Forecasting of breathing events during nocturnal sleep using encoder-decoder recurrent neural network based on a sensors data of consumer smartwatches.

Respiratory disorders during nocturnal sleep are the states of abnormal and difficult breathing, including snoring, hypopnea and different apnea types. Some of them have a negligible effect on health, while others can lead to a serious consequences. Therefore, the development of low-cost, portable, user-friendly devices and corresponding algorithms for diagnosis and forecasting of such events is of particular importance. In the current paper, an encoder-decoder recurrent neural network was developed for respiratory pattern forecasting. The system is based on a physiological sensors (accelerometer and photoplethysmography) data gathered from the consumer smartwatches during nocturnal sleep. The influence of the length of time series in the encoder part (available history for forecasting), and the length of time series at the output of decoder (forecasting length) is studied. The average achieved f1 score and Cohen's Kappa agreement of the proposed model varies in the range from 0.35 to 0.5 and from 0.25 to 0.4, respectively, depending on forecasting length. The efficiency of the forecasting largely depends on the model complexity, presence or absence of respiration events in the encoder part, and forecasting length.Clinical Relevance- Results of the current paper may be used for the development of the respiration events screening tool based on a wearable devices sensors data.

[Use of automated bactec MGIT 960 system in the diagnosis of resistance to reserve drugs agents in Samara].

The paper gives the results of a demonstration project to introduce a test for drug sensitivity to second-line antituberculous agents for patients with multidrug-resistant (MDR) tuberculosis at a routine large Russian laboratory. Two hundred and thirty MDR isolates were examined; of them 8.7% had extreme drug resistance. The cost of this test was estimated to be US $ 33.4. The introduction of this test is possible and essential for the precise and timely choice of antituberculous therapy for patients with MDR tuberculosis.

[The specific features of tuberculosis in children and adolescents previously receiving chemoprophylaxis].

Examining 261 cases of active forms of tuberculosis in children and adolescents in the Samara Region in 1996 to 2004 indicated that 115 (44.1%) had earlier received chemoprophylaxis in the outpatient setting. The specific features of tuberculosis were revealed in this group of patients as compared with the children and adolescents who had never been treated with antituberculous drugs (n = 146): there was a predominance of preschool children; severe, disseminated forms of tuberculosis, detectable from complaints were observed less frequently; clinically cured pulmonary tuberculosis was more frequently characterized by residual posttuberculous changes. Outpatient chemoprophylaxis reduces the severity of the disease, but is not always effective in preventing tuberculosis.

[Preponderance of Mycobacterium tuberculosis strains of the family Beijing and risk factors of their transmission in the Samara Region].

Current molecular and epidemiological studies could reveal individual families of Mycobacterium tuberculosis strains. The purpose of the present study was to reveal the spread of Mycobacterium tuberculosis strains of the family Beijing in the Samara Region and to define risk factors for their transmission. This was a cross-sectional populational molecular epidemiological study that showed that the Beijing genotype prevailed among the obtained isolates (66.6%; 586/880) and it was encountered among convicts and young persons (RR 1.3; 95% CI 1.2-1.5 and RR 1.2; 95% CI 1.0-1.3, respectively), which is indicative of active and recent transmission. Multifactorial analysis indicated that male sex (OR 1.5; 95% CI 1.1-1.9), younger age (OR 1.3; 95% CI 1.1-1.7), homelessness (OR 5.6; 95% CI 1.1-6.3), and prior or current confinement (OR 2.0; 95 CI 1.5-2.7) were substantially associated with the risk of contamination with the strain of the Beijung family. Drug resistance, including multidrug resistance, was twice higher among the strains of this family.

The Directly Observed Therapy Short-Course (DOTS) strategy in Samara Oblast, Russian Federation.

BACKGROUND: The World Health Organisation (WHO) defines Russia as one of the 22 highest-burden countries for tuberculosis (TB). The WHO Directly Observed Treatment Short Course (DOTS) strategy employing a standardised treatment for 6 months produces the highest cure rates for drug sensitive TB. The Russian TB service traditionally employed individualised treatment. The purpose of this study was to implement a DOTS programme in the civilian and prison sectors of Samara Region of Russia, describe the clinical features and outcomes of recruited patients, determine the proportion of individuals in the cohorts who were infected with drug resistant TB, the degree to which resistance was attributed to the Beijing TB strain family and establish risk factors for drug resistance. METHODS: Prospective study. RESULTS: 2,099 patients were recruited overall. Treatment outcomes were analysed for patients recruited up to the third quarter of 2003 (n = 920). 75.3% of patients were successfully treated. Unsuccessful outcomes occurred in 7.3% of cases; 3.6% of patients died during treatment, with a significantly higher proportion of smear-positive cases dying compared to smear-negative cases. 14.0% were lost and transferred out. A high proportion of new cases (948 sequential culture-proven TB cases) had tuberculosis that was resistant to first-line drugs; (24.9% isoniazid resistant; 20.3% rifampicin resistant; 17.3% multidrug resistant tuberculosis). Molecular epidemiological analysis demonstrated that half of all isolated strains (50.7%; 375/740) belonged to the Beijing family. Drug resistance including MDR TB was strongly associated with infection with the Beijing strain (for MDR TB, 35.2% in Beijing strains versus 9.5% in non-Beijing strains, OR-5.2. Risk factors for multidrug resistant tuberculosis were: being a prisoner (OR 4.4), having a relapse of tuberculosis (OR 3.5), being infected with a Beijing family TB strain (OR 6.5) and having an unsuccessful outcome from treatment (OR 5.0). CONCLUSION: The implementation of DOTS in Samara, Russia, was feasible and successful. Drug resistant tuberculosis rates in new cases were high and challenge successful outcomes from a conventional DOTS programme alone.

[Molecular typing of the Mycobacterium tuberculosis strains circulating in central Russia: efficiency of spoligotyping and VNTR-MIRU].

Current problems of molecular epidemiology of the Mycobacterium tuberculosis strains circulating in Samara Region, Russia are discussed. A total of 190 isolates of Mycobacterium tuberculosis were typed using two PCR-based molecular methods. The cultures were isolated from civil and prison patients with pulmonary tuberculosis recruited from different tuberculosis institutions across the Samara region. The usefulness of spoligotyping and 15-locii VNTR-MIRU was assessed for genotyping of Mycobacterium in population with high prevalence of Beijing strains (67.9%) using statistical analyses that included calculation of Hunter-Gaston index. The VNTR-MIRU method was demonstrated to be more efficient and was characterized by higher discrimination (index 0.747) compare to spoligotyping (index 0.572). VNTR-MIRU loci 10, 26, 31, 39, 40 and ETR-A were mostly polymorphic and therefore recommended for use in screening. It could be performed by manual electrophoresid, provided that automated sequencing is not available.

Social factors influencing hospital utilisation by tuberculosis patients in the Russian Federation: analysis of routinely collected data.

OBJECTIVE: To establish whether admissions, discharges and hospital utilisation for tuberculosis (TB) in Russia are independent of sex, age, disability and employment status. STUDY POPULATION AND METHODS: Analysis of hospital admissions, discharges and in-patient utilisation using routinely collected data in Samara Region of the Russian Federation. RESULTS: Male, unemployed and disabled adults were significantly more likely to be hospitalised (P < 0.001). The unemployed and pensioners were more likely to have multiple admissions. Unemployed adults were more likely to have longer average lengths of stay per admission (P < 0.001), with a cumulative length of stay for unemployed and disabled adults significantly greater than for employed adults and adults with no disability. Interruption of hospital care was significantly more frequent in male, disabled and unemployed patients (P < 0.001). CONCLUSIONS: Socio-economic factors influence hospital admission patterns and the length of stay for patients when hospitalised, as the providers of TB services attempt to mitigate the lack of social care provision for patients. For the WHO DOTS strategy to be effectively implemented and sustained in the Russian Federation health system, social sector linkage issues need to be addressed.

Variability in interpretation of chest radiographs among Russian clinicians and implications for screening programmes: observational study.

OBJECTIVE: To determine variability in interpretation of chest radiographs among tuberculosis specialists, radiologists, and respiratory specialists. DESIGN: Observational study. SETTING: Tuberculosis and respiratory disease services, Samara region, Russian Federation. PARTICIPANTS: 101 clinicians involved in the diagnosis and management of pulmonary tuberculosis and respiratory diseases. MAIN OUTCOME MEASURES: Interobserver and intraobserver agreement on the interpretation of 50 digital chest radiographs, using a scale of poor to very good agreement (kappa coefficient: < or = 0.20 poor, 0.21-0.40 fair, 0.41-0.60 moderate, 0.61-0.80 good, and 0.81-1.00 very good). RESULTS: Agreement on the presence or absence of an abnormality was fair only (kappa = 0.380, 95% confidence interval 0.376 to 0.384), moderate for localisation of the abnormality (0.448, 0.444 to 0.452), and fair for a diagnosis of tuberculosis (0.387, 0.382 to 0.391). The highest levels of agreement were among radiologists. Level of experience (years of work in the specialty) influenced agreement on presence of abnormalities and cavities. Levels of intraobserver agreement were fair. CONCLUSIONS: Population screening for tuberculosis in Russia may be less than optimal owing to limited agreement on interpretation of chest radiographs, and may have implications for radiological screening programmes in other countries.

Tuberculosis, HIV seroprevalence and intravenous drug abuse in prisoners.

High rates of tuberculosis (TB) and HIV are believed to exist in Russian prisons. Prisoners with TB were studied in order to identify the following: 1) prevalence of HIV, and risk factors for HIV and other blood-borne virus infections; and 2) clinical and social factors that might compromise TB treatment effectiveness and/or patient adherence and, hence, encourage treatment failure. A 1-yr cross-sectional prevalence study of 1,345 prisoners with TB was conducted at an in-patient TB facility in Samara, Russian Federation. HIV and hepatitis B and/or C co-infection occurred in 12.2% and 24.1% of prisoners, respectively, and rates were significantly higher than in civilians. Overall, 48.6% of prisoners used drugs, of which 88.3% were intravenous users. Prisoners were more likely to be intravenous drug users and HIV positive compared with civilians with TB, and 40.2% of prisoners shared needles. Two-thirds of prisoners (68.6%) had received previous TB drug therapy (frequently multiple, interrupted courses) and were significantly more likely than civilians to have had previous therapy consistent with the high drug-resistance rates seen. Prisons are major drivers of the tuberculosis and HIV epidemics. Novel strategies are needed to reduce the spread of blood borne diseases, particularly in intravenous drug users.

Seasonal variation and hospital utilization for tuberculosis in Russia: hospitals as social care institutions.

BACKGROUND: Clinical management of tuberculosis in Russia involves lengthy hospitalizations, in contrast to the recommended strategy advocated by the World Health Organization. METHODS: We used Fourier transform, spectral analysis and Student's t-test to analyse periodic and seasonal variations in admission and discharge rates for tuberculosis hospitalizations in 1999-2002, using routinely captured data from the Samara Region, Russia. RESULTS: Hospital admissions in colder months were significantly higher than in warmer months. The mean monthly adjusted number of admissions in colder and warmer months for all adults was 413 and 372 (P < 0.01), for unemployed adults 218 and 198 (P < 0.02) and for pensioners 104 and 82 (P < 0.05). Hospital discharges varied seasonally. Maximum differences between admissions and discharges occurred in colder months and minimum differences were observed in warmer months. CONCLUSIONS: As hospitalizations of tuberculosis patients in colder months fulfil an important social need, shifts to ambulatory care must be carefully managed.

[Analysis of risk factors of the occurrence of drug resistance in patients with tuberculosis from civil and penitentiary sectors in the Samara Region].

The true prevalence rates of multidrug-resistant tuberculosis (MDRT) are unknown for most regions of Russia. This study was conducted in the Samara Region that differs from other regions in the rapid spread of HIV infection. The purpose of this study was to determine the primary and acquired resistance of Mycobacterium tuberculosis (MBT) to first-line antituberculous drugs in patients from civil and penitentiary sectors and to reveal risk factors of drug resistance of MBT. Six hundred patients (309 civilians and 291 prisoners who had been bacteriologically diagnosed as having tuberculosis. The authors have established the following:--in new cases, primary drug resistance is as follows: to isoniazid [38.9% (95% CI, 31.3-36.9%)], to rifampicin [25.9% (95% CI, 19.4-33.4%)] and to MDRT [23.0% (95% CI, 16.7-30.3%)];--in prisoners, the primary resistance of MBT was statistically more significant than in civilians;--male sex, in adequate prior or current treatment for tuberculosis for more than 4 weeks, the presence of fibrocavernous tuberculosis and previous prison stay are essential risk factors of the development of resistance of MBT to both any first-line drug and MDRT;--HIV infection is unassociated with resistance.

Health system frailties in tuberculosis service provision in Russia: an analysis through the lens of formal nutritional support.

OBJECTIVE: The aim of this study was to describe health system challenges faced by tuberculosis (TB) treatment facilities in Russia through an analysis of formal institutional dietary provisions to patients in an inpatient facility that provides care for poor patients. METHODS: Analysis of formal dietary provisions by institutions and financing data from TB hospitals in Samara Oblast, Russia. RESULTS: Formal dietary provision for inpatients with TB has fallen substantially in recent years. In a hospital providing inpatient care for the poorest patients with fewest social support networks, this has been very pronounced. The likely reason for this is that financial support for other budget lines, principally salaries, has required protection. CONCLUSION: Formal institutional nutritional support in institutions providing care for the poorest patients with TB is unlikely to be enhancing the speed of recovery, or reducing the duration of infectiousness. Furthermore, the role that hospital may have played in the past in enabling patients to regain weight lost before admission may have been limited by reductions in formal financing. Reductions in state provision of food for patients may serve as an important illustration of wider TB control system frailties in the Russian Federation.

Barriers to sustainable tuberculosis control in the Russian Federation health system.

The Russian Federation has the eleventh highest tuberculosis burden in the world in terms of the total estimated number of new cases that occur each year. In 2003, 26% of the population was covered by the internationally recommended control strategy known as directly observed treatment (DOT) compared to an overall average of 61% among the 22 countries with the highest burden of tuberculosis. The Director-General of WHO has identified two necessary starting points for the scaling-up of interventions to control emerging infectious diseases. These are a comprehensive engagement with the health system and a strengthening of the health system. The success of programmes aimed at controlling infectious diseases is often determined by constraints posed by the health system. We analyse and evaluate the impact of the arrangements for delivering tuberculosis services in the Russian Federation, drawing on detailed analyses of barriers and incentives created by the organizational structures, and financing and provider-payment systems. We demonstrate that the systems offer few incentives to improve the efficiency of services or the effectiveness of tuberculosis control. Instead, the system encourages prolonged supervision through specialized outpatient departments in hospitals (known as dispensaries), multiple admissions to hospital and lengthy hospitalization. The implementation, and expansion and sustainability of WHO-approved methods of tuberculosis control in the Russian Federation are unlikely to be realized under the prevailing system of service delivery. This is because implementation does not take into account the wider context of the health system. In order for the control programme to be sustainable, the health system will need to be changed to enable services to be reconfigured so that incentives are created to reward improvements in efficiency and outcomes.

[Mutations linked with antimicrobial resistance in Mycobacterium tuberculosis isolated from tuberculosis patients in the Samara region].

A total of 234 M. tuberculosis isolates were used to demonstrate the leading role of mutations in, respectively, codon 531 of gene rpoB (90.0%) and codon 315 of gene katG (92.9%), in the development of resistance to rifampicin and isoniazid by the methods of reverse hybridization with oligonucleotide probes and the sequencing of gene stretches. The levels of primary resistance of M. tuberculosis to rifampicin, isoniazid and multiresistance, according to the molecular-genetic analysis, were 41.0%, 57.7% and 37.2% respectively. The coincidence of the results of the bacteriological and molecular-genetic analyses of the antimicrobial resistance of the isolates was 90.4% and 95.3% for isoniazid and rifampicin respectively. The prevalence of individual types of mutations, linked with antimicrobial resistance, in the presence of a considerable spread of strains of the family Beijing in the region may be indicative of the limited number of M. tuberculosis clones circulating in the region.

Rates of drug resistance and risk factor analysis in civilian and prison patients with tuberculosis in Samara Region, Russia.

BACKGROUND: Tuberculosis (TB) and HIV rates continue to escalate in Russia, but true rates for drug resistance, especially multidrug resistant tuberculosis (MDR TB), are unknown. A study was conducted with the aims of identifying first line drug resistance, both in the civilian and prison sectors, for new and previously treated cases; and risk factors for the development of drug resistance. METHODS: A cross sectional survey was undertaken of 600 patients (309 civilians, 291 prisoners) with bacteriologically confirmed pulmonary TB over a 1 year period during 2001-2 in Samara Oblast, Russia. RESULTS: The prevalence of isoniazid, rifampicin, streptomycin, ethambutol and pyrazinamide resistance in new TB cases (civilian and prison patients) was 38.0%, 25.2%, 34.6%, 14.7%, and 7.2%, respectively. The prevalence of MDR TB was 22.7%, 19.8%, and 37.3% in all new cases, new civilian cases, and new prison cases, respectively, with an overall prevalence of 45.5% and 55.3% in previously treated cases. Factors associated with resistance included previous TB treatment for more than 4 weeks, smoking (for isoniazid resistance), the presence of cavitations on the chest radiograph, and imprisonment. HIV was not associated with resistance in all patients. The rates of resistance were significantly higher in prisoners, with rate ratios (RR) of 1.9 (95% CI 1.1 to 3.2) for MDR TB, 1.9 (95% CI 1.1 to 3.2) for rifampicin, and 1.6 (95% CI 1.0 to 2.6) for isoniazid. CONCLUSIONS: Rates of first line drug resistance are high, particularly in prisoners and previously treated cases. TB control programmes should initially focus on standardised treatment to maximise cure, combined with measures to reduce institutional TB spread (particularly in prisons) coupled with early diagnosis of MDR TB to reduce the spread and development of resistance.

Multidrug-resistant tuberculosis in Russia: clinical characteristics, analysis of second-line drug resistance and development of standardized therapy.

The aim of the study presented here was to identify patients with multidrug resistant tuberculosis (MDRTB) in the Samara region of Russia and to analyze the susceptibility of their isolates to second-line drugs in order to develop an empirical, standard, second-line treatment regimen. Treatment of MDRTB can be individualized based on in vitro laboratory analysis or standardized. In the latter case there is still a need to ascertain local second-line drug-resistance patterns. Described here are the clinical characteristics of 251 MDRTB patients identified in the study and the second-line drug susceptibility of 69 MDRTB isolates obtained from them. Antimicrobial resistance to the following agents was detected in the isolates: rifabutin (88.2%), streptomycin (42.8%), amikacin (7.2%), doxycycline (7.4%), ciprofloxacin (4.3%), clofazimine (2.9%), cycloserine (7.4%), and prothionamide (1.5%). The results of the study indicate it is possible to develop a standard, effective, clinical treatment regimen using ethambutol, pyrazinamide, prothionamide, a fluoroquinolone and amikacin.

Increased risk of tuberculosis among health care workers in Samara Oblast, Russia: analysis of notification data.

SETTING: Samara Oblast, Russia. OBJECTIVE: To compare the rates of tuberculosis (TB) in health care workers (HCWs) working in TB services, general health services (GHS) and the general population in a region of the Russian Federation. DESIGN: Analysis of notification rates of TB among HCWs, GHS workers and the general population during the 9-year period from 1994 to 2002. RESULTS: During 1994-2002, TB incidence among staff employed at the TB services in Samara Oblast was ten times higher than among the general population, reaching 741.6/100 000 person years at risk. Staff working at in-patient TB facilities were found to be at highest risk, with an incidence rate ratio of 17.7 (95% CI 11.6-27.0) compared to HCWs at the GHS. CONCLUSIONS: HCWs at TB services in the Russian Federation are at substantially increased risk for TB, suggesting significant risks from nosocomial transmission. Control of institutional spread of TB in the Russian Federation is an area that requires urgent attention, especially given the epidemic of human immunodeficiency virus that Russia is currently witnessing.

Detection of mutations associated with isoniazid and rifampin resistance in Mycobacterium tuberculosis isolates from Samara Region, Russian Federation.

High incidence rates of isoniazid-, rifampin-, and multiple-drug-resistant tuberculosis have been reported in countries of the former Soviet Union (FSU). Genotypic (unlike phenotypic) drug resistance assays do not require viable cultures but require accurate knowledge of both the target gene and the mutations associated with resistance. For these assays to be clinically useful, they must be able to detect the range of mutations seen in isolates from the population of tuberculosis patients to which they are applied. Two novel macroarrays were applied to detect mutations associated with rifampin (rpoB) and isoniazid (katG and inhA) resistance. In a sample of 233 isolates from patients in Samara, central Russia, 46.5% of isolates possessed mutations in both the rpoB and the katG (or inhA) genes. Combined results from the macroarrays demonstrated concordance in 95.4 and 90.4% of phenotypically defined rifampin- and isoniazid-resistant isolates, respectively. The contribution of different mutations to resistance was comparable to that reported previously for non-FSU countries, with 90% of rifampin-resistant isolates and 93% of isoniazid resistant isolates due to rpoB531 and katG315 mutations, respectively. The percentage of phenotypically resistant rifampin isolates with no mutations in the rpoB codons 509 to 536 was 4.2%, which was similar to previous reports. Novel macroarrays offer a rapid, accurate, and relatively cheap system for the identification of rifampin-, isoniazid-, and multiple-drug-resistant Mycobacterium tuberculosis isolates.

[Spoligotyping of mycobacterium tuberculosis isolates obtained from patients in the Samara region]. / Spoligotipirovanie kul'tur mikobakterii tuberkuleza, vydelennykh ot bol'nykh iz Samarskoi oblasti.

The spoligotyping of 138 M. tuberculosis isolates obtained on the territory of the Samara region made it possible to classify them as belonging to 27 groups. The largest cluster including 94 strains (68.1%) belonged to Peking spoligotype. As shown with the use of the commercial system INNO-LiPA, 78 out of 134 strains (58.2%) had mutations in different sites of gene pro B. The analysis of the markers of resistance to rifampicin in Peking spoligotype revealed that 65 (83.9%) out of 90 such cultures had mutations in gene pro B, i.e. potentially these strains had multiple antimicrobial resistance. This work demonstrated the prevalence of Peking spoligotype in a prison antituberculosis colony (81.6%).