bluuebunny/crossref_metadata_2025_split huggingface dataset:
The interaction network of the YidC insertase with the SecYEG translocon, SRP and the SRP receptor FtsY
Authors: Petriman Narcis-Adrian , Jauß Benjamin , Hufnagel Antonia , Franz Lisa , Sachelaru Ilie , Drepper Friedel , Warscheid Bettina , Koch Hans-Georg 
Published: January 2018

AbstractYidC/Oxa1/Alb3 are essential proteins that operate independently or cooperatively with the Sec machinery during membrane protein insertion in bacteria, archaea and eukaryotic organelles. Although the interaction between the bacterial SecYEG translocon and YidC has been observed in multiple studies, it is still unknown which domains of YidC are in contact with the SecYEG translocon. By in vivo and in vitro site-directed and para-formaldehyde cross-linking we identified the auxiliary transmembrane domain 1 of E. coli YidC as a major contact site for SecY and SecG. Additional SecY contacts were observed for the tightly packed globular domain and the C1 loop of YidC, which reveals that the hydrophilic cavity of YidC faces the lateral gate of SecY. Surprisingly, YidC-SecYEG contacts were only observed when YidC and SecYEG were present at about stoichiometric concentrations, suggesting that the YidC-SecYEG contact in vivo is either very transient or only observed for a very small SecYEG sub-population. This is different for the YidC-SRP and YidC-FtsY interaction, which involves the C1 loop of YidC and is efficiently observed even at sub-stoichiometric concentrations of SRP/FtsY. In summary, our data provide a first detailed view on how YidC interacts with the SecYEG translocon and the SRP-targeting machinery.
Application of Hydrazine-Embedded Heterocyclic Compounds to High Voltage Rechargeable Lithium Organic Batteries
Authors: Shimizu Takeshi , Yamamoto Koji , Pandit Palash , Yoshikawa Hirofumi , Higashibayashi Shuhei 
Published: January 2018

AbstractHydrazine-embedded heterocyclic compounds with dimeric dimethylacridine (1b), carbazole (2b), and phenothiazine (3b) skeletons were applied to cathode active materials of rechargeable lithium organic batteries, and the performance of the batteries was evaluated. The charge/discharge curves exhibited clear plateaus in the high voltage range of 3.3–3.7 V. The capacities of the plateau regions were comparable to the calculated capacities corresponding to the one-electron redox of the molecules. The amount of the active compound 3b could be increased up to 30 wt% in the electrode composite, and fast charge/discharge performance was also observed.
Turning a normal microscope into a super-resolution instrument using a scanning microlens array
Authors: Huszka Gergely , Gijs Martin A. M. 
Published: January 2018

AbstractWe report dielectric microsphere array-based optical super-resolution microscopy. A dielectric microsphere that is placed on a sample is known to generate a virtual image with resolution better than the optical diffraction limit. However, a limitation of such type of super-resolution microscopy is the restricted field-of-view, essentially limited to the central area of the microsphere-generated image. We overcame this limitation by scanning a micro-fabricated array of ordered microspheres over the sample using a customized algorithm that moved step-by-step a motorized stage, meanwhile the microscope-mounted camera was taking pictures at every step. Finally, we stitched together the extracted central parts of the virtual images that showed super-resolution into a mosaic image. We demonstrated 130 nm lateral resolution (~λ/4) and 5 × 105 µm2 scanned surface area using a two by one array of barium titanate glass microspheres in oil-immersion environment. Our findings may serve as a basis for widespread applications of affordable optical super-resolution microscopy.
The Impact of COMT and Childhood Maltreatment on Suicidal Behaviour in Affective Disorders
Authors: Bernegger Alexandra , Kienesberger Klemens , Carlberg Laura , Swoboda Patrick , Ludwig Birgit , Koller Romina , Inaner Michelle , Zotter Melanie , Kapusta Nestor , Aigner Martin , Haslacher Helmuth , Kasper Siegfried , Schosser Alexandra 
Published: January 2018

AbstractThe inconsistent findings on the association between COMT (catecholamine-O-methyl-transferase) and suicidal behaviour gave reason to choose a clear phenotype description of suicidal behaviour and take childhood maltreatment as environmental factor into account. The aim of this candidate-gene-association study was to eliminate heterogeneity within the sample by only recruiting affective disorder patients and find associations between COMT polymorphisms and defined suicidal phenotypes. In a sample of 258 affective disorder patients a detailed clinical assessment (e.g. CTQ, SCAN, HAMD, SBQ-R, VI-SURIAS, LPC) was performed. DNA of peripheral blood samples was genotyped using TaqMan® SNP Genotyping Assays. We observed that the haplotype GAT of rs737865, rs6269, rs4633 is significantly associated with suicide attempt (p = 0.003 [pcorr = 0.021]), and that there is a tendency towards self-harming behaviour (p = 0.02 [pcorr = 0.08]) and also NSSI (p = 0.03 [pcorr = 0.08]), though the p values did not resist multiple testing correction. The same effect we observed with the 4-marker slide window haplotype, GATA of rs737865, rs6269, rs4633, rs4680 (p = 0.009 [pcorr = 0.045]). The findings support an association between the COMT gene and suicidal behaviour phenotypes with and without childhood maltreatment as environmental factor.
Evidence of s-wave superconductivity in the noncentrosymmetric La7Ir3
Authors: Li B. , Xu C. Q. , Zhou W. , Jiao W. H. , Sankar R. , Zhang F. M. , Hou H. H. , Jiang X. F. , Qian B. , Chen B. , Bangura A. F. , Xu Xiaofeng 
Published: January 2018

AbstractSuperconductivity in noncentrosymmetric compounds has attracted sustained interest in the last decades. Here we present a detailed study on the transport, thermodynamic properties and the band structure of the noncentrosymmetric superconductor La 7 Ir 3 (T
c
~ 2.3 K) that was recently proposed to break the time-reversal symmetry. It is found that La7Ir3 displays a moderately large electronic heat capacity (Sommerfeld coefficient γ
n
~ 53.1 mJ/mol K2) and a significantly enhanced Kadowaki-Woods ratio (KWR ~32 μΩ cm mol2 K2 J−2) that is greater than the typical value (~10 μΩ cm mol2 K2 J−2) for strongly correlated electron systems. The upper critical field Hc2 was seen to be nicely described by the single-band Werthamer-Helfand-Hohenberg model down to very low temperatures. The hydrostatic pressure effects on the superconductivity were also investigated. The heat capacity below T
c
reveals a dominant s-wave gap with the magnitude close to the BCS value. The first-principles calculations yield the electron-phonon coupling constant λ = 0.81 and the logarithmically averaged frequency ω
ln
= 78.5 K, resulting in a theoretical T
c
= 2.5 K, close to the experimental value. Our calculations suggest that the enhanced electronic heat capacity is more likely due to electron-phonon coupling, rather than the electron-electron correlation effects. Collectively, these results place severe constraints on any theory of exotic superconductivity in this system.
FDXR is a biomarker of radiation exposure in vivo
Authors: O’Brien Gráinne , Cruz-Garcia Lourdes , Majewski Matthäus , Grepl Jakub , Abend Michael , Port Matthias , Tichý Aleš , Sirak Igor , Malkova Andrea , Donovan Ellen , Gothard Lone , Boyle Sue , Somaiah Navita , Ainsbury Elizabeth , Ponge Lucyna , Slosarek Krzysztof , Miszczyk Leszek , Widlak Piotr , Green Edward , Patel Neel , Kudari Mahesh , Gleeson Fergus , Vinnikov Volodymyr , Starenkiy Viktor , Artiukh Sergii , Vasyliev Leonid , Zaman Azfar , Badie Christophe 
Published: January 2018

AbstractPrevious investigations in gene expression changes in blood after radiation exposure have highlighted its potential to provide biomarkers of exposure. Here, FDXR transcriptional changes in blood were investigated in humans undergoing a range of external radiation exposure procedures covering several orders of magnitude (cardiac fluoroscopy, diagnostic computed tomography (CT)) and treatments (total body and local radiotherapy). Moreover, a method was developed to assess the dose to the blood using physical exposure parameters. FDXR expression was significantly up-regulated 24 hr after radiotherapy in most patients and continuously during the fractionated treatment. Significance was reached even after diagnostic CT 2 hours post-exposure. We further showed that no significant differences in expression were found between ex vivo and in vivo samples from the same patients. Moreover, potential confounding factors such as gender, infection status and anti-oxidants only affect moderately FDXR transcription. Finally, we provided a first in vivo dose-response showing dose-dependency even for very low doses or partial body exposure showing good correlation between physically and biologically assessed doses. In conclusion, we report the remarkable responsiveness of FDXR to ionising radiation at the transcriptional level which, when measured in the right time window, provides accurate in vivo dose estimates.
Targeting melanoma stem cells with the Vitamin E derivative δ-tocotrienol
Authors: Marzagalli Monica , Moretti Roberta Manuela , Messi Elio , Marelli Marina Montagnani , Fontana Fabrizio , Anastasia Alessia , Bani Maria Rosa , Beretta Giangiacomo , Limonta Patrizia 
Published: January 2018

AbstractThe prognosis of metastatic melanoma is very poor, due to the development of drug resistance. Cancer stem cells (CSCs) may play a crucial role in this mechanism, contributing to disease relapse. We first characterized CSCs in melanoma cell lines. We observed that A375 (but not BLM) cells are able to form melanospheres and show CSCs traits: expression of the pluripotency markers SOX2 and KLF4, higher invasiveness and tumor formation capability in vivo with respect to parental adherent cells. We also showed that a subpopulation of autofluorescent cells expressing the ABCG2 stem cell marker is present in the A375 spheroid culture. Based on these data, we investigated whether δ-TT might target melanoma CSCs. We demonstrated that melanoma cells escaping the antitumor activity of δ-TT are completely devoid of the ability to form melanospheres. In contrast, cells that escaped vemurafenib treatment show a higher ability to form melanospheres than control cells. δ-TT also induced disaggregation of A375 melanospheres and reduced the spheroidogenic ability of sphere-derived cells, reducing the expression of the ABCG2 marker. These data demonstrate that δ-TT exerts its antitumor activity by targeting the CSC subpopulation of A375 melanoma cells and might represent a novel chemopreventive/therapeutic strategy against melanoma.
Induction of protein citrullination and auto-antibodies production in murine exposed to nickel nanomaterials
Authors: Mohamed Bashir M. , Boyle Noreen T. , Schinwald Anja , Murer Bruno , Ward Ronan , Mahfoud Omar K. , Rakovich Tatsiana , Crosbie-Staunton Kieran , Gray Steven G. , Donaldson Ken , Volkov Yuri , Prina-Mello Adriele 
Published: January 2018

AbstractCitrullination, or the post-translational deimination of polypeptide-bound arginine, is involved in several pathological processes in the body, including autoimmunity and tumorigenesis. Recent studies have shown that nanomaterials can trigger protein citrullination, which might constitute a common pathogenic link to disease development. Here we demonstrated auto-antibody production in serum of nanomaterials-treated mice. Citrullination-associated phenomena and PAD levels were found to be elevated in nanomaterials -treated cell lines as well as in the spleen, kidneys and lymph nodes of mice, suggesting a systemic response to nanomaterials injection, and validated in human pleural and pericardial malignant mesothelioma (MM) samples. The observed systemic responses in mice exposed to nanomaterials support the evidence linking exposure to environmental factors with the development of autoimmunity responses and reinforces the need for comprehensive safety screening of nanomaterials. Furthermore, these nanomaterials induce pathological processes that mimic those observed in Pleural MM, and therefore require further investigations into their carcinogenicity.
Automatic segmentation of the solid core and enclosed vessels in subsolid pulmonary nodules
Authors: Charbonnier Jean-Paul , Chung Kaman , Scholten Ernst T. , van Rikxoort Eva M. , Jacobs Colin , Sverzellati Nicola , Silva Mario , Pastorino Ugo , van Ginneken Bram , Ciompi Francesco 
Published: January 2018

AbstractSubsolid pulmonary nodules are commonly encountered in lung cancer screening and clinical routine. Compared to other nodule types, subsolid nodules are associated with a higher malignancy probability for which the size and mass of the nodule and solid core are important indicators. However, reliably measuring these characteristics on computed tomography (CT) can be hampered by the presence of vessels encompassed by the nodule, since vessels have similar CT attenuation as solid cores. This can affect treatment decisions and patient management. We present a method based on voxel classification to automatically identify vessels and solid cores in given subsolid nodules on CT. Three experts validated our method on 170 screen-detected subsolid nodules from the Multicentric Italian Lung Disease trial. The agreement between the proposed method and the observers was substantial for vessel detection and moderate for solid core detection, which was similar to the inter-observer agreement. We found a relatively high variability in the inter-observer agreement and low method-observer agreements for delineating the borders of vessels and solid cores, illustrating the difficulty of this task. However, 92.4% of the proposed vessel and 80.6% of the proposed solid core segmentations were labeled as usable in clinical practice by the majority of experts.
SESN2 facilitates mitophagy by helping Parkin translocation through ULK1 mediated Beclin1 phosphorylation
Authors: Kumar Ashish , Shaha Chandrima 
Published: January 2018

AbstractMitophagy, the selective degradation of mitochondria by autophagy, is crucial for the maintenance of healthy mitochondrial pool in cells. The critical event in mitophagy is the translocation of cytosolic Parkin, a ubiquitin ligase, to the surface of defective mitochondria. This study elucidates a novel role of SESN2/Sestrin2, a stress inducible protein, in mitochondrial translocation of PARK2/Parkin during mitophagy. The data demonstrates that SESN2 downregulation inhibits BECN1/Beclin1 and Parkin interaction, thereby preventing optimum mitochondrial accumulation of Parkin. SESN2 interacts with ULK1 (unc-51 like kinase 1) and assists ULK1 mediated phosphorylation of Beclin1 at serine-14 position required for binding with Parkin prior to mitochondrial translocation. The trigger for SESN2 activation and regulation of Parkin translocation is the generation of mitochondrial superoxide. Scavenging of mitochondrial superoxide lower the levels of SESN2, resulting in retardation of Parkin translocation. Importantly, we observe that SESN2 mediated cytosolic interaction of Parkin and Beclin1 is PINK1 independent but mitochondrial translocation of Parkin is PINK1 dependent. Together, these findings suggest the role of SESN2 as a positive regulator of Parkin mediated mitophagy.
HyphaTracker: An ImageJ toolbox for time-resolved analysis of spore germination in filamentous fungi
Authors: Brunk Michael , Sputh Sebastian , Doose Sören , van de Linde Sebastian , Terpitz Ulrich 
Published: January 2018

AbstractThe dynamics of early fungal development and its interference with physiological signals and environmental factors is yet poorly understood. Especially computational analysis tools for the evaluation of the process of early spore germination and germ tube formation are still lacking. For the time-resolved analysis of conidia germination of the filamentous ascomycete Fusarium fujikuroi we developed a straightforward toolbox implemented in ImageJ. It allows for processing of microscopic acquisitions (movies) of conidial germination starting with drift correction and data reduction prior to germling analysis. From the image time series germling related region of interests (ROIs) are extracted, which are analysed for their area, circularity, and timing. ROIs originating from germlings crossing other hyphae or the image boundaries are omitted during analysis. Each conidium/hypha is identified and related to its origin, thus allowing subsequent categorization. The efficiency of HyphaTracker was proofed and the accuracy was tested on simulated germlings at different signal-to-noise ratios. Bright-field microscopic images of conidial germination of rhodopsin-deficient F. fujikuroi mutants and their respective control strains were analysed with HyphaTracker. Consistent with our observation in earlier studies the CarO deficient mutant germinated earlier and grew faster than other, CarO expressing strains.
The RacGAP β-Chimaerin is essential for cerebellar granule cell migration
Authors: Estep Jason A. , Wong Wenny , Wong Yiu-Cheung E. , Loui Brian M. , Riccomagno Martin M. 
Published: January 2018

AbstractDuring mammalian cerebellar development, postnatal granule cell progenitors proliferate in the outer part of the External Granule Layer (EGL). Postmitotic granule progenitors migrate tangentially in the inner EGL before switching to migrate radially inward, past the Purkinje cell layer, to achieve their final position in the mature Granule Cell Layer (GCL). Here, we show that the RacGAP β-chimaerin is expressed by a small population of late-born, premigratory granule cells. β-chimaerin deficiency causes a subset of granule cells to become arrested in the EGL, where they differentiate and form ectopic neuronal clusters. These clusters of granule cells are able to recruit aberrantly projecting mossy fibers. Collectively, these data suggest a role for β-chimaerin as an intracellular mediator of Cerebellar Granule Cell radial migration.
Missing Value Imputation Approach for Mass Spectrometry-based Metabolomics Data
Authors: Wei Runmin , Wang Jingye , Su Mingming , Jia Erik , Chen Shaoqiu , Chen Tianlu , Ni Yan 
Published: January 2018

AbstractMissing values exist widely in mass-spectrometry (MS) based metabolomics data. Various methods have been applied for handling missing values, but the selection can significantly affect following data analyses. Typically, there are three types of missing values, missing not at random (MNAR), missing at random (MAR), and missing completely at random (MCAR). Our study comprehensively compared eight imputation methods (zero, half minimum (HM), mean, median, random forest (RF), singular value decomposition (SVD), k-nearest neighbors (kNN), and quantile regression imputation of left-censored data (QRILC)) for different types of missing values using four metabolomics datasets. Normalized root mean squared error (NRMSE) and NRMSE-based sum of ranks (SOR) were applied to evaluate imputation accuracy. Principal component analysis (PCA)/partial least squares (PLS)-Procrustes analysis were used to evaluate the overall sample distribution. Student’s t-test followed by correlation analysis was conducted to evaluate the effects on univariate statistics. Our findings demonstrated that RF performed the best for MCAR/MAR and QRILC was the favored one for left-censored MNAR. Finally, we proposed a comprehensive strategy and developed a public-accessible web-tool for the application of missing value imputation in metabolomics (https://metabolomics.cc.hawaii.edu/software/MetImp/).
Spatially selective responses to Kanizsa and occlusion stimuli in human visual cortex
Authors: de Haas Benjamin , Schwarzkopf Dietrich Samuel 
Published: January 2018

AbstractEarly visual cortex responds to illusory contours in which abutting lines or collinear edges imply the presence of an occluding surface, as well as to occluded parts of an object. Here we used functional magnetic resonance imaging (fMRI) and population receptive field (pRF) analysis to map retinotopic responses in early visual cortex using bar stimuli defined by illusory contours, occluded parts of a bar, or subtle luminance contrast. All conditions produced retinotopic responses in early visual field maps even though signal-to-noise ratios were very low. We found that signal-to-noise ratios and coherence with independent high-contrast mapping data increased from V1 to V2 to V3. Moreover, we found no differences of signal-to-noise ratios or pRF sizes between the low-contrast luminance and illusion conditions. We propose that all three conditions mapped spatial attention to the bar location rather than activations specifically related to illusory contours or occlusion.
Virtual Genome Walking across the 32 Gb Ambystoma mexicanum genome; assembling gene models and intronic sequence
Authors: Evans Teri , Johnson Andrew D. , Loose Matthew 
Published: January 2018

AbstractLarge repeat rich genomes present challenges for assembly using short read technologies. The 32 Gb axolotl genome is estimated to contain ~19 Gb of repetitive DNA making an assembly from short reads alone effectively impossible. Indeed, this model species has been sequenced to 20× coverage but the reads could not be conventionally assembled. Using an alternative strategy, we have assembled subsets of these reads into scaffolds describing over 19,000 gene models. We call this method Virtual Genome Walking as it locally assembles whole genome reads based on a reference transcriptome, identifying exons and iteratively extending them into surrounding genomic sequence. These assemblies are then linked and refined to generate gene models including upstream and downstream genomic, and intronic, sequence. Our assemblies are validated by comparison with previously published axolotl bacterial artificial chromosome (BAC) sequences. Our analyses of axolotl intron length, intron-exon structure, repeat content and synteny provide novel insights into the genic structure of this model species. This resource will enable new experimental approaches in axolotl, such as ChIP-Seq and CRISPR and aid in future whole genome sequencing efforts. The assembled sequences and annotations presented here are freely available for download fromhttps://tinyurl.com/y8gydc6n. The software pipeline is available fromhttps://github.com/LooseLab/iterassemble.
Controlled synthesis of Cu nanoparticle arrays with surface enhanced Raman scattering effect performance
Authors: Ding Qianqian , Hang Lifeng , Ma Liang 
Published: January 2018

Herein, we report the synthesis of a 350 nm Cu nanoparticle array with different period combinations by a method based on a monolayer and have further investigated its surface-enhanced Raman scattering (SERS) properties experimentally.