Robust joint modeling of longitudinal measurements and time to event data using normal/independent distributions: A Bayesian approach

Joint modeling of longitudinal data and survival data has been used widely for analyzing AIDS clinical trials, where a biological marker such as CD4 count measurement can be an important predictor of survival. In most of these studies, a normal distribution is used for modeling longitudinal responses, which leads to vulnerable inference in the presence of outliers in longitudinal measurements. Powerful distributions for robust analysis are normal/independent distributions, which include univariate and multivariate versions of the Student's t, the slash and the contaminated normal distributions in addition to the normal. In this paper, a linear‐mixed effects model with normal/independent distribution for both random effects and residuals and Cox's model for survival time are used. For estimation, a Bayesian approach using Markov Chain Monte Carlo is adopted. Some simulation studies are performed for illustration of the proposed method. Also, the method is illustrated on a real AIDS data set and the best model is selected using some criteria.     

The Rickettsia Endosymbiont of Ixodes pacificus Contains All the Genes of De Novo Folate Biosynthesis

Ticks and other arthropods often are hosts to nutrient providing bacterial endosymbionts, which contribute to their host’s fitness by supplying nutrients such as vitamins and amino acids. It has been detected, in our lab, that Ixodes pacificus is host to Rickettsia species phylotype G021. This endosymbiont is predominantly present, and 100% maternally transmitted in I. pacificus. To study roles of phylotype G021 in I. pacificus, bioinformatic and molecular approaches were carried out. MUMmer genome alignments of whole genome sequence of I. scapularis, a close relative to I. pacificus, against completely sequenced genomes of R. bellii OSU85-389, R. conorii, and R. felis, identified 8,190 unique sequences that are homologous to Rickettsia sequences in the NCBI Trace Archive. MetaCyc metabolic reconstructions revealed that all folate gene orthologues (folA, folC, folE, folKP, ptpS) required for de novo folate biosynthesis are present in the genome of Rickettsia buchneri in I. scapularis. To examine the metabolic capability of phylotype G021 in I. pacificus, genes of the folate biosynthesis pathway of the bacterium were PCR amplified using degenerate primers. BLAST searches identified that nucleotide sequences of the folA, folC, folE, folKP, and ptpS genes possess 98.6%, 98.8%, 98.9%, 98.5% and 99.0% identity respectively to the corresponding genes of Rickettsia buchneri. Phylogenetic tree constructions show that the folate genes of phylotype G021 and homologous genes from various Rickettsia species are monophyletic. This study has shown that all folate genes exist in the genome of Rickettsia species phylotype G021 and that this bacterium has the genetic capability for de novo folate synthesis.     

Experimental Adaptation of Wild-Type Canine Distemper Virus (CDV) to the Human Entry Receptor CD150

Canine distemper virus (CDV), a close relative of measles virus (MV), is widespread and well known for its broad host range. When the goal of measles eradication may be achieved, and when measles vaccination will be stopped, CDV might eventually cross the species barrier to humans and emerge as a new human pathogen. In order to get an impression how fast such alterations may occur, we characterized required adaptive mutations to the human entry receptors CD150 (SLAM) and nectin-4 as first step to infect human target cells. Recombinant wild-type CDV-A75/17^red adapted quickly to growth in human H358 epithelial cells expressing human nectin-4. Sequencing of the viral attachment proteins (hemagglutinin, H, and fusion protein, F) genes revealed that no adaptive alteration was required to utilize human nectin-4. In contrast, the virus replicated only to low titres (10² pfu/ml) in Vero cells expressing human CD150 (Vero-hSLAM). After three passages using these cells virus was adapted to human CD150 and replicated to high titres (10⁵ pfu/ml). Sequence analyses revealed that only one amino acid exchange in the H-protein at position 540 Asp→Gly (D540G) was required for functional adaptation to human CD150. Structural modelling suggests that the adaptive mutation D540G in H reflects the sequence alteration from canine to human CD150 at position 70 and 71 from Pro to Leu (P70L) and Gly to Glu (G71E), and compensates for the gain of a negative charge in the human CD150 molecule. Using this model system our data indicate that only a minimal alteration, in this case one adaptive mutation, is required for adaptation of CDV to the human entry receptors, and help to understand the molecular basis why this adaptive mutation occurs.     

Homing Genes Expression in Fucosyltransferase VI-Treated Umbilical Cord Blood CD133+ Cells which Expanded on Protein-Coated Nanoscaffolds

Umbilical cord blood (UCB)-derived hematopoietic stem cells (HSCs) are considered because of their self-renewing, differentiating, proliferating, and readily available properties. Moreover, HSCs? homing to the hematopoietic microenvironment is an important step in their transplantation process. But low content of progenitor cells in one unit of UCB and defect in the bone marrow (BM) homing limit their applications. Hence, we decided to correct this deficiency with ex vivo incubation of CD133+ cells using fucosyltransferase VI and GDP-fucose. Then C-X-C chemokines receptor-4 (CXCR4), very late activation antigen-4 (VLA4), very late activation antigen-5 (VLA5), lymphocyte function-associated antigen-1 (LFA-1), and E-cadherin (E-cad) genes expressions were investigated with the goal of homing evaluation. The purity of MACS isolated CD133+ cells and confirmation of fucosylation were done by flow cytometry, and the viability of cells seeded on protein-coated poly l-lactic acid (PLLA) scaffold was proven via MTT assay. Scanning electron microscopy (SEM), CFU assays, and expression assays of CXCR4, VLA4, VLA5, LFA-1 and E-cad by real-time PCR were performed, too. Flow cytometry data showed that isolated cells were suitable for fucosyltransferase VI (FT-VI) incubation and expansion on nanoscaffolds. MTT, CFU assays, and SEM micrographs demonstrated fibronectin (FN)–collagen–selectin (FCS)-coated scaffold serve as best environment for viability, clonogenicity, and cell attachment. High levels of homing genes expression were also observed in cells seeded on FCS-coated scaffolds. Also, CXCR4 flow cytometry analysis confirmed real-time data. FCS-PLLA scaffolds provided optimal conditions for viability of FT-VI-treated CD133+ cells, and clonogenicity with the goal of improving homing following UCB-HSCs transplantation.     

Achieving energy neutrality in wastewater treatment plants through energy savings and enhancing renewable energy production

Wastewater treatment plants (WWTPs) consume high amounts of energy which is mostly purchased from the grid. During the past years, many ongoing measures have taken place to analyze the possible solutions for both reducing the energy consumption and increasing the renewable energy production in the plants. This review contains all possible aspects which may assist to move towards energy neutrality in WWTPs. The sources of energy in wastewater were introduced and different indicators to express the energy consumption were discussed with examples of the operating WWTPs worldwide. Furthermore, the pathways for energy consumption reductions were reviewed including the operational strategies and the novel technological upgrades of the wastewater treatment processes. Then the methods of recovering the potential energy hidden in wastewater were described along with application of renewable energies in WWTPs. The available assessment methods, which may help in analyzing and comparing WWTPs in terms of energy and greenhouse gas emissions were introduced. Eventually, successful case studies on energy self-sufficiency of WWTPs were listed and the innovative projects in this area were presented.