist for Nur77, and Nur77 knockdown were adopted in the 6-hydroxydopamine (OHDA)-lesioned PC12 cells to investigate the mechanisms underlying Nur77-mediated injury. The 6-OHDA incubation caused Nur77 translocation from the nucleus to cytosol and Endoplasm reticulum (ER) and induced co-localization of Tom20/Nur77 and Protein Disulfide Isomerase (PDI)/Nur77. Nur77 activation further decreased cell viability, aggravated intracellular LDH release, intracellular Ca2+, ROS levels, apoptosis, ER tress and, mitochondrial transmembrane potential (ΔΨm) decline. In addition, Nur77 activation significantly enhanced the efficiency of autophagy as indicated by an up-regulation of Beclin-1/LC-3 and downregulation of p62, and aggravated mitochondrial dysfunctions and ER stress as shown by increased HSP60/Cytochrome C (Cyt C) and CHOP-ATF3 levels respectively. These changes could be partially reversed by Nur77 knockdown. Moreover, Nur77 activation upregulated PINK1 and downregulated Parkin levels. We conclude that Nur77 exacerbates PC12 cell death at least partially by aggravating the mitochondrial impairment and ER stress and enhancing autophagy. We propose that Nur77 is likely a critical target in the PD therapy.
Acidic Residues Control the Dimerization of the N-terminal Domain of Black Widow Spiders’ Major Ampullate Spidroin 1
Authors: Bauer Joschka , Schaal Daniel , Eisoldt Lukas , Schweimer Kristian , Schwarzinger Stephan , Scheibel Thomas 
Published: September 2016

AbstractDragline silk is the most prominent amongst spider silks and comprises two types of major ampullate spidroins (MaSp) differing in their proline content. In the natural spinning process, the conversion of soluble MaSp into a tough fiber is, amongst other factors, triggered by dimerization and conformational switching of their helical amino-terminal domains (NRN). Both processes are induced by protonation of acidic residues upon acidification along the spinning duct. Here, the structure and monomer-dimer-equilibrium of the domain NRN1 of Latrodectus hesperus MaSp1 and variants thereof have been investigated and the key residues for both could be identified. Changes in ionic composition and strength within the spinning duct enable electrostatic interactions between the acidic and basic pole of two monomers which prearrange into an antiparallel dimer. Upon naturally occurring acidification this dimer is stabilized by protonation of residue E114. A conformational change is independently triggered by protonation of clustered acidic residues (D39, E76, E81). Such step-by-step mechanism allows a controlled spidroin assembly in a pH- and salt sensitive manner, preventing premature aggregation of spider silk proteins in the gland and at the same time ensuring fast and efficient dimer formation and stabilization on demand in the spinning duct.
Molecular Characterization and Viral Origin of the 2015 Dengue Outbreak in Xishuangbanna, Yunnan, China
Authors: Zhao Yujiao , Li Lihua , Ma Dehong , Luo Jia , Ma Zhiqiang , Wang Xiaodan , Pan Yue , Chen Junying , Xi Juemin , Yang Jiajia , Qiu Lijuan , Bai Chunhai , Jiang Liming , Shan Xiyun , Sun Qiangming 
Published: September 2016

AbstractA total of 1067 serum samples were collected from febrile patients in Xishuangbanna, Yunnan, 2015. Of these, 852 cases were confirmed to be dengue NS1-positive. 76 structural protein genes were sequenced through RT-PCR based on the viral RNAs extracted from serum samples. Phylogenetic analysis revealed that all strains were classified as cosmopolitan genotype of DENV-2. After comparing with the DENV-2SS, 173 base substitutions were found in 76 sequences, resulting in 43 nonsynonymous mutations, of which 22 mutations existed among all samples. According to secondary structure prediction, 8 new possible nucelotide/protein binding sites were found and another 4 sites were lost among the 775 amino acids of DENV structural proteins as compared with DENV-2SS. Meanwhile, 6 distinct amino acid changes were found in the helix and strand regions, and the distribution of the exposed and buried regions was slightly altered. The results indicated that the epidemic dengue strains of Xishuangbanna in 2015 are most similar to the Indian strain in 2001 and the Sri Lankan strain in 2004. Moreover, it also show a very strong similarity to the epidemic strains of Fujian province in 1999 and 2010, which show that there is an internal recycling epidemic trend of DENV in China.
Liver DCE-MRI Registration in Manifold Space Based on Robust Principal Component Analysis
Authors: Feng Qianjin , Zhou Yujia , Li Xueli , Mei Yingjie , Lu Zhentai , Zhang Yu , Feng Yanqiu , Liu Yaqin , Yang Wei , Chen Wufan 
Published: September 2016

AbstractA technical challenge in the registration of dynamic contrast-enhanced magnetic resonance (DCE-MR) imaging in the liver is intensity variations caused by contrast agents. Such variations lead to the failure of the traditional intensity-based registration method. To address this problem, a manifold-based registration framework for liver DCE-MR time series is proposed. We assume that liver DCE-MR time series are located on a low-dimensional manifold and determine intrinsic similarities between frames. Based on the obtained manifold, the large deformation of two dissimilar images can be decomposed into a series of small deformations between adjacent images on the manifold through gradual deformation of each frame to the template image along the geodesic path. Furthermore, manifold construction is important in automating the selection of the template image, which is an approximation of the geodesic mean. Robust principal component analysis is performed to separate motion components from intensity changes induced by contrast agents; the components caused by motion are used to guide registration in eliminating the effect of contrast enhancement. Visual inspection and quantitative assessment are further performed on clinical dataset registration. Experiments show that the proposed method effectively reduces movements while preserving the topology of contrast-enhancing structures and provides improved registration performance.
Expansion and Contraction of the Indo-Pacific Tropical Rain Belt over the Last Three Millennia
Authors: Denniston Rhawn F. , Ummenhofer Caroline C. , Wanamaker Alan D. , Lachniet Matthew S. , Villarini Gabriele , Asmerom Yemane , Polyak Victor J. , Passaro Kristian J. , Cugley John , Woods David , Humphreys William F. 
Published: September 2016

AbstractThe seasonal north-south migration of the intertropical convergence zone (ITCZ) defines the tropical rain belt (TRB), a region of enormous terrestrial and marine biodiversity and home to 40% of people on Earth. The TRB is dynamic and has been shown to shift south as a coherent system during periods of Northern Hemisphere cooling. However, recent studies of Indo-Pacific hydroclimate suggest that during the Little Ice Age (LIA; AD 1400–1850), the TRB in this region contracted rather than being displaced uniformly southward. This behaviour is not well understood, particularly during climatic fluctuations less pronounced than those of the LIA, the largest centennial-scale cool period of the last millennium. Here we show that the Indo-Pacific TRB expanded and contracted numerous times over multi-decadal to centennial scales during the last 3,000 yr. By integrating precisely-dated stalagmite records of tropical hydroclimate from southern China with a newly enhanced stalagmite time series from northern Australia, our study reveals a previously unidentified coherence between the austral and boreal summer monsoon. State-of-the-art climate model simulations of the last millennium suggest these are linked to changes in the structure of the regional manifestation of the atmosphere’s meridional circulation.
Closed head experimental traumatic brain injury increases size and bone volume of callus in mice with concomitant tibial fracture
Authors: Brady Rhys D , Grills Brian L , Church Jarrod E , Walsh Nicole C , McDonald Aaron C , Agoston Denes V , Sun Mujun , O’Brien Terence J , Shultz Sandy R , McDonald Stuart J 
Published: September 2016

AbstractConcomitant traumatic brain injury (TBI) and long bone fracture are commonly observed in multitrauma and polytrauma. Despite clinical observations of enhanced bone healing in patients with TBI, the relationship between TBI and fracture healing remains poorly understood, with clinical data limited by the presence of several confounding variables. Here we developed a novel trauma model featuring closed-skull weight-drop TBI and concomitant tibial fracture in order to investigate the effect of TBI on fracture healing. Male mice were assigned into Fracture + Sham TBI (FX) or Fracture + TBI (MULTI) groups and sacrificed at 21 and 35 days post-injury for analysis of healing fractures by micro computed tomography (μCT) and histomorphometry. μCT analysis revealed calluses from MULTI mice had a greater bone and total tissue volume and displayed higher mean polar moment of inertia when compared to calluses from FX mice at 21 days post-injury. Histomorphometric results demonstrated an increased amount of trabecular bone in MULTI calluses at 21 days post-injury. These findings indicate that closed head TBI results in calluses that are larger in size and have an increased bone volume, which is consistent with the notion that TBI induces the formation of a more robust callus.