bluuebunny/crossref_metadata_2025_split huggingface dataset:
Volatile compounds emission from teratogenic human pluripotent stem cells observed during their differentiation in vivo
Authors: Capuano Rosamaria , Spitalieri Paola , Talarico Rosa Valentina , Catini Alexandro , Domakoski Ana Carolina , Martinelli Eugenio , Scioli Maria Giovanna , Orlandi Augusto , Cicconi Rosella , Paolesse Roberto , Novelli Giuseppe , Di Natale Corrado , Sangiuolo Federica 
Published: July 2018

AbstractSeveral investigations point out that the volatile fraction of metabolites, often called volatilome, might signal the difference processes occurring in living beings, both in vitro and in vivo. These studies have been recently applied to stem cells biology, and preliminary results show that the composition of the volatilome of stem cells in vitro changes along the differentiation processes leading from pluripotency to full differentiation. The identification of pluripotent stem cells is of great importance to improve safety in regenerative medicine avoiding the formation of teratomas. In this paper, we applied gas chromatography and gas sensor array to the study of the volatilome released by mice transplanted with human induced pluripotent stem cells (hiPSCs) or embryoid bodies (EBs) derived from hiPSCs at 5 days and spontaneously differentiated cells at 27 day. Gas chromatography analysis finds that, in mice transplanted with hiPSCs, the abundance of 13 volatile compounds increases four weeks after the implant and immediately before the formation of malignant teratomas (grade 3) become observable. The same behaviour is also followed by the signals of the gas sensors. Besides this event, the gas-chromatograms and the sensors signals do not show any appreciable variation related neither among the groups of transplanted mice nor respect to a placebo population. This is the first in vivo observation of the change of volatile metabolites released by human induced pluripotent stem cells and hiPSCs-derived cells during the differentiation process. These results shed further light on the differentiation mechanisms of stem cells and suggest possible applications for diagnostic purposes for an early detection of tumor relapse after surgery.
Computing Resonant Inelastic X-Ray Scattering Spectra Using The Density Matrix Renormalization Group Method
Authors: Nocera A. , Kumar U. , Kaushal N. , Alvarez G. , Dagotto E. , Johnston S. 
Published: July 2018

AbstractWe present a method for computing the resonant inelastic x-ray scattering (RIXS) spectra in one-dimensional systems using the density matrix renormalization group (DMRG) method. By using DMRG to address this problem, we shift the computational bottleneck from the memory requirements associated with exact diagonalization (ED) calculations to the computational time associated with the DMRG algorithm. This approach is then used to obtain RIXS spectra on cluster sizes well beyond state-of-the-art ED techniques. Using this new procedure, we compute the low-energy magnetic excitations observed in Cu L-edge RIXS for the challenging corner shared CuO4 chains, both for large multi-orbital clusters and downfolded t-J chains. We are able to directly compare results obtained from both models defined in clusters with identical momentum resolution. In the strong coupling limit, we find that the downfolded t-J model captures the main features of the magnetic excitations probed by RIXS only after a uniform scaling of the spectra is made.
Biostatistics mining associated method identifies AKR1B10 enhancing hepatocellular carcinoma cell growth and degenerated by miR-383-5p
Authors: Wang Junqing , Zhou Yunyun , Fei Xiaochun , Chen Xuehua , Chen Yongjun 
Published: July 2018

AbstractPrevious studies have reported that the aberrantly expressed AKR1B10 is associated with many cancer development, however the functional roles of AKR1B10 and its regulatory mechanisms in hepatocellular carcinoma (HCC) have been limited studied. In this project, we identified AKR1B10 functional as an oncogene in HCC through tumor/normal human tissue comparison from both GEO microarray and TCGA RNAseq dataset. Further experimental validations from three HCC cell lines (SMMC-7721, HePG2 and HeP3B) also suggested the ontogenetic functions of AKR1B10 in HCC tumor growth. By knocking down AKR1B10 through shRNA in HCC HeP3B cells, we showed it significantly induced cell cycle arrest and inhibited cell growth. Interestingly, integrative analysis of TCGA RNAseq data and miRNA-seq data predicted that miR-383-5p, a novel post-transcriptional tumor suppressor, is negatively associated with AKR1B10 expression. To further investigate the role of miR-383-5p in regulating AKR1B10 in HCC, we performed Dual-luciferase reporter assay experiments. Results showed that miR-383-5p is an upstream modulator targeting AKR1B10 in the post-transcriptional stage. Thus, we report AKR1B10 modulated regulated by miR-383-5p, promotes HCC tumor progress, and could be potentially a therapeutic target for precision medicine in HCC.
Adaptive Genetic Algorithm for Optical Metasurfaces Design
Authors: Jafar-Zanjani Samad , Inampudi Sandeep , Mosallaei Hossein 
Published: July 2018

AbstractAs optical metasurfaces become progressively ubiquitous, the expectations from them are becoming increasingly complex. The limited number of structural parameters in the conventional metasurface building blocks, and existing phase engineering rules do not completely support the growth rate of metasurface applications. In this paper, we present digitized-binary elements, as alternative high-dimensional building blocks, to accommodate the needs of complex-tailorable-multifunctional applications. To design these complicated platforms, we demonstrate adaptive genetic algorithm (AGA), as a powerful evolutionary optimizer, capable of handling such demanding design expectations. We solve four complex problems of high current interest to the optics community, namely, a binary-pattern plasmonic reflectarray with high tolerance to fabrication imperfections and high reflection efficiency for beam-steering purposes, a dual-beam aperiodic leaky-wave antenna, which diffracts TE and TM excitation waveguides modes to arbitrarily chosen directions, a compact birefringent all-dielectric metasurface with finer pixel resolution compared to canonical nano-antennas, and a visible-transparent infrared emitting/absorbing metasurface that shows high promise for solar-cell cooling applications, to showcase the advantages of the combination of binary-pattern metasurfaces and the AGA technique. Each of these novel applications encounters computational and fabrication challenges under conventional design methods, and is chosen carefully to highlight one of the unique advantages of the AGA technique. Finally, we show that large surplus datasets produced as by-products of the evolutionary optimizers can be employed as ingredients of the new-age computational algorithms, such as, machine learning and deep leaning. In doing so, we open a new gateway of predicting the solution to a problem in the fastest possible way based on statistical analysis of the datasets rather than researching the whole solution space.
Novel interactomics approach identifies ABCA1 as direct target of evodiamine, which increases macrophage cholesterol efflux
Authors: Wang Limei , Eftekhari Pierre , Schachner Daniel , Ignatova Irena D. , Palme Veronika , Schilcher Nicole , Ladurner Angela , Heiss Elke H. , Stangl Herbert , Dirsch Verena M. , Atanasov Atanas G. 
Published: July 2018

AbstractEvodiamine, a bioactive alkaloid from the fruits of the traditional Chinese medicine Evodia rutaecarpa (Juss.) Benth. (Fructus Evodiae, Wuzhuyu), recently gained attention as a dietary supplement for weight loss and optimization of lipid metabolism. In light of its use by patients and consumers, there is an urgent need to elucidate the molecular targets affected by this natural product. Using a novel interactomics approach, the Nematic Protein Organisation Technique (NPOT), we report the identification of ATP-binding cassette transporter A1 (ABCA1), a key membrane transporter contributing to cholesterol efflux (ChE), as a direct binding target of evodiamine. The binding of evodiamine to ABCA1 is confirmed by surface plasmon resonance (SPR) experiments. Examining the functional consequences of ABCA1 binding reveals that evodiamine treatment results in increased ABCA1 stability, elevated cellular ABCA1 protein levels, and ultimately increased ChE from THP-1-derived human macrophages. The protein levels of other relevant cholesterol transporters, ABCG1 and SR-B1, remain unaffected in the presence of evodiamine, and the ABCA1 mRNA level is also not altered.
A novel calix[4]pyrrole derivative as a potential anticancer agent that forms genotoxic adducts with DNA
Authors: Geretto Marta , Ponassi Marco , Casale Martina , Pulliero Alessandra , Cafeo Grazia , Malagreca Ferdinando , Profumo Aldo , Balza Enrica , Bersimbaev Rakhmetkazhi , Kohnke Franz Heinrich , Rosano Camillo , Izzotti Alberto 
Published: July 2018

Abstractmeso-(p-acetamidophenyl)-calix[4]pyrrole 3 was found to exhibit remarkable cytotoxicity towards A549 cancer cells. A comparative study including the isomer of 3meso-(m-acetamidophenyl)-calix[4]pyrrole 5, as well as molecules containing ‘fragments’ of these structures, demonstrated that both the calix[4]pyrrole and the acetamidophenyl units are essential for high cytotoxicity. Although calix[4]pyrroles and other anion-complexing ionophores have recently been reported to induce apoptosis by perturbing cellular chloride concentrations, in our study an alternative mechanism has emerged, as proven by the isolation of covalent DNA adducts revealed by the 32P postlabelling technique. Preliminary pharmacokinetic studies indicate that 3 is able to cross the Blood-Brain-Barrier, therefore being a potential drug that could kill primary and brain metastatic cancer cells simultaneously.
Mapping the genetic basis of breast microcalcifications and their role in metastasis
Authors: Rizwan Asif , Paidi Santosh Kumar , Zheng Chao , Cheng Menglin , Barman Ishan , Glunde Kristine 
Published: July 2018

AbstractBreast cancer screening and early stage diagnosis is typically performed by X-ray mammography, which detects microcalcifications. Despite being one of the most reliable features of nonpalpable breast cancer, the processes by which these microcalcifications form are understudied and largely unknown. In the current work, we have investigated the genetic drivers for the formation of microcalcifications in breast cancer cell lines, and have investigated their involvement in disease progression. We have shown that stable silencing of the Osteopontin (OPN) gene decreased the formation of hydroxyapatite in MDA-MB-231 breast cancer cells in response to osteogenic cocktail. In addition, OPN silencing reduced breast cancer cell migration. Furthermore, breast cancer cells that had spontaneously metastasized to the lungs in a mouse model of breast cancer had largely elevated OPN levels, while circulating tumor cells in the same mouse model contained intermediately increased OPN levels as compared to parental cells. The observed dual roles of the OPN gene reveal the existence of a direct relationship between calcium deposition and the ability of breast cancer cells to metastasize to distant organs, mediated by common genetic factors.
Comparative transcriptome analysis of field- and chamber-grown samples of Colobanthus quitensis (Kunth) Bartl, an Antarctic flowering plant
Authors: Cho Sung Mi , Lee Hyoungseok , Jo Hojin , Lee Horim , Kang Yoonjee , Park Hyun , Lee Jungeun 
Published: July 2018

AbstractColobanthus quitensisis one of the two vascular plants inhabiting the Antarctic. In natural habitats, it grows in the form of a cushion or mats, commonly observed in high latitudes or alpine vegetation. Although this species has been investigated over many years to study its geographical distribution and physiological adaptations to climate change, very limited genetic information is available. The high-throughput sequencing with ade novoassembly analysis yielded 47,070 contigs with blast-hits. Through the functional classification and enrichment analysis, we identified that photosynthesis and phenylpropanoid pathway genes show differential expression depending on the habitat environment. We found that the known ‘plant core environmental stress response (PCESR)’ genes were abundantly expressed in Antarctic samples, and confirmed that their expression is mainly induced by low-temperature. In addition, we suggest that differential expression of thermomorphogenesis-related genes may contribute to phenotypic plasticity of the plant, for instance, displaying a cushion-like phenotype to adapt to harsh environments.
Heterotic loci identified for maize kernel traits in two chromosome segment substitution line test populations
Authors: Wang Yafei , Zhang Xiangge , Shi Xia , Sun Canran , Jin Jiao , Tian Runmiao , Wei Xiaoyi , Xie Huiling , Guo Zhanyong , Tang Jihua 
Published: July 2018

AbstractHeterosis has been widely used to increase grain quality and yield, but its genetic mechanism remains unclear. In this study, the genetic basis of heterosis for four maize kernel traits was examined in two test populations constructed using a set of 184 chromosome segment substitution lines (CSSLs) and two inbred lines (Zheng58 and Xun9058) in two environments. 63 and 57 different heterotic loci (HL) were identified for four kernel traits in the CSSLs × Zheng58 and CSSLs × Xun9058 populations, respectively. Of these, nine HL and six HL were identified for four kernel traits in the CSSLs × Zheng58 and CSSLs × Xun9058 populations, at the two locations simultaneously. Comparative analysis of the HL for the four kernel traits identified only 21 HL in the two test populations simultaneously. These results showed that most HL for the four kernel traits differed between the two test populations. The common HL were important loci from the Reid × Tangsipingtou heterotic model, and could be used to predict hybrid performance in maize breeding.
Coherence as resource in scattering quantum walk search on complete graph
Authors: Su Yun-Long , Liu Si-Yuan , Wang Xiao-Hui , Fan Heng , Yang Wen-Li 
Published: July 2018

AbstractWe investigate the behavior of coherence in scattering quantum walk search on complete graph under the condition that the total number of vertices of the graph is significantly larger than the marked number of vertices we are searching, N ≫ v. We find that the consumption of coherence represents the increase of the success probability for the searching, also it is related to the efficiency of the algorithm in oracle queries. If no coherence is consumed or an incoherent state is utilized, the algorithm will behave as the classical blind search, implying that coherence is responsible for the speed-up in this quantum algorithm over its classical counterpart. The effect of noises, in particular of photon loss and random phase shifts, on the performance of algorithm is studied. Two types of noise are considered because they arise in the optical network used for experimental realization of scattering quantum walk. It is found that photon loss will reduce the coherence and random phase shifts will hinder the interference between the edge states, both leading to lower success probability compared with the noise-free case. We then conclude that coherence plays an essential role and is responsible for the speed-up in this quantum algorithm.
Exposure to galactic cosmic radiation compromises DNA repair and increases the potential for oncogenic chromosomal rearrangement in bronchial epithelial cells
Authors: Li Z. , Jella K. K. , Jaafar L. , Li S. , Park S. , Story M. D. , Wang H. , Wang Y. , Dynan W. S. 
Published: July 2018

AbstractParticipants in deep space missions face protracted exposure to galactic cosmic radiation (GCR). In this setting, lung cancer is a significant component of the overall risk of radiation-exposure induced death. Here we investigate persistent effects of GCR exposure on DNA repair capacity in lung-derived epithelial cells, using an enzyme-stimulated chromosomal rearrangement as an endpoint. Replicate cell cultures were irradiated with energetic 48Ti ions (a GCR component) or reference γ-rays. After a six-day recovery, they were challenged by expression of a Cas9/sgRNA pair that creates double-strand breaks simultaneously in the EML4 and ALK loci, misjoining of which creates an EML4-ALK fusion oncogene. Misjoining was significantly elevated in 48Ti-irradiated populations, relative to the baseline rate in mock-irradiated controls. The effect was not seen in γ-ray irradiated populations exposed to equal or higher radiation doses. Sequence analysis of the EML4-ALK joints from 48Ti-irradiated cultures showed that they were far more likely to contain deletions, sometimes flanked by short microhomologies, than equivalent samples from mock-irradiated cultures, consistent with a shift toward error-prone alternative nonhomologous end joining repair. Results suggest a potential mechanism by which a persistent physiological effect of GCR exposure may increase lung cancer risk.
Social context influences the expression of DNA methyltransferase genes in the honeybee
Authors: Cardoso-Júnior Carlos Antônio Mendes , Eyer Michael , Dainat Benjamin , Hartfelder Klaus , Dietemann Vincent 
Published: July 2018

AbstractDNA methylation is a reversible epigenetic modification that alters gene expression without altering the nucleotide sequence. Epigenetic modifications have been suggested as crucial mediators between social interactions and gene expression in mammals. However, little is known about the role of DNA methylation in the life cycle of social invertebrates. Recently, honeybees have become an attractive model to study epigenetic processes in social contexts. Although DNA methyltransferase (DNMT) enzymes responsible for DNA methylation are known in this model system, the influence of social stimuli on this process remains largely unexplored. By quantifying the expression of DNMT genes (dnmt1a, dnmt2 and dnmt3) under different demographical conditions characterized by the absence or presence of immatures and young adults, we tested whether the social context affected the expression of DNMT genes. The three DNMT genes had their expression altered, indicating that distinct molecular processes were affected by social interactions. These results open avenues for future investigations into regulatory epigenetic mechanisms underlying complex traits in social invertebrates.
Role of extrinsic mechanical force in the development of the RA-I tactile mechanoreceptor
Authors: Pham Trung Quang , Kawaue Takumi , Hoshi Takayuki , Tanaka Yoshihiro , Miyata Takaki , Sano Akihito 
Published: July 2018

AbstractRapidly adapting type I (RA-I) mechanoreceptors play an important role in sensing the low-frequency vibration aspects of touch. The structure of the RA-I mechanoreceptor is extremely complex regardless of its small size, limiting our understanding of its mechanotransduction. As a result of the emergence of bioengineering, we previously proposed an in vitro bioengineering approach for RA-I receptors to overcome this limitation. Currently, the in vitro bioengineering approach for the RA-I receptor is not realizable given the lack of knowledge of its morphogenesis. This paper demonstrates our first attempt to interpret the cellular morphogenesis of the RA-I receptor. We found indications of extrinsic mechanical force nearby the RA-I receptor in the developing fingertip. Using a mechanical compression device, the axon of dorsal root ganglion (DRG) neurons buckled in vitro into a profile that resembled the morphology of the RA-I receptor. This work encourages further implementation of this bioengineering approach in tactile receptor-related research.
Topical Curcumin Nanocarriers are Neuroprotective in Eye Disease
Authors: Davis Benjamin M. , Pahlitzsch Milena , Guo Li , Balendra Shiama , Shah Parth , Ravindran Nivedita , Malaguarnera Giulia , Sisa Claudia , Shamsher Ehtesham , Hamze Hisham , Noor Abdinasir , Sornsute Acom , Somavarapu Satyanarayana , Cordeiro M. Francesca 
Published: July 2018

AbstractCurcumin (1,7-bis-(4-hydroxy-3-methoxyphenyl)-1,6-heptadiene-3,5dione) is a polyphenol extracted from turmeric that has long been advocated for the treatment of a variety of conditions including neurodegenerative and inflammatory disorders. Despite this promise, the clinical use of curcumin has been limited by the poor solubility and low bioavailability of this molecule. In this article, we describe a novel nanocarrier formulation comprising Pluronic-F127 stabilised D-α-Tocopherol polyethene glycol 1000 succinate nanoparticles, which were used to successfully solubilize high concentrations (4.3 mg/mL) of curcumin. Characterisation with x-ray diffraction and in vitro release assays localise curcumin to the nanocarrier interior, with each particle measuring <20 nm diameter. Curcumin-loaded nanocarriers (CN) were found to significantly protect against cobalt chloride induced hypoxia and glutamate induced toxicity in vitro, with CN treatment significantly increasing R28 cell viability. Using established glaucoma-related in vivo models of ocular hypertension (OHT) and partial optic nerve transection (pONT), topical application of CN twice-daily for three weeks significantly reduced retinal ganglion cell loss compared to controls. Collectively, these results suggest that our novel topical CN formulation has potential as an effective neuroprotective therapy in glaucoma and other eye diseases with neuronal pathology.
Interleukin-27 controls basal pain threshold in physiological and pathological conditions
Authors: Sasaguri Tomoko , Taguchi Toru , Murata Yuzo , Kobayashi Kimiko , Iizasa Sayaka , Iizasa Ei’ichi , Tsuda Makoto , Hirakawa Naomi , Hara Hiromitsu , Yoshida Hiroki , Yasaka Toshiharu 
Published: July 2018

AbstractNumerous studies have shown that pain sensation is affected by various immune molecules, such as cytokines, in tissues comprising the sensory pathway. Specifically, it has been shown that interleukin (IL)-17 promotes pain behaviour, but IL-10 suppresses it. IL-27 has been reported to have an anti-inflammatory effect through regulation of T cell differentiation, resulting in reduced IL-17 and induction of IL-10. Thus, we hypothesised that IL-27 would have some regulatory role in pain sensation. Here, we provide evidence that endogenous IL-27 constitutively controls thresholds for thermal and mechanical sensation in physiological and pathological conditions. Mice lacking IL-27 or its receptor WSX-1 spontaneously showed chronic pain-like hypersensitivity. Reconstitution of IL-27 in IL-27-deficient mice reversed thermal and mechanical hypersensitive behaviours. Thus, unlike many other cytokines induced by inflammatory events, IL-27 appears to be constitutively produced and to control pain sensation. Furthermore, mice lacking IL-27/WSX-1 signalling showed additional hypersensitivity when subjected to inflammatory or neuropathic pain models. Our results suggest that the mechanisms underlying hypersensitive behaviours caused by the ablation of IL-27/WSX-1 signalling are different from those underlying established chronic pain models. This novel pain control mechanism mediated by IL-27 might indicate a new mechanism for the chronic pain hypersensitivity.