bluuebunny/crossref_metadata_2025_split huggingface dataset:
Software for improved field surveys of nesting marine turtles
Authors: Anastácio R. , Gonzalez J. M. , Slater K. , Pereira M. J. 
Published: September 2017

AbstractField data are still recorded on paper in many worldwide beach surveys of nesting marine turtles. The data must be subsequently transferred into an electronic database, and this can introduce errors in the dataset. To minimize such errors, the “Turtles” software was developed and piloted to record field data by one software user accompanying one Tortuguero in Akumal beaches, Quintana Roo, Mexico, from June 1st to July 31st during the night patrols. Comparisons were made between exported data from the software with the paper forms entered into a database (henceforth traditional). Preliminary assessment indicated that the software user tended to record a greater amount of metrics (i.e., an average of 18.3 fields ± 5.4 sd vs. 8.6 fields ± 2.1 sd recorded by the traditional method). The traditional method introduce three types of “errors” into a dataset: missing values in relevant fields (40.1%), different answers for the same value (9.8%), and inconsistent data (0.9%). Only 5.8% of these (missing values) were found with the software methodology. Although only tested by a single user, the software may suggest increased efficacy and warrants further examination to accurately assess the merit of replacing traditional methods of data recording for beach monitoring programmes.
Alpha subunit-dependent glycine receptor clustering and regulation of synaptic receptor numbers
Authors: Patrizio A. , Renner M. , Pizzarelli R. , Triller A. , Specht C. G. 
Published: September 2017

AbstractAccumulation of glycine receptors at synapses requires the interaction between the beta subunit of the receptor and the scaffold protein gephyrin. Here, we questioned whether different alpha subunits could modulate the receptors’ diffusion and propensity to cluster at spinal cord synapses. Using quantitative photoactivated localisation microscopy we found that alpha-1 and alpha-3 containing glycine receptors display the same α3:β2 stoichiometry and gephyrin binding. Despite these similarities, alpha-3 containing receptors are less mobile and cluster at higher density compared to alpha-1, with 1500 versus 1100 complexes µm−2, respectively. Furthermore, we identified a subunit-specific regulation of glycine receptor copy numbers at synapses: when challenged with interleukin 1β, the synaptic occupancy of alpha-1 but not alpha-3 receptors was reduced. This mechanism may play a role in the cell-type dependent regulation of glycinergic currents in response to interleukin 1β and highlights the capacity of the alpha subunits to affect receptor-gephyrin binding at synapses.
A massive tsunami promoted gene flow and increased genetic diversity in a near threatened plant species
Authors: Ohbayashi Kako , Hodoki Yoshikuni , I. Kondo Natsuko , Kunii Hidenobu , Shimada Masakazu 
Published: September 2017

AbstractThe magnitude and frequency of disturbances affect species diversity and spatial distributions, but the direct effects of large-scale disturbances on genetic diversity are poorly understood. On March 11, 2011, the Great Tohoku Earthquake in Japan caused a massive tsunami that resulted in substantial alteration of community compositions. Populations of a near-threatened tidal marsh Carex rugulosa inhabiting brackish sandbars was also affected. We found four out of six remnant C. rugulosa populations along the Pacific Ocean had become completely extinct. Newly emergent post-tsunami populations, however, had higher allelic numbers than pre-tsunami populations, indicating higher genetic diversity after the tsunami. In addition, genetic differentiation (Fst) between post-tsunami populations was significantly lower than that of pre-tsunami populations. We therefore conclude that the tsunami enhanced gene flow. Seeds of many Carex species persist for long periods in soil, which suggests that seed banks are important genetic resources for post-disturbance recovery of genetic diversity. When its brackish sandbar habitat is no longer subject to disturbance and changes to the land, C. rugulosa is outcompeted by terrestrial plant competitors and eliminated. Disturbance is a driving force for the recovery and maintenance of populations of species such as C. rugulosa—even after near-complete eradication.
Magneto-actuated cell apoptosis by biaxial pulsed magnetic field
Authors: Wong De Wei , Gan Wei Liang , Liu Ning , Lew Wen Siang 
Published: September 2017

AbstractWe report on a highly efficient magneto-actuated cancer cell apoptosis method using a biaxial pulsed magnetic field configuration, which maximizes the induced magnetic torque. The light transmissivity dynamics show that the biaxial magnetic field configuration can actuate the magnetic nanoparticles with higher responsiveness over a wide range of frequencies as compared to uniaxial field configurations. Its efficacy was demonstrated in in vitro cell destruction experiments with a greater reduction in cell viability. Magnetic nanoparticles with high aspect ratios were also found to form a triple vortex magnetization at remanence which increases its low field susceptibility. This translates to a larger magneto-mechanical actuated force at low fields and 12% higher efficacy in cell death as compared to low aspect ratio nanoparticles.
Tissue alkalosis in cold-ischemia time
Authors: Denninghoff V. , Olivieri E. H. R. , Fresno C. , Uceda A. , Mota L. , Suenaga A. P. , Carraro D. M. , Martins V. R. , Avagnina A. , Soares F. A. , Campos A. H. J. Fróes Marques 
Published: September 2017

AbstractThe control of pre-analytical-factors in human biospecimens collected for health research is currently required. Only two previous reports using post-mortem brain samples have tried to address the impact of cold-ischemia on tissue pH. Here we report pH variations according to time (third-order polynomial model) in mice for liver, kidney and lung samples. Tissue alkalosis in cold-ischemia time may be an underlying mechanism of gene expression changes. Therefore, tissue-pH regulation after organ removal may minimize biological stress in human tissue samples.
The effect of a high frequency electromagnetic field in the microwave range on red blood cells
Authors: Nguyen The Hong Phong , Pham Vy T. H. , Baulin Vladimir , Croft Rodney J. , Crawford Russell J. , Ivanova Elena P. 
Published: September 2017

AbstractThe effect of red blood cells (RBC) exposed to an 18 GHz electromagnetic field (EMF) was studied. The results of this study demonstrated for the first time that exposure of RBCs to 18 GHz EMF has the capacity to induce nanospheres uptake in RBCs. The uptake of nanospheres (loading efficiency 96% and 46% for 23.5 and 46.3 nm nanospheres respectively), their presence and locality were confirmed using three independent techniques, namely scanning electron microscopy, confocal laser scanning microscopy and transmission electron microscopy. It appeared that 23.5 nm nanospheres were translocated through the membrane into the cytosol, while the 46.3 nm-nanospheres were mostly translocated through the phospholipid-cholesterol bilayer, with only some of these nanospheres passing the 2D cytoskeleton network. The nanospheres uptake increased by up to 12% with increasing temperature from 33 to 37 °C. The TEM analysis revealed that the nanospheres were engulfed by the cell membrane itself, and then translocated into the cytosol. It is believed that EMF-induced rotating water dipoles caused disturbance of the membrane, initiating its deformation and result in an enhanced degree of membrane trafficking via a quasi-exocytosis process.
Evidence that endogenous formaldehyde produces immunogenic and atherogenic adduct epitopes
Authors: Nakamura Jun , Shimomoto Takasumi , Collins Leonard B. , Holley Darcy W. , Zhang Zhenfa , Barbee Jenna M. , Sharma Vyom , Tian Xu , Kondo Tomohiro , Uchida Koji , Yi Xianwen , Perkins Diana O. , Willis Monte S. , Gold Avram , Bultman Scott J. 
Published: September 2017

AbstractEndogenous formaldehyde is abundantly present in our bodies, at around 100 µM under normal conditions. While such high steady state levels of formaldehyde may be derived by enzymatic reactions including oxidative demethylation/deamination and myeloperoxidation, it is unclear whether endogenous formaldehyde can initiate and/or promote diseases in humans. Here, we show that fluorescent malondialdehyde-formaldehyde (M2FA)-lysine adducts are immunogenic without adjuvants in mice. Natural antibody titers against M2FA are elevated in atherosclerosis-prone mice. Staining with an antibody against M2FA demonstrated that M2FA is present in plaque found on the aortic valve of ApoE−/− mice. To mimic inflammation during atherogenesis, human myeloperoxidase was incubated with glycine, H2O2, malondialdehyde, and a lysine analog in PBS at a physiological temperature, which resulted in M2FA generation. These results strongly suggest that the 1,4-dihydropyridine-type of lysine adducts observed in atherosclerosis lesions are likely produced by endogenous formaldehyde and malondialdehyde with lysine. These highly fluorescent M2FA adducts may play important roles in human inflammatory and degenerative diseases.
Transcriptome profiling of genes involved in induced systemic salt tolerance conferred by Bacillus amyloliquefaciens FZB42 in Arabidopsis thaliana
Authors: Liu Shaofang , Hao Haiting , Lu Xiang , Zhao Xia , Wang Yun , Zhang Yubao , Xie Zhongkui , Wang Ruoyu 
Published: September 2017

AbstractPlant growth-promoting Bacillus amyloliquefaciens FZB42 induces systemic salt tolerance in Arabidopsis and enhances the fresh and dry weight. However, the underlying molecular mechanism that allows plants to respond to FZB42 and exhibit salt tolerance is largely unknown. Therefore, we performed large-scale transcriptome sequencing of Arabidopsis shoot tissues grown under salt stress with or without FZB42 inoculation by using Illumina sequencing to identify the key genes and pathways with important roles during this interaction. In total, 1461 genes were differentially expressed (FZB42-inoculated versus non-inoculated samples) at 0 mM NaCl, of which 953 were upregulated and 508 downregulated, while 1288 genes were differentially expressed at 100 mM NaCl, of which 1024 were upregulated and 264 were downregulated. Transcripts associated with photosynthesis, auxin-related, SOS scavenging, Na+ translocation, and osmoprotectant synthesis, such as trehalose and proline, were differentially expressed by FZB42 inoculation, which reduced the susceptibility to salt and facilitated salt adaptation. Meanwhile, etr1-3, eto1, jar1-1, and abi4-102 hormone-related mutants demonstrated that FZB42 might induce plant salt tolerance via activating plants ET/JA signaling but not ABA-dependent pathway. The results here characterize the plant transcriptome under salt stress with plant growth-promoting bacteria inoculation, thereby providing insights into the molecular mechanisms responsible for induced salt tolerance.
Differential impact of lipopolysaccharide defects caused by loss of RfaH in Yersinia pseudotuberculosis and Yersinia pestis
Authors: Hoffman Jared M. , Sullivan Shea , Wu Erin , Wilson Eric , Erickson David L. 
Published: September 2017

AbstractRfaH enhances transcription of a select group of operons controlling bacterial surface features such as lipopolysaccharide (LPS). Previous studies have suggested that rfaH may be required for Yersinia pseudotuberculosis resistance to antimicrobial chemokines and survival during mouse infections. In order to further investigate the role of RfaH in LPS synthesis, resistance to host defense peptides, and virulence of Yersinia, we constructed ΔrfaH mutants of Y. pseudotuberculosis IP32953 and Y. pestis KIM6+. Loss of rfaH affected LPS synthesis in both species, resulting in a shorter core oligosaccharide. Susceptibility to polymyxin and the antimicrobial chemokine CCL28 was increased by loss of rfaH in Y. pseudotuberculosis but not in Y. pestis. Transcription of genes in the ddhD-wzz O-antigen gene cluster, but not core oligosaccharide genes, was reduced in ΔrfaH mutants. In addition, mutants with disruptions in specific ddhD-wzz O-antigen cluster genes produced LPS that was indistinguishable from the ΔrfaH mutant. This suggests that both Y. pseudotuberculosis and Y. pestis produce an oligosaccharide core with a single O-antigen unit attached in an RfaH-dependent fashion. Despite enhanced sensitivity to host defense peptides, the Y. pseudotuberculosis ΔrfaH strain was not attenuated in mice, suggesting that rfaH is not required for acute infection.
Deamination-independent restriction of LINE-1 retrotransposition by APOBEC3H
Authors: Feng Yuqing , Goubran Mariam H. , Follack Tyson B. , Chelico Linda 
Published: September 2017

AbstractThe APOBEC3 family of cytosine deaminase enzymes are able to restrict replication of retroelements, such as LINE-1. However, each of the seven APOBEC3 enzymes have been reported to act differentially to prevent LINE-1 retrotransposition and the mechanisms of APOBEC3-mediated LINE-1 inhibition has not been well understood. The prevailing view for many years was that APOBEC3-mediated LINE-1 inhibition was deamination-independent and relied on APOBEC3s blocking the LINE-1 reverse transcriptase DNA polymerization or transport of the LINE-1 RNA into the nucleus. However, recently it was shown that APOBEC3A can deaminate cytosine, to form uracil, on transiently exposed single-stranded LINE-1 cDNA and this leads to LINE-1 cDNA degradation. In this study, we confirmed that APOBEC3A is a potent deamination-dependent inhibitor of LINE-1 retrotransposition, but show that in contrast, A3H haplotype II and haplotype V restrict LINE-1 activity using a deamination-independent mechanism. Our study supports the model that different APOBEC3 proteins have evolved to inhibit LINE-1 retrotransposition through distinct mechanisms.
Hysteretic Dynamics of Multi-Stable Early Afterdepolarisations with Repolarisation Reserve Attenuation: A Potential Dynamical Mechanism for Cardiac Arrhythmias
Authors: Tsumoto Kunichika , Kurata Yasutaka , Furutani Kazuharu , Kurachi Yoshihisa 
Published: September 2017

AbstractSome cardiovascular and non-cardiovascular drugs frequently cause excessive prolongation of the cardiac action potential (AP) and lead to the development of early afterdepolarisations (EADs), which trigger lethal ventricular arrhythmias. Combining computer simulations in APs with numerical calculations based on dynamical system theory, we investigated stability changes of APs observed in a paced human ventricular myocyte model by decreasing and/or increasing the rapid (IKr) and slow (IKs) components of delayed rectifying K+ current. Upon reducing IKr, the APs without EADs (no-EAD response) showed gradual prolongation of AP duration (APD), and were annihilated without AP configuration changes due to the occurrence of saddle-node bifurcations. This annihilation caused a transition to an AP with EADs as a new stable steady state. Furthermore, reducing repolarisation currents (repolarisation reserve attenuation) evoked multi-stable states consisting of APs with different APDs, and caused multiple hysteretic dynamics. Depending on initial ion circumstances within ventricular myocytes, these multi-stable AP states might increase the local/global heterogeneity of AP repolarisations in the ventricle. Thus, the EAD-induced arrhythmias with repolarisation reserve attenuation might be attributed to the APD variability caused by multi-stability in cardiac AP dynamics.
MITF and BRN2 contribute to metastatic growth after dissemination of melanoma
Authors: Simmons Jacinta L. , Pierce Carly J. , Al-Ejeh Fares , Boyle Glen M. 
Published: September 2017

AbstractMelanoma tumors are highly heterogeneous, comprising of different cell types that vary in their potential for growth and invasion. Heterogeneous expression of the Microphthalmia-associated Transcription Factor (MITF) and the POU domain transcription factor BRN2 (POU3F2) has been found in malignant melanoma. Changing expression of these transcription factors as the disease progresses has been linked to the metastatic mechanism of phenotype switching. We therefore investigated the effects of MITF and BRN2 expression in melanoma growth and metastasis. Depletion of MITF resulted in a cell population that had a slowed cell cycle progression, was less invasive in vitro and had hindered tumor and metastasis forming ability in mouse xenograft studies. BRN2 depletion left a cell population with intact proliferation and invasion in vitro; however metastatic growth was significantly reduced in the mouse xenograft model. These results suggest that the proliferative population within melanoma tumors express MITF, and both MITF and BRN2 are important for metastatic growth in vivo. This finding highlights the importance of BRN2 and MITF expression in development of melanoma metastasis.
β-catenin, Twist and Snail: Transcriptional regulation of EMT in smokers and COPD, and relation to airflow obstruction
Authors: Mahmood Malik Quasir , Walters Eugene Haydn , Shukla Shakti D. , Weston Steve , Muller Hans Konrad , Ward Chris , Sohal Sukhwinder Singh 
Published: September 2017

AbstractCOPD is characterised by poorly reversible airflow obstruction usually due to cigarette smoking. The transcription factor clusters of β-catenin/Snail1/Twist has been implicated in the process of epithelial mesenchymal transition (EMT), an intermediate between smoking and airway fibrosis, and indeed lung cancer. We have investigated expression of these transcription factors and their “cellular localization” in bronchoscopic airway biopsies from patients with COPD, and in smoking and non-smoking controls. An immune-histochemical study compared cellular protein expression of β-catenin, Snail1 and Twist, in these subject groups in 3 large airways compartment: epithelium (basal region), reticular basement membrane (Rbm) and underlying lamina propria (LP). β-catenin and Snail1 expression was generally high in all subjects throughout the airway wall with marked cytoplasmic to nuclear shift in COPD (P < 0.01). Twist expression was generalised in the epithelium in normal but become more basal and nuclear with smoking (P < 0.05). In addition, β-catenin and Snail1 expression, and to lesser extent of Twist, was related to airflow obstruction and to expression of a canonical EMT biomarker (S100A4). The β-catenin-Snail1-Twist transcription factor cluster is up-regulated and nuclear translocated in smokers and COPD, and their expression is closely related to both EMT activity and airway obstruction.
Quantifying the efficacy of first aid treatments for burn injuries using mathematical modelling and in vivo porcine experiments
Authors: Simpson Matthew J. , McInerney Sean , Carr Elliot J. , Cuttle Leila 
Published: September 2017

AbstractFirst aid treatment of burns reduces scarring and improves healing. We quantify the efficacy of first aid treatments using a mathematical model to describe data from a series of in vivo porcine experiments. We study burn injuries that are subject to various first aid treatments. The treatments vary in the temperature and duration. Calibrating the mathematical model to the experimental data provides estimates of the thermal diffusivity, the rate at which thermal energy is lost to the blood, and the heat transfer coefficient controlling the loss of thermal energy at the interface of the fat and muscle. A limitation of working with in vivo experiments is the difficulty of measuring variations in temperature across the tissue layers. This limitation motivates us to use a simple, single layer mathematical model. Using the solution of the calibrated mathematical model we visualise the temperature distribution across the thickness of the tissue. With this information we propose a novel measure of the potential for tissue damage. This measure quantifies two important factors: (i) the volume of tissue that rises above the threshold temperature associated with the accumulation of tissue damage; and (ii) the duration of time that the tissue remains above this threshold temperature.
Magnetic states of nanostructures containing Ni2+ ions at the surface of SiO2 nanospheres
Authors: Barrera Gabriele , Alberto Gabriele , Tiberto Paola , Martra Gianmario , Allia Paolo 
Published: September 2017

AbstractUltra-small magnetic particles containing Ni2+ions were grown at the surface of SiO2spheroidal nanoparticles (typical diameter: 50 nm) starting from NiCl2solutions. Depending on preparation details, two samples characterized by magnetic sub-nanostructures or lamellar sub-nanoparticles at the SiO2nanosphere surface were obtained. The decorated SiO2nanospheres were submitted to physico-chemical and magnetic characterization. In both samples, a magnetically blocked phase is observed at low temperature. Below 5 K, discontinuities in isothermal magnetization loops and magnetic relaxation effects suggest the onset of coherent quantum tunneling of nanoparticle magnetization (QTM). Relaxation effects give are described by a field- and temperature-dependent magnetic viscosity SV(H,T); the total spin number of magnetic units is estimated by fitting the isothermal SV(H) curve to a model for an assembly of particles with random anisotropy axes. The mean number of aligned spins involved in the low-temperature relaxation is 32 and 15 in the two considered samples. Phonon-assisted QTM plays an increasingly important role with raising temperature and the quantum regime gradually merges with the classical behavior. Above the blocking temperature the magnetic units behave as classical superparamagnetic particles. When the intra-particle ferromagnetic order disappears the Ni2+ions respond individually to the magnetic field.
Antibody production by in vivo RNA transfection
Authors: Romani Bizhan , Kavyanifard Amirarsalan , Allahbakhshi Elham 
Published: September 2017

AbstractMonoclonal antibodies have a variety of applications in research and medicine. Here, we report development of a new method for production of monoclonal antibodies. Our method relies on in vivo RNA transfection rather than peptide vaccination. We took advantage of RNA transcripts complexed with DOTMA and DOPE lipids to transfect mice. Intravenous administration of our RNA vaccine to mice resulted in expression of the antigenic peptides by splenic dendritic cells and detection of the antigens in the serum. The RNA vaccine stimulated production of specific antibodies against the RNA-encoded peptides. We produced monoclonal antibodies against viral, bacterial, and human antigens. In addition, we showed that our RNA vaccine stimulated humoral immunity and rescued mice infected with influenza A virus. Our method could be used as an efficient tool to generate monoclonal antibodies and to stimulate humoral immunity for research and medical purposes.
Information seeking about tool properties in great apes
Authors: Bohn Manuel , Allritz Matthias , Call Josep , Völter Christoph J. 
Published: September 2017

AbstractEvidence suggests that great apes engage in metacognitive information seeking for food items. To support the claim that a domain-general cognitive process underlies ape metacognition one needs to show that selective information seeking extends to non-food items. In this study, chimpanzees (Pan troglodytes) and orangutans (Pongo abelii) either had to determine the location of a desired food item or a property of a non-food item (length of a tool). We manipulated whether subjects received prior information about the item’s location or property. During the test, subjects had the opportunity to seek the respective information. Results show that apes engaged in more information seeking when they had no prior knowledge. Importantly, this selective pattern of information seeking applied to food as well as to tools.