Adaptive hybrid storage systems leveraging SSDs and HDDs in HPC cloud environments

Cloud computing should inherently support various types of data-intensive workloads with different storage access patterns. This makes a high-performance storage system in the Cloud an important component. Emerging flash device technologies such as solid state drives (SSDs) are a viable choice for building high performance computing (HPC) cloud storage systems to address more fine-grained data access patterns. However, the bit-per-dollar SSD price is still higher than the prices of HDDs. This study proposes an optimized progressive file layout (PFL) method to leverage the advantages of SSDs in a parallel file system such as Lustre so that small file I/O performance can be significantly improved. A PFL can dynamically adjust chunk sizes and stripe patterns according to various I/O traffics. Extensive experimental results show that this approach (i.e. building a hybrid storage system based on a combination of SSDs and HDDs) can actually achieve balanced throughput over mixed I/O workloads consisting of large and small file access patterns.     

EAD: elasticity aware deduplication manager for datacenters with multi-tier storage systems

The popularity of Big Data applications places pressures on storage systems to efficiently scale to meet the demand. At the same time, new developments like solid-state drives have changed to traditional storage hierarchy. Cloud storage systems are transitioning towards a hybrid architecture consisting of large amounts of memory, solid-state disks (SSDs), and traditional magnetic hard disks (HD). This paper presents elasticity aware deduplication (EAD), a data deduplication framework designed for multi-tier cloud storage architectures consisting of SSD and HD. EAD dynamically adjusts the deduplication parameters at runtime in order to improve performance. Experimental results indicate that EAD is able to detect more than 98% of all duplicate data, but it only consumes less than 5% of expected memory space. Additionally, EAD saves approximately 74% of overall IO access cost compared to the traditional design.     

Storability, post-storage conversion and genetic stability assessment of alginate-encapsulated shoot tips of monopodial orchid hybrid Aranda Wan Chark Kuan ‘Blue’ × Vanda coerulea Grifft. ex. Lindl.

An efficient short-term storage system of synthetic seeds, produced using in vitro shoot tips of the monopodial orchid hybrid Aranda Wan Chark Kuan ‘Blue’ × Vanda coerulea Grifft. ex. Lindl. (AV), was developed. In vitro shoot tips (3–4 mm) were successfully encapsulated, resulting in uniform spherical beads (capsules), using 3 % sodium alginate with 75 mM CaCl₂·2H₂O. Maximum (~100 %) conversion (into plantlets with shoot and root) of capsules (or synthetic seeds) was achieved on quarter-strength Murashige and Skoog regrowth medium, while full-strength MS medium was required for effective conversion of non-encapsulated shoot tips. The capsules showed distinct difference in their response to temperature during storage. The conversion efficiency declined upon storage duration at both 4 and 25 °C, with those stored at 25 °C being more tolerant to storage. Capsules stored at 4 °C had rapid deterioration and faced complete death within 160 days while those stored for 200 days at 25 °C showed relatively high conversion (71.6 %). An inter-simple sequence repeats fingerprinting approach, employed on indiscriminately chosen plantlets from converted capsules (following 4 and 25 °C of storage), ensured the post-storage genetic stability.     

Study of the Impact of Replacement Granularity and Associated Strategies on Video Caching

Partial caching of large media objects such as video files has been proposed recently as the caching of entire objects can easily exhaust the storage resources of a proxy server. In this paper the idea of segmenting video files into chunks and applying replacement decisions at the chunk level rather than on entire videos is examined. It is shown that a higher byte hit ratio (BHR) can be achieved by appropriately adjusting the replacement granularity. The price paid for the improved BHR performance is that the replacement algorithm takes a longer time to converge to the steady state BHR. For the segmentation of video into chunks two methods are presented. The Fixed Chunk Size segmentation scheme that is rather simple and reveals the basic trade-off between byte hit ratio (BHR) and responsiveness to changes of popularity; the Variable Chunk Size segmentation scheme that uses the request frequencies to dynamically adjust the size of the chunk and is shown to be capable of combining a small response time with high BHR. Moreover, a variation of the fixed chunk size segmentation scheme is presented, which is shown to improve its performance by switching between different chunk sizes. Video segmentation is also considered as a mechanism to provide for caching differentiation based on access costs. By employing access cost dependent chunk sizes an overall access cost reduction is demonstrated.     

Influence of Nanoemulsion Addition on the Stability of Conventional Emulsions

Interest in using nanoemulsions as delivery systems for lipophilic food ingredients is growing due to their high optical clarity, good physical stability, and ability to increase bioavailability. Nanoemulsion-based delivery systems may need to be incorporated into food matrices that also contain conventional emulsions. The aim of this work was to evaluate the effect of adding nanoemulsions (d?<?200 nm) to conventional emulsions (d?>?200 nm) on the creaming stability and microstructure of the mixed systems. Droplet flocculation and rapid creaming was observed when the nanoemulsion concentration exceeded a particular level: the critical flocculation concentration (CFC) was 3.75 % and 0.25 % (v/v) for conventional emulsions with average droplet diameters of 350 and 250 nm, respectively. Confocal microscopy indicated that there was appreciable droplet flocculation, and the fraction of individual droplets with diameters?<?100 nm decreased after 14 days storage, which was probably due to Ostwald ripening and/or coalescence. The results of the present study might have important implications for the incorporation of nanoemulsion-based delivery systems into food products containing larger fat droplets, such as dressings, sauces, or beverages.     

Point of Care Tuberculosis Sero-Diagnosis Kit for Wild Animals: Combination of Proteins for Improving the Diagnostic Sensitivity and Specificity

Tuberculosis is a significant problem globally for domestic animals as well as captive and free ranging wild life. Rapid point of care (POC) serology kits are well suited for the diagnosis of TB in wild animals. However, wild animals are invariably exposed to environmental non-pathogenic mycobacterium species with the development of cross reacting antibodies. In the present study, POC TB diagnosis kit was developed using a combination of pathogenic Mycobacteria specific recombinant antigens and purified protein derivatives of pathogenic and non-pathogenic Mycobacteria. To benchmark the TB antibody detection kit, particularly in respect to specificity which could not be determined in wildlife due to the lack of samples from confirmed uninfected animals, we first tested well-characterized sera from 100 M. bovis infected and 100 uninfected cattle. Then we investigated the kit’s performance using sera samples from wildlife, namely Sloth Bears (n = 74), Elephants (n = 9), Cervidae (n = 14), Felidae (n = 21), Cape buffalo (n = 2), Wild bear (n = 1) and Wild dog (n = 1).In cattle, a sensitivity of 81% and a specificity of 90% were obtained. The diagnostic sensitivity of the kit was 94% when the kit was tested using known TB positive sloth bear sera samples. 47.4% of the in-contact sloth bears turned seropositive using the rapid POC TB diagnostic kit. Seropositivity in other wild animals was 25% when the sera samples were tested using the kit. A point of care TB sero-diagnostic kit with the combination of proteins was developed and the kit was validated using the sera samples of wild animals.     

The novel human MRC1 gene polymorphisms are associated with susceptibility to pulmonary tuberculosis in Chinese Uygur and Kazak populations

The MRC1 gene, encoding the human mannose receptor (MR), is a member of the C-type lectin receptors family. MR can recognize and bind to Mycobacterium tuberculosis by the extracellular structure, and play a role in antigen-presenting and maintaining a stable internal environment. This study aimed to investigate potential associations of SNPs in exon 7 of the MRC1 gene with pulmonary tuberculosis (TB). G1186A, G1195A, T1212C, C1221G, C1303T and C1323T were genotyped using PCR and DNA sequencing in 595 Chinese Uygur and 513 Kazak subjects. In the Uygur, the frequency of allele G (P = 0.031, OR = 1.29, 95 % CI = 1.02–1.62) and AA genotype (P = 0.033, OR = 1.64, 95 % CI = 1.04–2.60) for G1186A was lower in the pulmonary TB than healthy control and were significantly correlated with pulmonary TB. After adjustment for age and gender, G1186A was found to be additive models in association with pulmonary TB (P = 0.04, OR = 1.27, 95 % CI = 1.01–1.60). By calculating linkage disequilibrium, the frequency of haplotype GGTCCT (P = 0.032, OR = 0.75, 95 % CI = 0.57–0.97) and GGTCCC (P = 0.044, OR = 0.57, 95 % CI = 0.33–0.99) was significantly associated with pulmonary TB. No association was found between other SNPs and pulmonary TB. In the Kazak, all SNPs were not associated with pulmonary TB. Our results suggest that genetic factors play an important role in susceptibility to pulmonary TB at the individual level, and provide an experimental basis to clarify the pathogenesis of pulmonary TB.     

IFNG polymorphisms are associated with tuberculosis in Han Chinese pediatric female population

Host genetic factors play a major role in determining differential susceptibility to human tuberculosis (TB), a re-emerging infectious disease throughout the world. Genetic variations in the IFNG gene coding for interferon gamma (IFN-γ), have been identified in TB patients. To investigate the association of the IFNG polymorphisms with TB susceptibility in Chinese pediatric population. A case–control study of 189 TB patients and 164 controls was performed using single-nucleotide polymorphism (SNP) analysis. Genomic DNA was extracted from leukocytes in peripheral blood. Three SNPs of IFNG, including ?1616C/T (rs2069705), +874A/T (rs2430561), and +3234C/T (rs2069718), were selected for genotyping and analysis. The +874A and +3234C alleles were more frequent among TB patients (P = 0.108 and P = 0.088), especially in females (both P = 0.029), although this difference was not significant since Bonferroni corrected significance threshold was 0.025 (two of three SNPs were found to be in linkage disequilibrium). More pronounced differences for the +874 and +3234 polymorphisms were found under the genotype comparison between TB cases and controls in the total population [P = 0.026 (borderline non-significance) and P = 0.020, respectively], and in the female subgroup (P = 0.020 and P = 0.020). The dominant model of inheritance was shown to be significant for +874A and +3234C alleles (both P = 0.019) in the female subgroup. The +874A and +3234C alleles were more frequently found in extrapulmonary TB patients than in controls (P = 0.039). Haplotype analysis carried out on these three SNPs showed the TTT haplotype to be more frequent in controls than in TB cases, and this difference showed a strong significance (P = 0.005). The +874A and +3234C alleles may be related to TB susceptibility in the female subgroup in the Chinese pediatric population of North China. The higher rate of +874A (known to correlate with lower IFN-γ expression) in the extrapulmonary TB subgroup suggests a sufficient IFN-γ expression to be not only an important factor for the onset of TB disease but also for limiting its dissemination to lungs.     

Association of polymorphisms in the Chr18q11.2 locus with tuberculosis in Chinese population

A GWAS study has reported that two single nucleotide polymorphisms (SNPs) were associated with predisposition to tuberculosis (TB) in African populations. These two loci represented the long-waited GWAS hits for TB susceptibility. To determine whether these two SNPs are associated with TB in Chinese population, we attempted an replication in a cohort of over one thousand Chinese TB patients and 1,280 healthy controls using melting temperature shift allele-specific genotyping analysis. We found that only SNP rs4331426 was significantly associated with TB in Chinese population (p = 0.011). However, the effect was opposite. The G allele of the SNP in Chinese population is a protective allele (OR = 0.62, 95 % CI 0.44–0.87), while it was the risk allele for African population (OR = 1.19, 95 % CI 1.12–1.26). No significance was found for SNP rs2335704. The results provided an independent support for a role in susceptibility to TB for SNP rs4331426. However, it also indicated that direct predisposition element to TB and the association effects may vary across ethnic groups.     

Analysis of the coat protein gene and untranslated region of RNA3 of Cucumber Mosaic Virus isolates infecting various Lilium species and hybrids: association of the isolate infecting asiatic hybrid lily with subgroup II

The variability in the coat protein gene of Cucumber mosaic virus (CMV) isolates from various Lilium species and hybrids namely L. longiflorum, L. tigrinum, Asiatic hybrid and Oriental hybrid lilies was studied by sequence comparison of ～900 bp regions spanning the entire coat protein, intercistronic regions and 3′-UTR. CMV isolate characterised from Asiatic hybrid lily showed the highest homology with subgroup II isolates (94 – 97%), whereas 73 – 76% homology was observed with those belonging to subgroup I. Similarly, another three isolates showed 91 – 98% amino acid sequence homology with subgroup I and 74 – 76% sequence homology with subgroup II. Based on the criteria for classification of CMV isolates all the Indian isolates fall in subgroup I, except the one characterized from Asiatic Hybrid lily which falls into subgroup II. Other lily isolates from world were placed in subgroup II. This is the first case of Asiatic hybrid lily CMV isolate belonging to subgroup II.     

The association between C-159T polymorphism in CD14 gene and susceptibility to tuberculosis: a meta-analysis

The association between CD14 gene C-159T polymorphism and tuberculosis (TB) susceptibility remains inconclusive. To derive a more precise estimation of the correlation, we performed a meta-analysis summarize the possible at a systematic manner. PubMed, HighWire and ScienceDirect databases covering all papers (up to November 2012) were searched. Statistical analyses were conducted by Rev-Man and STATA. Random- and fixed-effect models were used to estimate pooled odds ratios (ORs) and 95 % confidence intervals (CIs), based on between-study heterogeneity. Eight published case–control studies investigating the relationship between C-159T polymorphism in CD14 gene and TB susceptibility were included. Results showed that individuals with T allele have an increased risk of TB compared with those with C allele (OR (95 % CI) was 1.52 (1.11, 2.08) for TT vs. TC + CC, P < 0.001; 1.27 (1.01, 1.61) for T vs. C, P = 0.04). When stratified by ethnicity, variant TT homozygote carriers had an 86 % increased risk of TB in Asians (OR (95 % CI) was 1.86 (1.57, 2.20) for TT vs. TC + CC, P < 0.001), but not in Caucasians (OR (95 % CI) was TT vs. TC + CC: OR = 0.78, 95 % CI = 0.51–1.21, P = 0.61). This meta-analysis suggests that C-159T polymorphism in CD14 gene is associated with increased risk of TB, especially in Asians, but not in Caucasians.     

Synthetic Peptides are Better Than Native Antigens for Development of ELISA Assay for Diagnosis of Tuberculosis

Immunodiagnosis of both pulmonary tuberculosis (PTB) and extrapulmonary tuberculosis has remained challenging. In the present work, in-house developed synthetic peptide based antibody detection assay was assessed and validated with antigen based assay for effective diagnosis of tuberculosis (TB). The study population included both tuberculous meningitis (TBM) (n = 60) admitted to Neurology IPD wards of our Institute hospital and PTB cases (n = 57) recruited from high TB endemic zones. Peptides of five highly immunogenic Mycobacterium tuberculosis (MTB) proteins (Ag85B, 45 kDa, HSP-16, CFP-10 and ESAT-6) were designed and synthesized. The designed peptides were evaluated in samples of both TBM and PTB cases, respectively, using in-house developed antibody detection method. The developed tests were further compared and validated with MTB native proteins based antibody detection ELISA. Sensitivity and specificity of peptide assay were significantly higher or almost similar (p < 0.05) in TBM and PTB as compared to native proteins based ELISA. Among all peptides, diagnostic reliability of Ag 85B peptide A1 was higher for both forms of TB. Peptide-based antibody assay is cost effective, simple and may be interchangeable with conventional Antigen based ELISA assays for effective diagnosis of TB in the developing world.     

Serial femtosecond crystallography at the SACLA: breakthrough to dynamic structural biology

X-ray crystallography visualizes the world at the atomic level. It has been used as the most powerful technique for observing the three-dimensional structures of biological macromolecules and has pioneered structural biology. To determine a crystal structure with high resolution, it was traditionally required to prepare large crystals (> 200 μm). Later, synchrotron radiation facilities, such as SPring-8, that produce powerful X-rays were built. They enabled users to obtain good quality X-ray diffraction images even with smaller crystals (ca. 200–50 μm). In recent years, one of the most important technological innovations in structural biology has been the development of X-ray free electron lasers (XFELs). The SPring-8 Angstrom Compact free electron LAser (SACLA) in Japan generates the XFEL beam by accelerating electrons to relativistic speeds and directing them through in-vacuum, short-period undulators. Since user operation started in 2012, we have been involved in the development of serial femtosecond crystallography (SFX) measurement systems using XFEL at the SACLA. The SACLA generates X-rays a billion times brighter than SPring-8. The extremely bright XFEL pulses enable data collection with microcrystals (ca. 50–1 μm). Although many molecular analysis techniques exist, SFX is the only technique that can visualize radiation-damage-free structures of biological macromolecules at room temperature in atomic resolution and fast time resolution. Here, we review the achievements of the SACLA-SFX Project in the past 5 years. In particular, we focus on: (1) the measurement system for SFX; (2) experimental phasing by SFX; (3) enzyme chemistry based on damage-free room-temperature structures; and (4) molecular movie taken by time-resolved SFX.     

Development of doubled haploids from an elite <Emphasis Type="Italic">indica</Emphasis> rice hybrid (BS6444G) using anther culture

A total of 200 doubled haploids (DHs) were generated from an elite rice hybrid, ‘BS6444G’ for which an androgenic method was developed by manipulating the physical and chemical factors. The spike pretreated at 10?°C for 7–8 days was effective for callusing and green plant regeneration. The maximum callus frequency was achieved when the anthers cultured in N6 medium supplemented with 2.0 mg L^?1 2,4-diclorophenoxyacetic acid, 0.5 mg L^?1 6-benzylaminopurine and 3% maltose. Calli induced in N6 media also showed significant green shoot regeneration in MS medium supplemented with 0.5 mg L^?1 1-napthalene acetic acid, 0.5 mg L^?1 kinetin, 1.5 mg L^?1 benzylaminopurine and 3% sucrose producing 210 green plants. Assessment of the ploidy status showed 95.71% fertile diploids and 4.2% polyploids; no haploids were observed. A total of 38 sequence-tagged microsatellite (STMS) markers proved able to discriminate a heterozygote from all the 200 DHs. The DHs grown in the field showed significant variation for their agronomic traits. Comparison of traits with control indicates homogeneity within each DH line and significant variance of traits between DH lines. Nine DH lines produce higher grain yield than the hybrid parent which suggests the possibility of exploiting hybrid vigor in indica rice through the development of DH lines of high yielding hybrids.     

Systematic overestimation of Salicaceae seed survival using radicle emergence in response to drying and storage: implications for ex situ seed banking

Biodiversity conservation programmes are underpinned by seed banking following drying to low water contents (WC), and supported by both the assessment and prediction of seed viability over time. The means of judging viability is thus crucial to the comprehension of seed vigour. We selected seeds of three species and one hybrid in the Salicaceae likely to have variation in tolerance to drying, processing and storage, including in relation to cryobanking, and compared survival growth as radicle emergence (germination) and normal seedling production. With three seed lots of Salix gracilistyla, air-drying to 8–10 % WC enhanced seed survival after 40 days’ storage at 5 °C as compared with non-treated seeds at 14–20 % WC. Four seed lots of Populus alba × P. glandulosa showed equally high germination (88–100 %) and proportions of normal seedlings (81–99 %) when stored at 5 °C for 7–10 weeks. Among seven seed lots of S. gracilistyla, two groups with different storage behaviour could be statistically distinguished with normal seedling production ranging from 0 to 45 % after storage at 5 °C for 13 weeks. Seed tolerance to WC manipulation and cryopreservation was very variable among species and seed lots. Seed lots of S. hallaisanensis and S. gracilistyla with ~80 % germination survived cryopreservation at 10 % WC, but were sensitive to lower WCs. In contrast, Populus seeds had greater desiccation tolerance combined with cryopreservation capability. With seed lots of all species and hybrids, cryopreservation had little effect on viability unless the high moisture freezing limit had been exceeded (~10–20 % WC, depending on seed lot). However, under all conditions of handling (drying, rehydration, storage at 5 °C or cryopreservation) using germination as the only indicator of viability over-estimated survival compared with normal seedling production.     

Improving yield performance of Pleurotus pulmonarius through hyphal anastomosis fusion of dikaryons

High production and good quality are always the principal goals for agriculturally important crops, without the exception of mushrooms. P. pulmonarius is one of the commercially important edible mushrooms throughout the world. The yield performance improvement was carried out by cross bred P. pulmonarius with P. sapidus and P. ostreatus. The highest rate of 0.587 mm/days for spawn ramification and 53.33 % for percentage spawn productivity were obtained in hybrids LN LL910. The least day (11 and 12th) of the primodia mushroom sporophore were recorded in LL910 and LN 97 respectively, while longest day of 19th was recorded in wild type (NE 07). The highest biological efficiency (109.30 %) and production rate (3.77 %) obtained by LL910, while the least of 33.0 and 0.79 % were obtained by NE 07 for biological efficiency and production rate respectively. The morphological and molecular characterization of the hybrid strains established their true variation from their wild type. LL 910 (JF68088) is located at seventh subclusters from the root with boostrap value of 32 %, while only one parent (LAU 09: JF736658) out of the two has the close boostrap value of 43 % at the first subcluster to the root, with the other parent LAU 10 (JF736659) shows distance relationship after Blast. LN 97 (JF680992) is located at outgroup, while the parent strains NE 07 (boostrap value: 11 %) and LAU 09 (boostrap value: 44 %) located at tenth and second subclusters respectively. The results obtained from this study have shown the improved performance of the hybrids strain over wild type strains.     

Combining Instruction Prefetching with Partial Cache Locking to Improve WCET in Real-Time Systems

Caches play an important role in embedded systems to bridge the performance gap between fast processor and slow memory. And prefetching mechanisms are proposed to further improve the cache performance. While in real-time systems, the application of caches complicates the Worst-Case Execution Time (WCET) analysis due to its unpredictable behavior. Modern embedded processors often equip locking mechanism to improve timing predictability of the instruction cache. However, locking the whole cache may degrade the cache performance and increase the WCET of the real-time application. In this paper, we proposed an instruction-prefetching combined partial cache locking mechanism, which combines an instruction prefetching mechanism (termed as BBIP) with partial cache locking to improve the WCET estimates of real-time applications. BBIP is an instruction prefetching mechanism we have already proposed to improve the worst-case cache performance and in turn the worst-case execution time. The estimations on typical real-time applications show that the partial cache locking mechanism shows remarkable WCET improvement over static analysis and full cache locking.     

Recovery from topkill of shortleaf pine × loblolly pine hybrids compared to their parent populations

Hybrids between shortleaf pine (Pinus echinata Mill.) and loblolly pine (Pinus taeda L.) have increased since the 1950s throughout the southeastern USA. Previously, greater sprouting capacity and the formation of a basal crook that lowers the height of dormant buds may have favored pure shortleaf pine populations on fire prone sites. The objective of this study was to determine how seasonal timing of topkill by both fire and topclipping affect sprouting of shortleaf × loblolly pine F1 hybrids compared to their parent open-pollinated populations during their third growing season. A factorial combination of top-clipping (hand pruners) and girdling by fire (propane torch) was conducted on November 2010, January, March, and April 2011 and sprouting response was measured after the growing season. Survival of topkilled shortleaf pine (94 %) was greatest followed by hybrid (78 %) and loblolly pine (35 %). However, species effects varied with topkill treatment and treatment date because survival was relatively lower for loblolly and hybrid pines in the burn-only as well as the November and April treatment dates while survival of shortleaf pine was consistently high. The number of sprouts was greatest for shortleaf (32.3) intermediate for hybrid (23.8) and lowest for loblolly pine (12.0). Overall, 83 % of shortleaf pine, 35 % of hybrid pine, and 5 % of loblolly pine exhibited a basal crook. The height from ground line to the lowest sprout was shortest for shortleaf (3.5 mm), intermediate for hybrids (7.7 mm), and largest for loblolly pine (21.3 mm). While the hybrid saplings exhibited intermediate performance in survival, sprouting capacity, and crooking, pure shortleaf pine were superior and are probably better suited to recover from fire.     

Variants in toll-like receptors 2 and 9 influence susceptibility to pulmonary tuberculosis in Caucasians, African-Americans, and West Africans

Tuberculosis (TB) is a global public health problem and a source of preventable deaths each year, with 8.8 million new cases of TB and 1.6 million deaths worldwide in 2005. Approximately, 10% of infected individuals develop pulmonary or extrapulmonary TB, suggesting that host defense factors influence development of active disease. Toll-like receptor’ (TLR) polymorphisms have been associated with regulation of TLR expression and development of active TB. In the present study, 71 polymorphisms in TLR1, TLR2, TLR4, TLR6, and TLR9 were examined from 474 (295 cases and 179 controls) African-Americans, 381 (237 cases and 144 controls) Caucasians, and from 667 (321 cases and 346 controls) Africans from Guinea-Bissau for association with pulmonary TB using generalized estimating equations and logistic regression. Statistically significant associations were observed across populations at TLR9 and TLR2. The strongest evidence for association came at an insertion (I)/deletion (D) polymorphism (?196 to ?174) in TLR2 that associated with TB in both Caucasians (II vs. ID&DD, OR = 0.41 [95% CI 0.24–0.68], p = 0.0007) and Africans (II vs. ID&DD, OR = 0.70 [95% CI 0.51–0.95], p = 0.023). Our findings in three independent population samples indicate that variations in TLR2 and TLR9 might play important roles in determining susceptibility to TB.     

Smear positive pulmonary tuberculosis and associated factors among homeless individuals in Dessie and Debre Birhan towns,Northeast Ethiopia

Background

Tuberculosis (TB) remains one of the globe’s deadliest communicable diseases. The homeless individuals are at high risk to acquire TB and multi-drug resistant TB (MDR-TB), because of their poor living conditions and risky behaviors. Tuberculosis and MDR-TB in the homeless individuals can pose a risk to entire communities. However, the magnitude of the problem is not known in Ethiopia. Therefore, the aim of this study was to determine the prevalence and associated factors of smear positive pulmonary TB (PTB) and MDR-TB among homeless individuals in Dessie and Debre Birhan towns, Northeast Ethiopia.

Methods

A community based cross-sectional study design was conducted from September 2014 to June 2015. Using an active screening with cough of ≥2 weeks, 351 TB suspects homeless individuals were participated in this study. Data were collected by using pre-tested and structured questionnaire. Spot-morning-spot sputum sample was collected and examined for acid-fast bacilli (AFB) using fluorescence microscopy by Auramine O staining technique. All AFB positive sputum was further analyzed by GeneXpert for detection of Mycobacterium tuberculosis complex and rifampicin resistant gene. Univariate and multivariate logistic regressions were applied to identify factors associated with smear positive PTB and P value <0.05 was considered as statistically significant.

Results

The prevalence of smear positive PTB was 2.6 % (95 % CI 1.3–5) among TB suspect homeless individuals. Extrapolation of this study finding implies that there were 505 smear positive PTB per 100,000 homeless individuals. All smear positive PTB sputum specimens were further analyzed by GeneXpert assay, the assay confirmed that all were positive for MTBC but none were resistant to RIF or MDR. Smoking cigarette regularly for greater than 5 years (AOR 10.1, 95 % CI 1.1, 97.7), body mass index lower than 18.5 (AOR 6.9, 95 % CI 1.12, 41.1) and HIV infection (AOR 6.8, 95 % CI 1.1, 40.1) were significantly associated with smear positive PTB.

Conclusion

The prevalence of smear positive PTB among TB suspect homeless individuals was 2.6 %. Among smear positive PTB, prevalence of HIV co-infection was very high 5 (55.5 %). Smoking cigarette regularly for greater than 5 years, BMI lower than 18.5 and HIV infection were factors associated with smear positive PTB. Special emphasis is needed for homeless individuals to exert intensive effort to identify undetected TB cases to limit the circulation of the disease into the community.