bluuebunny/crossref_metadata_2025_split huggingface dataset:
The additive effects of atorvastatin and insulin on renal function and renal organic anion transporter 3 function in diabetic rats
Authors: Thongnak Laongdao , Pongchaidecha Anchalee , Jaikumkao Krit , Chatsudthipong Varanuj , Chattipakorn Nipon , Lungkaphin Anusorn 
Published: October 2017

AbstractHyperglycemia-induced oxidative stress is usually found in diabetic condition. 3-hydroxy-3-methylglutaryl coenzyme-A (HMG-CoA) reductase inhibitors, statins, are widely used as cholesterol-lowering medication with several “pleiotropic” effects in diabetic patients. This study aims to evaluate whether the protective effects of atorvastatin and insulin on renal function and renal organic anion transporter 3 (Oat3) function involve the modulation of oxidative stress and pancreatic function in type 1 diabetic rats. Type 1 diabetes was induced by intraperitoneal injection of streptozotocin (50 mg/kg BW). Atorvastatin and insulin as single or combined treatment were given for 4 weeks after diabetic condition had been confirmed. Diabetic rats demonstrated renal function and renal Oat3 function impairment with an increased MDA level and decreased SOD protein expression concomitant with stimulation of renal Nrf2 and HO-1 protein expression. Insulin plus atorvastatin (combined) treatment effectively restored renal function as well as renal Oat3 function which correlated with the decrease in hyperglycemia and oxidative stress. Moreover, pancreatic inflammation and apoptosis in diabetic rats were ameliorated by the combined drugs treatment. Therefore, atorvastatin plus insulin seems to exert the additive effect in improving renal functionby alleviating hyperglycemiaand the modulation of oxidative stress, inflammation and apoptosis.
Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogenetic Tree of the Paniceae Grasses
Authors: Washburn Jacob D. , Schnable James C. , Conant Gavin C. , Brutnell Thomas P. , Shao Ying , Zhang Yang , Ludwig Martha , Davidse Gerrit , Pires J. Chris 
Published: October 2017

AbstractThe past few years have witnessed a paradigm shift in molecular systematics from phylogenetic methods (using one or a few genes) to those that can be described as phylogenomics (phylogenetic inference with entire genomes). One approach that has recently emerged is phylo-transcriptomics (transcriptome-based phylogenetic inference). As in any phylogenetics experiment, accurate orthology inference is critical to phylo-transcriptomics. To date, most analyses have inferred orthology based either on pure sequence similarity or using gene-tree approaches. The use of conserved genome synteny in orthology detection has been relatively under-employed in phylogenetics, mainly due to the cost of sequencing genomes. While current trends focus on the quantity of genes included in an analysis, the use of synteny is likely to improve the quality of ortholog inference. In this study, we combine de novo transcriptome data and sequenced genomes from an economically important group of grass species, the tribe Paniceae, to make phylogenomic inferences. This method, which we call “genome-guided phylo-transcriptomics”, is compared to other recently published orthology inference pipelines, and benchmarked using a set of sequenced genomes from across the grasses. These comparisons provide a framework for future researchers to evaluate the costs and benefits of adding sequenced genomes to transcriptome data sets.
Dopamine-mediated photothermal theranostics combined with up-conversion platform under near infrared light
Authors: Lv Ruichan , Yang Piaoping , Chen Guanying , Gai Shili , Xu Jiating , Prasad Paras N. 
Published: October 2017

AbstractAn organic-inorganic hybrid core-shell nanostructure, based on mesoporous silica coated upconversion core-shell nanoparticles (NaGdF4:Yb,Er@NaGdF4:Yb@mSiO2-Dopa abbreviated here as UCNP@mSiO2-Dopa) that stably incorporates dopamine (Dopa) in the silica layer was introduced as a theranostic nanoplatform for optical imaging guided photothermal therapy (PTT) using NIR excitation. Silica-attaching polyethylenimine make the Dopa transforms into an active form (transferred Dopa) that strongly absorbs light under single 980 nm irradiation. We show that the activated UCNP@mSiO2-Dopa nanoplatform is able to produce a pronounced photothermal effect, that elevates water temperature from room temperature to 41.8 °C within 2 minutes, while concurrently emitting strong upconverted luminescence (UCL) for visualized guidance under 980 nm laser. In addition, we demonstrate the application of the same UCNP@mSiO2-Dopa nanoplatform for magnetic resonance imaging (MRI) and x-ray computed tomography (CT) enabled by the gadolinium (Gd) element contained in the UCNP. Importantly, thein vitroandin vivoanti-cancer therapeutic effects have been shown efficacious, implying the use of the described nanoplatform as an effective multi-modal imaging enabled PTT agent. Results from thein vivobiodistribution of UCNPs@mSiO2, cellular live/dead assay, and histologic analysis of main organs of treated mice, reveal that the UCNP@mSiO2-Dopa agents are bio-compatible with low toxicity.
Microtome-integrated microscope system for high sensitivity tracking of in-resin fluorescence in blocks and ultrathin sections for correlative microscopy
Authors: Lemercier Nicolas , Middel Volker , Hentsch Didier , Taubert Serge , Takamiya Masanari , Beil Tanja , Vonesch Jean-Luc , Baumbach Tilo , Schultz Patrick , Antony Claude , Strähle Uwe 
Published: October 2017

AbstractMany areas of biological research demand the combined use of different imaging modalities to cover a wide range of magnifications and measurements or to place fluorescent patterns into an ultrastructural context. A technically difficult problem is the efficient specimen transfer between different imaging modalities without losing the coordinates of the regions-of-interest (ROI). Here, we report a new and highly sensitive integrated system that combines a custom designed microscope with an ultramicrotome for in-resin-fluorescence detection in blocks, ribbons and sections on EM-grids. Although operating with long-distance lenses, this system achieves a very high light sensitivity. Our instrumental set-up and operating workflow are designed to investigate rare events in large tissue volumes. Applications range from studies of individual immune, stem and cancer cells to the investigation of non-uniform subcellular processes. As a use case, we present the ultrastructure of a single membrane repair patch on a muscle fiber in intact muscle in a whole animal context.
One-dimensional Confinement Effect on the Self-assembly of Symmetric H-shaped Copolymers in a Thin Film
Authors: Mu Dan , Li Jian-quan , Feng Sheng-yu 
Published: October 2017

AbstractThe self-assembly of a reformed symmetric H-shaped copolymer with four hydrophilic branches and one hydrophobic stem was systematically investigated. The existence of vacancies is vital to regulate the sizes of self-assembled cylinders to be able to form a hexagonal arrangement. With the introduction of horizontal-orientated confinement, a micellar structure is formed through a coalescence mechanism. The short acting distance and large influencing area of the confinement produces numerous small-sized micelles. Additionally, the cycled “contraction-expansion” change helps achieve hexagonal arrangement. In contrast, the introduction of lateral-oriented confinement with long acting distance and small influencing area cannot change the cylindrical structure. Under the fission mechanism, in which the larger cylinder splits into smaller ones, it is quite efficient to generate hierarchical-sized cylinders from larger-sized cylinders in the middle region and smaller-sized cylinders near both walls. The results indicate the possibility of regulating the characteristics of a nanomaterial by tuning the molecular structure of the copolymer and the parameters of the introduced confinement, which are closely related to the self-assembly structure.
Identification and characterization of a putative protein disulfide isomerase (HsPDI) as an alleged effector of Heterodera schachtii
Authors: Habash Samer S. , Sobczak Miroslaw , Siddique Shahid , Voigt Boris , Elashry Abdelnaser , Grundler Florian M. W. 
Published: October 2017

AbstractThe plant-parasitic nematode Heterodera schachtii is an obligate biotroph that induces syncytial feeding sites in roots of its hosts. Nematodes produce effectors that are secreted into the host and facilitate infection process. Here we identified H. schachtii protein disulphide isomerase (HsPDI) as a putative effector that interferes with the host’s redox status. In situ hybridization showed that HsPdi is specifically localized within esophageal glands of pre-parasitic second stage juveniles (J2). HsPdi is up-regulated in the early parasitic J2s. Silencing of HsPdi by RNA interference in the J2s hampers their development and leads to structural malfunctions in associated feeding sites induced in Arabidopsis roots. Expression of HsPDI in Arabidopsis increases plant’s susceptibility towards H. schachtii. HsPdi expression is up-regulated in the presence of exogenous H2O2, whereas HsPdi silencing results in increased mortality under H2O2 stress. Stable expression of HsPDI in Arabidopsis plants decreases ROS burst induced by flg22. Transiently expressed HsPDI in N. benthamiana leaves is localized in the apoplast. HsPDI plays an important role in the interaction between nematode and plant, probably through inducing local changes in the redox status of infected host tissue. It also contributes to protect the nematode from exogenous H2O2 stress.
The Orbiting Carbon Observatory (OCO-2) tracks 2–3 peta-gram increase in carbon release to the atmosphere during the 2014–2016 El Niño
Authors: Patra Prabir K. , Crisp David , Kaiser Johannes W. , Wunch Debra , Saeki Tazu , Ichii Kazuhito , Sekiya Takashi , Wennberg Paul O. , Feist Dietrich G. , Pollard David F. , Griffith David W. T. , Velazco Voltaire A. , De Maziere M. , Sha Mahesh K. , Roehl Coleen , Chatterjee Abhishek , Ishijima Kentaro 
Published: October 2017

AbstractThe powerful El Niño event of 2015–2016 – the third most intense since the 1950s – has exerted a large impact on the Earth’s natural climate system. The column-averaged CO2 dry-air mole fraction (XCO2) observations from satellites and ground-based networks are analyzed together with in situ observations for the period of September 2014 to October 2016. From the differences between satellite (OCO-2) observations and simulations using an atmospheric chemistry-transport model, we estimate that, relative to the mean annual fluxes for 2014, the most recent El Niño has contributed to an excess CO2 emission from the Earth’s surface (land + ocean) to the atmosphere in the range of 2.4 ± 0.2 PgC (1 Pg = 1015 g) over the period of July 2015 to June 2016. The excess CO2 flux is resulted primarily from reduction in vegetation uptake due to drought, and to a lesser degree from increased biomass burning. It is about the half of the CO2 flux anomaly (range: 4.4–6.7 PgC) estimated for the 1997/1998 El Niño. The annual total sink is estimated to be 3.9 ± 0.2 PgC for the assumed fossil fuel emission of 10.1 PgC. The major uncertainty in attribution arise from error in anthropogenic emission trends, satellite data and atmospheric transport.
Surface marker profiling of SH-SY5Y cells enables small molecule screens identifying BMP4 as a modulator of neuroblastoma differentiation
Authors: Ferlemann Fraua Christina , Menon Vishal , Condurat Alexandra Larisa , Rößler Jochen , Pruszak Jan 
Published: October 2017

AbstractNeuroblastoma is the most common extra-cranial solid tumor in children. Its broad spectrum of clinical outcomes reflects the underlying inherent cellular heterogeneity. As current treatments often do not lead to tumor eradication, there is a need to better define therapy-resistant neuroblastoma and to identify new modulatory molecules. To this end, we performed the first comprehensive flow cytometric characterization of surface molecule expression in neuroblastoma cell lines. Exploiting an established clustering algorithm (SPADE) for unbiased visualization of cellular subsets, we conducted a multiwell screen for small molecule modulators of neuroblastoma phenotype. In addition to SH-SY5Y cells, the SH-EP, BE(2)-M17 and Kelly lines were included in follow-up analysis as in vitro models of neuroblastoma. A combinatorial detection of glycoprotein epitopes (CD15, CD24, CD44, CD57, TrkA) and the chemokine receptor CXCR4 (CD184) enabled the quantitative identification of SPADE-defined clusters differentially responding to small molecules. Exposure to bone morphogenetic protein (BMP)-4 was found to enhance a TrkAhigh/CD15−/CD184− neuroblastoma cellular subset, accompanied by a reduction in doublecortin-positive neuroblasts and of NMYC protein expression in SH-SY5Y cells. Beyond yielding novel marker candidates for studying neuroblastoma pathology, our approach may provide tools for improved pharmacological screens towards developing novel avenues of neuroblastoma diagnosis and treatment.
The efficacy and further functional advantages of random-base molecular barcodes for absolute and digital quantification of nucleic acid molecules
Authors: Ogawa Taisaku , Kryukov Kirill , Imanishi Tadashi , Shiroguchi Katsuyuki 
Published: October 2017

AbstractAccurate quantification of biomolecules in system-wide measurements is in high demand, especially for systems with limited sample amounts such as single cells. Because of this, digital quantification of nucleic acid molecules using molecular barcodes has been developed, making, e.g., transcriptome analysis highly reproducible and quantitative. This counting scheme was shown to work using sequence-restricted barcodes, and non-sequence-restricted (random-base) barcodes that may provide a much higher dynamic range at significantly lower cost have been widely used. However, the efficacy of random-base barcodes is significantly affected by base changes due to amplification and/or sequencing errors and has not been investigated experimentally or quantitatively. Here, we show experimentally that random-base barcodes enable absolute and digital quantification of DNA molecules with high dynamic range (from one to more than 104, potentially up to 1015 molecules) conditional on our barcode design and variety, a certain range of sequencing depths, and computational analyses. Moreover, we quantitatively show further functional advantages of the molecular barcodes: the molecular barcodes enable one to find contaminants and misidentifications of target sequences. Our scheme here may be generally used to confirm that the digital quantification works in each platform.
A role for the purinergic receptor P2X3 in astrocytes in the mechanism of craniofacial neuropathic pain
Authors: Mah Won , Lee Sang Man , Lee Jaekwang , Bae Jin Young , Ju Jin Sook , Lee C. Justin , Ahn Dong Kuk , Bae Yong Chul 
Published: October 2017

AbstractThe purinergic receptor P2X3, expressed in the central terminals of primary nociceptive neurons in the brainstem, plays an important role in pathological pain. However, little is known about expression of P2X3 in the brainstem astrocytes and its involvement in craniofacial pathologic pain. To address this issue, we investigated the expression of P2X3 in astrocytes in the trigeminal caudal nucleus (Vc) in a rat model of craniofacial neuropathic pain, chronic constriction injury of infraorbital nerve (CCI-ION). We found that 1) P2X3-immunoreactivity is observed in the brainstem astrocytes, preferentially in their fine processes, 2) the number of P2X3-positive fine astrocytic processes and the density of P2X3 in these processes were increased significantly in CCI-ION rats, compared to control rats, and 3) administration of MPEP, a specific mGluR5 antagonist, alleviated the mechanical allodynia and abolished the increase in density of P2X3 in fine astrocytic processes caused by CCI-ION. These findings reveal preferential expression of P2X3 in the fine astrocytic processes in the brainstem, propose a novel role of P2X3 in the fine astrocytic process in the mechanism of craniofacial neuropathic pain, and suggest that the expression of astrocytic P2X3 may be regulated by astrocytic mGluR5.
Chronic antidepressant potentiates spontaneous activity of dorsal raphe serotonergic neurons by decreasing GABAB receptor-mediated inhibition of L-type calcium channels
Authors: Asaoka Nozomi , Nishitani Naoya , Kinoshita Haruko , Kawai Hiroyuki , Shibui Norihiro , Nagayasu Kazuki , Shirakawa Hisashi , Nakagawa Takayuki , Kaneko Shuji 
Published: October 2017

AbstractSpontaneous activity of serotonergic neurons of the dorsal raphe nucleus (DRN) regulates mood and motivational state. Potentiation of serotonergic function is one of the therapeutic strategies for treatment of various psychiatric disorders, such as major depression, panic disorder and obsessive-compulsive disorder. However, the control mechanisms of the serotonergic firing activity are still unknown. In this study, we examined the control mechanisms for serotonergic spontaneous activity and effects of chronic antidepressant administration on these mechanisms by using modified ex vivo electrophysiological recording methods. Serotonergic neurons remained firing even in the absence of glutamatergic and GABAergic ionotropic inputs, while blockade of L-type voltage dependent Ca2+ channels (VDCCs) in serotonergic neurons decreased spontaneous firing activity. L-type VDCCs in serotonergic neurons received gamma-aminobutyric acid B (GABAB) receptor-mediated inhibition, which maintained serotonergic slow spontaneous firing activity. Chronic administration of an antidepressant, citalopram, disinhibited the serotonergic spontaneous firing activity by weakening the GABAB receptor-mediated inhibition of L-type VDCCs in serotonergic neurons. Our results provide a new mechanism underlying the spontaneous serotonergic activity and new insights into the mechanism of action of antidepressants.
Emotion Regulating Attentional Control Abnormalities In Major Depressive Disorder: An Event-Related Potential Study
Authors: Hu Bin , Rao Juan , Li Xiaowei , Cao Tong , Li Jianxiu , Majoe Dennis , Gutknecht Jürg 
Published: October 2017

AbstractMajor depressive disorders (MDD) exhibit cognitive dysfunction with respect to attention. The deficiencies in cognitive control of emotional information are associated with MDD as compared to healthy controls (HC). However, the brain mechanism underlying emotion that influences the attentional control in MDD necessitates further research. The present study explores the emotion-regulated cognitive competence in MDD at a dynamic attentional stage. Event-Related Potentials (ERPs) were recorded from 35 clinical MDD outpatients and matched HCs by applying a modified affective priming dot-probe paradigm, which consisted of various emotional facial expression pairs. From a dynamic perspective, ERPs combined with sLORETA results showed significant differences among the groups. In compared to HC, 100 ms MDD group exhibited a greater interior-prefrontal N100, sensitive to negative-neutral faces. 200 ms MDD showed an activated parietal-occipital P200 linked to sad face, suggesting that the attentional control ability concentrated on sad mood-congruent cognition. 300 ms, a distinct P300 was observed at dorsolateral parietal cortex, representing a sustained attentional control. Our findings suggested that a negatively sad emotion influenced cognitive attentional control in MDD in the early and late attentional stages of cognition. P200 and P300 might be predictors of potential neurocognitive mechanism underlying the dysregulated attentional control of MDD.
Energy-efficient waveform for electrical stimulation of the cochlear nerve
Authors: Yip Marcus , Bowers Peter , Noel Victor , Chandrakasan Anantha , Stankovic Konstantina M. 
Published: October 2017

AbstractThe cochlear implant (CI) is the most successful neural prosthesis, restoring the sensation of sound in people with severe-to-profound hearing loss by electrically stimulating the cochlear nerve. Existing CIs have an external, visible unit, and an internal, surgically-placed unit. There are significant challenges associated with the external unit, as it has limited utility and CI users often report a social stigma associated with prosthesis visibility. A fully-implantable CI (FICI) would address these issues. However, the volume constraint imposed on the FICI requires less power consumption compared to today’s CI. Because neural stimulation by CI electrodes accounts for up to 90% of power consumption, reduction in stimulation power will result directly in CI power savings. To determine an energy-efficient waveform for cochlear nerve stimulation, we used a genetic algorithm approach, incorporating a computational model of a single mammalian myelinated cochlear nerve fiber coupled to a stimulator-electrode-tissue interface. The algorithm’s prediction was tested in vivo in human CI subjects. We find that implementation of a non-rectangular biphasic neural stimulation waveform may result in up to 25% charge savings and energy savings within the comfortable range of hearing for CI users. The alternative waveform may enable future development of a FICI.
Gastrointestinal Hemorrhage after Spontaneous Subarachnoid Hemorrhage: A Single-Center Cohort Study
Authors: Wang Shang-Po , Huang Yu-Hua 
Published: October 2017

AbstractSpontaneous subarachnoid hemorrhage (SAH) is a devastating disease, and gastrointestinal hemorrhage is one of several potential complications of acute strokes. We aim to analyze its prevalence, risk factors, and association with in-hospital prognosis following SAH. A total of 1047 adult patients with a primary diagnosis of spontaneous SAH were retrospectively enrolled. We retrieved medical information from the administrative database utilizing diagnostic and procedure codes of the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM). Patients with SAH included 418 men and 629 women, and their mean age was 57.2 (standard deviation 14.6) years (range, 18–93 years). Gastrointestinal hemorrhage occurred in 30 of the 1047 patients, accounting for 2.9%. In a multivariate logistic regression model, the independent risk factors for gastrointestinal hemorrhage were liver disease and hydrocephalus. The in-hospital mortality rates were 43.3% and 29.3% in patients with and without gastrointestinal hemorrhage, respectively, but the difference was not statistically significant. In conclusion, the prevalence of gastrointestinal hemorrhage was 2.9% in patients hospitalized for spontaneous SAH. Underlying liver disease and the presence of hydrocephalus were both independent risk factors for this complication, which is a reminder to clinicians to pay increased attention in such cases.