bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transient marine euxinia at the end of the terminal Cryogenian glaciation
Authors: Lang Xianguo , Shen Bing , Peng Yongbo , Xiao Shuhai , Zhou Chuanming , Bao Huiming , Kaufman Alan Jay , Huang Kangjun , Crockford Peter W. , Liu Yonggang , Tang Wenbo , Ma Haoran 
Published: July 2018

AbstractTermination of the terminal Cryogenian Marinoan snowball Earth glaciation (~650–635 Ma) is associated with the worldwide deposition of a cap carbonate. Modeling studies suggest that, during and immediately following deglaciation, the ocean may have experienced a rapid rise in pH and physical stratification followed by oceanic overturn. Testing these predictions requires the establishment of a high-resolution sequence of events within sedimentary records. Here we report the conspicuous occurrence of pyrite concretions in the topmost Nantuo Formation (South China) that was deposited in the Marinoan glacial deposits. Sedimentary facies and sulfur isotope data indicate pyrite precipitation in the sediments with H2S diffusing from the overlying sulfidic/euxinic seawater and Fe (II) from diamictite sediments. These observations suggest a transient but widespread presence of marine euxinia in an ocean characterized by redox stratification, high bioproductivity, and high-fluxes of sulfate from chemical weathering before the deposition of the cap carbonate.
Enhancement of adenovirus infection and adenoviral vector-mediated gene delivery by bromodomain inhibitor JQ1
Authors: Lv Baojie , Li Jingjing , Li Meng , Zhuo Yujie , Ren Ke , Li Erguang , Yang Guang 
Published: July 2018

AbstractAdenovirus-based vectors are among the most commonly used platforms for gene delivery and gene therapy studies. One of the obstacles for potential application is dose-related toxicity. We show here that adenovirus infection and Ad-mediated gene delivery can be enhanced by inhibitors of bromodomain and extra-terminal (BET) family proteins. We showed that JQ1, but not its inactive enantiomer (−)-JQ1, dose-dependently promoted Ad infection and Ad-mediated gene delivery in both epithelial and lymphocyte cells. Given orally, JQ1 also enhanced transgene expression in a murine tumor model. Inhibitors of histone deacetylases (HDACi) are among the commonly reported small molecule compounds which enhance Ad-mediated gene delivery. We found that JQ1 treatment did not cause histone acetylation nor expression of Ad attachment receptor CAR. Instead, JQ1 treatment induced an increase in BRD4 association with CDK9, a subunit of P-TEFb of transcription elongation. Concurrently, we showed that CDK9 inhibition blocked Ad infection and JQ1 enhancement on the infection. The study exemplifies the potentials of BET inhibitors like JQ1 in oncolytic virotherapy.
Characterization of the APETALA2/Ethylene-responsive factor (AP2/ERF) transcription factor family in sunflower
Authors: Najafi Somayeh , Sorkheh Karim , Nasernakhaei Fatemeh 
Published: July 2018

AbstractOne of the most prominent families of genes in plants is the AP2/ERF which play an important role in regulating plant growth and responses to various stresses. In this research, a genome-wide survey was conducted to recognize the AP2/ERF genes in sunflower (Helianthus annuus L.), and a total of 288 HaAP2/ERF was obtained. Phylogenetic analysis divided them into four sub-families, including 248 ERF, 4 RAV and 35 AP2, and one subgroup of the Soloist family. Localization of chromosome, gene structure, the conserved motif, gene ontology, interaction networks, homology modeling, the modeling of cis-regulatory elements and the analysis of events in the duplication of genes were carried out for HaAP2/ERF genes. Finally, 9AP2/ERF genes were chosen to confirm the gene expression of the selected genes in leaf and root tissues in various abiotic stress conditions by qPCR. The results confirmed that AP2/ERFs genes could effectively resist abiotic stress. Also, proline content was studied under drought, salinity, cold and heat stress. The results indicated that proline was increased under abiotic stress. This research has been done for the first time to determine the HaAP2/ERF family, which prepared valuable data for the evolutionary and practical research regarding AP2/ERF in sunflower.
A Rho-based reaction-diffusion system governs cell wall patterning in metaxylem vessels
Authors: Nagashima Yoshinobu , Tsugawa Satoru , Mochizuki Atsushi , Sasaki Takema , Fukuda Hiroo , Oda Yoshihisa 
Published: July 2018

AbstractRho GTPases play crucial roles in cell polarity and pattern formation. ROPs, Rho of plant GTPases, are widely involved in cell wall patterning in plants, yet the molecular mechanism underlying their action remains unknown. Arabidopsis ROP11 is locally activated to form plasma membrane domains, which direct formation of cell wall pits in metaxylem vessel cells through interaction with cortical microtubules. Here, we show that the pattern formation of cell wall pits is governed by ROP activation via a reaction-diffusion mechanism. Genetic analysis and reconstructive assays revealed that ROPGEF4/7 and ROPGAP3/4, which encode ROP activators and inactivators, respectively, regulated the formation of ROP-activated domains; these in turn determined the pattern of cell wall pits. Mathematical modelling showed that ROP-activation cycle generated ROP domains by reaction-diffusion mechanism. The model predicted that a positive feedback and slow diffusion of ROP11-ROPGEF4 complex were required to generate ROP-activated domains. ROPGEF4 formed a dimer that interacted with activated ROP11 in vivo, which could provide positive feedback for ROP activation. ROPGEF4 was highly stable on the plasma membrane and inhibited ROP11 diffusion. Our study indicated that ROP-based reaction-diffusion system self-organizes ROP-activated domains, thereby determines the pit pattern of metaxylem vessels.
Rapid Quaternary subsidence in the northwestern German North Sea
Authors: Arfai Jashar , Franke Dieter , Lutz Rüdiger , Reinhardt Lutz , Kley Jonas , Gaedicke Christoph 
Published: July 2018

Abstract3D and 2D seismic data reveal the base-reflection of the Quaternary in the northwestern German North Sea locally at depths of more than 1000 m. This indicates extremely fast subsidence, with a rate of up to 480 m/Ma during the Quaternary, resulting in a NNW-SSE oriented sedimentary depocentre. Distinct iceberg scour marks, identified in 3D seismic data are used to calibrate quantitative subsidence analysis and to document shallow marine conditions during the Quaternary interglacials. Previously, a number of mechanisms have been proposed to explain the Quaternary subsidence. Here we show that compaction and load-induced subsidence alone explain about 75% of the observed Quaternary subsidence. However, a certain portion of the subsidence needs additional processes to be invoked. The extensive seismic dataset interpreted here makes it possible to exclude a phase of renewed tectonic activity as the origin of the subsidence anomaly. From the orientation and extent of the depocentre, lithosphere buckling and subsidence due to salt movement are considered unlikely. Possibly a post-glacial collapse after the retreat of glaciers in the North Sea Basin, local lower crustal flow, or dynamic topography or a combination of these processes contributed to the residual subsidence.
Vinexin family (SORBS) proteins regulate mechanotransduction in mesenchymal stem cells
Authors: Kuroda Mito , Ueda Kazumitsu , Kioka Noriyuki 
Published: July 2018

AbstractThe stiffness of extracellular matrix (ECM) directs the differentiation of mesenchymal stem cells (MSCs) through the transcriptional co-activators Yes-associated protein (YAP) and transcriptional coactivator with a PDZ-binding motif (TAZ). Although a recent study revealed the involvement of vinexin α and CAP (c-Cbl-associated proteins), two of vinexin (SORBS) family proteins that bind to vinculin, in mechanosensing, it is still unclear whether these proteins regulate mechanotransduction and differentiation of MSCs. In the present study, we show that both vinexin α and CAP are necessary for the association of vinculin with the cytoskeleton and the promotion of YAP/TAZ nuclear localization in MSCs grown on rigid substrates. Furthermore, CAP is involved in the MSC differentiation in a stiffness-dependent manner, whereas vinexin depletion suppresses adipocyte differentiation independently of YAP/TAZ. These observations reveal a critical role of vinexin α and CAP in mechanotransduction and MSC differentiation.
Characterizing the activity of abundant, diverse and active CRISPR-Cas systems in lactobacilli
Authors: Crawley Alexandra B. , Henriksen Emily D. , Stout Emily , Brandt Katelyn , Barrangou Rodolphe 
Published: July 2018

AbstractCRISPR-Cas systems provide immunity against phages and plasmids in bacteria and archaea. Despite the popularity of CRISPR-Cas9 based genome editing, few endogenous systems have been characterized to date. Here, we sampled 1,262 publically available lactobacilli genomes found them to be enriched with CRISPR-Cas adaptive immunity. While CRISPR-Cas is ubiquitous in some Lactobacillus species, CRISPR-Cas content varies at the strain level in most Lactobacillus species. We identified that Type II is the most abundant type across the genus, with II-A being the most dominant sub-type. We found that many Type II-A systems are actively transcribed, and encode spacers that efficiently provide resistance against plasmid uptake. Analysis of various CRISPR transcripts revealed that guide sequences are highly diverse in terms of crRNA and tracrRNA length and structure. Interference assays revealed highly diverse target PAM sequences. Lastly, we show that these systems can be readily repurposed for self-targeting by expressing an engineered single guide RNA. Our results reveal that Type II-A systems in lactobacilli are naturally active in their native host in terms of expression and efficiently targeting invasive and genomic DNA. Together, these systems increase the possible Cas9 targeting space and provide multiplexing potential in native hosts and heterologous genome editing purpose.
Gomesin inhibits melanoma growth by manipulating key signaling cascades that control cell death and proliferation
Authors: Ikonomopoulou Maria P. , Fernandez-Rojo Manuel A. , Pineda Sandy S. , Cabezas-Sainz Pablo , Winnen Brit , Morales Rodrigo A. V. , Brust Andreas , Sánchez Laura , Alewood Paul F. , Ramm Grant A. , Miles John J. , King Glenn F. 
Published: July 2018

AbstractConsistent with their diverse pharmacology, peptides derived from venomous animals have been developed as drugs to treat disorders as diverse as hypertension, diabetes and chronic pain. Melanoma has a poor prognosis due in part to its metastatic capacity, warranting further development of novel targeted therapies. This prompted us to examine the anti-melanoma activity of the spider peptides gomesin (AgGom) and a gomesin-like homolog (HiGom). AgGom and HiGom dose-dependently reduced the viability and proliferation of melanoma cells whereas it had no deleterious effects on non-transformed neonatal foreskin fibroblasts. Concordantly, gomesin-treated melanoma cells showed a reduced G0/G1 cell population. AgGom and HiGom compromised proliferation of melanoma cells via activation of the p53/p21 cell cycle check-point axis and the Hippo signaling cascade, together with attenuation of the MAP kinase pathway. We show that both gomesin peptides exhibit antitumoral activity in melanoma AVATAR-zebrafish xenograft tumors and that HiGom also reduces tumour progression in a melanoma xenograft mouse model. Taken together, our data highlight the potential of gomesin for development as a novel melanoma-targeted therapy.
Familial Ovarian Cancer Clusters with Other Cancers
Authors: Zheng Guoqiao , Yu Hongyao , Kanerva Anna , Försti Asta , Sundquist Kristina , Hemminki Kari 
Published: July 2018

AbstractFamilial risk of ovarian cancer is well-established but whether ovarian cancer clusters with other cancers and the clusters differ by histology remains uncertain. Using data from the Swedish Family-Cancer Database, we explored familial associations of ovarian cancer with other cancers with a novel approach; relative risk for (histology-specific) ovarian cancer was estimated in families with patients affected by other cancers, and conversely, risks for other cancers in families with (histology-specific) ovarian cancer patients. Eight discordant cancers were associated with ovarian cancer risk, of which family history of breast cancer showed a dose-response (P-trend <0.0001). Conversely, risks of eight types of cancer increased in families with ovarian cancer patients, and dose-responses were shown for risks of liver (P-trend = 0.0083) and breast cancers (P-trend <0.0001) and cancer of unknown primary (P-trend = 0.0157). Some cancers were only associated with histology-specific ovarian cancers, e.g. endometrial cancer was only associated with endometrioid type but with highest significance. Novel associations with virus-linked cancers of the nose and male and female genitals were found. The results suggest that ovarian cancer shares susceptibility with a number of other cancers. This might alert genetic counselors and challenge approaches for gene and gene-environment identification.
Comparison of Computed Tomography derived Fractional Flow Reserve to invasive Fractional Flow Reserve in Diagnosis of Functional Coronary Stenosis: A Meta-Analysis
Authors: Agasthi Pradyumna , Kanmanthareddy Arun , Khalil Charl , Egbuche Obiora , Yarlagadda Vivek , Sachdeva Rajesh , Arsanjani Reza 
Published: July 2018

AbstractComputed Tomography derived Fractional Flow Reserve (CTFFR) is an emerging non-invasive imaging modality to assess functional significance of coronary stenosis. We performed a meta-analysis to compare the diagnostic performance of CTFFR to invasive Fractional Flow reserve (FFR). Electronic search was performed to identify relevant articles. Pooled Estimates of sensitivity, specificity, positive likelihood ratio (LR+), negative likelihood ratio (LR−) and diagnostic odds ratio (DOR) with corresponding 95% confidence intervals (CI) were calculated at the patient level as well as the individual vessel level using hierarchical logistic regression, summary receiver operating characteristic (SROC) curve and area under the curve were estimated. Our search yielded 559 articles and of these 17 studies was included in the analysis. A total of 2,191 vessels in 1294 patients were analyzed. Pooled estimates of sensitivity, specificity, LR+, LR− and DOR with corresponding 95% CI at per-patient level were 83% (79–87), 72% (68–76), 3.0 (2.6–3.5), 0.23 (0.18–0.29) and 13 (9–18) respectively. Pooled estimates of sensitivity, specificity, LR+, LR− and DOR with corresponding 95% CI at per-vessel level were 85% (83–88), 76% (74–79), 3.6 (3.3–4.0), 0.19 (0.16–0.22) and 19 (15–24). The area under the SROC curve was 0.89 for both per patient level and at the per vessel level. In our meta-analysis, CTFFR demonstrated good diagnostic performance in identifying functionally significant coronary artery stenosis compared to the FFR.
Evidence for functional state transitions in intensively-managed soil ecosystems
Authors: Todman L. C. , Fraser F. C. , Corstanje R. , Harris J. A. , Pawlett M. , Ritz K. , Whitmore A. P. 
Published: July 2018

AbstractSoils are fundamental to terrestrial ecosystem functioning and food security, thus their resilience to disturbances is critical. Furthermore, they provide effective models of complex natural systems to explore resilience concepts over experimentally-tractable short timescales. We studied soils derived from experimental plots with different land-use histories of long-term grass, arable and fallow to determine whether regimes of extreme drying and re-wetting would tip the systems into alternative stable states, contingent on their historical management. Prior to disturbance, grass and arable soils produced similar respiration responses when processing an introduced complex carbon substrate. A distinct respiration response from fallow soil here indicated a different prior functional state. Initial dry:wet disturbances reduced the respiration in all soils, suggesting that the microbial community was perturbed such that its function was impaired. After 12 drying and rewetting cycles, despite the extreme disturbance regime, soil from the grass plots, and those that had recently been grass, adapted and returned to their prior functional state. Arable soils were less resilient and shifted towards a functional state more similar to that of the fallow soil. Hence repeated stresses can apparently induce persistent shifts in functional states in soils, which are influenced by management history.
Longitudinal effects of aging on 18F-FDG distribution in cognitively normal elderly individuals
Authors: Ishibashi Kenji , Onishi Airin , Fujiwara Yoshinori , Oda Keiichi , Ishiwata Kiichi , Ishii Kenji 
Published: July 2018

AbstractPrevious studies of aging effects on fluorine-18-labeled fluorodeoxyglucose (18F-FDG) distribution have employed cross-sectional designs. We examined aging effects on 18F-FDG distribution using both cross-sectional and longitudinal assessments. We obtained two 18F-FDG positron emission tomography scans at two different time points from 107 cognitively normal elderly participants. The participants’ mean ages at baseline and second scans were 67.9 and 75.7, respectively. The follow-up period ranged from 4 to 11 years with a mean of 7.8 years. The voxel-wise analysis revealed significant clusters in which 18F-FDG uptake was decreased between baseline and second scans (p < 0.05, family-wise error corrected) in the anterior cingulate cortex (ACC), posterior cingulate cortex/precuneus (PCC/PC), and lateral parietal cortex (LPC). The cross-sectional analysis of 18F-FDG uptake and age showed significant correlations in the ACC (p = 0.016) but not the PCC/PC (p = 0.240) at baseline, and in the ACC (p = 0.004) and PCC/PC (p = 0.002) at the second scan. The results of longitudinal assessments suggested that 18F-FDG uptake in the ACC, PCC/PC, and LPC decreased with advancing age in cognitively normal elderly individuals, and those of the cross-sectional assessments suggested that the trajectories of age-associated 18F-FDG decreases differed between the ACC and PCC/PC.
Reproducibility of structural brain connectivity and network metrics using probabilistic diffusion tractography
Authors: Tsai Shang-Yueh 
Published: July 2018

AbstractThe structural connectivity network constructed using probabilistic diffusion tractography can be characterized by the network metrics. In this study, short-term test-retest reproducibility of structural networks and network metrics were evaluated on 30 subjects in terms of within- and between-subject coefficient of variance (CVws, CVbs), and intra class coefficient (ICC) using various connectivity thresholds. The short-term reproducibility under various connectivity thresholds were also investigated when subject groups have same or different sparsity. In summary, connectivity threshold of 0.01 can exclude around 80% of the edges with CVws = 73.2 ± 37.7%, CVbs = 119.3 ± 44.0% and ICC = 0.62 ± 0.19. The rest 20% edges have CVws < 45%, CVbs < 90%, ICC = 0.75 ± 0.12. The presence of 1% difference in the sparsity can cause additional within-subject variations on network metrics. In conclusion, applying connectivity thresholds on structural network to exclude spurious connections for the network analysis should be considered as necessities. Our findings suggest that a connectivity threshold over 0.01 can be applied without significant effect on the short-term when network metrics are evaluated at the same sparsity in subject group. When the sparsity is not the same, the procedure of integration over various connectivity thresholds can provide reliable estimation of network metrics.
A possible superconductor-like state at elevated temperatures near metal electrodes in an LaAlO3/SrTiO3 interface
Authors: Kim Taeyueb , Kim Shin-Ik , Joo Sungjung , Kim Sangsu , Jeon Jeehoon , Hong Jinki , Doh Yong-Joo , Baek Seung-Hyub , Koo Hyun Cheol 
Published: July 2018

AbstractWe experimentally investigated the transport properties near metal electrodes installed on a conducting channel in a LaAlO3/SrTiO3interface. The local region around the Ti and Al electrodes has a higher electrical conductance than that of other regions, where the upper limits of the temperature and magnetic field can be well defined. Beyond these limits, the conductance abruptly decreases, as in the case of a superconductor. The samples with the Ti- or Al-electrode have an upper-limit temperature of approximately 4 K, which is 10 times higher than the conventional superconducting critical temperature of LaAlO3/SrTiO3interfaces and delta-doped SrTiO3. This phenomenon is explained by the mechanism of electron transfer between the metal electrodes and electronicd-orbitals in the LaAlO3/SrTiO3interface. The transferred electrons trigger a phase transition to a superconductor-like state. Our results contribute to the deep understanding of the superconductivity in the LaAlO3/SrTiO3interface and will be helpful for the development of high-temperature interface superconductors.
Microbiomes of gall-inducing copepod crustaceans from the corals Stylophora pistillata (Scleractinia) and Gorgonia ventalina (Alcyonacea)
Authors: Shelyakin Pavel V. , Garushyants Sofya K. , Nikitin Mikhail A. , Mudrova Sofya V. , Berumen Michael , Speksnijder Arjen G. C. L. , Hoeksema Bert W. , Fontaneto Diego , Gelfand Mikhail S. , Ivanenko Viatcheslav N. 
Published: July 2018

AbstractCorals harbor complex and diverse microbial communities that strongly impact host fitness and resistance to diseases, but these microbes themselves can be influenced by stresses, like those caused by the presence of macroscopic symbionts. In addition to directly influencing the host, symbionts may transmit pathogenic microbial communities. We analyzed two coral gall-forming copepod systems by using 16S rRNA gene metagenomic sequencing: (1) the sea fan Gorgonia ventalina with copepods of the genus Sphaerippe from the Caribbean and (2) the scleractinian coral Stylophora pistillata with copepods of the genus Spaniomolgus from the Saudi Arabian part of the Red Sea. We show that bacterial communities in these two systems were substantially different with Actinobacteria, Alphaproteobacteria, and Betaproteobacteria more prevalent in samples from Gorgonia ventalina, and Gammaproteobacteria in Stylophora pistillata. In Stylophora pistillata, normal coral microbiomes were enriched with the common coral symbiont Endozoicomonas and some unclassified bacteria, while copepod and gall-tissue microbiomes were highly enriched with the family ME2 (Oceanospirillales) or Rhodobacteraceae. In Gorgonia ventalina, no bacterial group had significantly different prevalence in the normal coral tissues, copepods, and injured tissues. The total microbiome composition of polyps injured by copepods was different. Contrary to our expectations, the microbial community composition of the injured gall tissues was not directly affected by the microbiome of the gall-forming symbiont copepods.