bluuebunny/crossref_metadata_2025_split huggingface dataset:
LINC01088 inhibits tumorigenesis of ovarian epithelial cells by targeting miR-24-1-5p
Authors: Zhang Weijiang , Fei Jing , Yu Shuqian , Shen Jiayu , Zhu Xiaoqing , Sadhukhan Annapurna , Lu Weiguo , Zhou Jianwei 
Published: February 2018

AbstractThe roles of long non-coding RNAs (lncRNAs), a class of long non-protein-coding RNAs, in the tumorigenesis of ovarian epithelial cells remain unknown. In this study, we discovered that the expression of long intergenic non-coding RNA 1088 (LINC01088) was clearly reduced in benign epithelial ovarian tumor tissues compared to matched normal ovarian tissues. This was shown by global cDNA gene chip scanning and real-time qPCR, and validated in 42 clinical specimens. Furthermore, we found that LINC01088 inhibited the growth of ovarian cancer xenografts in nude mice. Correlation analysis between LINC01088 and mircoRNAs (miRNAs) conducted using primary clinical samples and RNA co-precipitation experiments revealed that miR-24-1-5p was one of the targets of LINC01088. Overexpression of miR-24-1-5p facilitated cell proliferation both in vitro and in vivo, however, LINC01088 could partially reverse the cell proliferation induced by miR-24-1-5p. Finally, we demonstrated that p21 activated kinase 4 (PAK4) was one of the downstream key targets of miR-24-1-5p by luciferase reporter assay and Western blotting; and our results showed a remarkable decrease in cell proliferation after overexpression of PAK4. We conclude that LINC01088 might function as a tumor suppressor, inhibiting the tumorigenesis of ovarian epithelial cells through LINC01088/ miR-24-1-5p/ PAK4 axis.
Age-related changes in the response of retinal structure, function and blood flow to pressure modification in rats
Authors: Zhao Da , Nguyen Christine T. O. , He Zheng , Wong Vickie H. Y. , van Koeverden Anna K. , Vingrys Algis J. , Bui Bang V. 
Published: February 2018

AbstractAge-related changes to the balance between the pressure inside the eye (intraocular pressure, IOP) and the pressure inside the brain (intracranial pressure, ICP) can modify the risk of glaucoma. In this study, we consider whether the optic nerve in older rat eyes is more susceptible to acute IOP and ICP modification. We systematically manipulate both ICP and IOP and quantify their effects on ganglion cell function (electroretinography, ERG), optic nerve structure (optical coherence tomography, OCT) and retinal blood flow (Doppler OCT). We show that ganglion cell function in older eyes was more susceptible to a higher optic nerve pressure difference (ONPD = IOP – ICP). This age-related susceptibility could not be explained by poorer blood flow with elevated ONPD. Rather, as ONPD increased the retinal nerve fibre layer showed greater compression, and the retinal surface showed less deformation in older eyes. Our data suggest that age-related changes to connective tissues in and around the rat optic nerve make it less flexible, which may result in greater strain on ganglion cell axons. This may account for greater functional susceptibility to higher optic nerve pressure differences in older rat eyes. Further studies in a species with a well-developed lamina cribrosa are needed to determine the clinical importance of these observations.
One-step noninvasive prenatal testing (NIPT) for autosomal recessive homozygous point mutations using digital PCR
Authors: Chang Mun Young , Ahn Soyeon , Kim Min Young , Han Jin Hee , Park Hye-Rim , Seo Han Kyu , Yoon Jinsun , Lee Seungmin , Oh Doo-Yi , Kang Changsoo , Choi Byung Yoon 
Published: February 2018

AbstractPreviously, we introduced a noninvasive prenatal testing (NIPT) protocol for diagnosing compound heterozygous autosomal recessive point mutations via maternal plasma DNA and simulated control genomic DNA sampling based on fetal DNA fraction. In our present study, we have improved our NIPT protocol to make it possible to diagnose homozygous autosomal recessive point mutations without the need to acquire fetal DNA fraction. Moreover, chi-squared test and empirical statistical range based on the proportion of mutant allele reads among the total reads served as the gatekeeping method. If this method yielded inconclusive results, then the Bayesian method was performed; final conclusion was drawn from the results of both methods. This protocol was applied to three families co-segregating congenital sensorineural hearing loss with monogenic homozygous mutations in prevalent deafness genes. This protocol successfully predicted the fetal genotypes from all families without the information about fetal DNA fraction using one-step dPCR reactions at least for these three families. Furthermore, we suspect that confirmatory diagnosis under this protocol is possible, not only by using picodroplet dPCR, but also by using the more readily available chip-based dPCR, making our NIPT protocol more useful in the diagnosis of autosomal recessive point mutations in the future.
Repercussion of Solid state vs. Liquid state synthesized p-n heterojunction RGO-copper phosphate on proton reduction potential in water
Authors: Samal Alaka , Das Dipti P. , Madras Giridhar 
Published: February 2018

AbstractThe same copper phosphate catalysts were synthesized by obtaining the methods involving solid state as well as liquid state reactions in this work. And then the optimised p-n hybrid junction photocatalysts have been synthesized following the same solid/liquid reaction pathways. The synthesized copper phosphate photocatalyst has unique rod, flower, caramel-treat-like morphology. The Mott-Schottky behavior is in accordance with the expected behavior of n-type semiconductor and the carrier concentration was calculated using the M-S analysis for the photocatalyst. And for the p-n hybrid junction of 8RGO-Cu3(PO4)2-PA (PA abbreviated for photoassisted synthesis method), 8RGO-Cu3(PO4)2-EG(EG abbreviated for Ethylene Glycol based synthesis method), 8RGO-Cu3(PO4)2-PEG (PEG abbreviated for Poly(ethylene glycol)-block-poly(propylene glycol)-block-poly(ethylene glycol based synthesis method)the amount of H2 synthesized was 7500, 6500 and 4500 µmol/h/g, respectively. The excited electrons resulting after the irradiation of visible light on the CB of p-type reduced graphene oxide (RGO) migrate easily to n-type Cu3(PO4)2via. the p-n junction interfaces and hence great charge carrier separation was achieved.
Soil-borne fungi challenge the concept of long-term biochemical recalcitrance of pyrochar
Authors: De la Rosa José M. , Miller Ana Z. , Knicker Heike 
Published: February 2018

AbstractPyrogenic organic matter (PyOM) is assumed to be biochemically recalcitrant, but recent studies indicated a quick decrease of PyOM in post-fire soils. Regardless erosion and abiotic degradation, microbial decomposition has been the explanation for this response, but no direct proof has been provided up to now. In the present study, we were able to demonstrate for the first time that the soil-borne fungus Fusarium oxysporum is not only colonizing the pore system of pyrochar (PyC) but is also involved in the degradation of its aromatic network. We showed that PyC not only stimulates microbial degradation of soil organic matter (SOM), but is also attacked and decomposed by microorganisms. Our observations are based on the chemical and morphological alterations of a sewage-sludge derived PyC produced at 600 °C after its amendment to a Calcic Cambisol by solid-state 13C nuclear magnetic resonance spectroscopy, analytical pyrolysis, elemental analysis, field emission scanning electron microscopy and DNA-based analysis of the isolated fungi. We showed that biofilms detected in the PyC play an essential role in the degradation process. These results are indispensable for a reliable assessment of the carbon sequestration potential of PyC in soils but also for improving global C cycling models.
Next-generation sequencing from bulked segregant analysis identifies a dwarfism gene in watermelon
Authors: Dong Wei , Wu Defeng , Li Guoshen , Wu Dewei , Wang Zicheng 
Published: February 2018

AbstractDwarfism is one of the most valuable traits in watermelon breeding mainly because of its contribution to yield as well as the decreased labor required to cultivate and harvest smaller plants. However, the underlying genetic mechanism is unknown. In this study, a candidate dwarfism gene was identified by applying next-generation sequencing technology to analyze watermelon plants. We completed a whole-genome re-sequencing of two DNA bulks (dwarf pool and vine pool) generated from plants in an F2 population. A genome-wide analysis of single nucleotide polymorphisms resulted in the detection of a genomic region harboring the candidate dwarfism gene Cla010726. The encoded protein was predicted to be a gibberellin 20-oxidase-like protein, which is a well-known “green revolution” protein in other crops. A quantitative real-time PCR investigation revealed that the Cla010726 expression level was significantly lower in the dwarf plants than in the normal-sized plants. The SNP analysis resulted in two SNP locating in the Cla010726 gene promoter of dsh F2 individuals. The results presented herein provide preliminary evidence that Cla010726 is a possible dwarfism gene.
Identification of inorganic compounds in composite alum-treated wooden artefacts from the Oseberg collection
Authors: McQueen Caitlin M. A. , Tamburini Diego , Braovac Susan 
Published: February 2018

AbstractAlum-treated wooden artefacts from the Oseberg collection display a great deal of morphological, structural and compositional inhomogeneity. Thus, an in-depth understanding of chemical processes underlying their degradation requires consideration of a variety of local environments. In addition to alum, sources of inorganic compounds include metal parts, corrosion products of which can migrate into the surrounding wood. In order to characterise the inorganic compounds a range of local environments, samples from several locations in a selection of composite objects have been investigated by X-ray diffraction (XRD), Fourier transform infrared (FTIR) spectroscopy, Raman spectroscopy and scanning electron microscopy (SEM)-energy dispersive X-ray spectroscopy (EDS). We have found that corrosion of iron rods used in reconstruction has formed iron(II) sulfates, which have migrated into the alum-treated wood to form sulfates containing combinations of potassium, aluminium, iron(II) and iron(III) cations. Reactions of alum were also evident from the presence of alunite in some samples. Areas with significant abundances of zinc sulfates, zinc sulfide and elemental sulfur were also detected. These results provide a first-time window into the complex array of inorganic species that can be present in such composite alum-treated objects.
RHYTHM: An Open Source Imaging Toolkit for Cardiac Panoramic Optical Mapping
Authors: Gloschat Christopher , Aras Kedar , Gupta Shubham , Faye N. Rokhaya , Zhang Hanyu , Syunyaev Roman A. , Pryamonosov Roman A. , Rogers Jack , Kay Matthew W. , Efimov Igor R. 
Published: February 2018

AbstractFluorescence optical imaging techniques have revolutionized the field of cardiac electrophysiology and advanced our understanding of complex electrical activities such as arrhythmias. However, traditional monocular optical mapping systems, despite having high spatial resolution, are restricted to a two-dimensional (2D) field of view. Consequently, tracking complex three-dimensional (3D) electrical waves such as during ventricular fibrillation is challenging as the waves rapidly move in and out of the field of view. This problem has been solved by panoramic imaging which uses multiple cameras to measure the electrical activity from the entire epicardial surface. However, the diverse engineering skill set and substantial resource cost required to design and implement this solution have made it largely inaccessible to the biomedical research community at large. To address this barrier to entry, we present an open source toolkit for building panoramic optical mapping systems which includes the 3D printing of perfusion and imaging hardware, as well as software for data processing and analysis. In this paper, we describe the toolkit and demonstrate it on different mammalian hearts: mouse, rat, and rabbit.
Mutations in the Drosophila homolog of human PLA2G6 give rise to age-dependent loss of psychomotor activity and neurodegeneration
Authors: Iliadi Konstantin G. , Gluscencova Oxana B. , Iliadi Natalia , Boulianne Gabrielle L. 
Published: February 2018

AbstractInfantile neuroaxonal dystrophy (INAD) is a fatal neurodegenerative disorder that typically begins within the first few years of life and leads to progressive impairment of movement and cognition. Several years ago, it was shown that >80% of patients with INAD have mutations in the phospholipase gene, PLA2G6. Interestingly, mutations in PLA2G6 are also causative in two other related neurodegenerative diseases, atypical neuroaxonal dystrophy and Dystonia-parkinsonism. While all three disorders give rise to similar defects in movement and cognition, some defects are unique to a specific disorder. At present, the cellular mechanisms underlying PLA2G6-associated neuropathology are poorly understood and there is no cure or treatment that can delay disease progression. Here, we show that loss of iPLA2-VIA, the Drosophila homolog of PLA2G6, gives rise to age-dependent defects in climbing and spontaneous locomotion. Moreover, using a newly developed assay, we show that iPLA2-VIA mutants also display impairments in fine-tune motor movements, motor coordination and psychomotor learning, which are distinct features of PLA2G6-associated disease in humans. Finally, we show that iPLA2-VIA mutants exhibit increased sensitivity to oxidative stress, progressive neurodegeneration and a severely reduced lifespan. Altogether, these data demonstrate that Drosophila iPLA2-VIA mutants provide a useful model to study human PLA2G6-associated neurodegeneration.
Synthetic Whole-Cell Biodevices for Targeted Degradation of Antibiotics
Authors: Xia Peng-Fei , Li Qian , Tan Lin-Rui , Liu Miao-Miao , Jin Yong-Su , Wang Shu-Guang 
Published: February 2018

AbstractSynthetic biology enables infinite possibilities in biotechnology via employing genetic modules. However, not many researches have explored the potentials of synthetic biology in environmental bioprocesses. In this study, we introduced a genetic module harboring the codon-optimized tetracycline degrading gene, tetX.co, into the model host, Escherichia coli, and generated a prototypal whole-cell biodevice for the degradation of a target antibiotic. Our results suggested that E. coli with the tetX.co-module driven by either the PJ23119 or PBAD promoters conferred resistance up to 50 μg/mL of tetracycline and degrades over 95% of tetracycline within 24 h. The detoxification ability of tetX was further verified in conditioned media by typical E. coli K-12 and B strains as well as Shewanella oneidensis. Our strategy demonstrated the feasibility of introducing genetic modules into model hosts to enable environmental functions, and this work will inspire more environmental innovations through synthetic biological devices.
Energy distribution of relativistic electrons in the kiloparsec scale jet of M 87 with Chandra
Authors: Sun Xiao-Na , Yang Rui-Zhi , Rieger Frank M. , Liu Ruo-Yu , Aharonian Felix 
Published: February 2018

The X-ray emission from the jets in active galactic nuclei (AGN) carries important information on the distributions of relativistic electrons and magnetic fields on large scales. We reanalysed archival Chandra observations on the jet of M 87 from 2000 to 2016 with a total exposure of 1460 kiloseconds to explore the X-ray emission characteristics along the jet. We investigated the variability behaviours of the nucleus and the inner jet component HST-1, and confirm indications for day-scale X-ray variability in the nucleus contemporaneous to the 2010 high TeV γ-ray state. HST-1 shows a general decline in X-ray flux over the last few years consistent with its synchrotron interpretation. We extracted the X-ray spectra for the nucleus and all knots in the jet, showing that they are compatible with a single power law within the X-ray band. There are indications that the resultant X-ray photon index exhibit a trend, with slight but significant index variations ranging from ≃ 2.2 (e.g. in knot D) to ≃ 2.4−2.6 (in the outer knots F, A, and B). When viewed in a multiwavelength context, a more complex situation can be seen. Fitting the radio to X-ray spectral energy distributions (SEDs) assuming a synchrotron origin, we show that a broken power-law electron spectrum with break energy Eb around 1 (300 μG/B)1/2 TeV allows a satisfactory description of the multiband SEDs for most of the knots. However, in the case of knots B, C, and D we find indications that an additional high-energy component is needed to adequately reproduce the broad-band SEDs. We discuss the implications and suggest that a stratified jet model may account for the differences.
Reanalysis of nearby open clusters usingGaiaDR1/TGAS and HSOY
Authors: Yen Steffi X. , Reffert Sabine , Schilbach Elena , Röser Siegfried , Kharchenko Nina V. , Piskunov Anatoly E. 
Published: February 2018

Context. Open clusters have long been used to gain insights into the structure, composition, and evolution of the Galaxy. With the large amount of stellar data available for many clusters in theGaiaera, new techniques must be developed for analyzing open clusters, as visual inspection of cluster color-magnitude diagrams is no longer feasible. An automatic tool will be required to analyze large samples of open clusters.Aims. We seek to develop an automatic isochrone-fitting procedure to consistently determine cluster membership and the fundamental cluster parameters.Methods. Our cluster characterization pipeline first determined cluster membership with precise astrometry, primarily from TGAS and HSOY. With initial cluster members established, isochrones were fitted, using a χ2minimization, to the cluster photometry in order to determine cluster mean distances, ages, and reddening. Cluster membership was also refined based on the stellar photometry. We used multiband photometry, which includes ASCC-2.5BV, 2MASSJHKs, andGaia Gband.Results. We present parameter estimates for all 24 clusters closer than 333 pc as determined by the Catalogue of Open Cluster Data and the Milky Way Star Clusters catalog. We find that our parameters are consistent to those in the Milky Way Star Clusters catalog.Conclusions. We demonstrate that it is feasible to develop an automated pipeline that determines cluster parameters and membership reliably. After additional modifications, our pipeline will be able to useGaiaDR2 as input, leading to better cluster memberships and more accurate cluster parameters for a much larger number of clusters.
Machine learning in APOGEE
Authors: Garcia-Dias Rafael , Prieto Carlos Allende , Almeida Jorge Sánchez , Ordovás-Pascual Ignacio 
Published: February 2018

Context.The volume of data generated by astronomical surveys is growing rapidly. Traditional analysis techniques in spectroscopy either demand intensive human interaction or are computationally expensive. In this scenario, machine learning, and unsupervised clustering algorithms in particular, offer interesting alternatives. The Apache Point Observatory Galactic Evolution Experiment (APOGEE) offers a vast data set of near-infrared stellar spectra, which is perfect for testing such alternatives.Aims.Our research applies an unsupervised classification scheme based onK-means to the massive APOGEE data set. We explore whether the data are amenable to classification into discrete classes.Methods.We apply theK-means algorithm to 153 847 high resolution spectra (R≈ 22 500). We discuss the main virtues and weaknesses of the algorithm, as well as our choice of parameters.Results.We show that a classification based on normalised spectra captures the variations in stellar atmospheric parameters, chemical abundances, and rotational velocity, among other factors. The algorithm is able to separate the bulge and halo populations, and distinguish dwarfs, sub-giants, RC, and RGB stars. However, a discrete classification in flux space does not result in a neat organisation in the parameters’ space. Furthermore, the lack of obvious groups in flux space causes the results to be fairly sensitive to the initialisation, and disrupts the efficiency of commonly-used methods to select the optimal number of clusters. Our classification is publicly available, including extensive online material associated with the APOGEE Data Release 12 (DR12).Conclusions.Our description of the APOGEE database can help greatly with the identification of specific types of targets for various applications. We find a lack of obvious groups in flux space, and identify limitations of theK-means algorithm in dealing with this kind of data.
Developing Foundational Counseling Skills for Addressing Adherence Issues in Auditory Rehabilitation
Authors: Jilla Anna , Danhauer Jeffrey , Johnson Carole 
Published: February 2018

AbstractSuccessfully getting patients with confirmed hearing loss to use hearing aids is a major challenge for hearing health care professionals. Treatment adherence has been defined as the active involvement of patients in collaborating with health care providers to plan and manage treatment regimens. Counseling patients with hearing loss on adherence to recommendations of hearing aid uptake and utilization is dependent upon building a patient-centered therapeutic relationship during the initial diagnostic evaluation. The purpose of this article is to provide resources, tools, and engaging learning activities for training students on the development of a hierarchy of counseling skills: informational counseling (e.g., checking comprehension and problem clarification), communication skills (e.g., promotion of shared-communication space, congruence, listening with the third ear, unconditional positive regard, and empathy), and health behavior change (e.g., Motivational Interviewing and the Teach-Back Method) that are prerequisites for addressing treatment adherence.
Teaching Patient-Centered Counseling Skills for Assessment, Diagnosis, and Management of Benign Paroxysmal Positional Vertigo
Authors: Roberts Richard , Johnson Carole , Jilla Anna 
Published: February 2018

AbstractAudiologists are an integral part of the management of those with dizziness and vestibular disorders. However, little research has been performed on counseling approaches for patients who present with dizziness as a primary concern. Accordingly, it is important that audiology students are provided with didactic and experiential learning opportunities for the assessment, diagnosis, and management of this population. Benign paroxysmal positional vertigo is the most common vestibular disorder among adults. Doctor of Audiology students, at a minimum, should be provided with learning opportunities for counseling patients with this particular disorder. Implementation of patient-centered counseling is applied across various parts of the patient encounter from initial intake to treatment and patient education. The purpose of this article is to present the available evidence and to apply widely accepted theories and techniques to counseling those with benign paroxysmal positional vertigo. Didactic resources and experiential learning activities are provided for use in coursework or as a supplement to clinical education.