bluuebunny/crossref_metadata_2025 huggingface dataset:
Suppression of initiation defects of chromosome replication in Bacillus subtilis dnaA and oriC-deleted mutants by integration of a plasmid replicon into the chromosomes
Authors: Hassan A K , Moriya S , Ogura M , Tanaka T , Kawamura F , Ogasawara N
Published: November 2016

We constructed Bacillus subtilis strains in which chromosome replication initiates from the minimal replicon of a plasmid isolated from Bacillus natto, independently of oriC. Integration of the replicon in either orientation at the proA locus (115 degrees on the genetic map) suppressed the temperature-sensitive phenotype caused by a mutation in dnaA, a gene required for initiation of replication from oriC. In addition, in a strain with the plasmid replicon integrated into the chromosome, we were able to delete sequences required for oriC function. These strains were viable but had a slower growth rate than the oriC+ strains. Marker frequency analysis revealed that both pyrD and metD, genes close to proA, showed the highest values among the markers (genes) measured, and those of other markers decreased symmetrically with distance from the site of the integration (proA). These results indicated that the integrated plasmid replicon operated as a new and sole origin of chromosome replication in these strains and that the mode of replication was bidirectional. Interestingly, these mutants produced anucleate cells at a high frequency (about 40% in exponential culture), and the distribution of chromosomes in the cells was irregular. A change in the site and mechanism (from oriC to a plasmid system) of initiation appears to have resulted in a drastic alteration in coordination between chromosome replication and chromosome partition or cell division.
The pst operon of Bacillus subtilis has a phosphate-regulated promoter and is involved in phosphate transport but not in regulation of the pho regulon
Authors: Qi Y , Kobayashi Y , Hulett F M
Published: November 2016

Genes from Bacillus subtilis predicted to encode a phosphate-specific transport (Pst) system were shown by mutation to affect high-affinity Pi uptake but not arsenate resistance or phosphate (Pho) regulation. The transcription start of the promoter upstream of the pstS gene was defined by primer extension. The promoter contains structural features analogous to the Escherichia coli pst promoter but not sequence similarity. Expression from this promoter was induced >5,000-fold upon phosphate starvation and regulated by the PhoP-PhoR two-component regulatory system. These data indicate that the pst operon is involved in phosphate transport and is a member of the Pho regulon but is not involved in Pi regulation.
Genetic characterization and expression in heterologous hosts of the 3-(3-hydroxyphenyl)propionate catabolic pathway of Escherichia coli K-12
Authors: Ferrández A , Garciá J L , Díaz E
Published: November 2016

We report the complete nucleotide sequence of the gene cluster encoding the 3-(3-hydroxyphenyl)propionate (3-HPP) catabolic pathway of Escherichia coli K-12. Sequence analysis revealed the existence of eight genes that map at min 8 of the chromosome, between the lac and hemB regions. Six enzyme-encoding genes account for a flavin-type monooxygenase (mhpA), the extradiol dioxygenase (mhpB), and the meta-cleavage pathway (mhpCDFE). The order of these catabolic genes, with the sole exception of mhpF, parallels that of the enzymatic steps of the pathway. The mhpF gene may encode the terminal acetaldehyde dehydrogenase (acylating) not reported previously in the proposed pathway. Enzymes that catalyze the early reactions of the pathway, MhpA and MhpB, showed the lowest level of sequence similarity to analogous enzymes of other aromatic catabolic pathways. However, the genes mhpCDFE present the same organization and appear to be homologous to the Pseudomonas xyl, dmp, and nah meta-pathway genes, supporting the hypothesis of the modular evolution of catabolic pathways and becoming the first example of this type of catabolic module outside the genus Pseudomonas. Two bacterial interspersed mosaic elements were found downstream of the mhpABCDFE locus and flank a gene, orfT, which encodes a protein related to the superfamily of transmembrane facilitators that might be associated with transport. All of the genes of the 3-HPP cluster are transcribed in the same direction, with the sole exception of mhpR. Inducible expression of the mhp catabolic genes depends upon the presence, in the cis or trans position, of a functional mhpR gene, which suggests that the mhpR gene product is the activator of the 3-HPP biodegradative pathway. The primary structure of MhpR revealed significant similarities to that of members of the IclR subfamily of transcriptional regulators. A 3-HPP catabolic DNA cassette was engineered and shown to be functional not only in enteric bacteria (E. coli and Salmonella typhimurium) but also in Pseudomonas putida and Rhizobium meliloti, thus facilitating its potential application to improve the catabolic abilities of bacterial strains for degradation of aromatic compounds.
The trp RNA-binding attenuation protein regulates TrpG synthesis by binding to the trpG ribosome binding site of Bacillus subtilis
Authors: Du H , Tarpey R , Babitzke P
Published: November 2016

The trpG gene of Bacillus subtilis encodes a glutamine amidotransferase subunit which is involved in the biosynthesis of L-tryptophan and folic acid. The trp RNA-binding attenuation protein (TRAP) is involved in controlling expression of trpG at the level of translation in response to changes in the intracellular concentration of tryptophan. We performed in vitro experiments using purified TRAP to elucidate the mechanism of TRAP-dependent trpG regulation. A TRAP-trpG RNA footprint analysis showed that tryptophan-activated TRAP interacts with one UAG, one AAG, and seven GAG repeats present in the trpG transcript. Results from ribosome and TRAP toeprint experiments indicated that the ribosome and TRAP binding sites overlap. Experiments with a B. subtilis cell-free translation system demonstrated that TRAP inhibits TrpG synthesis. Thus, TRAP regulates translation of trpG by blocking ribosome access to the trpG ribosome binding site. Our results are consistent with a model in which each tryptophan-activated TRAP subunit interacts with one trinucleotide repeat in an RNA target, thereby wrapping the transcript around the periphery of the TRAP complex.
Specificity of tRNA-mRNA interactions in Bacillus subtilis tyrS antitermination
Authors: Grundy F J , Hodil S E , Rollins S M , Henkin T M
Published: November 2016

The Bacillus subtilis tyrS gene, encoding tyrosyl-tRNA synthetase, is a member of the T-box family of genes, which are regulated by control of readthrough of a leader region transcriptional terminator. Readthrough is induced by interaction of the cognate uncharged tRNA with the leader; the system responds to decreased tRNA charging, caused by amino acid limitation or insufficient levels of the aminoacyl-tRNA synthetase. Recognition of the cognate tRNA is mediated by pairing of the anticodon of the tRNA with the specifier sequence of the leader, a codon specifying the appropriate amino acid; a second interaction between the acceptor end of the tRNA and an antiterminator structure is also important. Certain switches of the specifier sequence to a new codon result in a switch in the specificity of the amino acid response, while other switches do not. These effects may reflect additional sequence or structural requirements for the mRNA-tRNA interaction. This study includes investigation of the effects of a large number of specifier sequence switches in tyrS and analysis of structural differences between tRNA(Tyr) and tRNA species which interact inefficiently with the tyrS leader to promote antitermination.
Gene duplications in evolution of archaeal family B DNA polymerases
Authors: Edgell D R , Klenk H P , Doolittle W F
Published: November 2016

All archaeal DNA-dependent DNA polymerases sequenced to date are homologous to family B DNA polymerases from eukaryotes and eubacteria. Presently, representatives of the euryarchaeote division of archaea appear to have a single family B DNA polymerase, whereas two crenarchaeotes, Pyrodictium occultum and Sulfolobus solfataricus, each possess two family B DNA polymerases. We have found the gene for yet a third family B DNA polymerase, designated B3, in the crenarchaeote S. solfataricus P2. The encoded protein is highly divergent at the amino acid level from the previously characterized family B polymerases in S. solfataricus P2 and contains a number of nonconserved amino acid substitutions in catalytic domains. We have cloned and sequenced the ortholog of this gene from the closely related Sulfolobus shibatae. It is also highly divergent from other archaeal family B DNA polymerases and, surprisingly, from the S. solfataricus B3 ortholog. Phylogenetic analysis using all available archaeal family B DNA polymerases suggests that the S. solfataricus P2 B3 and S. shibatae B3 paralogs are related to one of the two DNA polymerases of P. occultum. These sequences are members of a group which includes all euryarchaeote family B homologs, while the remaining crenarchaeote sequences form another distinct group. Archaeal family B DNA polymerases together constitute a monophyletic subfamily whose evolution has been characterized by a number of gene duplication events.
Arginine biosynthesis and regulation in Lactobacillus plantarum: the carA gene and the argCJBDF cluster are divergently transcribed
Authors: Bringel F , Frey L , Boivin S , Hubert J C
Published: November 2016

A cluster of citrulline biosynthetic genes has been cloned and sequenced from a fragment of Lactobacillus plantarum CCM 1904 (ATCC 8014) DNA isolated as complementing a Bacillus subtilis argF mutation. The gene order was carA-argCJBDF, with carA transcribed divergently from the arg cluster. Although other gram-positive bacteria show similar arg clusters, this arrangement for carA is thus far unprecedented. Downstream from the arg cluster, two open reading frames (ORF7 and ORF8) having unknown functions were found. Sequence analysis of the end of a 10.5-kb cloned DNA fragment showed that argF was 3.5 kb from the ldhL gene coding for L-(+)-lactate dehydrogenase. A tree representation of amino acid sequence clustering relationships of 31 ornithine carbamoyltransferases (OTCases) from various organisms revealed two prokaryotic groups: one with ArgF of L. plantarum and one with ArgF of B. subtilis, which are paralogous. This divergence was not observed in vivo because an L. plantarum argF mutant (AM 1215) harboring no OTCase activity was complemented by the argF genes of L. plantarum and B. subtilis. No OTCase activity was detectable when L. plantarum was grown in the presence of saturating amounts of arginine or citrulline. Arginine may repress the citrulline biosynthetic genes in L. plantarum by using 11 identified DNA motifs which resemble the Escherichia coli ARG box consensus and which are in most cases separated by multiples of 11 bp, corresponding to a DNA helical turn. The carA and argCJBDF genes are divergently transcribed. Their putative promoters are 6 bp apart and are partially overlapped by putative ARG boxes, suggesting concerted transcription regulation.
A fusion promoter created by a new insertion sequence, IS1490, activates transcription of 2,4,5-trichlorophenoxyacetic acid catabolic genes in Burkholderia cepacia AC1100
Authors: Hübner A , Hendrickson W
Published: November 2016

Transposition and transcriptional activation by insertion sequences in Burkholderia cepacia AC1100 were investigated. Two closely related new elements, IS1413 and IS1490, were identified and characterized. These elements are not highly related to other insertion sequences identified in AC1100 or other B. cepacia isolates. Based on their structures and the sequences of the inverted terminal repeats and the putative transposase protein, the insertion elements (IS elements) are similar to IST2 of Thiobacillus ferrooxidans and several related elements. All the IS elements that have been identified in this strain are found in multiple copies (10 to 40), and they have high-level promoter activity capable of stimulating transcription from a distance up to 500 bp from a target gene. Strain AC1100 was originally isolated after prolonged selection for the ability to utilize the herbicide 2,4,5-trichlorophenoxyacetic acid (2,4,5-T) as a sole carbon source. Three IS elements are located near the first gene of the 2,4,5-T catabolic pathway, tftA. IS1490 inserted 110 bp upstream of tftA and created a fusion promoter responsible for constitutive transcription of the gene. Our results confirm the hypothesis that IS elements play a central role in transcription of 2,4,5-T genes and likely have stimulated rapid evolution of the metabolic pathway.
Unusual fatty acid compositions of the hyperthermophilic archaeon Pyrococcus furiosus and the bacterium Thermotoga maritima
Authors: Carballeira N M , Reyes M , Sostre A , Huang H , Verhagen M F , Adams M W
Published: November 2016

The fatty acid compositions of the hyperthermophilic microorganisms Thermotoga maritima and Pyrococcus furiosus were studied and compared. A total of 37 different fatty acids were identified in T. maritima, including the novel 13,14-dimethyloctacosanedioic acid. In contrast, a total of 18 different fatty acids were characterized, as minor components, in P. furiosus, and these included saturated, monounsaturated, and dicarboxylic acids. This is the first report of fatty acids from an archaeon.
Characterization of the genes encoding a receptor-like histidine kinase and a cognate response regulator from a biphenyl/polychlorobiphenyl-degrading bacterium, Rhodococcus sp. strain M5
Authors: Labbé D , Garnon J , Lau P C
Published: November 2016

We report the cloning, sequence, and expression of the bpdS and bpdT genes from Rhodococcus sp. strain M5, which are believed to encode the first two-component signal transduction system in the genus Rhodococcus, which potentially regulates biphenyl/polychlorobiphenyl metabolism in M5. BpdT has a typical responses regulator sequence (209 amino acids; 23 kDa), whereas BpdS, the predicted histidine kinase component, is an unusually large transmembrane protein (1,576 amino acids; 170 kDa) that contains ATP-binding and leucine-rich repeat motifs and some conserved residues of protein kinases. Expression of bpdST, like that of the bpdC1C2BADE degradative operon, is inducible by biphenyl.
Identification of Strain-Specific Sequences That Distinguish a Mycoplasma gallisepticum Vaccine Strain from Field Isolates
Authors: Ricketts Camir , Pickler Larissa , Maurer John , Ayyampalayam Saravanaraj , García Maricarmen , Ferguson-Noel Naola M.
Published: November 2016

Despite attempts to control avian mycoplasmosis through management, vaccination, and surveillance,
Mycoplasma gallisepticum
continues to cause significant morbidity, mortality, and economic losses in poultry production. Live attenuated vaccines are commonly used in the poultry industry to control avian mycoplasmosis; unfortunately, some vaccines may revert to virulence and vaccine strains are generally difficult to distinguish from natural field isolates. In order to identify genome differences among vaccine revertants, vaccine strains, and field isolates, whole-genome sequencing of the
M. gallisepticum
vaccine strain ts-11 and several “ts-11-like” strains isolated from commercial flocks was performed using Illumina and 454 pyrosequencing and the sequenced genomes compared to the
M. gallisepticum
R
low
reference genome. The collective contigs for each strain were annotated using the fully annotated
Mycoplasma
reference genome. The analysis revealed genetic differences among
vlhA
alleles, as well as among genes annotated as coding for a cell wall surface anchor protein (
mg0377
) and a hypothetical protein gene,
mg0359
, unique to
M. gallisepticum
ts-11 vaccine strain. PCR protocols were designed to target 5 sequences unique to the
M. gallisepticum
ts-11 strain:
vlhA
3.04a,
vlhA
3.04b,
vlhA
3.05,
mg0377
, and
mg0359
. All ts-11 isolates were positive for the five gene alleles tested by PCR; however, 5 to 36% of field isolates were also positive for at least one of the alleles tested. A combination of PCR tests for
vlhA
3.04a,
vlhA
3.05, and
mg0359
was able to distinguish the
M. gallisepticum
ts-11 vaccine strain from field isolates. This method will further supplement current approaches to quickly distinguish
M. gallisepticum
vaccine strains from field isolates.
Multicenter Pivotal Clinical Trial of Urine Malaria Test for Rapid Diagnosis of Plasmodium falciparum Malaria
Authors: Oyibo Wellington A. , Ezeigwe Nnenna , Ntadom Godwin , Oladosu Oladipo O. , Rainwater-Loveth Kaitlin , O'Meara Wendy , Okpokoro Evaezi , Brieger William
Published: November 2016

The need to expand malaria diagnosis capabilities alongside policy requirements for mandatory testing before treatment motivates exploration of noninvasive rapid diagnostic tests (RDTs). We report the outcome of the first cross-sectional, single-blind clinical performance evaluation of a urine malaria test (UMT) for diagnosis of
Plasmodium falciparum
malaria in febrile patients. Matched urine and finger-prick blood samples from participants ≥2 years of age with fever (axillary temperature of ≥37.5°C) or with a history of fever in the preceding 48 h were tested with UMT and microscopy (as the gold standard). BinaxNOW (Pf and Pan versions) blood RDTs were done to assess relative performance. Urinalysis and rheumatoid factor (RF) tests were conducted to evaluate possible interference. Diagnostic performance characteristics were computed at 95% confidence intervals (CIs). Of 1,800 participants screened, 1,691 were enrolled; of these 566 (34%) were febrile, and 1,125 (66%) were afebrile. Among enrolled participants, 341 (20%) tested positive by microscopy, 419 (25%) were positive by UMT, 676 (40%) were positive by BinaxNOW Pf, and 368 (22%) were positive by BinaxNow Pan. UMT sensitivity among febrile patients (for whom the test was indicated) was 85%, and specificity was 84%. Among febrile children ≤5 years of age, UMT sensitivity was 93%, and specificity was 83%. The area under the receiver-operator characteristic curve (AUC) of UMT (0.84) was not significantly different from that of BinaxNOW Pf (0.86) or of BinaxNOW Pan (0.87), indicating that the tests do not differ in overall performance. Gender, seasons, and RF did not impact UMT performance. Leukocytes, hematuria, and urobilinogen concentrations in urine were associated with lower UMT specificities. UMT performance was comparable to that of the BinaxNOW Pf/Pan tests, making UMT a promising tool to expand malaria testing in public and private health care settings where there are challenges to blood-based malaria diagnosis testing.
Underestimated Amoebic Appendicitis among HIV-1-Infected Individuals in Japan
Authors: Kobayashi Taiichiro , Watanabe Koji , Yano Hideaki , Murata Yukinori , Igari Toru , Nakada-Tsukui Kumiko , Yagita Kenji , Nozaki Tomoyoshi , Kaku Mitsuo , Tsukada Kunihisa , Gatanaga Hiroyuki , Kikuchi Yoshimi , Oka Shinichi
Published: November 2016

Entamoeba histolytica
is not a common causative agent of acute appendicitis. However, amoebic appendicitis can sometimes be severe and life threatening, mainly due to a lack of awareness. Also, its frequency, clinical features, and pathogenesis remain unclear. The study subjects were HIV-1-infected individuals who presented with acute appendicitis and later underwent appendectomy at our hospital between 1996 and 2014. Formalin-fixed paraffin-embedded preserved appendix specimens were reexamined by periodic acid-Schiff (PAS) staining and PCR to identify undiagnosed amoebic appendicitis. Appendectomies were performed in 57 patients with acute appendicitis. The seroprevalence of
E. histolytica
was 33% (14/43) from the available stored sera. Based on the medical records, only 3 cases were clinically diagnosed as amoebic appendicitis, including 2 diagnosed at the time of appendectomy and 1 case diagnosed by rereview of the appendix after the development of postoperative complications. Retrospective analyses using PAS staining and PCR identified 3 and 3 more cases, respectively. Thus,
E. histolytica
infection was confirmed in 9 cases (15.8%) in the present study. Apart from a significantly higher leukocyte count in
E. histolytica
-positive patients than in negative patients (median, 13,760 versus 10,385 cells/μl, respectively,
P
= 0.02), there were no other differences in the clinical features of the PCR-positive and -negative groups. In conclusion,
E. histolytica
infection was confirmed in 9 (15.8%) of the appendicitis cases. However, only 3, including one diagnosed after intestinal perforation, were diagnosed before the present analyses. These results strongly suggest there is frequently a failure to detect trophozoites in routine examination, resulting in an underestimation of the incidence of amoebic appendicitis.
Atypical presentation of appendicitis
Authors: Beaumont Oliver , Miller Robert , Guy Richard
Published: November 2016

A woman aged 64 years presented as an emergency with a mass in the right iliac fossa, clinically within the abdominal wall, but an otherwise soft abdomen. Systemically, she was quite well with normal vital signs. Blood tests revealed raised inflammatory markers, and an abdominal CT scan demonstrated a perforated appendix with associated large subcutaneous abscess. This represents a rare presentation of a common condition, demonstrating how appendicitis can still be a challenging problem for the clinician. The patient underwent incision and drainage of the abscess, resulting in the formation of an enterocutaneous fistula (ECF). This was managed with enteral nutritional support, wound dressings and antibiotics. Following normal CT imaging, an ileocaecal resection was planned in the expectation that the ECF would persist. The operation was postponed due to intercurrent illness, during which time her symptoms and the ECF fully resolved.
Screening and management of viral hepatitis and hepatocellular carcinoma in Mongolia: results from a survey of Mongolian physicians from all major provinces of Mongolia
Authors: Kim Yoona A , Estevez Jacqueline , Le An , Israelski Dennis , Baatarkhuu Oidov , Sarantuya Tserenchimed , Narantsetseg Sonom , Nymadawa Pagbajabyn , H Le Richard , Yuen Man-Fung , Dusheiko Geoffrey , Rizzetto Mario , Nguyen Mindie H
Published: November 2016

Background

According to Globocan, Mongolia has the highest worldwide hepatocellular carcinoma (HCC) incidence (78.1/100 000, 3.5× higher than China).

Aims and methods

We conducted an anonymous survey of physicians from major provinces who attended an educational liver symposium, analysing their demography, practice, knowledge, perceptions and proposed solutions. Multivariate logistic regression was used to estimate OR relating demography and practice factors with higher provider knowledge and improvement.

Results

Of the 121 attendees, 44–95 (36–79%) responded to each question. Most were female (87%), young (79% age <50), subspecialists (81%), university-affiliated (74%), and practised in urban areas (61%). The mean pretest and post-test scores per physician were 60.4±20.4 and 65.6±21.3, with no observed significant predictors for baseline knowledge or improvement. Most (>80%) noted that <50% of patients who need hepatitis or HCC screening receive it. The main perceived barriers to screening were inability to pay for tests, lack of guidelines and poor patient awareness. Hepatitis treatment rates were low; 83% treated hepatitis C virus in <10 patients in the past year, and 86% treated hepatitis B virus in <10 patients/month. Treatment barriers were multifactorial, with cost as a principal barrier. Proposed solutions were universal screening policies (46%), removal of financial barriers (28%) and provider education (20%).

Conclusions

Physicians from major regions of Mongolia noted low screening for viral hepatitis, even lower treatment rates, financial barriers and the need for increased educational efforts. We advocate broad-based medical education tailored to local needs and based on needs assessment and outcome measurements.
Maternal inflammatory bowel disease and hypospadias in male offspring: a population-based study in Denmark
Authors: Andersen Ane Birgitte Telén , Ehrenstein Vera , Erichsen Rune , Frøslev Trine , Sørensen Henrik Toft
Published: November 2016

Background

The occurrence of inflammatory bowel disease (IBD) and hypospadias has been concurrently increasing, possibly through shared environmental risk factors such as endocrine disrupting compounds. Also, maternal IBD may disturb the normal development of the fetal reproductive tract. However, whether maternal IBD increases the risk of hypospadias in male offspring is unknown. We compared hypospadias risk in sons of mothers with and without IBD.

Methods

We used Danish nationwide population-based registries to conduct a longitudinal prevalence study including all live-born boys from 1979 through 2009. We computed HRs, as estimates of prevalence ratios (PRs), with 95% CIs for hypospadias, using Cox proportional hazards regression, while adjusting for measured confounding.

Results

Among 966 038 live-born boys, 4688 (0.5%) had a mother with a history of IBD diagnosis before the relevant childbirth. Among the boys with maternal IBD, 36 (0.8%) were diagnosed with hypospadias any time after birth, whereas 6112 (0.6%) sons of mothers without IBD diagnosis had hypospadias (adjusted PR: 1.20, (95% CI 0.86 to 1.67). Adjusted PRs for maternal Crohn's disease and ulcerative colitis were 1.38 (95% CI 0.83 to 2.29) and 1.10 (95% CI 0.71 to 1.68), respectively. Analyses defining hypospadias diagnosis recorded <6 months postpartum showed similar results.

Conclusions

We found no convincing evidence of an association between maternal IBD and hypospadias.
Emotions and encounters with healthcare professionals as predictors for the self-estimated ability to return to work: a cross-sectional study of people with heart failure
Authors: Nordgren Lena , Söderlund Anne
Published: November 2016

Objectives

To live with heart failure means that life is delimited. Still, people with heart failure can have a desire to stay active in working life as long as possible. Although a number of factors affect sick leave and rehabilitation processes, little is known about sick leave and vocational rehabilitation concerning people with heart failure. This study aimed to identify emotions and encounters with healthcare professionals as possible predictors for the self-estimated ability to return to work in people on sick leave due to heart failure.

Design

A population-based cross-sectional study design was used.

Setting

The study was conducted in Sweden. Data were collected in 2012 from 3 different sources: 2 official registries and 1 postal questionnaire.

Participants

A total of 590 individuals were included.

Statistics

Descriptive statistics, correlation analysis and linear multiple regression analysis were used.

Results

3 variables, feeling strengthened in the situation (β=−0.21, p=0.02), feeling happy (β=−0.24, p=0.02) and receiving encouragement about work (β=−0.32, p≤0.001), were identified as possible predictive factors for the self-estimated ability to return to work.

Conclusions

To feel strengthened, happy and to receive encouragement about work can affect the return to work process for people on sick leave due to heart failure. In order to develop and implement rehabilitation programmes to meet these needs, more research is needed.
Factors facilitating a national quality registry to aid clinical quality improvement: findings of a national survey
Authors: Eldh Ann Catrine , Wallin Lars , Fredriksson Mio , Vengberg Sofie , Winblad Ulrika , Halford Christina , Dahlström Tobias
Published: November 2016

Objectives

While national quality registries (NQRs) are suggested to provide opportunities for systematic follow-up and learning opportunities, and thus clinical improvements, features in registries and contexts triggering such processes are not fully known. This study focuses on one of the world's largest stroke registries, the Swedish NQRRiksstroke, investigating what aspects of the registry and healthcare organisations facilitate or hinder the use of registry data in clinical quality improvement.

Methods

Following particular qualitative studies, we performed a quantitative survey in an exploratory sequential design. The survey, including 50 items on context, processes and the registry, was sent to managers, physicians and nurses engaged in Riksstroke in all 72 Swedish stroke units. Altogether, 242 individuals were presented with the survey; 163 responded, representing all but two units. Data were analysed descriptively and through multiple linear regression.

Results

A majority (88%) considered Riksstroke data to facilitate detection of stroke care improvement needs and acknowledged that their data motivated quality improvements (78%). The use of Riksstroke for quality improvement initiatives was associated (R2=0.76) with ‘Colleagues’ call for local results’ (p=<0.001), ‘Management Request of Registry data’ (p=<0.001), and it was said to be ‘Simple to explain the results to colleagues’ (p=0.02). Using stepwise regression, ‘Colleagues’ call for local results’ was identified as the most influential factor. Yet, while 73% reported that managers request registry data, only 39% reported that their colleagues call for the unit's Riksstroke results.

Conclusions

While an NQR like Riksstroke demonstrates improvement needs and motivates stakeholders to make progress, local stroke care staff and managers need to engage to keep the momentum going in terms of applying registry data when planning, performing and evaluating quality initiatives.
Protocol for the Mindful Student Study: a randomised controlled trial of the provision of a mindfulness intervention to support university students' well-being and resilience to stress
Authors: Galante Julieta , Dufour Geraldine , Benton Alice , Howarth Emma , Vainre Maris , Croudace Timothy J , Wagner Adam P , Stochl Jan , Jones Peter B
Published: November 2016

Introduction

Levels of stress in UK university students are high, with an increase in the proportion of students seeking help in recent years. Academic pressure is reported as a major trigger. Mindfulness training has been shown to reduce stress and is popular among students, but its effectiveness in this context needs to be ascertained. In this pragmatic randomised controlled trial, we hypothesise that the provision of a preventative mindfulness intervention in universities could reduce students' psychological distress during the examination period (primary outcome), improve their resilience to stress up to at least 1 year later, reduce their use of mental health support services and improve academic performance.

Methods and analysis

At least 550 University of Cambridge students free from active crises or severe mental illness will be randomised to joining an 8-week mindfulness course or to mental health provision as usual (one-to-one allocation rate). Psychological distress will be measured using the Clinical Outcomes in Routine Evaluation Outcome Measure at baseline, postintervention, examination term and 1-year follow-up. Other outcomes are use of mental health services, inability to sit examinations or special circumstance requests, examination grades, well-being, altruism and coping measured with ecological momentary assessment. Outcome assessment and intention-to-treat primary analysis using linear mixed models adjusted for baseline scores will be blind to intervention allocation. We will also conduct per-protocol, subgroup and secondary outcome analyses. An Independent Data Monitoring and Ethics Committee will be set up. We will systematically monitor for, and react to, possible adverse events. An advisory reference group will comprise student representatives, members of the University Counselling Service and other student welfare staff.

Ethics and dissemination

Approval has been obtained from Cambridge Psychology Research Ethics Committee (PRE.2015.060). Results will be published in peer-reviewed journals. A lay summary will be disseminated to a wider audience including other universities.

Trial registration number

ACTRN12615001160527; pre-results.
Prevalence and associated factors of facial palsy and lifestyle characteristics: data from the Korean National Health and Nutrition Examination Survey 2010–2012
Authors: Chang Young-Soo , Choi Ji Eun , Kim Seon Woo , Baek Sun-Young , Cho Yang-Sun
Published: November 2016

Objectives

To report the nationwide prevalence of facial palsy (FP) of grade III or worse in the House–Brackmann (H–B) grading system in South Korea and assess the associated factors.

Design

Cross-sectional analysis of a nationwide health survey.

Settings

South Korea.

Methods

We obtained data from the 2010 to 2012 Korea National Health and Nutrition Examination Surveys, which were cross-sectional surveys of the South Korean civilian population living in households and aged ≥1 year (N=23 533). A field survey team performed interviews, physical examinations and laboratory tests. Facial expression was evaluated based on the H–B grading system.

Results

Among the population aged ≥1 year, the prevalence of FP of grade III or worse in the H–B grading system was 0.12% (95% CI 0.07% to 0.17%). FP was more prevalent in women (p=0.01) and the prevalence rate increased with age (p<0.001). In participants aged ≥19 years, age, female gender, history of cardiovascular disease and the serum total cholesterol level were associated with FP in a multivariable analysis. In the evaluation of lifestyle, the individuals with FP had a higher rate of depressive mood and were more restricted in their daily activities.

Conclusions

Considering the significance of facial expression in psychosocial activities, public acknowledgement and further intervention are required to support patients with this distressing condition.
Managing antler problems in deer
Authors: Fletcher John , Foster Aiden , Goddard Pete , McSloy Alex
Published: November 2016

Antlers are one of the most amazing features of the mammal kingdom. They are, in mammals, the fastest growing tissue and the only example of the regeneration of an entire organ. Veterinarians encounter deer as a result of road traffic accidents, as young animals being bottle‐reared, or when veterinary problems occur in farmed or park deer or in animal collections. This article aims to provide information about antlers in terms of their growth and associated abnormalities, and discusses the particular issues faced by practitioners when dealing with castrated deer (especially reindeer) and orphan male calves.
Pig medicine for practising vets: an exercise in population medicine
Authors: Carr John , Howells Mark
Published: November 2016

This article explores the skillset required by a veterinary surgeon when dealing with population medicine problems in pigs. As with any clinical examination, the clinician needs to adopt a systematic approach. A systematic, consistent and disciplined approach to population medicine is essential to allow a veterinary clinician to form an objective assessment of the enterprise and, thereby, ensure that the health, welfare and wellbeing of the animals, stockpersons, farmers and owners are optimised. To illustrate the approach, this article focuses on six areas: biosecurity, animal flow, medicine controls, environmental medicine (water, food, floor and air), the animals themselves, and the people working with and caring for the animals.
Comments on the dilemma in the October issue: A request for euthanasia: advising a colleague
Authors: Brown Richard
Published: November 2016

In the dilemma discussed in the October issue of In Practice, a colleague reluctantly accepted the request to euthanase Bob, a healthy, two‐year‐old cat. The client was moving house and was not interested in rehoming. Later, a nurse said she could find a good home for the cat. What would you advise? (IP, October 2016, vol 38, pp 469‐470). Andrew Knight suggested that the colleague call the client and explain that a new option had arisen. Bob could go to a good home that was far away from the client, so there would be no chance of them seeing him again. However, if the client declined, the dilemma remained. One option might be to tell the client that, in view of the new circumstances, they could no longer agree to the euthanasia; instead they could offer to refund the payment and refer the client to another veterinarian for a second opinion.
Supporting new graduates
Authors: Hedberg Mark
Published: November 2016

Mark Hedberg offers some tips and advice on how practices can help new graduates find their feet.
Triage of the veterinary patient
Authors: Donnelly Emma , Lewis Daniel
Published: November 2016

Triage is a concept that dates back to the Napoleonic Wars. It is the process by which the stability of patients is determined, allowing those that are the most unstable to receive an examination, the implementation of essential treatment and further investigations as soon as possible. Well‐executed triage should allow the rapid ‘processing’ and initial assessment of multiple casualties to maximise the efficiency of the emergency team. This article discusses the aims of the triage process, the preparation required when waiting for the arrival of an emergency patient, and how to undertake primary and secondary surveys of the sick animal.
Avulsion fracture of the femoral attachment of the caudal cruciate ligament treated by arthroscopy in a Bernese Mountain puppy
Authors: Livet Véronique , Cachon Thibaut
Published: November 2016

A five‐month‐old male Bernese Mountain dog weighing 27.4 kg was presented for evaluation of an acute non‐weightbearing left pelvic limb lameness. Radiographs and CT revealed an avulsion fracture of the femoral attachment of the caudal cruciate ligament (CaCL). A left stifle arthroscopy was performed. Reduction and internal fixation were realised under arthroscopic guidance using a Kirschner wire (1.8 mm) and a single cortical screw (2.0 mm). Ten weeks postoperatively, the implants were removed via arthroscopy. A mild persistent intermittent weightbearing lameness was noted. Normal healing and resolution of lameness followed and the dog was clinically healthy 6 months postoperatively. As in human medicine, surgical treatment of a CaCL avulsion injury in dogs can be performed under arthroscopic guidance. Even though surgical treatment is not always required, it seemed indicated in this case and arthroscopic treatment was successful.
DInSAR data assimilation for settlement prediction: case study of a railway embankment in the Netherlands
Authors: Peduto Dario , Huber Maximilian , Speranza Gianluca , van Ruijven Joris , Cascini Leonardo
Published: November 2016

Secondary settlements in soft soils represent a significant fraction of the total settlement induced by external loads. Consequently, these settlements can play a key role in performance, serviceability, and safety of engineering works such as buildings, roads, embankments, and pipelines. This paper addresses the development of a predictive settlement model for a railway embankment built on soft clayey–peaty soils by following an original procedure consisting of three cascading steps: (i) preliminary detection of the most settlement-affected portions of the infrastructure; (ii) development of an equivalent subsoil model to study secondary settlements; (iii) back-calculation of the parameters of a predictive settlement model (design subsoil model) via a variational data assimilation scheme that exploits ground displacement measurements derived from differential interferometric synthetic aperture radar (DInSAR) data. The main achievement relies on the retrieval of a stochastic prediction of secondary settlements that can contribute to rationalize both conventional monitoring campaigns and management of key infrastructure.
Fatty acid composition and mechanisms of the protective effects of myrtle berry seed aqueous extract in alcohol-induced peptic ulcer in rat
Authors: Jabri Mohamed-Amine , Rtibi Kais , Tounsi Haifa , Hosni Karim , Marzouki Lamjed , Sakly Mohsen , Sebai Hichem
Published: November 2016

This study aimed to investigate the antiulcer and antioxidant activities of myrtle berry seed aqueous extract (MBSAE) in a peptic ulcer model induced by ethanol in male Wistar rats. MBSAE is rich in total polyphenols, total flavonoids, and unsaturated fatty acids, particularly linoleic (18:2) and oleic (18:1) acids. MBSAE also exhibited in vitro antioxidant activity using 2,2-diphenyl-1-picrylhydrazyl (DPPH) (IC50= 172.1 μg/mL) and superoxide anion (IC50= 200.24 μg/mL) scavenging activities. In vivo, MBSAE provided dose-dependent protection against ethanol-induced gastric and duodenal macroscopic and histological alterations. Also, it inhibited secretory profile disturbances and lipid peroxidation, and preserved normal antioxidant enzyme activities and nonenzymatic antioxidant levels. More importantly, we showed that acute alcohol intoxication increased gastric and duodenal calcium, hydrogen peroxide, and free iron levels, whereas MBSAE treatment protected against intracellular mediator deregulation. In conclusion, we suggest that MBSAE has potent protective effects against alcohol-induced peptic ulcer in rat. This protection might be related in part to its antioxidant properties as well as its opposite effects on some studied intracellular mediators.
Climate factors related to localized changes in snowshoe hare (Lepusamericanus) occupancy
Authors: Burt D.M. , Roloff G.J. , Etter D.R.
Published: November 2016

Information on climate that influences snowshoe hares (Lepus americanus Erxleben, 1777) can inform adaptation strategies. We identified climate factors correlated with localized changes in occupancy of snowshoe hares in Michigan, USA. A change in occupancy occurred if a site (∼7.5 ha) knowingly occupied by hares sometime in the past became unoccupied. We used local ecological knowledge to map sites where hares historically occurred and to assign a year of last-known occupancy. At 134 historically occupied sites, we conducted snow track surveys in 2013 to determine current occupancy status. We identified climate variables having relevance to hare population demographics and modeled the likelihood that those variables influenced current occupancy status. The top-ranking model included maximum temperature from 15 May to 19 January; as maximum temperature increased, the likelihood of a site becoming unoccupied increased. The second-ranked model included total number of days with measurable snow on the ground; as days with snow on the ground decreased, the likelihood of a site becoming unoccupied increased. Our data indicated that site occupancy status of hares can be described by climate variables and that the southern edge of snowshoe hare distribution in Michigan shifted northward by ∼45 km over the last 20 years.
Seesaw drift of bright solitons of the nonlinear Schrödinger equation with a periodic potential
Authors: Castro Camilo J. , Urzagasti Deterlino
Published: November 2016

Soliton solutions are investigated employing the nonlinear Schrödinger equation (NLSE) with an additional term corresponding to an external periodic field. In particular, we use this equation to describe the behavior of solitons in fiber optics in the case of anomalous dispersion. Employing the framework of variational analysis and analytical approximations, single peaked soliton solutions are derived, which exhibit variations of the solitonic parameters due to the effect of the periodic potential and a harmonic oscillator motion of the soliton center, when the frequency of the external field is small, whereas high values of the frequency of the external field produce static solitons. Finally, a variational-numerical analysis was developed and compared with a purely numerical model.
Moduli spaces of bundles on an abelian variety
Authors: Biswas Indranil
Published: November 2016

Let [Formula: see text] be a complex abelian variety and [Formula: see text] a complex reductive affine algebraic group. We describe the connected component, containing the trivial bundle, of the moduli spaces of topologically trivial principal [Formula: see text]-bundles and [Formula: see text]-Higgs bundles on [Formula: see text]. We also describe the moduli spaces of [Formula: see text]-connections and the [Formula: see text]-character variety for [Formula: see text].
Maxwell, Yang–Mills, Weyl and eikonal fields defined by any null shear-free congruence
Authors: Kassandrov Vladimir V. , Rizcallah Joseph A.
Published: November 2016

We show that (specifically scaled) equations of shear-free null geodesic congruences on the Minkowski space-time possess intrinsic self-dual, restricted gauge and algebraic structures. The complex eikonal, Weyl 2-spinor, [Formula: see text] Yang–Mills and complex Maxwell fields, the latter produced by integer-valued electric charges (“elementary” for the Kerr-like congruences), can all be explicitly associated with any shear-free null geodesic congruence. Using twistor variables, we derive the general solution of the equations of the shear-free null geodesic congruence (as a modification of the Kerr theorem) and analyze the corresponding “particle-like” field distributions, with bounded singularities of the associated physical fields. These can be obtained in a straightforward algebraic way and exhibit nontrivial collective dynamics simulating physical interactions.
The key technology research for integrated simulation of multi-disciplinary complex product system
Authors: Wu Jiani
Published: November 2016

Complex product system contains a number of different subsystems. The characteristics of multi-discipline and strong coupling exhibit due to the interconnection of subsystems. To achieve system-level optimization, integrated design on each subsystem is required. The traditional designing method using single simulation software is difficult to reflect the dynamic coupling among multiple subsystems. Therefore, the establishment of integrated design platform which is capable of multi-disciplinary and multi-domain simulation is necessary. This paper summarized the present design methods for multi-disciplinary integrated simulation platforms and the key technologies. Moreover, a case study with results was also provided to show the advantage of integrated multi-domain simulation. It will provide an important integrated authentication platform for the multi-disciplinary optimum design of complex product system.
A mathematical model to simulate Heap (bio)-leaching process: An exact conceptual model, Homotopy theory and comparative insights with conventional methods
Authors: Yaghobi Moghaddam M. , Shafaei Tonkaboni S. Z. , Noaparast M. , Doulati Ardejani F.
Published: November 2016

This paper attempts to address some nonlinear differential equations which describe main mechanisms governing heap (bio) leaching process as an important metallurgical facility in mining and mineral processing industries. The Homotopy Perturbation Method (HPM), Finite Volume Method and Analytical (Laplace) Method have been employed to provide proper solutions for these equations. Comparison was made between the methods and agreement was close; considering the fact that the proposed solution in comparison with the others provided a remarkable accuracy in dealing with nonlinear problems associated with mining and mineral processing industries. The maximum error of HPM in relation to the analytical solution was 0.02. The numerical finite volume method incorporating a computational fluid dynamics model termed PHOENICS provided rational and accurate results; describing that many chemical and biological processes extremely affect the transportation mechanism of the aqueous compounds in a heap structure and subsequently on the process efficiency. Besides, all solution methods presented to simulate heap leaching process provided valuable information related to the time dependence concentrations of dissolved compounds. The results obtained from this study can be effectively applied to manage the heap leaching costs to make the process feasible.