Compositional cubes: a new concept for multi-factorial compositions.

Compositional data are commonly known as multivariate observations carrying relative information. Even though the case of vector or even two-factorial compositional data (compositional tables) is already well described in the literature, there is still a need for a comprehensive approach to the analysis of multi-factorial relative-valued data. Therefore, this contribution builds around the current knowledge about compositional data a general theoretical framework for k-factorial compositional data. As a main finding it turns out that, similar to the case of compositional tables, also the multi-factorial structures can be orthogonally decomposed into an independent and several interactive parts and, moreover, a coordinate representation allowing for their separate analysis by standard analytical methods can be constructed. For the sake of simplicity, these features are explained in detail for the case of three-factorial compositions (compositional cubes), followed by an outline covering the general case. The three-dimensional structure is analyzed in depth in two practical examples, dealing with systems of spatial and time dependent compositional cubes. The methodology is implemented in the R package robCompositions.

Occurrence of virulence factors in Cronobacter sakazakii and Cronobacter malonaticus originated from clinical samples.

BACKGROUND: Cronobacter spp. are Gram-negative, facultative-anaerobic, non-spore forming, enteric coliform bacteria, which belongs to the Enterobacteriaceae family. Cronobacter spp. are opportunistic pathogens that have brought rare but life-threatening infections such as meningitis, necrotizing enterocolitis and bloodstream infections in neonates and infants. Information on the diversity, pathogenicity and virulence of Cronobacter species obtained from various sources is still relatively scarce and fragmentary. The aim of this study was to examine and analyse different pathogenicity and virulence factors among C. sakazakii and C. malonaticus strains isolated from clinical samples. METHODS: The thirty-six clinical Cronobacter strains have been used in this study. This bacterial collection consists of 25 strains of C. sakazakii and 11 strains of C. malonaticus, isolated from different clinical materials. Seven genes (ompA, inv, sip, aut, hly, fliC, cpa) were amplified by PCR. Moreover, the motility and the ability of these strains to adhere and invade human colorectal adenocarcinoma (HT-29) and mouse neuroblastoma (N1E-115) cell lines were investigated. RESULTS: Our results showed that all tested strains were able to adhere to both used cell lines, HT-29 and N1E-115 cells. The invasion assay showed that 66.7% (24/36) of isolates were able to invade N1-E115 cells while 83% (30/36) of isolates were able to invade HT-29 cells. On the average, 68% of the C. sakazakii strains exhibited seven virulence factors and only 18% in C. malonaticus. All strains amplified ompA and fliC genes. The other genes were detected as follow: sip 97% (35/36), hlyA 92% (33/36), aut 94% (34/36), cpa 67% (24/36), and inv 69% (25/36). CONCLUSIONS: C. sakazakii and C malonaticus strains demonstrate the diversity of the virulence factors present among these pathogens. It is necessary to permanently monitor the hospital environment to appropriately treat and resolve cases associated with disease. Furthermore, in-depth knowledge is needed about the source and transmission vehicles of pathogens in hospitals to adopt pertinent prevention measures.

Multivariate Independent Component Analysis Identifies Patients in Newborn Screening Equally to Adjusted Reference Ranges.

Newborn screening (NBS) of inborn errors of metabolism (IEMs) is based on the reference ranges established on a healthy newborn population using quantile statistics of molar concentrations of biomarkers and their ratios. The aim of this paper is to investigate whether multivariate independent component analysis (ICA) is a useful tool for the analysis of NBS data, and also to address the structure of the calculated ICA scores. NBS data were obtained from a routine NBS program performed between 2013 and 2022. ICA was tested on 10,213/150 free-diseased controls and 77/20 patients (9/3 different IEMs) in the discovery/validation phases, respectively. The same model computed during the discovery phase was used in the validation phase to confirm its validity. The plots of ICA scores were constructed, and the results were evaluated based on 5sd levels. Patient samples from 7/3 different diseases were clearly identified as 5sd-outlying from control groups in both phases of the study. Two IEMs containing only one patient each were separated at the 3sd level in the discovery phase. Moreover, in one latent variable, the effect of neonatal birth weight was evident. The results strongly suggest that ICA, together with an interpretation derived from values of the "average member of the score structure", is generally applicable and has the potential to be included in the decision process in the NBS program.

Clinical and Radiographic Outcomes of Immature Teeth Treated with Different Treatment Protocols of Regenerative Endodontic Procedures: A Retrospective Cohort Study.

Regenerative endodontic procedure (REP) is a progressive treatment modality for immature permanent teeth with necrotic pulp. The ambiguousness about the predictability of REP outcome in relation to complete disinfection of the root canal system and the occurrence of discoloration still exists. The aim of this retrospective study was to analyze two treatment protocols on clinical success rate, radiographic root development and the occurrence of discoloration. Eighteen patients were treated by a single operator by either treatment protocol according to the American Association of Endodontists (AAEP, n = 9) or a modified protocol (MP, n = 9) with the use of 5% sodium hypochlorite and sandblasting. Patients were followed up after 3, 6, 9, 12, 18 and 24 months and clinical success, radiographic root development and the occurrence of discoloration were assessed. The clinical success of MP was significantly higher in two years follow-up (p = 0.015), but the change in radiographic root area was higher for AAEP (p = 0.017) and the occurrence of discoloration was higher in AAEP (p = 0.029). The use of 5% sodium hypochlorite for a longer period of time leads to a higher success rate. The sandblasting of the access cavity reduces the occurrence of discoloration.

In Vitro Mechanical Properties of Mineral Trioxide Aggregate in Moist and Dry Intracanal Environments.

INTRODUCTION: The purpose of this study was to examine the microhardness and modulus of elasticity (MOE) of White ProRoot MTA (Dentsply Tulsa Dental, Tulsa, OK) after setting in moist or dry intracanal conditions. METHODS AND MATERIALS: To simulate root canal system, 14 polyethylen molds with internal diameter of 1 mm and height of 12 mm were used. These molds were filled with 9-mm thick layers of White ProRoot Mineral Trioxide Aggregate (MTA; Dentsply Tulsa Dental, Tulsa, OK). The experimental group (n=7) had a damp cotton pellet with 1.5 mm height and a 1.5 mm layer of resin composite placed on it. In control group (n=7) the whole 3 mm above MTA were filled with resin composite. The specimens were kept in 37°C and relative humidity of 80% for 4 days in order to simulate physiological conditions. Specimens were longitudinally sectioned and nanoindentation tests were carried out using Berkovich indenter at loading rate of 2 mN/s at 4×5 matrices of indents which were located in the coronal, middle and apical thirds of the specimen's cross section, to evaluate the microhardness and modulus of elasticity of the specimen to appraise the progression of the setting process. Differences were assessed using nonparametric generalized Friedman rank sum and Wilcoxon Rank-Sum tests. RESULTS: Statistical analysis showed that there was a significant difference in microhardness and MOE between control and experimental groups at coronal (P<0.001), middle (P<0.001) and apical (P<0.001) thirds of the simulated rod from simulated apical foramen. Kruskal-Wallis test showed no significant effect of depth on microhardness of material in experimental or control groups. CONCLUSION: Within limitations of this in vitro study, it seems that moist intracanal environment improves setting of MTA in various depths.

When less is more: a simple predictive model for repeated prostate biopsy outcomes.

OBJECTIVES: To present a new predictive model for repeated prostate biopsy outcomes. Several practical problems are described that arise when searching for a proper model among those that already exist. A new model is developed with only two explanatory variables and a simple graphical output. METHODS: This is a retrospective cohort study based on data collected from December 2006 to June 2011 at the Clinic of Urology of the University Hospital in Olomouc, Czech Republic. The cohort consists of 221 patients who underwent the first repeated biopsy after an initial biopsy with a negative outcome. All patients had prostate-specific antigen (PSA) levels between 1.5 and 16.5 ng/mL and a prostate volume not greater than 100mL. A logistic regression model was fitted. RESULTS: Of the 221 patients, 29 (13%) were diagnosed with prostate cancer on the repeated biopsy. The final model includes the PSA level and the transitory zone volume as predictors. Its accuracy is 76.4%. The cut-off point of 0.0687 in the predicted positive repeated biopsy outcome assures 95% sensitivity and prevents 42% of unnecessary biopsies. CONCLUSIONS: The accuracy of the model is comparable to that of more complex models (with more than two predictors) published in the literature. The model includes only two routinely measured variables, and hence it is accessible for a wide range of practitioners. The simple graphical outcome makes the model even more attractive.