bluuebunny/crossref_metadata_2025_split huggingface dataset:
miR-125b-5p enhances chemotherapy sensitivity to cisplatin by down-regulating Bcl2 in gallbladder cancer
Authors: Yang Dong , Zhan Ming , Chen Tao , Chen Wei , Zhang Yunhe , Xu Sunwang , Yan Jinchun , Huang Qihong , Wang Jian 
Published: March 2017

AbstractGallbladder cancer represents the most common malignancy of the biliary tract and is highly lethal with less than 5% overall 5-year survival rate. Chemotherapy remains the major treatment for late-stage patients. However, insensitivity to these chemotherapeutic agents including cisplatin is common. MicroRNAs (miRNAs) have been shown as modulators of drug resistance in many cancer types. We used genome-wide gene expression analysis in clinical samples to identify miR-125b-5p down-regulated in gallbladder cancer. miR-125b-5p up-regulation promoted cell death in gallbladder cancer cells in the presence of cisplatin. In contrast, knockdown of miR-125b-5p reduced cell death in gallbladder cancer cells treated with cisplatin. Up-regulation of miR-125b-5p significantly decreased tumor growth in combination with cisplatin in a mouse model. We identified Bcl2 as a direct target of miR-125b-5p which mediates the function of miR-125b-5p in gallbladder cancer. In clinical samples, miR-125b-5p was down-regulated in gallbladder cancer whereas Bcl2 was up-regulated and their expression was inversely correlated. Moreover, low miR-125b-5p expression or high expression of Bcl2 is correlated with poor prognosis in gallbladder cancer. Taken together, our findings indicate that miR-125b-5p is a potent chemotherapy sensitizer and may function as a new biomarker for the prognosis of gallbladder cancer patients.
Autophagy down regulates pro-inflammatory mediators in BV2 microglial cells and rescues both LPS and alpha-synuclein induced neuronal cell death
Authors: Bussi Claudio , Peralta Ramos Javier Maria , Arroyo Daniela S. , Gaviglio Emilia A. , Gallea Jose Ignacio , Wang Ji Ming , Celej Maria Soledad , Iribarren Pablo 
Published: March 2017

AbstractAutophagy is a fundamental cellular homeostatic mechanism, whereby cells autodigest parts of their cytoplasm for removal or turnover. Neurodegenerative disorders are associated with autophagy dysregulation, and drugs modulating autophagy have been successful in several animal models. Microglial cells are phagocytes in the central nervous system (CNS) that become activated in pathological conditions and determine the fate of other neural cells. Here, we studied the effects of autophagy on the production of pro-inflammatory molecules in microglial cells and their effects on neuronal cells. We observed that both trehalose and rapamycin activate autophagy in BV2 microglial cells and down-regulate the production of pro-inflammatory cytokines and nitric oxide (NO), in response to LPS and alpha-synuclein. Autophagy also modulated the phosphorylation of p38 and ERK1/2 MAPKs in BV2 cells, which was required for NO production. These actions of autophagy modified the impact of microglial activation on neuronal cells, leading to suppression of neurotoxicity. Our results demonstrate a novel role for autophagy in the regulation of microglial cell activation and pro-inflammatory molecule secretion, which may be important for the control of inflammatory responses in the CNS and neurotoxicity.
Production of the medaka derived from vitrified whole testes by germ cell transplantation
Authors: Seki Shinsuke , Kusano Kazunari , Lee Seungki , Iwasaki Yoshiko , Yagisawa Masaru , Ishida Mariko , Hiratsuka Tadashi , Sasado Takao , Naruse Kiyoshi , Yoshizaki Goro 
Published: March 2017

AbstractThe medaka (Oryzias latipes) is a teleost model distinguished from other model organisms by the presence of inbred strains, wild stocks, and related species. Cryopreservation guarantees preservation of these unique biological resources. However, because of their large size, cryopreservation techniques for their eggs and embryos have not been established. In the present study, we established a methodology to produce functional gametes from cryopreserved testicular cells (TCs). Whole testes taken from medaka were cryopreserved by vitrification. After thawing, the cells dissociated from cryopreserved testicular tissues were intraperitoneally transplanted into sterile triploid hatchlings. Some cells, presumably spermatogonial stem cells, migrated into the genital ridges of recipients and resulted in the production of eggs or sperm, based on sex of the recipient. Mating of recipients resulted in successful production of cryopreserved TC-derived offspring. We successfully produced individuals from the Kaga inbred line, an endangered wild population in Tokyo, and a sub-fertile mutant (wnt4b−/−) from cryopreserved their TCs. This methodology facilitates semi-permanent preservation of various medaka strains.
Limitations and challenges of genetic barcode quantification
Authors: Thielecke Lars , Aranyossy Tim , Dahl Andreas , Tiwari Rajiv , Roeder Ingo , Geiger Hartmut , Fehse Boris , Glauche Ingmar , Cornils Kerstin 
Published: March 2017

AbstractGenetic barcodes are increasingly used to track individual cells and to quantitatively assess their clonal contributions over time. Although barcode quantification relies entirely on counting sequencing reads, detailed studies about the method’s accuracy are still limited. We report on a systematic investigation of the relation between barcode abundance and resulting read counts after amplification and sequencing using cell-mixtures that contain barcodes with known frequencies (“miniBulks”). We evaluated the influence of protocol modifications to identify potential sources of error and elucidate possible limitations of the quantification approach. Based on these findings we designed an advanced barcode construct (BC32) to improved barcode calling and quantification, and to ensure a sensitive detection of even highly diluted barcodes. Our results emphasize the importance of using curated barcode libraries to obtain interpretable quantitative data and underline the need for rigorous analyses of any utilized barcode library in terms of reliability and reproducibility.
Multistability of the Brain Network for Self-other Processing
Authors: Chen Yi-An , Huang Tsung-Ren 
Published: March 2017

AbstractEarly fMRI studies suggested that brain areas processing self-related and other-related information were highly overlapping. Hypothesising functional localisation of the cortex, researchers have tried to locate “self-specific” and “other-specific” regions within these overlapping areas by subtracting suspected confounding signals in task-based fMRI experiments. Inspired by recent advances in whole-brain dynamic modelling, we instead explored an alternative hypothesis that similar spatial activation patterns could be associated with different processing modes in the form of different synchronisation patterns. Combining an automated synthesis of fMRI data with a presumption-free diffusion spectrum image (DSI) fibre-tracking algorithm, we isolated a network putatively composed of brain areas and white matter tracts involved in self-other processing. We sampled synchronisation patterns from the dynamical systems of this network using various combinations of physiological parameters. Our results showed that the self-other processing network, with simulated gamma-band activity, tended to stabilise at a number of distinct synchronisation patterns. This phenomenon, termed “multistability,” could serve as an alternative model in theorising the mechanism of processing self-other information.
An association between time-varying serum alkaline phosphatase concentrations and mortality rate in patients undergoing peritoneal dialysis: a five-year cohort study
Authors: Liu Ying , Zhu Jin-Gang , Cheng Ben-Chung , Liao Shang-Chih , Lee Chih-Hsiung , Chang Wen Xiu , Chen Jin-Bor 
Published: March 2017

AbstractThe relationship between serum alkaline phosphatase (ALP) concentrations and mortality in peritoneal dialysis (PD) patients is rarely reported. We enrolled 667 PD patients in one PD centre in Taiwan to retrospectively examine the association between three ALP concentrations (baseline, time-averaged, time-dependent) and mortality over a 5-year period (2011–2015). Baseline data collection included demographics, clinical, and laboratory parameters. Multivariable-adjusted Cox models were used to analyse the association. Four ALP quartiles were defined at the baseline: ≤62, 63–82, 83–118, and ≥119 U/L. Of 667 patients, 65 patients died, of which 8 patients died due to cardiovascular disease. Females were predominant in the higher ALP quartiles, and 24-h urine volume was significantly proportionately decreased in the higher ALP quartiles. ALP quartiles expressed by the three models were not associated with all-cause or cardiovascular mortalities after adjusting for demographics, liver function, bone metabolism, mortality, hemoglobin, and 24-h urine volume. In conclusion, ALP concentrations were not associated with death risk in PD patients over the 5-year period.
An inflammatory gene signature distinguishes neurofibroma Schwann cells and macrophages from cells in the normal peripheral nervous system
Authors: Choi Kwangmin , Komurov Kakajan , Fletcher Jonathan S. , Jousma Edwin , Cancelas Jose A. , Wu Jianqiang , Ratner Nancy 
Published: March 2017

AbstractNeurofibromas are benign peripheral nerve tumors driven by NF1 loss in Schwann cells (SCs). Macrophages are abundant in neurofibromas, and macrophage targeted interventions may have therapeutic potential in these tumors. We generated gene expression data from fluorescence-activated cell sorted (FACS) SCs and macrophages from wild-type and mutant nerve and neurofibroma to identify candidate pathways involved in SC-macrophage cross-talk. While in 1-month-old Nf1 mutant nerve neither SCs nor macrophages significantly differed from their normal counterparts, both macrophages and SCs showed significantly altered cytokine gene expression in neurofibromas. Computationally reconstructed SC-macrophage molecular networks were enriched for inflammation-associated pathways. We verified that neurofibroma SC conditioned medium contains macrophage chemo-attractants including colony stimulation factor 1 (CSF1). Network analysis confirmed previously implicated pathways and predict novel paracrine and autocrine loops involving cytokines, chemokines, and growth factors. Network analysis also predicted a central role for decreased type-I interferon signaling. We validated type-I interferon expression in neurofibroma by protein profiling, and show that treatment of neurofibroma-bearing mice with polyethylene glycolyated (PEGylated) type-I interferon-α2b reduces the expression of many cytokines overexpressed in neurofibroma. These studies reveal numerous potential targetable interactions between Nf1 mutant SCs and macrophages for further analyses.
Insula and somatosensory cortical myelination and iron markers underlie individual differences in empathy
Authors: Allen Micah , Frank Darya , Glen James C. , Fardo Francesca , Callaghan Martina F. , Rees Geraint 
Published: March 2017

AbstractEmpathy is a key component of our ability to engage and interact with others. In recent years, the neural mechanisms underlying affective and cognitive empathy have garnered intense interest. This work demonstrates that empathy for others depends upon a distributed network of regions such as the insula, parietal cortex, and somatosensory areas, which are also activated when we ourselves experience an empathized-with emotion (e.g., pain). Individuals vary markedly in their ability to empathize with others, which predicts the tendency to help others and relates to individual differences in the neuroanatomy of these areas. Here, we use a newly developed, high-resolution (800 μm isotropic), quantitative MRI technique to better elucidate the neuroanatomical underpinnings of individual differences in empathy. Our findings extend previous studies of the neuroanatomical correlates of cognitive and affective empathy. In particular, individual differences in cognitive empathy were associated with markers of myeloarchitectural integrity of the insular cortex, while affective empathy was predicted by a marker of iron content in second somatosensory cortex. These results indicate potential novel biomarkers of trait empathy, suggesting that microstructural features of an empathy and body-related network are crucial for understanding the mental and emotional states of others.
Antimicrobial efficacy against Pseudomonas aeruginosa biofilm formation in a three-dimensional lung epithelial model and the influence of fetal bovine serum
Authors: Crabbé Aurélie , Liu Yulong , Matthijs Nele , Rigole Petra , De La Fuente-Nùñez César , Davis Richard , Ledesma Maria A. , Sarker Shameema , Van Houdt Rob , Hancock Robert E. W. , Coenye Tom , Nickerson Cheryl A. 
Published: March 2017

AbstractIn vitro models that mimic in vivo host-pathogen interactions are needed to evaluate candidate drugs that inhibit bacterial virulence traits. We established a new approach to study Pseudomonas aeruginosa biofilm susceptibility on biotic surfaces, using a three-dimensional (3-D) lung epithelial cell model. P. aeruginosa formed antibiotic resistant biofilms on 3-D cells without affecting cell viability. The biofilm-inhibitory activity of antibiotics and/or the anti-biofilm peptide DJK-5 were evaluated on 3-D cells compared to a plastic surface, in medium with and without fetal bovine serum (FBS). In both media, aminoglycosides were more efficacious in the 3-D cell model. In serum-free medium, most antibiotics (except polymyxins) showed enhanced efficacy when 3-D cells were present. In medium with FBS, colistin was less efficacious in the 3-D cell model. DJK-5 exerted potent inhibition of P. aeruginosa association with both substrates, only in serum-free medium. DJK-5 showed stronger inhibitory activity against P. aeruginosa associated with plastic compared to 3-D cells. The combined addition of tobramycin and DJK-5 exhibited more potent ability to inhibit P. aeruginosa association with both substrates. In conclusion, lung epithelial cells influence the efficacy of most antimicrobials against P. aeruginosa biofilm formation, which in turn depends on the presence or absence of FBS.
Terahertz metamaterials and systems based on rolled-up 3D elements: designs, technological approaches, and properties
Authors: Prinz Victor Ya. , Naumova Elena V. , Golod Sergey V. , Seleznev Vladimir A. , Bocharov Andrey A. , Kubarev Vitaliy V. 
Published: March 2017

AbstractElectromagnetic metamaterials opened the way to extraordinary manipulation of radiation. Terahertz (THz) and optical metamaterials are usually fabricated by traditional planar-patterning approaches, while the majority of practical applications require metamaterials with 3D resonators. Making arrays of precise 3D micro- and nanoresonators is still a challenging problem. Here we present a versatile set of approaches to fabrication of metamaterials with 3D resonators rolled-up from strained films, demonstrate novel THz metamaterials/systems, and show giant polarization rotation by several chiral metamaterials/systems. The polarization spectra of chiral metamaterials on semiconductor substrates exhibit ultrasharp quasiperiodic peaks. Application of 3D printing allowed assembling more complex systems, including the bianisotropic system with optimal microhelices, which showed an extreme polarization azimuth rotation of 85° with drop by 150° at a frequency shift of 0.4%. We refer the quasiperiodic peaks in the polarization spectra of metamaterial systems to the interplay of different resonances, including peculiar chiral waveguide resonance. Formed metamaterials cannot be made by any other presently available technology. All steps of presented fabrication approaches are parallel, IC-compatible and allow mass fabrication with scaling of rolled-up resonators up to visible frequencies. We anticipate that the rolled-up meta-atoms will be ideal building blocks for future generations of commercial metamaterials, devices and systems on their basis.
Recovering the quantum formalism from physically realist axioms
Authors: Auffèves Alexia , Grangier Philippe 
Published: March 2017

AbstractWe present a heuristic derivation of Born’s rule and unitary transforms in Quantum Mechanics, from a simple set of axioms built upon a physical phenomenology of quantization. This approach naturally leads to the usual quantum formalism, within a new realistic conceptual framework that is discussed in details. Physically, the structure of Quantum Mechanics appears as a result of the interplay between the quantized number of “modalities” accessible to a quantum system, and the continuum of “contexts” that are required to define these modalities. Mathematically, the Hilbert space structure appears as a consequence of a specific “extra-contextuality” of modalities, closely related to the hypothesis of Gleason’s theorem, and consistent with its conclusions.
Capillary flow-driven microfluidic device with wettability gradient and sedimentation effects for blood plasma separation
Authors: Maria M. Sneha , Rakesh P. E. , Chandra T. S. , Sen A. K. 
Published: March 2017

AbstractWe report a capillary flow-driven microfluidic device for blood-plasma separation that comprises a cylindrical well between a pair of bottom and top channels. Exposure of the well to oxygen-plasma creates wettability gradient on its inner surface with its ends hydrophilic and middle portion hydrophobic. Due to capillary action, sample blood self-infuses into bottom channel and rises up the well. Separation of plasma occurs at the hydrophobic patch due to formation of a ‘self-built-in filter’ and sedimentation. Capillary velocity is predicted using a model and validated using experimental data. Sedimentation of RBCs is explained using modified Steinour’s model and correlation between settling velocity and liquid concentration is found. Variation of contact angle on inner surface of the well is characterized and effects of well diameter and height and dilution ratio on plasma separation rate are investigated. With a well of 1.0 mm diameter and 4.0 mm height, 2.0 μl of plasma was obtained (from <10 μl whole blood) in 15 min with a purification efficiency of 99.9%. Detection of glucose was demonstrated with the plasma obtained. Wetting property of channels was maintained by storing in DI water under vacuum and performance of the device was found to be unaffected over three weeks.
Insights into the sonochemical synthesis and properties of salt-free intrinsic plutonium colloids
Authors: Dalodière Elodie , Virot Matthieu , Morosini Vincent , Chave Tony , Dumas Thomas , Hennig Christoph , Wiss Thierry , Dieste Blanco Oliver , Shuh David K. , Tyliszcak Tolek , Venault Laurent , Moisy Philippe , Nikitenko Sergey I. 
Published: March 2017

AbstractFundamental knowledge on intrinsic plutonium colloids is important for the prediction of plutonium behaviour in the geosphere and in engineered systems. The first synthetic route to obtain salt-free intrinsic plutonium colloids by ultrasonic treatment of PuO2 suspensions in pure water is reported. Kinetics showed that both chemical and mechanical effects of ultrasound contribute to the mechanism of Pu colloid formation. In the first stage, fragmentation of initial PuO2 particles provides larger surface contact between cavitation bubbles and solids. Furthermore, hydrogen formed during sonochemical water splitting enables reduction of Pu(IV) to more soluble Pu(III), which then re-oxidizes yielding Pu(IV) colloid. A comparative study of nanostructured PuO2 and Pu colloids produced by sonochemical and hydrolytic methods, has been conducted using HRTEM, Pu LIII-edge XAS, and O K-edge NEXAFS/STXM. Characterization of Pu colloids revealed a correlation between the number of Pu-O and Pu-Pu contacts and the atomic surface-to-volume ratio of the PuO2 nanoparticles. NEXAFS indicated that oxygen state in hydrolytic Pu colloid is influenced by hydrolysed Pu(IV) species to a greater extent than in sonochemical PuO2 nanoparticles. In general, hydrolytic and sonochemical Pu colloids can be described as core-shell nanoparticles composed of quasi-stoichiometric PuO2 cores and hydrolyzed Pu(IV) moieties at the surface shell.
Thermographic Microstructure Monitoring in Electron Beam Additive Manufacturing
Authors: Raplee J. , Plotkowski A. , Kirka M. M. , Dinwiddie R. , Okello A. , Dehoff R. R. , Babu S. S. 
Published: March 2017

AbstractTo reduce the uncertainty of build performance in metal additive manufacturing, robust process monitoring systems that can detect imperfections and improve repeatability are desired. One of the most promising methods for in situ monitoring is thermographic imaging. However, there is a challenge in using this technology due to the difference in surface emittance between the metal powder and solidified part being observed that affects the accuracy of the temperature data collected. The purpose of the present study was to develop a method for properly calibrating temperature profiles from thermographic data to account for this emittance change and to determine important characteristics of the build through additional processing. The thermographic data was analyzed to identify the transition of material from metal powder to a solid as-printed part. A corrected temperature profile was then assembled for each point using calibrations for these surface conditions. Using this data, the thermal gradient and solid-liquid interface velocity were approximated and correlated to experimentally observed microstructural variation within the part. This work shows that by using a method of process monitoring, repeatability of a build could be monitored specifically in relation to microstructure control.
Transcriptional and post-transcriptional regulation of the ionizing radiation response by ATM and p53
Authors: Venkata Narayanan Ishwarya , Paulsen Michelle T. , Bedi Karan , Berg Nathan , Ljungman Emily A. , Francia Sofia , Veloso Artur , Magnuson Brian , di Fagagna Fabrizio d’Adda , Wilson Thomas E. , Ljungman Mats 
Published: March 2017

AbstractIn response to ionizing radiation (IR), cells activate a DNA damage response (DDR) pathway to re-program gene expression. Previous studies using total cellular RNA analyses have shown that the stress kinase ATM and the transcription factor p53 are integral components required for induction of IR-induced gene expression. These studies did not distinguish between changes in RNA synthesis and RNA turnover and did not address the role of enhancer elements in DDR-mediated transcriptional regulation. To determine the contribution of synthesis and degradation of RNA and monitor the activity of enhancer elements following exposure to IR, we used the recently developed Bru-seq, BruChase-seq and BruUV-seq techniques. Our results show that ATM and p53 regulate both RNA synthesis and stability as well as enhancer element activity following exposure to IR. Importantly, many genes in the p53-signaling pathway were coordinately up-regulated by both increased synthesis and RNA stability while down-regulated genes were suppressed either by reduced synthesis or stability. Our study is the first of its kind that independently assessed the effects of ionizing radiation on transcription and post-transcriptional regulation in normal human cells.