bluuebunny/crossref_metadata_2025 huggingface dataset:
Draft Genome Sequence of
Pseudomonas
sp. Strain CMAA 1215, a Plant Growth-Promoting Bacterium Isolated from a Brazilian Mangrove
Authors: Vasconcellos Rafael L. F. , Mendes Rodrigo , Taketani Rodrigo G. , Zucchi Tiago D. , Melo Itamar Soares
Published: November 2013

The aim of this study was to sequence the genome of the plant growth-promoting
Pseudomonas
sp. strain CMAA 1215, an osmotolerant bacterium isolated from mangrove soil.
Complete Genome Sequence of the Solvent Producer Clostridium saccharobutylicum NCP262 (DSM 13864)
Authors: Poehlein Anja , Hartwich Katrin , Krabben Preben , Ehrenreich Armin , Liebl Wolfgang , Dürre Peter , Gottschalk Gerhard , Daniel Rolf
Published: November 2013

Clostridium saccharobutylicum
was employed for the production of acetone and butanol in South Africa until the 1970s. The genome comprises a single replicon (5,107,814 bp) harboring all the genes necessary for solvent production and the degradation of various organic compounds, such as fructose, cellobiose, sucrose, and mannose.
Draft Genome Sequence of Lactobacillus fermentum Strain 3872
Authors: Karlyshev Andrey V. , Raju Kavita , Abramov Vyacheslav M.
Published: November 2013

This report describes a draft genome sequence of
Lactobacillus fermentum
strain 3872. The data revealed remarkable similarity to and dissimilarity with the published genome sequences of other strains of the species. The absence of and variation in structures of some adhesins and the presence of an additional adhesin may reflect adaptation of the bacterium to different host systems and may contribute to specific properties of this strain as a new probiotic.
Pyrosequencing for Rapid Detection of Extensively Drug-Resistant Mycobacterium tuberculosis in Clinical Isolates and Clinical Specimens
Authors: Lin S.-Y. Grace , Rodwell Timothy C. , Victor Thomas C. , Rider Errin C. , Pham Lucy , Catanzaro Antonino , Desmond Edward P.
Published: November 2013

Treating extensively drug-resistant (XDR) tuberculosis (TB) is a serious challenge. Culture-based drug susceptibility testing (DST) may take 4 weeks or longer from specimen collection to the availability of results. We developed a pyrosequencing (PSQ) assay including eight subassays for the rapid identification of
Mycobacterium tuberculosis
complex (MTBC) and concurrent detection of mutations associated with resistance to drugs defining XDR TB. The entire procedure, from DNA extraction to the availability of results, was accomplished within 6 h. The assay was validated for testing clinical isolates and clinical specimens, which improves the turnaround time for molecular DST and maximizes the benefit of using molecular testing. A total of 130 clinical isolates and 129 clinical specimens were studied. The correlations between the PSQ results and the phenotypic DST results were 94.3% for isoniazid, 98.7% for rifampin, 97.6% for quinolones (ofloxacin, levofloxacin, or moxifloxacin), 99.2% for amikacin, 99.2% for capreomycin, and 96.4% for kanamycin. For testing clinical specimens, the PSQ assay yielded a 98.4% sensitivity for detecting MTBC and a 95.8% sensitivity for generating complete sequencing results from all subassays. The PSQ assay was able to rapidly and accurately detect drug resistance mutations with the sequence information provided, which allows further study of the association of drug resistance or susceptibility with each mutation and the accumulation of such knowledge for future interpretation of results. Thus, reporting of false resistance for mutations known not to confer resistance can be prevented, which is a significant benefit of the assay over existing molecular diagnostic methods endorsed by the World Health Organization.
Clinical and Virologic Factors Associated with Reduced Sensitivity of Rapid Influenza Diagnostic Tests in Hospitalized Elderly Patients and Young Children
Authors: Chan Martin C. W. , Lee Nelson , Ngai Karry L. K. , Leung Ting F. , Chan Paul K. S.
Published: November 2013

Rapid influenza diagnostic tests (RIDTs) are commonly used by clinicians to guide patient management. Data on sensitivities among hospitalized patients are limited. Here, we evaluated the clinical and virologic factors affecting the sensitivities of 2 commercially available RIDTs (BinaxNOW Influenza A&B and QuickVue Influenza A+B) on nasopharyngeal aspirate (NPA) specimens collected from elderly patients and young children hospitalized for influenza. Influenza cases and age-matched negative controls were prospectively enrolled during the 2011-2012 influenza season in Hong Kong. NPA specimens were collected at presentation before antiviral treatment. Real-time reverse transcription-PCR (RT-PCR) results were used as references for the sensitivity analyses. One hundred patients (57 influenza cases and 43 controls) were studied. Both RIDTs had 100% specificities. The sensitivities of the BinaxNOW Influenza A&B and QuickVue Influenza A+B tests were 70% and 82%, respectively. For both tests, the sensitivities were lower in cases with presentation times beyond 2 days of illness onset than for those within this time (50 to 71% versus 85 to 91%, respectively). There were trends toward lower sensitivities for influenza B than for influenza A (66 to 81% versus 76 to 84%, respectively), among young children than among the elderly patients (63 to 78% versus 80 to 88%, respectively), and among cases with pneumonia than those without pneumonia (75% versus 82 to 94%, respectively). The sensitivities of the RIDTs decreased with reduced NPA viral RNA levels (5.6 to 15.0% reduction per 1-log decrease), which declined progressively after illness onset (Spearman's rho, −0.47 [P< 0.05] and −0.66 [P< 0.001] for influenza A and B, respectively). Collectively, late presentation, a low NPA viral load, and probably lower respiratory manifestation are factors associated with reduced sensitivities of RIDTs for diagnosing influenza in hospitalized patients. A negative RIDT result should be interpreted with caution.
Xpert GBS Assay for Rapid Detection of Group B Streptococcus in Gastric Fluid Samples from Newborns
Authors: Jost Christelle , Bercot Béatrice , Jacquier Hervé , Raskine Laurent , Barranger Emmanuel , Mouchnino Geneviève , Cambau Emmanuelle
Published: November 2013

The Xpert GBS real-time PCR assay was applied to gastric fluid samples from 143 newborns, and it detected group B streptococcus (GBS) within 1 h for 16 (11.2%) cases, while microscopic examination detected only 2 cases. The sensitivity and specificity of the Xpert GBS were 80% and 100%, respectively, with regard to 20 cases of GBS colonization or infection. Concordance of Xpert GBS results versus culture was 92.3%. This test detects in a timely manner newborns at risk for invasive GBS disease.
Development of a Loop-Mediated Isothermal Amplification Method for Detection of Histoplasma capsulatum DNA in Clinical Samples
Authors: Scheel Christina M. , Zhou Yitian , Theodoro Raquel C. , Abrams Bethany , Balajee S. Arunmozhi , Litvintseva Anastasia P.
Published: November 2013

Improved methods for the detection of
Histoplasma capsulatum
are needed in regions with limited resources in which the organism is endemic, where delayed diagnosis of progressive disseminated histoplasmosis (PDH) results in high mortality rates. We have investigated the use of a loop-mediated isothermal amplification (LAMP) assay to facilitate rapid inexpensive molecular diagnosis of this disease. Primers for LAMP were designed to amplify the
Hcp100
locus of
H. capsulatum
. The sensitivity and limit of detection were evaluated using DNA extracted from 91 clinical isolates of known geographic subspecies, while the assay specificity was determined using DNA extracted from 50 other fungi and
Mycobacterium tuberculosis
. Urine specimens (
n
= 6) collected from HIV-positive individuals with culture- and antigen-proven histoplasmosis were evaluated using the LAMP assay. Specimens from healthy persons (
n
= 10) without evidence of histoplasmosis were used as assay controls. The
Hcp100
LAMP assay was 100% sensitive and specific when tested with DNA extracted from culture isolates. The median limit of detection was ≤6 genomes (range, 1 to 300 genomes) for all except one geographic subspecies. The LAMP assay detected
Hcp100
in 67% of antigen-positive urine specimens (4/6 specimens), and results were negative for
Hcp100
in all healthy control urine specimens. We have shown that the
Hcp100
LAMP assay is a rapid affordable assay that can be used to expedite culture confirmation of
H. capsulatum
in regions in which PDH is endemic. Further, our results indicate proof of the concept that the assay can be used to detect
Histoplasma
DNA in urine. Further evaluation of this assay using body fluid samples from a larger patient population is warranted.
Economic Evaluation of Laboratory Testing Strategies for Hospital-Associated Clostridium difficile Infection
Authors: Schroeder Lee F. , Robilotti Elizabeth , Peterson Lance R. , Banaei Niaz , Dowdy David W.
Published: November 2013

Clostridium difficile
infection (CDI) is the most common cause of infectious diarrhea in health care settings, and for patients presumed to have CDI, their isolation while awaiting laboratory results is costly. Newer rapid tests for CDI may reduce this burden, but the economic consequences of different testing algorithms remain unexplored. We used decision analysis from the hospital perspective to compare multiple CDI testing algorithms for adult inpatients with suspected CDI, assuming patient management according to laboratory results. CDI testing strategies included combinations of on-demand PCR (odPCR), batch PCR, lateral-flow diagnostics, plate-reader enzyme immunoassay, and direct tissue culture cytotoxicity. In the reference scenario, algorithms incorporating rapid testing were cost-effective relative to nonrapid algorithms. For every 10,000 symptomatic adults, relative to a strategy of treating nobody, lateral-flow glutamate dehydrogenase (GDH)/odPCR generated 831 true-positive results and cost $1,600 per additional true-positive case treated. Stand-alone odPCR was more effective and more expensive, identifying 174 additional true-positive cases at $6,900 per additional case treated. All other testing strategies were dominated by (i.e., more costly and less effective than) stand-alone odPCR or odPCR preceded by lateral-flow screening. A cost-benefit analysis (including estimated costs of missed cases) favored stand-alone odPCR in most settings but favored odPCR preceded by lateral-flow testing if a missed CDI case resulted in less than $5,000 of extended hospital stay costs and <2 transmissions, if lateral-flow GDH diagnostic sensitivity was >93%, or if the symptomatic carrier proportion among the toxigenic culture-positive cases was >80%. These results can aid guideline developers and laboratory directors who are considering rapid testing algorithms for diagnosing CDI.
Differential Inhibitory Effects of Cyanovirin-N, Griffithsin, and Scytovirin on Entry Mediated by Envelopes of Gammaretroviruses and Deltaretroviruses
Authors: Jensen Stig M. R. , Ruscetti Francis W. , Rein Alan , Bertolette Daniel C. , Saucedo Carrie J. , O'Keefe Barry R. , Jones Kathryn S.
Published: November 2013

The antiviral lectins griffithsin (GRFT), cyanovirin-N (CV-N), and scytovirin (SVN), which inhibit several enveloped viruses, including lentiviruses, were examined for their ability to inhibit entry mediated by Env proteins of delta- and gammaretroviruses. The glycoproteins from human T-cell leukemia virus type 1 (HTLV-1) were resistant to the antiviral effects of all three lectins. For gammaretroviruses, CV-N inhibited entry mediated by some but not all of the envelopes examined, whereas GRFT and SVN displayed only little or no effect.
In VivoElectroporation of Minicircle DNA as a Novel Method of Vaccine Delivery To Enhance HIV-1-Specific Immune Responses
Authors: Wang Qingtao , Jiang Wei , Chen Yuhai , Liu Pengyu , Sheng Chunjie , Chen Shuai , Zhang Hui , Pan Changchuan , Gao Shijuan , Huang Wenlin
Published: November 2013

DNA vaccines offer advantage over conventional vaccines, as they are safer to use, easier to produce, and able to induce humoral as well cellular immune responses. Unfortunately, no DNA vaccines have been licensed for human use for the difficulties in developing an efficient and safein vivogene delivery system.In vivoelectroporation (EP)-based DNA delivery has attracted great attention for its potency to enhance cellular uptake of DNA vaccines and function as an adjuvant. Minicircle DNA (a new form of DNA containing only a gene expression cassette and lacking a backbone of bacterial plasmid DNA) is a powerful candidate of gene delivery in terms of improving the levels and the duration of transgene expressionin vivo. In this study, as a novel vaccine delivery system, we combinedin vivoEP and the minicircle DNA carrying a codon-optimized HIV-1gaggene (minicircle-gag) to evaluate the immunogenicity of this system. We found that minicircle-gag conferred persistent and high levels of gag expressionin vitroandin vivo. The use of EP delivery further increased minicircle-based gene expression. Moreover, when delivered by EP, minicircle-gag vaccination elicited a 2- to 3-fold increase in cellular immune response and a 1.5- to 3-fold augmentation of humoral immune responses compared with those elicited by a pVAX1-gag positive control. Increased immunogenicity of EP-assisted minicircle-gag may benefit from increasing local antigen expression, upregulating inflammatory genes, and recruiting immune cells. Collectively,in vivoEP of minicircle DNA functions as a novel vaccine platform that can enhance efficacy and immunogenicity of DNA vaccines.
The Rigid Amphipathic Fusion Inhibitor dUY11 Acts through Photosensitization of Viruses
Authors: Vigant Frederic , Hollmann Axel , Lee Jihye , Santos Nuno C. , Jung Michael E. , Lee Benhur
Published: November 2013

Rigid amphipathic fusion inhibitors (RAFIs) are lipophilic inverted-cone-shaped molecules thought to antagonize the membrane curvature transitions that occur during virus-cell fusion and are broad-spectrum antivirals against enveloped viruses (Broad-SAVE). Here, we show that RAFIs act like membrane-binding photosensitizers: their antiviral effect is dependent on light and the generation of singlet oxygen (
1
O
2
), similar to the mechanistic paradigm established for LJ001, a chemically unrelated class of Broad-SAVE. Photosensitization of viral membranes is a common mechanism that underlies these Broad-SAVE.
Laparoscopic upper pole splenectomy of the simple splenic cyst
Authors: Aparício David João Silva , Leichsenring Carlos , Rodrigues Ângela Reis , Alves Ana Catarina
Published: November 2013

Splenic cysts are rare clinic entities. Non-parasitic cysts are the most frequent cystic lesions of the spleen. In the last decade acknowledgment of the importance of the spleen function, along with development of imaging methods and surgery technics, allowed a conservative approach to be increasingly considered as the best approach in splenic cysts treatment. We present the case of a 34-year-old woman with an asymptomatic simple splenic cyst in the upper pole incidentally diagnosed in a thoracic CT. A laparoscopic upper pole splenectomy was performed on the patient, with no complications. Despite the rareness of this procedure and the fact that it was used in a simple splenic cyst, this article emphasises the idea that this approach is safe, reproducible and advantageous for the patient.
Joint effects of serum ferritin and body mass index on the risk of coronary artery disease: a case–control study
Authors: Zhou Yunping , Liu Tongtao , Jia Chongqi
Published: November 2013

Objectives

Serum ferritin and body mass index (BMI) have been reportedly associated with coronary artery disease (CAD) risk. The aim of the present study was to explore the interaction between serum ferritin and BMI on CAD risk.

Design

Hospital-based case–control study.

Setting

Patients with CAD and the controls were recruited from Qilu Hospital, Shandong University.

Participants

258 CAD cases and 282 healthy controls.

Methods

Multiplicative interaction was assessed through a cross-product interaction term in a multivariate logistic regression model. The effect of serum ferritin and BMI were evaluated per 50 µg/L and per 2 kg/m2, respectively. The presence of additive interaction between serum ferritin and BMI was evaluated by calculation of the relative excess risk due to interaction (RERI), attributable proportion due to interaction (AP) and synergy index (S).

Results

The ORs and 95% CI of the serum ferritin–BMI product term on a multiplicative scale in the univariate and multivariate models were 0.943 (0.904 to 0.984) and 1.004 (0.951 to 1.059), respectively. There was also evidence for interaction on an additive scale; the RERI (95% CI), AP (95% CI) and S (95% CI) in the univariate model were 0.314 (0.026 to 1.506), 0.107 (0.017 to 0.241) and 1.194 (1.053 to 1.406), respectively. After adjusting for the potential confounders, the estimates and 95% CIs for the aforementioned three measures were 0.004 (−0.016 to 0.311), 0.004 (−0.016 to 0.191) and 1.039 (0.774 to 1.285), respectively.

Conclusions

Serum ferritin and BMI had an additive interaction on the risk of CAD in Chinese population. Further investigations with big sample size are necessary for confirming this additive interaction.
A descriptive study of access to services in a random sample of Canadian rural emergency departments
Authors: Fleet Richard , Poitras Julien , Maltais-Giguère Julie , Villa Julie , Archambault Patrick
Published: November 2013

Objective

To examine 24/7 access to services and consultants in a sample of Canadian rural emergency departments (EDs).

Design

Cross-sectional study—mixed methods (structured interview, survey and government data bases) with random sampling of hospitals.

Setting

Canadian rural EDs (rural small town (RST) definition—Statistics Canada).

Participants

28% (95/336) of Canadian rural EDs providing 24/7 physician coverage located in hospitals with acute care hospitalisation beds.

Main outcome measures

General characteristics of the rural EDs, information about 24/7 access to consultants, equipment and services, and the proportion of rural hospitals more than 300 km from levels 1 and 2 trauma centres.

Results

Of the 336 rural EDs identified, 122 (36%) were randomly selected and contacted. Overall, 95 EDs participated in the study (participation rate, 78%). Hospitals had, on an average, 23 acute care beds, 7 ED stretchers and 13 500 annual ED visits. The proportion of rural hospitals with local access to the following 24/7 services was paediatrician, 5%; obstetrician, 10%; psychiatrist, 11%; internist, 12%; intensive care unit, 17%; CT scanner, 20%; surgeon, 26%; ultrasound, 28%; basic X-ray, 97% and laboratory services, 99%. Forty-four per cent and 54% of the RST EDs were more than 300 km from a level 1 and level 2 trauma centre, respectively.

Conclusions

This is the first study describing the services available in Canadian rural EDs. Apart from basic laboratory and X-ray services, most rural EDs have limited access to consultants, advanced imaging and critical care services. A detailed study is needed to evaluate the impact of these limited services on patient outcomes, costs and interfacility transport demands.
Urinary bisphenol A concentrations are associated with abnormal liver function in the elderly: a repeated panel study
Authors: Lee Mee-Ri , Park Hyunseung , Bae Sanghyuk , Lim Youn-Hee , Kim Jin Hee , Cho Soo-Hun , Hong Yun-Chul
Published: November 2013

Background

Bisphenol A (4,40-isopropylidenediphenol, BPA) is known to adversely affect various organs. The liver is reported to be affected by BPA in animal studies. However, there are few studies in humans on the effects of BPA on the liver. Therefore, we evaluated the relationship between urinary BPA levels and liver function in elderly subjects using repeated measurements.

Methods

From 2008 to 2010, a total of 560 elderly subjects residing in Seoul were each evaluated up to three times. At the first visit, demographic data, environmental exposure and lifestyle information were obtained from a systemised questionnaire. At each visit, blood and urine samples were collected and stored for analysis. Linear mixed and GLIMMIX model analyses were performed after adjusting for age, sex, Body Mass Index, alcohol consumption, urinary cotinine concentrations, exercise frequency, and low-density lipoprotein cholesterol level.

Results

The mean urinary BPA concentration was 1.13 μg/g creatinine. Significant relationships were observed between urinary BPA and aspartate aminotransferase, alanine aminotransferase, and gamma-glutamyl transferase after adjusting for potential confounders (p<0.05). When subjects were grouped according to urinary BPA concentrations divided by the median value, higher urinary BPA concentrations were associated with increased abnormal liver function (OR 2.66; 95% CI 1.15 to 5.90).

Conclusions

Community-level exposure to BPA was associated with abnormal liver function in the elderly, indicating that more stringent control of BPA is necessary to protect susceptible populations.
The madness of Gerard de Nerval
Authors: Beveridge Allan
Published: November 2013

This paper examines the madness of Gerard de Nerval, the nineteenth-century French writer. It looks at his account of mental disturbance, how he responded to the psychiatric profession and how he reacted to being diagnosed as insane. It considers his autobiographical novella of madness,Aurelia, which he began at the suggestion of his alienist, Dr Emile Blanche, and while he was still an asylum inmate. Nerval's story raises important questions about the nature of madness. Is it, as he contended, a mystical experience revealing truths about spiritual worlds inaccessible to the ‘sane’? Does psychiatry fail to understand it and inappropriately reduce it to the categories of scientific reason? Or are such notions of the spiritual value of madness guilty of the charge that they romanticise insanity? Do they make extravagant claims for an experience that is often disturbing and debilitating? What is the relationship between madness and recovery? Should an individual try to forget their experience of mental disturbance once they recover, or should they examine what the event reveals about themselves? Can the language of madness be decoded to unveil profound truths as Carl Jung and R.D. Laing have suggested, or is it, as the psychiatrist German Berrios maintains, merely a series of ‘empty speech acts’, signifying nothing? And finally, how does one avoid writing about madness, and instead write madness?
Adsorption of cadmium(II) ions from aqueous solution on exfoliated graphene nanosheets and its determination by flame atomic absorption spectrometry
Authors: Hallaj Rahman , Bahar Soleiman , Babamiri Bahareh , Zandi Shiva
Published: November 2013

In this study, we investigated the enrichment ability of exfoliated graphene nanosheets for determination of trace cadmium in water and vegetable samples with flame atomic absorption spectrometry. Various experimental parameters that could affect the extraction efficiency have been investigated. Under the optimum conditions, the enrichment factor of the method for the target analyte was 100. A liner response was achieved in the concentration range of 0.3–28.8 ng mL−1. The detection limit and precision of the method were 0.2 ng mL−1 and 0.8%, respectively. The proposed method was applied to determine the cadmium in water, onion, and tomato samples and recoveries of target analyte were in the range 97.6%–98.5%. All of these experimental results indicated that this new procedure could be applied for the determination of trace cadmium in real samples.
Spin-one Duffin–Kemmer–Petiau equation in the presence of Manning–Rosen potential plus a ring-shaped-like potential
Authors: Hassanabadi H. , Kamali M. , Yazarloo B.H.
Published: November 2013

We present the solution of the Duffin–Kemmer–Petiau equation for Manning–Rosen potential plus a ring-shaped-like potential in (1+3)-dimensional space–time for spin-one particles within the framework of an exponential approximation for the centrifugal term. We have used the Nikiforov–Uvarov method in our calculations. The radial wavefunction and the angular wavefunctions are expressed in terms of Jacobi polynomials. We have also represented some numerical results for the Manning–Rosen potential plus a ring-shaped-like potential.
Improved efficiency of ZnSe QDs—Si hybrid solar cell system by down shifting process
Authors: Liu Ni , Xu Ling , Wang Hongyu , Xu Jun , Su Weining , li Wei , Ma Zhongyuan , Chen Kunji
Published: November 2013

Traditional Si solar cells have a narrow active absorption cross section among the short wavelength range (200–400 nm). The down-shifting process can efficiently improve the spectral response of Si solar cells by converting shorter wavelengths (i.e., ultraviolet, UV) to longer wavelengths (i.e., the visible range). Here, ZnSe quantum dots (QDs), prepared by an aqueous solution method and employed as a luminescent down-shifting layer, were spin coated onto the upper surface of manufactured Si solar cells. Measurements under standard test conditions (AM1.5, 100 mW/cm2) show that the efficiency of the ZnSe QDs–Si hybrid solar cell is increased from 11.48% to12%. The improvement of the ZnSe QDs–Si hybrid solar cell is ascribed to the efficient down-shifting process of ZnSe QDs, which enhances spectra response in the UV region for Si solar cells. The mechanism of this optical coupling and efficiency enhancement is investigated in detail. These results support the case that low-cost ZnSe QDs can be employed as efficient down-shifting material on large-area solar cells.
Sequencing and annotation of the chloroplast DNAs and identification of polymorphisms distinguishing normal male-fertile and male-sterile cytoplasms of onion
Authors: von Kohn Christopher , Kiełkowska Agnieszka , Havey Michael J.
Published: November 2013

Male-sterile (S) cytoplasm of onion is an alien cytoplasm introgressed into onion in antiquity and is widely used for hybrid seed production. Owing to the biennial generation time of onion, classical crossing takes at least 4 years to classify cytoplasms as S or normal (N) male-fertile. Molecular markers in the organellar DNAs that distinguish N and S cytoplasms are useful to reduce the time required to classify onion cytoplasms. In this research, we completed next-generation sequencing of the chloroplast DNAs of N- and S-cytoplasmic onions; we assembled and annotated the genomes in addition to identifying polymorphisms that distinguish these cytoplasms. The sizes (153 538 and 153 355 base pairs) and GC contents (36.8%) were very similar for the chloroplast DNAs of N and S cytoplasms, respectively, as expected given their close phylogenetic relationship. The size difference was primarily due to small indels in intergenic regions and a deletion in the accD gene of N-cytoplasmic onion. The structures of the onion chloroplast DNAs were similar to those of most land plants with large and small single copy regions separated by inverted repeats. Twenty-eight single nucleotide polymorphisms, two polymorphic restriction-enzyme sites, and one indel distributed across 20 chloroplast genes in the large and small single copy regions were selected and validated using diverse onion populations previously classified as N or S cytoplasmic using restriction fragment length polymorphisms. Although cytoplasmic male sterility is likely associated with the mitochondrial DNA, maternal transmission of the mitochondrial and chloroplast DNAs allows for polymorphisms in either genome to be useful for classifying onion cytoplasms to aid the development of hybrid onion cultivars.
QUADRO-QUADRIC CREMONA MAPS AND VARIETIES 3-CONNECTED BY CUBICS: SEMI-SIMPLE PART AND RADICAL
Authors: PIRIO LUC , RUSSO FRANCESCO
Published: November 2013

Via the XJC-correspondence proved in [L. Pirio and F. Russo, Extremal varieties 3-rationally connected by cubics, quadro-quadric Cremona transformations and rank 3 Jordan algebras, submitted] we provide some structure theorems for quadro-quadric Cremona transformations and for extremal varieties 3-covered by twisted cubics by reinterpreting for these objects the algebraic results on the solvability of the radical of Jordan algebras. In this way, we can define the semi-simple part and the radical part of a quadro-quadric Cremona transformation, respectively of an extremal variety 3-covered by twisted cubics, and then describe how general objects are constructed from the semi-simple ones, which are completely classified modulo certain equivalences, via suitable null radical extensions.
BIOLOGICAL EFFECTS ON THE SOURCE OF GEONEUTRINOS
Authors: SLEEP NORMAN H. , BIRD DENNIS K. , ROSING MINIK T.
Published: November 2013

Detection of antineutrinos from U and Th series decay within the Earth (geoneutrinos) constrains the absolute abundance of these elements. Marine detectors will measure the ratio over the mantle beneath the site and provide spatial averaging. The measured mantle Th/U may well be significantly below its bulk earth value of ~4; Pb isotope measurements on mantle-derived rocks yield low Th/U values, effectively averaged over geological time. The physics of the modern biological process is complicated, but the net effect is that much of the U in the mantle comes from subducted marine sediments and subducted upper oceanic crust. That is, U subducts preferentially relative to Th. Oxygen ultimately from photosynthesis oxidizes U(IV) to U(VI), which is soluble during weathering and sediment transport. Dissolved U(VI) reacts with FeO in the oceanic crust and organic carbon within sediments to become immobile U(IV). These deep marine rocks are preferentially subducted relative to Th(IV)-bearing continental margin rocks. Ferric iron from anoxygenic photosynthesis and oxygen in local oases likely mobilized some U during the Archean Era when there was very little O2in the air. Conversely, these elements behave similarly in the absence of life, where the elements occur as U(IV) and Th(IV), which do not significantly fractionate during igneous processes. Neither do they fractionate during weathering, as they are essentially insoluble in water in surface environments. Th(IV) and U(IV) remain in solid clay-sized material. Overall, geoneutrino data constrain the masses of mantle chemical and isotopic domains recognized by studies of mantle-derived rocks and show the extent of recycling into the mantle over geological time.
THREE-ALGEBRA BFSS MATRIX THEORY
Authors: SATO MATSUO
Published: November 2013

We extend the BFSS matrix theory by means of Lie 3-algebra. The extended model possesses the same supersymmetry as the original BFSS matrix theory, and thus as the infinite momentum frame limit of M-theory. We study dynamics of the model by choosing the minimal Lie 3-algebra that includes u(N) algebra. We can solve a constraint in the minimal model and obtain two phases. In one phase, the model reduces to the original matrix model. In another phase, it reduces to a simple supersymmetric model.
FIBERED KNOTS AND VIRTUAL KNOTS
Authors: CHRISMAN MICAH W. , MANTUROV VASSILY O.
Published: November 2013

We introduce a new technique for studying classical knots with the methods of virtual knot theory. Let K be a knot and J be a knot in the complement of K with lk (J, K) = 0. Suppose there is covering space [Formula: see text], where V(J) is a regular neighborhood of J satisfying V(J) ∩ im (K) = ∅ and Σ is a connected compact orientable 2-manifold. Let K′ be a knot in Σ × (0, 1) such that πJ(K′) = K. Then K′ stabilizes to a virtual knot [Formula: see text], called a virtual cover of K relative to J. We investigate what can be said about a classical knot from its virtual covers in the case that J is a fibered knot. Several examples and applications to classical knots are presented. A basic theory of virtual covers is established.
EXACT RELATIVISTIC MODELS OF THIN DISKS AROUND STATIC BLACK HOLES IN A MAGNETIC FIELD
Authors: GUTIÉRREZ-PIÑERES ANTONIO C. , GARCÍA-REYES GONZALO , GONZÁLEZ GUILLERMO A.
Published: November 2013

The exact superposition of a central static black hole with surrounding thin disk in presence of a magnetic field is investigated. We consider two models of disk, one of infinite extension based on a Kuzmin–Chazy–Curzon metric and other finite based on the first Morgan–Morgan disk. We also analyze a simple model of active galactic nuclei (AGN) consisting of black hole, a Kuzmin–Chazy–Curzon disk and two rods representing jets, in presence of magnetic field. To explain the stability of the disks, we consider the matter of the disk made of two pressureless streams of counter-rotating charged particles (counter-rotating model) moving along electrogeodesic. Using the Rayleigh criterion, we derivate for circular orbits the stability conditions of the particles of the streams. The influence of the magnetic field on the matter properties of the disk and on its stability are also analyzed.
THE ROLE OF SHEAR IN DISSIPATIVE GRAVITATIONAL COLLAPSE
Authors: GOVENDER M. , REDDY K. P. , MAHARAJ S. D.
Published: November 2013

In this paper, we investigate the physics of a radiating star undergoing dissipative collapse in the form of a radial heat flux. Our treatment clearly demonstrates how the presence of shear affects the collapse process; we are in a position to contrast the physical features of the collapsing sphere in the presence of shear with the shear-free case. By employing a causal heat transport equation of the Maxwell–Cattaneo form we show that the shear leads to an enhancement of the core temperature thus emphasizing that relaxational effects cannot be ignored when the star leaves hydrostatic equilibrium.
THE TOLMAN–OPPENHEIMER–VOLKOFF EQUATIONS AND THE SPACETIME PROPERTIES OF THE SCHWARZSCHILD–DE SITTER CONSTANT DENSITY INTERIOR SOLUTION
Authors: ZOU LI , LI FANG-YU , LI TAO
Published: November 2013

In this paper, we first deduce the Tolman–Oppenheimer–Volkoff (TOV) equations and Schwarzschild–de Sitter (SdS) constant-density interior solutions of perfect fluid spheres in hydrostatic equilibrium by the Einstein equations with a nonzero cosmological constant. The TOV equations and the spacetime properties of exact solutions inside uniform perfect fluid spheres with different spatial curvature and cosmological constants will be respectively analyzed in detail. Moreover, a brief comparison between the internal static solutions of the SdS type and the dynamical Einstein–Strauss–de Sitter (ESdS) vacuole spacetime is obtained.
PERTURBATION OF FRW SPACETIME IN NP FORMALISM
Authors: SHARMA S. K. , KHANAL U.
Published: November 2013

Jacobi polynomials appear to play a very important role in describing all the spin field (s = 0, 1/2, 1, 2) perturbation of the Friedmann–Robertson–Walker (FRW) spacetime. The formulation becomes very transparent when done in Newman–Penrose (NP) formalism. All the variables are separable, and the spatial eigenfunctions turn out to be Jacobian polynomials in different forms. In particular, the angular ones are expressible as spin weighted spherical harmonics which are just the spherical harmonics formed with Jacobi polynomials. The radial eigenfunctions are also Jacobi polynomials but with unconventional parameters. Various properties of these polynomials are used to describe the scalar, vector and tensor modes of the perturbation. The Green's function of the scalar perturbations and also its Lienard–Wiechert type potentials are derived, and are shown to reduce to the familiar ones in the limit to flat FRW case. Some of the components of the perturbed metric tensor hμν have also been calculated.
THE ROLE OF SOCIAL TIES IN FOSTERING INNOVATION
Authors: SALARAN M. MEHDI , MARITZ ALEX
Published: November 2013

The purpose of this study is to examine the importance of social ties in encouraging innovative behaviour. There is limited empirical evidence of the interrelation between these two constructs in current academic literature. This research hypothesizes such relationship in higher academic institutions. To enhance innovativeness of academic staff within universities or R&D institutions, we examined the role of social ties in fostering innovativeness as a main factor in entrepreneurial activities. A survey was sent via a hyperlink to the target sample, facilitated by empirical analysis using correlation and regression analysis. It can be concluded that there is a significant relationship between spending time with social contacts and innovativeness. Limitations and further research are cited to enhance the understanding of the interrelation of the constructs.
Graded dimensions of principal subspaces and modular Andrews–Gordon-type series
Authors: Bringmann Kathrin , Calinescu Corina , Folsom Amanda , Kimport Susie
Published: November 2013

Our results in this paper are threefold: First, we establish the modular properties of the graded dimensions of principal subspaces of level one standard modules for [Formula: see text], and of principal subspaces of certain higher level standard modules for [Formula: see text]. Second, we establish the modular properties of families of q-series that appear in identities due to Warnaar and Zudilin, which generalize Macdonald's [Formula: see text] identities and the Rogers–Ramanujan identities. Third, we formulate a number of conjectures regarding the modularity of series of this type related to AN-1 root systems.
Minimal extension of General Relativity: Alternative gravity model with non-minimal coupling between matter and curvature
Authors: Bertolami Orfeu , Páramos Jorge
Published: November 2013

We examine an extension of General Relativity with an explicit non-minimal coupling between matter and curvature. The purpose of this work is to present an overview of the implications of the latter to various contexts, ranging from astrophysical matter distributions to a cosmological setting. Various results are discussed, including the impact of this non-minimal coupling on the choice of Lagrangian density, on a mechanism to mimic galactic and cluster dark matter, on the possibility of accounting for the accelerated expansion of the Universe, energy density fluctuations and modifications to post-inflationary reheating. The equivalence between a model exhibiting a non-minimal coupling and multi-scalar-theories is also discussed.
THERMODYNAMIC ANALYSES OF MULTIPLE EVAPORATORS VAPOR COMPRESSION REFRIGERATION SYSTEMS WITH R410A, R290, R1234YF, R502, R404A, R152A AND R134A
Authors: CHOPRA KAPIL , SAHNI V. , MISHRA R. S.
Published: November 2013

In this paper, comparative thermodynamic analysis of system-1 (multiple evaporators and compressors with individual expansion valves) and system-2 (multiple evaporators and compressors with multiple expansion valves) has been presented which is based on energy and exergy principles. The comparison of systems-1 and -2 using ecofriendly R410A, R290, R1234YF, R502, R404A, R152A and R134A refrigerants was done in terms of COP (energetic efficiency), exergetic efficiency and system defect. Numerical model has been developed for systems-1 and -2 for finding out irreversibility and it was observed that system-2 is better system in comparison with system-1 for selected refrigerants. It was also found that R152a shows better performances than other considered refrigerants for both systems.
Oxidative stress-inducible truncated serine/arginine-rich splicing factor 3 regulates interleukin-8 production in human colon cancer cells
Authors: Kano Shizuka , Nishida Kensei , Kurebe Hiroyuki , Nishiyama Chihiro , Kita Kentaro , Akaike Yoko , Kajita Keisuke , Kurokawa Ken , Masuda Kiyoshi , Kuwano Yuki , Tanahashi Toshihito , Rokutan Kazuhito
Published: November 2013

Serine/arginine-rich splicing factor 3 (SRSF3) is a member of the SR protein family and plays wide-ranging roles in gene expression. The human SRSF3 gene generates two alternative splice transcripts, a major mRNA isoform ( SRSF3-FL) encoding functional full-length protein and a premature termination codon (PTC)-containing isoform ( SRSF3-PTC). The latter is degraded through nonsense-mediated mRNA decay (NMD). Treatment of a human colon cancer cell line (HCT116) with 100 μM sodium arsenite increased SRSF3-PTC mRNA levels without changing SRSF3-FL mRNA levels. A chemiluminescence-based NMD reporter assay system demonstrated that arsenite treatment inhibited NMD activity and increased SRSF3-PTC mRNA levels in the cytoplasm, facilitating translation of a truncated SRSF3 protein (SRSF3-TR) from SRSF3-PTC mRNA. SRSF3-TR lacked two-thirds of the Arg/Ser-rich (RS) domain whose phosphorylation state is known to be crucial for subcellular distribution. SRSF3-FL was localized in the nucleus, while overexpressed SRSF3-TR was diffusely distributed in the cytoplasm and the nucleus. A part of SRSF3-TR was also associated with stress granules in the cytoplasm. Interestingly, treatment of HCT116 cells with a small interference RNA specifically targeting SRSF3-PTC mRNA significantly attenuated arsenite-stimulated induction of c-JUN protein, its binding activity to the AP-1 binding site (−126 to 120 bp) in the interleukin (IL)-8 gene promoter, and AP-1 promoter activity, resulting in significant reduction of arsenite-stimulated IL-8 production. Our results suggest that SRSF3-TR may function as a positive regulator of oxidative stress-initiated inflammatory responses in colon cancer cells.
Enhanced endoplasmic reticulum SERCA activity by overexpression of hepatic stimulator substance gene prevents hepatic cells from ER stress-induced apoptosis
Authors: Zhang Jing , Li Yuan , Jiang Shujun , Yu Hao , An Wei
Published: November 2013

Although the potential pathogenesis of nonalcoholic fatty liver disease (NAFLD) is unclear, increasing evidence indicates that endoplasmic reticulum (ER) stress may link free fatty acids to NAFLD. Since we previously reported that hepatic stimulator substance (HSS) could protect the liver from steatosis, this study is aimed to investigate whether HSS protection could be related with its inhibition on ER stress. The HSS gene was stably transfected into BEL-7402 hepatoma cells and effectively expressed in ER. The palmitic acid (PA)-induced heptocyte lipotoxicity was reproduced in the HSS-transfected cells, and HSS alleviation of the ER stress and apoptosis were subsequently examined. The results showed that PA treatment led to a heavy accumulation of fatty acids within the cells and a remarkable increase in reactive oxygen species (ROS). However, in the HSS-expressing cells, production of ROS was inhibited and ER stress-related marker glucose-regulated protein 78 (GRP-78), sterol regulatory element-binding protein (SREBP), anti-phospho-PRK-1ike ER kinase (p-PERK), anti-phospho-eukaryotic initiation factor 2α (p-eIF2α), and anti-C/EBP homologous protein (CHOP) were downregulated compared with the wild-type or mutant HSS-transfected cells. Furthermore, PA treatment severely impaired the activity of sarco-endoplasmic reticulum Ca2+-ATPase (SERCA), leading to imbalanced calcium homeostasis during ER stress, which could be rescued in the HSS-trasfected cells. The protection provided by HSS to the SERCA is identical to that observed with N-acetyl-l-cysteine (NAC) and sodium dimercaptopropane sulfonate (Na-DMPS), which are two typical free radical scavengers. As a consequence, the rate of ER stress-mediated apoptosis in the HSS-expressing cells was significantly reduced. In conclusion, the protective effect of HSS against ER stress may be associated with the removal of ROS to restore the activity of the SERCA.
Dynamic adhesion of eryptotic erythrocytes to immobilized platelets via platelet phosphatidylserine receptors
Authors: Walker Britta , Towhid Syeda T. , Schmid Evi , Hoffmann Sascha M. , Abed Majed , Münzer Patrick , Vogel Sebastian , Neis Felix , Brucker Sara , Gawaz Meinrad , Borst Oliver , Lang Florian
Published: November 2013

Glucose depletion of erythrocytes triggers suicidal erythrocyte death or eryptosis, which leads to cell membrane scrambling with phosphatidylserine exposure at the cell surface. Eryptotic erythrocytes adhere to endothelial cells by a mechanism involving phosphatidylserine at the erythrocyte surface and CXCL16 as well as CD36 at the endothelial cell membrane. Nothing has hitherto been known about an interaction between eryptotic erythrocytes and platelets, the decisive cells in primary hemostasis and major players in thrombotic vascular occlusion. The present study thus explored whether and how glucose-depleted erythrocytes adhere to platelets. To this end, adhesion of phosphatidylserine-exposing erythrocytes to platelets under flow conditions was examined in a flow chamber model at arterial shear rates. Platelets were immobilized on collagen and further stimulated with adenosine diphosphate (ADP, 10 μM) or thrombin (0.1 U/ml). As a result, a 48-h glucose depletion triggered phosphatidylserine translocation to the erythrocyte surface and augmented the adhesion of erythrocytes to immobilized platelets, an effect significantly increased upon platelet stimulation. Adherence of erythrocytes to platelets was blunted by coating of erythrocytic phosphatidylserine with annexin V or by neutralization of platelet phosphatidylserine receptors CXCL16 and CD36 with respective antibodies. In conclusion, glucose-depleted erythrocytes adhere to platelets. The adhesive properties of platelets are augmented by platelet activation. Erythrocyte adhesion to immobilized platelets requires phosphatidylserine at the erythrocyte surface and CXCL16 as well as CD36 expression on platelets. Thus platelet-mediated erythrocyte adhesion may foster thromboocclusive complications in diseases with stimulated phosphatidylserine exposure of erythrocytes.
Intestine of dystrophic mice presents enhanced contractile resistance to stretching despite morphological impairment
Authors: Alves Gabriel A. , Silva Luisa R. , Rosa Eloi F. , Aboulafia Jeannine , Freymüller-Haapalainen Edna , Souccar Caden , Nouailhetas Viviane L. A.
Published: November 2013

Protein dystrophin is a component of the dystrophin-associated protein complex, which links the contractile machinery to the plasma membrane and to the extracellular matrix. Its absence leads to a condition known as Duchenne muscular dystrophy (DMD), a disease characterized by progressive skeletal muscle degeneration, motor disability, and early death. In mdx mice, the most common DMD animal model, loss of muscle cells is observed, but the overall disease alterations are less intense than in DMD patients. Alterations in gastrointestinal tissues from DMD patients and mdx mice are not yet completely understood. Thus, we investigated the possible relationships between morphological (light and electron microscopy) and contractile function (by recording the isometric contractile response) with alterations in Ca2+handling in the ileum of mdx mice. We evidenced a 27% reduction in the ileal muscular layer thickness, a partial damage to the mucosal layer, and a partial damage to mitochondria of the intestinal myocytes. Functionally, the ileum from mdx presented an enhanced responsiveness during stretch, a mild impairment in both the electromechanical and pharmacomechanical signaling associated with altered calcium influx-induced contraction, with no alterations in the sarcoplasmic reticulum Ca2+storage (maintenance of the caffeine and thapsigargin-induced contraction) compared with control animals. Thus, it is evidenced that the protein dystrophin plays an important role in the preservation of both the microstructure and ultrastructure of mice intestine, while exerting a minor but important role concerning the intestinal contractile responsiveness and calcium handling.