bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mesenchymal stem cell transplantation can restore lupus disease-associated miRNA expression and Th1/Th2 ratios in a murine model of SLE
Authors: Choi Eun Wha , Lee MinJae , Song Ji Woo , Shin Il Seob , Kim Sung Joo 
Published: December 2016

AbstractC3.MRL-Faslpr/J mice spontaneously develop high titers of anti-dsDNA, mild glomerular nephritis, and severe lymphoproliferation symptoms. This study aimed to compare the effects of long-term serial administration of human adipose tissue-derived mesenchymal stem cells (ASCs), and cyclophosphamide treatment in C3.MRL-Faslpr/J mice using a murine SLE model. C3.MRL-Faslpr/J mice were divided into saline (C), cyclophosphamide (Y), and ASC (H) treatment groups. Background-matched control C3H mice treated with saline (N) were also compared. The Y group showed the greatest improvement in disease parameters, but with damaged trabecular integrity. ASC transplantation reduced anti-dsDNA levels, glomerular C3 deposition and CD138 proportion significantly, without trabecular damage. Furthermore, both cyclophosphamide and ASC treatment significantly decreased the ratio of Th1/Th2 compared with the saline-treatment. The expression levels of miR-31-5p, miR-96-5p, miR-182-5p, miR-183-5p, and miR-379-5p were significantly higher, while those of miR150-5p were significantly lower in the C group than in the N group. The expression levels of miR-96-5p, miR-182-5p in the Y and H groups were significantly lower than in the C group. Thus, treatment with cyclophosphamide or ASC can change miRNAs and decrease miR-96-5p and miR-182-5p expression, as well as decreasing the CD138 proportion and the Th1/Th2 ratio, which might be involved in the therapeutic mechanism.
Diverse specificity of cellulosome attachment to the bacterial cell surface
Authors: Brás Joana L. A. , Pinheiro Benedita A. , Cameron Kate , Cuskin Fiona , Viegas Aldino , Najmudin Shabir , Bule Pedro , Pires Virginia M. R. , Romão Maria João , Bayer Edward A. , Spencer Holly L. , Smith Steven , Gilbert Harry J. , Alves Victor D. , Carvalho Ana Luísa , Fontes Carlos M. G. A. 
Published: December 2016

AbstractDuring the course of evolution, the cellulosome, one of Nature’s most intricate multi-enzyme complexes, has been continuously fine-tuned to efficiently deconstruct recalcitrant carbohydrates. To facilitate the uptake of released sugars, anaerobic bacteria use highly ordered protein-protein interactions to recruit these nanomachines to the cell surface. Dockerin modules located within a non-catalytic macromolecular scaffold, whose primary role is to assemble cellulosomal enzymatic subunits, bind cohesin modules of cell envelope proteins, thereby anchoring the cellulosome onto the bacterial cell. Here we have elucidated the unique molecular mechanisms used by anaerobic bacteria for cellulosome cellular attachment. The structure and biochemical analysis of five cohesin-dockerin complexes revealed that cell surface dockerins contain two cohesin-binding interfaces, which can present different or identical specificities. In contrast to the current static model, we propose that dockerins utilize multivalent modes of cohesin recognition to recruit cellulosomes to the cell surface, a mechanism that maximises substrate access while facilitating complex assembly.
Diagnostic performance of peroxiredoxin 1 to determine time-of-onset of acute cerebral infarction
Authors: Richard Sébastien , Lapierre Vanessa , Girerd Nicolas , Bonnerot Mathieu , Burkhard Pierre R. , Lagerstedt Linnéa , Bracard Serge , Debouverie Marc , Turck Natacha , Sanchez Jean-Charles 
Published: December 2016

AbstractAccurately determining time-of-onset of cerebral infarction is important to clearly identify patients who could benefit from reperfusion therapies. We assessed the kinetics of peroxiredoxin 1 (PRDX1), a protein involved in oxidative stress during the acute phase of ischemia, and its ability to determine stroke onset in a population of patients with known onset of less than 24 hours and in a control group. Median PRDX1 levels were significantly higher in stroke patients compared to controls. PRDX1 levels were also higher from blood samples withdrawn beforevs.after 3 hours following stroke onset, and beforevs. after 6 hours. ROC analysis with area under the curve (AUC), sensitivity (Se) and specificity (Sp) determined from the Youden index was performed to assess the ability of PRDX1 levels to determine onset. Diagnostic performances of PRDX1 levels were defined by an AUC of 69%, Se of 53% and Sp of 86% for identifying cerebral infarction occurring <3 hours, and an AUC of 68%, Se of 49% and Sp of 88% for cerebral infarction occurring <6 hours. These first results suggest that PRDX1 levels could be the basis of a new method using biomarkers for determining cerebral infarction onset.
An Integrated Strategy for Global Qualitative and Quantitative Profiling of Traditional Chinese Medicine Formulas: Baoyuan Decoction as a Case
Authors: Ma Xiaoli , Guo Xiaoyu , Song Yuelin , Qiao Lirui , Wang Wenguang , Zhao Mingbo , Tu Pengfei , Jiang Yong 
Published: December 2016

AbstractClarification of the chemical composition of traditional Chinese medicine formulas (TCMFs) is a challenge due to the variety of structures and the complexity of plant matrices. Herein, an integrated strategy was developed by hyphenating ultra-performance liquid chromatography (UPLC), quadrupole time-of-flight (Q-TOF), hybrid triple quadrupole-linear ion trap mass spectrometry (Qtrap-MS), and the novel post-acquisition data processing software UNIFI to achieve automatic, rapid, accurate, and comprehensive qualitative and quantitative analysis of the chemical components in TCMFs. As a proof-of-concept, the chemical profiling of Baoyuan decoction (BYD), which is an ancient TCMF that is clinically used for the treatment of coronary heart disease that consists of Ginseng Radix et Rhizoma, Astragali Radix, Glycyrrhizae Radix et Rhizoma Praeparata Cum Melle, and Cinnamomi Cortex, was performed. As many as 236 compounds were plausibly or unambiguously identified, and 175 compounds were quantified or relatively quantified by the scheduled multiple reaction monitoring (sMRM) method. The findings demonstrate that the strategy integrating the rapidity of UNIFI software, the efficiency of UPLC, the accuracy of Q-TOF-MS, and the sensitivity and quantitation ability of Qtrap-MS provides a method for the efficient and comprehensive chemome characterization and quality control of complex TCMFs.
Next-generation systematics: An innovative approach to resolve the structure of complex prokaryotic taxa
Authors: Sangal Vartul , Goodfellow Michael , Jones Amanda L. , Schwalbe Edward C. , Blom Jochen , Hoskisson Paul A. , Sutcliffe Iain C. 
Published: December 2016

AbstractProkaryotic systematics provides the fundamental framework for microbiological research but remains a discipline that relies on a labour- and time-intensive polyphasic taxonomic approach, including DNA-DNA hybridization, variation in 16S rRNA gene sequence and phenotypic characteristics. These techniques suffer from poor resolution in distinguishing between closely related species and often result in misclassification and misidentification of strains. Moreover, guidelines are unclear for the delineation of bacterial genera. Here, we have applied an innovative phylogenetic and taxogenomic approach to a heterogeneous actinobacterial taxon, Rhodococcus, to identify boundaries for intrageneric and supraspecific classification. Seven species-groups were identified within the genus Rhodococcus that are as distantly related to one another as they are to representatives of other mycolic acid containing actinobacteria and can thus be equated with the rank of genus. It was also evident that strains assigned to rhodococcal species-groups are underspeciated with many misclassified using conventional taxonomic criteria. The phylogenetic and taxogenomic methods used in this study provide data of theoretical value for the circumscription of generic and species boundaries and are also of practical significance as they provide a robust basis for the classification and identification of rhodococci of agricultural, industrial and medical/veterinary significance.
Metabolic Adaptation to Nutritional Stress in Human Colorectal Cancer
Authors: Miyo Masaaki , Konno Masamitsu , Nishida Naohiro , Sueda Toshinori , Noguchi Kozo , Matsui Hidetoshi , Colvin Hugh , Kawamoto Koichi , Koseki Jun , Haraguchi Naotsugu , Nishimura Junichi , Hata Taishi , Gotoh Noriko , Matsuda Fumio , Satoh Taroh , Mizushima Tsunekazu , Shimizu Hiroshi , Doki Yuichiro , Mori Masaki , Ishii Hideshi 
Published: December 2016

AbstractTumor cells respond to their microenvironment, which can include hypoxia and malnutrition, and adapt their metabolism to survive and grow. Some oncogenes are associated with cancer metabolism via regulation of the related enzymes or transporters. However, the importance of metabolism and precise metabolic effects of oncogenes in colorectal cancer remain unclear. We found that colorectal cancer cells survived under the condition of glucose depletion, and their resistance to such conditions depended on genomic alterations rather than on KRAS mutation alone. Metabolomic analysis demonstrated that those cells maintained tricarboxylic acid cycle activity and ATP production under such conditions. Furthermore, we identified pivotal roles of GLUD1 and SLC25A13 in nutritional stress. GLUD1 and SLC25A13 were associated with tumor aggressiveness and poorer prognosis of colorectal cancer. In conclusion, GLUD1 and SLC25A13 may serve as new targets in treating refractory colorectal cancer which survive in malnutritional microenvironments.
Online flow cytometry reveals microbial dynamics influenced by concurrent natural and operational events in groundwater used for drinking water treatment
Authors: Besmer Michael D. , Epting Jannis , Page Rebecca M. , Sigrist Jürg A. , Huggenberger Peter , Hammes Frederik 
Published: December 2016

AbstractDetailed measurements of physical, chemical and biological dynamics in groundwater are key to understanding the important processes in place and their influence on water quality – particularly when used for drinking water. Measuring temporal bacterial dynamics at high frequency is challenging due to the limitations in automation of sampling and detection of the conventional, cultivation-based microbial methods. In this study, fully automated online flow cytometry was applied in a groundwater system for the first time in order to monitor microbial dynamics in a groundwater extraction well. Measurements of bacterial concentrations every 15 minutes during 14 days revealed both aperiodic and periodic dynamics that could not be detected previously, resulting in total cell concentration (TCC) fluctuations between 120 and 280 cells μL−1. The aperiodic dynamic was linked to river water contamination following precipitation events, while the (diurnal) periodic dynamic was attributed to changes in hydrological conditions as a consequence of intermittent groundwater extraction. Based on the high number of measurements, the two patterns could be disentangled and quantified separately. This study i) increases the understanding of system performance, ii) helps to optimize monitoring strategies, and iii) opens the possibility for more sophisticated (quantitative) microbial risk assessment of drinking water treatment systems.
Two genomic regions associated with fiber quality traits in Chinese upland cotton under apparent breeding selection
Authors: Su Junji , Li Libei , Pang Chaoyou , Wei Hengling , Wang Caixiang , Song Meizhen , Wang Hantao , Zhao Shuqi , Zhang Chi , Mao Guangzhi , Huang Long , Wang Chengshe , Fan Shuli , Yu Shuxun 
Published: December 2016

AbstractFiber quality is one of the most important agronomic traits of cotton, and understanding the genetic basis of its target traits will accelerate improvements to cotton fiber quality. In this study, a panel comprising 355 upland cotton accessions was used to perform genome-wide association studies (GWASs) of five fiber quality traits in four environments. A total of 16, 10 and 7 SNPs were associated with fiber length (FL), fiber strength (FS) and fiber uniformity (FU), respectively, based on the mixed linear model (MLM). Most importantly, two major genomic regions (MGR1 and MGR2) on chromosome Dt7 and four potential candidate genes for FL were identified. Analyzing the geographical distribution of favorable haplotypes (FHs) among these lines revealed that two favorable haplotype frequencies (FHFs) were higher in accessions from low-latitude regions than in accessions from high-latitude regions. However, the genetic diversity of lines from the low-latitude regions was lower than the diversity of lines from the high-latitude regions in China. Furthermore, the FHFs differed among cultivars developed during different breeding periods. These results indicate that FHs have undergone artificial selection during upland cotton breeding in recent decades in China and provide a foundation for the further improvement of fiber quality traits.
FOXA1, GATA3 and PPARɣ Cooperate to Drive Luminal Subtype in Bladder Cancer: A Molecular Analysis of Established Human Cell Lines
Authors: Warrick Joshua I. , Walter Vonn , Yamashita Hironobu , Chung Eunah , Shuman Lauren , Amponsa Vasty Osei , Zheng Zongyu , Chan Wilson , Whitcomb Tiffany L. , Yue Feng , Iyyanki Tejaswi , Kawasawa Yuka I. , Kaag Matthew , Guo Wansong , Raman Jay D. , Park Joo-Seop , DeGraff David J. 
Published: December 2016

AbstractDiscrete bladder cancer molecular subtypes exhibit differential clinical aggressiveness and therapeutic response, which may have significant implications for identifying novel treatments for this common malignancy. However, research is hindered by the lack of suitable models to study each subtype. To address this limitation, we classified bladder cancer cell lines into molecular subtypes using publically available data in the Cancer Cell Line Encyclopedia (CCLE), guided by genomic characterization of bladder cancer by The Cancer Genome Atlas (TCGA). This identified a panel of bladder cancer cell lines which exhibit genetic alterations and gene expression patterns consistent with luminal and basal molecular subtypes of human disease. A subset of bladder cancer cell lines exhibit in vivo histomorphologic patterns consistent with luminal and basal subtypes, including papillary architecture and squamous differentiation. Using the molecular subtype assignments, and our own RNA-seq analysis, we found overexpression of GATA3 and FOXA1 cooperate with PPARɣ activation to drive transdifferentiation of a basal bladder cancer cells to a luminial phenotype. In summary, our analysis identified a set of human cell lines suitable for the study of molecular subtypes in bladder cancer, and furthermore indicates a cooperative regulatory network consisting of GATA3, FOXA1, and PPARɣ drive luminal cell fate.
Caffeine prevents kidney stone formation by translocation of apical surface annexin A1 crystal-binding protein into cytoplasm: In vitro evidence
Authors: Peerapen Paleerath , Thongboonkerd Visith 
Published: December 2016

AbstractRecent large 3 cohorts have shown that caffeinated beverage consumption was associated with lower risk of kidney stone disease. However, its protective mechanisms remained unknown and had not been previously investigated. We thus evaluated protective effects of caffeine (1 μM–10 mM) on calcium oxalate monohydrate (COM) kidney stone formation, using crystallization, crystal growth, cell-crystal adhesion, Western blotting, and immunofluorescence assays. The results showed that caffeine reduced crystal number but, on the other hand, increased crystal size, resulting in unchanged crystal mass, consistent with crystal growth that was not affected by caffeine. However, caffeine significantly decreased crystal-binding capacity of MDCK renal tubular cells in a dose-dependent manner. Western blotting and immunofluorescence study of COM crystal-binding proteins revealed significantly decreased level of annexin A1 on apical surface and its translocation into cytoplasm of the caffeine-treated cells, but no significant changes in other COM crystal-binding proteins (annexin A2, α-enolase, HSP70, and HSP90) were observed. Moreover, caffeine decreased intracellular [Ca2+] but increased [Ca2+] secretory index. Taken together, our findings showed an in vitro evidence of the protective mechanism of caffeine against kidney stone formation via translocation of annexin A1 from apical surface into cytoplasm to reduce the crystal-binding capacity of renal tubular epithelial cells.
Endogenous testosterone is associated with lower amygdala reactivity to angry faces and reduced aggressive behavior in healthy young women
Authors: Buades-Rotger Macià , Engelke Christin , Beyer Frederike , Keevil Brian G. , Brabant Georg , Krämer Ulrike M. 
Published: December 2016

AbstractTestosterone and cortisol have been proposed to influence aggressive behavior by altering the neural processing of facial threat signals. However, this has not been investigated in direct social interactions. Here, we explored the joint impact of testosterone, cortisol, and brain reactivity to anger expressions on women’s reactive aggression in the Social Threat Aggression Paradigm (STAP). The STAP is a competitive reaction time task in which the purported opponent displays either an angry or a neutral facial expression at the beginning of each trial and delivers increasingly loud sound blasts to the participants, successfully provoking them. Strikingly, salivary testosterone at scan-time was negatively related to both aggression and basolateral amygdala (BLA) reactivity to angry faces, whereas cortisol had no effect. When the opponent looked angry, BLA-orbitofrontal coupling was reduced, and BLA reactivity was positively related to aggression. The latter relationship was fully mediated by bilateral superior temporal gyrus (STG) activation. Our results thus support previous neurobiological models of aggression, and extend them by demonstrating that fast amygdala responses to threat modulate STG activity in order to favor aggressive retaliation. Furthermore, our study agrees with recent evidence underscoring a fear-reducing and strategically prosocial effect of testosterone on human social behavior.
Exploring the coordination change of vanadium and structure transformation of metavanadate MgV2O6 under high pressure
Authors: Tang Ruilian , Li Yan , Xie Shengyi , Li Nana , Chen Jiuhua , Gao Chunxiao , Zhu Pinwen , Wang Xin 
Published: December 2016

AbstractRaman spectroscopy, synchrotron angle-dispersive X-ray diffraction (ADXRD), first-principles calculations, and electrical resistivity measurements were carried out under high pressure to investigate the structural stability and electrical transport properties of metavanadate MgV2O6. The results have revealed the coordination change of vanadium ions (from 5+1 to 6) at around 4 GPa. In addition, a pressure-induced structure transformation from the C2/m phase to the C2 phase in MgV2O6 was detected above 20 GPa, and both phases coexisted up to the highest pressure. This structural phase transition was induced by the enhanced distortions of MgO6 octahedra and VO6 octahedra under high pressure. Furthermore, the electrical resistivity decreased with pressure but exhibited different slope for these two phases, indicating that the pressure-induced structural phase transitions of MgV2O6 was also accompanied by the obvious changes in its electrical transport behavior.
A New SAR Image Segmentation Algorithm for the Detection of Target and Shadow Regions
Authors: Huang Shiqi , Huang Wenzhun , Zhang Ting 
Published: December 2016

AbstractThe most distinctive characteristic of synthetic aperture radar (SAR) is that it can acquire data under all weather conditions and at all times. However, its coherent imaging mechanism introduces a great deal of speckle noise into SAR images, which makes the segmentation of target and shadow regions in SAR images very difficult. This paper proposes a new SAR image segmentation method based on wavelet decomposition and a constant false alarm rate (WD-CFAR). The WD-CFAR algorithm not only is insensitive to the speckle noise in SAR images but also can segment target and shadow regions simultaneously, and it is also able to effectively segment SAR images with a low signal-to-clutter ratio (SCR). Experiments were performed to assess the performance of the new algorithm on various SAR images. The experimental results show that the proposed method is effective and feasible and possesses good characteristics for general application.
Unified rheology of vibro-fluidized dry granular media: From slow dense flows to fast gas-like regimes
Authors: Gnoli Andrea , Lasanta Antonio , Sarracino Alessandro , Puglisi Andrea 
Published: December 2016

AbstractGranular media take on great importance in industry and geophysics, posing a severe challenge to materials science. Their response properties elude known soft rheological models, even when the yield-stress discontinuity is blurred by vibro-fluidization. Here we propose a broad rheological scenario where average stress sums up a frictional contribution, generalizing conventional μ(I)-rheology, and a kinetic collisional term dominating at fast fluidization. Our conjecture fairly describes a wide series of experiments in a vibrofluidized vane setup, whose phenomenology includes velocity weakening, shear thinning, a discontinuous thinning transition, and gaseous shear thickening. The employed setup gives access to dynamic fluctuations, which exhibit a broad range of timescales. In the slow dense regime the frequency of cage-opening increases with stress and enhances, with respect to μ(I)-rheology, the decrease of viscosity. Diffusivity is exponential in the shear stress in both thinning and thickening regimes, with a huge growth near the transition.
Piezoelectric polymer gated OFET: Cutting-edge electro-mechanical transducer for organic MEMS-based sensors
Authors: Thuau Damien , Abbas Mamatimin , Wantz Guillaume , Hirsch Lionel , Dufour Isabelle , Ayela Cédric 
Published: December 2016

AbstractThe growth of micro electro-mechanical system (MEMS) based sensors on the electronic market is forecast to be invigorated soon by the development of a new branch of MEMS-based sensors made of organic materials. Organic MEMS have the potential to revolutionize sensor products due to their light weight, low-cost and mechanical flexibility. However, their sensitivity and stability in comparison to inorganic MEMS-based sensors have been the major concerns. In the present work, an organic MEMS sensor with a cutting-edge electro-mechanical transducer based on an active organic field effect transistor (OFET) has been demonstrated. Using poly(vinylidenefluoride/trifluoroethylene) (P(VDF-TrFE)) piezoelectric polymer as active gate dielectric in the transistor mounted on a polymeric micro-cantilever, unique electro-mechanical properties were observed. Such an advanced scheme enables highly efficient integrated electro-mechanical transduction for physical and chemical sensing applications. Record relative sensitivity over 600 in the low strain regime (<0.3%) was demonstrated, which represents a key-step for the development of highly sensitive all organic MEMS-based sensors.