bluuebunny/crossref_metadata_2025_split huggingface dataset:
IL-1α is a DNA damage sensor linking genotoxic stress signaling to sterile inflammation and innate immunity
Authors: Cohen Idan , Rider Peleg , Vornov Elena , Tomas Martin , Tudor Cicerone , Wegner Mareike , Brondani Lydia , Freudenberg Marina , Mittler Gerhard , Ferrando-May Elisa , Dinarello Charles A. , Apte Ron N. , Schneider Robert 
Published: October 2015

AbstractEnvironmental signals can be translated into chromatin changes, which alter gene expression. Here we report a novel concept that cells can signal chromatin damage from the nucleus back to the surrounding tissue through the cytokine interleukin-1alpha (IL-1α). Thus, in addition to its role as a danger signal, which occurs when the cytokine is passively released by cell necrosis, IL-1α could directly sense DNA damage and act as signal for genotoxic stress without loss of cell integrity. Here we demonstrate localization of the cytokine to DNA-damage sites and its subsequent secretion. Interestingly, its nucleo-cytosolic shuttling after DNA damage sensing is regulated by histone deacetylases (HDAC) and IL-1α acetylation. To demonstrate the physiological significance of this newly discovered mechanism, we used IL-1α knockout mice and show that IL-1α signaling after UV skin irradiation and DNA damage is important for triggering a sterile inflammatory cascade in vivo that contributes to efficient tissue repair and wound healing.
Identification of a FOXP3+CD3+CD56+ population with immunosuppressive function in cancer tissues of human hepatocellular carcinoma
Authors: Li Xiaofeng , Peng Jirun , Pang Yanli , Yu Sen , Yu Xin , Chen Pengcheng , Wang Wenzhen , Han Wenling , Zhang Jun , Yin Yanhui , Zhang Yu 
Published: October 2015

AbstractThe liver resident lymphoid population is featured by the presence of a large number of CD3+CD56+ cells referred as natural T cells. In human hepatocellular carcinoma (HCC) patients, the natural T cells were found to be sharply decreased in tumor (5.871 ± 3.553%) versus non-tumor (14.02 ± 6.151%) tissues. More intriguingly, a substantial fraction of the natural T cells (22.76 ± 18.61%) assumed FOXP3 expression. These FOXP3-expressing CD3+CD56+ cells lost the expression of IFN-γ and perforin, which are critical for the effector function of natural T cells. On the other hand, they acquired surface expression of CD25 and CTLA-4 typically found in regulatory T (Treg) cells. Consistent with the phenotypic conversion, they imposed an inhibitory effect on anti-CD3-induced proliferation of naive T cells. Further studies demonstrated that transforming growth factor β1 (TGF-β1) could effectively induce FOXP3 expression in CD3+CD56+ cells and the cells were thus endowed with a potent immunosuppressive capacity. Finally, Kaplan-Meier analysis revealed that the relative abundance of FOXP3-expressing CD3+CD56+ cells in tumor tissues was significantly correlated with the survival of HCC patients. In conclusion, the present study identified a new type of regulatory immune cells whose emergence in liver cancer tissues may contribute to tumor progression.
Identification of H2S3 and H2S produced by 3-mercaptopyruvate sulfurtransferase in the brain
Authors: Kimura Yuka , Toyofuku Yukiko , Koike Shin , Shibuya Norihiro , Nagahara Noriyuki , Lefer David , Ogasawara Yuki , Kimura Hideo 
Published: October 2015

AbstractHydrogen polysulfides (H2Sn) have a higher number of sulfane sulfur atoms than hydrogen sulfide (H2S), which has various physiological roles. We recently found H2Sn in the brain. H2Sn induced some responses previously attributed to H2S but with much greater potency than H2S. However, the number of sulfur atoms in H2Sn and its producing enzyme were unknown. Here, we detected H2S3 and H2S, which were produced from 3-mercaptopyruvate (3 MP) by 3-mercaptopyruvate sulfurtransferase (3MST), in the brain. High performance liquid chromatography with fluorescence detection (LC-FL) and tandem mass spectrometry (LC-MS/MS) analyses showed that H2S3 and H2S were produced from 3 MP in the brain cells of wild-type mice but not 3MST knockout (3MST-KO) mice. Purified recombinant 3MST and lysates of COS cells expressing 3MST produced H2S3 from 3 MP, while those expressing defective 3MST mutants did not. H2S3 was localized in the cytosol of cells. H2S3 was also produced from H2S by 3MST and rhodanese. H2S2 was identified as a minor H2Sn and 3 MP did not affect the H2S5 level. The present study provides new insights into the physiology of H2S3 and H2S, as well as novel therapeutic targets for diseases in which these molecules are involved.
PLD1 participates in BDNF-induced signalling in cortical neurons
Authors: Ammar Mohamed Raafet , Thahouly Tamou , Hanauer André , Stegner David , Nieswandt Bernhard , Vitale Nicolas 
Published: October 2015

AbstractThe brain-derived neurotrophic factor BDNF plays a critical role in neuronal development and the induction of L-LTP at glutamatergic synapses in several brain regions. However, the cellular and molecular mechanisms underlying these BDNF effects have not been firmly established. Using in vitro cultures of cortical neurons from knockout mice for Pld1 and Rsk2, BDNF was observed to induce a rapid RSK2-dependent activation of PLD and to stimulate BDNF ERK1/2-CREB and mTor-S6K signalling pathways, but these effects were greatly reduced in Pld1−/− neurons. Furthermore, phospho-CREB did not accumulate in the nucleus, whereas overexpression of PLD1 amplified the BDNF-dependent nuclear recruitment of phospho-ERK1/2 and phospho-CREB. This BDNF retrograde signalling was prevented in cells silenced for the scaffolding protein PEA15, a protein which complexes with PLD1, ERK1/2 and RSK2 after BDNF treatment. Finally PLD1, ERK1/2 and RSK2 partially colocalized on endosomal structures, suggesting that these proteins are part of the molecular module responsible for BDNF signalling in cortical neurons.
Multicopper oxidase-1 is required for iron homeostasis in Malpighian tubules of Helicoverpa armigera
Authors: Liu Xiaoming , Sun Chengxian , Liu Xiaoguang , Yin Xinming , Wang Baohai , Du Mengfang , An Shiheng 
Published: October 2015

AbstractMulticopper oxidases (MCOs) are enzymes that contain 10 conserved histidine residues and 1 cysteine residue. MCO1 has been extensively investigated in the midgut because this MCO is implicated in ascorbate oxidation, iron homeostasis and immune responses. However, information regarding the action of MCO1 in Malpighian tubules is limited. In this study, Helicoverpa armigera was used as a model to investigate the function of MCO1 in Malpighian tubules. Sequence analysis results revealed that HaMCO1 exhibits typical MCO characteristics, with 10 histidine and 1 cysteine residues for copper ion binding. HaMCO1 was also found to be highly abundant in Malpighian tubules. Temporal expression patterns indicated that HaMCO1 is mainly expressed during larval molting stages. Hormone treatments [the molting hormone 20-hydroxyecdysone (20E) and juvenile hormone (JH)] revealed that 20E inhibits HaMCO1 transcript expression via its heterodimer receptor, which consists of ecdysone receptor (EcR) and ultraspiracle (USP) and that JH counteracts the action of 20E to activate HaMCO1 transcript expression via its intracellular receptor methoprene-tolerant (Met). HaMCO1 knockdown caused a significant decrease in iron accumulation and also significantly reduced transferrin and ferritin transcript expression. Therefore, HaMCO1 is coordinately regulated by 20E and JH and is required for iron homeostasis in Malpighian tubules.
Thermal surface free energy and stress of iron
Authors: Schönecker Stephan , Li Xiaoqing , Johansson Börje , Kwon Se Kyun , Vitos Levente 
Published: October 2015

AbstractAbsolute values of surface energy and surface stress of solids are hardly accessible by experiment. Here, we investigate the temperature dependence of both parameters for the (001) and (110) surface facets of body-centered cubic Fe from first-principles modeling taking into account vibrational, electronic and magnetic degrees of freedom. The monotonic decrease of the surface energies of both facets with increasing temperature is mostly due to lattice vibrations and magnetic disorder. The surface stresses exhibit nonmonotonic behaviors resulting in a strongly temperature dependent excess surface stress and surface stress anisotropy.
Differential levels of p75NTR ectodomain in CSF and blood in patients with Alzheimer’s disease: a novel diagnostic marker
Authors: Jiao S-S , Bu X-L , Liu Y-H , Wang Q-H , Liu C-H , Yao X-Q , Zhou X-F , Wang Y-J 
Published: October 2015

AbstractAlzheimer’s disease (AD) is the primary cause of dementia in the elderly. The ectodomain of p75 neurotrophin receptor (p75NTR-ECD) has been suggested to play important roles in regulating beta-amyloid (Aβ) deposition and in protecting neurons from the toxicity of soluble Aβ. However, whether and how the serum and cerebrospinal fluid (CSF) levels of p75NTR-ECD change in patients with AD are not well documented. In the present study, we determined the concentrations of serum p75NTR-ECD in an AD group, a Parkinson disease group and a stroke group, as well as in a group of elderly controls without neurological disorders (EC). We also determined the levels of CSF p75NTR-ECD in a subset of the AD and EC groups. Our data showed that a distinct p75NTR-ECD profile characterized by a decreased CSF level and an increased serum level was present concomitantly with AD patients but not with other diseases. p75NTR-ECD levels in both the serum and CSF were strongly correlated with Mini-Mental State Examination (MMSE) scores and showed sound differential diagnostic value for AD. Moreover, when combining CSF Aβ42, CSF Aβ42/40, CSF ptau181 or CSF ptau181/Aβ42 with CSF p75NTR-ECD, the area under the receiver operating characteristic curve (AUC) and diagnostic accuracies improved. These findings indicate that p75NTR-ECD can serve as a specific biomarker for AD and the determination of serum and CSF p75NTR-ECD levels is likely to be helpful in monitoring AD progression.
Right external globus pallidus changes are associated with altered causal awareness in youth with depression
Authors: Griffiths K R , Lagopoulos J , Hermens D F , Hickie I B , Balleine B W 
Published: October 2015

AbstractCognitive impairment is a functionally disabling feature of depression contributing to maladaptive decision-making, a loss of behavioral control and an increased disease burden. The ability to calculate the causal efficacy of ones actions in achieving specific goals is critical to normal decision-making and, in this study, we combined voxel-based morphometry (VBM), shape analysis and diffusion tensor tractography to investigate the relationship between cortical–basal ganglia structural integrity and such causal awareness in 43 young subjects with depression and 21 demographically similar healthy controls. Volumetric analysis determined a relationship between right pallidal size and sensitivity to the causal status of specific actions. More specifically, shape analysis identified dorsolateral surface vertices where an inward location was correlated with reduced levels of causal awareness. Probabilistic tractography revealed that affected parts of the pallidum were primarily connected with the striatum, dorsal thalamus and hippocampus. VBM did not reveal any whole-brain gray matter regions that correlated with causal awareness. We conclude that volumetric reduction within the indirect pathway involving the right dorsolateral pallidum is associated with reduced awareness of the causal efficacy of goal-directed actions in young depressed individuals. This causal awareness task allows for the identification of a functionally and biologically relevant subgroup to which more targeted cognitive interventions could be applied, potentially enhancing the long-term outcomes for these individuals.
Structure and function of Caulobacter crescentus aldose–aldose oxidoreductase
Authors: Taberman Helena , Andberg Martina , Koivula Anu , Hakulinen Nina , Penttilä Merja , Rouvinen Juha , Parkkinen Tarja 
Published: October 2015

Aldose–aldose oxidoreductase (Cc AAOR) is a recently characterized enzyme from the bacterial strain Caulobacter crescentus CB15 belonging to the glucose-fructose oxidoreductase/inositol dehydrogenase/rhizopine catabolism protein (Gfo/Idh/MocA) family. Cc AAOR catalyses the oxidation and reduction of a panel of aldose monosaccharides using a tightly bound NADP(H) cofactor that is regenerated in the catalytic cycle. Furthermore, Cc AAOR can also oxidize 1,4-linked oligosaccharides. In the present study, we present novel crystal structures of the dimeric Cc AAOR in complex with the cofactor and glycerol, D-xylose, D-glucose, maltotriose and D-sorbitol determined to resolutions of 2.0, 1.8, 1.7, 1.9 and 1.8 Å (1 Å=0.1 nm), respectively. These complex structures allowed for a detailed analysis of the ligand-binding interactions. The structures showed that the C1 carbon of a substrate, which is either reduced or oxidized, is close to the reactive C4 carbon of the nicotinamide ring of NADP(H). In addition, the O1 hydroxy group of the substrate, which is either protonated or deprotonated, is unexpectedly close to both Lys104 and Tyr189, which may both act as a proton donor or acceptor. This led us to hypothesize that this intriguing feature could be beneficial for Cc AAOR to catalyse the reduction of a linear form of a monosaccharide substrate and the oxidation of a pyranose form of the same substrate in a reaction cycle, during which the bound cofactor is regenerated.
Yolk Sac Tumor of the Temporal Lobe: Case Report
Authors: Machado Ana , Taipa Ricardo , Pires Manuel , Silva Carla , Gomes Mário 
Published: October 2015

AbstractGerm cell tumors of the central nervous system (CNS) are usually located along the midline. Yolk sac tumor is a rare germ cell tumor very uncommonly located outside the midline, and, in such cases, it can be mistaken with other primary tumors. We report a case of a 32-year-old male patient who presented with a right temporal lobe tumor suggestive of a high grade glioma. He was submitted to a right temporal lobectomy with complete tumor removal. The histological exam revealed a germ cell tumor (later confirmed to be a yolk sac tumor). The search for a primary tumor outside of the CNS (including a positron emission tomography scan) was negative, making this a primary temporal lobe yolk sac tumor. The patient was submitted to chemotherapy and radiotherapy, but died 7 months after the surgery.
Region-wide synchrony and traveling waves of dengue across eight countries in Southeast Asia
Authors: van Panhuis Willem G. , Choisy Marc , Xiong Xin , Chok Nian Shong , Akarasewi Pasakorn , Iamsirithaworn Sopon , Lam Sai K. , Chong Chee K. , Lam Fook C. , Phommasak Bounlay , Vongphrachanh Phengta , Bouaphanh Khamphaphongphane , Rekol Huy , Hien Nguyen Tran , Thai Pham Quang , Duong Tran Nhu , Chuang Jen-Hsiang , Liu Yu-Lun , Ng Lee-Ching , Shi Yuan , Tayag Enrique A. , Roque Vito G. , Lee Suy Lyndon L. , Jarman Richard G. , Gibbons Robert V. , Velasco John Mark S. , Yoon In-Kyu , Burke Donald S. , Cummings Derek A. T. 
Published: October 2015

Significance
Persons living in the tropics and subtropics are at risk for dengue fever and dengue hemorrhagic fever, and large epidemics occur unexpectedly that can overburden healthcare systems. The spatial and temporal dynamics of dengue transmission are poorly understood, limiting disease control efforts. We compiled a large-scale dataset and analyzed continental-scale patterns of dengue in Southeast Asia. Our analysis shows that periods of elevated temperatures can drive the occurrence of synchronous dengue epidemics across the region. This multicountry collaborative study improved insight that may lead to improved prediction of dengue transmission patterns and more effective disease surveillance and control efforts.
A holistic picture of Austronesian migrations revealed by phylogeography of Pacific paper mulberry
Authors: Chang Chi-Shan , Liu Hsiao-Lei , Moncada Ximena , Seelenfreund Andrea , Seelenfreund Daniela , Chung Kuo-Fang 
Published: October 2015

Significance
Paper mulberry, a common East Asian tree used for paper making, is propagated across the Pacific for making barkcloth, a practical and symbolic component of Austronesian material culture. Using chloroplast DNA sequences, we demonstrate a tight genealogical link between its populations in South China and North Taiwan, and South Taiwan and Remote Oceania by way of Sulawesi and New Guinea, presenting the first study, to our knowledge, of a commensal plant species transported to Polynesia whose phylogeographic structure concurs with expectations of the “out of Taiwan” hypothesis of Austronesian expansion. As a commensal plant likely transported across the full range of Austronesian expansion from South China to East Polynesia, paper mulberry may also be the most widely transported fiber crop in human prehistory.
Optofluidic wavelength division multiplexing for single-virus detection
Authors: Ozcelik Damla , Parks Joshua W. , Wall Thomas A. , Stott Matthew A. , Cai Hong , Parks Joseph W. , Hawkins Aaron R. , Schmidt Holger 
Published: October 2015

Significance
The ability to simultaneously detect and identify multiple biological particles or biomarkers is one of the key requirements for molecular diagnostic tests that are becoming even more important as personalized and precision medicine place increased emphasis on such capabilities. Integrated optofluidic platforms can help create such highly sensitive, multiplexed assays on a small, dedicated chip. We introduce a method for multiplex fluorescence detection of single bioparticles by creating color-dependent excitation spot patterns from a single integrated waveguide structure. Detection and identification of individual virus particles from three different influenza subtypes are demonstrated. The principle can be readily applied to amplification-free detection of nucleic acid biomarkers as well as larger target numbers using combinatorial color coding.
Variable genetic architectures produce virtually identical molecules in bacterial symbionts of fungus-growing ants
Authors: Sit Clarissa S. , Ruzzini Antonio C. , Van Arnam Ethan B. , Ramadhar Timothy R. , Currie Cameron R. , Clardy Jon 
Published: October 2015

Significance
Bacterially produced natural products comprise a group of molecules with highly diverse and generally complex structures that possess a remarkable array of biological activities. These molecules are separated into families sharing a common structural core and, accordingly, conserved sets of genes encoding the biosynthetic enzymes required to generate these shared structural features. Genomic characterization of related bacteria that produce remarkably similar molecules led to the surprising discovery that gene context was not conserved for the respective biosynthetic pathways. A comparison of these variable arrangements documents one way in which closely related symbiotic bacteria acquire the capacity to produce new molecules with new functions.
Photon gating in four-dimensional ultrafast electron microscopy
Authors: Hassan Mohammed T. , Liu Haihua , Baskin John Spencer , Zewail Ahmed H. 
Published: October 2015

Significance
In this contribution, we demonstrate a unique concept in the use of photon-induced near-field electron microscopy—combining one electron pulse and two optical pulses—as a probe for ultrafast dynamics of matter in electron microscopy. Photon–electron coupling permits the use of a short optical pulse to gate the electron pulse, which is serving as a probe of the ultrafast dynamics triggered by another optical pulse. This technique provides the high spatial and temporal resolution of the electron pulse and optical laser pulses, respectively, both in ultrafast electron microscopy (UEM) measurements. This development paves the way for numerous studies in imaging of matter not only with few femtosecond resolution but also with the potential for attosecond imaging in UEM.
Mapping of histone modifications in episomal HBV cccDNA uncovers an unusual chromatin organization amenable to epigenetic manipulation
Authors: Tropberger Philipp , Mercier Alexandre , Robinson Margaret , Zhong Weidong , Ganem Don E. , Holdorf Meghan 
Published: October 2015

Significance
Chronic hepatitis B virus (HBV) infection is maintained by the persistence of episomal HBV closed circular DNA (cccDNA) in infected hepatocytes. Current therapeutic regimes have no or limited impact on cccDNA, and the development of cccDNA-targeted therapies is complicated by our limited understanding of cccDNA regulation. We present a novel approach and first detailed analysis to our knowledge of cccDNA chromatin from de novo infected cells and infected liver tissue and reveal general features of cccDNA chromatin organization, and features that are unique to each source of cccDNA. We show that cccDNA chromatin is modulated by innate immunity and manipulated with an epigenetic agent, thereby establishing the importance of chromatin for cccDNA regulation and as a potential target for therapy of chronic HBV infection.
Detailed structure of the outer disk around HD 169142 with polarized light in H-band
Authors: Momose Munetake , Morita Ayaka , Fukagawa Misato , Muto Takayuki , Takeuchi Taku , Hashimoto Jun , Honda Mitsuhiko , Kudo Tomoyuki , Okamoto Yoshiko K. , Kanagawa Kazuhiro D. , Tanaka Hidekazu , Grady Carol A. , Sitko Michael L. , Akiyama Eiji , Currie Thayne , Follette Katherine B. , Mayama Satoshi , Kusakabe Nobuhiko , Abe Lyu , Brandner Wolfgang , Brandt Timothy D. , Carson Joseph C. , Egner Sebastian , Feldt Markus , Goto Miwa , Guyon Olivier , Hayano Yutaka , Hayashi Masahiko , Hayashi Saeko S. , Henning Thomas , Hodapp Klaus W. , Ishii Miki , Iye Masanori , Janson Markus , Kandori Ryo , Knapp Gillian R. , Kuzuhara Masayuki , Kwon Jungmi , Matsuo Taro , McElwain Michael W. , Miyama Shoken , Morino Jun-Ichi , Moro-Martin Amaya , Nishimura Tetsuo , Pyo Tae-Soo , Serabyn Eugene , Suenaga Takuya , Suto Hiroshi , Suzuki Ryuji , Takahashi Yasuhiro H. , Takami Michihiro , Takato Naruhisa , Terada Hiroshi , Thalmann Christian , Tomono Daigo , Turner Edwin L. , Watanabe Makoto , Wisniewski John , Yamada Toru , Takami Hideki , Usuda Tomonori , Tamura Motohide 
Published: October 2015

Abstract
Coronagraphic imagery of the circumstellar disk around HD 169142 in H-band polarized intensity (PI) with Subaru/HiCIAO is presented. The emission scattered by dust particles at the disk surface in 0${^{\prime\prime}_{.}}$2 ≤ r ≤ 1${^{\prime\prime}_{.}}$2, or 29 ≤ r ≤ 174 au, is successfully detected. The azimuthally averaged radial profile of the PI shows a double power-law distribution, in which the PIs in r = 29–52 au and r = 81.2–145 au respectively show r−3 dependence. These two power-law regions are connected smoothly with a transition zone (TZ), exhibiting an apparent gap in r = 40–70 au. The PI in the inner power-law region shows a deep minimum whose location seems to coincide with the point source at λ = 7 mm. This can be regarded as another sign of a protoplanet in the TZ. The observed radial profile of the PI is reproduced by a minimally flaring disk with an irregular surface density distribution, an irregular temperature distribution, or with a combination of both. The depletion factor of surface density in the inner power-law region (r &lt; 50 au) is derived to be ≥ 0.16 from a simple model calculation. The obtained PI image also shows small-scale asymmetries in the outer power-law region. Possible origins for these asymmetries include corrugation of the scattering surface in the outer region, and a shadowing effect by a puffed-up structure in the inner power-law region.