bluuebunny/crossref_metadata_2025_split huggingface dataset:
PathoPhenoDB, linking human pathogens to their phenotypes in support of infectious disease research
Authors: Kafkas Şenay , Abdelhakim Marwa , Hashish Yasmeen , Kulmanov Maxat , Abdellatif Marwa , Schofield Paul N. , Hoehndorf Robert 
Published: June 2019

AbstractUnderstanding the relationship between the pathophysiology of infectious disease, the biology of the causative agent and the development of therapeutic and diagnostic approaches is dependent on the synthesis of a wide range of types of information. Provision of a comprehensive and integrated disease phenotype knowledgebase has the potential to provide novel and orthogonal sources of information for the understanding of infectious agent pathogenesis, and support for research on disease mechanisms. We have developed PathoPhenoDB, a database containing pathogen-to-phenotype associations. PathoPhenoDB relies on manual curation of pathogen-disease relations, on ontology-based text mining as well as manual curation to associate host disease phenotypes with infectious agents. Using Semantic Web technologies, PathoPhenoDB also links to knowledge about drug resistance mechanisms and drugs used in the treatment of infectious diseases. PathoPhenoDB is accessible at http://patho.phenomebrowser.net/, and the data are freely available through a public SPARQL endpoint.
CFTI5Med, the new release of the catalogue of strong earthquakes in Italy and in the Mediterranean area
Authors: Guidoboni Emanuela , Ferrari Graziano , Tarabusi Gabriele , Sgattoni Giulia , Comastri Alberto , Mariotti Dante , Ciuccarelli Cecilia , Bianchi Maria Giovanna , Valensise Gianluca 
Published: June 2019

AbstractA key element for assessing seismic hazard and risk is the availability of a comprehensive dataset on past earthquakes. Here we present the rationale, structure and contents of CFTI5Med (https://doi.org/10.6092/ingv.it-cfti5), the 2018 version of the Catalogue of Strong Earthquakes in Italy: a large multidisciplinary effort including historians, seismologists and geologists. It was conceived in 1989, following the inception of GIS technology, and first published in 1995 to offer a full account of Italy’s strongest earthquakes, of their territorial impact and associated social and economic upheaval. Subsequent versions (1997, 2000, 2007) entailed a fine tuning of research methodologies, included additional research on Italian earthquakes, and were extended to large earthquakes of the Mediterranean area. CFTI5Med comprised an opportunity to streamline the structure of the Catalogue database and propose a renovated user interface. The new front-end (1) grants an easier, intuitive access to the data, including earthquake effects on the environment, and (2) allows all data to be displayed jointly with relevant topographic, geological and seismological overlays published as web services.
In-feed bacitracin methylene disalicylate modulates the turkey microbiota and metabolome in a dose-dependent manner
Authors: Johnson Timothy A. , Sylte Matthew J. , Looft Torey 
Published: June 2019

AbstractBeginning in 2017, the subtherapeutic use of most antibiotic compounds for growth promotion in food producing animals in the US was prohibited, highlighting the need to discover alternative growth promotants. Identifying the mechanism of action of growth promoting antibiotics may aid in the discovery of antibiotic alternatives. We describe the effects of feeding a subtherapeutic (50 g/ton of feed) and therapeutic (200 g/ton) concentration of bacitracin methylene disalicylate (BMD) to commercial turkeys for 14 weeks, and its effect on turkey intestinal microbial communities and cecal metabolomes. Both BMD concentrations had an immediate and lasting impact on the microbiota structure, and reduced bacterial richness through the end of the study (12 weeks). Metabolomic analysis identified 712 biochemicals, and 69% of metabolites were differentially present in BMD treated turkeys for at least one time point (q < 0.1). Amino acids, carbohydrates, nucleotides, peptides, and lipids were decreased in the turkey ceca early after BMD administration. Long-term metabolome alterations continued even after withdrawal of BMD. The microbial composition, determined by 16S rRNA gene sequencing, was predictive of the metabolome, indicating a connection between the microbiome and metabolome. In-feed BMD may cause bacterial metabolic shifts, leading to beneficial traits that can be targeted to improve animal health and production.
Spatial and temporal relationship between native mammals and free-roaming dogs in a protected area surrounded by a metropolis
Authors: Yen Shih-Ching , Ju Yu-Ten , Shaner Pei-Jen Lee , Chen Hsiang Ling 
Published: June 2019

AbstractWith rapid urbanization worldwide, anthropogenic impacts such as human settlements and invasive carnivores (dogs Canis familiaris, cats Felis catus) are altering spatial distributions and temporal activity patterns of native species. In this study, we focused on spatiotemporal responses of native mammals to anthropogenic impacts in a protected area surrounded by a large metropolis (i.e. Yangmingshan National Park inside Taipei-Keelung metropolis in northern Taiwan). We collected site use data of 11 mammal species (i.e. dogs, cats, nine native species) between 2012 and 2017 with a camera system comprising 121 camera sites. We quantified anthropogenic disturbances as distance to human settlements and activity levels of free-roaming dogs and cats. Species richness and occurrences of the native mammals increased with increasing distances to human settlements and decreasing activity level of dogs, with the latter having a stronger effect than the former. Diel activity overlap between native mammals and dogs was lower during April–July season, coinciding with the breeding season for several native mammals. In contrast, activity level of cats showed no relationships with species richness, occurrences or diel activities of the native mammals. This study demonstrated negative impacts of human settlements and free-roaming dogs on native mammal communities for protected areas in urban environments, and highlights dog activity as a major anthropogenic threat to wildlife.
A synthetic male-specific sterilization system using the mammalian pro-apoptotic factor in a malaria vector mosquito
Authors: Yamamoto Daisuke S. , Sumitani Megumi , Kasashima Katsumi , Sezutsu Hideki , Matsuoka Hiroyuki , Kato Hirotomo 
Published: June 2019

AbstractConditional cell death systems are useful for various aspects of basic science with a wide range of applications, including genetic pest control. We recently demonstrated that expression of the mammalian pro-apoptotic factor, B-cell leukaemia/lymphoma 2-associated X protein (Bax), can induce apoptosis in specific tissues by using tissue specific promoters in silkworm and mosquito. Here, we newly identified a functional promoter in the Asian malaria vector, Anopheles stephensi, which enables gene expression specifically in the testis. We produced a transgenic mosquito line that expresses mouse Bax under the control of this testis-specific promoter. Transgenic mosquito males exhibited aberrant testes without functional sperm and complete sterility, whereas transgenic females maintained normal fecundity. Despite their abnormal testes, the transgenic males maintained normal function of male accessory glands and typical mating behaviour. As a result of mating with these males, females showed refractoriness to further mating. These results suggest that transgenic males induce female sterility via mating. The mosquito is one of the most important disease vectors, and the control of their population benefits global public health. Thus, this Bax-mediated synthetic male-specific sterilization system could be applied to population control of mosquitoes.
The LL-100 panel: 100 cell lines for blood cancer studies
Authors: Quentmeier Hilmar , Pommerenke Claudia , Dirks Wilhelm G. , Eberth Sonja , Koeppel Max , MacLeod Roderick A. F. , Nagel Stefan , Steube Klaus , Uphoff Cord C. , Drexler Hans G. 
Published: June 2019

AbstractFor many years, immortalized cell lines have been used as model systems for cancer research. Cell line panels were established for basic research and drug development, but did not cover the full spectrum of leukemia and lymphoma. Therefore, we now developed a novel panel (LL-100), 100 cell lines covering 22 entities of human leukemia and lymphoma including T-cell, B-cell and myeloid malignancies. Importantly, all cell lines are unequivocally authenticated and assigned to the correct tissue. Cell line samples were proven to be free of mycoplasma and non-inherent virus contamination. Whole exome sequencing and RNA-sequencing of the 100 cell lines were conducted with a uniform methodology to complement existing data on these publicly available cell lines. We show that such comprehensive sequencing data can be used to find lymphoma-subtype-characteristic copy number aberrations, mRNA isoforms, transcription factor activities and expression patterns of NKL homeobox genes. These exemplary studies confirm that the novel LL-100 panel will be useful for understanding the function of oncogenes and tumor suppressor genes and to develop targeted therapies.
Density Functional Theory description of the order-disorder transformation in Fe-Ni
Authors: Tian Li-Yun , Levämäki Henrik , Eriksson Olle , Kokko Kalevi , Nagy Ágnes , Délczeg-Czirják Erna Krisztina , Vitos Levente 
Published: June 2019

AbstractThe thermodynamic ordering transformation of tetragonal FeNi system is investigated by the Exact Muffin-Tin Orbitals (EMTO) method. The tetragonal distortion of the unit cell is taken into account and the free energy is calculated as a function of long-range order and includes the configurational, vibrational, electronic and magnetic contributions. We find that both configurational and vibrational effects are important and that the vibrational effect lowers the predicted transformation temperature by about 480 K compared to the value obtained merely from the configurational free energy. The predicted temperature is in excellent agreement with the experimental value when all contributions are taken into account. We also perform spin dynamics calculations for the magnetic transition temperature and find it to be in agreement with the experiments. The present research opens new opportunities for quantum-mechanical engineering of the chemical and magnetic ordering in tetrataenite.
Fate of Barium Sulfate Nanoparticles Deposited in the Lungs of Rats
Authors: Molina Ramon M. , Konduru Nagarjun V. , Queiroz Priscila M. , Figueroa Benjamin , Fu Dan , Ma-Hock Lan , Groeters Sibylle , Schaudien Dirk , Brain Joseph D. 
Published: June 2019

AbstractWe have shown that barium [from BaSO4 nanoparticles (NPs)] was cleared from the lungs faster than other poorly soluble NPs and translocated mostly to bone. We now studied barium biokinetics in rats during Study 1: two-year inhalation exposure to 50 mg/m3 BaSO4 NP aerosols, and Study 2: single intratracheal (IT) instillation of increasing doses of BaSO4 NPs or BaCl2. Study 1 showed that lung barium content measured by inductively coupled plasma mass spectrometry increased during 360 days of BaSO4 NP aerosol exposures. An equilibrium was established from that time until 2 years. Barium concentrations in BaSO4-exposed animals were in the order (lungs > lymph nodes > hard bone > bone marrow > liver). In Study 2, there was an increase in lung barium post-IT instillation of BaSO4 NPs while barium from BaCl2 was mostly cleared by day 28. Transmission electron microscopy showed intact BaSO4 NPs in alveolar macrophages and type II epithelial cells, and in tracheobronchial lymph nodes. Using stimulated Raman scattering microscopy, specific BaSO4 Raman spectra were detected in BaSO4 NP-instilled lungs and not in other organs. Thus, we posit that barium from BaSO4 NPs translocates from the lungs mainly after dissolution. Barium ions are then incorporated mostly into the bone and other organs.
Effects of short-term exposure to particulate matter air pollution on cognitive performance
Authors: Shehab M. A. , Pope F. D. 
Published: June 2019

AbstractThis paper assesses the effect of short-term exposure to particulate matter (PM) air pollution on human cognitive performance via a double cross over experimental design. Two distinct experiments were performed, both of which exposed subjects to low and high concentrations of PM. Firstly, subjects completed a series of cognitive tests after being exposed to low ambient indoor PM concentrations and elevated PM concentrations generated via candle burning, which is a well-known source of PM. Secondly, a different cohort underwent cognitive tests after being exposed to low ambient indoor PM concentrations and elevated ambient outdoor PM concentrations via commuting on or next to roads. Three tests were used to assess cognitive performance: Mini-Mental State Examination (MMSE), the Stroop Color and Word test, and Ruff 2 & 7 test. The results from the MMSE test showed a statistically robust decline in cognitive function after exposure to both the candle burning and outdoor commuting compared to ambient indoor conditions. The similarity in the results between the two experiments suggests that PM exposure is the cause of the short-term cognitive decline observed in both. The outdoor commuting experiment also showed a statistically significant short-term cognitive decline in automatic detection speed from the Ruff 2 and 7 selective attention test. The other cognitive tests, for both the candle and commuting experiments, showed no statistically significant difference between the high and low PM exposure conditions. The findings from this study are potentially far reaching; they suggest that elevated PM pollution levels significantly affect short term cognition. This implies average human cognitive ability will vary from city to city and country to country as a function of PM air pollution exposure.
Closed and open state dependent block of potassium channels cause opposing effects on excitability – a computational approach
Authors: Ågren Richard , Nilsson Johanna , Århem Peter 
Published: June 2019

AbstractBlock of voltage-gated potassium (Kv) channels has been demonstrated to affect neuronal activity described as increasing excitability. The effect has been associated with a closed-state dependent block. However, the block of Kv channels in e.g. local anesthetic and antiarrhythmics, is open state-dependent. Since the reduced excitability in this case mainly is due to sodium channel block, the role of the Kv channel block is concealed. The present investigation aims to analyse the specific role of state-dependent Kv channel block for excitability. Using a computational approach, with introduced blocked states in the Kv channel of the Frankenhaeuser-Huxley axon membrane model, we calculated the effects on threshold, firing and presynaptic Ca influx. The Ca influx was obtained from an N-type Cav channel model linked to the Frankenhaeuser-Huxley membrane. The results suggested that a selective block of open Kv channels decreased the rate of repetitive firing and the consequent Ca influx, thus challenging the traditional view. In contrast, presence of a closed-state block, increased the firing rate and the Ca influx. These findings propose that Kv channel block may either increase or decrease cellular excitability, thus highlighting the importance of further investigating the role of state-specific blocking mechanisms.
Witnessing Entanglement In Compton Scattering Processes Via Mutually Unbiased Bases
Authors: Hiesmayr Beatrix C. , Moskal Pawel 
Published: June 2019

AbstractWe present a quantum information theoretic version of the Klein-Nishina formula. This formulation singles out the quantity, the a priori visibility, that quantifies the ability to deduce the polarisation property of single photons. The Kraus-type structure allows a straightforward generalisation to the multiphoton cases, relevant in the decay of positronium which is utilized e.g. for metabolic PET-imaging (Positron- Emission- Tomograph). Predicted by theory but never experimentally proven, the two- or three-photon states should be entangled. We provide an experimentally feasible method to witness entanglement for these processes via MUBs (Mutually Unbiased Bases), exploiting Bohr’s complementarity. Last but not least we present explicit cases exemplifying the interrelation of geometry and entanglement including relations to its potentiality for teleportation schemes or Bell inequality violations or in future for detecting cancer in human beings.
Combination of TLR2 and TLR3 agonists derepress infectious bursal disease virus vaccine-induced immunosuppression in the chicken
Authors: Bashir Khalid , Kappala Deepthi , Singh Yogendra , Dar Javeed Ahmad , Mariappan Asok Kumar , Kumar Ajay , Krishnaswamy Narayanan , Dey Sohini , Chellappa Madhan Mohan , Goswami Tapas Kumar , Gupta Vivek Kumar , Ramakrishnan Saravanan 
Published: June 2019

AbstractLive intermediate plus infectious bursal disease virus (IBDV) vaccines (hot vaccines) are used for protection against the virulent IBDV strains in young chickens. We evaluated the potential of Toll-like receptor (TLR) agonists to alleviate hot vaccine-induced immunosuppression. The combination of Pam3CSK4 and poly I:C synergistically upregulated IFN-β, IFN-γ, IL-12, IL-4, and IL-13 transcripts and cross-inhibited IL-1β, IL-10, and iNOS transcripts in the chicken peripheral blood mononuclear cells (PBMCs) as analyzed by quantitative real-time PCR. Further, four-week old specific pathogen free White Leghorn chickens (n = 60) were randomly divided into six groups and either immunized with hot IBDV vaccine with or without Pam3CSK4 and/or poly I:C or not vaccinated to serve as controls. The results indicated that poly I:C alone and in combination with Pam3CSK4 alleviated vaccine-induced immunosuppression, as evidenced by greater weight gain, increased overall antibody responses to both sheep erythrocytes and live infectious bronchitis virus vaccine, upregulated IFN-γ transcripts and nitric oxide production by PBMCs (P < 0.05), and lower bursal lesion score in the experimental birds. In conclusion, poly I:C alone and its combination with Pam3CSK4 reduced the destruction of B cells as well as bursal damage with restoration of function of T cells and macrophages when used with a hot IBDV vaccine.
Fbxo41 Promotes Disassembly of Neuronal Primary Cilia
Authors: King Cillian R. , A. A. Quadros Ana R. , Chazeau Anaël , Saarloos Ingrid , van der Graaf Anne Jolien , Verhage Matthijs , Toonen Ruud F. 
Published: June 2019

AbstractNeuronal primary cilia are signaling organelles with crucial roles in brain development and disease. Cilia structure is decisive for their signaling capacities but the mechanisms regulating it are poorly understood. We identify Fbxo41 as a novel Skp1/Cullin1/F-box (SCF) E3-ligase complex subunit that targets to neuronal centrioles where its accumulation promotes disassembly of primary cilia, and affects sonic hedgehog signaling, a canonical ciliary pathway. Fbxo41 targeting to centrioles requires its Coiled-coil and F-box domains. Levels of Fbxo41 at the centrioles inversely correlate with neuronal cilia length, and mutations that disrupt Fbxo41 targeting or assembly into SCF-complexes also disturb its function in cilia disassembly and signaling. Fbxo41 dependent cilia disassembly in mitotic and post-mitotic cells requires rearrangements of the actin-cytoskeleton, but requires Aurora A kinase activation only in mitotic cells, highlighting important mechanistical differences controlling cilia size between mitotic and post-mitotic cells. Phorbol esters induce recruitment of overexpressed Fbxo41 to centrioles and cilia disassembly in neurons, but disassembly can also occur in absence of Fbxo41. We propose that Fbxo41 targeting to centrosomes regulates neuronal cilia structure and signaling capacity in addition to Fbxo41-independent pathways controlling cilia size.
Soluble Forms of the Receptor for Advanced Glycation Endproducts (RAGE) in Periodontitis
Authors: Detzen Laurent , Cheng Bin , Chen Ching-Yuan , Papapanou Panos N. , Lalla Evanthia 
Published: June 2019

AbstractThe receptor for advanced glycation endproducts (RAGE) is critically involved in the pathobiology of chronic inflammatory diseases. Soluble forms of RAGE have been proposed as biomarkers of severity in inflammatory and metabolic conditions, and in monitoring therapeutic responses. The aim of the present study was to determine circulating levels of the soluble forms of RAGE in periodontitis and to evaluate the expression of cell-bound, full-length RAGE and its antagonist AGER1 locally, in gingival tissues. Periodontitis patients and periodontally healthy, sex- and age-matched controls (50 per group) were included. Serum levels of total soluble RAGE and cleaved RAGE (cRAGE) were significantly lower in periodontitis patients. Levels of the endogenous secretory esRAGE were similar in the two groups. cRAGE remained significantly lower in the periodontitis group following multiple adjustments, and had a statistically significant inverse correlation with body mass index and all periodontal parameters. In periodontitis patients, gene expression of full-length RAGE and of AGER1 were significantly higher in periodontitis-affected gingival tissues compared to healthy gingiva. Soluble forms of RAGE, particularly cRAGE, may serve as biomarkers for the presence and severity/extent of periodontitis, and may be implicated in its pathogenesis and its role as a systemic inflammatory stressor.
Observations and Projections of Heat Waves in South America
Authors: Feron S. , Cordero R. R. , Damiani A. , Llanillo P. J. , Jorquera J. , Sepulveda E. , Asencio V. , Laroze D. , Labbe F. , Carrasco J. , Torres G. 
Published: June 2019

AbstractAlthough Heat Waves (HWs) are expected to increase due to global warming, they are a regional phenomenon that demands for local analyses. In this paper, we assess four HW metrics (HW duration, HW frequency, HW amplitude, and number of HWs per season) as well as the share of extremely warm days (TX95, according to the 95th percentile) in South America (SA). Our analysis included observations as well as simulations from global and regional models. In particular, Regional Climate Models (RCMs) from the Coordinated Regional Climate Downscaling Experiment (CORDEX), and Global Climate Models (GCMs) from the Coupled Model Intercomparison Project Phase 5 (CMIP5) were used to project both TX95 estimates and HW metrics according to two representative concentration pathways (RCP4.5 and RCP8.5). We found that in recent decades the share of extremely warm days has at least doubled over the period December–January–February (DJF) in northern SA; less significant increases have been observed in southern SA. We also found that by midcentury, under the RCP4.5 scenario, extremely warm DJF days (as well as the number of HWs per season) are expected to increase by 5–10 times at locations close to the Equator and in the Atacama Desert. Increases are expected to be less pronounced in southern SA. Projections under the RCP8.5 scenario are more striking, particularly in tropical areas where half or more of the days could be extremely warm by midcentury.