bluuebunny/crossref_metadata_2025_split huggingface dataset:
SalmoNet, an integrated network of ten Salmonella enterica strains reveals common and distinct pathways to host adaptation
Authors: Métris Aline , Sudhakar Padhmanand , Fazekas David , Demeter Amanda , Ari Eszter , Olbei Marton , Branchu Priscilla , Kingsley Rob A. , Baranyi Jozsef , Korcsmáros Tamas 
Published: October 2017

AbstractSalmonella entericais a prominent bacterial pathogen with implications on human and animal health.Salmonellaserovars could be classified as gastro-intestinal or extra-intestinal. Genome-wide comparisons revealed that extra-intestinal strains are closer relatives of gastro-intestinal strains than to each other indicating a parallel evolution of this trait. Given the complexity of the differences, a systems-level comparison could reveal key mechanisms enabling extra-intestinal serovars to cause systemic infections. Accordingly, in this work, we introduce a unique resource, SalmoNet, which combines manual curation, high-throughput data and computational predictions to provide an integrated network forSalmonellaat the metabolic, transcriptional regulatory and protein-protein interaction levels. SalmoNet provides the networks separately for five gastro-intestinal and five extra-intestinal strains. As a multi-layered, multi-strain database containing experimental data, SalmoNet is the first dedicated network resource forSalmonella. It comprehensively contains interactions between proteins encoded inSalmonellapathogenicity islands, as well as regulatory mechanisms of metabolic processes with the option to zoom-in and analyze the interactions at specific loci in more detail. Application of SalmoNet is not limited to strain comparisons as it also provides aSalmonellaresource for biochemical network modeling, host-pathogen interaction studies, drug discovery, experimental validation of novel interactions, uncovering new pathological mechanisms from emergent properties and epidemiological studies. SalmoNet is available athttp://salmonet.org.
Effects of vessel traffic and underwater noise on the movement, behaviour and vocalisations of bottlenose dolphins in an urbanised estuary
Authors: Marley Sarah A. , Salgado Kent Chandra P. , Erbe Christine , Parnum Iain M. 
Published: October 2017

AbstarctThe potential disturbance of dolphins from tourism boats has been widely discussed in the literature, in terms of both physical vessel presence and associated underwater noise. However, less attention has been paid to the potential impact of non-tourism vessels, despite these being much more widespread and occurring in greater numbers throughout coastal dolphin habitats. The Indo-Pacific bottlenose dolphin (T. aduncus) community using the Fremantle Inner Harbour, Western Australia, is exposed to high levels of vessel traffic. To investigate whether behavioural responses could be occurring, a non-invasive combination of visual and acoustic monitoring was conducted using a theodolite and an autonomous acoustic logger. Dolphins significantly increased their average movement speeds in high vessel densities, but only for some activity states. Behavioural budgets also changed in the presence of vessels, with animals spending greater time travelling and less time resting or socialising. Finally, multiple whistle characteristics varied with rising levels of broadband noise, and other contextual variables. Despite being acoustically specialised for higher frequencies, dolphins had the strongest acoustic variation during low-frequency noise. This study highlights the complexity of disturbance responses in this species, confirming the need for consideration of both surface and acoustic behaviour alongside appropriate contextual data.
Priming with FGF2 stimulates human dental pulp cells to promote axonal regeneration and locomotor function recovery after spinal cord injury
Authors: Nagashima Kosuke , Miwa Takahiro , Soumiya Hitomi , Ushiro Daisuke , Takeda-Kawaguchi Tomoko , Tamaoki Naritaka , Ishiguro Saho , Sato Yumi , Miyamoto Kei , Ohno Takatoshi , Osawa Masatake , Kunisada Takahiro , Shibata Toshiyuki , Tezuka Ken-ichi , Furukawa Shoei , Fukumitsu Hidefumi 
Published: October 2017

AbstractHuman dental pulp cells (DPCs), adherent cells derived from dental pulp tissues, are potential tools for cell transplantation therapy. However, little work has been done to optimize such transplantation. In this study, DPCs were treated with fibroblast growth factor-2 (FGF2) for 5–6 consecutive serial passages and were transplanted into the injury site immediately after complete transection of the rat spinal cord. FGF2 priming facilitated the DPCs to promote axonal regeneration and to improve locomotor function in the rat with spinal cord injury (SCI). Additional analyses revealed that FGF2 priming protected cultured DPCs from hydrogen-peroxide–induced cell death and increased the number of DPCs in the SCI rat spinal cord even 7 weeks after transplantation. The production of major neurotrophic factors was equivalent in FGF2-treated and untreated DPCs. These observations suggest that FGF2 priming might protect DPCs from the post-trauma microenvironment in which DPCs infiltrate and resident immune cells generate cytotoxic reactive oxygen species. Surviving DPCs could increase the availability of neurotrophic factors in the lesion site, thereby promoting axonal regeneration and locomotor function recovery.
Diabetes in Iran: Prospective Analysis from First Nationwide Diabetes Report of National Program for Prevention and Control of Diabetes (NPPCD-2016)
Authors: Esteghamati Alireza , Larijani Bagher , Aghajani Mohammad Haji , Ghaemi Fatemeh , Kermanchi Jamshid , Shahrami Ali , Saadat Mohammad , Esfahani Ensieh Nasli , Ganji Morsaleh , Noshad Sina , Khajeh Elias , Ghajar Alireza , Heidari Behnam , Afarideh Mohsen , Mechanick Jeffrey I. , Ismail-Beigi Faramarz 
Published: October 2017

AbstractWe estimated proportions of different types of diabetes, comorbidities, treatment (the use of oral glucose-lowering agents and insulin), control (hyperglycemia, dyslipidemia and hypertension) and chronic microvascular and macrovascular complications among people with diabetes presenting to the tertiary-care academic diabetes outpatient clinics in Iran. This study is the prospective analysis of data (n = 30,202) from the registry of university-affiliated adult outpatient diabetes clinics in the country during 2015–2016. The proportions of type 1 diabetes, types 2 diabetes, and other types of diabetes were 11.4%, 85.5%, and 1.3%, respectively. The frequencies of drug-naivety, use of oral agents, insulin monotherapy and insulin combination therapy were 2.9%, 60.5%, 11.5%, and 25.1%, respectively. Around 13.2%, 11.9% and 43.3% of patients with diabetes had controlled hyperglycemia, hyperlipidemia and hypertension, respectively. The proportions of retinopathy, nephropathy, peripheral neuropathy, diabetic foot, and ischemic heart disease were 21.9%, 17.6%, 28.0%, 6.2%, and 23.9%, respectively. Despite the wide availability of medications and insulin coverage in Iran, the estimated national control of hyperglycemia, hyperlipidemia and hypertension (especially for young men and old women) remains subpar. The present study further suggests that the frequencies of chronic vascular complications among patients with diabetes are relatively high in Iran.
A high-speed single sideband generator using a magnetic tunnel junction spin torque nano-oscillator
Authors: Sharma Raghav , Sisodia Naveen , Iacocca Ezio , Awad Ahmad A. , Åkerman Johan , Muduli P. K. 
Published: October 2017

Abstract An important property of spin-torque nano-oscillators (STNOs) is their ability to produce a frequency modulated (FM) signal, which is very critical for communication applications. We here demonstrate a novel single sideband (SSB) modulation phenomenon using a magnetic tunnel junction (MTJ)-based STNO, which saves transmission bandwidth and in principle should minimize attenuation for wireless communication. Experimentally, lower single sidebands (LSSBs) have been successfully demonstrated over a wide range of modulation frequency, f
m
= 150 MHz-1 GHz. The observed LSSBs are determined by the intrinsic properties of the device, which can be modeled well by a nonlinear frequency and amplitude modulation formulation and reproduced in macrospin simulations. Moreover, our macrospin simulation results show that the range of modulation current and modulation frequency for generating SSBs can be controlled by the field-like torque and biasing conditions.
Characterization of a New Protein Family Associated With the Silica Deposition Vesicle Membrane Enables Genetic Manipulation of Diatom Silica
Authors: Tesson Benoit , Lerch Sarah J. L. , Hildebrand Mark 
Published: October 2017

AbstractDiatoms are known for their intricate, silicified cell walls (frustules). Silica polymerization occurs in a compartment called the silica deposition vesicle (SDV) and it was proposed that the cytoskeleton influences silica patterning through the SDV membrane (silicalemma) via interactions with transmembrane proteins. In this work we identify a family of proteins associated with the silicalemma, named SAPs for Silicalemma Associated Proteins. The T. pseudonana SAPs (TpSAPs) are characterized by their motif organization; each contains a transmembrane domain, serine rich region and a conserved cytoplasmic domain. Fluorescent tagging demonstrated that two of the TpSAPs were localized to the silicalemma and that the intralumenal region of TpSAP3 remained embedded in the silica while the cytoplasmic region was cleaved. Knockdown lines of TpSAP1 and 3 displayed malformed valves; which confirmed their roles in frustule morphogenesis. This study provides the first demonstration of altering silica structure through manipulation of a single gene.
Modeling and Preventing Progressive Hearing Loss in Usher Syndrome III
Authors: Geng Ruishuang , Omar Akil , Gopal Suhasini R. , Chen Daniel H.-C. , Stepanyan Ruben , Basch Martin L. , Dinculescu Astra , Furness David N. , Saperstein David , Hauswirth William , Lustig Lawrence R. , Alagramam Kumar N. 
Published: October 2017

AbstractUsher syndrome type III (USH3) characterized by progressive loss of vision and hearing is caused by mutations in the clarin-1 gene (CLRN1). Clrn1 knockout (KO) mice develop hair cell defects by postnatal day 2 (P2) and are deaf by P21-P25. Early onset profound hearing loss in KO mice and lack of information about the cochlear cell type that requires Clrn1 expression pose challenges to therapeutic investigation. We generated KO mice harboring a transgene, TgAC1, consisting of Clrn1-UTR (Clrn1 cDNA including its 5′ and 3′ UTR) under the control of regulatory elements (Atoh1 3′ enhancer/β-globin basal promoter) to direct expression of Clrn1 in hair cells during development and down regulate it postnatally. The KO-TgAC1 mice displayed delayed onset progressive hearing loss associated with deterioration of the hair bundle structure, leading to the hypothesis that hair cell expression of Clrn1 is essential for postnatal preservation of hair cell structure and hearing. Consistent with that hypothesis, perinatal transfection of hair cells in KO-TgAC1 mice with a single injection of AAV-Clrn1-UTR vector showed correlative preservation of the hair bundle structure and hearing through adult life. Further, the efficacy of AAV-Clrn1 vector was significantly attenuated, revealing the potential importance of UTR in gene therapy.
Global Identification, Classification, and Expression Analysis of MAPKKK genes: Functional Characterization of MdRaf5 Reveals Evolution and Drought-Responsive Profile in Apple
Authors: Sun Meihong , Xu Yang , Huang Jinguang , Jiang Zesheng , Shu Huairui , Wang Huasen , Zhang Shizhong 
Published: October 2017

AbstractMitogen-activated protein kinase kinase kinases (MAPKKKs) are pivotal components of Mitogen-activated protein kinase (MAPK) cascades, which play a significant role in many biological processes. Although genome-wide analysis of MAPKKKs has been conducted in many species, extant results in apple are scarce. In this study, a total of 72 putative MdMAPKKKs in Raf-like group, 11 in ZIK-like group and 37 in MEEK were identified in apple firstly. Predicted MdMAPKKKs were located in 17 chromosomes with diverse densities, and there was a high-level of conservation in and among the evolutionary groups. Encouragingly, transcripts of 12 selected MdMAPKKKs were expressed in at least one of the tested tissues, indicating that MdMAPKKKs might participate in various physiological and developmental processes in apple. Moreover, they were found to respond to drought stress in roots and leaves, which suggested a possible conserved response to drought stress in different species. Overexpression of MdRaf5 resulted in a hyposensitivity to drought stress, which was at least partially due to the regulation of stomatal closure and transpiration rates. To the best of our knowledge, this is the first genome-wide functional analysis of the MdMAPKKK genes in apple, and it provides valuable information for understanding MdMAPKKKs signals and their putative functions.
Structural and Mechanistic Analysis of Drosophila melanogaster Agmatine N-Acetyltransferase, an Enzyme that Catalyzes the Formation of N-Acetylagmatine
Authors: Dempsey Daniel R. , Nichols Derek A. , Battistini Matthew R. , Pemberton Orville , Ospina Santiago Rodriguez , Zhang Xiujun , Carpenter Anne-Marie , O’Flynn Brian G. , Leahy James W. , Kanwar Ankush , Lewandowski Eric M. , Chen Yu , Merkler David J. 
Published: October 2017

AbstractAgmatine N-acetyltransferase (AgmNAT) catalyzes the formation of N-acetylagmatine from acetyl-CoA and agmatine. Herein, we provide evidence that Drosophila melanogaster AgmNAT (CG15766) catalyzes the formation of N-acetylagmatine using an ordered sequential mechanism; acetyl-CoA binds prior to agmatine to generate an AgmNAT•acetyl-CoA•agmatine ternary complex prior to catalysis. Additionally, we solved a crystal structure for the apo form of AgmNAT with an atomic resolution of 2.3 Å, which points towards specific amino acids that may function in catalysis or active site formation. Using the crystal structure, primary sequence alignment, pH-activity profiles, and site-directed mutagenesis, we evaluated a series of active site amino acids in order to assign their functional roles in AgmNAT. More specifically, pH-activity profiles identified at least one catalytically important, ionizable group with an apparent pKa of ~7.5, which corresponds to the general base in catalysis, Glu-34. Moreover, these data led to a proposed chemical mechanism, which is consistent with the structure and our biochemical analysis of AgmNAT.
Enterococci Mediate the Oviposition Preference of Drosophila melanogaster through Sucrose Catabolism
Authors: Liu Wei , Zhang Ke , Li Yujuan , Su Wanzhen , Hu Kunkun , Jin Shan 
Published: October 2017

AbstractSucrose, one of the main products of photosynthesis in plants, functions as a universal biomarker for nutritional content and maturity of different fruits across diverse ecological niches. Drosophila melanogaster congregates to lay eggs in rotting fruits, yet the factors that influence these decisions remains uncovered. Here, we report that lactic acid bacteria Enterococci are critical modulators to attract Drosophila to lay eggs on decaying food. Drosophila-associated Enterococci predominantly catabolize sucrose for growing their population in fly food, and thus generate a unique ecological niche with depleted sucrose, but enriched bacteria. Female flies navigate these favorable oviposition sites by probing the sucrose cue with their gustatory sensory neurons. Acquirement of indigenous microbiota facilitated the development and systemic growth of Drosophila, thereby benefiting the survival and fitness of their offspring. Thus, our finding highlights the pivotal roles of commensal bacteria in influencing host behavior, opening the door to a better understanding of the ecological relationships between the microbial and metazoan worlds.
Modulating hemispheric lateralization by brain stimulation yields gain in mental and physical activity
Authors: Zich Catharina , Harty Siobhán , Kranczioch Cornelia , Mansfield Karen L. , Sella Francesco , Debener Stefan , Cohen Kadosh Roi 
Published: October 2017

AbstractImagery plays an important role in our life. Motor imagery is the mental simulation of a motor act without overt motor output. Previous studies have documented the effect of motor imagery practice. However, its translational potential for patients as well as for athletes, musicians and other groups, depends largely on the transfer from mental practice to overt physical performance. We used bilateral transcranial direct current stimulation (tDCS) over sensorimotor areas to modulate neural lateralization patterns induced by unilateral mental motor imagery and the performance of a physical motor task. Twenty-six healthy older adults participated (mean age = 67.1 years) in a double-blind cross-over sham-controlled study. We found stimulation-related changes at the neural and behavioural level, which were polarity-dependent. Specifically, for the hand contralateral to the anode, electroencephalographic activity induced by motor imagery was more lateralized and motor performance improved. In contrast, for the hand contralateral to the cathode, hemispheric lateralization was reduced. The stimulation-related increase and decrease in neural lateralization were negatively related. Further, the degree of stimulation-related change in neural lateralization correlated with the stimulation-related change on behavioural level. These convergent neurophysiological and behavioural effects underline the potential of tDCS to improve mental and physical motor performance.
Materials analysis and focused ion beam nanofabrication of topological insulator Bi2Se3
Authors: Friedensen Sarah , Mlack Jerome T. , Drndić Marija 
Published: October 2017

AbstractFocused ion beam milling allows manipulation of the shape and size of nanostructures to create geometries potentially useful for opto-electronics, thermoelectrics, and quantum computing. We focus on using the ion beam to control the thickness of Bi2Se3 and to create nanowires from larger structures. Changes in the material structure of Bi2Se3 nanomaterials that have been milled using a focused ion beam are presented. In order to characterize the effects of ion beam processing on the samples, we use a variety of techniques including analytical transmission electron microscopy and atomic force microscopy. The results show that while part of the material remains intact after shaping, amorphous regions form where the beam has been used to thin the sample. For wires created by thinning the material down to the substrate, the sidewalls of the wires appear intact based on diffraction images from samples cut at an angle, but thin crystalline regions remain at the wire edges. Even with the resulting defects and limitations when thinning, focused ion beam milling can be used to fabricate custom geometries of Bi2Se3 nanostructures.
The histone variant H3.3 G34W substitution in giant cell tumor of the bone link chromatin and RNA processing
Authors: Lim Jinyeong , Park Joo Hyun , Baude Annika , Yoo Yeongran , Lee Yeon Kyu , Schmidt Christopher R. , Park Jong Bae , Fellenberg Jörg , Zustin Josef , Haller Florian , Krücken Irene , Kang Hyun Guy , Park Yoon Jung , Plass Christoph , Lindroth Anders M. 
Published: October 2017

AbstractWhile transcription as regulated by histones and their post-translational modifications has been well described, the function of histone variants in this process remains poorly characterized. Potentially important insight into this process pertain to the frequently occurring mutations of H3.3, leading to G34 substitutions in childhood glioblastoma and giant cell tumor of the bone (GCTB). In this study, we have established primary cell lines from GCTB patients and used them to uncover the influence of H3.3 G34W substitutions on cellular growth behavior, gene expression, and chromatin compaction. Primary cell lines with H3.3 G34W showed increased colony formation, infiltration and proliferation, known hallmarks of tumor development. Isogenic cell lines with H3.3 G34W recapitulated the increased proliferation observed in primary cells. Transcriptomic analysis of primary cells and tumor biopsies revealed slightly more downregulated gene expression, perhaps by increased chromatin compaction. We identified components related to splicing, most prominently hnRNPs, by immunoprecipitation and mass spectrometry that specifically interact with H3.3 G34W in the isogenic cell lines. RNA-sequencing analysis and hybridization-based validations further enforced splicing aberrations. Our data uncover a role for H3.3 in RNA processing and chromatin modulation that is blocked by the G34W substitution, potentially driving the tumorigenic process in GCTB.
Palmitate-induced lipotoxicity alters acetylation of multiple proteins in clonal β cells and human pancreatic islets
Authors: Ciregia Federica , Bugliani Marco , Ronci Maurizio , Giusti Laura , Boldrini Claudia , Mazzoni Maria R , Mossuto Sandra , Grano Francesca , Cnop Miriam , Marselli Lorella , Giannaccini Gino , Urbani Andrea , Lucacchini Antonio , Marchetti Piero 
Published: October 2017

AbstractType 2 diabetes is characterized by progressive β cell dysfunction, with lipotoxicity playing a possible pathogenetic role. Palmitate is often used to examine the direct effects of lipotoxicity and it may cause mitochondrial alterations by activating protein acetylation. However, it is unknown whether palmitate influences protein acetylation in β cells. We investigated lysine acetylation in mitochondrial proteins from INS-1E β cells (INS-1E) and in proteins from human pancreatic islets (HPI) after 24 h palmitate exposure. First, we confirmed that palmitate damages β cells and demonstrated that chemical inhibition of deacetylation also impairs INS-1E function and survival. Then, by 2-D gel electrophoresis, Western Blot and Liquid Chromatography-Mass Spectrometry we evaluated the effects of palmitate on protein acetylation. In mitochondrial preparations from palmitate-treated INS-1E, 32 acetylated spots were detected, with 13 proteins resulting over-acetylated. In HPI, 136 acetylated proteins were found, of which 11 were over-acetylated upon culture with palmitate. Interestingly, three proteins, glutamate dehydrogenase, mitochondrial superoxide dismutase, and SREBP-1, were over-acetylated in both INS-1E and HPI. Therefore, prolonged exposure to palmitate induces changes in β cell protein lysine acetylation and this modification could play a role in causing β cell damage. Dysregulated acetylation may be a target to counteract palmitate-induced β cell lipotoxicity.
Proteomic Analysis Reveals Dab2 Mediated Receptor Endocytosis Promotes Liver Sinusoidal Endothelial Cell Dedifferentiation
Authors: Lao Yuanxiang , Li Yanyan , Hou Yufang , Chen Huahai , Qiu Bintao , Lin Weiran , Sun Aihua , Wei Handong , Jiang Ying , He Fuchu 
Published: October 2017

AbstractSinusoidal dedifferentiation is a complicated process induced by several factors, and exists in early stage of diverse liver diseases. The mechanism of sinusoidal dedifferentiation is poorly unknown. In this study, we established a NaAsO2-induced sinusoidal dedifferentiation mice model. Liver sinusoidal endothelial cells were isolated and isobaric tag for relative and absolute quantitation (iTRAQ) based proteomic approach was adopted to globally examine the effects of arsenic on liver sinusoidal endothelial cells (LSECs) during the progression of sinusoidal dedifferentiation. In all, 4205 proteins were identified and quantified by iTRAQ combined with LC-MS/MS analysis, of which 310 proteins were significantly changed in NaAsO2 group, compared with the normal control. Validation by western blot showed increased level of clathrin-associated sorting protein Disabled 2 (Dab2) in NaAsO2 group, indicating that it may regulate receptor endocytosis, which served as a mechanism to augment intracellular VEGF signaling. Moreover, we found that knockdown of Dab2 reduced the uptake of VEGF in LSECs, furthermore blocking VEGF-mediated LSEC dedifferentiation and angiogenesis.