bluuebunny/crossref_metadata_2025 huggingface dataset:
Security in Public Space: An Empirical Assessment of Three US Cities
Authors: Németh Jeremy
Published: October 2010

Critics often mourn a loss of publicness in cities due to the increased presence of antiterror security zones and related behavioral and access controls, although recent work suggests that security landscapes have shifted from the hard, intense, militarized architecture of the late 1990s–early 2000s to a softer, less obtrusive approach more commonly seen today. Nonetheless, these studies are mostly anecdotal in nature: few studies attempt to back these claims with empirical evidence and even fewer connect this physical security imposition with the policies and plans governing its implementation and operation. In this paper I describe results of site visits to Civic Centers and Financial Districts in New York City, Los Angeles, and San Francisco. In each neighborhood I catalog security landscapes using a simple tool to assess the intensity, duration, and location of individual security zones. I find that the security landscape covers between 3.4% and 35.7% of publicly accessible space in the districts studied, and that this landscape is most prevalent and intense in New York City. I also find that security zones governed by multistakeholder networks are more intense and militarized than zones managed by a single entity. By understanding how the policies impact physical security, albeit in a relatively small sample of cities and districts, we can better predict what the future of urban security measures might hold. This paper provides empirical grounding to more common theoretical speculations regarding the future of the urban security landscape in the global West.
Cryo-scanning electron microscopy (CSEM) in the advancement of functional plant biology: energy dispersive X-ray microanalysis (CEDX) applications
Authors: McCully Margaret E. , Canny Martin J. , Huang Cheng X. , Miller Celia , Brink Frank
Published: October 2010

The capacity to make measurements of elemental concentrations at the level of single cells by energy dispersive X-ray microanalysis of cryo-fixed, inherently-hydrated plant parts (CEDX) is changing or extending our understanding of many plant functions. We include in this review a wide-ranging catalogue of studies that have used CEDX which provides access to the literature on elements measured, plants and tissues studied, techniques used, level of quantitation and the significant findings. These findings include new perspectives on the following areas: salt tolerance; xylem maturation and solute content, root pressure and embolism refilling; the contents of intercellular spaces; sequestration of toxic elements; biomineralisation with silicon; movement of tracer homologues of native cations; indirect localisation of molecules with a distinctive element component; transfer of nutrients from vesicular-arbuscular (VA) mycorrhizas; the role of mucilages in protection and in generating mechanical force. In an Appendix we discuss the procedures involved in CEDX: cryo-fixation, specimen planing, etching, elemental quantitation and mapping. Limitations on sample numbers, elements measurable, spatial resolution, sensitivity and threshold concentrations quantifiable are outlined. A brief discussion of the potential of emerging technologies for cell-specific analysis of cryo-fixed, hydrated specimens is included. In the Accessory Publication we list our standard protocol for CEDX.
Structural, electronic and magnetic properties of partially inverse spinel CoFe2O4: a first-principles study
Authors: Hou Y H , Zhao Y J , Liu Z W , Yu H Y , Zhong X C , Qiu W Q , Zeng D C , Wen L S
Published: October 2010

Partially inverse spinel CoFe2O4, which may be prepared through various heat treatments, differs remarkably from the ideal inverse spinel in many properties. The structure of partially inverse spinel CoFe2O4 as well as its electronic and magnetic properties through a systemic theoretical calculation of (Co1−x
Fe
x
)Tet(Co
x
Fe2−x
)OctO4 (x = 0, 0.25, 0.5, 0.75 and 1.0) have been investigated by the generalized gradient approximation (GGA) + U approach. It is found that the Co and Fe ions prefer their high spin configurations with higher spin moments at octahedral sites in all the studied cases, in line with experimental observations. The Co ions at the octahedral sites favour being far away from each other in the partial inverse spinels, which also show half metallicity at certain inversion degrees.
Graphene and its one-dimensional patterns: from basic properties towards applications
Authors: Do Van Nam , Pham Thanh Huy
Published: October 2010

Graphene, a carbon material discovered in 2004 by a group of scientists at the University of Manchester, UK, has been attracting significant attention in both fundamental and applied studies. Due to the rapid increase in the number of articles on this material since its discovery, a range of readers, particularly those just beginning to learn about this material, are turning to various different sources. The purpose of this article is to create a bridge between the key aspects of this material in experimental and theoretical investigations, as well as in fundamental and applied studies, aiming to provide a basic understanding of this material for those who are new to it. The presentation in this article is thus not particularly academic. The content focuses on four themes, including fabrication methods, basic properties, potential for application and some typical research directions for this magic carbon material.
Are U.S. Corn and Soybeans Becoming More Drought Tolerant?
Authors: Yu Tian , Babcock Bruce A.
Published: October 2010

The hypothesis that corn and soybeans have become more drought tolerant is tested by regressing county yields on a drought index and time. Results indicate that corn yield losses from drought of a given severity, whether measured in quantity terms or as a percentage of mean yields, have decreased over time. Soybean percentage yield losses have also declined, but absolute losses have remained largely constant. The potential impact of increased drought tolerance on U.S. crop insurance rates is illustrated by comparing Group Risk Plan premium rates assuming time‐invariant susceptibility to drought with rates generated from this article's regression results.
SmashCell: a software framework for the analysis of single-cell amplified genome sequences
Authors: Harrington Eoghan D. , Arumugam Manimozhiyan , Raes Jeroen , Bork Peer , Relman David A.
Published: October 2010

Summary: Recent advances in single-cell manipulation technology, whole genome amplification and high-throughput sequencing have now made it possible to sequence the genome of an individual cell. The bioinformatic analysis of these genomes, however, is far more complicated than the analysis of those generated using traditional, culture-based methods. In order to simplify this analysis, we have developed SmashCell (Simple Metagenomics Analysis SHell-for sequences from single Cells). It is designed to automate the main steps in microbial genome analysis—assembly, gene prediction, functional annotation—in a way that allows parameter and algorithm exploration at each step in the process. It also manages the data created by these analyses and provides visualization methods for rapid analysis of the results.

Availability: The SmashCell source code and a comprehensive manual are available at http://asiago.stanford.edu/SmashCell

Contact:  eoghanh@stanford.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
CNAseg—a novel framework for identification of copy number changes in cancer from second-generation sequencing data
Authors: Ivakhno Sergii , Royce Tom , Cox Anthony J. , Evers Dirk J. , Cheetham R. Keira , Tavaré Simon
Published: October 2010

Motivation: Copy number abnormalities (CNAs) represent an important type of genetic mutation that can lead to abnormal cell growth and proliferation. New high-throughput sequencing technologies promise comprehensive characterization of CNAs. In contrast to microarrays, where probe design follows a carefully developed protocol, reads represent a random sample from a library and may be prone to representation biases due to GC content and other factors. The discrimination between true and false positive CNAs becomes an important issue.

Results: We present a novel approach, called CNAseg, to identify CNAs from second-generation sequencing data. It uses depth of coverage to estimate copy number states and flowcell-to-flowcell variability in cancer and normal samples to control the false positive rate. We tested the method using the COLO-829 melanoma cell line sequenced to 40-fold coverage. An extensive simulation scheme was developed to recreate different scenarios of copy number changes and depth of coverage by altering a real dataset with spiked-in CNAs. Comparison to alternative approaches using both real and simulated datasets showed that CNAseg achieves superior precision and improved sensitivity estimates.

Availability: The CNAseg package and test data are available at http://www.compbio.group.cam.ac.uk/software.html.

Contact:  Sergii.Ivakhno@cancer.org.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Free Radical Scavenging, Cytotoxic and Hemolytic Activities from Leaves of Acacia nilotica (L.) Wild. ex. Delile subsp. indica (Benth.) Brenan
Authors: Kalaivani T. , Rajasekaran C. , Suthindhiran K. , Mathew Lazar
Published: October 2010

Dietary intake of phytochemicals having antioxidant activity is associated with a lower risk of mortality from many diseases. Therefore, the aim of this study was to determine the free radical scavenging, cytotoxic and hemolytic activities of leaves of Acacia nilotica by using various methods. The results of the present study revealed that ethanol extract was the most effective and IC50 value was found to be 53.6 μg mL−1 for Vero cell lines and 28.9 μg mL−1 for Hela cell lines in cytotoxicity assays. The zone of color retention was 14.2 mm in β‐carotene bleaching assay, which was as significant as positive control, butylated hydroxy toluene. None of the tested extracts possessed any hemolytic activity against rat and human erythrocytes revealing their cytotoxic mechanism and non‐toxicity. Thus, only the ethanol extract could be considered as a potential source of anticancer and antioxidant compounds. Further phytochemical studies will be performed for specification of the biologically active principles.
Revisiting the Sham: Is It all Smoke and Mirrors?
Authors: Horn Brandon , Balk Judith , Gold Jeffrey I.
Published: October 2010

The misuse of sham controls in examining the efficacy or effectiveness of Complementary and Alternative Medicine has created numerous problems. The theoretical justification for incorporating a sham is questionable. The sham does not improve our control of bias and leads to relativistic data that, in most instances, has no appropriate interpretation with regards to treatment efficacy. Even the concept of a sham or placebo control in an efficacy trial is inherently paradoxical. Therefore, it is prudent to re‐examine how we view sham controls in the context of medical research. Extreme caution should be used in giving weight to any sham‐controlled study claiming to establish efficacy or safety.
Dilong: Role in Peripheral Nerve Regeneration
Authors: Chang Yung-Ming , Chi Wei-Yi , Lai Tung-Yuan , Chen Yueh-Sheng , Tsai Fuu-Jen , Tsai Chang-Hai , Kuo Wei-Wen , Cheng Yi-Chang , Lin Chien-Chung , Huang Chih-Yang
Published: October 2010

Dilong, also known as earthworm, has been widely used in traditional Chinese medicine (TCM) for thousands of years. Schwann cell migration and proliferation are critical for the regeneration of injured nerves and Schwann cells provide an essentially supportive role for neuron regeneration. However, the molecular mechanisms of migration and proliferation induced by dilongs in Schwann cells remain unclear. Here, we discuss the molecular mechanisms that includes (i) migration signaling, MAPKs (mitogen‐activated protein kinases), mediated PAs and MMP2/9 pathway; (ii) survival and proliferative signaling, IGF‐I (insulin‐like growth factor‐I)‐mediated PI3K/Akt pathways and (iii) cell cycle regulation. Dilong stimulate RSC96 cell proliferation and migration. It can induce phosphorylation of ERK1/2 and p38, but not JNK, and activate the downstream signaling expression of PAs (plasminogen activators) and MMPs (matrix metalloproteinases) in a time‐dependent manner. In addition, Dilong stimulated ERK1/2 and p38 phosphorylation was attenuated by pretreatment with chemical inhibitors (U0126 and SB203580), and small interfering ERK1/2 and p38 RNA, resulting in migration and uPA‐related signal pathway inhibition. Dilong also induces the phosphorylation of IGF‐I‐mediated PI3K/Akt pathway, activates protein expression of PCNA (proliferating cell nuclear antigen) and cell cycle regulatory proteins (cyclin D1, cyclin E and cyclin A) in a time‐dependent manner. In addition, it accelerates G1‐phase progression with earlier S‐phase entry and significant numbers of cells entered the S‐phase. The siRNA‐mediated knockdown of PI3K that significantly reduces PI3K protein expression levels, resulting in Bcl2 survival factor reduction, revealing a marked blockage of G1 to S transition in proliferating cells. These results reveal the unknown RSC96 cell migration and proliferation mechanism induced by dilong, which find use as a new medicine for nerve regeneration.
Challenges Facing Muslim GPs and Muslim Patients
Authors: Safdar Asim , Ahmed Farah , Mearza Talib , Mearza Talib , Mearza Talib
Published: October 2010

General practice is a wide and varied field which throws up many challenges and ethical dilemmas on a regular basis. To understand the challenges and thought processes that Muslim GPs specifically go through when dealing with these requires some discussion. It is also worth clarifying some mainstream Muslim beliefs and to understand some of the logic and reasons behind some requests that patients may make from their GPs from time to time.
Hip and Knee Arthroplasty
Authors: Avis Duncan , Newman Alex , Rowland Megan
Published: October 2010

The incidence of hip and knee replacement surgery is increasing rapidly as a consequence of our ageing and increasingly obese society. In the UK, 50 000 hip replacements are being performed each year, and this is expected to treble by 2030. The aim of this article is to discuss the principles behind hip and knee arthroplasty, the types of prostheses, the surgeon's aims and the potential complications that may be encountered.
Etiology of Esophageal Food Impactions in Children
Authors: Hurtado Christine Waasdorp , Furuta Glenn T , Kramer Robert E
Published: October 2010

Objective:

The aim of the study was to measure clinicopathological features of children presenting to a tertiary care emergency department with esophageal food impaction.

Materials and Methods:

A retrospective chart review of children with esophageal food impaction seen between January 1, 2005 and June 30, 2009, including all patients from age 1 month to 18 years with esophageal food impaction at a pediatric emergency department, was performed.

Results:

Initial screening ofInternational Classification of Disease, 9th Revision, discharge diagnosis identified 698 children with an esophageal foreign body. Of this group, 72 esophageal food impaction events were identified in 65 children (69% boys), 49 of whom required endoscopic intervention. Endoscopic appearances of the esophageal mucosa were abnormal in 40 (82%), revealing evidence of esophagitis (55%) or stricture (27%). Twenty‐four of the subjects had biopsies taken at the time of endoscopy. Inflammation, described as increased eosinophils, basilar hyperplasia, rete peg elongation, and/or microabscess, was present in 76% of mucosal samples. Follow‐up endoscopy in 12 children identified an etiology in 9, five of whom were found to have eosinophilic esophagitis.

Conclusions:

The majority of children with esophageal food impaction who underwent endoscopic evaluation and biopsy have an underlying potentially treatable cause. We therefore recommend that all of the children with esophageal food impaction have mucosal biopsies at the time of endoscopic disimpaction with appropriate follow‐up to allow for diagnosis and management of the underlying etiology.
Surgery in Children With Crohn Disease Refractory to Medical Therapy
Authors: Pacilli Maurizio , Eaton Simon , Fell John M , Rawat David , Clarke Simon , Haddad Munther J
Published: October 2010

Objective:

The aim of this study was to evaluate the results of surgery in children with Crohn disease (CD) not responding to medical therapy and establish whether surgery improves growth and nutrition.

Patients and Methods:

Children with CD diagnosed between 1998 and 2008 were reviewed. Relapse was defined by Harvey‐Bradshaw index >5. Data, reported as median (range), were compared by Fisher exact test and repeated‐measures ANOVA.

Results:

One hundred forty‐one children, ages 12.7 years (3.5–16.8), were identified; 27 (19%) required surgery 14.5 months (1.1–61.8) after diagnosis. Twenty‐one had elective surgery (19 isolated ileocaecal disease and stricture, 2 diffuse disease of ileum); 6 had emergency surgery (3 peritonitis, 2 haemorrhage, 1 perforation). Surgery included 18 ileocaecal resection and end‐to‐end anastomosis, 5 stoma formation, 2 left hemicolectomy and end‐to‐end anastomosis, and 2 stricturoplasty. Follow‐up was 2.5 years (1–9.4). Growth and nutrition improved by 6 and 12 months after surgery, with a significant increase in weight z score (P < 0.0001), height z score (P < 0.0001), albumin (30 [13–36] vs 39 [30–46] vs 40 [33–45], P < 0.0001), and haemoglobin [10 (6.8–13.2) vs 11.7 (8.2–13.7) vs 12.0 (9.3–14.7), P < 0.0001]. All patients of the received azathioprine (2–2.5 mg · kg−1 · day−1) after surgery. Fifteen patients (55%) relapsed with a modified Harvey‐Bradshaw index of 8 (6–11) within 11.5 months (4.2–33.4). Of these, 5 patients (18%) relapsed within 1 year. Five patients (18%) had further surgery (2 anastomotic strictures, 2 diseased stoma, and 1 enterocutaneous fistula).

Conclusions:

Growth and nutrition following surgery for CD improve, but there is a high relapse rate. Despite this, the improved growth and nutrition before relapse may be beneficial during puberty and justify surgery in children not responding to medications.
Gluten‐free Sourdough Wheat Baked Goods Appear Safe for Young Celiac Patients: A Pilot Study
Authors: Di Cagno Raffaella , Barbato Maria , Di Camillo Chiara , Rizzello Carlo Giuseppe , De Angelis Maria , Giuliani Giammaria , De Vincenzi Massimo , Gobbetti Marco , Cucchiara Salvatore
Published: October 2010

Objectives:

This study was aimed at showing the safety, for young patients with celiac disease (CD), of sweet baked goods made of wheat flour, which was rendered gluten‐free during sourdough fermentation.

Methods and Results:

As shown by R5 antibody‐based sandwich and competitive enzyme‐linked immunosorbent assay (ELISA), selected lactobacilli and fungal proteases, routinely used in bakeries, degraded gluten to <10 ppm during sourdough fermentation. The resulting flour was mainly a mixture of water‐/salt‐soluble low‐size peptides and free amino acids. Gliadin and glutenin fractions extracted from the pepsin‐trypsin (PT) digest of the fermented wheat flour induced the expression of interferon (IFN)‐γ at the level comparable with the negative control. After fermentation, the wheat flour was spray dried and used for making sweet baked goods. Eight patients with CD in remission were enrolled for the clinical challenge, and they daily consumed 200 g of sweet baked goods equivalent to 10 g of native gluten. Hematology, serology (total serum IgA, IgG and IgA antigluten, endomysial and tissue transglutaminase IgA antibodies), and intestinal permeability analyses were carried out over time. One patient interrupted the trial after 15 days and another after 30 days only due to difficulties in the compliance of the daily consumption. All of the other patients showed normal values of hematology, serology, and intestinal permeability during 60 days of challenge.

Conclusions:

This study showed that a wheat flour–fermented product, having gluten completely degraded, is not toxic for patients with CD. Nevertheless, these foods should not be recommended for patients with celiac disease until a formal trial has been done.
Rhodococcus erythropolis septicaemia in a patient with acute lymphocytic leukaemia
Authors: Park Soon Deok , Uh Young , Jang In Ho , Yoon Kap Jun , Kim Hwang Min , Bae Yon Jung
Published: October 2010

Rhodococcus erythropolis rarely causes infection in humans. We report the second case of R. erythropolis septicaemia in a 7-year-old child. However, to our knowledge it is the first case in a patient with acute lymphocytic leukaemia who had been undergoing chemotherapy. The identification was performed using 16S rRNA gene sequencing. Even though R. erythropolis is rarely associated with human infections, it should be considered as a potential causative agent of bacteraemia, rather than overlooked as a contaminant.
Bacteriophage versus antimicrobial agents for the treatment of murine burn wound infection caused by Klebsiella pneumoniae B5055
Authors: Kumari Seema , Harjai Kusum , Chhibber Sanjay
Published: October 2010

This study was planned to evaluate the efficacy of silver nitrate and gentamicin in the treatment of burn wound infection and to compare it with phage therapy using an isolated and well-characterizedKlebsiella-specific phage, Kpn5. A full-thickness burn wound was induced in mice and infected withKlebsiella pneumoniaeB5055 via the topical route. Different concentrations of silver nitrate or gentamicin were applied topically daily after establishment of infection. Phage Kpn5 mixed in hydrogel was also applied topically at an m.o.i. of 200 on the burn wound site. The efficacy of these antimicrobial agents was assessed on the basis of percentage survival of infected mice following treatment. The results showed that a single dose of phage Kpn5 resulted in a significant reduction in mortality (P<0.001). Daily applications of silver nitrate and gentamicin at 0.5 % and 1000 mg l−1, respectively, provided significant protection (P<0.001) compared to lower concentrations of the two agents. However, the level of protection given by these two agents was lower than that given by the phage therapy. The results strongly suggest that phage Kpn5 has therapeutic utility in treating burn wound infection in mice as a single topical application of this phage was able to rescue mice from infection caused byK. pneumoniaeB5055 in comparison to multiple applications of silver nitrate and gentamicin.
Continued control of pneumococcal disease in the UK – the impact of vaccination
Authors: Gladstone R. A. , Jefferies J. M. , Faust S. N. , Clarke S. C.
Published: October 2010

Streptococcus pneumoniae, also known as the pneumococcus, is an important cause of morbidity and mortality in the developed and developing world. Pneumococcal conjugate vaccines were first introduced for routine use in the USA in 2000, although the seven-valent pneumococcal conjugate vaccine (PCV7) was not introduced into the UK's routine childhood immunization programme until September 2006. After its introduction, a marked decrease in the incidence of pneumococcal disease was observed, both in the vaccinated and unvaccinated UK populations. However, pneumococci are highly diverse and serotype prevalence is dynamic. Conversely, PCV7 targets only a limited number of capsular types, which appears to confer a limited lifespan to the observed beneficial effects. Shifts in serotype distribution have been detected for both non-invasive and invasive disease reported since PCV7 introduction, both in the UK and elsewhere. The pneumococcalHaemophilus influenzaeprotein D conjugate vaccine (PHiD-CV, Synflorix; GlaxoSmithKline) and 13-valent pneumococcal conjugate vaccine (PCV13, Prevenar 13; Pfizer) have been newly licensed. The potential coverage of the 10- and 13-valent conjugate vaccines has also altered alongside serotype shifts. Nonetheless, the mechanism of how PCV7 has influenced serotype shift is not clear-cut as the epidemiology of serotype prevalence is complex. Other factors also influence prevalence and incidence of pneumococcal carriage and disease, such as pneumococcal diversity, levels of antibiotic use and the presence of risk groups. Continued surveillance and identification of factors influencing serotype distribution are essential to allow rational vaccine design, implementation and continued effective control of pneumococcal disease.
Antibiotic resistance patterns of intestinal Escherichia coli isolates from Nicaraguan children
Authors: Amaya Erick , Reyes Daniel , Vilchez Samuel , Paniagua Margarita , Möllby Roland , Nord Carl Erik , Weintraub Andrej
Published: October 2010

In developing countries, diarrhoeal diseases are one of the major causes of death in children under 5 years of age. It is known that diarrhoeagenic Escherichia coli (DEC) is an important aetiological agent of infantile diarrhoea in Nicaragua. However, there are no recent studies on antimicrobial resistance among intestinal E. coli isolates in Nicaraguan children. The aim of the present study was to determine the antimicrobial resistance pattern in a collection of 727 intestinal E. coli isolates from the faeces of children in León, Nicaragua, between March 2005 and September 2006. All samples had been screened previously for the presence of DEC by multiplex PCR. Three hundred and ninety-five non-DEC isolates (270 from children with diarrhoea and 125 from children without diarrhoea) and 332 DEC isolates (241 from children with diarrhoea and 91 from children without diarrhoea) were analysed in this study. In general, antimicrobial resistance among the 727 intestinal E. coli isolates was high for ampicillin (60 %), trimethoprim–sulfamethoxazole (64 %) and chloramphenicol (11 %). Among individual E. coli categories, enteroaggregative E. coli isolates from children with and without diarrhoea exhibited significantly higher levels of resistance (P<0.05) to ampicillin and trimethoprim–sulfamethoxazole compared to the other E. coli categories. Resistance to ceftazidime and/or ceftriaxone and a pattern of multi-resistance was related to CTX-M-5- or CTX-M-15-producing E. coli isolates. The results suggest that E. coli isolates from Nicaraguan children have not reached the high levels of resistance to the most common antibiotics used for diarrhoea treatment as in other countries.
Co-regulation of β-lactam resistance, alginate production and quorum sensing in Pseudomonas aeruginosa
Authors: Balasubramanian Deepak , Kong Kok-Fai , Jayawardena Suriya Ravi , Leal Sixto Manuel , Sautter Robert Todd , Mathee Kalai
Published: October 2010

Development ofβ-lactam resistance, production of alginate and modulation of virulence factor expression that alters host immune responses are the hallmarks of chronicPseudomonas aeruginosainfection in cystic fibrosis patients. In this study, we propose that a co-regulatory network exists between these mechanisms. We compared the promoter activities ofampR,algT/U,lasR,lasI,rhlR,rhlIandlasAgenes, representing theβ-lactam antibiotic resistance master regulatory gene, the alginate switch operon, thelasandrhlquorum-sensing (QS) genes, and the LasA staphylolytic protease, respectively. Four isogenicP. aeruginosastrains, the prototypic Alg−PAO1, Alg−PAOampR, the mucoid Alg+PAOmucA22(Alg+PDO300) and Alg+PAOmucA22ampR(Alg+PDOampR) were used. We found that in the presence of AmpR regulator andβ-lactam antibiotic, the extracytoplasmic function sigma factor AlgT/U positively regulated PampR, whereas AmpR negatively regulated PalgT/U. On the basis of this finding we suggest the presence of a negative feedback loop to limitalgT/Uexpression. In addition, the functional AlgT/U caused a significant decrease in the expression of QS genes, whereas loss ofampRonly resulted in increased PlasIand PlasRtranscription. The upregulation of thelasQS system is likely to be responsible for the increasedlasApromoter and the LasA protease activities in Alg−PAOampRand Alg+PDOampR. The enhanced expression of virulence factors in theampRstrains correlated with a higher rate ofCaenorhabditis elegansparalysis. Hence, this study shows that the loss ofampRresults in increased virulence, and is indicative of the existence of a co-regulatory network betweenβ-lactam resistance, alginate production, QS and virulence factor production, with AmpR playing a central role.
Using extracellular polymeric substances (EPS)-producing cyanobacteria for the bioremediation of heavy metals: do cations compete for the EPS functional groups and also accumulate inside the cell?
Authors: Pereira Sara , Micheletti Ernesto , Zille Andrea , Santos Arlete , Moradas-Ferreira Pedro , Tamagnini Paula , De Philippis Roberto
Published: October 2010

Many cyanobacteria produce extracellular polymeric substances (EPS) mainly of polysaccharidic nature. These EPS can remain associated to the cell surface as sheaths, capsules and/or slimes, or be liberated into the surrounding environment as released polysaccharides (RPS). The ability of EPS-producing cyanobacteria to remove heavy metals from aqueous solutions has been widely reported in the literature, focusing mainly on the biotechnological potential. However, the knowledge of the effects of the metals in the cell's survival/growth is still scarce, particularly when they are simultaneously exposed to more than one metal. This work evaluated the effects of different concentrations of Cu2+and/or Pb2+in the growth/survival ofGloeothecesp. PCC 6909 and its sheathless mutantGloeothecesp. CCY 9612. The results obtained clearly showed that both phenotypes are more severely affected by Cu2+than Pb2+, and that the mutant is more sensitive to the former metal than the wild-type. Evident ultrastructural changes were also observed in the wild-type and mutant cells exposed to high levels (10 mg l−1) of Cu2+. Moreover, in bi-metal systems, Pb2+was preferentially removed compared with Cu2+, being the RPS of the mutant that is the most efficient polysaccharide fraction in metal removal. In these systems, the simultaneous presence of Cu2+and Pb2+caused a mutual inhibition in the adsorption of each metal.
Characterization of a broad-specificity non-haem iron N-demethylase from Pseudomonas putida CBB5 capable of utilizing several purine alkaloids as sole carbon and nitrogen source
Authors: Summers Ryan M. , Louie Tai Man , Yu Chi Li , Subramanian Mani
Published: October 2010

N-Demethylation of many xenobiotics and naturally occurring purine alkaloids such as caffeine and theobromine is primarily catalysed in higher organisms, ranging from fungi to mammals, by the well-studied membrane-associated cytochrome P450s. In contrast, there is no well-characterized enzyme forN-demethylation of purine alkaloids from bacteria, despite several reports on their utilization as sole source of carbon and nitrogen. Here, we provide what we believe to be the first detailed characterization of a purifiedN-demethylase fromPseudomonas putidaCBB5. The solubleN-demethylase holoenzyme is composed of two components, a reductase component with cytochromecreductase activity (Ccr) and a two-subunitN-demethylase component (Ndm). Ndm, with a native molecular mass of 240 kDa, is composed of NdmA (40 kDa) and NdmB (35 kDa). Ccr transfers reducing equivalents from NAD(P)H to Ndm, which catalyses an oxygen-dependentN-demethylation of methylxanthines to xanthine, formaldehyde and water. Paraxanthine and 7-methylxanthine were determined to be the best substrates, with apparentKmandkcatvalues of 50.4±6.8 μM and 16.2±0.6 min−1, and 63.8±7.5 μM and 94.8±3.0 min−1, respectively. Ndm also displayed activity towards caffeine, theobromine, theophylline and 3-methylxanthine, all of which are growth substrates for this organism. Ndm was deduced to be a Rieske [2Fe–2S]-domain-containing non-haem iron oxygenase based on (i) its distinct absorption spectrum and (ii) significant identity of the N-terminal sequences of NdmA and NdmB with the gene product of an uncharacterized caffeine demethylase inP. putidaIF-3 and a hypothetical protein inJanthinobacteriumsp. Marseille, both predicted to be Rieske non-haem iron oxygenases.
Duplication of the chromosomal bla
SHV-11 gene in a clinical hypermutable strain of Klebsiella pneumoniae
Authors: Duvernay Chloé , Coulange Laure , Dutilh Brigitte , Dubois Véronique , Quentin Claudine , Arpin Corinne
Published: October 2010

In a collection of 110 clinical isolates of Klebsiella pneumoniae, a single strain, Kp593, was found to exhibit a mutator phenotype with a rifampicin mutation frequency 100-fold higher than the modal value for this species. Complementation experiments with the wild-type MutL, one of the main components of the methyl-directed mismatch repair system, allowed the mutator phenotype to be reversed. Sequencing revealed substitution of the conserved residue Lys307 to Arg and site-directed mutagenesis followed by complementation experiments confirmed the critical role of this mutation. The patient infected with Kp593 relapsed a month later and the strain isolated then, Kp869, was identical to Kp593, as verified by PFGE analysis. Phenotypically, Kp869 colonies were more mucoid than those of Kp593, probably due to increased capsule synthesis as shown by electron microscopy. In addition, Kp869 exhibited a 16-fold higher amoxicillin resistance level related to a 36.4 kb tandem duplication encompassing the chromosomal bla
SHV-11 gene, which was unstable in vitro. These data suggest that the mutator phenotype found in Kp593/Kp869 is associated with beneficial mutations conferring a selective advantage, such as increased virulence factor production and antibiotic resistance. The latter was due to resistance gene duplication, an event rarely described in natural isolates. This is the first description of the in vivo occurrence of gene duplication in a mutator background.
Mycoplasma gallisepticum and Mycoplasma synoviae express a cysteine protease CysP, which can cleave chicken IgG into Fab and Fc
Authors: Cizelj Ivanka , Berčič Rebeka Lucijana , Dušanić Daliborka , Narat Mojca , Kos Janko , Dovč Peter , Benčina Dušan
Published: October 2010

Major poultry pathogens M. gallisepticum and M. synoviae share a gene encoding a putative cysteine protease CysP similar to papain cysteine protease (C1A subfamily). Comparison of the cysP gene sequences of 18 M. synoviae and 10 M. gallisepticum strains sequenced in this study showed polymorphisms, including deletions. Seven M. synoviae strains, including the type strain WVU 1853, had a 39 bp deletion in the 3′ end of the cysP gene. In the same cysP region, all M. gallisepticum strains showed a deletion of 66 bp. Immunoblot analysis with specific antibodies demonstrated that M. synoviae strains expressed CysP, which was approximately 65 kDa. Both M. synoviae and M. gallisepticum were able to digest chicken IgG (cIgG). Incubation of cIgG (∼170 kDa) with M. synoviae or M. gallisepticum cells (∼15 h at 37 °C) resulted in a papain-like cleavage pattern of cIgG and fragments corresponding to the antigen-binding fragment of IgG (Fab, ∼45 kDa) and the crystallizable region fragment (Fc) of the IgG heavy chain (dimer of ∼60 kDa). Iodoacetamide (50 mM) prevented cleavage of cIgG by both Mycoplasma species. Following site-directed mutagenesis (eight TGA codons were changed to TGG) the cysP gene of M. synoviae ULB 925 was expressed as a His-tagged protein in a cell-free system. Purified recombinant CysP (rCysP; ∼67 kDa, pI∼8) cleaved cIgG into Fab and Fc fragments. This indicates that CysP is responsible for the cIgG cleavage caused by M. synoviae and, probably, by M. gallisepticum. This is the first evidence to our knowledge that mycoplasmas have enzymes that can cleave the host IgG and indicates a novel strategy used by M. gallisepticum and M. synoviae for prolonged survival despite the antibody response of their host.
Neonatal immune function and inflammatory illnesses in later life: lessons to be learnt from the developing world?
Authors: Lisciandro J. G. , Van Den Biggelaar A. H. J.
Published: October 2010

With the emergence of allergic and autoimmune diseases in populations that have started to transit to a western lifestyle, there has been an increasing interest in the role of environmental factors modulating early immune function. Yet, most of the information concerning neonatal immune function has been derived from studies in westernized countries. We postulate that comparative studies of early immune development in children born under conditions that are typical for a westernized vs. that of a still more traditional setting will provide a crucial insight into the environmental‐driven immunological mechanisms that are responsible for the world‐wide rise in inflammatory disorders. In this review, we summarize the current understanding of early‐life immune function in humans in general and the literature on some major lifestyle factors that may influence neonatal immune function and potentially the risk for disease in later life. An understanding of the mechanisms of ‘prenatal/early‐life programming’ in populations living in traditional compared with modern societies is crucial to develop strategies to prevent a further rise in ‘western diseases’ such as allergic disorders. Indications exist that prenatal conditioning of the innate immune system by low‐grade inflammatory responses is key to inducing more tightly regulated postnatal adaptive immune responses.

Cite this as: J. G. Lisciandro and A. H. J. van den Biggelaar, Clinical & Experimental Allergy, 2010 (40) 1719–1731.
STUDIES ON THE DECOMPOSITION OF PLANT MATERIAL IN SOIL. IV. THE EFFECT OF RATE OF ADDITION
Authors: JENKINSON D. S.
Published: October 2010

Different amounts of ryegrass roots and tops, both uniformly labelled with 1
4 C, were mixed with soil and allowed to decompose for 155 days under controlled conditions in the laboratory at 25°C. Initially the roots decomposed more slowly than the tops but by 155 days this difference had disappeared. About a third of the added plant C remained in the soil at the end of 155 days, about as much as when the same plant materials were incubated in the same soils for 6 months in the field.

To a first approximation, the amount of labelled CO2–C evolved was directly proportional to the amount of labelled plant C added. This held throughout the incubations. However, a slightly smaller percentage of the added plant C was evolved with small additions than with large, although this effect was on the limits of detection. Slightly more labelled plant C was retained in a soil rich in organic matter (2.43% C) than in an otherwise similar soil with less organic matter (0.97% C).
Continuing connections: the experiences of retired and senior working nurse mentors
Authors: McDonald Glenda , Mohan Shantala , Jackson Debra , Vickers Margaret H , Wilkes Lesley
Published: October 2010

Aims and objectives.  This paper reports the benefits and challenges of a mentoring programme through which retired and senior nurses continued to support and nurture nurses and midwives currently working in the health system.

Background.  Nursing has an ageing workforce and faces significant loss of expertise because of retirements. Previously, mentoring programmes have been instituted in a range of nursing contexts and they have been a retention strategy for older nurses and midwives.

Design.  Mentors and their mentees worked together towards mutually agreed on professional and personal goals. They were asked to meet or speak together a minimum of twice per month for at least six months.

Method.  As part of a collective case study, 15 mentoring dyads were established. Participants and mentors took part in qualitative, semi‐structured interviews about their perceptions and experiences of the mentoring programme. Interviews were audio‐taped, transcribed and analysed thematically.

Results.  Mentors reported the mentoring experience to be rewarding experience that enabled them to re‐connect with nursing‐related activities and brought new challenges in retirement. They perceived the mentees were visibly helped by their support and influence.

Conclusions.  The mentors studied reinforced a positive self‐concept as nurses and midwives in their mentees and assisted their development. Retired nurses and midwives in particular may have several characteristics that make them effective mentors.

Relevance to clinical practice.  Potential benefits are demonstrated for nurses and midwives vulnerable to workplace adversity, especially those new to Australia who may have limited professional and social networks. For health organisations, mentoring programmes may be an innovative method of retention that engages both mid‐career nurses and midwives and those recently retired.
The relationships between organisational citizenship behaviour, job satisfaction and turnover intention
Authors: Tsai Yafang , Wu Shih‐Wang
Published: October 2010

Aim. This study aims to explore the relationships between organisational citizenship behaviour, job satisfaction and turnover intention.

Background. Because of the changing health policies landscape, Taiwan’s hospital administrators are facing major cost reduction challenges. Specifically, the high turnover rate of nurses represents a hindrance and a human resource cost. This study focuses on ways of reducing the employee turnover rate through enhanced organisational citizenship behaviour and job satisfaction.

Design. A cross‐sectional study.

Methods. This study focuses on hospital nurses in Taiwan. Our research samples were obtained from one medical centre, three regional hospitals and seven district hospitals. Out of 300 questionnaires distributed among samples, 237 were completed and returned. Pearson’s correlation was used to test for relationships among the main variables. One‐way analysis of variance and Scheffé’spost hocanalysis were employed to test the influence of demographic data on the main variables.

Results. The results reveal that the nurses’ job satisfaction has a significantly positive correlation with organisational citizenship behaviour and a negative correlation with turnover intention.

Conclusions. This study has proven that the turnover intention of clinical nurses is related to their organisational citizenship behaviour and job satisfaction. Hospital administrators can reduce the turnover intention by meeting nurses’ needs and by promoting their organisational citizenship behaviour.

Relevance to clinical practice. Organisational citizenship behaviour involves behaviour that encourages staff to endeavour to voluntarily improve organisational performance without lobbying for compensation. Employees’ job satisfaction includes satisfaction with the working environment or welfare programme in the context of human resource initiatives. Similarly, human resource protocols may serve as the starting point for promoting staff organisational citizenship behaviour. Administrators in clinical healthcare are encouraged to meet their employees’ working needs through human resource practices.
An exploratory study of the follow‐up care needs of patients treated for colorectal cancer
Authors: Beaver Kinta , Latif Saima , Williamson Susan , Procter Debbie , Sheridan Janet , Heath Jonathan , Susnerwala Shabbir , Luker Karen
Published: October 2010

Aims and objectives.  To explore patient perceptions of their experiences of follow‐up care after treatment for colorectal cancer.

Background.  The optimal follow‐up strategy for colorectal cancer is not known, and although patients are seen in traditional outpatient follow‐up clinics, this system may not meet psycho‐social and information needs.

Design.  An exploratory qualitative study.

Method.  In‐depth interviews were conducted with 27 patients who had completed treatment for colorectal cancer. The data were analysed using thematic analysis.

Results.  One dominant theme emerged from the data with several sub‐themes. The dominant theme was ‘knowing what to expect’ after bowel surgery. The subthemes related to ‘living with altered bowel function’, the ways patients gathered information about their condition through ‘trial and error’ and ‘information and support from specialist nurses’. Patients who did not have a stoma were particularly vulnerable and expressed a need for more information on knowing what to expect after surgery. The role of the colorectal nurse specialist was vital in providing information and support; in particular, nurse‐led clinics provided continuity of care and information that was tailored to individual need.

Conclusions.  Traditional hospital follow‐up does not always address patients’ psycho‐social and information needs. Nurse‐led services were commented on favourably in terms of providing information that was tailored to individual need as well as being responsive to urgent patient concerns; future innovative strategies for providing follow‐up care for patients with colorectal cancer should draw on the specialist knowledge and skills of these nurses.

Relevance to clinical practice.  Nurse‐led clinics and/or telephone follow‐up by specialist nurses may be effective models of care for this particular patient group, providing appropriate access for meeting clinical, psycho‐social and information needs.
Evolutionary history of the conifer root rot fungus Heterobasidion annosum sensu lato
Authors: DALMAN K. , OLSON Å. , STENLID J.
Published: October 2010

We investigated two hypotheses for the origin of the root rot fungus Heterobasidion annosum species complex: (i) that geology has been an important factor for the speciation (ii) that co‐evolutionary processes with the hosts drove the divergence of the pathogen species. The H. annosum species complex consists of five species: three occur in Europe, H. annosum s.s., Heterobasidion parviporum and Heterobasidion abietinum, and two in North America, Heterobasidion irregulare and Heterobasidion occidentale; all with different but partially overlapping host preferences. The evolution of the H. annosum species complex was studied using six partially sequenced genes, between 10 and 30 individuals of each species were analysed. Neighbour‐joining trees were constructed for each gene, and a Bayesian tree was built for the combined data set. In addition, haplotype networks were constructed to illustrate the species relationships. For three of the genes, H. parviporum and H. abietinum share haplotypes supporting recent divergence and/or possible gene flow. We propose that the H. annosum species complex originated in Laurasia and that the H. annosum s.s./H. irregulare and H. parviporum/H. abietinum/H. occidentale ancestral species emerged between 45 and 60 Ma in the Palaearctic, well after the radiation of the host genera. Our data imply that H. irregulare and H. occidentale were colonizing North America via different routes. In conclusion, plate tectonics are likely to have been the main factor influencing Heterobasidion speciation and biogeography.