A compositional data analysis package for R providing multiple approaches

���compositions��� is a new R-package for the analysis of compositional and positive data.It contains four classes corresponding to the four different types of compositional andpositive geometry (including the Aitchison geometry). It provides means for computation,plotting and high-level multivariate statistical analysis in all four geometries.These geometries are treated in an fully analogous way, based on the principle of workingin coordinates, and the object-oriented programming paradigm of R. In this way,called functions automatically select the most appropriate type of analysis as a functionof the geometry. The graphical capabilities include ternary diagrams and tetrahedrons,various compositional plots (boxplots, barplots, piecharts) and extensive graphical toolsfor principal components. Afterwards, ortion and proportion lines, straight lines andellipses in all geometries can be added to plots. The package is accompanied by ahands-on-introduction, documentation for every function, demos of the graphical capabilitiesand plenty of usage examples. It allows direct and parallel computation inall four vector spaces and provides the beginner with a copy-and-paste style of dataanalysis, while letting advanced users keep the functionality and customizability theydemand of R, as well as all necessary tools to add own analysis routines. A completeexample is included in the appendix

Potential risk factors for multiple sclerosis in Rio de Janeiro: a case-control study.

PURPOSE. To evaluate potential risk factors for the development of multiple sclerosis in Brazilian patients. METHOD. A case control study was carried out in 81 patients enrolled at the Department of Neurology of the Hospital da Lagoa in Rio de Janeiro, and 81 paired controls. A standardized questionnaire on demographic, social and cultural variables, and medical and family history was used. Statistical analysis was performed using descriptive statistics and conditional logistic regression models with the SPSS for Windows software program. RESULTS. Having standard vaccinations (vaccinations specified by the Brazilian government) (OR=16.2; 95% CI=2.3-115.2), smoking (OR=7.6; 95% CI=2.1-28.2), being single (OR=4.7; 95% CI=1.4-15.6) and eating animal brain (OR=3.4; 95% CI=1.2-9.8) increased the risk of developing MS. CONCLUSIONS. RESULTS of this study may contribute towards better awareness of the epidemiological characteristics of Brazilian patients with multiple sclerosis.

Cervical myelopathy in hereditary multiple exostoses.

Spinal cord compression due to cervical exostoses is a rare but recognized complication of hereditary multiple exostosis (HME), an autosomal dominant disorder. This disease, also called multiple osteochondromatosis, is characterised by osteocartilaginous exostoses, typically involving the juxtaepiphyseal regions of long bones. Complications such as transformation to sarcoma (1 to 5%) or neurological compression (of the spinal cord, 1 to 9%) can arise during the course of the disease. We report the case of a 64-year-old man with progressive difficulties in walking over many years, ascribed to congenital rachitism. A diagnosis of HME was not made until late in the disease course. Investigations revealed cervical myelopathy due to vertebral exostosis as well as multiple exostoses in other sites. His gait was not improved after surgical decompression. A better knowledge of this disease could have prevented this neurological complication.

Neptune: a hil simulator for multiple UUVs

This paper overviews the field of graphical simulators used for AUV development, presents the taxonomy of these applications and proposes a classification. It also presents Neptune, a multivehicle, real-time, graphical simulator based on OpenGL that allows hardware in the loop simulations

Differential cognitive impairment for diverse forms of multiple sclerosis.

BACKGROUND Cognitive impairment is a common feature in multiple sclerosis (MS) patients and occurs in 60% of all cases. Unfortunately, neurological examination does not always agree with the neuropsychological evaluation in determining the cognitive profile of the patient. On the other hand, psychophysiological techniques such as event-related potentials (ERPs) can help in evaluating cognitive impairment in different pathologies. Behavioural responses and EEG signals were recorded during the experiment in three experimental groups: 1) a relapsing-remitting group (RRMS), 2) a benign multiple sclerosis group (BMS) and 3) a Control group. The paradigm employed was a spatial attention task with central cues (Posner experiment). The main aim was to observe the differences in the performance (behavioural variables) and in the latency and amplitude of the ERP components among these groups. RESULTS Our data indicate that both MS groups showed poorer task performance (longer reaction times and lower percentage of correct responses), a latency delay for the N1 and P300 component, and a different amplitude for the frontal N1. Moreover, the deficit in the BMS group, indexed by behavioural and pyschophysiological variables, was more pronounced compared to the RRMS group. CONCLUSION The present results suggest a cognitive impairment in the information processing in all of these patients. Comparing both pathological groups, cognitive impairment was more accentuated in the BMS group compared to the RMSS group. This suggests a silent deterioration of cognitive skills for the BMS that is not usually treated with pharmacological or neuropsychological therapy.

Analysis of selectin ligands supporting hematologic malignancy cell interactions with their microenvironment : focus on leukemia and multiple myeloma

CONTEXTE: Les s��lectines sont une famille de trois prot��ines qui r��glent la capture et le roulement des leucocytes et qui initient la cascade d'adh��sion. Elles contr��lent ��galement la migration des leucocytes en r��ponse �� un stimulus physiologique ou inflammatoire pour atteindre un organe cible. Le r��le des s��lectines et des leurs ligands est bien connu dans l'adh��sion des leucocytes normaux �� l'endoth��lium; en revanche, la nature des ligands des s��lectines exprim��s par les cellules leuc��miques et le my��lome multiple est peu connue. La r��cente d��couverte que la E- et la P-s��lectine sont exprim��es par les cellules endoth��liales et du stroma de la moelle osseuse, nous a incit�� �� examiner leur r��le dans les interactions des cellules malignes avec leur environnement m��dullaire. R��SULTATS: Les analyses ont ��t�� conduites sur les cellules du sang ou de la moelle osseuse pr��lev��es �� des patients atteints de leuc��mie aigu�� ou de my��lome multiple et sur des lign��es cellulaires. Les ligands des s��lectines qui ont ��t�� identifi��s sur les blastes leuc��miques ou les plasmocytes, sont �� P-selectin glycoprotein ligand-1 �� (PSGL-1), CD44, CD43 et l'endoglycan (EGC), ainsi que les saccharides fucosyl��s sLex et CLA. Nous avons v��rifi�� dans des exp��riences d'adh��sion cellulaire effectu��es dans des conditions de flux que ces ligands sont fonctionnels, ��tant porteurs des sucres mentionn��s, et qu'ils sont capables de supporter le roulement cellulaire d��pendant des s��lectines. De plus, nous avons montr�� que la liaison de ces ligands g��n��re des signaux intracellulaires favorisant la prolif��ration et la survie des cellules de my��lome. CONCLUSION. Les donn��es pr��sent��es ici montrent que la E- et la P- s��lectine du microenvironnement m��dullaire interagissent avec les cellules leuc��miques et de my��lome multiple, et que ces interactions activent des voies de signalisation contr��lant la prolif��ration et la survie cellulaire. Ces effets protecteurs sont impliqu��s dans la persistance de clones cellulaires malins r��sistant aux traitements et peuvent conduire �� la r��cidive de la maladie. L'inhibition de ces interactions pourrait fournir de nouvelles options th��rapeutiques pour le traitement de ces maladies de mauvais pronostic. - BACKGROUND: Selectins are a family of glycoproteins involved in the first steps of the adhesion cascade, tethering and rolling, during which leukocytes sense tissue specific signals and commit the cells to enter in a particular organ or inflammation site. While the role of selectins and their ligands is well established in supporting normal leukocyte adhesion to vascular endothelium, our knowledge of selectin ligands in two hematological malignancies, acute leukemia and multiple myeloma, is incomplete. The recent discovery that E- and P- selectin are also expressed on bone marrow (BM) endothelial and stromal cells, prompted us to investigate a potential role in selectin-mediated interaction of malignant cells with its protective BM microenvironment. RESULTS. Using cells obtained from blood or BM of patients affected by acute myeloid or lymphoblastic leukemia, or multiple myeloma, as well as cell lines, we characterized the expression of selectin ligands on blasts and plasma cells and identified P-selectin glycoprotein ligand-1 (PSGL-1), CD44, CD43 and endoglycan (EGC), as well as sLex/CLA determinants. Rolling assays under flow conditions allowed us to verify that these ligands are functional, i.e. correctly glycosylated and able to support selectin-mediated rolling. Moreover, we demonstrated that these ligands trigger proliferation and pro-survival signals upon engagement on myeloma cells. CONCLUSIONS. Data presented here demonstrate that E- and P-selectin in the BM microenvironment interact with leukemia and myeloma cells, and suggest that they have an impact on proliferation and survival of malignant plasma cells. These protective effects may induce drug resistance in malignant clones, leading to disease relapse. Interfering with these interactions could provide new therapeutic options. - Le corps humain d��pend du syst��me immunitaire pour sa protection face aux agressions, notamment des bact��ries ou des virus, ou face �� une dysfonction de l'organisme. Ce syst��me est compos�� de plusieurs types cellulaires, regroup��s sous le nom de leucocytes, qui participent �� son fonctionnement. Ces cellules se d��veloppent �� partir d'une cellule souche h��matopo'i��tique commune qui r��side dans la moelle osseuse. Comme c'est le cas dans les autres tissus, les cellules du syst��me immunitaire peuvent aussi d��velopper des cancers, appel��s tumeurs h��matopo����tiques ou tumeurs du sang. Bien que ces maladies puissent ��tre trait��es avec succ��s gr��ce �� de fortes doses de chimioth��rapies ou �� d'autres moyens comme les greffes, les patients connaissent un fort taux de rechute. La raison de ces r��cidives est la survie d'une partie des cellules malignes dans la moelle osseuse, o�� elles re��oivent une protection au traitement par le biais de l'interaction avec d'autres cellules. Les s��lectines (E-, P- et L-s��lectine) r��gulent l'interaction des leucocytes avec l'endoth��lium (la paroi des vaisseaux sanguins), d'autres leucocytes et les plaquettes ; ces interactions surviennent quand les leucocytes atteignent un site d'inflammation ou un organe cible. Dans la moelle osseuse, la E- et la P-s��lectine se trouvent sur les cellules de l'endoth��lium et sur les macrophages, qui sont d'autres leucocytes faisant partie du stroma de la moelle. Elles pourraient ��tre impliqu��es dans la protection des cellules canc��reuses ��voqu��e plus haut. Les mol��cules d'adh��sion avec lesquelles les s��lectines s'associent, autrement dit les ligands des s��lectines, sont des glycoprot��ines. Ces prot��ines ont besoin de sucres sp��cifiques pour acqu��rir une telle capacit�� d'adh��sion. Dans le cadre de cette th��se, nous avons ��tudi�� deux types de cellules extraites du sang et de la moelle osseuse des patients atteints d'une leuc��mie aigu�� (les blastes) ou de my��lome multiple (les plasmocytes), et leur capacit�� �� se lier aux s��lectines. Nous avons d��montr�� une interaction entre ces cellules malignes et la E- et/ou la P-s��lectine, �� condition que les ligands soient correctement d��cor��s. De plus, lors que les plasmocytes se lient aux s��lectines, une cascade de signaux �� l'int��rieur des cellules stimule leur prolif��ration et leur survie. L'ensemble de ces r��sultats permet l'identification de nouvelles cibles th��rapeutiques potentielles de ces h��mopathies de mauvais pronostic.

A novel study of copy number variations in Hirschsprung disease using the multiple ligation-dependent probe amplification (MLPA) technique.

BACKGROUND Hirschsprung disease (HSCR) is a congenital malformation of the hindgut produced by a disruption in neural crest cell migration during embryonic development. HSCR has a complex genetic etiology and mutations in several genes, mainly the RET proto-oncogene, have been related to the disease. There is a clear predominance of missense/nonsense mutations in these genes whereas copy number variations (CNVs) have been seldom described, probably due to the limitations of conventional techniques usually employed for mutational analysis. METHODS In this study we have aimed to analyze the presence of CNVs in some HSCR genes (RET, EDN3, GDNF and ZFHX1B) using the Multiple Ligation-dependent Probe Amplification (MLPA) approach. RESULTS Two alterations in the MLPA profiles of RET and EDN3 were detected, but a detailed inspection showed that the decrease in the corresponding dosages were due to point mutations affecting the hybridization probes regions. CONCLUSION Our results indicate that CNVs of the gene coding regions analyzed here are not a common molecular cause of Hirschsprung disease. However, further studies are required to determine the presence of CNVs affecting non-coding regulatory regions, as well as other candidate genes.

Pulmonary Sarcoid-like Granulomatosis after Multiple Vaccinations of a Long-term Surviving Patient with Metastatic Melanoma.

Autoimmune side effects are frequent in patients with cancer treated with immune checkpoint-targeting antibodies, but are rare with cancer vaccines. Here, we present a case report on a patient with metastatic melanoma who developed pulmonary sarcoid-like granulomatosis following repetitive vaccinations with peptides and CpG. Despite multiple metastases, including one lesion in the brain, the patient is alive and well more than 13 years after the diagnosis of metastatic disease. The strongly activated tumor-specific CD8(+) T cells showed robust long-term memory and effector functions. It is possible that long-term survival and adverse autoimmune events may become more common for vaccines inducing robust anticancer immune responses as were present in this patient. Cancer Immunol Res; 2(12); 1148-53. ��2014 AACR.

Genome-wide association study of multiple sclerosis confirms a novel locus at 5p13.1.

Multiple Sclerosis (MS) is the most common progressive and disabling neurological condition affecting young adults in the world today. From a genetic point of view, MS is a complex disorder resulting from the combination of genetic and non-genetic factors. We aimed to identify previously unidentified loci conducting a new GWAS of Multiple Sclerosis (MS) in a sample of 296 MS cases and 801 controls from the Spanish population. Meta-analysis of our data in combination with previous GWAS was done. A total of 17 GWAS-significant SNPs, corresponding to three different loci were identified:HLA, IL2RA, and 5p13.1. All three have been previously reported as GWAS-significant. We confirmed our observation in 5p13.1 for rs9292777 using two additional independent Spanish samples to make a total of 4912 MS cases and 7498 controls (ORpooled = 0.84; 95%CI: 0.80-0.89; p = 1.36 �� 10-9). This SNP differs from the one reported within this locus in a recent GWAS. Although it is unclear whether both signals are tapping the same genetic association, it seems clear that this locus plays an important role in the pathogenesis of MS.

On-pump beating heart coronary surgery for high risk patients requiring emergency multiple coronary artery bypass grafting.

BACKGROUND: Cardiopulmonary bypass (CPB) with aortic cross-clamping and cardioplegic arrest remains the method of choice for patients requiring standard myocardial revascularization. Therefore, very high-risk patients presenting with acute coronary syndrome, unstable angina, onset of cardiac decompensation and requiring emergency multiple myocardial revascularization, can have a poor outcome. The on-pump beating heart technique can reduce the mortality and the morbidity in such a selected group of patients and this report describes our clinical experience. METHODS: Out of 290 patients operated for CABG from January 2005 to January 2006, 25 (8.6%) selected high-risk patients suffering from life threatening coronary syndrome (mean age 69 +/- 7 years) and requiring emergency multiple myocardial revascularization, underwent on-pump beating heart surgery. The mean pre-operative left ventricle ejection fraction (LVEF) was 27 +/- 8%. The majority of them (88%) suffered of tri-vessel coronary disease and 6 (24%) had a left main stump disease. Nine patients (35%) were on severe cardiac failure and seven among them (28%) received a pre-operative intra-aortic balloon pump. The pre-operative EuroScore rate was equal or above 8 in 18 patients (73%). RESULTS: All patients underwent on-pump-beating heart coronary revascularization. The mean number of graft/patient was 2.9 +/- 0.6 and the internal mammary artery was used in 23 patients (92%). The mean CPB time was 84 +/- 19 minutes. Two patients died during the recovery stay in the intensive care unit, and there were no postoperative myocardial infarctions between the survivors. Eight patients suffered of transitorily renal failure and 1 patient developed a sternal wound infection. The mean hospital stay was 12 +/- 7 days. The follow-up was complete for all 23 patients survived at surgery and the mean follow-up time was 14 +/- 5 months. One patient died during the follow-up for cardiac arrest and 2 patients required an implantable cardiac defibrillator. One year after surgery they all had a standard trans-thoracic echocardiogram showing a mean LVEF rate of 36 +/- 11.8%. CONCLUSION: Standard on-pump arrested heart coronary surgery has higher mortality and morbidity in emergencies. The on-pump beating heart myocardial revascularization seems to be a valid alternative for the restricted and selected cohort of patients suffering from life threatening coronary syndrome and requiring multiple emergency CABG.

Multiple insecticide resistance in Aedes aegypti (Diptera: Culicidae) populations compromises the effectiveness of dengue vector control in French Guiana

In French Guiana, pyrethroids and organophosphates have been used for many years against Aedes aegypti. We aimed to establish both the resistance level of Ae. aegypti and the ultra low volume spray efficacy to provide mosquito control services with practical information to implement vector control and resistance management. Resistance to deltamethrin and fenitrothion was observed. In addition, the profound loss of efficacy of AquaK'othrine�� and the moderate loss of efficacy of Paluthion�� 500 were recorded. Fenitrothion remained the most effective candidate for spatial application in French Guiana until its removal in December 2010. Further investigation of the mechanism of resistance to deltamethrin demonstrated the involvement of mixed-function oxidases and, to a lesser extent, of carboxylesterases. However, these observations alone cannot explain the level of insecticide resistance we observed during tube and cage tests.

Multiple miscarriages are associated with the risk of ovarian cancer: results from the European Prospective Investigation into Cancer and Nutrition.

While the risk of ovarian cancer clearly reduces with each full-term pregnancy, the effect of incomplete pregnancies is unclear. We investigated whether incomplete pregnancies (miscarriages and induced abortions) are associated with risk of epithelial ovarian cancer. This observational study was carried out in female participants of the European Prospective Investigation into Cancer and Nutrition (EPIC). A total of 274,442 women were followed from 1992 until 2010. The baseline questionnaire elicited information on miscarriages and induced abortions, reproductive history, and lifestyle-related factors. During a median follow-up of 11.5 years, 1,035 women were diagnosed with incident epithelial ovarian cancer. Despite the lack of an overall association (ever vs. never), risk of ovarian cancer was higher among women with multiple incomplete pregnancies (HR(���4vs.0): 1.74, 95% CI: 1.20-2.70; number of cases in this category: n���=���23). This association was particularly evident for multiple miscarriages (HR(���4vs.0): 1.99, 95% CI: 1.06-3.73; number of cases in this category: n���=���10), with no significant association for multiple induced abortions (HR(���4vs.0): 1.46, 95% CI: 0.68-3.14; number of cases in this category: n���=���7). Our findings suggest that multiple miscarriages are associated with an increased risk of epithelial ovarian cancer, possibly through a shared cluster of etiological factors or a common underlying pathology. These findings should be interpreted with caution as this is the first study to show this association and given the small number of cases in the highest exposure categories.

Multiple cytokine expression profiles reveal immune-based differences in occult hepatitis B genotype H-infected Mexican Nahua patients

A high prevalence of occult hepatitis B (OHB) genotype H infections has been observed in the native Mexican Nahua population. In addition, a low incidence of hepatitis B virus (HBV)-associated hepatocellular carcinoma has been described in Mexico. The immune response to infection among OHB-infected patients has been poorly evaluated in vivo. Therefore, we assessed the expression profiles of 23 cytokines in OHB genotype H-infected Nahua patients. A total of 41 sera samples from natives of the Nahua community were retrospectively analysed. Based on their HBV antibody profiles, patients were stratified into two groups: OHB patients (n = 21) and patients that had recovered from HBV infection (n = 20). Herein, we report distinctive cytokines profiles in OHB-infected individuals. Compared to healthy controls (n = 20) and patients who resolved HBV infection, OHB-infected patients displayed an increase in interleukin (IL)-2 secretion in addition to a characteristic inflammation profile (decrease in IL-8 and tumour necrosis factor-alpha levels and increased levels of tumour growth factor-beta). IL-15 and interferon-gamma levels were reduced in OHB-infected individuals when compared to those patients who resolved HBV infection. In contrast, OHB patients showed an increase in monocyte chemoattractant protein (MCP)-1 and MCP-2 compared to healthy controls and patients who resolved HBV infection. These findings suggest that cytokine expression can influence the severity of OHB disease and could lead to new investigation into the treatment of liver and other infectious diseases.

Adherence to interferon ��-1b treatment in patients with multiple sclerosis in Spain

BACKGROUND Adherence to interferon ��-1b (INF��-1b) therapy is essential to maximize the beneficial effects of treatment in multiple sclerosis (MS). For that reason, the main objectives of this study are to assess adherence to INF��-1b in patients suffering from MS in Spain, and to identify the factors responsible for adherence in routine clinical practice. METHODOLOGY/PRINCIPAL FINDINGS This was an observational, retrospective, cross-sectional study including 120 Spanish patients with MS under INF��-1b treatment. Therapeutic adherence was assessed with Morisky-Green test and with the percentage of doses received. The proportion of adherent patients assessed by Morisky-Green test was 68.3%, being indicative of poor adherence. Nevertheless, the percentage of doses received, which was based on the number of injected medication, was 94.3%. The main reason for missing INF��-1b injections was forgetting some of the administrations (64%). Therefore, interventions that diminish forgetfulness might have a positive effect in the proportion of adherent patients and in the percentage of doses received. In addition, age and comorbidities had a significant effect in the number of doses injected per month, and should be considered in the management of adherence in MS patients. CONCLUSION/SIGNIFICANCE Among all the available methods for assessing adherence, the overall consumption of the intended dose has to be considered when addressing adherence.