bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extraction of the Rashba spin-orbit coupling constant from scanning gate microscopy conductance maps for quantum point contacts
Authors: Kolasiński K. , Sellier H. , Szafran B. 
Published: October 2017

AbstractWe study the possibility for the extraction of the Rashba spin-orbit coupling constant for a two-dimensional electron gas with the conductance microscopy technique. Due to the interplay between the effective magnetic field due to the Rashba spin-orbit coupling and the external magnetic field applied within the plane of confinement, the electron backscattering induced by a charged tip of an atomic force microscope located above the sample leads to the spin precession and spin mixing of the incident and reflected electron waves between the QPC and the tip-induced 2DEG depletion region. This mixing leads to a characteristic angle-dependent beating pattern visible in the conductance maps. We show that the structure of the Fermi level, bearing signatures of the spin-orbit coupling, can be extracted from the Fourier transform of the interference fringes in the conductance maps as a function of the magnetic field direction. We propose a simple analytical model which can be used to fit the experimental data in order to obtain the spin-orbit coupling constant.
VP2 of Chicken Anaemia Virus Interacts with Apoptin for Down-regulation of Apoptosis through De-phosphorylated Threonine 108 on Apoptin
Authors: Lai Guan-Hua , Lien Yi-Yang , Lin Ming-Kuem , Cheng Jai-Hong , Tzen Jason TC , Sun Fang-Chun , Lee Meng-Shiunn , Chen Hsi-Jien , Lee Meng-Shiou 
Published: October 2017

AbstractChicken anaemia virus (CAV) is an important contagious agent that causes immunosuppressive disease in chickens. CAV Apoptin is a nucleoplasmic shuffling protein that induces apoptosis in chicken lymphoblastoid cells. In the present study, confocal microscopy revealed co-localisation of expressed CAV non-structural protein VP2 with Apoptin in the nucleus of MDCC-MSB1 cells and the nucleoplasmic compartment of CHO-K1 cells. In vitro pull-down and ex vivo biomolecular fluorescent complementation (BiFC) assays further showed that the VP2 protein directly interacts with Apoptin. Transient co-expression of VP2 and Apoptin in MDCC-MSB1 cells significantly decreased the rate of apoptosis compared with that in cells transfected with the Apoptin gene alone. In addition, the phosphorylation status of threonine 108 (Thr108) of Apoptin was found to decrease upon interaction with VP2. Although dephosphorylated Thr108 did not alter the subcellular distribution of Apoptin in the nucleus of MDCC-MSB1 cells, it did suppress apoptosis. These findings provide the first evidence that VP2 directly interacts with Apoptin in the nucleus to down-regulate apoptosis through alterations in the phosphorylation status of the latter. This information will be useful to further elucidate the underlying mechanism of viral replication in the CAV life cycle.
The genetic variation in the R1a clade among the Ashkenazi Levites’ Y chromosome
Authors: Behar Doron M. , Saag Lauri , Karmin Monika , Gover Meir G. , Wexler Jeffrey D. , Sanchez Luisa Fernanda , Greenspan Elliott , Kushniarevich Alena , Davydenko Oleg , Sahakyan Hovhannes , Yepiskoposyan Levon , Boattini Alessio , Sarno Stefania , Pagani Luca , Carmi Shai , Tzur Shay , Metspalu Ene , Bormans Concetta , Skorecki Karl , Metspalu Mait , Rootsi Siiri , Villems Richard 
Published: October 2017

AbstractApproximately 300,000 men around the globe self-identify as Ashkenazi Levites, of whom two thirds were previously shown to descend from a single male. The paucity of whole Y-chromosome sequences precluded conclusive identification of this ancestor’s age, geographic origin and migration patterns. Here, we report the variation of 486 Y-chromosomes within the Ashkenazi and non-Ashkenazi Levite R1a clade, other Ashkenazi Jewish paternal lineages, as well as non-Levite Jewish and non-Jewish R1a samples. Cumulatively, the emerging profile is of a Middle Eastern ancestor, self-affiliating as Levite, and carrying the highly resolved R1a-Y2619 lineage, which was likely a minor haplogroup among the Hebrews. A star-like phylogeny, coalescing similarly to other Ashkenazi paternal lineages, ~1,743 ybp, suggests it to be one of the Ashkenazi paternal founders; to have expanded as part of the overall Ashkenazi demographic expansion, without special relation to the Levite affiliation; and to have subsequently spread to non-Ashkenazi Levites.
Palmitate inhibits arthritis by inducing t-bet and gata-3 mRNA degradation in iNKT cells via IRE1α-dependent decay
Authors: Ko Jae Sung , Koh Jae Moon , So Jae-Seon , Jeon Yoon Kyung , Kim Hye Young , Chung Doo Hyun 
Published: October 2017

AbstractLong chain fatty acids (LCFAs) exert pro-inflammatory effectsin vivo. However, little is known regarding the effect of LCFAs on invariant (i) NKT cell functions. Here, we report an inhibitory effect of saturated LCFAs on transcription factors iniNKT cells. Among the saturated LCFAs, palmitic acid (PA) specifically inhibited IL-4 and IFN-γ production and reducedgata-3andt-bettranscript levels iniNKT cells during TCR-mediated activation. IniNKT cells, PA was localized and induced dilation in the endoplasmic reticulum and increased the mRNA levels of downstream molecules of IRE1α RNase. Moreover, PA increased the degradation rates ofgata-3andt-betmRNA, which was restored by IRE1α inhibition or transfection with mutantgata-3ort-bet, indicating thatgata-3andt-betare cleaved via regulated IRE1α-dependent decay (RIDD). A PA-rich diet and PA injection suppressed IL-4 and IFN-γ production byiNKT cells in C57BL/6, but not Jα18 knockout mice, which was restored by injection of STF083010, an IRE1α-specific inhibitor. Furthermore, a PA-rich diet and PA injection attenuated arthritis in aniNKT cell-dependent manner. Taken together, our experiments demonstrate that a saturated LCFA induced RIDD-mediatedt-betandgata-3mRNA degradation iniNKT cells, thereby suppressing arthritis.
Identification of pharmacological agents that induce HMGB1 release
Authors: Liu Peng , Zhao Liwei , Loos Friedemann , Iribarren Kristina , Lachkar Sylvie , Zhou Heng , Gomes-da-Silva Lígia C. , Chen Guo , Bezu Lucillia , Boncompain Gaelle , Perez Franck , Zitvogel Laurence , Kepp Oliver , Kroemer Guido 
Published: October 2017

AbstractThe translocation of the protein high mobility group box 1 (HMGB1) from the nucleus to the cytoplasm and its secretion or passive release through the permeabilized plasma membrane, constitutes a major cellular danger signal. Extracellular HMGB1 can interact with pattern recognition receptors to stimulate pro-inflammatory and immunostimulatory pathways. Here, we developed a screening assay to identify pharmacological agents endowed with HMGB1 releasing properties. For this, we took advantage of the “retention using selective hooks” (RUSH) system in which a streptavidin-NLS3 fusion protein was used as a nuclear hook to sequestrate streptavidin-binding peptide (SBP) fused with HMGB1 and green fluorescent protein (GFP). When combined with biotin, which competitively disrupts the interaction between streptavidin-NLS3 and HMGB1-SBP-GFP, immunogenic cell death (ICD) inducers such as anthracyclines were able to cause the nucleo-cytoplasmic translocation of HMGB1-SBP-GFP. This system, was used in a high-content screening (HCS) campaign for the identification of HMGB1 releasing agents. Hits fell into three functional categories: known ICD inducers, microtubule inhibitors and epigenetic modifiers. These agents induced ICD through a panoply of distinct mechanisms. Their effective action was confirmed by multiple methods monitoring nuclear, cytoplasmic and extracellular HMGB1 pools, both in cultured human or murine cells, as well as in mouse plasma.
Author Correction: Pancreatic cancer: Circulating Tumor Cells and Primary Tumors show Heterogeneous KRAS Mutations
Authors: Kulemann Birte , Rösch Stephanie , Seifert Sindy , Timme Sylvia , Bronsert Peter , Seifert Gabriel , Martini Verena , Kuvendjiska Jasmina , Glatz Torben , Hussung Saskia , Fritsch Ralph , Becker Heiko , Pitman Martha B. , Hoeppner Jens 
Published: October 2017

AbstractA correction to this article has been published and is linked from the HTML version of this paper. The error has been fixed in the paper.
Proof-of-concept Raman spectroscopy study aimed to differentiate thyroid follicular patterned lesions
Authors: Rau Julietta V. , Fosca Marco , Graziani Valerio , Taffon Chiara , Rocchia Massimiliano , Caricato Marco , Pozzilli Paolo , Onetti Muda Andrea , Crescenzi Anna 
Published: October 2017

AbstractInter-observer variability and cancer over-diagnosis are emerging clinical problems, especially for follicular patterned thyroid lesions. This challenge strongly calls for a new clinical tool to reliably identify neoplastic lesions and to improve the efficiency of differentiation between benign and malignant neoplasms, especially considering the increased diagnosis of small carcinomas and the growing number of thyroid nodules. In this study, we employed a Raman spectroscopy (RS) microscope to investigate frozen thyroid tissues from fourteen patients with thyroid nodules. To generate tissue classification models, a supervised statistical analysis of the Raman spectra was performed. The results obtained demonstrate an accuracy of 78% for RS based diagnosis to discriminate between normal parenchyma and follicular patterned thyroid nodules, and 89% accuracy – for very challenging follicular lesions (carcinoma versus adenoma). RS translation into intraoperative diagnosis of frozen sections and in preoperative analysis of biopsies can be very helpful to reduce unnecessary surgery in patients with indeterminate cytological reports.
Spermine oxidase promotes bile canalicular lumen formation through acrolein production
Authors: Uemura Takeshi , Takasaka Tomokazu , Igarashi Kazuei , Ikegaya Hiroshi 
Published: October 2017

AbstractSpermine oxidase (SMOX) catalyzes oxidation of spermine to generate spermidine, hydrogen peroxide (H2O2) and 3-aminopropanal, which is spontaneously converted to acrolein. SMOX is induced by a variety of stimuli including bacterial infection, polyamine analogues and acetaldehyde exposure. However, the physiological functions of SMOX are not yet fully understood. We investigated the physiological role of SMOX in liver cells using human hepatocellular carcinoma cell line HepG2. SMOX localized to the bile canalicular lumen, as determined by F-actin staining. Knockdown of SMOX reduced the formation of bile canalicular lumen. We also found that phospho-Akt (phosphorylated protein kinase B) was localized to canalicular lumen. Treatment with Akt inhibitor significantly reduced the formation of bile canalicular lumen. Acrolein scavenger also inhibited the formation of bile canalicular lumen. PTEN, phosphatase and tensin homolog and an inhibitor of Akt, was alkylated in a SMOX-dependent manner. Our results suggest that SMOX plays a central role in the formation of bile canalicular lumen in liver cells by activating Akt pathway through acrolein production.
Secretoneurin A regulates neurogenic and inflammatory transcriptional networks in goldfish (Carassius auratus) radial glia
Authors: Da Fonte Dillon F. , Martyniuk Christopher J. , Xing Lei , Pelin Adrian , Corradi Nicolas , Hu Wei , Trudeau Vance L. 
Published: October 2017

AbstractRadial glial cells (RGCs) are the most abundant macroglia in the teleost brain and have established roles in neurogenesis and neurosteroidogenesis; however, their transcriptome remains uncharacterized, which limits functional understanding of this important cell type. Using cultured goldfish RGCs, RNA sequencing and de novo transcriptome assembly were performed, generating the first reference transcriptome for fish RGCs with 17,620 unique genes identified. These data revealed that RGCs express a diverse repertoire of receptors and signaling molecules, suggesting that RGCs may respond to and synthesize an array of hormones, peptides, cytokines, and growth factors. Building upon neuroanatomical data and studies investigating direct neuronal regulation of RGC physiology, differential gene expression analysis was conducted to identify transcriptional networks that are responsive to the conserved secretogranin II-derived neuropeptide secretoneurin A (SNa). Pathway analysis of the transcriptome indicated that cellular processes related to the central nervous system (e.g., neurogenesis, synaptic plasticity, glial cell development) and immune functions (e.g., immune system activation, leukocyte function, macrophage response) were preferentially modulated by SNa. These data reveal an array of new functions that are proposed to be critical to neuronal-glial interactions through the mediator SNa.
iDNAProt-ES: Identification of DNA-binding Proteins Using Evolutionary and Structural Features
Authors: Chowdhury Shahana Yasmin , Shatabda Swakkhar , Dehzangi Abdollah 
Published: October 2017

AbstractDNA-binding proteins play a very important role in the structural composition of the DNA. In addition, they regulate and effect various cellular processes like transcription, DNA replication, DNA recombination, repair and modification. The experimental methods used to identify DNA-binding proteins are expensive and time consuming and thus attracted researchers from computational field to address the problem. In this paper, we present iDNAProt-ES, a DNA-binding protein prediction method that utilizes both sequence based evolutionary and structure based features of proteins to identify their DNA-binding functionality. We used recursive feature elimination to extract an optimal set of features and train them using Support Vector Machine (SVM) with linear kernel to select the final model. Our proposed method significantly outperforms the existing state-of-the-art predictors on standard benchmark dataset. The accuracy of the predictor is 90.18% using jack knife test and 88.87% using 10-fold cross validation on the benchmark dataset. The accuracy of the predictor on the independent dataset is 80.64% which is also significantly better than the state-of-the-art methods. iDNAProt-ES is a novel prediction method that uses evolutionary and structural based features. We believe the superior performance of iDNAProt-ES will motivate the researchers to use this method to identify DNA-binding proteins. iDNAProt-ES is publicly available as a web server at:http://brl.uiu.ac.bd/iDNAProt-ES/.
Heparanase and macrophage interplay in the onset of liver fibrosis
Authors: Secchi Maria Francesca , Crescenzi Marika , Masola Valentina , Russo Francesco Paolo , Floreani Annarosa , Onisto Maurizio 
Published: October 2017

AbstractThe heparan sulfate endoglycosidase heparanase (HPSE) is involved in tumor growth, chronic inflammation and fibrosis. Since a role for HPSE in chronic liver disease has not been demonstrated to date, the current study was aimed at investigating the involvement of HPSE in the pathogenesis of chronic liver injury. Herein, we revealed that HPSE expression increased in mouse livers after carbon tetrachloride (CCl4)-mediated chronic induction of fibrosis, but with a trend to decline during progression of the disease. In mouse fibrotic liver tissues HPSE immunostaining was restricted in necro-inflammatory areas, co-localizing with F4/80 macrophage marker and TNF-α. TNF-α treatment induced HPSE expression as well as HPSE secretion in U937 macrophages. Moreover, macrophage-secreted HPSE regulated the expression of α-SMA and fibronectin in hepatic stellate LX-2 cells. Finally, HPSE activity increased in the plasma of patients with liver fibrosis but it inversely correlated with liver stiffness. Our results suggest the involvement of HPSE in early phases of reaction to liver damage and inflammatory macrophages as an important source of HPSE. HPSE seems to play a key role in the macrophage-mediated activation of hepatic stellate cells (HSCs), thus suggesting that HPSE targeting could be a new therapeutic option in the treatment of liver fibrosis.
Implications of mitochondrial network organization in mitochondrial stress signalling in NARP cybrid and Rho0 cells
Authors: Walczak Jarosław , Partyka Małgorzata , Duszyński Jerzy , Szczepanowska Joanna 
Published: October 2017

AbstractMitochondrial dysfunctions lead to the generation of signalling mediators that influence the fate of that organelle. Mitochondrial dynamics and their positioning within the cell are important elements of mitochondria-nucleus communication. The aim of this project was to examine whether mitochondrial shape, distribution and fusion/fission proteins are involved in the mitochondrial stress response in a cellular model subjected to specifically designed chronic mitochondrial stress: WT human osteosarcoma cells as controls, NARP cybrid cells as mild chronic stress and Rho0 as severe chronic stress. We characterized mitochondrial distribution in these cells using confocal microscopy and evaluated the level of proteins directly involved in the mitochondrial dynamics and their regulation. We found that the organization of mitochondria within the cell is correlated with changes in the levels of proteins involved in mitochondrial dynamics and proteins responsible for regulation of this process. Induction of the autophagy/mitophagy process, which is crucial for cellular homeostasis under stress conditions was also shown. It seems that mitochondrial shape and organization within the cell are implicated in retrograde signalling in chronic mitochondrial stress.
HIF-1α- Targeting Acriflavine Provides Long Term Survival and Radiological Tumor Response in Brain Cancer Therapy
Authors: Mangraviti Antonella , Raghavan Tula , Volpin Francesco , Skuli Nicolas , Gullotti David , Zhou Jinyuan , Asnaghi Laura , Sankey Eric , Liu Ann , Wang Yuan , Lee Dong-Hoon , Gorelick Noah , Serra Riccardo , Peters Michael , Schriefer Destiny , Delaspre Fabien , Rodriguez Fausto J. , Eberhart Charles G. , Brem Henry , Olivi Alessandro , Tyler Betty 
Published: October 2017

AbstractTumor progression, limited efficacy of current standard treatments, and the rise in patient mortality are associated with gene expression caused by the synergistic action of intratumoral hypoxia and HIF-1α activation. For this reason, recent investigations have focused on HIF-targeting therapeutic agents, with encouraging preclinical and clinical results in solid tumors. Here we describe the efficacy of a HIF-1α inhibitor, Acriflavine, and demonstrate its potency against brain cancer. This safe antibacterial dye induces cell death and apoptosis in several glioma cell lines, targets HIF-1α–mediated pathways, and decreases the level of PGK1, VEGF and HIF-1α in vitro and in vivo. Administered locally via biodegradable polymers, Acriflavine provides significant benefits in survival resulting in nearly 100% long term survival, confirmed by MRI and histological analyses. This study reports preclinical evidence that this safe, small molecule can contribute to brain tumor therapy and highlights the significance of HIF-1α-targeting molecules.
Two-dimensional negative capacitance transistor with polyvinylidene fluoride-based ferroelectric polymer gating
Authors: Wang Xudong , Chen Yan , Wu Guangjian , Li Dan , Tu Luqi , Sun Shuo , Shen Hong , Lin Tie , Xiao Yongguang , Tang Minghua , Hu Weida , Liao Lei , Zhou Peng , Sun Jinglan , Meng Xiangjian , Chu Junhao , Wang Jianlu 
Published: October 2017

AbstractConventional field-effect transistors (FETs) are not expected to satisfy the requirements of future large integrated nanoelectronic circuits because of these circuits’ ultra-high power dissipation and because the conventional FETs cannot overcome the subthreshold swing (SS) limit of 60 mV/decade. In this work, the ordinary oxide of the FET is replaced only by a ferroelectric (Fe) polymer, poly(vinylidene difluoride-trifluoroethylene) (P(VDF-TrFE)). Additionally, we employ a two-dimensional (2D) semiconductor, such as MoS2 and MoSe2, as the channel. This 2D Fe-FET achieves an ultralow SS of 24.2 mV/dec over four orders of magnitude in drain current at room temperature; this sub-60 mV/dec switching is derived from the Fe negative capacitance (NC) effect during the polarization of ferroelectric domain switching. Such 2D NC-FETs, realized by integrating of 2D semiconductors and organic ferroelectrics, provide a new approach to satisfy the requirements of next-generation low-energy-consumption integrated nanoelectronic circuits as well as the requirements of future flexible electronics.
A compendium of multi-omic sequence information from the Saanich Inlet water column
Authors: Hawley Alyse K. , Torres-Beltrán Mónica , Zaikova Elena , Walsh David A. , Mueller Andreas , Scofield Melanie , Kheirandish Sam , Payne Chris , Pakhomova Larysa , Bhatia Maya , Shevchuk Olena , Gies Esther A. , Fairley Diane , Malfatti Stephanie A. , Norbeck Angela D. , Brewer Heather M. , Pasa-Tolic Ljiljana , del Rio Tijana Glavina , Suttle Curtis A. , Tringe Susannah , Hallam Steven J. 
Published: October 2017

AbstractMarine oxygen minimum zones (OMZs) are widespread regions of the ocean that are currently expanding due to global warming. While inhospitable to most metazoans, OMZs are hotspots for microbial mediated biogeochemical cycling of carbon, nitrogen and sulphur, contributing disproportionately to marine nitrogen loss and climate active trace gas production. Our current understanding of microbial community responses to OMZ expansion is limited by a lack of time-resolved data sets linking multi-omic sequence information (DNA, RNA, protein) to geochemical parameters and process rates. Here, we present six years of time-resolved multi-omic observations in Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island, British Columbia, Canada that undergoes recurring changes in water column oxygenation status. This compendium provides a unique multi-omic framework for studying microbial community responses to ocean deoxygenation along defined geochemical gradients in OMZ waters.
Predicting Intelligibility Gains in Individuals With Dysarthria From Baseline Speech Features
Authors: Fletcher Annalise R. , McAuliffe Megan J. , Lansford Kaitlin L. , Sinex Donal G. , Liss Julie M. 
Published: October 2017

Purpose
Across the treatment literature, behavioral speech modifications have produced variable intelligibility changes in speakers with dysarthria. This study is the first of two articles exploring whether measurements of baseline speech features can predict speakers’ responses to these modifications.

Methods
Fifty speakers (7 older individuals and 43 speakers with dysarthria) read a standard passage in habitual, loud, and slow speaking modes. Eighteen listeners rated how easy the speech samples were to understand. Baseline acoustic measurements of articulation, prosody, and voice quality were collected with perceptual measures of severity.

Results
Cues to speak louder and reduce rate did not confer intelligibility benefits to every speaker. The degree to which cues to speak louder improved intelligibility could be predicted by speakers' baseline articulation rates and overall dysarthria severity. Improvements in the slow condition could be predicted by speakers' baseline severity and temporal variability. Speakers with a breathier voice quality tended to perform better in the loud condition than in the slow condition.

Conclusions
Assessments of baseline speech features can be used to predict appropriate treatment strategies for speakers with dysarthria. Further development of these assessments could provide the basis for more individualized treatment programs.