bluuebunny/crossref_metadata_2025 huggingface dataset:
Stress induction of clpC in Bacillus subtilis and its involvement in stress tolerance
Authors: Krüger E , Völker U , Hecker M
Published: November 2016

A member of the clpC subfamily of stress response-related Clp ATPases was cloned from Bacillus subtilis. The B. subtilis clpC gene was induced in response to various stresses, including heat shock. Its product was identified as a general stress protein (Gsp12) described previously. A dramatic increase in the amount of clpC mRNA immediately after exposure to multiple stresses suggested regulation on a transcriptional level. Induction by heat shock was independent of the alternative sigma factor SigB, indicating a new mechanism of heat shock induction in B. subtilis. A clpC insertional mutant had an impaired tolerance for heat shock and salt stress. Furthermore, the mutation triggered the formation of elongated cells, a phenomenon particularly pronounced during stress.
Patient-Specific
Bacteroides
Genome Variants in Pouchitis
Authors: Vineis Joseph H. , Ringus Daina L. , Morrison Hilary G. , Delmont Tom O. , Dalal Sushila , Raffals Laura H. , Antonopoulos Dionysios A. , Rubin David T. , Eren A. Murat , Chang Eugene B. , Sogin Mitchell L.
Published: November 2016

A 2-year longitudinal microbiome study of 22 patients who underwent colectomy with an ileal pouch anal anastomosis detected significant increases in distinct populations of
Bacteroides
during 9 of 11 patient visits that coincided with inflammation (pouchitis). Oligotyping and metagenomic short-read annotation identified
Bacteroides
populations that occurred in early samples, bloomed during inflammation, and reappeared after antibiotic treatment. Targeted cultivation of
Bacteroides
isolates from the same individual at multiple time points and from several patients detected subtle genomic changes, including the identification of rapidly evolving genomic elements that differentiate isogenic strains of
Bacteroides fragilis
from the mucosa versus lumen. Each patient harbored
Bacteroides
spp. that are closely related to commonly occurring clinical isolates, including
Bacteroides ovatus
,
B. thetaiotaomicron
,
B. vulgatus
, and
B. fragilis
, which contained unique loci in different patients for synthesis of capsular polysaccharides. The presence of unique
Bacteroides
capsular polysaccharide loci within different hosts and between the lumen and mucosa may represent adaptations to stimulate, suppress, and evade host-specific immune responses at different microsites of the ileal pouch.

IMPORTANCE
This longitudinal study provides an opportunity to describe shifts in the microbiomes of individual patients who suffer from ulcerative colitis (UC) prior to and following inflammation. Pouchitis serves as a model for UC with a predictable incidence of disease onset and enables prospective longitudinal investigations of UC etiology prior to inflammation. Because of insufficient criteria for predicting which patients will develop UC or pouchitis, the interpretation of cross-sectional study designs suffers from lack of information about the microbiome structure and host gene expression patterns that directly correlate with the onset of disease. Our unique longitudinal study design allows each patient to serve as their own control, providing information about the state of the microbiome and host prior to and during the course of disease. Of significance to the broader community, this study identifies microbial strains that may have genetic elements that trigger the onset of disease in susceptible hosts.
The Paralogous Histone Deacetylases Rpd3 and Rpd31 Play Opposing Roles in Regulating the White-Opaque Switch in the Fungal Pathogen Candida albicans
Authors: Xie Jing , Jenull Sabrina , Tscherner Michael , Kuchler Karl
Published: November 2016

Chromatin modifications affect gene regulation in response to environmental stimuli in numerous biological processes. For example,
N
-acetyl-glucosamine and CO
2
induce a morphogenetic conversion between white (W) and opaque (O) cells in
MTL
(mating-type locus) homozygous and heterozygous (
a
/α) strains of the human fungal pathogen
Candida albicans
. Here, we identify 8 histone-modifying enzymes playing distinct roles in the regulation of W/O switching in
MTL
homozygous and heterozygous strains. Most strikingly, genetic removal of the paralogous genes
RPD3
and
RPD31
, both of which encode almost identical orthologues of the yeast histone deacetylase (HDAC) Rpd3, reveals opposing roles in W/O switching of
MTL
a
/α strains. We show that Rpd3 and Rpd31 functions depend on
MTL
genotypes. Strikingly, we demonstrate that Rpd3 and Rpd31, which are almost identical except for a divergent C-terminal extension present in Rpd31, exert their functions in distinct regulatory complexes referred to as CaRpd3L and CaRpd31S complexes. Moreover, we identify the
Candida
orf19.7185 product Ume1, the orthologue of yeast Ume1, as a shared core subunit of CaRpd3L and CaRpd31S. Mechanistically, we show that the opposing roles of Rpd3 and Rpd31 require their deacetylase activities. Importantly, CaRpd3L interacts with the heterodimeric transcriptional repressor
a
1/α2, thus controlling expression of
WOR1
encoding the master regulator of W/O switching. Thus, our work provides novel insight about regulation mechanisms of W/O switching in
MTL
a
/α strains. This is the first example of two highly conserved HDACs exerting opposing regulatory functions in the same process in a eukaryotic cell.

IMPORTANCE
RPD3
-like histone deacetylases (also called class I HDACs) are conserved from unicellular eukaryotes to mammals. Specifically, the genome of the human fungal pathogen
Candida albicans
, the most frequent cause of invasive fungal infections of high morbidity and mortality, harbors two almost identical paralogous HDACs, Rpd3 and Rpd31. We show here for the first time that Rpd3 and Rpd31 acquired functional divergence related to a distinct C-terminal domain. Rpd3 and Rpd31 associate with different complexes in the control regions of the master regulator gene
WOR1
, which is required for white-opaque (W/O) morphogenesis, respectively. The ability to switch is important for fungal pathogenesis, since it enables distinct host niche colonization. This work is to the best of our knowledge the first description of two paralogous HDACs playing opposing functional roles in the same developmental process. Our work adds a new angle concerning the molecular understanding of HDACs in the regulation of cell fate decisions.
Capsular Polysaccharide Expression in CommensalStreptococcusSpecies: Genetic and Antigenic Similarities to Streptococcus pneumoniae
Authors: Skov Sørensen Uffe B. , Yao Kaihu , Yang Yonghong , Tettelin Hervé , Kilian Mogens
Published: November 2016

Expression of a capsular polysaccharide is considered a hallmark of most invasive species of bacteria, includingStreptococcus pneumoniae, in which the capsule is among the principal virulence factors and is the basis for successful vaccines. Consequently, it was previously assumed that capsule production distinguishesS. pneumoniaefrom closely related commensals of the mitis group streptococci. Based on antigenic and genetic analyses of 187 mitis group streptococci, including 90 recognized serotypes ofS. pneumoniae, we demonstrated capsule production by the Wzy/Wzx pathway in 74% of 66S. mitisstrains and in virtually all tested strains ofS. oralis(subspeciesoralis,dentisani, andtigurinus) andS. infantis. Additional analyses of genomes ofS. cristatus,S. parasanguinis,S. australis,S. sanguinis,S. gordonii,S. anginosus,S. intermedius, andS. constellatusrevealed complete capsular biosynthesis (cps) loci in all strains tested. Truncatedcpsloci were detected in three strains ofS. pseudopneumoniae, in 26% ofS. mitisstrains, and in a singleS. oralisstrain. The level of sequence identities ofcpslocus genes confirmed that the structural polymorphism of capsular polysaccharides inS. pneumoniaeevolved by import ofcpsfragments from commensalStreptococcusspecies, resulting in a mosaic of genes of different origins. The demonstrated antigenic identity of at least eight of the numerous capsular polysaccharide structures expressed by commensal streptococci with recognized serotypes ofS. pneumoniaeraises concerns about potential misidentifications in addition to important questions concerning the consequences for vaccination and host-parasite relationships both for the commensals and for the pathogen.

IMPORTANCEExpression of a capsular polysaccharide is among the principal virulence factors ofStreptococcus pneumoniaeand is the basis for successful vaccines against infections caused by this important pathogen. Contrasting with previous assumptions, this study showed that expression of capsular polysaccharides by the same genetic mechanisms is a general property of closely related species of streptococci that form a significant part of our commensal microbiota. The demonstrated antigenic identity of many capsular polysaccharides expressed by commensal streptococci andS. pneumoniaeraises important questions concerning the consequences for vaccination and host-parasite relationships both for the commensals and the pathogen.
A Stress-Induced Bias in the Reading of the Genetic Code in Escherichia coli
Authors: Oron-Gottesman Adi , Sauert Martina , Moll Isabella , Engelberg-Kulka Hanna
Published: November 2016

Escherichia coli
mazEF
is an extensively studied stress-induced toxin-antitoxin (TA) system. The toxin MazF is an endoribonuclease that cleaves RNAs at ACA sites. Thereby, under stress, the induced MazF generates a stress-induced translation machinery (STM), composed of MazF-processed mRNAs and selective ribosomes that specifically translate the processed mRNAs. Here, we further characterized the STM system, finding that MazF cleaves only ACA sites located in the open reading frames of processed mRNAs, while out-of-frame ACAs are resistant. This in-frame ACA cleavage of MazF seems to depend on MazF binding to an extracellular-death-factor (EDF)-like element in ribosomal protein bS1 (bacterial S1), apparently causing MazF to be part of STM ribosomes. Furthermore, due to the in-frame MazF cleavage of ACAs under stress, a bias occurs in the reading of the genetic code causing the amino acid threonine to be encoded only by its synonym codon ACC, ACU, or ACG, instead of by ACA.

IMPORTANCE
The genetic code is a universal characteristic of all living organisms. It defines the set of rules by which nucleotide triplets specify which amino acid will be incorporated into a protein. Our results represent the first existing report on a stress-induced bias in the reading of the genetic code. We found that in
E. coli
, under stress, the amino acid threonine is encoded only by its synonym codon ACC, ACU, or ACG, instead of by ACA. This is because under stress, MazF generates a stress-induced translation machinery (STM) in which MazF cleaves in-frame ACA sites of the processed mRNAs.
Indications for antiviral therapy for chronic hepatitis B in pregnant mothers
Authors: Yoo Eric Raeyoon , Perumpail Ryan Babu , Cholankeril George , Ahmed Aijaz
Published: November 2016

The use of antiviral therapy for chronic hepatitis B virus (HBV) infection in the setting of pregnancy needs to be individualised based on limited data. We report a case of a 34-year-old Korean-American woman with a history of pregnancy with emergent caesarean section due to prolonged labour in the setting of HBV e-antigen (HBeAg) positive chronic HBV with a pretreatment baseline HBV DNA level of 110000 000 million copies per mL. Her first delivery was complicated by mother-to-child transmission (MTCT) of HBV infection to her daughter despite standard active and passive immunoprophylaxis. Our case report highlights an important clinical decision-making step regarding the timing of antiviral therapy in the management of chronic HBV in pregnant women with high risk of MTCT.
Massive symptomatic right-sided Bochdalek hernia in an adult man
Authors: Kohli Naman , Mitreski Goran , Yap Cheng-Hon , Leong Matthew
Published: November 2016

A 22-year-old man presented to a rural hospital in Australia with right-sided pleuritic chest pain, right shoulder pain and dyspnoea. The patient had been receiving chronic asthma therapy without improvement. CT of the chest was performed after an abnormal X-ray, incidentally revealing one of the largest documented right-sided diaphragmatic hernias, with left lung compression due to mediastinal shift. The patient was definitively managed with thoracotomy alone. The contents of the hernia sac included colon and multiple loops of small bowel with a 10 cm neck. Definitive treatment was achieved with significant reduction in hernia size and formation of a neo-diaphragm with composite mesh. The postoperative period was complicated only by a wound infection. Two weeks after discharge the patient remained clinically well. Repeat chest X-ray showed no recurrence of the hernia. Congenital diaphragmatic hernias should be considered in patients with ongoing respiratory symptoms. Thoracotomy provides a safe approach.
Interesting case of base of skull mass infiltrating cavernous sinuses
Authors: Singh Achintya Dinesh , Soneja Manish , Memon Saba Samad , Vyas Surabhi
Published: November 2016

A man aged 35 years presented with chronic headache and earache of 1-year duration. He had progressive vision loss and diplopia since last 9 months. He also had pain over the face and episodic profuse epistaxis. On examination, perception of light was absent in the right eye and hand movements were detected at 4 m distance in the left eye. Imaging revealed a lobulated mass in the nasopharynx extending into the bilateral cavernous sinuses and sphenoid sinus with bony erosions. Biopsy of the nasopharyngeal mass revealed pathological features which are characteristic of IgG4 disease. His serum IgG4 levels and acute inflammatory markers were also elevated. The patient was started on oral corticosteroid therapy. Fever, headache and earache resolved early and there was gradual improvement in the vision of the left eye. After 6 months, visual acuity in the left eye was 6/9, but right eye visual acuity had no change. Follow-up imaging revealed a significant reduction in the size of the mass.
DisseminatedMycobacterium tuberculosisfollowing renal transplant with alemtuzumab induction
Authors: Baghban Adam , Azar Marwan Mikheal , Bernardo Raffaele Mario , Malinis Maricar
Published: November 2016

Mycobacterium tuberculosispresents unique challenges in the peritransplant period. Here, we describe a case of disseminated tuberculosis following renal transplantation with alemtuzumab induction immunosuppression in a patient with remotely treated pulmonary tuberculosis and ongoing risk factors for re-infection. We also review the available literature regarding the prevalence of tuberculosis infection following solid organ transplant and management of high-risk patients, including the role for isoniazid preventative therapy.
Oncolytic reovirus as a combined antiviral and anti-tumour agent for the treatment of liver cancer
Authors: Samson Adel , Bentham Matthew J , Scott Karen , Nuovo Gerard , Bloy Abigail , Appleton Elizabeth , Adair Robert A , Dave Rajiv , Peckham-Cooper Adam , Toogood Giles , Nagamori Seishi , Coffey Matthew , Vile Richard , Harrington Kevin , Selby Peter , Errington-Mais Fiona , Melcher Alan , Griffin Stephen
Published: November 2016

Objective

Oncolytic viruses (OVs) represent promising, proinflammatory cancer treatments. Here, we explored whether OV-induced innate immune responses could simultaneously inhibit HCV while suppressing hepatocellular carcinoma (HCC). Furthermore, we extended this exemplar to other models of virus-associated cancer.

Design and results

Clinical grade oncolytic orthoreovirus (Reo) elicited innate immune activation within primary human liver tissue in the absence of cytotoxicity and independently of viral genome replication. As well as achieving therapy in preclinical models of HCC through the activation of innate degranulating immune cells, Reo-induced cytokine responses efficiently suppressed HCV replication both in vitro and in vivo. Furthermore, Reo-induced innate responses were also effective against models of HBV-associated HCC, as well as an alternative endogenous model of Epstein–Barr virus-associated lymphoma. Interestingly, Reo appeared superior to the majority of OVs in its ability to elicit innate inflammatory responses from primary liver tissue.

Conclusions

We propose that Reo and other select proinflammatory OV may be used in the treatment of multiple cancers associated with oncogenic virus infections, simultaneously reducing both virus-associated oncogenic drive and tumour burden. In the case of HCV-associated HCC (HCV-HCC), Reo should be considered as an alternative agent to supplement and support current HCV-HCC therapies, particularly in those countries where access to new HCV antiviral treatments may be limited.
Synthesis of spiropyran derivatives over 1-(carboxymethyl) pyridinium iodide as nanostructured pyridinium salt under aqueous media
Authors: Moosavi-Zare Ahmad Reza , Zolfigol Mohammad Ali , Salehi-Moratab Rasoul , Noroozizadeh Ehsan
Published: November 2016

In this work, acetic acid functionalized pyridinium salt, namely 1-(carboxymethyl)pyridinium iodide {[cmpy]I}, has been applied as reusable nanostructured catalyst for green, simple and efficient preparation of spiropyrans by the one-pot domino Knoevenagel–Michael–cyclization reaction of isatin derivatives or acenaphthenquinone, with malononitrile, and 1,3-dicarbonyl compounds under aqueous media. Moreover, 1H and 13C NMR, mass, CHN analysis, Fourier transform infrared spectroscopy (FTIR), scanning electron microscope (SEM), thermal gravimetric analysis (TGA), differential thermal gravimetric (DTG), X-ray diffraction analysis (XRD), and calculation of crystallite size and interplaner distance of the catalyst have been studied.
Comparative study on performance and physical properties of CsI, NaI, RbI, and KBr materials
Authors: Belameiri Nadia , Tebboune Abdelghani , Mokaddem Allel , Sayed Ahmed , Asma Saim , Temimi Lahouari , Belbachir Ahmed Hafid
Published: November 2016

In the present work we report the results of our investigation using the full potential linear muffin tin orbital method (FP-LMTO) to calculate the structural and electronic properties of NaI, KBr, RbI, and CsI materials, in particular, the lattice constant and bulk modulus. The electronic band structures are also studied and discussed. Our aim is to find the relationship between the physical properties of these materials and their efficiency for detection. For this, Geant4 simulation has been performed for studying the absolute and photopeak detection efficiencies for the different materials as scintillation detectors at several photon energies. The range of gamma ray energy was between 662 and 1332.5 keV. The measurement results are compared with the available theoretical and experimental data.
Estimation of long terminal repeat element content in theHelicoverpa zeagenome from high-throughput sequencing of bacterial artificial chromosome pools
Authors: Coates Brad S. , Abel Craig A. , Perera Omaththage P.
Published: November 2016

The lepidopteran pest insect Helicoverpa zea feeds on cultivated corn and cotton across the Americas where control remains challenging owing to the evolution of resistance to chemical and transgenic insecticidal toxins, yet genomic resources remain scarce for this species. A bacterial artificial chromosome (BAC) library having a mean genomic insert size of 145 ± 20 kbp was created from a laboratory strain of H. zea, which provides ∼12.9-fold coverage of a 362.8 ± 8.8 Mbp (0.37 ± 0.09 pg) flow cytometry estimated haploid genome size. Assembly of Illumina HiSeq 2000 reads generated from 14 pools that encompassed all BAC clones resulted in 165 485 genomic contigs (N50= 3262 bp; 324.6 Mbp total). Long terminal repeat (LTR) protein coding regions annotated from 181 contigs included 30 Ty1/copia, 78 Ty3/gypsy, and 73 BEL/Pao elements, of which 60 (33.1%) encoded all five functional polyprotein (pol) domains. Approximately 14% of LTR elements are distributed non-randomly across pools of BAC clones.
Pharmacological Effects of Active Components of Chinese Herbal Medicine in the Treatment of Alzheimer's Disease: A Review
Authors: Wang Zhi-Yong , Liu Jian-Gang , Li Hao , Yang Hui-Ming
Published: November 2016

Alzheimer's disease (AD), the most common neurodegenerative disorder associated with dementia, not only severely decreases the quality of life for its victims, but also brings a heavy economic burden to the family and society. Unfortunately, few chemical drugs designed for clinical applications have reached the expected preventive or therapeutic effect so far, and combined with their significant side-effects, there is therefore an urgent need for new strategies to be developed for AD treatment. Traditional Chinese Medicine has accumulated many experiences in the treatment of dementia during thousands of years of practice; modern pharmacological studies have confirmed the therapeutic effects of many active components derived from Chinese herbal medicines (CHM). Ginsenoside Rg1, extracted from Radix Ginseng, exerts a [Formula: see text]-secretase inhibitor effect so as to decrease A[Formula: see text] aggregation. It can also inhibit the apoptosis of neuron cells. Tanshinone IIA, extracted from Radix Salviae miltiorrhizae, and baicalin, extracted from Radix Scutellariae[Formula: see text] can inhibit the oxidative stress injury in neuronal cells. Icariin, extracted from Epimedium brevicornum, can decrease A[Formula: see text] levels and the hyperphosphorylation of tau protein, and can also inhibit oxidative stress and apoptosis. Huperzine A, extracted from Huperzia serrata, exerts a cholinesterase inhibitor effect. Evodiamine, extracted from Fructus Evodiae, and curcumin, extracted from Rhizoma Curcumae Longae, exert anti-inflammatory actions. Curcumin can act on A[Formula: see text] and tau too. Due to the advantages of multi-target effects and fewer side effects, Chinese medicine is more appropriate for long-term use. In this present review, the pharmacological effects of commonly used active components derived from Chinese herbal medicines in the treatment of AD are discussed.
Standardized Extract from Caesalpinia spinosa is Cytotoxic Over Cancer Stem Cells and Enhance Anticancer Activity of Doxorubicin
Authors: Sandoval Tito A. , Urueña Claudia P. , Llano Mónica , Gómez-Cadena Alejandra , Hernández John F. , Sequeda Luis Gonzalo , Loaiza Alix E. , Barreto Alfonso , Li Shaoping , Fiorentino Susana
Published: November 2016

Cancer stem cells (CSC) are the primary cell type responsible for metastasis and relapse. ABC-transporters are integral membrane proteins involved in the translocation of substrates across membranes protecting CSC from chemotherapeutic agents. A plant extract derived from C. spinosa (P2Et) previously investigated for its antitumor activity has been shown to reduce lung and spleen metastasis in mice that have been transplanted with breast cancer cells, suggesting that P2Et has a significant activity against cancer stem cells (CSC). P2Et extract was thoroughly characterized by HPLC/MS. The cytotoxicity of P2Et extract was evaluated using a MTT assay in human and murine cell lines with different profiles of resistance, by Pgp overexpression or by enrichment in cancer stem cells. The synergistic effect of P2Et with doxorubicin was evaluated in vitro in several cell lines and in vivo in mice transplanted with TS/A cells, a highly resistant cell line and enriched in CD44[Formula: see text]CD24[Formula: see text]CSC. The chromatographic fingerprint of P2Et extract revealed 13 gallotannins. We also found that P2Et extract was cytotoxic to cells regardless of their resistant phenotype. Similarly, complementary activities were observed as drug efflux reversion and antioxidant activity. Short-treatment with P2Et extract, revealed a synergistic effect with doxorubicin in resistant cell lines. In vivo the P2Et increases mice survival in a TS/A breast cancer model associated with augmentation of calreticulin expression. Our results suggest that P2Et treatment could be used as adjuvant along with conventional chemotherapy to treat tumors with a MDR phenotype or with high frequency of CSC.
de Sitter and power-law solutions in some models of modified gravity
Authors: Zhong Yi , Elizalde Emilio
Published: November 2016

Inspired by some recent works of Lovelock Brans–Dicke (BD) gravity and mimetic gravity, cosmology solutions in extensions of these two modified gravities are investigated. A nonlocal term is added to the Lovelock BD action and Gauss–Bonnet (GB) terms to the mimetic action, correspondingly. de Sitter and power scale factor solutions are then obtained in both theories. They can provide natural new approaches to a more accurate description of the unverse evolution.
On the rapidity distribution of nucleons participating in elliptical flow at intermediate energies
Authors: Kaur Kamaldeep , Kumar Suneel
Published: November 2016

The distribution of nucleons participating in elliptical flow is studied for the reactions of [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text] and [Formula: see text] using isospin-dependent quantum molecular dynamics (IQMD) model for various centrality ranges and over the wide range of intermediate energy. Our findings reveal that the sigma (width) of rapidity distribution obtained varies with mass of colliding system at a given energy. The peak of rapidity distribution decreases with decrease in the mass of colliding nuclei. Transition energy as well as width of rapidity distribution depends on the mass of fragment for a given centrality. Influence of isospin dependent symmetry energy and nucleon–nucleon cross-section can be studied using rapidity distribution. Second transition energy depends on the mass of the fragment. Rotational phenomenon of nucleons can be observed for nucleons participating in elliptical flow.
On augmented superfield approach to vector Schwinger model
Authors: Gupta Saurabh , Kumar R.
Published: November 2016

We exploit the techniques of Bonora–Tonin superfield formalism to derive the off-shell nilpotent and absolutely anticommuting (anti-)BRST as well as (anti-)co-BRST symmetry transformations for the (1[Formula: see text]+[Formula: see text]1)-dimensional (2D) bosonized vector Schwinger model. In the derivation of above symmetries, we invoke the (dual)-horizontality conditions as well as gauge and (anti-)co-BRST invariant restrictions on the superfields that are defined onto the (2,[Formula: see text]2)-dimensional supermanifold. We provide geometrical interpretation of the above nilpotent symmetries (and their corresponding charges). We also express the nilpotency and absolute anticommutativity of the (anti-)BRST and (anti-)co-BRST charges within the framework of augmented superfield formalism.
The effect of position-dependent mass on nonlinear optical absorption coefficients and refractive index changes in a quantum well
Authors: Hu Meilin , Guo Kangxian , Zhang Zhongmin , Jiang Xiancong , Li Keyin , Liu Dongfeng
Published: November 2016

The influence of position-dependent mass (PDM) on nonlinear optical absorption (OA) coefficients and refractive index changes (RICs) is theoretically studied, within the framework of the iterative method and the compact-density-matrix approach. Through solving Schrödinger equation, the eigenfunctions and energy eigenvalues are obtained. The analytic expressions of the optical absorption coefficients and the refraction index changes are derived theoretically. The results reveal that the OA coefficients and the RICs are strongly affected by PDM, and both the peaks of them increase when considering PDM.
A graph model for preventing railway accidents based on the maximal information coefficient
Authors: Shao Fubo , Li Keping
Published: November 2016

A number of factors influences railway safety. It is an important work to identify important influencing factors and to build the relationship between railway accident and its influencing factors. The maximal information coefficient (MIC) is a good measure of dependence for two-variable relationships which can capture a wide range of associations. Employing MIC, a graph model is proposed for preventing railway accidents which avoids complex mathematical computation. In the graph, nodes denote influencing factors of railway accidents and edges represent dependence of the two linked factors. With the increasing of dependence level, the graph changes from a globally coupled graph to isolated points. Moreover, the important influencing factors are identified from many factors which are the monitor key. Then the relationship between railway accident and important influencing factors is obtained by employing the artificial neural networks. With the relationship, a warning mechanism is built by giving the dangerous zone. If the related factors fall into the dangerous zone in railway operations, the warning level should be raised. The built warning mechanism can prevent railway accidents and can promote railway safety.
Majorana fermion wavefunctions in carbon nanotubes and carbynes
Authors: Sadykov N. R. , Aporoski A. V.
Published: November 2016

Electron properties of semiconducting zigzag carbon nanotubes (CNTs) can be described by two uncoupled Dirac equations of dimension (1+1) for the particle with nonzero mass. The solutions of these equations are two charge-neutral Majorana fields. An analogous equation is obtained for the carbon chains. We use the approach, wherein wavefunction of charged particle is represented as the production of a rapidly oscillating exponent and the slowly varying function amplitude depending on the longitudinal coordinate.
High energy oxygen irradiation-induced defects in Fe-doped semi-insulating indium phosphide by positron annihilation technique
Authors: Pan S. , Mandal A. , Sohel Md. A. , Saha A. K. , Das D. , Sen Gupta A.
Published: November 2016

Positron annihilation technique is applied to study the recovery of radiation-induced defects in 140 MeV oxygen (O[Formula: see text]) irradiated Fe-doped semi-insulating indium phosphide during annealing over a temperature region of 25[Formula: see text]C–650[Formula: see text]C. Lifetime spectra of the irradiated sample are fitted with three lifetime components. Trapping model analysis is used to characterize defect states corresponding to the de-convoluted lifetime values. After irradiation, the observed average lifetime of positron [Formula: see text] ps at room temperature is higher than the bulk lifetime by 21 ps which reveals the presence of radiation-induced defects in the material. A decrease in [Formula: see text] occurs during room temperature 25[Formula: see text]C to 200[Formula: see text]C indicating the dissociation of higher order defects, might be due to positron trapping in acceptor-type of defects ([Formula: see text]). A reverse annealing stage is found at temperature range of 250[Formula: see text]C–425[Formula: see text]C for [Formula: see text]-parameter probably due to the migration of vacancies and the formation of vacancy clusters. Increase in [Formula: see text]-parameter from 325[Formula: see text]C to 425[Formula: see text]C indicates the change in the nature of predominant positron trapping sites. Beyond 425[Formula: see text]C, [Formula: see text], [Formula: see text]-parameter and [Formula: see text]-parameter starts decreasing and around 650[Formula: see text]C, [Formula: see text] and [Formula: see text]-parameter approached almost the bulk value showing the annealing out of radiation-induced defects.
Dynamical study of Debye temperature and combined density of states of TiO2
Authors: Srivastava U. C.
Published: November 2016

In present paper, it is focused on theoretical study of TiO2 with particular emphasis on vibrational phonon properties by means of van der Waals three-body force shell model (VTBFSM). Present model includes van der Waals interactions (VWI) and three-body interactions (TBI) in the framework of both ion polarizable rigid shell model (RSM) with short-range interactions effective up to the second neighbor. The Coulombic ion–ion interaction contribution to the dynamical matrix is calculated by the Kellerman.1 Therefore, it may be inferred that the present model is the most realistic model for complete harmonic dynamical behavior of the crystals. The lattice dynamical study of phonon properties of transition metal titanium dioxide (TiO2) has been presented by means of VTBFS model. Titanium is an extremely light semiconducting material, exhibiting stable bcc structure in a certain temperature range 0–300 K normal pressures Debye temperature variation and combined density of states (CDS) of TiO2 has been studied in this work. At high temperature, strength and oxidation resistance of Ti alloys has improved. The model predictions are found to be in reasonable agreement with experimental data.2
Fitting of adaptive neuron model to electrophysiological recordings using particle swarm optimization algorithm
Authors: Shan Bonan , Wang Jiang , Zhang Lvxia , Deng Bin , Wei Xile
Published: November 2016

In order to fit neural model’s spiking features to electrophysiological recordings, in this paper, a fitting framework based on particle swarm optimization (PSO) algorithm is proposed to estimate the model parameters in an augmented multi-timescale adaptive threshold (AugMAT) model. PSO algorithm is an advanced evolutionary calculation method based on iteration. Selecting a reasonable criterion function will ensure the effectiveness of PSO algorithm. In this work, firing rate information is used as the main spiking feature and the estimation error of firing rate is selected as the criterion for fitting. A series of simulations are presented to verify the performance of the framework. The first step is model validation; an artificial training data is introduced to test the fitting procedure. Then we talk about the suitable PSO parameters, which exhibit adequate compromise between speediness and accuracy. Lastly, this framework is used to fit the electrophysiological recordings, after three adjustment steps, the features of experimental data are translated into realistic spiking neuron model.
AND and OR logic gates based on a phononic crystal ring resonator cavity
Authors: Xu Zhenlong , Wu Fugen , Guo Zhongning
Published: November 2016

We propose AND and OR logic gates based on a phononic crystal (PNC) ring resonator cavity. The proposed devices consist of ring resonator cavities coupled to PNC line defect waveguides. The logic gate performance has been analyzed and investigated using finite element methods. The design specifies a logical 0 as a transmission rate of 0.3 or less and a logical 1 as a transmission rate of 0.6 or more. The results show that such a design has stable transmission peaks, meeting the requirements of acoustic logic gates. The design has the potential to be a key component in future phononic integrated circuits.
AN OPTIMIZATION OF MAXIMAL INVARIANCE IN A CLASS OF MULTIPLE VALUED ITERATIVE DYNAMICS MODELS OF NONLINEAR DISTURBED CONTROL SYSTEMS
Authors: KAHNG BYUNGIK
Published: November 2016

We discuss an optimization problem on the maximal invariance of a class of multiple-valued iterative dynamics (MVID) models of discrete-time nonlinear control dynamical systems with singular disturbance. We study the inner and outer bounds of the maximal invariance, between which all noninterfering MVID models of nonlinear discrete-time control dynamical systems with singular disturbance reside. We also study the invariant fractal structure and an optimization of Lyapunov multipliers associated to it.
PAIRS TRADING OF TWO ASSETS WITH UNCERTAINTY IN CO-INTEGRATION'S LEVEL OF MEAN REVERSION
Authors: LEE SANGMIN , PAPANICOLAOU ANDREW
Published: November 2016

This paper considers a stochastic control problem derived from a model for pairs trading under incomplete information. We decompose an individual asset's drift into two parts: an industry drift plus some additional stochasticity. The extra stochasticity may be unobserved, which means the investor has only partial information. We solve the control problem under both full and partial informations for utility function [Formula: see text], and we make comparisons. We show the existence of stable solution to the associated matrix Riccati equations in both cases for [Formula: see text], but for [Formula: see text] there remains potential for infinite value functions in finite time. Also, we quantify the expected loss in utility due to partial information, and present a numerical study to illustrate the contribution of this paper.
Fracture Mechanical Analysis of Open Cell Ceramic Foams Under Thermal Shock Loading
Authors: Settgast C. , Abendroth M. , Kuna M.
Published: November 2016

Ceramic foams made by replica techniques containing sharp-edged cavities, which are potential crack initiators and therefore have to be analyzed using fracture mechanical methods. The ceramic foams made of novel carbon bonded alumina are used as filters in metal melt filtration applications, where the filters are exposed to a thermal shock. During the casting process the filters experience a complex thermo-mechanical loading, which is difficult to measure. Modern numerical methods allow the simulation of such complex processes.

As a simplified foam structure an open Kelvin cell is used as a representative volume element. A three-dimensional finite element model containing realistic sharp-edged cavities and three-dimensional sub-models along these sharp edges are used to compute the transient temperature, stress and strain fields at the Kelvin foam. The sharp edges are evaluated using fracture mechanical methods like the [Formula: see text]-integral technique.

The results of this study describe the influence of the pore size, relative density of the ceramic foam, the heat transfer and selected material parameters on the fracture mechanical behaviour.
Toughness Enhancement of Commercial Poly (Hydroxybutyrate-co-Valerate) (PHBV) by Blending with a Thermoplastic Polyurethane (TPU)
Authors: González-Ausejo Jennifer , Sánchez-Safont Estefania , Cabedo Luis , Gamez-Perez Jose
Published: November 2016

Poly(hydroxyl butyrate-co-valerate) (PHBV) is a biopolymer synthesized by microorganisms that is fully biodegradable with improved thermal and tensile properties with respect to some commodity plastics. However, it presents an intrinsic brittleness that limits its potential application in replacing plastics in packaging applications. Films made of blends of PHBV with different contents of thermoplastic polyurethane (TPU) were prepared by single screw extruder and their fracture toughness behavior was assessed by means of the essential work of fracture (EWF) Method. As the crack propagation was not always stable, a partition method has been used to compare all formulations and to relate results with the morphology of the blends. Indeed, fully characterization of the different PHBV/TPU blends showed that PHBV was incompatible with TPU. The blends showed an improvement of the toughness fracture, finding a maximum with intermediate TPU contents.
Electromechanical Catastrophe
Authors: Lu Tongqing , Cheng Sibo , Li Tiefeng , Wang Tiejun , Suo Zhigang
Published: November 2016

A transducer is a system that couples two loads. For example, an electromechanical transducer couples a mechanical force and an electrical voltage. A two-load, nonlinear system can exhibit rich behavior of bifurcation, which can be displayed in a three-dimensional space, with the horizontal plane representing the two loads, and the vertical axis representing the state of the system. In this three-dimensional space, a state of equilibrium at fixed loads corresponds to a point on a surface. The surface is smooth, but its projection to the load plane results in singularities of two types: fold and cusp. Here we identify the fold and cusp for a dielectric elastomer transducer by a combination of experiment and calculation. We conduct two kinds of experiment: electrical actuation under a constant force and mechanical pulling under a constant voltage. The theory and the experiment agree well. The fold and cusp are essential in the design of loading paths to avoid or harness the bifurcation.
A method for threshold selection in load extrapolation based on multiple criteria decision-making technology
Authors: Wang Jixin , Liu Qingsong , Zhai Xinting
Published: November 2016

In order to establish an accurate peak over threshold (POT) model for reasonable load extrapolation, a new threshold selection method based on multiple criteria decision making (MCDM) technology is proposed. The fitting test criterion is taken into consideration in the method. For each candidate threshold, the fitting values of several fitting test criteria are integrated into a comprehensive evaluation value through entropy method and MCDM technology. The threshold corresponding to the minimum comprehensive evaluation value is assumed as the optimal threshold. A random simulation study is carried out to evaluate the performance of the method and to compare them with other literature methods. Genuine load data are applied the proposed method. Both the results shown that the proposed method could be seen as an additional method that complements existing threshold selection methods.
Controversies in the history of geology and their educational importance for facilitating understanding of the nature of science
Authors: Clary Renee M.
Published: November 2016

Controversies in the history of geology are inherently interesting to students, and offer an effective method for conveying the scientific process and the cultural and social influences under which science progresses. Historical controversies can also address the basic understandings of the nature of science (NOS), which students need in order to develop an authentic understanding of the scientific process. Four controversial vignettes in the history of geology are overviewed: Agassiz's Glacial Theory, Darwin's theory on reef formation, the Cope–Marsh dinosaur wars and Byrd's flight over the North Pole. The controversies are analysed using the NOS matrix to demonstrate their effectiveness for teaching the nature of science via historical episodes in geology. Surveys of practising teachers also provide further documentation for the importance of historical controversies in the science classroom, as well as student interest in them.
Obesity-associated extracellular mtDNA activates central TGFβ pathway to cause blood pressure increase
Authors: Alé Albert , Zhang Yalin , Han Cheng , Cai Dongsheng
Published: November 2016

Hypothalamic inflammation was recently found to mediate obesity-related hypertension, but the responsible upstream mediators remain unexplored. In this study, we show that dietary obesity is associated with extracellular release of mitochondrial DNA (mtDNA) into the cerebrospinal fluid and that central delivery of mtDNA mimics transforming growth factor-β (TGFβ) excess to activate downstream signaling pathways. Physiological study reveals that central administration of mtDNA or TGFβ is sufficient to cause hypertension in mice. Knockout of the TGFβ receptor in proopiomelanocortin neurons counteracts the hypertensive effect of not only TGFβ but also mtDNA excess, while the hypertensive action of central mtDNA can be blocked pharmacologically by a TGFβ receptor antagonist or genetically by TGFβ receptor knockout. Finally, we confirm that obesity-induced hypertension can be reversed through central treatment with TGFβ receptor antagonist. In conclusion, circulating mtDNA in the brain employs neural TGFβ pathway to mediate a central inflammatory mechanism of obesity-related hypertension.
Total CAD/CAM Supported Method for Manufacturing Removable Complete Dentures
Authors: de Mendonça Arthur Furtado , Furtado de Mendonça Mario , White George Shelby , Sara Georges , Littlefair Darren
Published: November 2016

The incorporation of computer-aided design/computer-aided manufacturing (CAD/CAM) technology into complete denture fabrication brings about several advantages to the fabrication process, providing better predictability of the desired outcomes and high accuracy of denture fit, mainly because the milling of prepolymerized acrylic resin eliminates the shrinkage of the acrylic base. Also, there is a decrease in the porosity when compared to a conventionally processed denture, and consequently there is a decrease in the retention of Candida albicans on the denture base. The presented workflow for complete denture fabrication presents a totally wax-free manufacturing process, combining rapid prototyping (RP) and rapid milling. With the presented technique, the maxillomandibular relation (MMR) and the ideal setup of the tooth arrangement are developed by using occlusion rims and trial setup made with RP. For the definitive final denture, the denture base and the basal surfaces of the conventional denture teeth were milled according to the individual clinical situation. Posteriorly, the teeth were adapted and bonded into the milled sockets of the milled base.
A New Method to Solve Numeric Solution of Nonlinear Dynamic System
Authors: Hu Min , Li Fengjun
Published: November 2016

It is well known that the cubic spline function has advantages of simple forms, good convergence, approximation, and second-order smoothness. A particular class of cubic spline function is constructed and an effective method to solve the numerical solution of nonlinear dynamic system is proposed based on the cubic spline function. Compared with existing methods, this method not only has high approximation precision, but also avoids the Runge phenomenon. The error analysis of several methods is given via two numeric examples, which turned out that the proposed method is a much more feasible tool applied to the engineering practice.
Palatal Swelling: A Diagnostic Enigma
Authors: Suganya Ramalingam , Malathi Narasimhan , Thamizhchelvan Harikrishnan , Ramkumar Subramaniam , Giri G. V. V.
Published: November 2016

Giant cell tumor (GCT) of bone is a giant-cell-rich bony lesion associated with abundant multinucleated osteoclast-type giant cells. It is a primary neoplasm of bone with characteristic clinical, radiological, and pathological features. It is an expansive and lytic lesion without periosteal reaction and prominent peripheral sclerosis. Giant cells are also seen in other diseases like giant cell granuloma of the jaws, traumatic bone cyst, aneurysmal bone cyst, and jaw tumor of hyperparathyroidism. We present a unique case of GCT of palate in a 30-year-old female.
Anomalous Origin of the Left Common Carotid Artery from the Main Pulmonary Artery: A Rare Association in an Infant with CHARGE Syndrome
Authors: Osakwe Onyekachukwu , Jones Blaise , Hirsch Russel
Published: November 2016

Case Report. Isolated carotid artery originating from the pulmonary trunk is an exceedingly rare anomalous origin of head and neck vessels. We present this finding, along with a persistent embryonic trigeminal artery, in a male infant with multiple cardiac defects and other congenital anomalies associated with CHARGE syndrome. After extensive investigations, cardiac catheterization revealed the anomalous left common carotid artery arising from the cranial aspect of the main pulmonary artery. There was retrograde flow in this vessel, resulting from the lower pulmonary pressure, essentially stealing arterial supply from the left anterior cerebral circulation. The persistent left-sided trigeminal artery provided collateral flow from the posterior circulation to the left internal carotid artery territory, allowing for safe ligation of the anomalous origin of the left common carotid artery, thereby reversing the steal of arterial blood flow into the pulmonary circulation and resulting in a net improvement of cerebral perfusion.Conclusion. The possibility of this vascular anomaly should be considered in all infants with CHARGE syndrome. Surgical repair or ligation should be tailored to the specific patient circumstances, following a careful delineation of all sources of cerebral perfusion.