bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crop wild relative populations of Beta vulgaris allow direct mapping of agronomically important genes
Authors: Capistrano-Gossmann Gina G. , Ries D. , Holtgräwe D. , Minoche A. , Kraft T. , Frerichmann S.L.M. , Rosleff Soerensen T. , Dohm J. C. , González I. , Schilhabel M. , Varrelmann M. , Tschoep H. , Uphoff H. , Schütze K. , Borchardt D. , Toerjek O. , Mechelke W. , Lein J. C. , Schechert A. W. , Frese L. , Himmelbauer H. , Weisshaar B. , Kopisch-Obuch F. J. 
Published: June 2017

AbstractRapid identification of agronomically important genes is of pivotal interest for crop breeding. One source of such genes are crop wild relative (CWR) populations. Here we used a CWR population of <200 wild beets (B. vulgaris ssp. maritima), sampled in their natural habitat, to identify the sugar beet (Beta vulgaris ssp. vulgaris) resistance gene Rz2 with a modified version of mapping-by-sequencing (MBS). For that, we generated a draft genome sequence of the wild beet. Our results show the importance of preserving CWR in situ and demonstrate the great potential of CWR for rapid discovery of causal genes relevant for crop improvement. The candidate gene for Rz2 was identified by MBS and subsequently corroborated via RNA interference (RNAi). Rz2 encodes a CC-NB-LRR protein. Access to the DNA sequence of Rz2 opens the path to improvement of resistance towards rhizomania not only by marker-assisted breeding but also by genome editing.
Small extracellular vesicles secreted from senescent cells promote cancer cell proliferation through EphA2
Authors: Takasugi Masaki , Okada Ryo , Takahashi Akiko , Virya Chen David , Watanabe Sugiko , Hara Eiji 
Published: June 2017

AbstractCellular senescence prevents the proliferation of cells at risk for neoplastic transformation. However, the altered secretome of senescent cells can promote the growth of the surrounding cancer cells. Although extracellular vesicles (EVs) have emerged as new players in intercellular communication, their role in the function of senescent cell secretome has been largely unexplored. Here, we show that exosome-like small EVs (sEVs) are important mediators of the pro-tumorigenic function of senescent cells. sEV-associated EphA2 secreted from senescent cells binds to ephrin-A1, that is, highly expressed in several types of cancer cells and promotes cell proliferation through EphA2/ephrin-A1 reverse signalling. sEV sorting of EphA2 is increased in senescent cells because of its enhanced phosphorylation resulting from oxidative inactivation of PTP1B phosphatase. Our results demonstrate a novel mechanism of reactive oxygen species (ROS)-regulated cargo sorting into sEVs, which is critical for the potentially deleterious growth-promoting effect of the senescent cell secretome.
Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex
Authors: Xu Youwei , Bernecky Carrie , Lee Chung-Tien , Maier Kerstin C. , Schwalb Björn , Tegunov Dimitry , Plitzko Jürgen M. , Urlaub Henning , Cramer Patrick 
Published: June 2017

AbstractThe conserved polymerase-associated factor 1 complex (Paf1C) plays multiple roles in chromatin transcription and genomic regulation. Paf1C comprises the five subunits Paf1, Leo1, Ctr9, Cdc73 and Rtf1, and binds to the RNA polymerase II (Pol II) transcription elongation complex (EC). Here we report the reconstitution of Paf1C from Saccharomyces cerevisiae, and a structural analysis of Paf1C bound to a Pol II EC containing the elongation factor TFIIS. Cryo-electron microscopy and crosslinking data reveal that Paf1C is highly mobile and extends over the outer Pol II surface from the Rpb2 to the Rpb3 subunit. The Paf1-Leo1 heterodimer and Cdc73 form opposite ends of Paf1C, whereas Ctr9 bridges between them. Consistent with the structural observations, the initiation factor TFIIF impairs Paf1C binding to Pol II, whereas the elongation factor TFIIS enhances it. We further show that Paf1C is globally required for normal mRNA transcription in yeast. These results provide a three-dimensional framework for further analysis of Paf1C function in transcription through chromatin.
Understanding the origin of Paris Agreement emission uncertainties
Authors: Rogelj Joeri , Fricko Oliver , Meinshausen Malte , Krey Volker , Zilliacus Johanna J. J. , Riahi Keywan 
Published: June 2017

AbstractThe UN Paris Agreement puts in place a legally binding mechanism to increase mitigation action over time. Countries put forward pledges called nationally determined contributions (NDC) whose impact is assessed in global stocktaking exercises. Subsequently, actions can then be strengthened in light of the Paris climate objective: limiting global mean temperature increase to well below 2 °C and pursuing efforts to limit it further to 1.5 °C. However, pledged actions are currently described ambiguously and this complicates the global stocktaking exercise. Here, we systematically explore possible interpretations of NDC assumptions, and show that this results in estimated emissions for 2030 ranging from 47 to 63 GtCO2e yr−1. We show that this uncertainty has critical implications for the feasibility and cost to limit warming well below 2 °C and further to 1.5 °C. Countries are currently working towards clarifying the modalities of future NDCs. We identify salient avenues to reduce the overall uncertainty by about 10 percentage points through simple, technical clarifications regarding energy accounting rules. Remaining uncertainties depend to a large extent on politically valid choices about how NDCs are expressed, and therefore raise the importance of a thorough and robust process that keeps track of where emissions are heading over time.
Sequence variants in ARHGAP15, COLQ and FAM155A associate with diverticular disease and diverticulitis
Authors: Sigurdsson Snaevar , Alexandersson Kristjan F. , Sulem Patrick , Feenstra Bjarke , Gudmundsdottir Steinunn , Halldorsson Gisli H. , Olafsson Sigurgeir , Sigurdsson Asgeir , Rafnar Thorunn , Thorgeirsson Thorgeir , Sørensen Erik , Nordholm-Carstensen Andreas , Burcharth Jakob , Andersen Jens , Jørgensen Henrik Stig , Possfelt-Møller Emma , Ullum Henrik , Thorleifsson Gudmar , Masson Gisli , Thorsteinsdottir Unnur , Melbye Mads , Gudbjartsson Daniel F. , Stefansson Tryggvi , Jonsdottir Ingileif , Stefansson Kari 
Published: June 2017

AbstractDiverticular disease is characterized by pouches (that is, diverticulae) due to weakness in the bowel wall, which can become infected and inflamed causing diverticulitis, with potentially severe complications. Here, we test 32.4 million sequence variants identified through whole-genome sequencing (WGS) of 15,220 Icelanders for association with diverticular disease (5,426 cases) and its more severe form diverticulitis (2,764 cases). Subsequently, 16 sequence variants are followed up in a diverticular disease sample from Denmark (5,970 cases, 3,020 controls). In the combined Icelandic and Danish data sets we observe significant association of intronic variants inARHGAP15(Rho GTPase-activating protein 15; rs4662344-T:P=1.9 × 10−18, odds ratio (OR)=1.23) andCOLQ(collagen-like tail subunit of asymmetric acetylcholinesterase; rs7609897-T:P=1.5 × 10−10, OR=0.87) with diverticular disease and inFAM155A(family with sequence similarity 155A; rs67153654-A:P=3.0 × 10−11, OR=0.82) with diverticulitis. These are the first loci shown to associate with diverticular disease in a genome-wide study.
Quantum gambling based on Nash-equilibrium
Authors: Zhang Pei , Zhou Xiao-Qi , Wang Yun-Long , Liu Bi-Heng , Shadbolt Pete , Zhang Yong-Sheng , Gao Hong , Li Fu-Li , O’Brien Jeremy L. 
Published: June 2017

AbstractThe problem of establishing a fair bet between spatially separated gambler and casino can only be solved in the classical regime by relying on a trusted third party. By combining Nash-equilibrium theory with quantum game theory, we show that a secure, remote, two-party game can be played using a quantum gambling machine which has no classical counterpart. Specifically, by modifying the Nash-equilibrium point we can construct games with arbitrary amount of bias, including a game that is demonstrably fair to both parties. We also report a proof-of-principle experimental demonstration using linear optics.
NMR structure of the Bacillus cereus hemolysin II C-terminal domain reveals a novel fold
Authors: Kaplan Anne R. , Kaus Katherine , De Swastik , Olson Rich , Alexandrescu Andrei T. 
Published: June 2017

AbstractIn addition to multiple virulence factors, Bacillus cereus a pathogen that causes food poisoning and life-threatening wound infections, secretes the pore-forming toxin hemolysin II (HlyII). The HlyII toxin has a unique 94 amino acid C-terminal domain (HlyIIC). HlyIIC exhibits splitting of NMR resonances due to cis/trans isomerization of a single proline near the C-terminus. To overcome heterogeneity, we solved the structure of P405M-HlyIIC, a mutant that exclusively stabilizes the trans state. The NMR structure of HlyIIC reveals a novel fold, consisting of two subdomains αA-β1-β2 and β3-β4-αB-β5, that come together in a barrel-like structure. The barrel core is fastened by three layers of hydrophobic residues. The barrel end opposite the HlyIIC-core has a positively charged surface, that by binding negatively charged moieties on cellular membranes, may play a role in target-cell surface recognition or stabilization of the heptameric pore complex. In the WT domain, dynamic flexibility occurs at the N-terminus and the first α-helix that connects the HlyIIC domain to the HlyII-core structure. In the destabilizing P405M mutant, increased flexibility is evident throughout the first subdomain, suggesting that the HlyIIC structure may have arisen through gene fusion.
CXCL12 and osteopontin from bone marrow-derived mesenchymal stromal cells improve muscle regeneration
Authors: Maeda Yasushi , Yonemochi Yasuhiro , Nakajyo Yuki , Hidaka Hideaki , Ikeda Tokunori , Ando Yukio 
Published: June 2017

AbstractMuscle satellite cells are essential for muscle regeneration. However, efficient regeneration does not occur without muscle-resident mesenchymal progenitor cells. We show here that bone marrow-derived mesenchymal stromal cells (Bm-MSCs) also facilitate muscle regeneration in Duchenne muscular dystrophy (DMD) model mice. Bm-MSCs transplanted into peritoneal cavities of DMD model mice with severe muscle degeneration strongly suppressed dystrophic pathology and improved death-related symptoms, which resulted in dramatic lifespan extension. Isolated single myofibers from Bm-MSC-transplanted mice manifested considerably less myofiber splitting compared with myofibers from non-transplanted mice, which indicated that transplantation significantly ameliorated abnormal regeneration. With regard to the number of satellite cells, several cells remained on myofibers from Bm-MSC-transplanted model mice, but satellite cells rarely occurred on myofibers from non-transplanted mice. Also, CXCL12 was crucial for muscle regeneration. CXCL12 facilitated muscle regeneration and paired box protein–7 (PAX7) expression after cardiotoxin-related muscle injury in vivo. The majority of primary muscle satellite cells sorted by integrin-α7 and CD34 expressed CXCR4, a receptor specific for CXCL12. CXCL12 strongly suppressed p-STAT3 expression in these sorted cells in vitro. CXCL12 may therefore influence muscle regeneration through STAT3 signaling in satellite cells. Targeting these proteins in or on muscle satellite cells may improve many degenerative muscle diseases.
Exogenous interleukin 37 ameliorates atherosclerosis via inducing the Treg response in ApoE-deficient mice
Authors: Ji Qingwei , Meng Kai , Yu Kunwu , Huang Song , Huang Ying , Min Xiaohong , Zhong Yucheng , Wu Bangwei , Liu Yuzhou , Nie Shaoping , Zhang Jianwei , Zhou Yujie , Zeng Qiutang 
Published: June 2017

AbstractOur previous study indicated that interleukin (IL)-37 is involved in atherosclerosis. In the present study, Anterior tibial arteries were collected from diabetes patients and controls. A histopathological analysis showed that IL-37 was over-expressed in human atherosclerotic plaques. Many types of cells including macrophages, vascular smooth muscle cells (VSMCs), endothelial cells and T lymphocyte expressed IL-37 in human atherosclerotic plaques. ApoE−/− mice were divided into a control group and a recombinant human IL-37-treated group. The IL-37 treatment resulted in a significant decrease in macrophages and CD4+ T lymphocytes and a substantial increase in VSMCs and collagen in atherosclerotic plaques, resulting in a reduction in atherosclerotic plaque size. Furthermore, the IL-37 treatment modulated the CD4+ T lymphocyte activity, including a decrease in T helper cell type 1 (Th1) and Th17 cells and an increase in regulatory T (Treg) cells, and inhibited the maturity of dendritic cells both in vivo and in vitro. In addition, treatment with anti-IL-10 receptor monoclonal antibody abrogated the anti-atherosclerotic effects of IL-37. These data suggest that exogenous IL-37 ameliorates atherosclerosis via inducing the Treg response. IL-37 may be a novel therapeutic to prevent and treat atherosclerotic disease.
Discovering overlapped protein complexes from weighted PPI networks by removing inter-module hubs
Authors: Maddi A. M. A. , Eslahchi Ch. 
Published: June 2017

AbstractDetecting known protein complexes and predicting undiscovered protein complexes from protein-protein interaction (PPI) networks help us to understand principles of cell organization and its functions. Nevertheless, the discovery of protein complexes based on experiment still needs to be explored. Therefore, computational methods are useful approaches to overcome the experimental limitations. Nevertheless, extraction of protein complexes from PPI network is often nontrivial. Two major constraints are large amount of noise and ignorance of occurrence time of different interactions in PPI network. In this paper, an efficient algorithm, Inter Module Hub Removal Clustering (IMHRC), is developed based on inter-module hub removal in the weighted PPI network which can detect overlapped complexes. By removing some of the inter-module hubs and module hubs, IMHRC eliminates high amount of noise in dataset and implicitly considers different occurrence time of the PPI in network. The performance of the IMHRC was evaluated on several benchmark datasets and results were compared with some of the state-of-the-art models. The protein complexes discovered with the IMHRC method show significantly better agreement with the real complexes than other current methods. Our algorithm provides an accurate and scalable method for detecting and predicting protein complexes from PPI networks.
Sb2Se3 assembling Sb2O3@ attapulgite as an emerging composites for catalytic hydrogenation of p-nitrophenol
Authors: Tan Lin , Tang Aidong , Zou Yue , Long Mei , Zhang Yi , Ouyang Jin , Chen Jing 
Published: June 2017

AbstractThe construction and application of a new type of composite material are achieved more and more attention. However, expected Sb2Se3/attapulgite composites aim to use the low price, and high adsorption of attapulgite in assembling Sb2Se3 is quite difficult to be acquired by a facile and benign environmental hydrothermal method. In this manuscript, we developed a new way for preparation of an emerging composite by means of Sb2O3 as a media linking Sb2Se3 and attapulgite together, and finally won an emerging composite Sb2Se3/Sb2O3@attapulgite, which presented an excellent catalytic properties for catalytic hydrogenation of p-nitrophenol. It was noted that the Sb2Se3/Sb2O3@attapulgite composites exhibited a high conversion rate for the hydrogenation of p-nitrophenol that was up to 90.7% within 15 min, which was far more than the 61.5% of Sb2Se3 sample. The excellent catalytic performance was attributed to the highly dispersion Sb2Se3 microbelts and Sb2Se3@Sb2O3@attapulgite rods, which would improve the adsorption of the reactant species and facility electronic transfer process of the catalytic hydrogenation of p-nitrophenol.
Visual adaptation reveals an objective electrophysiological measure of high-level individual face discrimination
Authors: Retter Talia L. , Rossion Bruno 
Published: June 2017

AbstractThe ability to individualize faces is a fundamental human brain function. Following visual adaptation to one individual face, the suppressed neural response to this identity becomes discriminable from an unadapted facial identity at a neural population level. Here, we investigate a simple and objective measure of individual face discrimination with electroencephalographic (EEG) frequency tagging following adaptation. In a first condition, (1) two facial identities are presented in alternation at a rate of six images per second (6 Hz; 3 Hz identity repetition rate) for a 20 s testing sequence, following 10-s adaptation to one of the facial identities; this results in a significant identity discrimination response at 3 Hz in the frequency domain of the EEG over right occipito-temporal channels, replicating our previous findings. Such a 3 Hz response is absent for two novel conditions, in which (2) the faces are inverted and (3) an identity physically equidistant from the two faces is adapted. These results indicate that low-level visual features present in inverted or unspecific facial identities are not sufficient to produce the adaptation effect found for upright facial stimuli, which appears to truly reflect identity-specific perceptual representations in the human brain.
Prognostic nutritional index predicts clinical outcome in patients with acute ST-segment elevation myocardial infarction undergoing primary percutaneous coronary intervention
Authors: Chen Qing-Jie , Qu Hui-Juan , Li Dong-Ze , Li Xiao-Mei , Zhu Jia-Jun , Xiang Yang , Li Lei , Ma Yi-Tong , Yang Yi-Ning 
Published: June 2017

AbstractWe aimed to investigate whether the prognostic nutritional index (PNI), a combined nutritional-inflammatory score based on serum albumin levels and lymphocyte count, was associated with mortality in patients with acute ST-segment elevation myocardial infarction (STEMI) undergoing primary percutaneous coronary intervention (pPCI). From September 2011 to November 2014, 309 consecutive patients with STEMI undergoing pPCI were prospectively enrolled. Patients with a combined score of albumin (g/L) + 5 × total lymphocyte count × 109/L ≥ 45 or <45 were assigned a PNI score of 0 or 1, respectively. Of the 309 STEMI patients, 24 (7.74%) died in the hospital, and 15 (4.83%) died during long-term follow-up (median follow-up time, 19.5 [3–36] months). Compared to patients with a PNI of 0, patients with a PNI of 1 had significantly higher in-hospital (14.2% vs. 3.7%; P < 0.001) and long-term follow-up (21.7% vs. 6.9%, P < 0.001) mortality rates. PNI (1/0, HR, 2.414; 95% CI, 1.016 to 5.736; P = 0.046) was a significant independent predictor of mortality in patients with STEMI undergoing pPCI. Moreover, cumulative survival was significantly lower for patients with a PNI of 1 compared to patients with a PNI of 0 (78.3% vs. 93.1%, log-rank P < 0.001). PNI appears useful for the risk stratification of STEMI patients undergoing pPCI.
PTH [1–34] induced differentiation and mineralization of mandibular condylar cartilage
Authors: O’ Brien Mara Heather , Dutra Eliane Hermes , Lima Alexandro , Nanda Ravindra , Yadav Sumit 
Published: June 2017

AbstractIntermittent Parathyroid Hormone (I-PTH) is the only FDA approved anabolic drug therapy available for the treatment of osteoporosis in males and postmenopausal females. The effects of I-PTH on the chondrogenic lineage of the mandibular condylar cartilage (MCC) are not well understood. To investigate the role of I-PTH on the MCC and subchondral bone, we carried out our studies using 4 to 5 week old triple transgenic mice (Col1a1XCol2a1XCol10a1). The experimental group was injected with PTH (80 μg/kg) daily for 2 weeks, while control group was injected with saline. Our histology showed that the I-PTH treatment led to an increased number of cells expressing Col1a1, Col2a1 and Col10a1. Additionally, there was an increase in cellular proliferation, increased proteoglycan distribution, increased cartilage thickness, increased TRAP activity, and mineralization. Immunohistochemical staining showed increased expression of pSMAD158 and VEGF in the MCC and subchondral bone. Furthermore our microCT data showed that I-PTH treatment led to an increased bone volume fraction, tissue density and trabecular thickness, with a decrease in trabecular spacing. Morphometric measurements showed increased mandibular length and condyle head length following I-PTH treatment. In conclusion, our study suggests that I-PTH plays a critical role in cellular proliferation, proteoglycan distribution, and mineralization of the MCC.
Amplifying the signal of localized surface plasmon resonance sensing for the sensitive detection of Escherichia coli O157:H7
Authors: Song Liping , Zhang Lei , Huang Youju , Chen Liming , Zhang Ganggang , Shen Zheyu , Zhang Jiawei , Xiao Zhidong , Chen Tao 
Published: June 2017

AbstractGold nanorods (Au NRs) based localized surface plasmon resonance (LSPR) sensors have been widely employed in various fields including biology, environment and food safety detection, but their size- and shape-dependent sensitivity limits their practical applications in sensing and biological detection. In our present work, we proposed an approach to maximally amplify the signal of Au NRs based LSPR sensing by coating an optimized thickness of mesoporous silica onto Au NRs. The plasmonic peaks of Au NRs@SiO2 with different shell thickness showed finely linear response to the change of surrounding refractive index. The optimized thickness of mesoporous silica of Au NRs@SiO2 not only provided high stability for LSPR sensor,but also displayed much higher sensitivity (390 nm/RIU) than values of Au NRs from previous reports. The obtained Au NRs@SiO2 based LSPR sensor was further used in practical application for selectively detection of the E. coli O157:H7, and the detection limit achieved 10 CFU, which is much lower than conventional methods such as electrochemical methods and lateral-flow immunochromatography.
Diagnostic capability of Pulsar perimetry in pre-perimetric and early glaucoma
Authors: Hirasawa Kazunori , Takahashi Natsumi , Matsumura Kazuhiro , Kasahara Masayuki , Shoji Nobuyuki 
Published: June 2017

AbstractThis study aimed to compare the diagnostic capability of Pulsar perimetry (Pulsar) in pre-perimetric glaucoma (PPG) and early glaucoma (EG) with that of Flicker perimetry (Flicker) and spectral-domain optical conference tomography (SD-OCT). This prospective cross-sectional study included 25 eyes of 25 PPG patients, 35 eyes of 35 EG patients, and 42 eyes of 42 healthy participants. The diagnostic capability using the area under the curve (AUC) of the best parameter and agreement of detectability between structural and functional measurements were compared. For PPG patients, the AUC of Pulsar, Flicker, OCT-disc, and OCT-macular was 0.733, 0.663, 0.842, and 0.780, respectively. The AUC of Flicker was significantly lower than that of OCT-disc (p = 0.016). For EG patients, the AUC of Pulsar, Flicker, OCT-disc, and OCT-macular were 0.851, 0.869, 0.907, and 0.861, respectively. There was no significant difference in AUC among these methods. The agreement between structural and functional measurements expressed by kappa value ranged from −0.16 to 0.07 for PPG and from 0.01 to 0.25 for EG. Although the diagnostic capability of Pulsar in the PPG and EG groups was equal to that of Flicker and SD-OCT, the agreements between structural and functional measurements for both PPG and EG were poor.