Computation of multiple correspondence analysis, with code in R

The generalization of simple correspondence analysis, for two categorical variables, to multiple correspondence analysis where they may be three or more variables, is not straighforward, both from a mathematical and computational point of view. In this paper we detail the exact computational steps involved in performing a multiple correspondence analysis, including the special aspects of adjusting the principal inertias to correct the percentages of inertia, supplementary points and subset analysis. Furthermore, we give the algorithm for joint correspondence analysis where the cross-tabulations of all unique pairs of variables are analysed jointly. The code in the R language for every step of the computations is given, as well as the results of each computation.

Specificity revisited: The role of cross-investments

Previous analysis has shown that traders may opt for specific technologies with nojoint productivity advantage as a way to commit themselves to trading jointly, butonly when long-term contracting is infeasible. This paper proves that speciÞcity canalso be optimal (by relaxing the budget-balance constraint) in settings with long-termcontracting. Traders will opt for specificity when one trader makes a cross-investmentand either (1) this cross-investment has a direct externality on the other trader, (2) bothparties invest, or (3) private information is present. The specificity (e.g. from non-salvageable investments, specific assets and technologies, narrow business strategies,and exclusivity restrictions) is equally effective regardless of which trader's alternativetrade payoff is reduced. Specificity supports long-term contracts in a broad rangeof settings - both with and without renegotiation. The theory also offers a novelperspective on franchising and vertical integration.

Trunk neuromuscular responses to a single whole-body vibration session in patients with chronic low back pain: a cross-sectional study.

OBJECTIVE: Whole-body vibration (WBV) exercise is progressively adopted as an alternative therapeutic modality for enhancing muscle force and muscle activity via neurogenic potentiation. So far, possible changes in the recruitment patterns of the trunk musculature after WBV remain undetermined. The main objective of this study was to evaluate the short-term effects of a single WBV session on trunk neuromuscular responses in patients with chronic low back pain (cLBP) and healthy participants. METHODS: Twenty patients with cLBP and 21 healthy participants performed 10 trunk flexion-extensions before and after a single WBV session consisting of five 1-minute vibration sets. Surface electromyography (EMG) of erector spinae at L2-L3 and L4-L5 and lumbopelvic kinematic variables were collected during the trials. Data were analyzed using 2-way mixed analysis of variance models. RESULTS: The WBV session led to increased lumbar EMG activity during the flexion and extension phases but yielded no change in the quiet standing and fully flexed phases. Kinematic data showed a decreased contribution to the movement of the lumbar region in the second extension quartile. These effects were not different between patients with cLBP and healthy participants. CONCLUSIONS: Increased lumbar EMG activity after a single WBV session most probably results from potentiation effects of WBV on lumbar muscles reflex responses. Decreased EMG activity in full trunk flexion, usually observed in healthy individuals, was still present after WBV, suggesting that the ability of the spine stabilizing mechanisms to transfer the extension torque from muscles to passive structures was not affected.

Signaling cross-talk between peroxisome proliferator-activated receptor/retinoid X receptor and estrogen receptor through estrogen response elements.

Peroxisome proliferator-activated receptors (PPARs) and retinoid X receptors (RXRs) are nuclear hormone receptors that are activated by fatty acids and 9-cis-retinoic acid, respectively. PPARs and RXRs form heterodimers that activate transcription by binding to PPAR response elements (PPREs) in the promoter of target genes. The PPREs described thus far consist of a direct tandem repeat of the AGGTCA core element with one intervening nucleotide. We show here that the vitellogenin A2 estrogen response element (ERE) can also function as a PPRE and is bound by a PPAR/RXR heterodimer. Although this heterodimer can bind to several other ERE-related palindromic response elements containing AGGTCA half-sites, only the ERE is able to confer transactivation of test reporter plasmids, when the ERE is placed either close to or at a distance from the transcription initiation site. Examination of natural ERE-containing promoters, including the pS2, very-low-density apolipoprotein II and vitellogenin A2 genes, revealed considerable differences in the binding of PPAR/RXR heterodimers to these EREs. In their natural promoter context, these EREs did not allow transcriptional activation by PPARs/RXRs. Analysis of this lack of stimulation of the vitellogenin A2 promoter demonstrated that PPARs/RXRs bind to the ERE but cannot transactivate due to a nonpermissive promoter structure. As a consequence, PPARs/RXRs inhibit transactivation by the estrogen receptor through competition for ERE binding. This is the first example of signaling cross-talk between PPAR/RXR and estrogen receptor.

Analysis of antiviral immunity in primary and chronic infections

Several evidences in humans underscored the contribution of CD4 and CD8 T-cell responses in controlling viral and bacterial infections. However, CD4 and CD8 Τ cells have distinct and specific effector functions leading to a hierarchical importance in responding to different types of pathogens. In this context, the present work aimed to investigate distinct CD8 T-cell features potentially influencing T-cell efficacy against viral infection. To achieve this-objective, CD8 Τ cells derived from HIV-infected patients and healthy donors harbouring virus-specific immune responses or immunized with an HTV vaccine candidate were studied. In particular, we performed a comprehensive cross-sectional and longitudinal analysis to characterize the function, the phenotype and the functional avidity of HIV-specific CD8 Τ cells during acute (PHI) and chronic infection and, in particular, we investigated immunological parameters potentially associated with the functional avidity of HIV-specific CD8 Τ cells. In addition, we studied the expression pattern of co-inhibitory molecules and the influence of CD 160 on the functions of CD8 Τ cells in absence of chronic infections. From these analyses we observed that the functional avidity of HIV-specific CD8 T- cell responses was significantly lower in acute than in chronic infection, but was not different between chronic progressive and non-progressive patients. Functional avidity remained low after several years of antiretroviral therapy in PHI patients, but increased in patients experiencing a virus rebound following treatment interruption in association with a massive renewal of the global CD8 complementarity-determining region 3 of the TCR. The functional avidity was also directly associated to T-cell exhaustion. In individuals with no sign of HIV or Hepatitis A, Β or C virus infection, CD8 Τ cells expressed higher levels of co-inhibitory molecules than CD4 Τ cells and this was dependent on the stage of T-cell differentiation and activation. The expression of CD 160 impaired the proliferation capacity and IL-2 production of CD8 Τ cells and was reduced upon CD8 T-cell activation, entitling CD 160 as unique marker of CD8 T-cell exhaustion. The CD 160 blockade restored the proliferation capacity of virus-specific CD8 Τ cells providing a potential new target for immunotherapy. All together, these results expand our knowledge regarding the interplay between the immune system and the viruses. - De nombreuses études chez l'Homme ont mis en évidence la contribution des réponses cellulaires Τ CD4 et CD8 dans le contrôle des infections virales et bactériennes. En particulier, les lymphocytes Τ ont différentes fonctions effectrices spécifiques qui leur confèrent un rôle clé lors d'infections par différents pathogènes. Ce travail vise à étudier différentes caractéristiques des cellules Τ CD8 affectant l'efficacité des réponses cellulaires contre les virus. Pour atteindre cet objectif nous avons étudié les cellules Τ CD8 provenant de patients infectés par le VIH et de donneurs sains avec des réponses immunitaires naturelles ou vaccinales contre des virus. Nous avons effectué plusieurs analyses transversales et longitudinales des fonctions, du phénotype et de l'avidité fonctionnelle des lymphocytes Τ CD8 spécifiques au VIH au cours d'infections aiguës et chroniques; en particulier, nous avons étudié les paramètres immunologiques qui pourraient être associés à l'avidité fonctionnelle. De plus, nous avons investigué le profil d'expression des principales molécules co-inhibitrices et en particulier le rôle du CD 160 dans les fonctions des lymphocytes Τ CD8. Sur la base de ces analyses, nous avons constaté que l'avidité fonctionnelle des cellules Τ CD8 spécifiques au VIH était significativement plus faible lors infections aiguës que lors d'infections chroniques, mais n'était, par contre, pas différente entre les patients avec des infections chroniques progressives et non progressives. L'avidité fonctionnelle reste faible après plusieurs années de traitement antirétroviral, mais augmente chez les patients subissant un rebond viral, et donc exposés à des hautes virémies, suite à l'interruption du traitement. Cette augmentation d'avidité des lymphocytes Τ CD8, liée à un épuisement fonctionnel accru, était quantitativement directement associée à un renouvellement massif du TCR. Indépendamment de l'infection par le VIH, les cellules Τ CD8 expriment des niveaux plus élevés de molécules co-inhibitrices (PD-1, 2B4 et CD 160) par rapport aux cellules Τ CD4 et ceci dépend de leur stade de différenciation et d'activation. En particulier, CD 160 semble être un marqueur clé d'épuisement cellulaire des cellules Τ CD8, et donc une nouvelle cible potentielle pour l'immunothérapie, car a) son expression réduit la capacité proliférative et la production d'IL-2 b) CD 160 diminue suite à 1'activation et c) le blocage de CD 160 redonne la capacité proliférative aux cellules Τ CD8 spécifiques aux virus. - Le système immunitaire est un ensemble de cellules, tissus et organes indispensables pour limiter l'entrée des pathogènes à travers la peau et les muqueuses. Parmi les différentes cellules composant le système immunitaire, les cellules Τ CD4 et CD8 sont fondamentales pour le contrôle des infections virales et bactériennes. Les moyens pour combattre les différents pathogènes peuvent être cependant très variables. Les cellules Τ CD8, qui sont indispensables pour la lutte contre les virus, peuvent avoir différents niveaux de sensibilité; les cellules qui répondent à de faibles quantités d'antigène ont une forte sensibilité. Suite à une première infection virale, les cellules Τ CD8 ont une sensibilité plus faible que lors d'expositions répétées au même virus. En effet, la réexposition au pathogène induit une augmentation de sensibilité, grâce au recrutement et/ou à l'expansion de cellules Τ dotées d'une sensibilité plus élevée. Les cellules Τ CD8 avec une plus haute sensibilité semblent être caractérisées par une perte de fonctionnalité (épuisement fonctionnel associé à une haute expression de molécules dites inhibitrices). En absence d'infection, la fonction des molécules inhibitrices n'est pas encore clairement définie. Les cellules Τ CD8 montrent un niveau d'expression plus élevé de ces molécules par rapport aux cellules Τ CD4. Ceci dépend de l'état des cellules. Parmi ces molécules, le CD160 est associé à l'incapacité des cellules à proliférer et à produire de l'IL-2, une protéine importante pour la prolifération et la survie cellulaire. L'incapacité des cellules exprimant le CD 160 à proliférer en réponse à des virus peut être restaurée par le blocage fonctionnel du récepteur CD 160. Cette étude étoffe notre connaissance du rôle des cellules Τ CD8 ainsi que des conséquences induites par leur épuisement fonctionnel. Ces informations sont fondamentales pour le développement de nouvelles stratégies thérapeutiques et vaccinales.

Candida bloodstream infections in intensive care units: analysis of the extended prevalence of infection in intensive care unit study.

OBJECTIVES: To provide a global, up-to-date picture of the prevalence, treatment, and outcomes of Candida bloodstream infections in intensive care unit patients and compare Candida with bacterial bloodstream infection. DESIGN: A retrospective analysis of the Extended Prevalence of Infection in the ICU Study (EPIC II). Demographic, physiological, infection-related and therapeutic data were collected. Patients were grouped as having Candida, Gram-positive, Gram-negative, and combined Candida/bacterial bloodstream infection. Outcome data were assessed at intensive care unit and hospital discharge. SETTING: EPIC II included 1265 intensive care units in 76 countries. PATIENTS: Patients in participating intensive care units on study day. INTERVENTIONS: None. MEASUREMENT AND MAIN RESULTS: Of the 14,414 patients in EPIC II, 99 patients had Candida bloodstream infections for a prevalence of 6.9 per 1000 patients. Sixty-one patients had candidemia alone and 38 patients had combined bloodstream infections. Candida albicans (n = 70) was the predominant species. Primary therapy included monotherapy with fluconazole (n = 39), caspofungin (n = 16), and a polyene-based product (n = 12). Combination therapy was infrequently used (n = 10). Compared with patients with Gram-positive (n = 420) and Gram-negative (n = 264) bloodstream infections, patients with candidemia were more likely to have solid tumors (p < .05) and appeared to have been in an intensive care unit longer (14 days [range, 5-25 days], 8 days [range, 3-20 days], and 10 days [range, 2-23 days], respectively), but this difference was not statistically significant. Severity of illness and organ dysfunction scores were similar between groups. Patients with Candida bloodstream infections, compared with patients with Gram-positive and Gram-negative bloodstream infections, had the greatest crude intensive care unit mortality rates (42.6%, 25.3%, and 29.1%, respectively) and longer intensive care unit lengths of stay (median [interquartile range]) (33 days [18-44], 20 days [9-43], and 21 days [8-46], respectively); however, these differences were not statistically significant. CONCLUSION: Candidemia remains a significant problem in intensive care units patients. In the EPIC II population, Candida albicans was the most common organism and fluconazole remained the predominant antifungal agent used. Candida bloodstream infections are associated with high intensive care unit and hospital mortality rates and resource use.

Mutational analysis of class A and class B penicillin-binding proteins in Streptococcus gordonii.

High-molecular-weight (HMW) penicillin-binding proteins (PBPs) are divided into class A and class B PBPs, which are bifunctional transpeptidases/transglycosylases and monofunctional transpeptidases, respectively. We determined the sequences for the HMW PBP genes of Streptococcus gordonii, a gingivo-dental commensal related to Streptococcus pneumoniae. Five HMW PBPs were identified, including three class A (PBPs 1A, 1B, and 2A) and two class B (PBPs 2B and 2X) PBPs, by homology with those of S. pneumoniae and by radiolabeling with [3H]penicillin. Single and double deletions of each of them were achieved by allelic replacement. All could be deleted, except for PBP 2X, which was essential. Morphological alterations occurred after deletion of PBP 1A (lozenge shape), PBP 2A (separation defect and chaining), and PBP 2B (aberrant septation and premature lysis) but not PBP 1B. The muropeptide cross-link patterns remained similar in all strains, indicating that cross-linkage for one missing PBP could be replaced by others. However, PBP 1A mutants presented shorter glycan chains (by 30%) and a relative decrease (25%) in one monomer stem peptide. Growth rate and viability under aeration, hyperosmolarity, and penicillin exposure were affected primarily in PBP 2B-deleted mutants. In contrast, chain-forming PBP 2A-deleted mutants withstood better aeration, probably because they formed clusters that impaired oxygen diffusion. Double deletion could be generated with any PBP combination and resulted in more-altered mutants. Thus, single deletion of four of the five HMW genes had a detectable effect on the bacterial morphology and/or physiology, and only PBP 1B seemed redundant a priori.

Prevalence of vascular disease in systemic lupus erythematosus compared with type-1 diabetes mellitus: A cross-sectional study of two cohorts.

OBJECTIVES: Systemic lupus erythematosus (SLE) is associated with considerable cardiovascular morbidity that has not yet been directly compared with other diseases with known cardiovascular risk. METHODS: Two hundred and forty-one patients of the multicentre Swiss SLE cohort study (SSCS) were cross-sectionally assessed for coronary heart disease (CHD), cerebrovascular disease (CVD) and peripheral artery disease (PAD). SLE patients were compared with a cohort of 193 patients with type-1 diabetes mellitus being followed at the University Hospital Basel. A subgroup analysis of 50 age- and sex-matched patients from the University Hospital Basel was performed. RESULTS: Of patients within the SSCS 13.3% had one or more vascular events: 8.3% CHD, 5% CVD and 1.2% PAD. In type-1 diabetes mellitus patients, 15% had vascular events: 9.3% CHD, 3.1% CVD and 5.6% PAD. In the matched subgroup, 26% of SLE patients had vascular events (14% CHD) compared with 12% in type-1 DM patients (2% CHD). Cardiovascular risk factors were similar in both groups. Vascular events in SLE patients were associated with age, longer disease duration, dyslipidaemia, and hypertension. CONCLUSION: Cardiovascular morbidity in SLE is at least as frequent as in age- and sex-matched type-1 diabetes mellitus patients. Therefore, aggressive screening and management of cardiovascular risk factors should be performed.

Analysis of IRAS stellar sources in Alpha Persei region

The present study is an analysis of IR sources in the Alpha Persei open cluster region from the IRAS Point Source Catalog and from ground-based photometric observations. Cross-identification between stars in the region and IRAS Point Source Catalog was performed and nine new associations were found. BVRI Johnson photometry for 24 of the matched objects have been carried out. Physical identity of visual and IRAS sources and relationship to the Alpha Persei open cluster are discussed.

Deviant trajectories of cortical maturation in 22q11.2 deletion syndrome (22q11DS): a cross-sectional and longitudinal study.

22q11.2 deletion syndrome (22q11DS) is associated with an increased susceptibility to develop schizophrenia. Despite a large body of literature documenting abnormal brain structure in 22q11DS, cerebral changes associated with brain maturation in 22q11DS remained largely unexplored. To map cortical maturation from childhood to adulthood in 22q11.2 deletion syndrome, we used cerebral MRI from 59 patients with 22q11DS, aged 6 to 40, and 80 typically developing controls; three year follow-up assessments were also available for 32 patients and 31 matched controls. Cross-sectional cortical thickness trajectories during childhood and adolescence were approximated in age bins. Repeated-measures were also conducted with the longitudinal data. Within the group of patients with 22q11DS, exploratory measures of cortical thickness differences related to COMT polymorphism, IQ, and schizophrenia were also conducted. We observed deviant trajectories of cortical thickness changes with age in patients with 22q11DS. In affected preadolescents, larger prefrontal thickness was observed compared to age-matched controls. Afterward, we observed greater cortical loss in 22q11DS with a convergence of cortical thickness values by the end of adolescence. No compelling evidence for an effect of COMT polymorphism on cortical maturation was observed. Within 22q11DS, significant differences in cortical thickness were related to cognitive level in children and adolescents, and to schizophrenia in adults. Deviant trajectories of cortical thickness from childhood to adulthood provide strong in vivo cues for a defect in the programmed synaptic elimination, which in turn may explain the susceptibility of patients with 22q11DS to develop psychosis.

A fully adaptive numerical approximation for a two-dimensional epidemic model with nonlinear cross-diffusion

An epidemic model is formulated by a reactionâeuro"diffusion system where the spatial pattern formation is driven by cross-diffusion. The reaction terms describe the local dynamics of susceptible and infected species, whereas the diffusion terms account for the spatial distribution dynamics. For both self-diffusion and cross-diffusion, nonlinear constitutive assumptions are suggested. To simulate the pattern formation two finite volume formulations are proposed, which employ a conservative and a non-conservative discretization, respectively. An efficient simulation is obtained by a fully adaptive multiresolution strategy. Numerical examples illustrate the impact of the cross-diffusion on the pattern formation.

Re-thinking cell cycle regulators: the cross-talk with metabolism.

Analysis of genetically engineered mice deficient in cell cycle regulators, including E2F1, cdk4, and pRB, showed that the major phenotypes are metabolic perturbations. These key cell cycle regulators contribute to lipid synthesis, glucose production, insulin secretion, and glycolytic metabolism. It has been shown that deregulation of these pathways can lead to metabolic perturbations and related metabolic diseases, such as obesity and type II diabetes. The cyclin-cdk-Rb-E2F1 pathway regulates adipogenesis in addition to its well-described roles in cell cycle regulation and cancer. It was also shown that E2F1 directly participates in the regulation of pancreatic growth and function. Similarly, cyclin D3, cdk4, and cdk9 are also adipogenic factors with strong effects on whole organism metabolism. These examples support the emerging notion that cell cycle regulatory proteins also modulate metabolic processes. These cell cycle regulators are activated by insulin and glucose, even in non-proliferating cells. Most importantly, these cell cycle regulators trigger the adaptive metabolic switch that normal and cancer cells require in order to proliferate. These changes include increased lipid synthesis, decreased oxidative metabolism, and increased glycolytic metabolism. In summary, these factors are essential regulators of anabolic biosynthetic processes, blocking at the same time oxidative and catabolic pathways, which is reminiscent of cancer cell metabolism.

High proportion of healthcare-associated urinary tract infection in the absence of prior exposure to urinary catheter: a cross-sectional study.

BACKGROUND: Exposure to urinary catheters is considered the most important risk factor for healthcare-associated urinary tract infection (UTI) and is associated with significant morbidity and substantial extra-costs. In this study, we assessed the impact of urinary catheterisation (UC) on symptomatic healthcare-associated UTI among hospitalized patients. METHODS: A nationwide period prevalence survey of healthcare-associated infections was conducted during 1 May to 30 June 2004 in 49 Swiss hospitals and included 8169 adult patients (4313 female; 52.8%) hospitalised in medical, surgical, intermediate, and intensive care wards. Additional data were collected on exposure to UC to investigate factors associated with UTI among hospitalised adult patients exposed and non-exposed to UC. RESULTS: 1917 (23.5%) patients were exposed to UC within the week prior to survey day; 126 (126/8169; 1.5%) developed UTI. Exposure to UC preceded UTI only in 73 cases (58%). By multivariate logistic regression analysis, UTI was independently associated with exposure to UC (odds ratio [OR], 3.9 [95% CI, 2.6-5.9]), female gender (OR, 2.1 [95% CI, 1.4-3.1]), an American Society of Anesthesiologists' score > 2 points (OR, 3.2 [95% CI, 1.1-9.4], and prolonged hospital stay >20 days (OR, 1.9 [95% CI, 1.4-3.2]. Further analysis showed that the only significant factor for UTI with exposure to UC use was prolonged hospital stay >40 days (OR, 2.9 [95% CI, 1.3-6.1], while female gender only showed a tendency (OR, 1.6 [95% CI, 1.0-2.7]. In the absence of exposure to UC, the only significant risk factor for UTI was female gender (OR, 3.3 [95% CI, 1.7-6.5]). CONCLUSIONS: Exposure to UC was the most important risk factor for symptomatic healthcare-associated UTI, but only concerned about half of all patients with UTI. Further investigation is warranted to improve overall infection control strategies for UTI.

Growth and externalities across economies : an empirical analysis using spatial econometrics

Recent theoretical models of economic growth have emphasised the role of external effects on the accumulation of factors of production. Although most of the literature has considered the externalities across firms within a region, in this paper we go a step further and consider the possibility that these externalities cross the barriers of regional economies. We assess the role of these external effects in explaining growth and economic convergence. We present a simple growth model, which includes externalities across economies, developing a methodology for testing their existence and estimating their strength. In our view, spatial econometrics is naturally suited to an empirical consideration of these externalities. We obtain evidence on the presence of significant externalities both across Spanish and European regions.

Analysis of the near-intrinsic and extrinsic photocapacitance due to the EL2 level in boron implanted GaAs

A detailed analysis of the photocapacitance signal at the near‐band and extrinsic energetic ranges in Schottky barriers obtained on horizontal Bridgman GaAs wafers, which were implanted with boron at different doses and annealed at several temperatures, has been carried out by using the optical isothermal transient spectroscopy, OITS. The optical cross sections have been determined as well as the quenching efficiency of the EL2 level which has been found to be independent of the annealing temperature. Moreover, the quenching relaxation presents two significant features: (i) a strong increase of the quenching efficiency from 1.35 eV on and (ii) a diminution of the quenching transient amplitude in relation with that shown by the fundamental EL2 level. In order to explain this behavior, different cases are discussed assuming the presence of several energy levels, the existence of an optical recuperation, or the association of the EL2 trap with two levels located, respectively, at Ev+0.45 eV and Ec−0.75 eV. The theoretical simulation, taking into account these two last cases, is in agreement with the experimental photocapacitance data at low temperature, as well as at room temperature where the EL2 filling phototransient shows an anomalous behavior. Moreover, unlike the previous data reported for the EL2 electron optical cross section, the values found using our experimental technique are in agreement with the behavior deduced from the theoretical calculation. The utilization of the OITS method has also allowed the determination of another level, whose faster optical contribution is often added to that of the EL2 level when the DLOS or standard photocapacitance is used.