Performance Comparison of Three Rapid Tests for the Diagnosis of Drug-Resistant Tuberculosis

Background

The aim of this study was to compare the performance of several recently developed assays for the detection of multi- and extensively drug-resistant tuberculosis (M/XDR-TB) in a large, multinational field trial.

Methods

Samples from 1,128 M/XDR-TB suspects were examined by Line Probe Assay (LPA), Pyrosequencing (PSQ), and Microscopic Observation of Drug Susceptibility (MODS) and compared to the BACTEC MGIT960 reference standard to detect M/XDR-TB directly from patient sputum samples collected at TB clinics in India, Moldova, and South Africa.

Results

Specificity for all three assays was excellent: 97–100% for isoniazid (INH), rifampin (RIF), moxifloxacin (MOX) and ofloxacin (OFX) and 99–100% for amikacin (AMK), capreomycin (CAP) and kanamycin (KAN) resistance. Sensitivities were lower, but still very good: 94–100% for INH, RIF, MOX and OFX, and 84–90% for AMK and CAP, but only 48–62% for KAN. In terms of agreement, statistically significant differences were only found for detection of RIF (MODS outperformed PSQ) and KAN (MODS outperformed LPA and PSQ) resistance. Mean time-to-result was 1.1 days for LPA and PSQ, 14.3 days for MODS, and 24.7 days for MGIT.

Conclusions

All three rapid assays evaluated provide clinicians with timely detection of resistance to the drugs tested; with molecular results available one day following laboratory receipt of samples. In particular, the very high specificity seen for detection of drug resistance means that clinicians can use the results of these rapid tests to avoid the use of toxic drugs to which the infecting organism is resistant and develop treatment regiments that have a higher likelihood of yielding a successful outcome.     

Diurnal variation in CREB phosphorylation and PER1 protein levels in lactotroph cells of melatonin-proficient C3H and melatonin-deficient C57BL mice: similarities and differences

The pineal hormone melatonin plays an important role in the maintenance of rhythmic functions of the hypophyseal pars tuberalis, which controls the lactotroph cells of the pars distalis. To analyze the effects of melatonin deficiency on the activity state of these cells, we have investigated the levels of Ser133-phosphorylated (p)CREB and PER1 protein in immunocytochemically identified lactotroph cells of melatonin-proficient C3H and melatonin-deficient C57BL mice at four different time points of a 12/12 LD cycle. At night, the percentage of lactotroph cells showing a positive nuclear pCREB and PER1 immunoreaction is significantly smaller in C57BL than in C3H mice. In both mouse strains, the percentage of pCREB-immunoreactive cells is minimal in the early morning and gradually increases to reach a maximum in the late night. PER1 levels show a parallel temporal variation in C3H, but in C57BL, they are drastically reduced in the early afternoon. The observation that, during darkness, the percentage of lactotroph cells with nuclear pCREB immunoreaction is significantly higher in C3H than in C57BL mice suggests the existence of a distinct cell population that is under the control of melatonin-dependent intrapituitary signaling. Interestingly, the percentage of pCREB- and PER1-immunoreactive lactotroph cells reaches minimal and maximal values at the same time points. This suggests that the correlation between CREB phosphorylation and PER1 induction differs between these cells and other neuroendocrine centers, e.g., the pineal organ and suprachiasmatic nucleus, displaying a temporal gap between CREB phosphorylation and PER1 induction.This study was supported by grants from the Deutsche Forschungsgemeinschaft (KO758/7-3)     

Using 2H2O to study the influence of feeding on protein synthesis: effect of isotope equilibration in vivo vs. in cell culture

We previously reported that 2H2O can be used to measure rates of protein synthesis during prolonged steady-state conditions (Previs SF, Fatica R, Chandramouli V, Alexander JC, Brunengraber H, and Landau BR. Am J Physiol Endocrinol Metab 286: E665-E672, 2004). The underlying premise of our method is that following the administration of 2H2O, 2H atoms in body water rapidly equilibrate with free alanine before it is incorporated into newly synthesized proteins. We have now directly examined whether 2H2O can be used to measure the influence of a single meal on protein synthesis. In addition, we have compared the use of 2H2O for measuring rates of protein synthesis in vivo vs. in cell culture. Using a rat model, we observed rapid equilibration between 2H in body water and free alanine; therefore we were able to study the response of protein synthesis to a single meal. We observed that approximately 50% of the plasma albumin that is synthesized over the course of 24 h is made within approximately 5 h after eating (in rats trained to eat a complete 24-h ration of food in a single meal). Contrary to what we observed in vivo, feeding (the replenishment of cell culture medium) does influence the use of 2H2O for in vitro studies. In particular, since there can be slow equilibration of 2H between water and alanine in the cell culture medium, special consideration must be made to avoid underestimating the rate of protein synthesis in vitro.     

Structural variation and rates of genome evolution in the grass family seen through comparison of sequences of genomes greatly differing in size

Homology was searched with genes annotated in the Aegilops tauschii pseudomolecules against genes annotated in the pseudomolecules of tetraploid wild emmer wheat, Brachypodium distachyon, sorghum and rice. Similar searches were performed with genes annotated in the rice pseudomolecules. Matrices of collinear genes and rearrangements in their order were constructed. Optical BioNano genome maps were constructed and used to validate rearrangements unique to the wild emmer and Ae. tauschii genomes. Most common rearrangements were short paracentric inversions and short intrachromosomal translocations. Intrachromosomal translocations outnumbered segmental intrachromosomal duplications. The densities of paracentric inversion lengths were approximated by exponential distributions in all six genomes. Densities of collinear genes along the Ae. tauschii chromosomes were highly correlated with meiotic recombination rates but those of rearrangements were not, suggesting different causes of the erosion of gene collinearity and evolution of major chromosome rearrangements. Frequent rearrangements sharing breakpoints suggested that chromosomes have been rearranged recurrently at some sites. The distal 4 Mb of the short arms of rice chromosomes Os11 and Os12 and corresponding regions in the sorghum, B. distachyon and Triticeae genomes contain clusters of interstitial translocations including from 1 to 7 collinear genes. The rates of acquisition of major rearrangements were greater in the large wild emmer wheat and Ae. tauschii genomes than in the lineage preceding their divergence or in the B. distachyon, rice and sorghum lineages. It is suggested that synergy between large quantities of dynamic transposable elements and annual growth habit have been the primary causes of the fast evolution of the Triticeae genomes.     

Mapping QTLs for physiological and biochemical traits related to grain yield under control and terminal heat stress conditions in bread wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.)

In order to detect genomic regions with different effects for some of the physiological and biochemical traits of wheat, four experiments were conducted at Research Farm of Agricultural and Natural Resources Research Center of Zabol in 2015–2016 and 2016–2017 growing seasons. The experiments were carried out using four alpha lattice designs with two replications under non-stress and terminal heat stress conditions. Plant materials used in this study included 167 recombinant inbred lines and their parents (‘SeriM82’ and ‘Babax’). Six traits including grain yield (GY), proline content (PRO), water soluble carbohydrates (WSC), maximum efficiency of photosystem II (Fv/Fm), cytoplasmic membrane stability (CMS) and chlorophyll content (CHL) were evaluated. Genetic linkage map consisted of 211 AFLP marker, 120 SSR marker and 144 DArT markers with 1864 cm length and 4.4 cm mean distance. QTL analysis was carried out using a mixed-model-based composite interval mapping (MCIM) method. By the combined analysis of normal phenotypic values, 27 additive QTLs and five pairs of epistatic effects were identified for studied traits, among which two additive and one epistatic QTL showed significant QTL?×?environment interactions. By the combined analysis of stress phenotypic values, a total of 26 QTLs with additive effects and 5 epistatic QTLs were detected, among which one additive and one epistatic QTL showed QTL?×?environment interactions. Six QTLs with major effects (QGY-2B, QGY-2D, QPro-5B, QWSC-4A, QFv/Fm-6A and QCMS-4B), which were common between two conditions could be useful for marker-assisted selection (MAS) in order to develop heat tolerant and high-performance wheat varieties.     

The positive effects of Mediterranean-neutropenic diet on nutritional status of acute myeloid leukemia patients under chemotherapy

Introduction

Cancer and chemotherapy-induced malnutrition increase death, reduce the response to treatment, and increase multiple kinds of side effects. The aim of this study was to investigate the effects of Mediterranean-neutropenic diet on the nutritional status of acute myeloid leukemia patients under chemotherapy.

Materials and Methods

50 patients were divided into two groups by a random allocation scheme: the Mediterranean-neutropenic diet (n = 25) and the neutropenic diet group (n = 25). The intervention was implemented during a one month period. The nutritional status was evaluated based on PG-SGA. Serum albumin levels and dietary intake were also measured.

Results

After the intervention, the mean serum albumin level in the intervention group was significantly higher than the beginning of the study (p = 0.09) and in comparison with the control group (p = 0.01). Also, the mean serum albumin level in the control group significantly decreased at the end of the study compared to the beginning of the study (p = 0.03). After intervention, the nutritional status of the patients in the intervention group was significantly improved compared to the control group.

Conclusion

In general, based on the results of this study, the Mediterranean neutropenic diet improves nutritional status during chemotherapy by increasing food intake, preventing weight loss and increasing serum albumin levels

     

The network structure affects the fixation probability when it couples to the birth-death dynamics in finite population

The study of evolutionary dynamics on graphs is an interesting topic for researchers in various fields of science and mathematics. In systems with finite population, different model dynamics are distinguished by their effects on two important quantities: fixation probability and fixation time. The isothermal theorem declares that the fixation probability is the same for a wide range of graphs and it only depends on the population size. This has also been proved for more complex graphs that are called complex networks. In this work, we propose a model that couples the population dynamics to the network structure and show that in this case, the isothermal theorem is being violated. In our model the death rate of a mutant depends on its number of neighbors, and neutral drift holds only in the average. We investigate the fixation probability behavior in terms of the complexity parameter, such as the scale-free exponent for the scale-free network and the rewiring probability for the small-world network.     

Pollen morphological studies in subfamily Suaedoideae (Chenopodiaceae)

The pollen morphology of two Bienertia species and 28 Suaeda species from the Old World has been studied with light and scanning electron microscopy. Pollen morphological characters used in this study include pollen diameter, pore number, pore diameter, operculum diameter, chord distance, exine thickness, plus number and characteristics of exine spinules and operculum spinules. Using these characters, the pollen of Bienertia is clearly distinguished from that of Suaeda. In addition, pollen data support recent molecular studies which merge the genus Borszczowia into Suaeda. The pollen grains of Suaeda show notable variation; in some cases this allows morphological distinctions to be made between species. Taxonomically, pore number is observed to be a more useful character than pollen diameter. Principal components analysis (PCA) shows only a weak correlation between pollen characters and habit (life form), habitat, mode of photosynthesis or phylogenetic relationships. Interestingly, however, the annual C₃ and C₄ species of section Schoberia are usually characterised by a higher pore number than the perennial C₄ species.     

Bioinformatics Analysis of Domain 1 of HCV-Core Protein: Iran

International Journal of Peptide Research and Therapeutics - Hepatitis C virus (HCV) infection is a serious global health problem and a cause of chronic hepatitis, liver cirrhosis, and...     

Application of a dissimilarity index of EEG and its sub-bands on prediction of induced epileptic seizures from rat's EEG signals

ObjectiveEpileptic seizures are defined as manifest of excessive and hyper-synchronous activity of neurons in the cerebral cortex that cause frequent malfunction of the human central nervous system. Therefore, finding precursors and predictors of epileptic seizure is of utmost clinical relevance to reduce the epileptic seizure induced nervous system malfunction consequences. Researchers for this purpose may even guide us to a deep understanding of the seizure generating mechanisms. The goal of this paper is to predict epileptic seizures in epileptic rats.MethodsSeizures were induced in rats using pentylenetetrazole (PTZ) model. EEG signals in interictal, preictal, ictal and postictal periods were then recorded and analyzed to predict epileptic seizures. Epileptic seizures were predicted by calculating an index in consecutive windows of EEG signal and comparing the index with a threshold. In this work, a newly proposed dissimilarity index called Bhattacharyya Based Dissimilarity Index (BBDI), dynamical similarity index and fuzzy similarity index were investigated.ResultsBBDI, dynamical similarity index and fuzzy similarity index were examined on case and control groups and compared to each other. The results show that BBDI outperforms dynamical and fuzzy similarity indices. In order to improve the results, EEG sub-bands were also analyzed. The best result achieved when the proposed dissimilarity index was applied on Delta sub-band that predicts epileptic seizures in all rats with a mean of 299.5 s.ConclusionThe dissimilarity of neural network activity between reference window and present window of EEG signal has a significant increase prior to an epileptic seizure and the proposed dissimilarity index (BBDI) can reveal this variation to predict epileptic seizures. In addition, analyzing EEG sub-bands results in more accurate information about constituent neuronal activities underlying the EEG since certain changes in EEG signal may be amplified when each sub-band is analyzed separately.SignificanceThis paper presents application of a dissimilarity index (BBDI) on EEG signals and its sub-bands to predict PTZ-induced epileptic seizures in rats. Based on the results of this work, BBDI will predict epileptic seizures more accurately and more reliably compared to current indices that increases epileptic patient comfort and improves patient outcomes.