bluuebunny/crossref_metadata_2025_split huggingface dataset:
A perfusion incubator liver chip for 3D cell culture with application on chronic hepatotoxicity testing
Authors: Yu Fang , Deng Rensheng , Hao Tong Wen , Huan Li , Chan Way Ng , IslamBadhan Anik , Iliescu Ciprian , Yu Hanry 
Published: October 2017

AbstractLiver chips have been developed to recapitulate in vivo physiological conditions to enhance hepatocyte functions for assessing acute responses to drugs. To develop liver chips that can assess repeated dosing chronic hepatotoxicity, we need to ensure that hepatocyte functions be maintained at constant values over two weeks in stable culture conditions of sterility, temperature, pH, fluidic-flow of culture media and drugs. We have designed a perfusion-incubator-liver-chip (PIC) for 3D cell culture, that assures a tangential flow of the media over the spheroids culture. Rat hepatocyte spheroids constrained between a cover glass and a porous-ultrathin Parylene C membrane experienced optimal mass transfer and limited shear stress from the flowing culture media; maintained cell viability over 24 days. Hepatocyte functions were significantly improved and maintained at constant values (urea, albumin synthesis, and CYP450 enzyme activities) for 14 days. The chip act as an incubator, having 5% CO2 pressure-driven culture-media flow, on-chip heater and active debubbler. It operates in a biosafety cabinet, thus minimizing risk of contamination. The chronic drug response to repeated dosing of Diclofenac and Acetaminophen evaluated in PIC were more sensitive than the static culture control.
Machine learning model for sequence-driven DNA G-quadruplex formation
Authors: Sahakyan Aleksandr B. , Chambers Vicki S. , Marsico Giovanni , Santner Tobias , Di Antonio Marco , Balasubramanian Shankar 
Published: October 2017

AbstractWe describe a sequence-based computational model to predict DNA G-quadruplex (G4) formation. The model was developed using large-scale machine learning from an extensive experimental G4-formation dataset, recently obtained for the human genome via G4-seq methodology. Our model differentiates many widely accepted putative quadruplex sequences that do not actually form stable genomic G4 structures, correctly assessing the G4 folding potential of over 700,000 such sequences in the human genome. Moreover, our approach reveals the relative importance of sequence-based features coming from both within the G4 motifs and their flanking regions. The developed model can be applied to any DNA sequence or genome to characterise sequence-driven intramolecular G4 formation propensities.
Predictors of Liver Fat and Stiffness in Non-Alcoholic Fatty Liver Disease (NAFLD) – an 11-Year Prospective Study
Authors: Lallukka Susanna , Sädevirta Sanja , Kallio Markus T. , Luukkonen Panu K. , Zhou You , Hakkarainen Antti , Lundbom Nina , Orho-Melander Marju , Yki-Järvinen Hannele 
Published: October 2017

AbstractLiver fat can be non-invasively measured by proton magnetic resonance spectroscopy (1H-MRS) and fibrosis estimated as stiffness using transient elastography (FibroScan). There are no longitudinal data on changes in liver fat in Europids or on predictors of liver stiffness using these methods. We determined liver fat (1H-MRS) and clinical characteristics including features of insulin resistance at baseline and after a median follow-up period of 11.3 (range 7.3–13.4) years in 97 Finnish subjects. Liver stiffness was measured at 11.3 years. Liver fat content decreased by 5% (p < 0.05) over time. Values at baseline and 11.3 years were closely interrelated (r = 0.81, p < 0.001). Baseline liver fat (OR 1.32; 95%CI: 1.15–1.50) and change in BMI (OR 1.67; 95%CI: 1.24–2.25) were independent predictors of liver fat at 11.3 years (AUROC 0.90; 95%CI: 0.83–0.96). Baseline liver fat (AUROC 0.84; 95%CI: 0.76–0.92) predicted liver fat at 11.3 years more accurately than routinely available parameters (AUROC 0.76; 95%CI: 0.65–0.86, p = 0.02). At 11.3 years, 29% of the subjects had increased liver stiffness. Baseline liver fat (OR 2.17; 95%CI: 1.05–4.46) was an independent predictor of increased liver stiffness. These data show that liver fat is more important than the associated metabolic abnormalities as the predictor of future liver fat and fibrosis.
Candidate proteins from predegenerated nerve exert time-specific protection of retinal ganglion cells in glaucoma
Authors: Pietrucha-Dutczak Marita , Smedowski Adrian , Liu Xiaonan , Matuszek Iwona , Varjosalo Markku , Lewin-Kowalik Joanna 
Published: October 2017

AbstractGlaucoma is thought to be the main cause of severe visual impairment or permanent loss of vision. Current therapeutic strategies are not sufficient to protect against glaucoma. Thus, new therapies and potential novel therapeutic targets must be developed to achieve progress in the treatment of this insidious disease. This study was undertaken to verify whether the time of administration of an extract from predegenerated rat sciatic nerves as well as exposure time of this extract onto retinal ganglion cells (RGCs) influences the survival of RGCs in a rat glaucoma model. We have demonstrated that extract obtained from the predegenerated sciatic nerves protects RGCs in a rat glaucoma model. The neuroprotective effect depends mostly on the time of administration of the extract and less clearly on the time of exposure to the extract and is associated with stimulation of endogenous BDNF expression both in RGCs and glial cells. The 14th day following glaucoma induction represents a therapeutic window for effective treatment in a glaucoma model. Mass Spectrometry analysis demonstrated that metallothionein 2 (MT2) may be a key molecule responsible for neuroprotective effects on RGC survival.
Numerical Investigation of Tunable Plasmonic Tweezers based on Graphene Stripes
Authors: Samadi Mohsen , Darbari Sara , Moravvej-Farshi Mohammad Kazem 
Published: October 2017

AbstractWe are proposing tunable plasmonic tweezers, consisting two parallel graphene stripes, which can be utilized to effectively trap and sort nanoparticles. We show that by electrostatically tuning the chemical potential of a graphene stripe by about 100 meV (equivalent to ΔVG ≈ 4.4 V), the plasmonic force can be switched efficiently, without a need to switch the laser intensity. This enables high speed and low power switching with a large number of switching cycles. By applying two independent and appropriate gate bias voltages to the stripes, the direction of the plasmonic force can be reversed, which leads to separation of nanoparticles that satisfy the trapping conditions. Numerical simulations show that the potential depths obtained for polystyrene nanoparticles of refractive index n = 1.5717 and radii r ≥ 50 nm is deeper than −10 kBT , confirming the ability of the proposed system to effectively separate such nanoparticles. This capability holds for smaller nanoparticles with larger refractive indices. Finally, performing thermal simulations, we have demonstrated that the heat induced by the illumination increases the fluid temperature by at most 9 °C, having negligible effect on the trapping mechanism. The proposed system opens up new possibilities in developing tunable on-chip manipulation devices, suitable for biological applications.
Identification of unusual peptides with new Cys frameworks in the venom of the cold-water sea anemone Cnidopus japonicus
Authors: Babenko Vladislav V. , Mikov Alexander N. , Manuvera Valentin A. , Anikanov Nickolay A. , Kovalchuk Sergey I. , Andreev Yaroslav A. , Logashina Yulia A. , Kornilov Daniil A. , Manolov Alexander I. , Sanamyan Nadya P. , Sanamyan Karen E. , Kostryukova Elena S. , Kozlov Sergey A. , Grishin Eugene V. , Govorun Vadim M. , Lazarev Vassili N. 
Published: October 2017

AbstractSea anemones (Actiniaria) are intensely popular objects of study in venomics. Order Actiniaria includes more than 1,000 species, thus presenting almost unlimited opportunities for the discovery of novel biologically active molecules. The venoms of cold-water sea anemones are studied far less than the venoms of tropical sea anemones. In this work, we analysed the molecular venom composition of the cold-water sea anemone Cnidopus japonicus. Two sets of NGS data from two species revealed molecules belonging to a variety of structural classes, including neurotoxins, toxin-like molecules, linear polypeptides (Cys-free), enzymes, and cytolytics. High-throughput proteomic analyses identified 27 compounds that were present in the venoms. Some of the toxin-like polypeptides exhibited novel Cys frameworks. To characterise their function in the venom, we heterologously expressed 3 polypeptides with unusual Cys frameworks (designated CjTL7, CjTL8, and AnmTx Cj 1c-1) in E. coli. Toxicity tests revealed that the CjTL8 polypeptide displays strong crustacean-specific toxicity, while AnmTx Cj 1c-1 is toxic to both crustaceans and insects. Thus, an improved NGS data analysis algorithm assisted in the identification of toxins with unusual Cys frameworks showing no homology according to BLAST. Our study shows the advantage of combining omics analysis with functional tests for active polypeptide discovery.
Network-pharmacology-based validation of TAMS/CXCL-1 as key mediator of XIAOPI formula preventing breast cancer development and metastasis
Authors: Wang Neng , Zheng Yifeng , Gu Jiangyong , Cai Youli , Wang Shengqi , Zhang Fengxue , Chen Jianping , Situ Honglin , Lin Yi , Wang Zhiyu 
Published: October 2017

AbstractNetwork pharmacology has become a powerful means of understanding the mechanisms underlying the action of Chinese herbs in cancer treatment. This study aims to validate the preventive effects and molecular mechanisms of a clinical prescription XIAOPI formula against breast cancer. In vivo breast cancer xenograft data showed that XIAOPI delayed breast cancer development and efficiently inhibited lung metastasis, accompanied by prolonged survival benefits and decreased cancer stem cell subpopulations. However, similar phenomenon were not observed in a cell model. The herb-ingredient-target network analysis further identified a total of 81 genes closely correlated with the breast cancer chemoprevention effects of XIAOPI. Cytokine array analysis further validated CXCL-1 as the key target of XIAOPI both in vitro and in vivo. Evaluation of the mechanism demonstrated that CXCL-1 administration significantly abrogated the metastatic inhibition effects of XIAOPI on breast cancer migration, invasion, stem cells subpopulations, epithelial-mesenchymal transition(EMT), or mammosphere formation abilities. Overall, our study provides experimental evidence and molecular mechanisms that may facilitate the safe and effective use of herbal medicine for the prevention of breast cancer growth or metastasis, and may lead to CXCL-1-based therapeutic strategies for mammary malignancies.
Penicillin induces alterations in glutamine metabolism in Streptococcus pneumoniae
Authors: El Khoury Jessica Y. , Boucher Nancy , Bergeron Michel G. , Leprohon Philippe , Ouellette Marc 
Published: October 2017

AbstractPenicillin is a bactericidal antibiotic that inhibits the synthesis of the peptidoglycan by targeting penicillin-binding proteins. This study aimed to assess through transcriptional profiling the stress response of S. pneumoniae strains after exposure to lethal penicillin concentrations to understand further the mode of action of penicillin. Two experimental designs (time-course and dose-response) were used for monitoring the effect of penicillin on the transcriptional profile. The expression of some genes previously shown to be modulated by penicillin was altered, including ciaRH, pstS and clpL. Genes of the glnRA and glnPQ operons were among the most downregulated genes in the three strains. These genes are involved in glutamine synthesis and uptake and LC-MS work confirmed that penicillin treatment increases the intracellular glutamine concentrations. Glutamine conferred a protective role against penicillin when added to the culture medium. Glutamine synthetase encoded by glnA catalyses the transformation of glutamate and ammonium into glutamine and its chemical inhibition by the inhibitor L-methionine sulfoximine is shown to sensitize S. pneumoniae to penicillin, including penicillin-resistant clinical isolates. In summary, a combination of RNA-seq and metabolomics revealed that penicillin interferes with glutamine metabolism suggesting strategies that could eventually be exploited for combination therapy or for reversal of resistance.
The comprehensive expression analysis of circular RNAs in gastric cancer and its association with field cancerization
Authors: Vidal Amanda Ferreira , Ribeiro-dos-Santos André M. , Vinasco-Sandoval Tatiana , Magalhães Leandro , Pinto Pablo , Anaissi Ana K. M. , Demachki Samia , de Assumpção Paulo Pimentel , dos Santos Sidney Emanuel Batista , Ribeiro-dos-Santos Ândrea 
Published: October 2017

AbstractCircular RNAs comprise a new class of long noncoding RNAs characterized by their 5′ and 3′ ends covalently joined. Previous studies have demonstrated that some circular RNAs act as microRNA sponges, and are associated with cellular proliferation in cancer. We were the first to analyze the global expression of circular RNAs in samples of patients without gastric cancer, gastric cancer, and matched tumor-adjacent gastric tissue. Among the samples, we identified 736 previously annotated circular RNAs by RNA-Seq. The tumor-adjacent tissue presented the higher abundance of circular RNAs and could not be considered as a normal tissue, reinforcing the notion of field effect in gastric cancer. We identified five differentially expressed circular RNAs that may be potential biomarkers of this type of cancer. We also predicted candidate microRNAs targets of the highest expressed circular RNAs in gastric tissues and found five miRNAs. Overall, our results support the hypothesis of circular RNAs representing a novel factor in the dynamic epigenetic network of gene regulation, which involves the microRNAs, its mRNAs targets, and the circular RNAs-derived genes. Further studies are needed to elucidate the roles and the functional relevance of the circular RNAs in human diseases.
Centimeter-wide worm-like fossils from the lowest Cambrian of South China
Authors: Zhang Xingliang , Liu Wei , Isozaki Yukio , Sato Tomohiko 
Published: October 2017

AbstractThe trace fossil record implies that large worm-like animals were in place along with the skeletonizing organisms during the initial stage of the Cambrian explosion. Body fossils of large worms, however, have so far not been found. Here, we describe a large, soft-bodied, worm-like organism, Vittatusivermis annularius gen. et sp. nov. from the lowest Cambrian of South China, which is constrained to the Fortunian Age (541–529 Ma) of the Cambrian Period. The elongate body of Vittatusivermis was large enough to have supported organ systems and a fluid skeleton that facilitated peristaltic locomotion, thus allowing for more complex patterns of movement than those of flatworms. Its occurrence on the same bedding surface as trace fossils suggests that Vittatusivermis might have produced epichnial trails and shallow burrows on and within sediments. Therefore, Vittatusivermis is likely to have been one of the long expected producers of trace fossils in the earliest Cambrian.
Identification of claudin-4 binder that attenuates tight junction barrier function by TR-FRET-based screening assay
Authors: Watari Akihiro , Kodaka Miki , Matsuhisa Koji , Sakamoto Yuta , Hisaie Kota , Kawashita Norihito , Takagi Tatsuya , Yamagishi Yoshiaki , Suzuki Hidehiko , Tsujino Hirofumi , Yagi Kiyohito , Kondoh Masuo 
Published: October 2017

AbstractClaudins are key functional and structural components of tight junctions (TJs) in epithelial cell sheets. The C-terminal fragment of Clostridium perfringens enterotoxin (C-CPE) binds to claudin-4 and reversibly modulates intestinal TJ seals, thereby enhancing paracellular transport of solutes. However, the use of C-CPE as an absorption enhancer is limited by the molecule’s immunogenicity and manufacturing cost. Here, we developed a high-throughput screening system based on the Time-Resolved Fluorescence Resonance Energy Transfer (TR-FRET) method to identify claudin-4 binders in a library collection of 32,560 compounds. Thiostrepton, identified from the screen, decreased transepithelial electrical resistance and increased flux of 4-kDa fluorescein isothiocyanate–labelled dextran (FD-4) in Caco-2 cell monolayers, a model of intestinal epithelium. Thiostrepton changed the expression, but not the localisation, of TJ components. Treatment of rat jejunum with thiostrepton increased the absorption of FD-4 without tissue toxicity, indicating that thiostrepton is a novel claudin-4 binder that enhances intestinal permeability. The screening system may therefore be a useful tool for identifying claudin-4 binders to enhance drug absorption in mucosa.
A role for small secreted proteins (SSPs) in a saprophytic fungal lifestyle: Ligninolytic enzyme regulation in Pleurotus ostreatus
Authors: Feldman Daria , Kowbel David J. , Glass N. Louise , Yarden Oded , Hadar Yitzhak 
Published: October 2017

AbstractSmall secreted proteins (SSPs), along with lignocellulose degrading enzymes, are integral components of the secretome ofPleurotus ostreatus, a white rot fungus. In this study, we identified 3 genes (ssp1,2and3) encoding proteins that are annotated as SSPs and that exhibited of ~4,500- fold expression, 24 hr following exposure to the toxic compound 5-hydroxymethylfurfural (HMF). Homologues to genes encoding these SSPs are present in the genomes of other basidiomycete fungi, however the role of SSPs is not yet understood. SSPs, aryl-alcohol oxidases (AAO) and the intracellular aryl-alcohol dehydrogenases (AAD) were also produced after exposure to other aryl-alcohols, known substrates and inducers of AAOs, and during idiophase (after the onset of secondary metabolism). A knockdown strain ofssp1exhibited reduced production of AAO-and AAD-encoding genes after HMF exposure. Conversely, a strain overexpressingssp1exhibited elevated expression of genes encoding AAOs and ADD, resulting in a 3-fold increase in enzymatic activity of AAOs, as well as increased expression and protein abundance of versatile peroxidase 1, which directly degrades lignin. We propose that in addition to symbionts and pathogens, SSPs also have roles in saprophytes and function inP. ostreatusas components of the ligninolytic system.
Discovering geothermal supercritical fluids: a new frontier for seismic exploration
Authors: Piana Agostinetti Nicola , Licciardi Andrea , Piccinini Davide , Mazzarini Francesco , Musumeci Giovanni , Saccorotti Gilberto , Chiarabba Claudio 
Published: October 2017

AbstractExploiting supercritical geothermal resources represents a frontier for the next generation of geothermal electrical power plant, as the heat capacity of supercritical fluids (SCF),which directly impacts on energy production, is much higher than that of fluids at subcritical conditions. Reconnaissance and location of intensively permeable and productive horizons at depth is the present limit for the development of SCF geothermal plants. We use, for the first time, teleseismic converted waves (i.e. receiver function) for discovering those horizons in the crust. Thanks to the capability of receiver function to map buried anisotropic materials, the SCF-bearing horizon is seen as the 4km-depth abrupt termination of a shallow, thick, ultra-high (>30%) anisotropic rock volume, in the center of the Larderello geothermal field. The SCF-bearing horizon develops within the granites of the geothermal field, bounding at depth the vapor-filled heavily-fractured rock matrix that hosts the shallow steam-dominated geothermal reservoirs. The sharp termination at depth of the anisotropic behavior of granites, coinciding with a 2 km-thick stripe of seismicity and diffuse fracturing, points out the sudden change in compressibility of the fluid filling the fractures and is a key-evidence of deep fluids that locally traversed the supercritical conditions. The presence of SCF and fracture permeability in nominally ductile granitic rocks open new scenarios for the understanding of magmatic systems and for geothermal exploitation.
Enhancing reading performance through action video games: the role of visual attention span
Authors: Antzaka A. , Lallier M. , Meyer S. , Diard J. , Carreiras M. , Valdois S. 
Published: October 2017

AbstractRecent studies reported that Action Video Game-AVG training improves not only certain attentional components, but also reading fluency in children with dyslexia. We aimed to investigate the shared attentional components of AVG playing and reading, by studying whether the Visual Attention (VA) span, a component of visual attention that has previously been linked to both reading development and dyslexia, is improved in frequent players of AVGs. Thirty-six French fluent adult readers, matched on chronological age and text reading proficiency, composed two groups: frequent AVG players and non-players. Participants performed behavioural tasks measuring the VA span, and a challenging reading task (reading of briefly presented pseudo-words). AVG players performed better on both tasks and performance on these tasks was correlated. These results further support the transfer of the attentional benefits of playing AVGs to reading, and indicate that the VA span could be a core component mediating this transfer. The correlation between VA span and pseudo-word reading also supports the involvement of VA span even in adult reading. Future studies could combine VA span training with defining features of AVGs, in order to build a new generation of remediation software.
Highly Performance Core-Shell TiO2(B)/anatase Homojunction Nanobelts with Active Cobalt phosphide Cocatalyst for Hydrogen Production
Authors: Yang Guang , Ding Hao , Feng Jiejie , Hao Qiang , Sun Sijia , Ao Weihua , Chen Daimei 
Published: October 2017

AbstractIn this paper, a highly efficient core-shell structure of TiO2(B)/anatase photocatalyst with CoP cocatalyst has been synthesized via hydrothermal processes and a mechanical milling method. The designed core-shell TiO2(B)/anatase photocatalysts exhibit excellent performance by compared with pure TiO2(B) and anatase phase. With the participation of CoP particles, there is drastically enhanced photocatalytic activity of TiO2(B)/anatase, and the H2-production rate can be up to 7400 μmol·g−1, which is about 3.2 times higher than TiO2(B)/anatase photocatalyst. The improved activity is attributed to the contribution of the well-matched core-shell structure and cooperative effect of CoP cocatalyst. The photogenerated holes of anatase can migrate more promptly to the adjacent TiO2(B) core than the photogenerated electrons, which result in an accumulation of electrons in the anatase, and CoP nanoparticles can contribute significantly to transferring electrons from the surface of TiO2(A). It was found that the efficient separation of electron-hole pairs greatly improved the photocatalytic hydrogen evolution in water under UV light irradiation.