bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional control of motility enables directional movement of Escherichia coli in a signal gradient
Authors: Ravichandar Jayamary Divya , Bower Adam G. , Julius A. Agung , Collins Cynthia H. 
Published: August 2017

AbstractManipulation of cellular motility using a target signal can facilitate the development of biosensors or microbe-powered biorobots. Here, we engineered signal-dependent motility in Escherichia coli via the transcriptional control of a key motility gene. Without manipulating chemotaxis, signal-dependent switching of motility, either on or off, led to population-level directional movement of cells up or down a signal gradient. We developed a mathematical model that captures the behaviour of the cells, enables identification of key parameters controlling system behaviour, and facilitates predictive-design of motility-based pattern formation. We demonstrated that motility of the receiver strains could be controlled by a sender strain generating a signal gradient. The modular quorum sensing-dependent architecture for interfacing different senders with receivers enabled a broad range of systems-level behaviours. The directional control of motility, especially combined with the potential to incorporate tuneable sensors and more complex sensing-logic, may lead to tools for novel biosensing and targeted-delivery applications.
Windows of opportunity for Ebola virus infection treatment and vaccination
Authors: Nguyen Van Kinh , Hernandez-Vargas Esteban A. 
Published: August 2017

AbstractEbola virus (EBOV) infection causes a high death toll, killing a high proportion of EBOV-infected patients within 7 days. Comprehensive data on EBOV infection are fragmented, hampering efforts in developing therapeutics and vaccines against EBOV. Under this circumstance, mathematical models become valuable resources to explore potential controlling strategies. In this paper, we employed experimental data of EBOV-infected nonhuman primates (NHPs) to construct a mathematical framework for determining windows of opportunity for treatment and vaccination. Considering a prophylactic vaccine based on recombinant vesicular stomatitis virus expressing the EBOV glycoprotein (rVSV-EBOV), vaccination could be protective if a subject is vaccinated during a period from one week to four months before infection. For the case of a therapeutic vaccine based on monoclonal antibodies (mAbs), a single dose might resolve the invasive EBOV replication even if it was administrated as late as four days after infection. Our mathematical models can be used as building blocks for evaluating therapeutic and vaccine modalities as well as for evaluating public health intervention strategies in outbreaks. Future laboratory experiments will help to validate and refine the estimates of the windows of opportunity proposed here.
Metabolic unhealthiness is an important predictor for the development of advanced colorectal neoplasia
Authors: Kim Tae Jun , Kim Eun Ran , Hong Sung Noh , Kim Young-Ho , Chang Dong Kyung , Ji Jaehwan , Kim Jee Eun , Kim Hye Seung , Kim Kyunga , Son Hee Jung 
Published: August 2017

AbstractObesity is a well-known risk factor for colorectal neoplasia. Yet, the associations of both metabolic and obesity status with metachronous colorectal neoplasia remain unclear. We conducted a cohort study of 9,331 adults who underwent screening colonoscopy and surveillance colonoscopy. Participants were classified as metabolically healthy if they had no metabolic syndrome component. Participants were categorized into four groups according to body mass index and metabolic status: metabolically healthy non-obese (MHNO; n = 2,745), metabolically abnormal non-obese (MANO; n = 3,267), metabolically healthy obese (MHO; n = 707), and metabolically abnormal obese (MAO; n = 2,612). MAO individuals [n = 159 advanced colorectal neoplasia (AN) cases, 6.1%] and MANO individuals (n = 167 AN cases, 5.1%) had a higher incidence of AN compared with MHNO individuals (n = 79 AN cases, 2.9%). In a multivariable model, the risk of metachronous AN was higher in MANO (hazard ratio [HR] 1.43, 95% confidence interval [CI] 1.12–1.84) and MAO (HR 1.52, 95% CI 1.18–1.96) than in MHNO. In contrast, the risk of metachronous AN was not significantly elevated in MHO. In subgroup analyses, with or without adenoma at baseline, MAO was a risk group for metachronous AN, and MHO was not. Our findings suggest that metabolic unhealthiness is a significant predictor for metachronous AN.
Label-free in vivo Raman microspectroscopic imaging of the macromolecular architecture of oocytes
Authors: Heraud Philip , Marzec Katarzyna Maria , Zhang Qing‒Hua , Yuen Wai Shan , Carroll John , Wood Bayden R. 
Published: August 2017

AbstractConfocal Raman spectroscopy (CRS) can provide information about oocyte competency through measurement of changes in the macromolecular architecture during oocyte development and maturation. Hitherto most spectroscopic studies have been limited to fixed oocytes due to the inherent difficulties working with live cells. Here we report the first three-dimensional images of living murine oocytes using CRS. We show that fixation induces significant changes in the macromolecular chemistry compared to living oocytes. A band at 1602 cm−1, assigned to a marker for mitochondria function was found in living oocytes but absent from fixed oocytes providing an in vivo marker. Fixation resulted in significant changes in protein and nucleic acid bands and the spatial distribution of organelles. Raman imaging of Metaphase I and II (MI, MII) and germinal vesicle stage oocytes showed changes in nuclear organisation and cytoplasm macromolecular architecture during these development and maturation stages related to changes in chromosome condensation, mitochondria aggregation and lipid droplet numbers.
Application of sebomics for the analysis of residual skin surface components to detect potential biomarkers of type-1 diabetes mellitus
Authors: Shetage Satyajit S. , Traynor Matthew J. , Brown Marc B. , Galliford Thomas M. , Chilcott Robert P. 
Published: August 2017

AbstractMetabolic imbalance in chronic diseases such as type-1 diabetes may lead to detectable perturbations in the molecular composition of residual skin surface components (RSSC). This study compared the accumulation rate and the composition of RSSC in type-1 diabetic patients with those in matched controls in order to identify potential biomarkers of the disease. Samples of RSSC were collected from the foreheads of type-1 diabetic (n = 55) and non-diabetic (n = 58) volunteers. Samples were subsequently analysed to identify individual components (sebomic analysis). There was no significant difference in the rate of accumulation of RSSC between type-1 diabetics and controls. In terms of molecular composition, 171 RSSC components were common to both groups, 27 were more common in non-diabetics and 18 were more common in type-1 diabetic patients. Statistically significant (P < 0.05) differences between diabetic and non-diabetic volunteers were observed in the recovered amounts of one diacylglyceride (m/z 594), six triacylglycerides (m/z 726–860) and six free fatty acids (m/z 271–345). These findings indicate that sebomic analysis can identify differences in the molecular composition of RSSC components between type-1 diabetic and non-diabetic individuals. Further work is required to determine the practical utility and identity of these potential biomarkers.
The Calabrian Arc: three-dimensional modelling of the subduction interface
Authors: Maesano Francesco E. , Tiberti Mara M. , Basili Roberto 
Published: August 2017

AbstractThe Calabrian Arc is a one-of-a-kind subduction zone, featuring one of the shortest slab segments (<150 km), one of the thickest accretionary wedges, and one of the oldest oceanic crust in the world. Despite a convergence rate of up to 5 mm/y and well-known intraslab seismicity below 40 km, its shallow interface shows little signs of seismic activity. Nonetheless, it has been attributed as generating historical large earthquakes and tsunamis. To gain insights into this subduction zone, we first made a geological reconstruction of the shallower slab interface (<20 km) and its overlying accretionary wedge by interpreting a grid of 54 seismic reflection lines (8,658 km) with 438 intersections within an area of 105 km2. Then, we constrained a deeper portion of the slab surface (40–350 km) using the seismicity distribution. Finally, we interpolated the two parts to obtain a seamless 3D surface highlighting geometric details of the subduction interface, its lateral terminations and down-dip curvature, and a slab tear at 70–100 km depth. Our 3D slab model of the Calabrian Arc will contribute to understanding of the geodynamics of a cornerstone in the Mediterranean tectonic puzzle and estimates of seismic and tsunami hazards in the region.
Molecular Diversity and Potential Anti-neuroinflammatory Activities of Cyathane Diterpenoids from the Basidiomycete Cyathus africanus
Authors: Wei Jing , Cheng Yuanyuan , Guo Wan-Hui , Wang Da-Cheng , Zhang Qiang , Li Ding , Rong Jianhui , Gao Jin-Ming 
Published: August 2017

AbstractTen new polyoxygenated cyathane diterpenoids, named neocyathins A–J (1–10), together with four known diterpenes (11–14), were isolated from the liquid culture of the medicinal basidiomycete fungus Cyathus africanus. The structures and configurations of these new compounds were elucidated through comprehensive spectroscopic analyses including 1D NMR, 2D NMR (HSQC, HMBC, NOESY) and HRESIMS, and electronic circular dichroism (ECD) data. Neuroinflammation is implicated in the pathogenesis of various neurodegenerative diseases, such as Alzheimers’ disease (AD). All isolated compounds were evaluated for the potential anti-neuroinflammatory activities in BV2 microglia cells. Several compounds showed differential effects on the expression of inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) in lipopolysaccharide (LPS)-stimulated and Aβ1–42-treated mouse microglia cell line BV-2. Molecular docking revealed that bioactive compounds (e.g., 11) could interact with iNOS protein other than COX-2 protein. Collectively, our results suggested that this class of cyathane diterpenoids might serve as important lead compounds for drug discovery against neuroinflammation in AD.
A clue to unprecedented strategy to HIV eradication: “Lock-in and apoptosis”
Authors: Tateishi Hiroshi , Monde Kazuaki , Anraku Kensaku , Koga Ryoko , Hayashi Yuya , Ciftci Halil Ibrahim , DeMirci Hasan , Higashi Taishi , Motoyama Keiichi , Arima Hidetoshi , Otsuka Masami , Fujita Mikako 
Published: August 2017

AbstractDespite the development of antiretroviral therapy against HIV, eradication of the virus from the body, as a means to a cure, remains in progress. A “kick and kill” strategy proposes “kick” of the latent HIV to an active HIV to eventually be “killed”. Latency-reverting agents that can perform the “kick” function are under development and have shown promise. Management of the infected cells not to produce virions after the “kick” step is important to this strategy. Here we show that a newly synthesized compound, L-HIPPO, captures the HIV-1 protein Pr55Gag and intercepts its function to translocate the virus from the cytoplasm to the plasma membrane leading to virion budding. The infecting virus thus “locked-in” subsequently induces apoptosis of the host cells. This “lock-in and apoptosis” approach performed by our novel compound in HIV-infected cells provides a means to bridge the gap between the “kick” and “kill” steps of this eradication strategy. By building upon previous progress in latency reverting agents, our compound appears to provide a promising step toward the goal of HIV eradication from the body.
Dose-related liver injury of Geniposide associated with the alteration in bile acid synthesis and transportation
Authors: Tian Jingzhuo , Zhu Jingjing , Yi Yan , Li Chunying , Zhang Yushi , Zhao Yong , Pan Chen , Xiang Shixie , Li Xiaolong , Li Guiqin , Newman John W , Feng Xiaoyi , Liu Jing , Han Jiayin , Wang Lianmei , Gao Yue , La Frano Michael R. , Liang Aihua 
Published: August 2017

AbstractFructus Gardenia (FG), containing the major active constituent Geniposide, is widely used in China for medicinal purposes. Currently, clinical reports of FG toxicity have not been published, however, animal studies have shown FG or Geniposide can cause hepatotoxicity in rats. We investigated Geniposide-induced hepatic injury in male Sprague-Dawley rats after 3-day intragastric administration of 100 mg/kg or 300 mg/kg Geniposide. Changes in hepatic histomorphology, serum liver enzyme, serum and hepatic bile acid profiles, and hepatic bile acid synthesis and transportation gene expression were measured. The 300 mg/kg Geniposide caused liver injury evidenced by pathological changes and increases in serum alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP) and γ-glutamytransferase (γ-GT). While liver, but not sera, total bile acids (TBAs) were increased 75% by this dose, dominated by increases in taurine-conjugated bile acids (t-CBAs). The 300 mg/kg Geniposide also down-regulated expression of Farnesoid X receptor (FXR), small heterodimer partner (SHP) and bile salt export pump (BSEP). In conclusion, 300 mg/kg Geniposide can induce liver injury with associated changes in bile acid regulating genes, leading to an accumulation of taurine conjugates in the rat liver. Taurocholic acid (TCA), taurochenodeoxycholic acid (TCDCA) as well as tauro-α-muricholic acid (T-α-MCA) are potential markers for Geniposide-induced hepatic damage.
Enhancement of spontaneous emission in Tamm plasmon structures
Authors: Gubaydullin A. R. , Symonds C. , Bellessa J. , Ivanov K. A. , Kolykhalova E. D. , Sasin M. E. , Lemaitre A. , Senellart P. , Pozina G. , Kaliteevski M. A. 
Published: August 2017

AbstractIt was theoretically and experimentally demonstrated that in metal/semiconductor Tamm plasmon structures the probability of spontaneous emission can be increased despite losses in metal, and theoretical analysis of experimental results suggested that the enhancement could be as high as one order of magnitude. Tamm plasmon structure with quantum dots has been fabricated and the emission pattern has been measured. Electromagnetic modes of the structure have been analyzed and modification of spontaneous emission rates has been calculated showing a good agreement with experimentally observed emission pattern.
Small molecules enhance CRISPR/Cas9-mediated homology-directed genome editing in primary cells
Authors: Li Guoling , Zhang Xianwei , Zhong Cuili , Mo Jianxin , Quan Rong , Yang Jie , Liu Dewu , Li Zicong , Yang Huaqiang , Wu Zhenfang 
Published: August 2017

AbstractCRISPR/Cas9 is an efficient customizable nuclease to generate double-strand breaks (DSBs) in the genome. This process results in knockout of the targeted gene or knock-in of a specific DNA fragment at the targeted locus in the genome of various species. However, efficiency of knock-in mediated by homology-directed repair (HDR) pathway is substantially lower compared with the efficiency of knockout mediated by the nonhomologous end-joining (NHEJ) pathway. Suppressing NHEJ pathway or enhancing HDR pathway has been proven to enhance the nuclease-mediated knock-in efficiency in cultured cells and model organisms. We here investigated the effect of small molecules, Scr7, L755507 and resveratrol, on promoting HDR efficiency in porcine fetal fibroblasts. Results from eGFP reporter assay showed that these small molecules could increase the HDR efficiency by 2–3-fold in porcine fetal fibroblasts. When transfecting with the homologous template DNA and CRISPR/Cas9 plasmid and treating with small molecules, the rate of knock-in porcine fetal fibroblast cell lines with large DNA fragment integration could reach more than 50% of the screened cell colonies, compared with 26.1% knock-in cell lines in the DMSO-treated group. The application of small molecules offers a beneficial approach to improve the frequency of precise genetic modifications in primary somatic cells.
De novo transcriptome assembly for the spiny mouse (Acomys cahirinus)
Authors: Mamrot Jared , Legaie Roxane , Ellery Stacey J. , Wilson Trevor , Seemann Torsten , Powell David R. , Gardner David K. , Walker David W. , Temple-Smith Peter , Papenfuss Anthony T. , Dickinson Hayley 
Published: August 2017

AbstractSpiny mice of the genus Acomys display several unique physiological traits, including menstruation and scar-free wound healing; characteristics that are exceedingly rare in mammals, and of considerable interest to the scientific community. These unique attributes, and the potential for spiny mice to accurately model human diseases, are driving increased use of this genus in biomedical research, however little genetic information is accessible for this species. This project aimed to generate a draft transcriptome for the Common spiny mouse (Acomys cahirinus). Illumina sequencing of RNA from 15 organ types (male and female) produced 451 million, 150 bp paired-end reads (92.4Gbp). An extensive survey of de novo transcriptome assembly approaches using Trinity, SOAPdenovo-Trans, and Oases at multiple kmer lengths was conducted, producing 50 single-kmer assemblies from this dataset. Non-redundant transcripts from all assemblies were merged into a meta-assembly using the EvidentialGene tr2aacds pipeline, producing the largest gene catalogue to date for Acomys cahirinus. This study provides the first detailed characterization of the spiny mouse transcriptome. It validates use of the EvidentialGene tr2aacds pipeline in mammals to augment conventional de novo assembly approaches, and provides a valuable scientific resource for further investigation into the unique physiological characteristics inherent in the genus Acomys.
Omalizumab efficacy in cases of chronic spontaneous urticaria is not explained by the inhibition of sera activity in effector cells
Authors: Serrano-Candelas Eva , Martínez-Aranguren Rubén , Vega Olga , Gastaminza Gabriel , Bartra Joan , Audicana Maria Teresa , Núñez-Córdoba Jorge M. , Algorta Jaime , Valero Antonio , Martin Margarita , Ferrer Marta 
Published: August 2017

AbstractOmalizumab (OmAb) is a humanized anti-IgE antibody approved for the treatment of chronic spontaneous urticaria (CSU). OmAb’s mechanism of action is known to include actions on free IgE and on pre-bound IgE. However, OmAb is equally and rapidly effective against autoimmune and non-autoimmune urticaria where IgE involvement is not clear, suggesting the involvement of additional mechanisms of action. In this study, we sought to investigate the ability of OmAb to inhibit mast cell and basophil degranulation induced by sera from CSU patients. For this purpose, we performed a comparison between thein vitroincubation of sera from CSU patients treated with OmAb and thein vivoadministration of OmAb in a clinical trial. We found that OmAb addedin vitroto sera from CSU patients did not modify the ability of the sera to induce cell degranulation. Similarly, the sera from patients treated with OmAb in the context of the clinical trial who had a good clinical outcome maintained the capacity to activate mast cells and basophils. Thus, we conclude that the beneficial activity of OmAb does not correlate with the ability of patient sera to induce cell degranulation.
A highly sensitive plasma-based amyloid-β detection system through medium-changing and noise cancellation system for early diagnosis of the Alzheimer’s disease
Authors: Yoo Yong Kyoung , Kim Jinsik , Kim Gangeun , Kim Young Soo , Kim Hye Yun , Lee Sejin , Cho Won Woo , Kim Seongsoo , Lee Sang-Myung , Lee Byung Chul , Lee Jeong Hoon , Hwang Kyo Seon 
Published: August 2017

AbstractWe developed an interdigitated microelectrode (IME) sensor system for blood-based Alzheimer’s disease (AD) diagnosis based on impedimetric detection of amyloid-β (Aβ) protein, which is a representative candidate biomarker for AD. The IME sensing device was fabricated using a surface micromachining process. For highly sensitive detection of several tens to hundreds of picogram/mL of Aβ in blood, medium change from plasma to PBS buffer was utilized with signal cancellation and amplification processing (SCAP) system. The system demonstrated approximately 100-folds higher sensitivity according to the concentrations. A robust antibody-immobilization process was used for stability during medium change. Selectivity of the reaction due to the affinity of Aβ to the antibody and the sensitivity according to the concentration of Aβ were also demonstrated. Considering these basic characteristics of the IME sensor system, the medium change was optimized in relation to the absolute value of impedance change and differentiated impedance changes for real plasma based Aβ detection. Finally, the detection of Aβ levels in transgenic and wild-type mouse plasma samples was accomplished with the designed sensor system and the medium-changing method. The results confirmed the potential of this system to discriminate between patients and healthy controls, which would enable blood-based AD diagnosis.
New approaches to high-resolution mapping of marine vertical structures
Authors: Robert Katleen , Huvenne Veerle A. I. , Georgiopoulou Aggeliki , Jones Daniel O. B. , Marsh Leigh , D. O. Carter Gareth , Chaumillon Leo 
Published: August 2017

AbstractVertical walls in marine environments can harbour high biodiversity and provide natural protection from bottom-trawling activities. However, traditional mapping techniques are usually restricted to down-looking approaches which cannot adequately replicate their 3D structure. We combined sideways-looking multibeam echosounder (MBES) data from an AUV, forward-looking MBES data from ROVs and ROV-acquired videos to examine walls from Rockall Bank and Whittard Canyon, Northeast Atlantic. High-resolution 3D point clouds were extracted from each sonar dataset and structure from motion photogrammetry (SfM) was applied to recreate 3D representations of video transects along the walls. With these reconstructions, it was possible to interact with extensive sections of video footage and precisely position individuals. Terrain variables were derived on scales comparable to those experienced by megabenthic individuals. These were used to show differences in environmental conditions between observed and background locations as well as explain spatial patterns in ecological characteristics. In addition, since the SfM 3D reconstructions retained colours, they were employed to separate and quantify live coral colonies versus dead framework. The combination of these new technologies allows us, for the first time, to map the physical 3D structure of previously inaccessible habitats and demonstrates the complexity and importance of vertical structures.
Enhancement of Plasmonic Performance in Epitaxial Silver at Low Temperature
Authors: Sun Liuyang , Zhang Chendong , Wang Chun-Yuan , Su Ping-Hsiang , Zhang Matt , Gwo Shangjr , Shih Chih-Kang , Li Xiaoqin , Wu Yanwen 
Published: August 2017

AbstractWe report longer surface plasmon polariton propagation distance based on crystalline crystal silver at low temperature. Although enhanced plasmonic performance at low temperature has been predicted for a long time, it has not been directly observed on polycrystalline silver films which suffer from significant plasmonic losses due to grain boundaries and rough silver surface. Here we show that longer propagation distance can be achieved with epitaxial silver at low temperature. Importantly, the enhancement at low temperature are consistent across silver films grown with different methods.