Performance of the Genotype? MTBDRPlus assay in the diagnosis of tuberculosis and drug resistance in Samara, Russian Federation

Background  

Russia is a high tuberculosis (TB) burden country with a high prevalence of multidrug resistant tuberculosis (MDRTB). Molecular assays for detection of MDRTB on clinical specimens are not widely available in Russia.     

Energy Structure and Luminescence of CeF3 Crystals

The results of the calculation of the energy band structure and luminescent research of CeF₃ crystals are presented. The existence of two 5d1 and 5d2 subbands of the conduction band genetically derived from 5d states of Ce³⁺ ions with different effective electron masses of 4.9 m_e and 0.9 m_e, respectively, is revealed. The large electron effective mass in the 5d1 subband facilitates the localization of electronic excitations forming the 4f-5d cerium Frenkel self-trapped excitons responsible for the CeF₃ luminescence. The structure of the excitation spectra of the exciton luminescence peaked at 290 nm, and the defect luminescence at 340 nm confirms the aforementioned calculated features of the conduction band of CeF₃ crystals. The peculiarities of the excitation spectra of the luminescence of CaF₂:Ce crystals dependent on the cerium concentration are considered with respect to the phase formation possibility of CeF₃.     

3D-QSAR comparative molecular field analysis on opioid receptor antagonists: pooling data from different studies

Three-dimensional quantitative structure-activity relationship (3D-QSAR) models were constructed using comparative molecular field analysis (CoMFA) on a series of opioid receptor antagonists. To obtain statistically significant and robust CoMFA models, a sizable data set of naltrindole and naltrexone analogues was assembled by pooling biological and structural data from independent studies. A process of "leave one data set out", similar to the traditional "leave one out" cross-validation procedure employed in partial least squares (PLS) analysis, was utilized to study the feasibility of pooling data in the present case. These studies indicate that our approach yields statistically significant and highly predictive CoMFA models from the pooled data set of delta, mu, and kappa opioid receptor antagonists. All models showed excellent internal predictability and self-consistency: q(2) = 0.69/r(2) = 0.91 (delta), q(2) = 0.67/r(2) = 0.92 (mu), and q(2) = 0.60/r(2) = 0.96 (kappa). The CoMFA models were further validated using two separate test sets: one test set was selected randomly from the pooled data set, while the other test set was retrieved from other published sources. The overall excellent agreement between CoMFA-predicted and experimental binding affinities for a structurally diverse array of ligands across all three opioid receptor subtypes gives testimony to the superb predictive power of these models. CoMFA field analysis demonstrated that the variations in binding affinity of opioid antagonists are dominated by steric rather than electrostatic interactions with the three opioid receptor binding sites. The CoMFA steric-electrostatic contour maps corresponding to the delta, mu, and kappa opioid receptor subtypes reflected the characteristic similarities and differences in the familiar "message-address" concept of opioid receptor ligands. Structural modifications to increase selectivity for the delta over mu and kappa opioid receptors have been predicted on the basis of the CoMFA contour maps. The structure-activity relationships (SARs) together with the CoMFA models should find utility for the rational design of subtype-selective opioid receptor antagonists.     

Molecular and electrophysiological evidence for net synaptic potentiation in wake and depression in sleep

Plastic changes occurring during wakefulness aid in the acquisition and consolidation of memories. For some memories, further consolidation requires sleep, but whether plastic processes during wakefulness and sleep differ is unclear. We show that, in rat cortex and hippocampus, GluR1-containing AMPA receptor (AMPAR) levels are high during wakefulness and low during sleep, and changes in the phosphorylation states of AMPARs, CamKII and GSK3beta are consistent with synaptic potentiation during wakefulness and depression during sleep. Furthermore, slope and amplitude of cortical evoked responses increase after wakefulness, decrease after sleep and correlate with changes in slow-wave activity, a marker of sleep pressure. Changes in molecular and electrophysiological indicators of synaptic strength are largely independent of the time of day. Finally, cortical long-term potentiation can be easily induced after sleep, but not after wakefulness. Thus, wakefulness appears to be associated with net synaptic potentiation, whereas sleep may favor global synaptic depression, thereby preserving an overall balance of synaptic strength.     

Assessing the quality of clinical and administrative data extracted from hospitals: the General Medicine Inpatient Initiative (GEMINI) experience

ObjectiveLarge clinical databases are increasingly used for research and quality improvement. We describe an approach to data quality assessment from the General Medicine Inpatient Initiative (GEMINI), which collects and standardizes administrative and clinical data from hospitals.MethodsThe GEMINI database contained 245 559 patient admissions at 7 hospitals in Ontario, Canada from 2010 to 2017. We performed 7 computational data quality checks and iteratively re-extracted data from hospitals to correct problems. Thereafter, GEMINI data were compared to data that were manually abstracted from the hospital’s electronic medical record for 23 419 selected data points on a sample of 7488 patients.ResultsComputational checks flagged 103 potential data quality issues, which were either corrected or documented to inform future analysis. For example, we identified the inclusion of canceled radiology tests, a time shift of transfusion data, and mistakenly processing the chemical symbol for sodium (“Na”) as a missing value. Manual validation identified 1 important data quality issue that was not detected by computational checks: transfusion dates and times at 1 site were unreliable. Apart from that single issue, across all data tables, GEMINI data had high overall accuracy (ranging from 98%–100%), sensitivity (95%–100%), specificity (99%–100%), positive predictive value (93%–100%), and negative predictive value (99%–100%) compared to the gold standard.Discussion and ConclusionComputational data quality checks with iterative re-extraction facilitated reliable data collection from hospitals but missed 1 critical quality issue. Combining computational and manual approaches may be optimal for assessing the quality of large multisite clinical databases.     

Synaptic potentiation and sleep need: clues from molecular and electrophysiological studies

Sleep is homeostatically regulated in all species that have been carefully studied. In mammals and birds, the best characterized marker of sleep pressure is slow wave activity (SWA), defined as the electroencephalogram (EEG) power between 0.5 and 4 Hz during NREM sleep. SWA peaks at sleep onset and decreases with time spent asleep, and reflects the synchronous firing of cortical neurons coordinated by an underlying slow oscillation, the fundamental cellular phenomenon of NREM sleep. We have recently proposed the synaptic homeostasis hypothesis of sleep, which claims that an important function of sleep is to maintain synaptic balance. This hypothesis states that plastic processes during wake are biased towards synaptic potentiation, resulting in a net increase in synaptic strength in many brain circuits. Such increased synaptic weight would be unsustainable in the long run, due to increased demand for energy, space and supplies, and risk of synaptic saturation. Thus, according to the synaptic homeostasis hypothesis, sleep is important to renormalize synaptic strength to a baseline level that is sustainable and beneficial for memory and performance. There is strong evidence that the amplitude and slope of EEG slow waves is related to the number of neurons that enter an up state or a down state of the slow oscillation near-synchronously, and that synchrony is directly related to the number, strength, and efficacy of synaptic connections among them. Thus, the average synaptic strength (number or efficacy of synapses) reached in a given cortical area at the end of the major wake phase should be reflected by the level of SWA in the EEG at sleep onset. Moreover, according to the hypothesis, sleep SWA is not only a useful proxy of wake-related cortical synaptic strength, but could mediate the renormalization of neural circuits by favoring net synaptic depression, perhaps aided by low levels of norepinephrine, serotonin, and acetylcholine during NREM sleep. Here we briefly review human and animal studies showing that, consistent with this hypothesis, 1) in the adult cerebral cortex wake is associated with a net increase in synaptic strength, and sleep with a net decrease; and 2) SWA reflects not just prior "use" of specific neuronal circuits, but rather the occurrence of plastic changes, with increases in SWA after synaptic potentiation, and decreases in SWA after synaptic depression. We end by discussing current challenges to this hypothesis and future research directions.     

Molecular epidemiology of Mycobacterium tuberculosis clinical isolates in Southwest Ireland

Tuberculosis has had significant effects on Ireland over the past two centuries, causing persistently higher morbidity and mortality than in neighbouring countries until the last decade. This study describes the results of genotyping and drug susceptibility testing of 171 strains of Mycobacterium tuberculosis complex isolated between January 2004 and December 2006 in a region of Ireland centred on the city of Cork. Spoligotype comparisons were made with the SpolDB4 database and clustered 130 strains in 23 groups, forty-one strains showed unique Spoligotyping patterns. The commonest spoligotypes detected were ST0137 (X2) (16.9%), and ST0351 (15.8%) (‘U’ clade). The major spoligotype clades were X (26.2%), U (19.3%), T (15.2%), Beijing (5.9%), Haarlem (4.7%), LAM (4.1%), BOVIS (1.75%), with 12.9% unassigned strains. A 24-locus VNTR genotyping produced 15 clusters containing 49 isolates, with high discrimination index (HGDI > 0.99). A combination of Spoligotyping and VNTR reduced the number of clustered isolates to 47 in 15 clusters (27.5%). This study identified ST351 as common among Irish nationals, and found a low rate of drug resistance with little evidence of transmission of drug resistant strains. Strain clustering was significantly associated with age under 55 years and Irish nationality. Only strains of Euro-American lineage formed clusters. Molecular typing did not completely coincide with the results of contact investigations.