bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection and characterisation of coronaviruses in migratory and non-migratory Australian wild birds
Authors: Chamings Anthony , Nelson Tiffanie M. , Vibin Jessy , Wille Michelle , Klaassen Marcel , Alexandersen Soren 
Published: April 2018

AbstractWe evaluated the presence of coronaviruses by PCR in 918 Australian wild bird samples collected during 2016–17. Coronaviruses were detected in 141 samples (15.3%) from species of ducks, shorebirds and herons and from multiple sampling locations. Sequencing of selected positive samples found mainly gammacoronaviruses, but also some deltacoronaviruses. The detection rate of coronaviruses was improved by using multiple PCR assays, as no single assay could detect all coronavirus positive samples. Sequencing of the relatively conserved Orf1 PCR amplicons found that Australian duck gammacoronaviruses were similar to duck gammacoronaviruses around the world. Some sequenced shorebird gammacoronaviruses belonged to Charadriiformes lineages, but others were more closely related to duck gammacoronaviruses. Australian duck and heron deltacoronaviruses belonged to lineages with other duck and heron deltacoronaviruses, but were almost 20% different in nucleotide sequence to other deltacoronavirus sequences available. Deltacoronavirus sequences from shorebirds formed a lineage with a deltacoronavirus from a ruddy turnstone detected in the United States. Given that Australian duck gammacoronaviruses are highly similar to those found in other regions, and Australian ducks rarely come into contact with migratory Palearctic duck species, we hypothesise that migratory shorebirds are the important vector for moving wild bird coronaviruses into and out of Australia.
Role of the Interplay Between the Internal and External Conditions in Invasive Behavior of Tumors
Authors: Azimzade Youness , Saberi Abbas Ali , Sahimi Muhammad 
Published: April 2018

AbstractTumor growth, which plays a central role in cancer evolution, depends on both the internal features of the cells, such as their ability for unlimited duplication, and the external conditions, e.g., supply of nutrients, as well as the dynamic interactions between the two. A stem cell theory of cancer has recently been developed that suggests the existence of a subpopulation of self-renewing tumor cells to be responsible for tumorigenesis, and is able to initiate metastatic spreading. The question of abundance of the cancer stem cells (CSCs) and its relation to tumor malignancy has, however, remained an unsolved problem and has been a subject of recent debates. In this paper we propose a novel model beyond the standard stochastic models of tumor development, in order to explore the effect of the density of the CSCs and oxygen on the tumor’s invasive behavior. The model identifies natural selection as the underlying process for complex morphology of tumors, which has been observed experimentally, and indicates that their invasive behavior depends on both the number of the CSCs and the oxygen density in the microenvironment. The interplay between the external and internal conditions may pave the way for a new cancer therapy.
Methane release from the southern Brazilian margin during the last glacial
Authors: Portilho-Ramos R. C. , Cruz A. P. S. , Barbosa C. F. , Rathburn A. E. , Mulitza S. , Venancio I. M. , Schwenk T. , Rühlemann C. , Vidal L. , Chiessi C. M. , Silveira C. S. 
Published: April 2018

AbstractSeafloor methane release can significantly affect the global carbon cycle and climate. Appreciable quantities of methane are stored in continental margin sediments as shallow gas and hydrate deposits, and changes in pressure, temperature and/or bottom-currents can liberate significant amounts of this greenhouse gas. Understanding the spatial and temporal dynamics of marine methane deposits and their relationships to environmental change are critical for assessing past and future carbon cycle and climate change. Here we present foraminiferal stable carbon isotope and sediment mineralogy records suggesting for the first time that seafloor methane release occurred along the southern Brazilian margin during the last glacial period (40–20 cal ka BP). Our results show that shallow gas deposits on the southern Brazilian margin responded to glacial−interglacial paleoceanographic changes releasing methane due to the synergy of sea level lowstand, warmer bottom waters and vigorous bottom currents during the last glacial period. High sea level during the Holocene resulted in an upslope shift of the Brazil Current, cooling the bottom waters and reducing bottom current strength, reducing methane emissions from the southern Brazilian margin.
Texture analysis- and support vector machine-assisted diffusional kurtosis imaging may allow in vivo gliomas grading and IDH-mutation status prediction: a preliminary study
Authors: Bisdas Sotirios , Shen Haocheng , Thust Steffi , Katsaros Vasileios , Stranjalis George , Boskos Christos , Brandner Sebastian , Zhang Jianguo 
Published: April 2018

AbstractWe sought to investigate, whether texture analysis of diffusional kurtosis imaging (DKI) enhanced by support vector machine (SVM) analysis may provide biomarkers for gliomas staging and detection of the IDH mutation. First-order statistics and texture feature extraction were performed in 37 patients on both conventional (FLAIR) and mean diffusional kurtosis (MDK) images and recursive feature elimination (RFE) methodology based on SVM was employed to select the most discriminative diagnostic biomarkers. The first-order statistics demonstrated significantly lower MDK values in the IDH-mutant tumors. This resulted in 81.1% accuracy (sensitivity = 0.96, specificity = 0.45, AUC 0.59) for IDH mutation diagnosis. There were non-significant differences in average MDK and skewness among the different tumour grades. When texture analysis and SVM were utilized, the grading accuracy achieved by DKI biomarkers was 78.1% (sensitivity 0.77, specificity 0.79, AUC 0.79); the prediction accuracy for IDH mutation reached 83.8% (sensitivity 0.96, specificity 0.55, AUC 0.87). For the IDH mutation task, DKI outperformed significantly the FLAIR imaging. When using selected biomarkers after RFE, the prediction accuracy achieved 83.8% (sensitivity 0.92, specificity 0.64, AUC 0.88). These findings demonstrate the superiority of DKI enhanced by texture analysis and SVM, compared to conventional imaging, for gliomas staging and prediction of IDH mutational status.
Consistent differences in fitness traits across multiple generations of Olympia oysters
Authors: Silliman Katherine E. , Bowyer Tynan K. , Roberts Steven B. 
Published: April 2018

AbstractAdaptive evolution and plasticity are two mechanisms that facilitate phenotypic differences between populations living in different environments. Understanding which mechanism underlies variation in fitness-related traits is a crucial step in designing conservation and restoration management strategies for taxa at risk from anthropogenic stressors. Olympia oysters (Ostrea lurida) have received considerable attention with regard to restoration, however there is limited information on adaptive population structure. Using oysters raised under common conditions for up to two generations (F1s and F2s), we tested for evidence of divergence in reproduction, larval growth, and juvenile growth among three populations in Puget Sound, Washington. We found that the population with the fastest growth rate also exhibited delayed and reduced reproductive activity, indicating a potential adaptive trade-off. Our results corroborate and extend upon a previous reciprocal transplant study on F1 oysters from the same populations, indicating that variation in growth rate and differences in reproductive timing are consistent across both natural and laboratory environments and have a strongly heritable component that cannot be entirely attributed to plasticity.
Alterations in the health of hibernating bats under pathogen pressure
Authors: Bandouchova Hana , Bartonička Tomáš , Berkova Hana , Brichta Jiri , Kokurewicz Tomasz , Kovacova Veronika , Linhart Petr , Piacek Vladimir , Pikula Jiri , Zahradníková Alexandra , Zukal Jan 
Published: April 2018

AbstractIn underground hibernacula temperate northern hemisphere bats are exposed to Pseudogymnoascus destructans, the fungal agent of white-nose syndrome. While pathological and epidemiological data suggest that Palearctic bats tolerate this infection, we lack knowledge about bat health under pathogen pressure. Here we report blood profiles, along with body mass index (BMI), infection intensity and hibernation temperature, in greater mouse-eared bats (Myotis myotis). We sampled three European hibernacula that differ in geomorphology and microclimatic conditions. Skin lesion counts differed between contralateral wings of a bat, suggesting variable exposure to the fungus. Analysis of blood parameters suggests a threshold of ca. 300 skin lesions on both wings, combined with poor hibernation conditions, may distinguish healthy bats from those with homeostatic disruption. Physiological effects manifested as mild metabolic acidosis, decreased glucose and peripheral blood eosinophilia which were strongly locality-dependent. Hibernating bats displaying blood homeostasis disruption had 2 °C lower body surface temperatures. A shallow BMI loss slope with increasing pathogen load suggested a high degree of infection tolerance. European greater mouse-eared bats generally survive P. destructans invasion, despite some health deterioration at higher infection intensities (dependant on hibernation conditions). Conservation measures should minimise additional stressors to conserve constrained body reserves of bats during hibernation.
A quantitative LumiFluo assay to test inhibitory compounds blocking p53 degradation induced by human papillomavirus oncoprotein E6 in living cells
Authors: Messa Lorenzo , Celegato Marta , Bertagnin Chiara , Mercorelli Beatrice , Nannetti Giulio , Palù Giorgio , Loregian Arianna 
Published: April 2018

AbstractHigh-risk human papillomaviruses (HR-HPVs) are the causative agents for the onset of several epithelial cancers in humans. The deregulated expression of the viral oncoproteins E6 and E7 is the driving force sustaining the progression of malignant transformation in pre-neoplastic lesions. Targeting the viral E6 oncoprotein through inhibitory compounds can counteract the survival of cancer cells due to the reactivation of p53-mediated pathways and represents an intriguing strategy to treat HPV-associated neoplasias. Here, we describe the development of a quantitative and easy-to-perform assay to monitor the E6-mediated degradation of p53 in living cells to be used for small-molecule testing. This assay allows to unbiasedly determine whether a compound can protect p53 from the E6-mediated degradation in cells, through a simple 3-step protocol. We validated the assay by testing two small molecules, SAHA and RITA, reported to impair the E6-mediated p53 degradation. Interestingly, we observed that only SAHA efficiently rescued p53, while RITA could not provide the same degree of protection. The possibility to specifically and quantitatively monitor the ability of a selected compound to rescue p53 in a cellular context through our LumiFluo assay could represent an important step towards the successful development of anti-HPV drugs.
Lignin peroxidase ligand access channel dysfunction in the presence of atrazine
Authors: Ecker János , Fülöp László 
Published: April 2018

AbstractStudies have determined that the white-rot basidiomycete Phanerochaete chrysosporium is capable of biodegrading the atrazine herbicide with its broad-specificity enzymes, but the particular role of biocatalysts is still unclear. In the case of lignin peroxidase, a ligand access channel connected to the active heme cofactor provides access to the active site for potential small-sized substrates. Experimental results show that lignin peroxidase is unable to degrade atrazine, therefore, the primary goal was to determine whether there is any connection between the structural and dynamical properties of the enzyme and its incapability to degrade atrazine. The results of protein-ligand docking and molecular dynamics study correlate with relevant, published NMR and molecular dynamics data, and give the answer to the lack of atrazine degradation by lignin peroxidase which has already been established by numerous authors using experimental methods. Atrazine has no access to heme edge due to the electric charges of the delocalized s-triazine ring. The detected phenomenon suggests that the small size of the ligands only is not a sufficient condition to access the active site. Their physicochemical properties influence the structural behaviour of the channel.
Towards a generalized toxicity prediction model for oxide nanomaterials using integrated data from different sources
Authors: Choi Jang-Sik , Ha My Kieu , Trinh Tung Xuan , Yoon Tae Hyun , Byun Hyung-Gi 
Published: April 2018

AbstractA generalized toxicity classification model for 7 different oxide nanomaterials is presented in this study. A data set extracted from multiple literature sources and screened by physicochemical property based quality scores were used for model development. Moreover, a few more preprocessing techniques, such as synthetic minority over-sampling technique, were applied to address the imbalanced class problem in the data set. Then, classification models using four different algorithms, such as generalized linear model, support vector machine, random forest, and neural network, were developed and their performances were compared to find the best performing preprocessing methods as well as algorithms. The neural network model built using the balanced data set was identified as the model with best predictive performance, while applicability domain was defined using k-nearest neighbours algorithm. The analysis of relative attribute importance for the built neural network model identified dose, formation enthalpy, exposure time, and hydrodynamic size as the four most important attributes. As the presented model can predict the toxicity of the nanomaterials in consideration of various experimental conditions, it has the advantage of having a broader and more general applicability domain than the existing quantitative structure-activity relationship model.
p52 expression enhances lung cancer progression
Authors: Saxon Jamie A. , Yu Hui , Polosukhin Vasiliy V. , Stathopoulos Georgios T. , Gleaves Linda A. , McLoed Allyson G. , Massion Pierre P. , Yull Fiona E. , Zhao Zhongming , Blackwell Timothy S. 
Published: April 2018

AbstractWhile many studies have demonstrated that canonical NF-κB signaling is a central pathway in lung tumorigenesis, the role of non-canonical NF-κB signaling in lung cancer remains undefined. We observed frequent nuclear accumulation of the non-canonical NF-κB component p100/p52 in human lung adenocarcinoma. To investigate the impact of non-canonical NF-κB signaling on lung carcinogenesis, we employed transgenic mice with doxycycline-inducible expression of p52 in airway epithelial cells. p52 over-expression led to increased tumor number and progression after injection of the carcinogen urethane. Gene expression analysis of lungs from transgenic mice combined within vitrostudies suggested that p52 promotes proliferation of lung epithelial cells through regulation of cell cycle-associated genes. Using gene expression and patient information from The Cancer Genome Atlas (TCGA) database, we found that expression of p52-associated genes was increased in lung adenocarcinomas and correlated with reduced survival, even in early stage disease. Analysis of p52-associated gene expression in additional human lung adenocarcinoma datasets corroborated these findings. Together, these studies implicate the non-canonical NF-κB component p52 in lung carcinogenesis and suggest modulation of p52 activity and/or downstream mediators as new therapeutic targets.
Indistinguishability as nonlocality constraint
Authors: Amorim Cássio Sozinho 
Published: April 2018

AbstractA physical explanation for quantum bounds to nonlocality (Tsirelson’s bound) is a fundamental problem in quantum theory, for it is known that no-signaling alone fails to reproduce this limit. Here, information indistinguishability is presented as the indistinguishability of qubits or more general bits, and it suggests an answer to the nonlocality conundrum, ultimately placing it as the origin to quantum limits. Indistinguishability is also connected to exclusivity principle, and it is shown that indistinguishability leads to quantum correlation bounds. This suggests indistinguishability be as fundamental as non-locality and relativistic causality for nonlocal realism.
Exposure to Phthalate, an Endocrine Disrupting Chemical, Alters the First Trimester Placental Methylome and Transcriptome in Women
Authors: Grindler N. M. , Vanderlinden L. , Karthikraj R. , Kannan K. , Teal S. , Polotsky A. J. , Powell T. L. , Yang I. V. , Jansson T. 
Published: April 2018

AbstractPhthalates are known endocrine disruptors and associated with decreased fecundity, pregnancy loss, and adverse obstetrical outcomes, however the underlying mechanisms remain to be established. Environmental factors can influence gene expression and cell function by modifying epigenetic marks, impacting the developing embryo as well as future generations of offspring. The impact of phthalates on placental gene methylation and expression is largely unknown. We studied the effect of maternal phthalate exposure on the human placental DNA methylome and transcriptome. We determined epigenome-wide DNA methylation marks (Illumina Infinium Human Methylation 850k BeadChip) and gene expression (Agilent whole human genome array) associated with phthalate exposure in first trimester placenta. Integrative genomic analysis of candidate genes was performed to define gene methylation-expression relationships. We identified 39 genes with significantly altered methylation and gene expression in the high phthalate exposure group. Most of these relationships were inversely correlated. This analysis identified epidermal growth factor receptor (EGFR) as a critical candidate gene mediating the effects of phthalates on early placental function. Although additional studies are needed to determine the functional consequences of these changes, our findings are consistent with the model that phthalates impact placental function by modulating the expression of critical placental genes through epigenetic regulation.
Increased Abundance and Nursery Habitat Use of the Bull Shark (Carcharhinus leucas) in Response to a Changing Environment in a Warm-Temperate Estuary
Authors: Bangley Charles W. , Paramore Lee , Shiffman David S. , Rulifson Roger A. 
Published: April 2018

AbstractA general northward shift in marine species distributions has been observed in the western North Atlantic Ocean, which may have significant ecological consequences. Large coastal sharks can have wide migratory distributions but show fidelity to specific nursery habitats. Here we show evidence for nursery range expansion into Pamlico Sound, North Carolina by a marine apex predator, the Bull Shark (Carcharhinus leucas). Previous assessments have shown little to no use of estuarine North Carolina waters as nursery habitat by Bull Sharks from 1965–2011. Juvenile sharks were rarely captured in a fishery-independent gillnet survey conducted by the North Carolina Division of Marine Fisheries (NCDMF) from 2003–2011, but were present every year from 2011–2016. Juvenile Bull Shark presence in the Sound was strongly related to early summer temperatures and late summer salinities, which have increased in the estuary over the 13 survey years, and further evidence for increasing water temperatures in Pamlico Sound was found in a 45-year data set for the NCDMF estuarine trawl survey. These results suggest that increasing water temperature and salinity have allowed Bull Sharks to expand their nursery habitat. This shift will have unknown, but potentially strong, impacts on both the local ecosystem and interactions with humans.
Expression of KK-LC-1, a cancer/testis antigen, at non-tumour sites of the stomach carrying a tumour
Authors: Fukuyama Takashi , Futawatari Nobue , Yamamura Rui , Yamazaki Taiga , Ichiki Yoshinobu , Ema Akira , Ushiku Hideki , Nishi Yatsushi , Takahashi Yoshihito , Otsuka Toshikazu , Yamazaki Hitoshi , Koizumi Wasaburo , Yasumoto Kosei , Kobayashi Noritada 
Published: April 2018

AbstractKita-Kyushu lung cancer antigen-1 (KK-LC-1) is a cancer/testis antigen (CTA) and predominant target for cancer immunotherapy. Our previous study indicated that KK-LC-1 was expressed in 82% of gastric cancers, and also in 79% of early stage of gastric cancers, with a correlation to Helicobacter pylori (H. pylori) infection. In addition, we found that KK-LC-1 was occasionally expressed at non-tumour sites of stomachs carrying tumours. Here, we investigated the characteristics of KK-LC-1 expression at non-tumour sites and the clinical utility of these phenomena. The gene expression of KK-LC-1 was detected at the non-tumour sites including pyloric glands. The most detectable corpus/gland subset had a KK-LC-1 expression rate of 77% in the pyloric gland of the lower corpus where H. pylori preferentially exists. KK-LC-1 expression rates were 67% or 32% with or without intestinal metaplasia, which also induced by H. pylori, respectively. Consequently, KK-LC-1 would be detected at the pre-cancerous condition of the stomach, and may be a useful marker to predict gastric cancer.
Optical Coherence Tomography Angiography Vessel Density Changes after Acute Intraocular Pressure Elevation
Authors: Zhang Qi , Jonas Jost B. , Wang Qian , Chan Szy Yann , Xu Liang , Wei Wen Bin , Wang Ya Xing 
Published: April 2018

AbstractTo investigate changes in retinal vessel density in optic nerve head (ONH) and macula after acute intraocular pressure (IOP) elevation, we conducted a prospective observational study. Eyes with IOP rise ≥5 mmHg after 2-hour dark room prone provocative test (DRPPT) were included. Vasculature of ONH and macula was examined by optical coherence tomography angiography (OCTA) at baseline and after DRPPT. Among the 65 eyes of 42 individuals, 40 eyes with qualified images were enrolled. Mean IOP rise was 9.6 ± 4.2 mmHg (5.0–23.3 mmHg) after DRPPT. Retinal vessel density did not differ after IOP rise for either the papillary region (optic nerve head and radial peripapillary capillary layer) or the macula region (superficial, deep and outer retinal layer) (P > 0.05). Vessel density in each subregion did not change either. If only enrolled eyes with IOP rise ≥10 mmHg, similar results were obtained in condition of IOP increase by 15.0 ± 3.6 mmHg. To conclude, eyes with an acute IOP elevation by 10 or 15 mmHg for two hours, while the blood pressure remained constant, the vessel density in both ONH and macula region examined by OCTA did not show significant changes. The observations fit with an IOP-related autoregulation in retinal blood flow for a moderate elevation of IOP.