bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implementation of a method to visualize noise-induced hearing loss in mass stranded cetaceans
Authors: Morell Maria , Brownlow Andrew , McGovern Barry , Raverty Stephen A. , Shadwick Robert E. , André Michel 
Published: February 2017

AbstractAssessment of the impact of noise over-exposure in stranded cetaceans is challenging, as the lesions that lead to hearing loss occur at the cellular level and inner ear cells are very sensitive to autolysis. Distinguishing ante-mortem pathology from post-mortem change has been a major constraint in diagnosing potential impact. Here, we outline a methodology applicable to the detection of noise-induced hearing loss in stranded cetaceans. Inner ears from two mass strandings of long-finned pilot whales in Scotland were processed for scanning electron microscopy observation. In one case, a juvenile animal, whose ears were fixed within 4 hours of death, revealed that many sensory cells at the apex of the cochlear spiral were missing. In this case, the absence of outer hair cells would be compatible with overexposure to underwater noise, affecting the region which transduces the lowest frequencies of the pilot whales hearing spectrum. Perfusion of cochlea with fixative greatly improved preservation and enabled diagnostic imaging of the organ of Corti, even 30 hours after death. This finding supports adopting a routine protocol to detect the pathological legacy of noise overexposure in mass stranded cetaceans as a key to understanding the complex processes and implications that lie behind such stranding events.
Modulation of Microglial Cell Fcγ Receptor Expression Following Viral Brain Infection
Authors: Chauhan Priyanka , Hu Shuxian , Sheng Wen S. , Prasad Sujata , Lokensgard James R. 
Published: February 2017

AbstractFcγ receptors (FcγRs) for IgG couple innate and adaptive immunity through activation of effector cells by antigen-antibody complexes. We investigated relative levels of activating and inhibitory FcγRs on brain-resident microglia following murine cytomegalovirus (MCMV) infection. Flow cytometric analysis of microglial cells obtained from infected brain tissue demonstrated that activating FcγRs were expressed maximally at 5 d post-infection (dpi), while the inhibitory receptor (FcγRIIB) remained highly elevated during both acute and chronic phases of infection. The highly induced expression of activating FcγRIV during the acute phase of infection was also noteworthy. Furthermore,in vitroanalysis using cultured primary microglia demonstrated the role of interferon (IFN)γ and interleukin (IL)-4 in polarizing these cells towards a M1 or M2 phenotype, respectively. Microglial cell-polarization correlated with maximal expression of either FcγRIV or FcγRIIB following stimulation with IFNγ or IL-4, respectively. Finally, we observed a significant delay in polarization of microglia towards an M2 phenotype in the absence of FcγRs in MCMV-infected Fcer1g and FcgR2b knockout mice. These studies demonstrate that neuro-inflammation following viral infection increases expression of activating FcγRs on M1-polarized microglia. In contrast, expression of the inhibitory FcγRIIB receptor promotes M2-polarization in order to shut-down deleterious immune responses and limit bystander brain damage.
Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity
Authors: Kuhn Benjamin M. , Nodzyński Tomasz , Errafi Sanae , Bucher Rahel , Gupta Shibu , Aryal Bibek , Dobrev Petre , Bigler Laurent , Geisler Markus , Zažímalová Eva , Friml Jiří , Ringli Christoph 
Published: February 2017

AbstractThe phytohormone auxin is a major determinant and regulatory component important for plant development. Auxin transport between cells is mediated by a complex system of transporters such as AUX1/LAX, PIN, and ABCB proteins, and their localization and activity is thought to be influenced by phosphatases and kinases. Flavonols have been shown to alter auxin transport activity and changes in flavonol accumulation in the Arabidopsis thaliana rol1-2 mutant cause defects in auxin transport and seedling development. A new mutation in ROOTS CURL IN NPA 1 (RCN1), encoding a regulatory subunit of the phosphatase PP2A, was found to suppress the growth defects of rol1-2 without changing the flavonol content. rol1-2 rcn1-3 double mutants show wild type-like auxin transport activity while levels of free auxin are not affected by rcn1-3. In the rol1-2 mutant, PIN2 shows a flavonol-induced basal-to-apical shift in polar localization which is reversed in the rol1-2 rcn1-3 to basal localization. In vivo analysis of PINOID action, a kinase known to influence PIN protein localization in a PP2A-antagonistic manner, revealed a negative impact of flavonols on PINOID activity. Together, these data suggest that flavonols affect auxin transport by modifying the antagonistic kinase/phosphatase equilibrium.
A Noise Trimming and Positional Significance of Transposon Insertion System to Identify Essential Genes in Yersinia pestis
Authors: Yang Zheng Rong , Bullifent Helen L. , Moore Karen , Paszkiewicz Konrad , Saint Richard J. , Southern Stephanie J. , Champion Olivia L. , Senior Nicola J. , Sarkar-Tyson Mitali , Oyston Petra C. F. , Atkins Timothy P. , Titball Richard W. 
Published: February 2017

AbstractMassively parallel sequencing technology coupled with saturation mutagenesis has provided new and global insights into gene functions and roles. At a simplistic level, the frequency of mutations within genes can indicate the degree of essentiality. However, this approach neglects to take account of the positional significance of mutations - the function of a gene is less likely to be disrupted by a mutation close to the distal ends. Therefore, a systematic bioinformatics approach to improve the reliability of essential gene identification is desirable. We report here a parametric model which introduces a novel mutation feature together with a noise trimming approach to predict the biological significance of Tn5 mutations. We show improved performance of essential gene prediction in the bacterium Yersinia pestis, the causative agent of plague. This method would have broad applicability to other organisms and to the identification of genes which are essential for competitiveness or survival under a broad range of stresses.
High-throughput sequencing of multiple amplicons for barcoding and integrative taxonomy
Authors: Cruaud Perrine , Rasplus Jean-Yves , Rodriguez Lillian Jennifer , Cruaud Astrid 
Published: February 2017

AbstractUntil now, the potential of NGS for the construction of barcode libraries or integrative taxonomy has been seldom realised. Here, we amplified (two-step PCR) and simultaneously sequenced (MiSeq) multiple markers from hundreds of fig wasp specimens. We also developed a workflow for quality control of the data. Illumina and Sanger sequences accumulated in the past years were compared. Interestingly, primers and PCR conditions used for the Sanger approach did not require optimisation to construct the MiSeq library. After quality controls, 87% of the species (76% of the specimens) had a valid MiSeq sequence for each marker. Importantly, major clusters did not always correspond to the targeted loci. Nine specimens exhibited two divergent sequences (up to 10%). In 95% of the species, MiSeq and Sanger sequences obtained from the same sampling were similar. For the remaining 5%, species were paraphyletic or the sequences clustered into divergent groups on the Sanger + MiSeq trees (>7%). These problematic cases may represent coding NUMTS or heteroplasms. Our results illustrate that Illumina approaches are not artefact-free and confirm that Sanger databases can contain non-target genes. This highlights the importance of quality controls, working with taxonomists and using multiple markers for DNA-taxonomy or species diversity assessment.
Lead-free piezoelectrics: V3+ to V5+ ion conversion promoting the performances of V-doped Zinc Oxide
Authors: Laurenti M. , Castellino M. , Perrone D. , Asvarov A. , Canavese G. , Chiolerio A. 
Published: February 2017

AbstractVanadium doped ZnO (VZO) thin films were grown by RF magnetron sputtering, starting from a ZnO:V ceramic target. The crystal structure, chemical composition, electric and piezoelectric properties of the films were investigated either on the as-grown thin films or after a post-deposition rapid thermal annealing (RTA) treatment performed at 600 °C for different lengths of time (1 and 5 min) in an oxygen atmosphere. Substitutional doping of Zn2+ with V3+ and V5+ ions strongly deteriorated the hexagonal wurtzite ZnO structure of the as-grown thin films due to lattice distortion. The resulting slight amorphization led to a poor piezoelectric response and higher resistivity. After the RTA treatment, strong c-axis oriented VZO thin films were obtained, together with a partial conversion of the starting V3+ ions into V5+. The improvement of the crystal structure and the stronger polarity of both V3+ – O and V5+ – O chemical bonds, together with the corresponding easier rotation under the application of an external electric field, positively affected the piezoelectric response and increased conductivity. This was confirmed by closed-loop butterfly piezoelectric curves, by a maximum d33 piezoelectric coefficient of 85 pm·V−1, and also by ferroelectric switching domains with a well-defined polarization hysteresis curve, featuring a residual polarization of 12.5 μC∙cm−2.
Expression of human endogenous retrovirus-K is strongly associated with the basal-like breast cancer phenotype
Authors: Johanning Gary L. , Malouf Gabriel G. , Zheng Xiaofeng , Esteva Francisco J. , Weinstein John N. , Wang-Johanning Feng , Su Xiaoping 
Published: February 2017

AbstractHuman endogenous retroviruses (HERVs), which make up approximately 8% of the human genome, are overexpressed in some breast cancer cells and tissues but without regard to cancer subtype. We, therefore, analyzed TCGA RNA-Seq data to evaluate differences in expression of the HERV-K family in breast cancers of the various subtypes. Four HERV-K loci on different chromosomes were analyzed in basal, Her2E, LumA, and LumB breast cancer subtypes of 512 breast cancer patients with invasive ductal carcinoma (IDC). The results for all four loci showed higher HERV-K expression in the basal subtype, suggesting similar mechanisms of regulation regardless of locus. Expression of the HERV-K envelope gene (env) was highly significantly increased in basal tumors in comparison with the also-upregulated expression of other HERV-K genes. Analysis of reverse-phase protein array data indicated that increased expression of HERV-K is associated with decreased mutation of H-Ras (wild-type). Our results show elevation of HERV-K expression exclusively in the basal subtype of IDC breast cancer (as opposed to the other subtypes) and suggest HERV-K as a possible target for cancer vaccines or immunotherapy against this highly aggressive form of breast cancer.
Electromagnetic Tunneling and Resonances in Pseudochiral Omega Slabs
Authors: Razzaz Faroq , Alkanhal Majeed A. S. 
Published: February 2017

AbstractThis paper presents theoretical investigation of the electromagnetic wave tunneling and anomalous transmission around the trapped modes in a pseudochiral omega slab. The dispersion relation, the conditions of the trapped modes, and the evanescent wave coupling and tunneling in two different reciprocal pseudochiral omega slab structures are derived. The Berreman’s matrix method is applied to obtain the transmission coefficients across the pseudochiral omega slab. When the structure is perturbed, a resonance phenomenon is detected around the trapped modes. This resonance results in transmission anomalies (total transmission and total reflection) and dramatic field amplifications around the trapped modes. The number of the discrete trapped modes and then the resonance frequencies are prescribed by the parameters of the pseudochiral omega slab such as the value of the omega parameter and its orientation and the slab thickness.
Micheliolide provides protection of mice against Staphylococcus aureus and MRSA infection by down-regulating inflammatory response
Authors: Jiang Xinru , Wang Yuli , Qin Yifei , He Weigang , Benlahrech Adel , Zhang Qingwen , Jiang Xin , Lu Zhenhui , Ji Guang , Zheng Yuejuan 
Published: February 2017

AbstractA major obstacle to therapy in intensive care units is sepsis caused by severe infection. In recent years gram-positive (G+) bacteria, most commonly staphylococci, are thought to be the main pathogens. Micheliolide (MCL) was demonstrated to provide a therapeutic role in rheumatoid arthritis, inflammatory intestinal disease, colitis-associated cancer, and lipopolysaccharide (LPS, the main component of G−bacterial cell wall) induced septic shock. We proved here that MCL played an anti-inflammatory role inStaphylococcus aureus (S. aureus) and methicillin-resistantS. aureus(MRSA) induced peritonitis. It inhibited the expression of inflammatory cytokines and chemokines in macrophages and dendritic cells upon stimulation with peptidoglycan (PGN, the main cell wall composition of G+bacteria). PI3K/Akt and NF-κB pathways account for the anti-inflammatory role of MCL after PGN stimulation. MCL reduced IL-6 secretion through down-regulating NF-κB activation and improved the survival status in mice challenged with a lethal dose ofS. aureus. In MRSA infection mouse model, MCL down-regulated the expression of IL-6, TNF-α, MCP-1/CCL2 and IFN-γ in sera, and ameliorated the organ damage of liver and kidney. In conclusion, MCL can help maintain immune equilibrium and decrease PGN,S. aureusand MRSA-triggered inflammatory response. These provide the rationality for the potential usage of MCL in sepsis caused by G+bacteria (e.g.,S. aureus) and antibiotic-resistant bacteria (e.g., MRSA).
Magnetic Lifshitz transition and its consequences in multi-band iron-based superconductors
Authors: Ptok Andrzej , Kapcia Konrad J. , Cichy Agnieszka , Oleś Andrzej M. , Piekarz Przemysław 
Published: February 2017

AbstractIn this paper we address Lifshitz transition induced by applied external magnetic field in a case of iron-based superconductors, in which a difference between the Fermi level and the edges of the bands is relatively small. We introduce and investigate a two-band model with intra-band pairing in the relevant parameters regime to address a generic behaviour of a system with hole-like and electron-like bands in external magnetic field. Our results show that two Lifshitz transitions can develop in analysed systems and the first one occurs in the superconducting phase and takes place at approximately constant magnetic field. The chosen sets of the model parameters can describe characteristic band structure of iron-based superconductors and thus the obtained results can explain the experimental observations in FeSe and Co-doped BaFe2As2 compounds.
Insights into structure and activity of natural compound inhibitors of pneumolysin
Authors: Li Hongen , Zhao Xiaoran , Deng Xuming , Wang Jianfeng , Song Meng , Niu Xiaodi , Peng Liping 
Published: February 2017

AbstractPneumolysin is the one of the major virulence factor of the bacterium Streptococcus pneumoniae. In previous report, it is shown that β-sitosterol, a natural compound without antimicrobial activity, is a potent antagonist of pneumolysin. Here, two new pneumolysin natural compound inhibitors, with differential activity, were discovered via haemolysis assay. To explore the key factor of the conformation for the inhibition activity, the interactions between five natural compound inhibitors with differential activity and pneumolysin were reported using molecular modelling, the potential of mean force profiles. Interestingly, it is found that incorporation of the single bond (C22-C23-C24-C25) to replace the double bond (hydrocarbon sidechain) improved the anti-haemolytic activity. In view of the molecular modelling, binding of the five inhibitors to the conserved loop region (Val372, Leu460, and Tyr461) of the cholesterol binding sites led to stable complex systems, which was consistent with the result of β-sitosterol. Owing to the single bond (C22-C23-C24-C25), campesterol and brassicasterol could form strong interactions with Val372 and show higher anti-haemolytic activity, which indicated that the single bond (C22-C23-C24-C25) in inhibitors was required for the anti-haemolytic activity. Overall, the current molecular modelling work provides a starting point for the development of rational design and higher activity pneumolysin inhibitors.
Microbial nitrification, denitrification and respiration in the leached cinnamon soil of the upper basin of Miyun Reservoir
Authors: Xu Wen , Cai Yan-Peng , Yang Zhi-Feng , Yin Xin-An , Tan Qian 
Published: February 2017

AbstractLeached cinnamon soil is the main agricultural soil distributed in the North China Plain. In this research, leached cinnamon soil samples were collected in the upper basin of Miyun Reservoir (northeast of Beijing, China). The BaPS method (Barometric Process Separation) was applied to measure nitrification, denitrification and respiration rates. The rates of nitrification, denitrification and respiration were 0–120.35 μg N/kg SDW h, 0–246.86 μg N/kg SDW h and 0.17–225.85 μg C/kg SDW h (Soil Dry Weight, SDW), respectively. The emission rates of CO2 and NxOy through nitrification, denitrification and respiration were 1.00–547.80 and 6.00–4850.65 μmol/h, respectively. The analysis of relationships between nitrification, denitrification and respiration rates indicated that these three microbial processes were interacted, which posed impacts on soil nitrogen availability. As indicated by the results, C:N ratio coupled with "Equation missing" content could be taken as the indicators of "Equation missing" content, which is usually the predominant form of N available to plants growing in soil. Results showed that "Equation missing" content was the highest (i.e., >62.4 mg/kg) when C:N ratio was 5.30–8.40, meanwhile "Equation missing" content was 3.71–4.39 mg/kg. Nevertheless, "Equation missing" content was the lowest (i.e., <6.40 mg/kg) when C:N ratio was 9.2–12.10, meanwhile "Equation missing" content was 3.41–4.35 mg/kg.
The Demographic Features, Clinicopathological Characteristics and Cancer-specific Outcomes for Patients with Microinvasive Breast Cancer: A SEER Database Analysis
Authors: Wang Wenna , Zhu Wenjie , Du Feng , Luo Yang , Xu Binghe 
Published: February 2017

AbstractTo investigate the clinicopathological characteristics and survival outcomes of microinvasive breast cancer, we conducted an observational study of female diagnosed with DCIS or DCIS with microinvasion (DCISM) from 1990 to 2012 using the Surveillance, Epidemiology, and End Results (SEER) database. There were 87695 DCIS and 8863 DCISM identified. In DCISM group, patients appeared to be younger and more black patients were identified in comparison with DCIS group. Furthermore, DCISM was associated with more aggressive tumor characteristics like higher rates of oestrogen receptor (ER) and progesterone receptor (PR) negativity, HER2 positivity, and lymph node metastasis. With a median follow-up of 91 months, patients with DCISM had worse cancer-specific survival (CSS) (hazard ratio [HR], 2.475; P < 0.001) and overall survival (OS) (HR, 1.263; P < 0.001). In the multivariable analysis, microinvasion was an independent prognostic factor for worse CSS (HR, 1.919; P < 0.001) and OS (HR, 1.184; P < 0.001). The 10-year cancer-specific mortality rate was 1.49% in DCIS and 4.08% in DCISM (HR, 2.771; P < 0.001). The 20-year cancer-specific mortality rate was 4.00% in DCIS and 9.65% in DCISM (HR, 2.482; P < 0.001). Deepening understanding of the nature of microinvasive breast cancer will be valuable for clinical treatment recommendations.
A universal computational model for predicting antigenic variants of influenza A virus based on conserved antigenic structures
Authors: Peng Yousong , Wang Dayan , Wang Jianhong , Li Kenli , Tan Zhongyang , Shu Yuelong , Jiang Taijiao 
Published: February 2017

AbstractRapid determination of the antigenicity of influenza A virus could help identify the antigenic variants in time. Currently, there is a lack of computational models for predicting antigenic variants of some common hemagglutinin (HA) subtypes of influenza A viruses. By means of sequence analysis, we demonstrate here that multiple HA subtypes of influenza A virus undergo similar mutation patterns of HA1 protein (the immunogenic part of HA). Further analysis on the antigenic variation of influenza A virus H1N1, H3N2 and H5N1 showed that the amino acid residues’ contribution to antigenic variation highly differed in these subtypes, while the regional bands, defined based on their distance to the top of HA1, played conserved roles in antigenic variation of these subtypes. Moreover, the computational models for predicting antigenic variants based on regional bands performed much better in the testing HA subtype than those did based on amino acid residues. Therefore, a universal computational model, named PREDAV-FluA, was built based on the regional bands to predict the antigenic variants for all HA subtypes of influenza A viruses. The model achieved an accuracy of 0.77 when tested with avian influenza H9N2 viruses. It may help for rapid identification of antigenic variants in influenza surveillance.
Bet-hedging in bacteriocin producing Escherichia coli populations: the single cell perspective
Authors: Bayramoglu Bihter , Toubiana David , van Vliet Simon , Inglis R. Fredrik , Shnerb Nadav , Gillor Osnat 
Published: February 2017

AbstractProduction of public goods in biological systems is often a collaborative effort that may be detrimental to the producers. It is therefore sustainable only if a small fraction of the population shoulders the cost while the majority reap the benefits. We modelled this scenario using Escherichia coli populations producing colicins, an antibiotic that kills producer cells’ close relatives. Colicin expression is a costly trait, and it has been proposed that only a small fraction of the population actively expresses the antibiotic. Colicinogenic populations were followed at the single-cell level using time-lapse microscopy, and showed two distinct, albeit dynamic, subpopulations: the majority silenced colicin expression, while a small fraction of elongated, slow-growing cells formed colicin-expressing hotspots, placing a significant burden on expressers. Moreover, monitoring lineages of individual colicinogenic cells showed stochastic switching between expressers and non-expressers. Hence, colicin expressers may be engaged in risk-reducing strategies—or bet-hedging—as they balance the cost of colicin production with the need to repel competitors. To test the bet-hedging strategy in colicin-mediated interactions, competitions between colicin-sensitive and producer cells were simulated using a numerical model, demonstrating a finely balanced expression range that is essential to sustaining the colicinogenic population.