bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk management in Indian companies: EWRM concerns and issues
Authors: Gupta P.K. 
Published: February 2011

PurposeThe purpose of this paper is to examine the current status of risk management in Indian companies and explore the reasons for the adoption or lack of adoption of integrated approach to risk management. It identifies the imperatives for implementation of comprehensive risk management solutions leading to enterprise‐wide risk management (EWRM). The paper shows that effective risk management can improve organizational performance but adequate infrastructure is not available in companies for implementing EWRM.Design/methodology/approachExploratory design using the survey research methodology that includes structured questionnaires and interviews of 130 companies.FindingsRisk management in Indian companies is currently facing the problem of integration and incentivisation. The risk management function is not suitably blended into the corporate strategy and use of information technology for risk management is minimal. The portfolio approach to risk management titled as integrated risk management or EWRM is ineffective from an implementation perspective and a sea change in risk perception is required which accentuates the need for building up of risk culture across business segments and adequate incentivisation for risk management.Practical implicationsRisk management is an integral part of the decision‐making process and effective risk management can proactively help in overcoming the possibilities of the business failures.Originality/valueThe paper highlights the fact that knowledge of risk management in Indian companies is inadequate and sample companies hesitate to respond thinking that it may reflect inefficiencies.
Post‐crisis developments in international financial markets
Authors: Suetin Alexander 
Published: February 2011

PurposeThe purpose of this paper is to investigate what affected the post‐crisis developments in international financial markets with special reference to current innovations in the financial industry.Design/methodology/approachThe paper revisits banks failures in recession years occurred in presence of a huge unprecedented guarantee programmes worth 16.4 per cent of gross domestic product in a median advanced economy.FindingsFinancial markets are indispensable despite finance's risks are everyone's because banks rely both directly and indirectly on taxpayers' support. Still the finance industry enables more trade to take place than would otherwise occur. The rally after crisis is driven by liquidity. In this context, special attention is paid to the situation on the gold market. The paper underscores that the dollar declinism is overblown. Still the situation with shifting and reorganising the world demand stays open.Originality/valueThe paper adds insight into post‐crisis developments in international financial markets.
Growth in Baumslag–Solitar groups I: subgroups and rationality
Authors: Freden Eric M. , Knudson Teresa , Schofield Jennifer 
Published: February 2011

AbstractThe computation of growth series for the higher Baumslag–Solitar groups is an open problem first posed by de la Harpe and Grigorchuk. We study the growth of the horocyclic subgroup as the key to the overall growth of these Baumslag–Solitar groups BS(p,q), where 1<p<q. In fact, the overall growth series can be represented as a modified convolution product with one of the factors being based on the series for the horocyclic subgroup. We exhibit two distinct algorithms that compute the growth of the horocyclic subgroup and discuss the time and space complexity of these algorithms. We show that when p divides q, the horocyclic subgroup has a geodesic combing whose words form a context-free (in fact, one-counter) language. A theorem of Chomsky–Schützenberger allows us to compute the growth series for this subgroup, which is rational. When p does not divide q, we show that no geodesic combing for the horocyclic subgroup forms a context-free language, although there is a context-sensitive geodesic combing. We exhibit a specific linearly bounded Turing machine that accepts this language (with quadratic time complexity) in the case of BS(2,3) and outline the Turing machine construction in the general case.
Metagenomic Analysis of Kimchi, a Traditional Korean Fermented Food
Authors: Jung Ji Young , Lee Se Hee , Kim Jeong Myeong , Park Moon Su , Bae Jin-Woo , Hahn Yoonsoo , Madsen Eugene L. , Jeon Che Ok 
Published: February 2011

ABSTRACTKimchi, a traditional food in the Korean culture, is made from vegetables by fermentation. In this study, metagenomic approaches were used to monitor changes in bacterial populations, metabolic potential, and overall genetic features of the microbial community during the 29-day fermentation process. Metagenomic DNA was extracted from kimchi samples obtained periodically and was sequenced using a 454 GS FLX Titanium system, which yielded a total of 701,556 reads, with an average read length of 438 bp. Phylogenetic analysis based on 16S rRNA genes from the metagenome indicated that the kimchi microbiome was dominated by members of three genera:Leuconostoc,Lactobacillus, andWeissella. Assignment of metagenomic sequences to SEED categories of the Metagenome Rapid Annotation using Subsystem Technology (MG-RAST) server revealed a genetic profile characteristic of heterotrophic lactic acid fermentation of carbohydrates, which was supported by the detection of mannitol, lactate, acetate, and ethanol as fermentation products. When the metagenomic reads were mapped onto the database of completed genomes, theLeuconostoc mesenteroidessubsp.mesenteroidesATCC 8293 andLactobacillus sakeisubsp.sakei23K genomes were highly represented. These same two genera were confirmed to be important in kimchi fermentation when the majority of kimchi metagenomic sequences showed very high identity toLeuconostoc mesenteroidesandLactobacillusgenes. Besides microbial genome sequences, a surprisingly large number of phage DNA sequences were identified from the cellular fractions, possibly indicating that a high proportion of cells were infected by bacteriophages during fermentation. Overall, these results provide insights into the kimchi microbial community and also shed light on fermentation processes carried out broadly by complex microbial communities.
Quantitative Metagenomic Analyses Based on Average Genome Size Normalization
Authors: Frank Jeremy A. , Sørensen Søren J. 
Published: February 2011

ABSTRACTOver the past quarter-century, microbiologists have used DNA sequence information to aid in the characterization of microbial communities. During the last decade, this has expanded from single genes to microbial community genomics, or metagenomics, in which the gene content of an environment can provide not just a census of the community members but direct information on metabolic capabilities and potential interactions among community members. Here we introduce a method for the quantitative characterization and comparison of microbial communities based on the normalization of metagenomic data by estimating average genome sizes. This normalization can relieve comparative biases introduced by differences in community structure, number of sequencing reads, and sequencing read lengths between different metagenomes. We demonstrate the utility of this approach by comparing metagenomes from two different marine sources using both conventional small-subunit (SSU) rRNA gene analyses and our quantitative method to calculate the proportion of genomes in each sample that are capable of a particular metabolic trait. With both environments, to determine what proportion of each community they make up and how differences in environment affect their abundances, we characterize three different types of autotrophic organisms: aerobic, photosynthetic carbon fixers (theCyanobacteria); anaerobic, photosynthetic carbon fixers (theChlorobi); and anaerobic, nonphotosynthetic carbon fixers (theDesulfobacteraceae). These analyses demonstrate how genome proportionality compares to SSU rRNA gene relative abundance and how factors such as average genome size and SSU rRNA gene copy number affect sampling probability and therefore both types of community analysis.
Natural Competence in the Hyperthermophilic ArchaeonPyrococcus furiosusFacilitates Genetic Manipulation: Construction of Markerless Deletions of Genes Encoding the Two Cytoplasmic Hydrogenases
Authors: Lipscomb Gina L. , Stirrett Karen , Schut Gerrit J. , Yang Fei , Jenney Francis E. , Scott Robert A. , Adams Michael W. W. , Westpheling Janet 
Published: February 2011

ABSTRACTIn attempts to develop a method of introducing DNA intoPyrococcus furiosus, we discovered a variant within the wild-type population that is naturally and efficiently competent for DNA uptake. ApyrFgene deletion mutant was constructed in the genome, and the combined transformation and recombination frequencies of this strain allowed marker replacement by direct selection using linear DNA. We have demonstrated the use of this strain, designated COM1, for genetic manipulation. Using genetic selections and counterselections based on uracil biosynthesis, we generated single- and double-deletion mutants of the two gene clusters that encode the two cytoplasmic hydrogenases. The COM1 strain will provide the basis for the development of more sophisticated genetic tools allowing the study and metabolic engineering of this important hyperthermophile.
Identification of Genetic Markers for Differentiation of Shiga Toxin-Producing, Enteropathogenic, and Avirulent Strains ofEscherichia coliO26
Authors: Bugarel Marie , Beutin Lothar , Scheutz Flemming , Loukiadis Estelle , Fach Patrick 
Published: February 2011

ABSTRACTShiga toxin-producingEscherichia coli(STEC) O26 is one of the top five enterohemorrhagicE. coli(EHEC) O groups most often associated with hemorrhagic colitis and hemolytic uremic syndrome (HUS) worldwide. STEC O26 is considered to have evolved from enteropathogenic (EPEC) O26 strains through the acquisition of Shiga toxin (Stx)-encoding genes. Our PCR data identified several STEC-like strains expressing all features of STEC except Stx production and carrying remnants of Stx phages that were probably derivatives of EHEC O26. EHEC and EPEC O26 strains phenotypically resemble O26 EHEC-like and apathogenicE. coliO26 strains and are therefore undistinguishable by cultural methods. A clear discrimination between the different O26 groups is required for diagnostics in patients and for control of food safety. To develop an assay for specific detection of EHEC and EHEC-like O26 strains, we used a high-throughput PCR approach for selection of discriminative genetic markers among 33 tested genes mostly encoding type III secretion system effector proteins. The genesECs1822,nleH1-2,nleA,nleC,nleH1-1,nleG,nleG2,nleG6-1,nleG6-2,espJ,espM2,nleG8-2,espG,ent(orespL2),nleB,nleE,efa1, andespBwere detected at different frequencies in O26 EHEC, EHEC-like, and EPEC strains, indicating the possible role of these genes in virulence of human pathogenic O26 strains. TheespKandespNgenes were detected only in EHEC and EHEC-like O26 strains.espKwas present in 99.14% of EHEC and 91.14% of EHEC-like O26 strains and was hence the best candidate as a genetic marker for characterizing these pathogroups. These data were corroborated by a genotyping real-time PCR test based on allelic discrimination of thearcA(aerobic respiratory control protein A) gene. The results indicate that a combination of molecular detection tools for O26wzx(wzxO26),eae-beta,stx,espK, andarcAgenotyping is highly discriminative for clear identification of EHEC and EHEC-likeE. coliO26 strains. This simple diagnostic test might be applicable in hospital service laboratories or public health laboratories to test strains isolated from stools of patients suffering from diarrhea.
Structure of the Periplasmic Stress Response Protein CpxP
Authors: Thede Gina L. , Arthur David C. , Edwards Ross A. , Buelow Daelynn R. , Wong Julia L. , Raivio Tracy L. , Glover J. N. Mark 
Published: February 2011

ABSTRACT

CpxP is a novel bacterial periplasmic protein with no homologues of known function. In Gram-negative enteric bacteria, CpxP is thought to interact with the two-component sensor kinase, CpxA, to inhibit induction of the Cpx envelope stress response in the absence of protein misfolding. CpxP has also been shown to facilitate DegP-mediated proteolysis of misfolded proteins. Six mutations that negate the ability of CpxP to function as a signaling protein are localized in or near two conserved LTXXQ motifs that define a class of proteins with similarity to CpxP, Pfam PF07813. To gain insight into how these mutations might affect CpxP signaling and/or proteolytic adaptor functions, the crystal structure of CpxP from
Escherichia coli
was determined to 2.85-Å resolution. The structure revealed an antiparallel dimer of intertwined α-helices with a highly basic concave surface. Each protomer consists of a long, hooked and bent hairpin fold, with the conserved LTXXQ motifs forming two diverging turns at one end. Biochemical studies demonstrated that CpxP maintains a dimeric state but may undergo a slight structural adjustment in response to the inducing cue, alkaline pH. Three of the six previously characterized
cpxP
loss-of-function mutations, M59T, Q55P, and Q128H, likely result from a destabilization of the protein fold, whereas the R60Q, D61E, and D61V mutations may alter intermolecular interactions.
Identification of a Chitin-Induced Small RNA That Regulates Translation of thetfoXGene, Encoding a Positive Regulator of Natural Competence in Vibrio cholerae
Authors: Yamamoto Shouji , Izumiya Hidemasa , Mitobe Jiro , Morita Masatomo , Arakawa Eiji , Ohnishi Makoto , Watanabe Haruo 
Published: February 2011

ABSTRACTThetfoX(also calledsxy) gene product is the central regulator of DNA uptake in the naturally competent bacteriaHaemophilus influenzaeandVibrio cholerae. However, the mechanisms regulatingtfoXgene expression in both organisms are poorly understood. Our previous studies revealed that inV. cholerae, chitin disaccharide (GlcNAc)2is needed to activate the transcription and translation ofV. cholerae tfoX(tfoXVC) to induce natural competence. In this study, we screened a multicopy library ofV. choleraeDNA fragments necessary for translational regulation oftfoXVC. A clone carrying theVC2078-VC2079intergenic region, designatedtfoR, increased the expression of atfoXVC::lacZtranslational fusion constructed inEscherichia coli. Using atfoXVC::lacZreporter system inV. cholerae, we confirmed thattfoRpositively regulatedtfoXVCexpression at the translational level. Deletion oftfoRabolished competence for exogenous DNA even when (GlcNAc)2was provided. The introduction of a plasmid clone carrying thetfoR+gene into thetfoRdeletion mutant complemented the competence deficiency. We also found that thetfoRgene encodes a 102-nucleotide small RNA (sRNA), which was transcriptionally activated in the presence of (GlcNAc)2. Finally, we showed that this sRNA activated translation fromtfoXVCmRNA in a highly purifiedin vitrotranslation system. Taking these results together, we propose that in the presence of (GlcNAc)2, TfoR sRNA is expressed to activate the translation oftfoXVC, which leads to the induction of natural competence.
Subpopulation-Specific Transcriptome Analysis of Competence-Stimulating-Peptide-Induced Streptococcus mutans
Authors: Lemme André , Gröbe Lothar , Reck Michael , Tomasch Jürgen , Wagner-Döbler Irene 
Published: February 2011

ABSTRACT

Competence-stimulating-peptide (CSP)-mediated competence development in
Streptococcus mutans
is a transient and biphasic process, since only a subpopulation induces the expression of ComX in the presence of CSP, and the activation of the DNA uptake machinery in this fraction shuts down ∼3 to 4 h postinduction. Here, we combine for the first time, to our knowledge, the bacterial flow-cytometric sorting of cells and subpopulation-specific transcriptome analysis of both the competent and noncompetent fraction of CSP-treated
S. mutans
cells. Sorting was guided by a ComX-green fluorescent protein (ComX-GFP) reporter, and the transcriptome analysis demonstrated the successful combination of both methods, because a strong enrichment of transcripts for
comX
and its downstream genes was achieved. Three two-component systems were expressed in the competent fraction, and among them was ComDE. Moreover, the recently identified regulator system ComR/S was expressed exclusively in the competent fraction. In contrast, the expression of bacteriocin-related genes was at the same level in all cells. GFP reporter strains for ComE and CipB (mutacin V) confirmed this expression pattern on the single-cell level. Fluorescence microscopy revealed that some ComX-expressing cells committed autolysis in an early stage of competence initiation. In viable ComX-expressing cells, the uptake of DNA could be shown on the single-cell level. This study demonstrates that all cells in the population respond to CSP through the activation of bacteriocin-related genes. Some of these cells start to activate ComX expression but then segregate into two subpopulations, one becoming competent and another one that lyses, resulting in intrapopulation diversity.
Transarterial embolization with ONYX for treatment of intracranial non-cavernous dural arteriovenous fistula with or without cortical venous reflux
Authors: De Keukeleire Katrien , Vanlangenhove Peter , Kalala Okito Jean-Pierre , Hallaert Giorgio , Van Roost Dirk , Defreyne Luc 
Published: February 2011

Background and purposeTo report our experience with transarterial ONYX embolization of intracranial non-cavernous dural arteriovenous fistulas (DAVFs) with or without cortical venous reflux.Materials and methodsRetrospective analysis of transarterial ONYX embolization in 20 patients with 21 DAVFs, presenting with intracranial hemorrhage (n=7), pulsatile bruit (n=7), vertigo (n=3), non-pulsatile bruit (n=1), headache (n=1) and epilepsy (n=1). Risk grading of DAVFs was Borden type I (n=6), type II (n=4) and type III (n=11).Results18 of 21 (85.7%) DAVFs were angiographically occluded immediately after embolization, with ONYX embolization only, in either one (n=12) or two sessions (n=2); with a combination of ONYX and glue or transvenous coiling in a single session (n=2) or in two sessions (n=1); or after previous transvenous coiling/glue embolization (n=1). At the 6 (4–14) month control digital subtraction angiography (DSA), available in 14 of 18 occluded DAVFs, one patient showed a small residual fistula (17/21 or 81% occluded). Mid-term DSA was not available because of early death (n=2) or patients were awaiting the examination (n=2). In three cases, treatment was incomplete. Of six Borden type I DAVFs, four were cured and two partially occluded with resolution of symptoms. In two DAVFs, neurosurgical access to the feeding artery allowed distal microcatheterization and successful embolization.ConclusionTransarterial ONYX embolization offers an effective and safe treatment for all non-cavernous DAVFs, whether with or without cortical venous reflux.
Trends in mortality from appendicitis and from gallstone disease in English populations, 1979–2006: study of multiple-cause coding of deaths
Authors: Goldacre Michael J , Duncan Marie E , Griffith Myfanwy , Davidson Matt 
Published: February 2011

ABSTRACT

Objective
To report on trends in mortality from appendicitis and from gallstone disease.

Design and setting
Analysis of data from death certificates including all certified causes of death, termed ‘mentions’, not just the underlying cause, using data from Oxford (‘mentions’ available from 1979 to 2006) and all England (‘mentions’ available from 1995 to 2006).

Outcome measures
Mortality rates across all years studied, and in periods defined by changes to national rules in selecting the underlying cause of death.

Results
In the Oxford region, mortality rates for appendicitis based on underlying cause fluctuated between periods defined by coding rule changes. Those based on mentions were more stable: they were 3.3 per million population in 1979–83 and 3.5 in 2001–6. Nationally, mentions-based rates fell from 3.4 per million in 1995–2000 to 3.1 in 2001–2006, a small but statistically significant decline. For gallstone disease in Oxford, rates fell in the early years but then levelled off. Mortality rates for gallstones in England actually rose slightly between 1995–2000 (15.0 deaths per million) and 2001–6 (15.6 per million). The majority of deaths from appendicitis and gallstone disease were in the elderly.

Conclusions
Appendicitis and gallstones are considered to be avoidable causes of death. Mortality rates for each cause have not shown any substantial falls in the recent periods covered by this study. It is possible that deaths were not, in fact, avoidable, but audits into the circumstances of deaths from these diseases may be warranted. Mortality data based on underlying cause alone substantially underestimate deaths from these two conditions.
Using the ISBAR handover tool in junior medical officer handover: a study in an Australian tertiary hospital
Authors: Thompson James E , Collett Luke W , Langbart Marc J , Purcell Natalie J , Boyd Stephanie M , Yuminaga Yuigi , Ossolinski Gemma , Susanto Clarissa , McCormack Ann 
Published: February 2011

ABSTRACT

Background
Despite being essential to patient care, current clinical handover practices are inconsistent and error prone. Efforts to improve handover have attracted attention recently, with the ISBAR tool increasingly utilised as a format for structured handover communication. However, ISBAR has not been validated in a junior medical officer setting.

Objective
To assess the effect of the ISBAR handover tool on junior medical officer (JMO) handover communication in an Australian hospital.

Methods
JMOs who participated in after-hours handover during an 11 week clinical term from June to August 2009 were recruited. After-hours handover was audiotaped, and JMOs completed a survey to assess current handover perception and practice. JMOs then participated in a 1 h education session on handover and use of the ISBAR handover tool, and were encouraged to handover using this method. Following the education session, participants were surveyed to measure perceived changes in handover with use of ISBAR, and handover was again audiotaped to assess differences in information transfer and duration.

Results
Following the introduction of ISBAR, 25/36 (71%) of JMOs felt there was an overall improvement in handover communication. Specifically, they perceived improvement in the structure and consistency of handover, they felt more confident receiving handover, and they believed patient care and safety were improved. Audio-tape data demonstrated increased transfer of key clinical information during handover with no significant effect on handover duration.

Conclusions
Use of the ISBAR tool improves JMO perception of handover communication in a time neutral fashion. Consideration should be given to the introduction of ISBAR in all JMO handover settings.
International disease monitoring, October to December, 2010
Authors: Roberts H. , Lopez M. , Hartley M. 
Published: February 2011

African swine fever in the Caucasus and Leningrad regions of Russia
Equine infectious anaemia in several EU member states
Foot‐and‐mouth disease in Bulgaria – the first in an EU member state since 2007
Highly pathogenic avian influenza H5N1 in the Far East
West Nile virus in southern Europe
These are among matters discussed in the international disease monitoring report for October to December 2010, prepared by Defra's Food and Farming Group, Veterinary Science Team