bluuebunny/crossref_metadata_2025 huggingface dataset:
Bloodstream Infections Caused by Metallo-β-Lactamase/Klebsiella pneumoniae Carbapenemase–Producing K. pneumoniae among Intensive Care Unit Patients in Greece: Risk Factors for Infection and Impact of Type of Resistance on Outcomes
Authors: Mouloudi Eleni , Protonotariou Euthymia , Zagorianou Alexia , Iosifidis Elias , Karapanagiotou Areti , Giasnetsova Tatiana , Tsioka Agoritsa , Roilides Emmanuel , Sofianou Danai , Gritsi-Gerogianni Nikoleta
Published: October 2010

Objective.

To determine risk factors for bloodstream infections (BSIs) caused by Klebsiella pneumoniae producing metallo-β-lactamases (MBLs) or K. pneumoniae carbapenemases (KPCs), as well as risk factors for mortality associated with carbapenem-resistant K. pneumoniae, among intensive care unit (ICU) patients.

Methods.

Two case-control studies were conducted in a patient cohort with K. pneumoniae BSIs in an 8-bed ICU in a Greek hospital from January 1, 2007, through December 31, 2008. In study 1, patients with K. pneumoniae BSIs were allocated among 3 groups according to isolate susceptibility profile: (1) carbapenem-susceptible insolates (control group), (2) MBL-producing isolates, or (3) KPC-producing isolates. The MBL and KPC groups were compared with the control group to identify risk factors for development of K. pneumoniae BSI. In study 2, patients with K. pneumoniae BSIs who died were compared with survivors to identify risk factors for mortality.

Results.

Fifty-nine patients had K. pneumoniae BSIs (22 with carbapenem-susceptible isolates, 18 with MBL-producing isolates, and 19 with KPC-producing isolates). All KPC-producing isolates carried the blaKPC-2 gene, and 17 of 18 MBL-producing isolates carried blaVIM-1 Acute Physiology and Chronic Health Evaluation II score (odds ratio, 1.13 [95% confidence interval, 1.03–1.25]; P = .02) was independently associated with KPC-producing K. pneumoniae BSIs. Nine (41%) of 22 control patients, 8 (44%) of 18 MBL group patients, and 13 (68%) of 19 KPC group patients died in the ICU. Nine (41%) of 22 control patients, 10 (56%) of 18 MBL group patients, and 15 (79%) of 19 KPC group patients died in the hospital. Isolation of KPC-producing K. pneumoniae was an independent predictor of ICU death (P = .04) and in-hospital death (P = .03) but not infection-attributable death.

Conclusions.

BSIs due to KPC-producing K. pneumoniae resulted in significantly increased mortality. The accurate and rapid detection of these pathogens is necessary for therapeutic considerations and for the implementation of infection control measures to contain them.
Interoperability between phenotype and anatomy ontologies
Authors: Hoehndorf Robert , Oellrich Anika , Rebholz-Schuhmann Dietrich
Published: October 2010

Motivation: Phenotypic information is important for the analysis of the molecular mechanisms underlying disease. A formal ontological representation of phenotypic information can help to identify, interpret and infer phenotypic traits based on experimental findings. The methods that are currently used to represent data and information about phenotypes fail to make the semantics of the phenotypic trait explicit and do not interoperate with ontologies of anatomy and other domains. Therefore, valuable resources for the analysis of phenotype studies remain unconnected and inaccessible to automated analysis and reasoning.

Results: We provide a framework to formalize phenotypic descriptions and make their semantics explicit. Based on this formalization, we provide the means to integrate phenotypic descriptions with ontologies of other domains, in particular anatomy and physiology. We demonstrate how our framework leads to the capability to represent disease phenotypes, perform powerful queries that were not possible before and infer additional knowledge.

Availability:  http://bioonto.de/pmwiki.php/Main/PheneOntology

Contact:  rh497@cam.ac.uk
Generalized random set framework for functional enrichment analysis using primary genomics datasets
Authors: Freudenberg Johannes M. , Sivaganesan Siva , Phatak Mukta , Shinde Kaustubh , Medvedovic Mario
Published: October 2010

Motivation: Functional enrichment analysis using primary genomics datasets is an emerging approach to complement established methods for functional enrichment based on predefined lists of functionally related genes. Currently used methods depend on creating lists of ‘significant’ and ‘non-significant’ genes based on ad hoc significance cutoffs. This can lead to loss of statistical power and can introduce biases affecting the interpretation of experimental results.

Results: We developed and validated a new statistical framework, generalized random set (GRS) analysis, for comparing the genomic signatures in two datasets without the need for gene categorization. In our tests, GRS produced correct measures of statistical significance, and it showed dramatic improvement in the statistical power over other methods currently used in this setting. We also developed a procedure for identifying genes driving the concordance of the genomics profiles and demonstrated a dramatic improvement in functional coherence of genes identified in such analysis.

Availability: GRS can be downloaded as part of the R package CLEAN from http://ClusterAnalysis.org/. An online implementation is available at http://GenomicsPortals.org/.

Contact:  mario.medvedovic@uc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
The GMOD Drupal Bioinformatic Server Framework
Authors: Papanicolaou Alexie , Heckel David G.
Published: October 2010

Motivation: Next-generation sequencing technologies have led to the widespread use of -omic applications. As a result, there is now a pronounced bioinformatic bottleneck. The general model organism database (GMOD) tool kit (http://gmod.org) has produced a number of resources aimed at addressing this issue. It lacks, however, a robust online solution that can deploy heterogeneous data and software within a Web content management system (CMS).

Results: We present a bioinformatic framework for the Drupal CMS. It consists of three modules. First, GMOD-DBSF is an application programming interface module for the Drupal CMS that simplifies the programming of bioinformatic Drupal modules. Second, the Drupal Bioinformatic Software Bench (biosoftware_bench) allows for a rapid and secure deployment of bioinformatic software. An innovative graphical user interface (GUI) guides both use and administration of the software, including the secure provision of pre-publication datasets. Third, we present genes4all_experiment, which exemplifies how our work supports the wider research community.

Conclusion: Given the infrastructure presented here, the Drupal CMS may become a powerful new tool set for bioinformaticians. The GMOD-DBSF base module is an expandable community resource that decreases development time of Drupal modules for bioinformatics. The biosoftware_bench module can already enhance biologists' ability to mine their own data. The genes4all_experiment module has already been responsible for archiving of more than 150 studies of RNAi from Lepidoptera, which were previously unpublished.

Availability and implementation: Implemented in PHP and Perl. Freely available under the GNU Public License 2 or later from http://gmod-dbsf.googlecode.com

Contact:  alexie@butterflybase.org
GAMES identifies and annotates mutations in next-generation sequencing projects
Authors: Sana Maria Elena , Iascone Maria , Marchetti Daniela , Palatini Jeff , Galasso Marco , Volinia Stefano
Published: October 2010

Motivation: Next-generation sequencing (NGS) methods have the potential for changing the landscape of biomedical science, but at the same time pose several problems in analysis and interpretation. Currently, there are many commercial and public software packages that analyze NGS data. However, the limitations of these applications include output which is insufficiently annotated and of difficult functional comprehension to end users.

Results: We developed GAMES (Genomic Analysis of Mutations Extracted by Sequencing), a pipeline aiming to serve as an efficient middleman between data deluge and investigators. GAMES attains multiple levels of filtering and annotation, such as aligning the reads to a reference genome, performing quality control and mutational analysis, integrating results with genome annotations and sorting each mismatch/deletion according to a range of parameters. Variations are matched to known polymorphisms. The prediction of functional mutations is achieved by using different approaches. Overall GAMES enables an effective complexity reduction in large-scale DNA-sequencing projects.

Availability: GAMES is available free of charge to academic users and may be obtained from http://aqua.unife.it/GAMES.

Contact:  stefano.volinia@unife.it
Controls on pathogen species richness in plants’ introduced and native ranges: roles of residence time, range size and host traits
Authors: Mitchell Charles E. , Blumenthal Dana , Jarošík Vojtěch , Puckett Emily E. , Pyšek Petr
Published: October 2010

Ecology Letters(2010) 13: 1525–1535

Introduced species escape many pathogens and other enemies, raising three questions. How quickly do introduced hosts accumulate pathogen species? What factors control pathogen species richness? Are these factors the same in the hosts’ native and introduced ranges? We analysed fungal and viral pathogen species richness on 124 plant species in both their native European range and introduced North American range. Hosts introduced 400 years ago supported six times more pathogens than those introduced 40 years ago. In hosts’ native range, pathogen richness was greater on hosts occurring in more habitat types, with a history of agricultural use and adapted to greater resource supplies. In hosts’ introduced range, pathogen richness was correlated with host geographic range size, agricultural use and time since introduction, but not any measured biological traits. Introduced species have accumulated pathogens at rates that are slow relative to most ecological processes, and contingent on geographic and historic circumstance.
After Elizabeth: representations of female rule in Massinger's tragicomedies
Authors: TOSI LAURA
Published: October 2010

The perception, memories and representations of Elizabeth in the early seventeenth century can hardly be separated by political concerns. As Jacobean and Caroline governments were progressively distancing themselves from the values Elizabeth had been known to support, the idealized memory of good Queen Bess could also be effectively reframed and used as a form of opposition to the rule of James and Charles. The representation of women rulers in Philip Massinger's tragicomedies may be read as a crucial example of the way a nostalgic vision of Elizabeth blends in with more contemporary considerations about female authority as well as representations of ideal relationships between the sexes and between the monarch and his/her people. The purpose of this article is to investigate some of the implications of the so‐called myth of Elizabeth, and the way some dramatic representations of the female governor complicate and integrate the example of Elizabeth as idealized monarch and become part of a wider investigation on hierarchy and the private/public conduct of rulers in Jacobean and Caroline times.
Landlord Attitudes and Behaviors Regarding Smoke‐Free Policies: Implications for Voluntary Policy Change
Authors: Cramer Mary E. , Roberts Sara , Stevens Elizabeth
Published: October 2010

ABSTRACT
Objective: Objective: The study purpose was to describe multiunit landlord attitudes and behaviors toward smoke‐free policies.

Design and Sample: This was a descriptive, cross‐sectional survey of multiunit landlords in Douglas County (N=392). Measures: A 25‐item survey was developed and pilot tested. It was administered by telephone (n=143) and mail (n=249) to multiunit landlords.

Results: Combined response rate was 30.1% (81/143 telephone, 37/249 mail) representing 24,080 units on 974 properties with 34,399 tenants. Most respondents (73.7%) allowed smoking. Reasons for not implementing smoke‐free policies were potential enforcement problems (57.0%), tenant objections (43.0%), loss of market share (39.5%). Respondents without smoke‐free policies expected vacancy (53.6%) and turnover (50.0%) rates to increase, which was significantly different (p <.0001) than respondents with smoke‐free policies where only 10.7% reported increased vacancy and only 3.7% reported increased turnover.

Conclusions: Expected adverse impacts of smoke‐free policies do not reflect real experiences of smoke‐free policy implementation. Public health advocates can use these study findings to develop community‐based education and social marketing messages directed at voluntary smoke‐free policy changes. Respondents without smoke‐free policies expressed interest at the end of the survey in learning how to implement smoke‐free policies indicating a readiness for change.
Mapping Restoration Opportunity for Collaborating with Land Managers in a Carbon Credit‐Funded Restoration Program in the Makana Municipality, Eastern Cape, South Africa
Authors: Curran Patrick , Smedley David , Thompson Peter , Knight Andrew T.
Published: October 2010

Spatial prioritization techniques are commonly used in conservation planning, but are relatively new for planning restoration programs. Typically, ecological data, and more recently data on economic costs and vulnerability of sites, are used. However, the effectiveness of restoration action ultimately relies on a combination of the appropriate ecological restoration techniques and the human and social dynamics of social‐ecological systems. Surveys were conducted with 29 land managers within the Makana Municipality of the Eastern Cape, South Africa, to identify a range of human and social factors hypothesized to define the potential effectiveness of restoration action. Land managers with similar characteristics were grouped using a cluster analysis, and the groups ranked and mapped in geographical information system (GIS) to provide a spatial representation of restoration opportunity. The total number of questions were reduced by 35.6%, a step toward developing a rapid assessment approach for assessing land managers' potential participation in restoration initiatives. Identifying and incorporating human and social factors that directly influence restoration prioritization should promote efficient and effective implementation of restoration actions by the Working for Woodlands programme, who are looking to funding landscape‐scale restoration through carbon trading.
Peri‐implant reconstruction using autologous periosteum‐derived cells and guided bone regeneration
Authors: Ribeiro Fernanda Vieira , Suaid Fabricia Ferreira , Ruiz Karina Gonzales Silverio , Rodrigues Thaisângela Lopes , Carvalho Marcelo Diniz , Nociti Francisco Humberto , Sallum Enilson Antonio , Casati Márcio Zaffalon
Published: October 2010

Ribeiro FV, Suaid FF, Ruiz KGS, Rodrigues TL, Carvalho MD, Nociti FH, Sallum EA, Casati MZ. Peri‐implant reconstruction using autologous periosteum‐derived cells and guided bone regeneration. J Clin Periodontol 2010; doi: 10.1111/j.1600‐051X.2010.01635.x.

Aim: This investigation evaluated the bone healing in peri‐implant defects treated with periosteum‐derived cells (PCs) and guided bone regeneration (GBR).

Material and Methods: PCs were harvested from six beagle dogs and characterized in vitro with regard to their osteogenic properties. The animals were subjected to teeth extraction in the mandible, and after 3 months of healing, implant sites were drilled, bone dehiscences were created and implants were placed. Dehiscences were randomly assigned to: PCs+GBR, GBR, PCs and non‐treated defects. After 3 months, the implants/adjacent tissues were processed. Bone‐to‐implant contact (BIC) bone fill (BF) within implant threads, and bone area (BA) in a zone lateral to the implant were obtained.

Results: In vitro analyses confirmed the osteogenic potential of PCs. Histometrically, no statistically significant differences were observed among the PCs+GBR, GBR and PCs groups for both BF and BIC (p>0.05), whereas these groups showed statistically higher values, as compared with the non‐treated group (p<0.05). With respect to BA, the PCs+GBR and GBR groups presented significantly higher means, as compared with the PCs and non‐treated groups (p<0.05).

Conclusion: Although successful outcomes have been promoted by using the combined approach, PCs in conjunction with membranes did not provide additional benefit during peri‐implant bone regeneration, when compared with the therapeutic approaches used alone.
Cytotoxicity of calcium enriched mixture cement compared with mineral trioxide aggregate and intermediate restorative material
Authors: Mozayeni Mohammad A. , Milani Amin S. , Marvasti Laleh A. , Asgary Saeed
Published: October 2010

Calcium enriched mixture (CEM) cement has been recently invented by the last author. It is composed of calcium oxide, calcium phosphate, calcium silicate and calcium sulphate; however, it has a different chemical composition to mineral trioxide aggregate (MTA). The purpose of this ex vivo study was to investigate the cytotoxicity of CEM cement, and compare it with intermediate restorative material (IRM) and MTA. The materials were tested in fresh and set states on L929 fibroblasts to assess their cytotoxicity. The cell viability responses were evaluated with methyl‐tetrazolium bromide assay and Elisa reader at 1, 24 and 168 h (7 days). The tested materials were eluted with L929 culture medium according to international standard organisation 109935 standard. Distilled water and culture medium served as positive and negative controls, respectively. Differences in cytotoxicity were evaluated by one‐way anova and t‐tests. The cytotoxicity of the materials was statistically different at the three time intervals (P < 0.01). The lowest cytotoxic values recorded were expressed by MTA subgroups followed by CEM cement; IRM subgroups were the most cytotoxic root‐end/dental material (P < 0.001). CEM cement and MTA are reasonable alternatives to IRM because of lower cytotoxicity. CEM cement also has good biocompatibility as well as lower estimated cost to MTA and seems to be a promising dental material.
Prophylactic intraligamentary injection of piroxicam (feldene) for the management of post‐endodontic pain in molar teeth with irreversible pulpitis
Authors: Atbaei Adnan , Mortazavi Nazanin
Published: October 2010

The purpose of this prospective research was to evaluate the post‐endodontic pain‐reducing effect of piroxicam (feldene), a non‐selective non‐steroidal anti‐inflammatory drug. Pain following endodontic treatment is often linked to the inflammatory process as well as additional central mechanisms. The effects of intraligamentary injection of piroxicam have not previously been studied. Sixty‐five patients with irreversible pulpitis were randomly divided into two groups. The active group received intraligamentary injections totalling 0.4 mL of piroxicam, while the placebo group received the same amount of lidocaine. One‐appointment endodontic therapy was performed by a single endodontist. Visual Analogue Scale was used to record pain before treatment and 4, 8, 12, 24 and 48 h postoperatively. The decrease in the intensity of post‐treatment pain between the two groups was very significant. Intraligamentary injection of piroxicam can be considered an effective method for reducing post‐endodontic pain.
IntestinalBacteroidesspecies associated with coeliac disease
Authors: Sánchez Ester , Donat Ester , Ribes-Koninckx Carmen , Calabuig Miguel , Sanz Yolanda
Published: October 2010

Aims

To characterise the predominant species of bacterial populations associated with duodenal biopsies of paediatric patients with active and treated coeliac disease.

Methods

20 biopsy specimens from patients with active coeliac disease, 12 from patients with treated coeliac disease, and eight from age-matched controls were evaluated for comparative purposes.Bacteroides,Bifidobacteriumand lactic acid bacteria (LAB) populations were analysed by PCR-denaturing gradient gel electrophoresis using group-specific primers.

Results

Bacteroidesdiversity was higher in biopsy specimens from controls than in those from patients with active and treated coeliac disease.Bacteroides distasonis,Bacteroides fragilis/Bacteroides thetaiotaomicron,Bacteroides uniformisandBacteroides ovatuswere more abundant in controls than in patients with coeliac disease (p<0.05).Bacteroides vulgatuswas more frequently detected in controls than in patients with treated coeliac disease (p<0.01).Bacteroides doreiwas more common in patients with active coeliac disease than in those with treated coeliac disease and control children (p<0.01).Bifidobacteriumdiversity was higher in patients with coeliac disease than in controls.Bifidobacterium adolescentisandBifidobacterium animalissubsplactiswere more prevalent in patients with active coeliac disease than in patients with treated coeliac disease and control children. A higher LAB diversity was found in patients with treated coeliac disease and controls than in patients with active coeliac disease.Weissellaspp andLactobacillus fermentumwere more frequently detected in patients with treated coeliac disease than in controls and patients with active coeliac disease.

Conclusions

Bacteroides,Bifidobacteriumand LAB populations in the duodenum of Spanish children with typical coeliac disease (active and treated) and controls differ in diversity and species composition; this could contribute to features of the disease.
Endovascular treatment of venous sinus thrombosis: a case report and review of the literature
Authors: Nimjee Shahid M , Powers Ciaran J , Kolls Bradley J , Smith Tony , Britz Gavin W , Zomorodi Ali R
Published: October 2010

Dural venous sinus thrombosis (DVST) is a pathological phenomenon resulting from vascular occlusion of the cerebral venous sinuses. The mainstay of therapy for DVST is anticoagulation but more aggressive interventional therapies must be considered when medical therapy fails. A case is presented of a patient who was diagnosed with DVST, medically treated immediately but continued to deteriorate. Invasive endovascular therapies ultimately obliterated the thrombi in her sinuses. A brief review of the literature is reported.
Transarterial Onyx embolization of sacral chordoma: case report and review of the literature: Figure 1
Authors: Hu Yin C , Newman C Benjamin , Porter Randall W , Albuquerque Felipe C
Published: October 2010

Aim

To report a successful transarterial Onyx embolization of a highly vascularized sacral chordoma.

Case presentation

A 74-year-old patient presented with progressive lower back pain and anorectal and urogenital dysfunction complicated by excessive intraoperative blood loss requiring emergent endovascular intervention.

Intervention

Emergent pelvic angiography demonstrated a highly vascularized sacral chordoma. Transarterial embolization with Onyx was performed successfully via a single arterial pedicle, the median sacral artery. Surgical extirpation was achieved with the expected amount of intraoperative blood loss without further complications.

Conclusion

Preoperative transarterial Onyx embolization can be performed safely and effectively to assist in the surgical resection of sacral chordomas.
Ignition strength of 25 international cigarette brands
Authors: Seidenberg Andrew B , Rees Vaughan W , Alpert Hillel R , O'Connor Richard J , Connolly Gregory N
Published: October 2010

Background

Cigarette-ignited fires are a leading cause of fire death and injury throughout the world and remain a global public health and safety problem. To reduce this harm, a small number of countries now require cigarettes to have reduced ignition propensity (RIP). It is not known if cigarette manufacturers are voluntarily introducing RIP cigarettes in other countries to help save lives.

Methods

Using the ASTM E2187-04 test method, per cent full length burn (%FLB) was measured for three popular brands from each of seven countries that did not have RIP legislation at the time of purchase. Results were compared with %FLB measurements from four popular US brands purchased in a jurisdiction (Vermont) with an RIP law. SRM 1082 reference cigarette was also tested to assure laboratory quality control.

Results

All cigarette brands purchased in countries not requiring fire safety standards for cigarettes exceeded 75% FLB. In contrast, none of the cigarette brands from the USA exceeded 10% FLB. The SRM 1082 reference cigarette demonstrated 5% FLB.

Conclusion

Cigarette ignition propensity can be greatly reduced through legislation that requires cigarette fire safety standards. RIP cigarettes have the potential to significantly decrease the number of fire deaths, injuries and destruction of property caused by cigarette-ignited fires. Appropriate standards should be applied in cigarette markets globally.
Resistance to Legality
Authors: Brisbin Richard A.
Published: October 2010

The contingency of legality creates opportunities for individuals and collective associations to oppose its norms and requirements. This article examines the context and dimensions of resistance or opposition to legality, why resistance occurs, the strategies and tactics used to conduct resistance, the outcomes of acts of resistance, and whether resistance is a meaningful social and political activity.
Entry Regulation under Asymmetric Information about Demand
Authors: Sarmento Paula , Brandão António
Published: October 2010

We investigate how an incumbent firm can use the regulatory policy about entry and the informational advantage to protect his market position. This question is studied through the construction of a signalling game where we assume that the regulator has less information about demand than the firms. We conclude that there is a pooling equilibrium and partially separating equilibria in which entry is deterred and, if demand is high, there will be insufficient entry. The final effect on welfare depends on the tradeoff between short‐run benefits (lower price) and long‐run losses (weaker competition).
Fluorescence and Photochemical Investigations of Phytochrome in Higher Plants
Authors: Sineshchekov Vitaly A.
Published: October 2010

In higher plants, photoreceptor phytochrome (phy)—photoisomerizing biliprotein working as a light-driven molecular switch—is represented by a small family of phytochrome gene products with phyA and phyB as major species. phyA is unique among other phytochromes mediating photoresponse modes specific only for this pigment (far-red light induced) and also photoresponses characteristic of phyB and other minor phys (red light induced). In our group,in vivofluorescence investigations of phytochrome were initiated and two native phyA pools—posttranslationally modifiedPHYAgene products designated phyA′and phyA″—were detected in dicots and monocots. They differ by spectroscopic and photochemical parameters, by abundance and distribution in etiolated plant tissues, by light stability, and other phenomenological characteristics, and, most importantly, by their functional properties. This may explain, at least partially, the nature of the uniqueness of the phyA action. In this paper, the data on the phyA polymorphism are summarized with attention to the applied experimental approach.
Complete Genome Sequence of Rothia mucilaginosa DY-18: A Clinical Isolate with Dense Meshwork-Like Structures from a Persistent Apical Periodontitis Lesion
Authors: Yamane Kazuyoshi , Nambu Takayuki , Yamanaka Takeshi , Mashimo Chiho , Sugimori Chieko , Leung Kai-Poon , Fukushima Hisanori
Published: October 2010

Rothia mucilaginosa is an opportunistic pathogen in the human oral cavity and pharynx. We found that R. mucilaginosa DY-18, a clinical isolate from a persistent apical periodontitis lesion, had biofilm-like structures. Similar structures were also observed on R. mucilaginosa ATCC25296. To further study these structures, we determined the complete genome sequence of DY-18 and found it a 2.26-Mb chromosome. Regarding stress responsive systems known to affect biofilm formation in many bacteria, DY-18 genome possessed only two sigma factor genes. One of these encoded an additional sigma factor whose promoter-binding activity may be regulated in response to environmental stimuli. Additionally, several genes assigned to two-component signal transduction systems were presented in this genome. To the best of our knowledge, this is the first complete genome of R. mucilaginosa species and our data raise the possibility that this organism regulates the biofilm phenotype through these stress responsive systems.
The Distribution of the Size of the Union of Cycles for Two Types of Random Permutations
Authors: Lengyel Tamás
Published: October 2010

We discuss some problems and permutation statistics involving two different types of random permutations. Under the usual model of random permutations, we prove that the shifted coverage of the elements of {1, 2, …, k} of a random permutation over {1, 2, …, n}; that is, the size of the union of the cycles containing these elements, excluding these elements themselves, follows a negative hypergeometric distribution. This fact gives a probabilistic model for the coverage via the canonical cycle representation. For a different random model, we determine some random permutation statistics regarding the problem of the
lost boarding pass and its variations.
The Social Cognitive Evaluation Battery for Children with Autism: A New Tool for the Assessment of Cognitive and Social Development in Children with Autism Spectrum Disorders
Authors: Thiébaut Eric , Adrien Jean-Louis , Blanc Romuald , Barthelemy Catherine
Published: October 2010

The Social Cognitive Evaluation Battery (SCEB) is a new instrument for the psychological evaluation of children with autism. The battery consists of 16 scales that measure different cognitive and socioemotional functions. This study reports the results of a reliability analysis and some elements of validation. Analyses are based on the observed performance of 100 children with autism and a convenience sample of 35 normal children. Validation is based on the examination of the structure of the relations between the 16 scale scores of the SCEB, their relations with other measurements, the correspondence between the theoretical developmental ages, and the observed chronological ages and the SCEB's sensitivity to specific disorders. The results show that this new instrument is useful and relevant for the psychological assessment of children with autism.
Carbazole Containing Copolymers: Synthesis, Characterization, and Applications in Reversible Holographic Recording
Authors: Mailhot-Jensen Bénédicte , Robu Stefan , Rivaton Agnès , Pilichowski Jean-François , Chirita Arcadi , Chilat Ekaterina , Dragalina Galina
Published: October 2010

Carbazolic copolymers have been developed to be used in reversible holographic recording. This paper describes a complete analysis, from synthesis of the material to its applications, together with the corresponding characterizations. The investigated materials were photosensitive copolymers obtained from carbazolylalkylmethacrylates (CEM) and octylmethacrylate (OMA). A detailed investigation was undertaken involving infrared spectroscopy and NMR techniques,1H,13C, COSY, and HSQC, in order to establish the chemical structure and the composition of the copolymers. Holographic recording characteristics were investigated with one- and two-layer photothermoplastic carriers. The two-layer carrier contains separate photosensitive and thermoplastic layers and gives the best holographic response. The surface of microstructured samples has been characterized by atomic force microscopy analysis. It is shown that via a photothermoplastic recording process, it is possible to record and read holograms practically in real time (~3 s) with a diffraction efficiency of 10% and a spatial resolution higher than 1000 .
Hodgkin's Lymphomas: A Tumor Recognized by Its Microenvironment
Authors: Montes-Moreno S.
Published: October 2010

Thomas Hodgkin's and Samuel Wilks first recognized Hodgkin disease in the first half of the 19th century. Initially described as lymphogranulomatosis, it was later recognized to be a lymphoid neoplasm derived from B cells and was classified on the basis of its histopathological features. Hodgkin lymphomas are now regarded as encompassing two clearly defined entities according to the WHO classification: nodular lymphocyte-predominant Hodgkin Lymphoma (NLPHL) and classical Hodgkin Lymphoma (CHL). This paper focuses on the current knowledge about the biological features that characterize both NLPHL and CHL, highlighting those relevant to correct pathological diagnosis and those that might be associated with patient outcome.
Fixed Point Results in Quasimetric Spaces
Authors: Latif Abdul , Al-Mezel Saleh A
Published: October 2010

In the setting of quasimetric spaces, we prove some new results on the existence of fixed points for contractive type maps with respect to "Equation missing"-function. Our results either improve or generalize many known results in the literature.
Role of Radiotherapy in Modern Treatment of Hodgkin's Lymphoma
Authors: Yeoh Kheng-Wei , Mikhaeel N. George
Published: October 2010

Hodgkin's Lymphoma was incurable until the advent of effective therapeutic radiation around the first half of the 20th century. As survival rates improved, the long-term toxicities from radiotherapy began to emerge. This together with the availability of effective chemotherapy has encouraged a combined modality approach for early-staged disease and the omission of radiotherapy in advanced-staged disease. The differing toxicities of radiotherapy and chemotherapy has promoted ongoing research to identify the utility of each of these modalities in the modern management of Hodgkin's Lymphoma. This article will provide a critical review of the developments and indications for modern radiotherapy, in context with advances in chemotherapy, for the treatment of Hodgkin's Lymphoma.
Focus on Basal Cell Carcinoma
Authors: Samarasinghe Venura , Madan Vishal , Lear John T.
Published: October 2010

Nonmelanoma skin cancers (NMSCs), which include basal and squamous cell cancers are the most common human cancers. BCCs have a relatively low metastatic rate and slow growth and are frequently underreported. Whilst there is a definite role of sunexposure in the pathogenesis of BCC, several additional complex genotypic, phenotypic and environmental factors are contributory. The high prevalence and the frequent occurrence of multiple primary BCC in affected individuals make them an important public health problem. This has led to a substantial increase in search for newer noninvasive treatments for BCC. Surgical excision with predetermined margins remains the mainstay treatment for most BCC. Of the newer non-invasive treatments only photodynamic therapy and topical imiquimod have become established in the treatment of certain BCC subtypes, while the search for other more effective and tissue salvaging therapies continues. This paper focuses on the pathogenesis and management of BCC.
Comparative Phylogeography of the Coral Triangle and Implications for Marine Management
Authors: Carpenter Kent E. , Barber Paul H. , Crandall Eric D. , Ablan-Lagman Ma. Carmen A. , Ambariyanto  , Mahardika Gusti Ngurah , Manjaji-Matsumoto B. Mabel , Juinio-Meñez Marie Antonette , Santos Mudjekeewis D. , Starger Craig J. , Toha Abdul Hamid A.
Published: October 2010

Extreme concentration of marine biodiversity and exploitation of marine resources in the Coral Triangle pose challenges to biogeographers and resource managers. Comparative phylogeography provides a powerful tool to test biogeographic hypotheses evoked to explain species richness in the Coral Triangle. It can also be used to delineate management units for marine resources. After about a decade of phylogeographical studies, patterns for the Coral Triangle are emerging. Broad connectivity in some species support the notion that larvae have maintained gene flow among distant populations for long periods. Other phylogeographic patterns suggest vicariant events resulting from Pleistocene sea level fluctuations, which have, at least occasionally, resulted in speciation. Divergence dates ranging back to the Miocene suggest that changing land configurations may have precipitated an explosion of species diversification. A synthesis of the marine phylogeographic studies reveals repeated patterns that corroborate hypothesized biogeographic processes and suggest improved management schemes for marine resources.
Not All Larvae Stay Close to Home: Insights into Marine Population Connectivity with a Focus on the Brown Surgeonfish (Acanthurus nigrofuscus)
Authors: Eble Jeff A. , Rocha Luiz A. , Craig Matthew T. , Bowen Brian W.
Published: October 2010

Recent reports of localized larval recruitment in predominately small-range fishes are countered by studies that show high genetic connectivity across large oceanic distances. This discrepancy may result from the different timescales over which genetic and demographic processes operate or rather may indicate regular long-distance dispersal in some species. Here, we contribute an analysis of mtDNA cytochromebdiversity in the widely distributed Brown Surgeonfish (Acanthurus nigrofuscus;N=560), which revealed significant genetic structure only at the extremes of the range (ΦCT=0.452;P<.001). Collections from Hawaii to the Eastern Indian Ocean comprise one large, undifferentiated population. This pattern of limited genetic subdivision across reefs of the central Indo-Pacific has been observed in a number of large-range reef fishes. Conversely, small-range fishes are often deeply structured over the same area. These findings demonstrate population connectivity differences among species at biogeographic and evolutionary timescales, which likely translates into differences in dispersal ability at ecological and demographic timescales. While interspecific differences in population connectivity complicate the design of management strategies, the integration of multiscale connectivity patterns into marine resource planning will help ensure long-term ecosystem stability by preserving functionally diverse communities.
The Role of the IL-12 Cytokine Family in Directing T-Cell Responses in Oral Candidosis
Authors: Wei Xiao-Qing , Rogers Helen , Lewis Michael A. O. , Williams David W.
Published: October 2010

Candida albicansis an opportunistic fungal pathogen that normally exists as a harmless commensal in humans. In instances where host debilitation occurs,Candidacan cause a range of clinical infections, and whilst these are primarily superficial, effecting mucosal membranes, systemic infections can develop in severely immunocompromised individuals. The mechanism of host immunity during commensal carriage ofC. albicanshas been intensively studied. In this paper, we present the most recent information concerning host recognition ofC. albicansleading to cytokine production and the subsequent T-cell responses generated in response toC. albicans. Particular focus is given to the role of the IL-12 cytokine family including IL-12, IL-23, IL-27, and IL-35, in host immunity toCandida. T-cells are considered crucial in the regulation of immunity and inflammation. In this regard, the role of Th1/2, helper cells, together with the recently identified Th17 and Treg cells in candidosis will be discussed. Understanding the detailed mechanisms that underlie host immunity toCandidanot only will be of benefit in terms of the infections caused by this organism but could also be exploited in the development of therapeutic interventions for other diseases.
The Sensorium: A Multimodal Neurofeedback Environment
Authors: Hinterberger Thilo
Published: October 2010

The Sensorium is a neurofeedback environment that allows people to experience signals from their nonperceptible body processes visually and auditorily. Various (neuro-)physiological rhythms and frequencies are projected simultaneously as soundscapes and “lightscapes” into the environment. A wireless physiological amplifier device sends signals such as EEG and ECG to a computer for real-time processing using the modified brain-computer interface software “Thought Translation Device” (TTD). The TTD performs signal filtering, parametric orchestral sonification, and light control. In a pilot study, 20 participants have been exposed to their ongoing brain and heart signals while sitting inside the Sensorium, a small room equipped with a speaker and lighting system. Almost all of them reported an increase in contentment, relaxation, happiness, and inner harmony. They also reported a widening in their body consciousness. In future, therapeutic paradigms will be developed and the treatment effects on people with psychosomatic diseases will be evaluated.
Influence of Hsp90 and HDAC Inhibition and Tubulin Acetylation on Perinuclear Protein Aggregation in Human Retinal Pigment Epithelial Cells
Authors: Ryhänen Tuomas , Viiri Johanna , Hyttinen Juha M. T. , Uusitalo Hannu , Salminen Antero , Kaarniranta Kai
Published: October 2010

Retinal pigment epithelial (RPE) cells are continually exposed to oxidative stress that contributes to protein misfolding, aggregation and functional abnormalities during aging. The protein aggregates formed at the cell periphery are delivered along the microtubulus network by dynein‐dependent retrograde trafficking to a juxtanuclear location. We demonstrate that Hsp90 inhibition by geldanamycin can effectively suppress proteasome inhibitor, MG‐132‐induced protein aggregation in a way that is independent of HDAC inhibition or the tubulin acetylation levels in ARPE‐19 cells. However, the tubulin acetylation and polymerization state affects the localization of the proteasome‐inhibitor‐induced aggregation. These findings open new perspectives for understanding the pathogenesis of protein aggregation in retinal cells and can be useful for the development of therapeutic treatments to prevent retinal cell deterioration.
Influence of Lithium on Nanosized Films of Fe2O3
Authors: Turković A. , Ivanda M. , Bitenc M. , Crnjak Orel Z.
Published: October 2010

We have investigated nanosized thin films ofα-Fe2O3(hematite) andα-Fe2O3with addition of Li, by the impedance spectroscopy (IS), the Raman spectroscopy, scanning electron microscopy (SEM), and X-ray diffraction (XRD). Combining all of these methods, and earlier obtained thermally stimulated currents (TSC) on the same samples, the dependence of structural and electrical properties upon percentage of Li added into the matrix of these metal-oxide films was found. The comparison of IS, Raman, SEM, XRD, and TSC results reveals the increase of the size of nanoparticles upon inducing 1% of Li inFe2O3matrix followed by the decrease of the size of nanoparticles in the case of samples with 10% Li, as well as the decrease (increase) of conductivity, respectively. These changes are explained by the structural and morphological changes caused by the impact ofLi+ions in the charge transfers. This material is suitable for application in the galvanic cell of second generation that could be used as solar-cells backup.
Inhibitory Effect of Chinese Propolis on Phosphatidylcholine‐Specific Phospholipase C Activity in Vascular Endothelial Cells
Authors: Xuan Hongzhuan , Zhu Ruiliang , Li Yajing , Hu Fuliang
Published: October 2010

To understand the mechanisms underlying the anti‐inflammatory action of Chinese propolis, we investigated its effect on the activity of phosphatidylcholine‐specific phospholipase C (PC‐PLC) that plays critical roles in control of vascular endothelial cell (VEC) function and inflammatory responses. Furthermore, p53 and reactive oxygen species (ROS) levels and mitochondrial membrane potential (Δψm) were investigated. Our data indicated that treatment of Chinese propolis 6.25 and 12.5 μg/ml for 12 hours increased VEC viability obviously. Exposure to Chinese propolis 6.25, 12.5, and 25 μg/ml for 6 and 12 hours significantly decreased PC‐PLC activity and p53 level, and ROS levels were depressed by Chinese propolis 12.5 μg/ml and 25 μg/ml dramatically. The Δψm of VECs was not affected by Chinese propolis at low concentration but disrupted by the propolis at 25 μg/ml significantly, which indicated that Chinese propolis depressed PC‐PLC activity and the levels of p53 and ROS in VECs but disrupted Δψm at a high concentration.
Impact of residual and intrafractional errors on strategy of correction for image-guided accelerated partial breast irradiation
Authors: Cai Gang , Hu Wei-Gang , Chen Jia-Yi , Yu Xiao-Li , Pan Zi-Qiang , Yang Zhao-Zhi , Guo Xiao-Mao , Shao Zhi-Min , Jiang Guo-Liang
Published: October 2010

Background

The cone beam CT (CBCT) guided radiation can reduce the systematic and random setup errors as compared to the skin-mark setup. However, the residual and intrafractional (RAIF) errors are still unknown. The purpose of this paper is to investigate the magnitude of RAIF errors and correction action levels needed in cone beam computed tomography (CBCT) guided accelerated partial breast irradiation (APBI).

Methods

Ten patients were enrolled in the prospective study of CBCT guided APBI. The postoperative tumor bed was irradiated with 38.5 Gy in 10 fractions over 5 days. Two cone-beam CT data sets were obtained with one before and one after the treatment delivery. The CBCT images were registered online to the planning CT images using the automatic algorithm followed by a fine manual adjustment. An action level of 3 mm, meaning that corrections were performed for translations exceeding 3 mm, was implemented in clinical treatments. Based on the acquired data, different correction action levels were simulated, and random RAIF errors, systematic RAIF errors and related margins before and after the treatments were determined for varying correction action levels.

Results

A total of 75 pairs of CBCT data sets were analyzed. The systematic and random setup errors based on skin-mark setup prior to treatment delivery were 2.1 mm and 1.8 mm in the lateral (LR), 3.1 mm and 2.3 mm in the superior-inferior (SI), and 2.3 mm and 2.0 mm in the anterior-posterior (AP) directions. With the 3 mm correction action level, the systematic and random RAIF errors were 2.5 mm and 2.3 mm in the LR direction, 2.3 mm and 2.3 mm in the SI direction, and 2.3 mm and 2.2 mm in the AP direction after treatments delivery. Accordingly, the margins for correction action levels of 3 mm, 4 mm, 5 mm, 6 mm and no correction were 7.9 mm, 8.0 mm, 8.0 mm, 7.9 mm and 8.0 mm in the LR direction; 6.4 mm, 7.1 mm, 7.9 mm, 9.2 mm and 10.5 mm in the SI direction; 7.6 mm, 7.9 mm, 9.4 mm, 10.1 mm and 12.7 mm in the AP direction, respectively.

Conclusions

Residual and intrafractional errors can significantly affect the accuracy of image-guided APBI with nonplanar 3DCRT techniques. If a 10-mm CTV-PTV margin is applied, a correction action level of 5 mm or less is necessary so as to maintain the RAIF errors within 10 mm for more than 95% of fractions. Pre-treatment CBCT guidance is not a guarantee for safe delivery of the treatment despite its known benefits of reducing the initial setup errors. A patient position verification and correction during the treatment may be a method for the safe delivery.