bluuebunny/crossref_metadata_2025 huggingface dataset:
Sequencing Assays for Failed Genotyping with the Versant Hepatitis C Virus Genotype Assay (LiPA), Version 2.0
Authors: Larrat Sylvie , Poveda Jean-Dominique , Coudret Camille , Fusillier Katia , Magnat Nelly , Signori-Schmuck Anne , Thibault Vincent , Morand Patrice
Published: April 2013

For optimal antiviral therapy, the hepatitis C virus (HCV) genotype needs to be determined, as it remains a strong predictor of sustained viral response. In this study, we assessed the number of HCV genotyping results that could not be determined using the commercially available line probe assay (LiPA) (Versant hepatitis C virus genotype 2.0 assay) in a large international panel of samples from 9,874 HCV-positive patients. In-house sequencing assays targeting the 5′ untranslated region (UTR), core region, NS3 region, and NS5B region of the HCV genome and phylogenetic analyses were used to resolve these LiPA failures. Among all cases, the genotypes of 51 samples (0.52%) could not be determined with the LiPA. These undetermined results were observed more frequently among samples from non-European regions (mainly the Arabian Peninsula). The use of sequencing assays coupled with phylogenetic analysis provided reliable genotype results for 86% of the LiPA failures, which exhibited higher rates of genotypes 4, 5, and 6 than did LiPA-resolved genotypes. As expected, the 5′ UTR was not sufficiently variable for clear discrimination between genotypes 1 and 6, but it also resulted in errors in classification of some genotype 3 and 4 cases using well-known Web-based BLAST programs. This study demonstrates the low frequency of genotyping failures with the Versant hepatitis C virus genotype 2.0 assay (LiPA) and also underlines the need for a complex combination of sequences and phylogenetic analyses in order to genotype these particular HCV strains correctly.
Molecular Analysis of an Outbreak of Lethal Postpartum Sepsis Caused by Streptococcus pyogenes
Authors: Turner Claire E. , Dryden Matthew , Holden Matthew T. G. , Davies Frances J. , Lawrenson Richard A. , Farzaneh Leili , Bentley Stephen D. , Efstratiou Androulla , Sriskandan Shiranee
Published: April 2013

Sepsis is now the leading direct cause of maternal death in the United Kingdom, and
Streptococcus pyogenes
is the leading pathogen. We combined conventional and genomic analyses to define the duration and scale of a lethal outbreak. Two postpartum deaths caused by
S. pyogenes
occurred within 24 h; one was characterized by bacteremia and shock and the other by hemorrhagic pneumonia. The women gave birth within minutes of each other in the same maternity unit 2 days earlier. Seven additional infections in health care and household contacts were subsequently detected and treated. All cluster-associated
S. pyogenes
isolates were genotype
emm
1 and were initially indistinguishable from other United Kingdom
emm
1 isolates. Sequencing of the virulence gene
sic
revealed that all outbreak isolates had the same unique
sic
type. Genome sequencing confirmed that the cluster was caused by a unique
S. pyogenes
clone. Transmission between patients occurred on a single day and was associated with casual contact only. A single isolate from one patient demonstrated a sequence change in
sic
consistent with longer infection duration. Transmission to health care workers was traced to single clinical contacts with index cases. The last case was detected 18 days after the first case. Following enhanced surveillance, the outbreak isolate was not detected again. Mutations in bacterial regulatory genes played no detectable role in this outbreak, illustrating the intrinsic ability of
emm
1
S. pyogenes
to spread while retaining virulence. This fast-moving outbreak highlights the potential of
S. pyogenes
to cause a range of diseases in the puerperium with rapid transmission, underlining the importance of immediate recognition and response by clinical infection and occupational health teams.
Exposure to Human and Bovine Noroviruses in a Birth Cohort in Southern India from 2002 to 2006
Authors: Menon Vipin Kumar , George Santosh , Shanti Aruna A. , Saravanabavan Anuradha , Samuel Prasanna , Ramani Sasirekha , Estes Mary K. , Kang Gagandeep
Published: April 2013

Human and bovine norovirus virus-like particles were used to evaluate antibodies in Indian children at ages 6 and 36 months and their mothers. Antibodies to genogroup II viruses were acquired early and were more prevalent than antibodies to genogroup I. Low levels of IgG antibodies against bovine noroviruses indicate possible zoonotic transmission.
Analysis of Mutations in Streptomycin-Resistant Strains Reveals a Simple and Reliable Genetic Marker for Identification of the Mycobacterium tuberculosis Beijing Genotype
Authors: Villellas Cristina , Aristimuño Liselotte , Vitoria María-Asunción , Prat Cristina , Blanco Silvia , García de Viedma Darío , Domínguez José , Samper Sofía , Aínsa José A.
Published: April 2013

The
Mycobacterium tuberculosis
pandemic is a major health problem, further complicated by an increasing incidence of drug-resistant isolates and the existence of highly transmissible strains, such as those in the Beijing family. Streptomycin (STR)-resistant
M. tuberculosis
clinical isolates have been analyzed to look for mutations in the
rpsL
,
rrs
, and
gidB
genes. In addition, the
Rv1258c
gene, which encodes Tap, an efflux pump that transports STR, has been sequenced. Mutations affecting codons 43 and 88 of the
rpsL
gene were found in 44.4% of the strains, and 16.7% of the strains carried mutations in the
rrs
gene, both of which probably contribute to STR resistance. Many strains presented with mutations in the
gidB
gene, but the implication of those mutations in STR resistance remains unclear. Interestingly, a cytosine nucleotide insertion between positions 580 and 581 (denominated Tap
580
) in the
Rv1258c
gene has been found in all Beijing isolates included in this study, suggesting that it might be a novel polymorphism specific to the Beijing family of
M. tuberculosis
. A simple and fast restriction fragment length polymorphism (RFLP)-PCR method for detecting the Tap
580
insertion has been developed and used to screen a collection of 220 DNA samples obtained from cultures of
M. tuberculosis
isolates and 30 respiratory specimens. In all cases, the Beijing and non-Beijing representative samples were identified correctly. Tap
580
is a novel polymorphism specific to the highly transmissible Beijing family, which allows for fast detection of these strains even at the very early stages of infection.
Quantitative and Qualitative Involvement of P3N-PIPO in Overcoming Recessive Resistance against Clover Yellow Vein Virus in Pea Carrying the
cyv1
Gene
Authors: Choi Sun Hee , Hagiwara-Komoda Yuka , Nakahara Kenji S. , Atsumi Go , Shimada Ryoko , Hisa Yusuke , Naito Satoshi , Uyeda Ichiro
Published: April 2013

In pea carrying
cyv1
, a recessive gene for resistance to
Clover yellow vein virus
(ClYVV), ClYVV isolate Cl-no30 was restricted to the initially infected cells, whereas isolate 90-1 Br2 overcame this resistance. We mapped the region responsible for breaking of
cyv1
-mediated resistance by examining infection of
cyv1
pea with chimeric viruses constructed from parts of Cl-no30 and 90-1 Br2. The breaking of resistance was attributed to the P3 cistron, which is known to produce two proteins: P3, from the main open reading frame (ORF), and P3N-PIPO, which has the N-terminal part of P3 fused to amino acids encoded by a small open reading frame (ORF) called PIPO in the +2 reading frame. We introduced point mutations that were synonymous with respect to the P3 protein but nonsynonymous with respect to the P3N-PIPO protein, and vice versa, into the chimeric viruses. Infection of plants with these mutant viruses revealed that both P3 and P3N-PIPO were involved in overcoming
cyv1
-mediated resistance. Moreover, P3N-PIPO quantitatively affected the virulence of Cl-no30 in
cyv1
pea. Additional expression in
trans
of the P3N-PIPO derived from Cl-no30, using
White clover mosaic virus
as a vector, enabled Cl-no30 to move to systemic leaves in
cyv1
pea. Susceptible pea plants infected with chimeric ClYVV possessing the P3 cistron of 90-1 Br2, and which were therefore virulent toward
cyv1
pea, accumulated more P3N-PIPO than did those infected with Cl-no30, suggesting that the higher level of P3N-PIPO in infected cells contributed to the breaking of resistance by 90-1 Br2. This is the first report showing that P3N-PIPO is a virulence determinant in plants resistant to a potyvirus.
The Four and a Half LIM Family Members Are Novel Interactants of the Human T-Cell Leukemia Virus Type 1 Tax Oncoprotein
Authors: McCabe Áine , Hashimoto Kenichi , Hall William W. , Sheehy Noreen
Published: April 2013

Human T-cell leukemia virus type 1 (HTLV-1) is the etiologic agent of adult T-cell leukemia (ATL). The viral regulatory protein Tax1 plays a pivotal role in T-cell transformation and ATL development. Previous studies in our laboratory, using the yeast 2-hybrid approach to screen a T-cell library for Tax1-interacting partners, identified the cellular Four and a Half Lim domain protein 3 (FHL3) as a possible Tax1-interacting candidate. FHL3 is a member of the FHL family of proteins, which function as transcriptional coactivators and cytoskeleton regulators and have a role in cancer progression and development. The aim of this study was to investigate the physical and functional interaction between Tax1 and members of the FHL family of proteins. We show that Tax1 and FHL3 interact both
in vitro
and
in vivo
. Furthermore, both FHL1 and -2 also interact with Tax1. We have demonstrated that FHL3 enhances Tax1-mediated activation of the viral long terminal repeat (LTR) without affecting basal activity and that FHL1 to -3 regulate NF-κB activation by Tax1 in a cell-specific manner. In addition, we have found that the interaction between Tax1 and FHL1 to -3 affects the localization of these proteins, leading to their redistribution in cells. Tax1 also affected FHL3 cytoskeleton function by increasing FHL3-mediated cell spreading. Overall, our results suggest that the interaction between Tax1 and the FHL family alters both the transactivating activity and the subcellular localization of Tax1 and provide new insights into molecular mechanisms that underlie the oncogenic nature of this HTLV-1 protein.
The Cytokine Response of U937-Derived Macrophages Infected through Antibody-Dependent Enhancement of Dengue Virus Disrupts Cell Apical-Junction Complexes and Increases Vascular Permeability
Authors: Puerta-Guardo Henry , Raya-Sandino Arturo , González-Mariscal Lorenza , Rosales Victor H. , Ayala-Dávila José , Chávez-Mungía Bibiana , Martínez-Fong Daniel , Medina Fernando , Ludert Juan E. , del Angel Rosa María
Published: April 2013

Severe dengue (SD) is a life-threatening complication of dengue that includes vascular permeability syndrome (VPS) and respiratory distress. Secondary infections are considered a risk factor for developing SD, presumably through a mechanism called antibody-dependent enhancement (ADE). Despite extensive studies, the molecular bases of how ADE contributes to SD and VPS are largely unknown. This work compares the cytokine responses of differentiated U937 human monocytic cells infected directly with dengue virus (DENV) or in the presence of enhancing concentrations of a humanized monoclonal antibody recognizing protein E (ADE-DENV infection). Using a cytometric bead assay, ADE-DENV-infected cells were found to produce significantly higher levels of the proinflammatory cytokines interleukin 6 (IL-6), IL-12p70, and tumor necrosis factor alpha (TNF-α), as well as prostaglandin E
2
(PGE
2
), than cells directly infected. The capacity of conditioned supernatants (conditioned medium [CM]) to disrupt tight junctions (TJs) in MDCK cell cultures was evaluated. Exposure of MDCK cell monolayers to CM collected from ADE-DENV-infected cells (ADE-CM) but not from cells infected directly led to a rapid loss of transepithelial electrical resistance (TER) and to delocalization and degradation of apical-junction complex proteins. Depletion of either TNF-α, IL-6, or IL-12p70 from CM from ADE-DENV-infected cells fully reverted the disrupting effect on TJs. Remarkably, mice injected intraperitoneally with ADE-CM showed increased vascular permeability in sera and lungs, as indicated by an Evans blue quantification assay. These results indicate that the cytokine response of U937-derived macrophages to ADE-DENV infection shows an increased capacity to disturb TJs, while results obtained with the mouse model suggest that such a response may be related to the vascular plasma leakage characteristic of SD.
Identification of Multiple Novel Viruses, Including a Parvovirus and a Hepevirus, in Feces of Red Foxes
Authors: Bodewes Rogier , van der Giessen Joke , Haagmans Bart L. , Osterhaus Albert D. M. E. , Smits Saskia L.
Published: April 2013

Red foxes (
Vulpes vulpes
) are the most widespread members of the order of
Carnivora
. Since they often live in (peri)urban areas, they are a potential reservoir of viruses that transmit from wildlife to humans or domestic animals. Here we evaluated the fecal viral microbiome of 13 red foxes by random PCR in combination with next-generation sequencing. Various novel viruses, including a parvovirus, bocavirus, adeno-associated virus, hepevirus, astroviruses, and picobirnaviruses, were identified.
The Small Molecules AZD0530 and Dasatinib Inhibit Dengue Virus RNA Replication via Fyn Kinase
Authors: de Wispelaere Melissanne , LaCroix Amy J. , Yang Priscilla L.
Published: April 2013

In this study, we characterized the antiviral mechanism of action of AZD0530 and dasatinib, two pharmacological inhibitors of host kinases, that also inhibit dengue virus (DV) infection. Using Northern blot and reporter replicon assays, we demonstrated that both small molecules inhibit the DV2 infectious cycle at the step of steady-state RNA replication. In order to identify the cellular target of AZD0530 and dasatinib mediating this anti-DV2 activity, we examined the effects of RNA interference (RNAi)-mediated depletion of the major kinases known to be inhibited by these small molecules. We determined that Fyn kinase, a target of both AZD0530 and dasatinib, is involved in DV2 RNA replication and is probably a major mediator of the anti-DV activity of these compounds. Furthermore, serial passaging of DV2 in the presence of dasatinib led to the identification of a mutation in the transmembrane domain 3 of the NS4B protein that overcomes the inhibition of RNA replication by AZD0530, dasatinib, and Fyn RNAi. Although we observed that dasatinib also inhibits DV2 particle assembly and/or secretion, this activity does not appear to be mediated by Src-family kinases. Together, our results suggest that AZD0530 and dasatinib inhibit DV at the step of viral RNA replication and demonstrate a critical role for Fyn kinase in this viral process. The antiviral activity of these compounds
in vitro
makes them useful pharmacological tools to validate Fyn or other host kinases as anti-DV targets
in vivo
.
Adaptation of Avian Influenza A Virus Polymerase in Mammals To Overcome the Host Species Barrier
Authors: Mänz Benjamin , Schwemmle Martin , Brunotte Linda
Published: April 2013

Avian influenza A viruses, such as the highly pathogenic avian H5N1 viruses, sporadically enter the human population but often do not transmit between individuals. In rare cases, however, they establish a new lineage in humans. In addition to well-characterized barriers to cell entry, one major hurdle which avian viruses must overcome is their poor polymerase activity in human cells. There is compelling evidence that these viruses overcome this obstacle by acquiring adaptive mutations in the polymerase subunits PB1, PB2, and PA and the nucleoprotein (NP) as well as in the novel polymerase cofactor nuclear export protein (NEP). Recent findings suggest that synthesis of the viral genome may represent the major defect of avian polymerases in human cells. While the precise mechanisms remain to be unveiled, it appears that a broad spectrum of polymerase adaptive mutations can act collectively to overcome this defect. Thus, identification and monitoring of emerging adaptive mutations that further increase polymerase activity in human cells are critical to estimate the pandemic potential of avian viruses.
Modulation of Hepatitis C Virus Genome Encapsidation by Nonstructural Protein 4B
Authors: Han Qingxia , Manna David , Belton Kerry , Cole Richard , Konan Kouacou V.
Published: April 2013

Hepatitis C Virus (HCV) NS4B protein has many roles in HCV genome replication. Recently, our laboratory (Q. Han, J. Aligo, D. Manna, K. Belton, S. V. Chintapalli, Y. Hong, R. L. Patterson, D. B. van Rossum, and K. V. Konan, J. Virol. 85:6464–6479, 2011) and others (D. M. Jones, A. H. Patel, P. Targett-Adams, and J. McLauchlan, J. Virol. 83:2163–2177, 2009; D. Paul, I. Romero-Brey, J. Gouttenoire, S. Stoitsova, J. Krijnse-Locker, D. Moradpour, and R. Bartenschlager, J. Virol. 85:6963–6976, 2011) have also reported NS4B's function in postreplication steps. Indeed, replacement of the NS4B C-terminal domain (CTD) in the HCV JFH1 (genotype 2a [G2a]) genome with sequences from Con1 (G1b) or H77 (G1a) had a negligible impact on JFH1 genome replication but attenuated virus production. Since NS4B interacts weakly with the HCV genome, we postulated that NS4B regulates the function of host or virus proteins directly involved in HCV production. In this study, we demonstrate that the integrity of the JFH1 NS4B CTD is crucial for efficient JFH1 genome encapsidation. Further, two adaptive mutations (NS4B N216S and NS5A C465S) were identified, and introduction of these mutations into the chimera rescued virus production to various levels, suggesting a genetic interaction between the NS4B and NS5A proteins. Interestingly, cells infected with chimeric viruses displayed a markedly decreased NS5A hyperphosphorylation state (NS5A p58) relative to JFH1, and the adaptive mutations differentially rescued NS5A p58 formation. However, immunofluorescence staining indicated that the decrease in NS5A p58 did not alter NS5A colocalization with the core around lipid droplets (LDs), the site of JFH1 assembly, suggesting that NS5A fails to facilitate the transfer of HCV RNA to the capsid protein on LDs. Alternatively, NS4B's function in HCV genome encapsidation may entail more than its regulation of the NS5A phosphorylation state.
Investigation of a safety-engineered device to prevent needlestick injury: why has not StatLock stuck?
Authors: Griswold Sharon , Bonaroti Alisha , Rieder Christopher J , Erbayri John , Parsons Jessica , Nocera Romy , Hamilton Richard
Published: April 2013

Objective

This article sought to define whether an alternative safety-engineered device (SED) could help prevent needlestick injury (NSI) in healthcare workers (HCWs) who place central venous catheters (CVCs).

Design

The study involved three phases: (1) A retrospective analysis of deidentified occupational health records from our tertiary care urban US hospital to clearly identify NSI risk and rates to an HCW during invasive catheter placement; (2) 95 residents were surveyed regarding their knowledge and experience with NSIs and SEDs; (3) A random sample of six residents participated in a focus group session discussing barriers to the use of SED.

Setting

A single urban US tertiary care teaching hospital.

Participants

A retrospective analysis of NSI to HCWs in a tertiary care urban US hospital was conducted over a 4-year period (July 2007–June 2011). Ninety-five residents from specialties that often place CVC during training (surgery, surgical subspecialties, internal medicine, anaesthesia and emergency medicine) were surveyed regarding their experience with NSIs and SEDs. A random sample of six residents participated in a focus group session discussing barriers to the use of SED.

Results

314 NSIs were identified via occupational health records. 16% (21 of 131) of NSIs occurring in residents and fellows occurred during the securement of an invasive catheter such as a CVC. If an SED device had been used, the 5.25 NSIs/year could have been avoided. Each NSI occurring in an HCW incurred at least $2723 in charges. Thus, utilisation of the SED could have saved a minimum of $57 183 over the 4-year period.

Conclusions

SEDs are currently available and can be used as an alternative to sharps. If safety and efficacy can be demonstrated, then implementation of such devices can significantly reduce the number of NSIs.
How accurate are medical record data in Afghanistan's maternal health facilities? An observational validity study
Authors: Broughton Edward I , Ikram Abdul Naser , Sahak Ihsanullah
Published: April 2013

Objectives

Improvement activities, surveillance and research in maternal and neonatal health in Afghanistan rely heavily on medical record data. This study investigates accuracy in delivery care records from three hospitals across workshifts.

Design

Observational cross-sectional study.

Setting

The study was conducted in one maternity hospital, one general hospital maternity department and one provincial hospital maternity department. Researchers observed vaginal deliveries and recorded observations to later check against data recorded in patient medical records and facility registers.

Outcome measures

We determined the sensitivity, specificity, area under the receiver operator characteristics curves (AUROCs), proportions correctly classified and the tendency to make performance seem better than it actually was.

Results

600 observations across the three shifts and three hospitals showed high compliance with active management of the third stage of labour, measuring blood loss and uterine contraction at 30 min, cord care, drying and wrapping newborns and Apgar scores and low compliance with monitoring vital signs. Compliance with quality indicators was high and specificity was lower than sensitivity. For adverse outcomes in birth registries, specificity was higher than sensitivity. Overall AUROCs were between 0.5 and 0.6. Of 17 variables that showed biased errors, 12 made performance or outcomes seem better than they were, and five made them look worse (71% vs 29%, p=0.143). Compliance, sensitivity and specificity varied less among the three shifts than among hospitals.

Conclusions

Medical record accuracy was generally poor. Errors by clinicians did not appear to follow a pattern of self-enhancement of performance. Because successful improvement activities, surveillance and research in these settings are heavily reliant on collecting accurate data on processes and outcomes of care, substantial improvement is needed in medical record accuracy.
Social network analysis of Iranian researchers on emergency medicine: a sociogram analysis
Authors: Ghafouri Hamed Basir , Mohammadhassanzadeh Hafez , Shokraneh Farhad , Vakilian Maryam , Farahmand Shervin
Published: April 2013

Background

The purpose of this study was to report interaction patterns among Iranian authors of emergency medicine using social network analysis methodology, focusing on coauthorship network.

Methods

The bibliographic data of Iranian authors on the ‘emergency medicine’ field during the years 2001–2011 were retrieved from the Science Citation Index Expanded database. Co-occurrence matrices were made by BibExcel and were imported to Ucinet and NetDraw to delineate coauthorship network. To detect structural patterns among authors, we considered some measures of social network analysis, such as density, centralisation indices, component analysis and cut-points. Lastly, subject experts separately analysed the content of papers.

Results

Of 116 papers published, the network was composed of 10 components, with the largest component having 25 authors. Using social network analysis measures, we identified science bottlenecks in knowledge sharing, hub authors and accelerators of information flow. Topic analysis showed ‘Wounds and Injuries’ as the most recent theme in all components because of existence of national registry for trauma, high burden of road traffic injuries and research priority of injuries in Iran.

Conclusions

because of Iranian low productivity in the emergency medicine field, social network analysis seems to be a proper option for bibliometrics to identify central authors and detect knowledge structure in this field.
Use of ulipristal acetate, levonorgestrel and the copper-intrauterine device for emergency contraception following the introduction of new FSRH guidelines
Authors: Baird Aisling Susan
Published: April 2013

Objectives

The UK Faculty of Sexual & Reproductive Healthcare (FSRH) has recommended that for emergency contraception (EC) the health professional should discuss individual needs and inform women of the different methods, efficacy, adverse effects, interactions, eligibility and additional contraception. In our sexual and reproductive health care service (Liverpool and Knowsley, UK), revised guidance was issued in early 2012, reflecting Faculty advice. We studied (1) how our use of EC changed, (2) which methods were offered and how this changed, (3) which method was chosen by women who were offered all three UK licensed methods of EC and (4) the appropriateness of the offer of only levonorgestrel (LNG).

Methods

We studied a total of 2989 case records in the 3 months before and 3 months following the adoption by our service of the 2011 FSRH guidance. This was a retrospective review of charts undertaken by interrogating our computerised Excelicare®system of clinical records. All EC episodes in the two 3-month periods were analysed, covering October–December 2011 and March–May 2012. Additionally, three non-probabilistic, purposeful samples of representative practitioners’ charts were examined in groups of women offered all methods [and choosing either ulipristal acetate (UPA) or LNG] or who were offered LNG only.

Results

The use of LNG fell from 93.0% of EC issued to 76.0%; UPA use rose from 3.0% to 18.7%. In the second 3-month period, of the women offered all three methods, 54.9% chose LNG and 39.8% UPA. LNG-only offers in our judgement were clinically appropriate in 62.5% cases of such offers.

Conclusions

Comparing the second period with the first, more women were offered all three methods, the use of LNG fell (93.0% to 76.0%) and that of UPA increased (3.0% to 18.7%). Women were encouraged to exercise choice. However, increasing choice in our service did not lead to a wholesale change from LNG to UPA.
LT COL DS JOLLlFFE, RAMC
Authors: Hopkins G O.
Published: April 2013

Eight patients suffering from cutaneous leishmaniasis acquired in Belize were treated with 800 mg oral ketoconazole daily for 28 days . Four were infected withLeishmania mexicana mexicanaand four withLeishmania braziliensis braziliensis. On complelion of therapy, all cases ofLeishmania mexicalla mexicanainfection and one ofLeishmania braziliensis braziliensisinfection showed significant clinical improvement. No side-effects were observed during this study which suggests that ketoconazole might be a safe and effective form of therapy for cutaneous leishmaniasis caused byLeishmania mexicona mexicana.
Highly efficient iron phthalocyanine catalyzed oxidative synthesis of imines from alcohols and amines
Authors: Bala Manju , Verma Praveen Kumar , Kumar Neeraj , Sharma Upendra , Singh Bikram
Published: April 2013

An efficient iron phthalocyanine catalyzed method was developed for direct oxidative coupling of alcohols with amines to afford corresponding imines. The present protocol is applicable to various substituted aromatic and aliphatic alcohols and amines. The reaction is believed to proceed via activation of alcohols by iron phthalocyanines through Lewis acid–base interaction to form aldehydes, which by nucleophilic attack of amines are converted into the corresponding imines.
Evaluating the impact of fluvial geomorphology on river ice cover formation based on a global sensitivity analysis of a river ice model
Authors: Lindenschmidt Karl-Erich , Chun Kwok P.
Published: April 2013

In 2011, Manitoba was stricken by wide-scale flooding causing high flows along the Dauphin River. The unprecedented high discharges at freeze-up created the potential for excessive ice cover thickening and backwater staging exacerbating the flood risk already threatening the communities along the river and upstream-lying Lake St. Martin. Hence, the river ice model RIVICE was implemented to determine flood protection elevations to which existing dikes needed to be raised and extended. Two reaches of the river were modelled separately representing distinct geomorphological characteristics: mildly sloping, more sinuous upper reach and steeper, more channelized lower reach. A global sensitivity analysis based on a Monte Carlo analysis was carried out to determine how differences in these morphological features influence different processes of the ice cover formation. It was found that the sinuous and braided morphology of the upper reach has a marked impact on the sensitivity of the hydraulic roughness and strength parameters. The structure of the ice (porosity) and the discharge were most sensitive to the backwater level outcomes of the steeper and straighter lower reach.
What is the added value of including fleet dynamics processes in fisheries models?
Authors: Marchal Paul , De Oliveira José A.A. , Lorance Pascal , Baulier Loïc , Pawlowski Lionel
Published: April 2013

We develop a spatially and seasonally explicit bioeconomic model with three fleet dynamics processes built in endogenously. The model has been applied to the large French trawlers harvesting a medium-depth demersal stock, North Sea saithe (i.e., pollock, Pollachius virens), and a mix of deepwater species over a 10-year period (1999–2008), and the predictions have been contrasted with observations. The best overall fit was achieved where effort allocation was determined to be 80% by traditions and 20% by economic opportunism and where harvest efficiency increased by 8% a year. With this fleet dynamics parameterization, annual trends in fishing effort and profit were well reproduced by the model over the whole time period. Time series of the observed fishing effort by métier were generally well fitted by the model over the period 1999–2003, but less so over 2004–2008. The model also reasonably reproduced the catches by species over most of the time series, except for black scabbardfish (Aphanopus carbo).
The “firing cannons” of Dipodascopsis uninucleata var. uninucleata
Authors: Olivier Andries P.S. , Swart Chantel W. , Pohl Carolina H. , van Wyk Pieter W.J. , Swart Hendrik C. , Coetsee Elizabeth , Schoombie Schalk W. , Smit Jon , Kock Johan Lodewyk F.
Published: April 2013

According to literature, the elongated ascospores of Dipodascopsis uninucleata var. uninucleata exhibit smart movement when forcefully ejected from bottle-shaped asci. This type of movement is defined as the unique patterns of non-random movement of ascospores with specialized morphology thereby facilitating release from asci. Smart movement is required to actively release ascospores individually through the narrow ascus neck, without causing an obstruction and blocking ascospore release. However, little is known about the propulsion mechanism of this cannon-type release system. We show that asci of this yeast contain a central channel (barrel) filled with ascospores. These are surrounded by a sheath-like structure that lines the inner surface of the ascus wall. We found that this sheath is responsible for forcing the naked ascospores out of the ascus by exerting turgor pressure from the bottom towards the tip of the ascus. This cannon firing system is in contrast to that found in Dipodascus geniculatus, where no sheaths lining the ascus interior were observed. Instead, sheaths were found enveloping each ascospore.
CELL GAS MODEL OF CLASSICAL STATISTICAL SYSTEMS
Authors: REBENKO ALEXEI L.
Published: April 2013

The work is a brief review of articles by the author and his young colleagues to describe the classical statistical systems with the use of properties of integrals with respect to Poisson measure on configuration space. A variant of cell gas model which is an approximation of the continuous classical gas is proposed. Cell gas (CG) model for continuous classical system of interacting point particles is defined as follows. For a given partition [Formula: see text] of the space ℝd into an infinite set of mutually disjoint hypercubes with edges a, every point of a phase space of an infinite particle system is a configuration in which every hypercube [Formula: see text] contains no more than one particle. We present a structure of measurable sets of the configuration space and show that for strong superstable interaction the pressure and correlation functions of the system pointwise converge to the corresponding values of the conventional continuous system if the edges a of cubes [Formula: see text] tend to zero. We also define lattice gas (LG) model which approximates the CG model and thus provides a continuous transition LG model in the model of continuous gas.
ENHANCING TRAFFIC CAPACITY OF TWO-LAYER COMPLEX NETWORKS
Authors: JIANG ZHONG-YUAN , LIANG MAN-GUI , ZHANG SHUAI , ZHOU WEIXING , JIN HUIQIN
Published: April 2013

As two-layer or multi-layer network model can more accurately reveal many real structures of complex systems such as peer-to-peer (P2P) networks on IP networks, to better understand the traffic dynamics and improve the network traffic capacity, we propose to efficiently construct the structure of upper logical layer network which can be possibly implemented. From the beginning, we assume that the logical layer network has the same structure as the lower physical layer network, and then we use link-removal strategy in which a fraction of links with maximal product (ki* kj) are removed from the logical layer, where ki and kj are the degrees of node i and node j, respectively. Traffic load is strongly redistributed from center nodes to noncenter nodes. The traffic capacity of whole complex system is enhanced several times at the expense of a little average path lengthening. In two-layer network model, the physical layer network structure is unchanged and the shortest path routing strategy is used. The structure of upper layer network can been constructed freely under our own methods. This mechanism can be employed in many real complex systems to improve the network traffic capacity.
JET PHYSICS IN HEAVY-ION COLLISIONS
Authors: MEHTAR-TANI YACINE , MILHANO JOSÉ GUILHERME , TYWONIUK KONRAD
Published: April 2013

Jets are expected to play a prominent role in the ongoing efforts to characterize the hot and dense QCD medium created in ultrarelativistic heavy-ion collisions. The success of this program depends crucially on the existence of a full theoretical account of the dynamical effects of the medium on the jets that develop within it. By focussing on the discussion of the essential ingredients underlying such a theoretical formulation, we aim to set the appropriate context in which current and future developments can be understood.
MODELING CITATION DIFFUSION: INNOVATION MANAGEMENT LITERATURE
Authors: PILKINGTON ALAN
Published: April 2013

Citation patterns are important to understanding the spread of technological ideas as science is essentially a cumulative activity. One feature only now being appreciated is the obsolescence or ageing patterns in citations and the insights their study can bring. There have been a number of studies examining, predicting, modeling and plotting citation delays, ageing and the publication cycle. These normally apply lognormal, log-logistic and Weibull distributions to scientific papers. This paper adds to this body of work by examining a set of 18 other distributions, and tests their predictive power on a new data set based on 10 years of ISI Citation data for 10 innovation centered journals. The resulting grouping of journals appears to be a useful proxy for academic-practitioner involvement and warrants further investigation. The finding that the three-parameter Inverse Gaussian provides the best fit to the data extends the understanding of this process. As well as allowing the classification of literature, this improved representation of citation obsolescence will allow us to predict earlier and more precisely those scientific ideas which are generating noteworthy attention or may be suitable for early exploitation.
PROPER HYPERSUBSTITUTIONS OF VARIETIES OF PSEUDO-COMPLEMENTED SEMILATTICES
Authors: Denecke Klaus , Srithus Ratana
Published: April 2013

We determine all V-proper hypersubstitutions for the variety of pseudo-complemented semilattices. Moreover, for any monoid [Formula: see text] of hypersubstitutions we will give the greatest M-solid variety of pseudo-complemented semilattices.
ON ANNIHILATOR IDEALS OF C-ALGEBRAS
Authors: RAO M. SAMBASIVA
Published: April 2013

The concept of annihilator ideals is introduced in C-algebras. Some properties of these annihilator ideals are studied and then proved that the class of all annihilator ideals forms a complete Boolean algebra. A set of equivalent conditions are obtained for every ideal of a C-algebra to become an annihilator ideal. Some properties of homomorphic images and inverse images of annihilators ideals of a C-algebra are studied.
CONSTRUCTION OF SMOOTH COMPACTLY SUPPORTED WINDOWS GENERATING DUAL PAIRS OF GABOR FRAMES
Authors: Christiansen Lasse Hjuler , Christensen Ole
Published: April 2013

Let g be any real-valued, bounded and compactly supported function, whose integer-translates {Tkg}k∈ℤ form a partition of unity. Based on a new construction of dual windows associated with Gabor frames generated by g, we present a method to explicitly construct dual pairs of Gabor frames. This new method of construction is based on a family of polynomials which is closely related to the Daubechies polynomials, used in the construction of compactly supported wavelets. For any k ∈ ℕ ∪ {∞} we consider the Meyer scaling functions and use these to construct compactly supported windows g ∈ Ck(ℝ) associated with a family of smooth compactly supported dual windows [Formula: see text]. For any n ∈ ℕ the pair of dual windows g, hn ∈ Ck(ℝ) have compact support in the interval [-2/3, 2/3] and share the property of being constant on half the length of their support. We therefore obtain arbitrary smoothness of the dual pair of windows g, hn without increasing their support.
SURGING CAPITAL FLOWS TO EMERGING ASIA: FACTS, IMPACTS AND RESPONSES
Authors: BALAKRISHNAN RAVI , NOWAK SYLWIA , PANTH SANJAYA , WU YIQUN
Published: April 2013

Net capital flows to Emerging Asia rebounded at a record pace following the global financial crisis, raising concerns about overheating and financial stability. This paper documents the size and composition of the most recent surge to Asian emerging markets from a historical perspective and compares developments in the broader economy, asset prices, and corporate variables across the different episodes of strong inflows. We find little evidence of a significant build-up of imbalances and resource misallocation during the most recent surge. We also review country experiences in managing the risks associated with inflows and argue that Asian countries have used regulatory measures during past surges.
GLOBAL FINANCIAL SHOCKS AND THEIR ECONOMIC IMPACT ON EMERGING MARKET ECONOMIES
Authors: ADLER GUSTAVO , TOVAR CAMILO E.
Published: April 2013

The world has experienced episodes of global financial stress every 2.5 years on average over the past two decades, with repercussions on a global scale. Over the same period, emerging economies have improved their macroeconomic fundamentals while becoming increasingly integrated with the world. Against this backdrop, are these economies more or less vulnerable to large global financial shocks? What roles have macroeconomic fundamentals and financial integration played in amplifying or buffering the impact of these shocks? This paper addresses these questions by examining the output cost associated with these events in 40 emerging and nine "small" advanced economies during the period 1990–2010.
The significance of copper concentrations in natural gold alloy for reconnaissance exploration and understanding gold-depositing hydrothermal systems
Authors: Moles N. R. , Chapman R. J. , Warner R. B.
Published: April 2013

Analytical studies of placer (detrital) gold grains, intended to track bedrock sources and styles of mineralization, mainly consider alloy Ag content and inclusion mineralogy to generate ‘microchemical signatures’. Occasionally Hg and Pd help discriminate gold from different sources; Cu infrequently because electron microprobes seldom detect the low concentrations. Reporting of Cu has been largely confined to gold from porphyry–epithermal environments, and this has biased subsequent interpretations of observed Cu-bearing gold alloys.

This study focuses on placer gold in the Mourne Mountains, Northern Ireland, where auriferous bedrock remains undiscovered and the complex geology is consistent with either orogenic or intrusion-related mineralization. Over 500 gold grains analysed average 0.17% Cu ranging to >1% Cu and show a wide variation in Ag content. Inclusion mineralogy mainly matches that of orogenic gold elsewhere in the host terrane; however, some signatures are suggestive of zonation within an orogenic hydrothermal mineralizing system, or possibly metamorphic-hydrothermal remobilized gold associated with subsequent intrusive activity. One locality in the study area has placer gold of a distinctive Cu-rich alloy composition containing Cu sulphide inclusions, an association noted elsewhere in gold derived from alkali Cu-Au porphyries.

Consideration of Cu-bearing gold alloys worldwide indicates that previously proposed compositional correlations with deposit type are of limited value. We show that Cu contents to at least 0.8% are permissible within orogenic gold – the first time that such compositions have been clearly ascribed to orogenic mineralization. The result is particularly important considering on-going exploration in northern Canada which employs gold grain analysis to help define exploration targets.
Riparian eucalypt biogeochemical expression of groundwater salinity, Murray River, South Australia
Authors: McLennan Stephanie M. , Hill Steven M. , Hatch Michael , Barovich Karin , Berens Volmer
Published: April 2013

Salinisation of floodplains along the Murray River is a significant environmental and social problem in south-eastern Australia that can be expensive and time-consuming to monitor. The potential of plant biogeochemistry as an environmental monitoring tool, specifically its innovative application to groundwater salinity detection, is explored in this paper. Major and trace element biogeochemical data were compared to data from three geophysical surveys in the study area as well as field observations of the underlying stratigraphy. The result is an understanding of how groundwater chemistry can be characterised by plants, specifically river red gum (
Eucalyptus camaldulensis
) and black box (
Eucalyptus largiflorens
) leaves. From the survey it is evident that
E. camaldulensis
and
E. largiflorens
were both successful in expressing high salinity levels in the subsurface. Molybdenum was the most suitable pathfinder element for high salinity groundwater. The study has important implications for interpreting biogeochemical mineral exploration results; anomalous element concentrations need to be interpreted in relation to salinity levels.
Metal migration at the North Miitel Ni sulphide deposit in the southern Yilgarn Craton: Part 2, vegetation and organic soil
Authors: Lintern M.J. , Noble R.R.P. , Reid N. , Anand R.R.
Published: April 2013

Transported regolith cover hinders exploration for economically important komatiite-hosted sulphide ore bodies in the Yilgarn Craton. Biogeochemistry offers a surface sampling technique to explore for these buried deposits that has not been extensively tested in this region. In this study, eucalypt trees and some other common plants were investigated at the North Miitel Ni deposit for their use in exploration targeting and to understand what role vegetation is taking in creating near surface anomalous geochemical signatures. Primary ore is deep (
c.
400 m) with a thin, weakly-enriched (compared to primary mineralisation),
in situ
weathered zone 10–20 m below the surface, under a cover sequence of 5–10 m deep. This study investigated the efficacy of several sample media including leaves, bark, litter, and organic-rich soils in an orientation traverse and a more extensive (150 m - spaced, 9 km
2
) grid-based survey (footprint). The organic-rich soil and biogeochemistry were influenced by contamination from the haul road. Directly over mineralisation some elements showed anomalous concentrations but data were erratic, not statistically significant and, therefore, not useful for mineral exploration. High groundwater salinity and low pH, lack of supergene development, weak subsurface signature and aeolian contamination contribute to why Ni anomalies have not been readily indentified at the surface. Nickel is also essential to plant physiology and is actively absorbed in a controlled manner. Investigation of plant-soil-water interactions is valuable in understanding metal mobility in the environment. Here we refined the viable exploration techniques in this setting where Ni sulphide discoveries through cover are important for future economic and resource development.
Island slopes and jumbled shell beds
Authors: Donovan Stephen K. , Van Waveren Isabel M. , Portell Roger W.
Published: April 2013

Shell beds pose questions of provenance, but determining the degree of pre-depositional transport of bioclasts can be speculative. Bioclastic beds deposited on a broad, shallow continental shelf may consist of a minimally transported accumulation. In contrast, islands may have steep shelves and accumulate disharmonious bioclastic assemblages in deeper water. The latter are a signature of the stratigraphic record on many islands. Herein, we contrast differing examples of jumbled shell beds preserved around islands. The Lower Permian Mengkarang Formation of Sumatra preserves deep-water facies at the base of a volcanic section. Nektonic cephalopods overlie a fine-grained ash containing a diverse association of terrestrial pollen. The Lower Miocene Montpelier Formation of Jamaica yields allochthonous packstones and slide blocks of reef limestone embedded in chalk; the ichthyofauna indicates deposition in ≥200 m water depth. Abundant evidence that deposition occurred in a deep-water turbidite basin flanking a volcanic island is found in the Middle Miocene Grand Bay Formation of Carriacou, the Grenadines. Diverse, deeper water taxa are preserved in association with land snails, hermatypic scleractinians, algal balls and planktic pteropods. The famous Upper Pliocene Bowden shell beds, Jamaica, preserve terrestrial, shallow-water, deep-water and planktic taxa.
A review of volcanic island evolution and magma production rate: an example from a Cenozoic island arc in the Caribbean
Authors: Jackson Trevor A.
Published: April 2013

Different stages of volcanic island evolution are evident in the Cenozoic Lesser Antilles arc developed near the eastern edge of the Caribbean Plate. The early stage of seamount evolution is represented by the Kick-em-Jenny submarine volcano near the southern end of the arc. The volcanically active islands known as the Volcanic Caribbées are composed of a series of composite volcanoes and are examples of an emergent volcanic island stage. Those islands that were formerly active, known as the Limestone Caribbées, provide evidence that an erosional to submergent stage occurred in the northern part of the island arc during the Oligocene and Miocene epochs. Growth of the islands and underlying crust is dependent upon the magma production rate along the arc, which has for the last 100 ka ranged from less than 1 km
3
to 40 km
3
. These differences in magma production and volcanic rock composition along the arc are attributed to the obliquity of plate convergence and the plate convergence rates.