Genomic islands: tools of bacterial horizontal gene transfer and evolution.

Abstract Bacterial genomes evolve through mutations, rearrangements or horizontal gene transfer. Besides the core genes encoding essential metabolic functions, bacterial genomes also harbour a number of accessory genes acquired by horizontal gene transfer that might be beneficial under certain environmental conditions. The horizontal gene transfer contributes to the diversification and adaptation of microorganisms, thus having an impact on the genome plasticity. A significant part of the horizontal gene transfer is or has been facilitated by genomic islands (GEIs). GEIs are discrete DNA segments, some of which are mobile and others which are not, or are no longer mobile, which differ among closely related strains. A number of GEIs are capable of integration into the chromosome of the host, excision, and transfer to a new host by transformation, conjugation or transduction. GEIs play a crucial role in the evolution of a broad spectrum of bacteria as they are involved in the dissemination of variable genes, including antibiotic resistance and virulence genes leading to generation of hospital 'superbugs', as well as catabolic genes leading to formation of new metabolic pathways. Depending on the composition of gene modules, the same type of GEIs can promote survival of pathogenic as well as environmental bacteria.

Maximising the duration of disease control in metastatic renal cell carcinoma with targeted agents: an expert agreement.

With six targeted agents approved (sorafenib, sunitinib, temsirolimus, bevacizumab [+interferon], everolimus and pazopanib), many patients with metastatic renal cell carcinoma (mRCC) will receive multiple therapies. However, the optimum sequencing approach has not been defined. A group of European experts reviewed available data and shared their clinical experience to compile an expert agreement on the sequential use of targeted agents in mRCC. To date, there are few prospective studies of sequential therapy. The mammalian target of rapamycin (mTOR) inhibitor everolimus was approved for use in patients who failed treatment with inhibitors of vascular endothelial growth factor (VEGF) and VEGF receptors (VEGFR) based on the results from a Phase III placebo-controlled study; however, until then, the only licensed agents across the spectrum of mRCC were VEGF(R) inhibitors (sorafenib, sunitinib and bevacizumab + interferon), and as such, a large body of evidence has accumulated regarding their use in sequence. Data show that sequential use of VEGF(R) inhibitors may be an effective treatment strategy to achieve prolonged clinical benefit. The optimal place of each targeted agent in the treatment sequence is still unclear, and data from large prospective studies are needed. The Phase III AXIS study of second-line sorafenib vs. axitinib (including post-VEGF(R) inhibitors) has completed, but the data are not yet published; other ongoing studies include the Phase III SWITCH study of sorafenib-sunitinib vs. sunitinib-sorafenib (NCT00732914); the Phase III 404 study of temsirolimus vs. sorafenib post-sunitinib (NCT00474786) and the Phase II RECORD 3 study of sunitinib-everolimus vs. everolimus-sunitinib (NCT00903175). Until additional data are available, consideration of patient response and tolerability to treatment may facilitate current decision-making regarding when to switch and which treatment to switch to in real-life clinical practice.

Identifying the unmet health needs of patients with congenital hypogonadotropic hypogonadism using a web-based needs assessment: implications for online interventions and peer-to-peer support.

BACKGROUND: Patients with rare diseases such as congenital hypogonadotropic hypogonadism (CHH) are dispersed, often challenged to find specialized care and face other health disparities. The internet has the potential to reach a wide audience of rare disease patients and can help connect patients and specialists. Therefore, this study aimed to: (i) determine if web-based platforms could be effectively used to conduct an online needs assessment of dispersed CHH patients; (ii) identify the unmet health and informational needs of CHH patients and (iii) assess patient acceptability regarding patient-centered, web-based interventions to bridge shortfalls in care. METHODS: A sequential mixed-methods design was used: first, an online survey was conducted to evaluate health promoting behavior and identify unmet health and informational needs of CHH men. Subsequently, patient focus groups were held to explore specific patient-identified targets for care and to examine the acceptability of possible online interventions. Descriptive statistics and thematic qualitative analyses were used. RESULTS: 105 male participants completed the online survey (mean age 37 ± 11, range 19-66 years) representing a spectrum of patients across a broad socioeconomic range and all but one subject had adequate healthcare literacy. The survey revealed periods of non-adherence to treatment (34/93, 37%) and gaps in healthcare (36/87, 41%) exceeding one year. Patient focus groups identified lasting psychological effects related to feelings of isolation, shame and body-image concerns. Survey respondents were active internet users, nearly all had sought CHH information online (101/105, 96%), and they rated the internet, healthcare providers, and online community as equally important CHH information sources. Focus group participants were overwhelmingly positive regarding online interventions/support with links to reach expert healthcare providers and for peer-to-peer support. CONCLUSION: The web-based needs assessment was an effective way to reach dispersed CHH patients. These individuals often have long gaps in care and struggle with the psychosocial sequelae of CHH. They are highly motivated internet users seeking information and tapping into online communities and are receptive to novel web-based interventions addressing their unmet needs.

The atypical faces of neuroblastoma : pictorial essay : P49

Purpose: Neuroblastoma represents 8 to 10% of all pediatric tumors and account for 15% of cancer deaths in children. Neuroblastoma may arise anywhere sympathetic tissue is present and its clinical presentation may be very variable. Therefore, a significant number of unusual tumor presentation and imaging findings are possible.The purpose of this pictorial essay is to review the unusual imaging findings of neuroblastoma. Methods and materials: We retrospectively revised the 25 cases f neuroblastoma detected and treated at our institution in the last 3 years and selected those cases with atypical imaging findings at the initial diagnosis and the follow-up studies. Results: A significant number of our studies showed atypical imaging findings concerning the site of origin, the initial characteristics and extension of the primary tumor or the site of metastasis. Conclusion: The variability of origin and the changing clinical evolution of neuroblastoma may originate a wide spectrum of unusual imaging findings, which should be recognized to allow a correct diagnosis.

Systemic-onset juvenile idiopathic arthritis: the changing life of a rare disease.

Systemic-onset juvenile idiopathic arthritis (SoJIA), sometimes called Still's disease, is a systemic inflammatory disease classified within the spectrum of juvenile idiopathic arthritis (JIA). It is an orphan disease with often a chronic course and a major impact on the affected children and their families. This disorder is unique in terms of clinical manifestations, prognosis and response to conventional immunosuppressants. The objectives of this review are to describe SoJIA and emphasise the recent advances in the pathogenesis and treatment, which have transformed the care and the prognosis of this potentially life-threatening paediatric condition.

Rhea-a manually curated resource of biochemical reactions.

Rhea (http://www.ebi.ac.uk/rhea) is a comprehensive resource of expert-curated biochemical reactions. Rhea provides a non-redundant set of chemical transformations for use in a broad spectrum of applications, including metabolic network reconstruction and pathway inference. Rhea includes enzyme-catalyzed reactions (covering the IUBMB Enzyme Nomenclature list), transport reactions and spontaneously occurring reactions. Rhea reactions are described using chemical species from the Chemical Entities of Biological Interest ontology (ChEBI) and are stoichiometrically balanced for mass and charge. They are extensively manually curated with links to source literature and other public resources on metabolism including enzyme and pathway databases. This cross-referencing facilitates the mapping and reconciliation of common reactions and compounds between distinct resources, which is a common first step in the reconstruction of genome scale metabolic networks and models.

In vitro selection of bacteria with potential for use as probiotics in marine shrimp culture

The objective of this work was to isolate strains of lactic acid bacteria with probiotic potential from the digestive tract of marine shrimp (Litopenaeus vannamei), and to carry out in vitro selection based on multiple characters. The ideotype (ideal proposed strain) was defined by the highest averages for the traits maximum growth velocity, final count of viable cells, and inhibition halo against nine freshwater and marine pathogens, and by the lowest averages for the traits duplication time and resistance of strains to NaCl (1.5 and 3%), pH (6, 8, and 9), and biliary salts (5%). Mahalanobis distance (D²) was estimated among the evaluated strains, and the best ones were those with the shortest distances to the ideotype. Ten bacterial strains were isolated and biochemically identified as Lactobacillus plantarum (3), L. brevis (3), Weissella confusa (2), Lactococcus lactis (1), and L. delbrueckii (1). Lactobacillus plantarum strains showed a wide spectrum of action and the largest inhibition halos against pathogens, both Gram-positive and negative, high growth rate, and tolerance to all evaluated parameters. In relation to ideotype, L. plantarum showed the lowest Mahalanobis (D²) distance, followed by the strains of W. confusa, L. brevis, L. lactis, and L. delbrueckii. Among the analyzed bacterial strains, those of Lactobacillus plantarum have the greatest potential for use as a probiotic for marine shrimp.

Neck complaints in the pediatric emergency department: a consecutive case series of 170 children.

OBJECTIVES: To describe the spectrum of pathologies responsible for neck ailments in a primary care pediatric emergency setting and evaluate their outcome. METHODS: All children aged 16 years or younger, who presented to the emergency department of the Children's Hospital of Lausanne during a 1-year period, were retrospectively identified and charts were reviewed. Causes of neck complaints were classified as traumatic (group 1), infectious (group 2), postural (group 3), or miscellaneous (group 4) according to the final diagnosis. History and physical examination findings, radiological and laboratory results, as well as patient outcomes were recorded. RESULTS: During the study period, 28,722 children were observed in the emergency department, and 170 were identified as having neck complaints. The number of patients with neck ailments in group 1 was 105 (62%). Group 2 contained 33 patients (19%), of which 28 (16.5%) had a viral infection and 5 (2.9%) had a bacterial infection. Group 3 contained 30 children (17.6%) and group 4 contained 2 children (1.2%). Cervical spine radiography was performed on an emergency basis in 60 children (57 in group 1, 2 in group 2, and 1 in group 3). Significant abnormalities were observed in 6 children. Cervical computed tomography (CT) was performed in 9 children, from which 5 were in group 1, 3 were in group 2, and 1 was in group 4. The CT scan revealed pathologic findings in 6 children. Follow-up data were available in 135 patients (79.4%), of which 129 (95.6%) experienced complete recovery in less than 2 weeks. Admission to the hospital was necessary in 4 children (1 in group 1 and 3 in group 2), including 2 for emergency surgical drainage of retropharyngeal abscesses. One child with posttraumatic torticollis was treated conservatively as an outpatient and recovered in 7 weeks. One child was had his/her condition eventually diagnosed with osteoid osteoma and treated with oral nonsteroidal anti-inflammatory drug. CONCLUSIONS: Most cases of neck ailments in children presenting to the emergency department were due to trauma or infection, which were effectively managed as outpatients. When signs and symptoms suggested an emergent cause, CT provided a definitive diagnosis. The evaluation of a child presenting with acute neck complaints should be based on history and physical examination. Plain radiographs and CT scan are contributive in selected cases.

Diabetic neuropathy is a more important determinant of baroreflex sensitivity than carotid elasticity in type 2 diabetes.

The object of this study was to evaluate the contribution of carotid distensibilty on baroreflex sensitivity in patients with type 2 diabetes mellitus with at least 2 additional cardiovascular risk factors. Carotid distensibility was measured bilaterally at the common carotid artery in 79 consecutive diabetic patients and 60 matched subjects without diabetes. Spontaneous baroreflex sensitivity assessment was obtained using time and frequency methods. Baroreflex sensitivity was lower in diabetic subjects as compared with nondiabetic control subjects (5.25+/-2.80 ms/mm Hg versus 7.55+/-3.79 ms/mm Hg; P<0.01, respectively). Contrary to nondiabetic subjects, diabetic subjects showed no significant correlation between carotid distensibility and baroreflex sensitivity (r2=0.08, P=0.04 and r2=0.04, P=0.13, respectively). In diabetic subjects, baroreflex sensitivity was significantly lower in subjects with peripheral neuropathy than in those with preserved vibration sensation (4.1+/-0.5 versus 6.1+/-0.4 ms/mm Hg, respectively; P=0.005). Age in nondiabetic subjects, diabetes duration, systolic blood pressure, peripheral or sensitive neuropathy, and carotid distensibility were introduced in a stepwise multivariate analysis to identify the determinants of baroreflex sensitivity. In diabetic patients, neuropathy is a more sensitive determinant of baroreflex sensitivity than the reduced carotid distensibility (stepwise analysis; F ratio=5.1, P=0.028 versus F ratio=1.9, P=0.16, respectively). In diabetic subjects with 2 additional cardiovascular risk factors, spontaneous baroreflex sensitivity is not related to carotid distensibility. Diabetic subjects represent a particular population within the spectrum of cardiovascular risk situations because of the marked neuropathy associated with their metabolic disorder. Therefore, neuropathy is a more significant determinant of baroreflex sensitivity than carotid artery elasticity in patients with type 2 diabetes.

Volcanic debris avalanche deposits of the upper Maronne valley (Cantal Volcano, France): evidence for contrasted formation and transport mechanisms

The deposits of two volcanic debris avalanches (VDA I and II) that occur in the upper Maronne valley, northwest sector of Cantal Volcano, France, were studied to establish their mechanisms of formation, transport and deposition. These two volcanic debris avalanches that clearly differ with regard to their structures, textures and extensions, exemplify the wide spectrum of events associated with large-scale sector collapse. VDA I is voluminous (similar to1 km(3) in the upper Maronne valley) and widespread. The deposits comprise two distinct facies: the block facies that forms the intermediate and upper part of the unit and the mixed facies that crops out essentially at the base of the unit. The block facies consists of more or less brecciated lava, block-and-ash-flow breccia and pumice-flow tuff megablocks set in breccias resulting from block disaggregation. Mixing and differential movements are almost absent in this part of the VDA. The mixed facies consists of breccias rich in fine particles that originate from block disagregation, as well as being picked up from the substratum during movement. Mixing and differential movements are predominant in this zone. Analysis of fractures on lava megablocks suggests that shear stress during the initial sliding is the principal cause of fracture. These data strongly indicate that VDA I is purely gravitational and argue for a model in which the initial sliding mass transforms into a flow due to differential in situ fragmentation caused by the shear stress. VDA II is restricted to low-topography areas. Its volume, in the studied area, is about 0.3 km(3). The deposits consist of brecciated, rounded blocks and megablocks set in a fine-grained matrix composed essentially of volcanic glass. This unit is stratified, with a massive layer that contains all the megablocks at the base and in the intermediate part, and in the upper part a normally graded layer that contains only blocks <1 m in size. The different lithologies present are totally mixed. These observations suggest that VDA II may be of the Bezymianny-type and that it underwent a flow transformation from a turbulent to a stratified flow consisting of a basal hyperconcentrated laminar body overlain by a dilute layer. (C) 2000 Elsevier Science B.V. All rights reserved.

Multisystem Langerhans' cell histiocytosis (Hand-Schüller-Christian disease) in an adult: a case report and review of the literature.

Langerhans' cell histiocytosis (LCH) is a rare and enigmatic clonal disorder that affects mainly children. It is characterized by single or multiple granulomatous mass lesions composed of cells with the Langerhans' cell phenotype. Clinical presentation and behavior are heterogeneous and can range from a solitary lytic bone lesion (i.e., eosinophilic granuloma) with a favorable course to a fatal disseminated leukaemia-like form, with a wide spectrum of intermediate clinical presentations between these two extremes. Although LCH typically involves the bone, lesions can be found in almost all organs. We are reporting the case of a multisystem LCH in a 47-year-old patient who presented with a panhypopituitarism and diabetes insipidus, and who, 5 years later, developed mandibular, mastoid and femoral lesions. The final diagnosis of LCH was made on mandibular biopsy.

Patulin in food: state-of-the-art and analytical trends

Patulin is a mycotoxin produced by several fungal species of the genera Penicillium and Aspergillus, found on several fruit species and, remarkably, in apples and apple products. Patulin has a broad spectrum of toxicity, including carcinogenicity and teratogenicity in animals. Due to the stability of the molecule, considerable amounts of patulin still remain in apple products after processing. This paper reviews different analytical methods for patulin determination and methods to reduce levels of patulin in apple products as well.

Spectral energy distribution of the gamma-ray microquasar LS 5039

The microquasar LS 5039 has recently been detected as a source of very high energy (VHE) $\gamma$-rays. This detection, that confirms the previously proposed association of LS 5039 with the EGRET source 3EG~J1824$-$1514, makes of LS 5039 a special system with observational data covering nearly all the electromagnetic spectrum. In order to reproduce the observed spectrum of LS 5039, from radio to VHE $\gamma$-rays, we have applied a cold matter dominated jet model that takes into account accretion variability, the jet magnetic field, particle acceleration, adiabatic and radiative losses, microscopic energy conservation in the jet, and pair creation and absorption due to the external photon fields, as well as the emission from the first generation of secondaries. The radiative processes taken into account are synchrotron, relativistic Bremsstrahlung and inverse Compton (IC). The model is based on a scenario that has been characterized with recent observational results, concerning the orbital parameters, the orbital variability at X-rays and the nature of the compact object. The computed spectral energy distribution (SED) shows a good agreement with the available observational data.

Childhood adversities as specific contributors to the co-occurrence of posttraumatic stress and alcohol use disorders.

There is much evidence that alcohol use disorders (AUD) often co-occur with posttraumatic stress disorders (PTSD), and that the comorbid condition is associated with a more severe clinical profile than that of PTSD without AUD. However, little is known about the role of childhood adversities as specific risk factors for the development of AUD in individuals presenting with PTSD. The aim of the study was to explore whether specific stressors from the spectrum of trauma and childhood adversities contribute to the development of AUD among subjects with PTSD. From a large community sample, of N=140 individuals with PTSD, N=24 (17.14%) received an additional diagnosis of AUD with an onset after the onset of PTSD. Those with comorbid PTSD/AUD and those with PTSD only were compared regarding type and features of their trauma, childhood adversities and psychiatric comorbidity. Compared to PTSD alone, PTSD/AUD was associated with higher levels of stress in terms of childhood adversities; in particular, sexual abuse below the age of 16, but also with having been brought up in a foster home. PTSD/AUD was also associated with an earlier age of adverse events. Treatment of AUD should include standardized assessments of trauma, especially of trauma experienced during childhood.

The Role of Logistics as a Competitiveness Factor when Entering New Markets

Tämän diplomityön tarkoituksena on löytää halvin tapa kohdeyrityksen tuotteiden saamiseksi määritellyille kohdemarkkinoille. Logistiset kustannukset ovat erityisen tärkeässä asemassa esimerkkitoimialalla, ja käytettävissä olevien logististen ratkaisujen kirjo tekee tehtävästä erityisen haastavan. Yrityksen ja teollisuudenalan erityispiirteiden esittelyn jälkeen valitaan sopiva tapa päästä markkinoille, minkä lisäksi pohditaan erilaisia kilpailustrategioita yrityksen aikaisempien kokemusten ja teoreettisen käsittelyn pohjalta. Tämä pohdinta on erilaisten analyysimenetelmien esittelyn lisäksi työn empiirisen osan taustalla. Logistiikkaympäristön ymmärtäminen ja sen tarjoamien mahdollisuuksien tunnistaminen ovat tärkeimmällä sijalla koko tutkimuksen ajan. Työssä tarkastellaan myös vientilogistiikan ja kohdemarkkinoiden erityispiirteitä, joita sovelletaan harkitsemisenarvoisiin kuljetustapoihin. Mahdollisten logististen ratkaisujen kustannusrakenteen ja kilpailukyvyn selvittämiseksi päätöksenteon tueksi luodaan yksilölliset vuokaaviot yrityksen omien kokemusten ja eri logistiikkapalvelujen tarjoajien lausuntojen perusteella. Näin voidaan edelleen tunnistaa mielekkäimmät logistiset ketjut ja arvioida niiden kustannustehokkuutta sekä suorien logististen että laatukustannusten suhteen. Lisäksi esimerkkien avulla tarkastellaan mahdollisuuksia benchmarkkaukseen. Työn lopuksi suositellaan johtopäätösten pohjalta tulevia toimenpiteitä, jotta myös jatkossa saataisiin aikaan vastaavaa pohdintaa ja toimintaa.