Toward Mapping an NGSI-LD Context Model on RDF Graph Approaches: A Comparison Study.

A considerable number of Internet of Things deployments are isolated from specific solutions, from devices to data platforms. Standardized data models were proposed to overcome the interoperability gap between these deployments. Next generation service interfaces-linked data (NGSI-LD) is one of the proposed platforms that exploits linked data and proposes an information model and an application programming interface (API) for easy use and standard management of context information. The NGSI-LD information model is based on JSON for Linked Data (JSON-LD) as a serialization format for context information. This efficiently exploits the potential of semantics and linked open data. However, the NGSI-LD graph API and query language are still theoretically defined and limited to some preliminary works. Consequently, current NGSI-LD implementations are mainly based on traditional databases, where the JSON-LD serialization is supported but not exploited owing to the difficulties in defining and implementing new NGSI-LD based Graph APIs. One of the basic solutions is the use of an RDF store for NGSI-LD payloads because these types of databases are well defined and maintained and will not need any added effort for JSON-LD based payloads. However, the main complication at this level is the use of reification to annotate relationships. This study focused on both aspects of exploiting the semantics of NGSI-LD by proposing standardized mapping mechanisms to RDF graphs without reifying JSON-LD payloads and with respect to the NGSI-LD context model and API. Our main proposals highlight that exploiting the RDF store for processing NGSI-LD data semantically is feasible and uncomplicated. We illustrated the proposed mapping approaches with real use-case examples and a possible exploitation of semantic approaches.

Evaluation of GeneXpert MTB/RIF system performances in the diagnosis of extrapulmonary tuberculosis.

BACKGROUND: Tuberculosis represents a serious public health problem and a significant diagnostic and therapeutic challenge worldwide. Molecular diagnostic techniques are crucial in the World Health Organization's new tuberculosis control strategy. This study aims to evaluate the performance of GeneXpert MTB/RIF (Cepheid Sunnyvale, CA, United States) in diagnosis of extra-pulmonary tuberculosis then compare it's performance in detecting Rifampicin resistance to GenoType MTBDRplus (HAIN Life Sciences, Nehren, Germany). METHODS: Samples from pulmonary and/or extra-pulmonary origins were analysed in a 21 months retrospective study. Samples were sent to the bacteriology laboratory for Mycobacterium tuberculosis detection using conventional bacteriological and molecular methods (GeneXpert MTB/RIF and MTBDRplus). Sensitivity and specificity were calculated for the stained smear and GeneXpert according to culture (Gold Standard) as well as for GeneXpert MTB/RIF in both negative and positive microscopy tuberculosis cases. Data's statistical analysis was performed with SPSS13.0 software. RESULTS: Seven hundred fourteen patients' samples were analysed; the average age was 47.21 ± 19.98 years with a male predominance (66.4%). Out of 714 samples: 285 were from pulmonary and 429 were from extra-pulmonary origins. The positivity rates for microscopy, GeneXpert MTB/RIF and culture were 12.88, 20.59 and 15.82%, respectively. These rates were 18.9, 23.85 and 20.35% for pulmonary samples and 9.71, 18.41 and 12.82% for extra-pulmonary samples, respectively. The sensitivity and specificity of GeneXpert MTB/RIF were almost the same in both pulmonary and extra-pulmonary samples (78.2 and 90.4%) and (79,3 and 90.3%) respectively. Rifampicin resistance rate found by GeneXpert MTB/RIF was 0.84%. Comparison of Rifampicin resistance obtained by GeneXpert MTB/RIF and Genotype MTBDRplus, showed 100% agreement between the two techniques for studied samples. CONCLUSIONS: This confirms GeneXpert MTB/RIF advantage for tuberculosis diagnosis, particularly extra-pulmonary tuberculosis with negatively stained smear. The performance of GeneXpert and Genotype MTBDRplus are similar in detection of Rifampicin resistance. However, variability of detection performance according to tuberculosis endemicity deserves more attention in the choice of screening techniques of Rifampicin resistance, hence the interest of conducting comparative studies of detection performance under low and medium endemicity on large samples of tuberculosis populations.

Prevalence, antibiotic resistance, and MLST typing of Helicobacter pylori in Algiers, Algeria.

BACKGROUND: Helicobacter pylori infection is common in Algeria, but there are few data on the characterization of isolated strains. The aim of this study was to update data on the prevalence of H. pylori in patients submitted to endoscopy, antibiotic resistance, and phylogeography of H. pylori strains isolated in Algiers. MATERIALS AND METHODS: This is a prospective study carried out between November 2015 and August 2016. The culture of H. pylori was performed on antral and fundic gastric biopsies of adult patients from 3 hospitals. A real-time PCR using the fluorescence resonance energy transfer (FRET) principle for the detection of H. pylori followed by a melting curve analysis for the detection of mutations associated with resistance to clarithromycin was applied. Differentiation between antral and fundic isolates of the same patient was also determined by RAPD, and an MLST typing was performed for characterization of the phylogeographic group of H. pylori. RESULTS: By real-time PCR, the prevalence of H. pylori infection among the 147 patients included was 57%. Culture was positive in only 29% of the cases. Twenty-seven percent of patients had received H. pylori eradication treatment. The primary and secondary resistance rates to clarithromycin were 23% and 36%, respectively, and to metronidazole, 45% and 71%, respectively. Only one isolate was resistant to levofloxacin, and no resistance to amoxicillin, tetracycline, and rifampicin was detected. A double population was present in 14 patients. The MLST analysis classified the 42 H. pylori strains from 38 patients in 2 haplotypes: hpEurope (33) and hpNEAfrica (9). CONCLUSION: The prevalence of H. pylori remains high in Algeria but appears to be decreasing in recent years. High resistance to clarithromycin requires increased monitoring of the evolution of antibiotic resistance and adaptation of eradication therapy.

Age-dependent association between pulmonary tuberculosis and common TOX variants in the 8q12-13 linkage region.

Only a small fraction of individuals infected with Mycobacterium tuberculosis develop clinical tuberculosis (TB) in their lifetime. Genetic epidemiological evidence suggests a genetic determinism of pulmonary TB (PTB), but the molecular basis of genetic predisposition to PTB remains largely unknown. We used a positional-cloning approach to carry out ultrafine linkage-disequilibrium mapping of a previously identified susceptibility locus in chromosomal region 8q12-13 by genotyping 3,216 SNPs in a family-based Moroccan sample including 286 offspring with PTB. We observed 44 PTB-associated SNPs (p < 0.01), which were genotyped in an independent set of 317 cases and 650 controls from Morocco. A single signal, consisting of two correlated SNPs close to TOX, rs1568952 and rs2726600 (combined p = 1.1 × 10(-5) and 9.2 × 10(-5), respectively), was replicated. Stronger evidence of association was found in individuals who developed PTB before the age of 25 years (combined p for rs1568952 = 4.4 × 10(-8); odds ratio of PTB for AA versus AG/GG = 3.09 [1.99-4.78]). The association with rs2726600 (p = 0.04) was subsequently replicated in PTB-affected subjects under 25 years in a study of 243 nuclear families from Madagascar. Stronger evidence of replication in Madagascar was obtained for additional SNPs in strong linkage disequilibrium with the two initial SNPs (p = 0.003 for rs2726597), further confirming the signal. We thus identified around rs1568952 and rs2726600 a cluster of SNPs strongly associated with early-onset PTB in Morocco and Madagascar. SNP rs2726600 is located in a transcription-factor binding site in the 3' region of TOX, and further functional explorations will focus on CD4 T lymphocytes.

Association study of genes controlling IL-12-dependent IFN-γ immunity: STAT4 alleles increase risk of pulmonary tuberculosis in Morocco.

BACKGROUND: Only a minority of individuals infected with Mycobacterium tuberculosis develop clinical tuberculosis. Genetic epidemiological evidence suggests that pulmonary tuberculosis has a strong human genetic component. Previous genetic findings in Mendelian predisposition to more severe mycobacterial infections, including by M. tuberculosis, underlined the importance of the interleukin 12 (IL-12)/interferon γ (IFN-γ) circuit in antimycobacterial immunity. METHODS: We conducted an association study in Morocco between pulmonary tuberculosis and a panel of single-nucleotide polymorphisms (SNPs) covering 14 core IL-12/IFN-γ circuit genes. The analyses were performed in a discovery family-based sample followed by replication in a case-control population. RESULTS: Out of 228 SNPs tested in the family-based sample, 6 STAT4 SNPs were associated with pulmonary tuberculosis (P = .0013-.01). We replicated the same direction of association for 1 cluster of 3 SNPs encompassing the promoter region of STAT4. In the combined sample, the association was stronger among younger subjects (pulmonary tuberculosis onset <25 years) with an odds ratio of developing pulmonary tuberculosis at rs897200 for GG vs AG/AA subjects of 1.47 (1.06-2.04). Previous functional experiments showed that the G allele of rs897200 was associated with lower STAT4 expression. CONCLUSIONS: Our present findings in a Moroccan population support an association of pulmonary tuberculosis with STAT4 promoter-region polymorphisms that may impact STAT4 expression.

Assessment of the Association of Chlamydia e pneumoniae Infection with Lung Cancer in a Moroccan Patients' Cohort.

BACKGROUND: Chlamydia pneumoniae (C. pneumoniae) is a respiratory pathogen associated with chronic inflammatory and its detection in human lung cancer suggests its involvement in cancerogenesis. Our study aimed to evaluate the association between C. pneumoniae  infection and Lung Cancer disease in Moroccans patients and control cohorts, through a molecular investigation. METHODS: The study comprised 42 lung cancer patients and 43 healthy controls. All participants provided demographics, Clinical, and Toxic behaviors datas, and a peripheral blood sample for testing, a Nested Polymerase Chain Reaction (PCR) was performed for C. pneumoniae Deoxyribonucleic acid (DNA) detection. Statistical analysis was performed using IBM®SPSS®software. RESULTS: Positive Nested PCR results for cases and controls were respectively 33.3% and 4.7%, there by  significant difference between cases and controls   infection was identified (p <0.05). Data analysis also showed that tobacco could act synergically with C. pneumoniae infection as a risk factor of lung cancer. In fact a significant difference between patients and controls was shown for tobacco and alcohol use (p < 0.05). CONCLUSION: C. pneumoniae infection is potentially associated with primary Lung cancer in the Moroccan population and has combined effects with Tabaco consumption.

Right Intraventricular Metastasis of Lung Squamous Cell Carcinoma Detected on 18F-Fluorodeoxyglucose Positron Emission Tomography-Computed Tomography.

Cardiac metastasis from lung cancer is rare. They are clinically silent and often diagnosed only postmortem. Cardiac magnetic resonance imaging (MRI) provides interesting information about the tissue characterization and vascularization of the tumor. The 18F-fluorodeoxyglucose positron emission tomography-computed tomography (18F-FDG PET/CT) shows hypermetabolism in the cardiac metastasis. We present a case of a 74-year-old male, diagnosed with squamous cell carcinoma of the lung, who underwent cardiac MRI which showed a right intracavitary mass. We share interesting images, detected on 18F-FDG PET/CT, of cardiac metastasis.

[IManagement of patients with relapsed primary naso-sinusal tuberculosis]. / Gestion de la rechute d'une tuberculose naso-sinusienne primaire.

Primary naso-sinusal tuberculosis (TB) is a relatively rare or exceptional disorder characterized by polymorphic or non-specific clinical manifestation. Diagnosis is based on anatomo-pathological examination and mycobacteriology test of biopsy specimen. Predictor of good outcome is early conventional anti-tuberculous antibiotic therapy. However, our study reports recurrence at this rare site in an immunocompetent patient despite early suitable TB treatment and good adherence with therapy. Relapse was correlated with underdosing of rifampicin. This study highlights the diagnostic, etiological and therapeutic management of this relapse. Our experience could help clinicians to better manage this uncommon condition.

Typical presentation of pulmonary lepidic adenocarcinoma: a rare case report.

Bronchioloalveolar carcinoma (BAC) is a rare subtype of adenocarcinoma of lung with distinct features and distinctive characteristics. It accounts approximately for 4% of lung cancers. In the following study we report a rare observation of a 50 years old female with a clinical, radiological and histological presentation, which is typical of an invasive mucinous lepidic adenocarcinoma formerly named BAC.

Prevalence and risk factors for latent tuberculosis infection among healthcare workers in Morocco.

Increased prevalence of latent tuberculosis infection (LTBI) has been observed among high-risk populations such as healthcare workers (HCWs). The results may depend on the method of LTBI assessment, interferon-gamma release assay (IGRA) and/or tuberculin skin test (TST). Here, we investigated the prevalence and risk factors for LTBI assessed by both IGRAs and TST in HCWs living in Morocco, a country with intermediate tuberculosis (TB) endemicity and high BCG vaccination coverage. HCWs were recruited in two Moroccan hospitals, Rabat and Meknes. All the participants underwent testing for LTBI by both IGRA (QuantiFERON-TB Gold In-Tube, QFT-GIT) and TST. Different combinations of IGRA and TST results defined the LTBI status. Risk factors associated with LTBI were investigated using a mixed-effect logistic regression model. The prevalence of LTBI among 631 HCWs (age range 18-60 years) varied from 40.7% (95%CI 36.9-44.5%) with QFT-GIT to 52% (95%CI 48.2-56.0%) with TST using a 10 mm cut-off. The highest agreement between QFT-GIT and TST (κ = 0.50; 95%CI 0.43-0.56) was observed with the 10 mm cut-off for a positive TST. For a definition of LTBI status using a double positive result for both QFT-GIT and TST, significant associations were found with the following risk factors: being male (OR = 2.21; 95%CI 1.40-3.49; p = 0.0007), belonging to age groups 35-44 years (OR = 2.43; 95%CI 1.45-4.06; p = 0.0007) and even more 45-60 years (OR = 4.81; 95%CI 2.72-8.52; p = 7.10-8), having a family history of TB (OR = 6.62; 95%CI 2.59-16.94; p = 8.10-5), and working at a pulmonology unit (OR = 3.64; 95%CI 1.44-9.23; p = 0.006). Smoking was associated with LTBI status when defined by a positive QFT-GIT result (OR = 1.89; 95%CI 1.12-3.21; p = 0.02). A high prevalence of LTBI was observed among HCWs in two Moroccan hospitals. Male gender, increased age, family history of TB, and working at a pulmonology unit were consistent risk factors associated with LTBI.

[Spinal cord compression in a patient with tuberculous spondylodiscitis]. / Compression médullaire au cours d'une spondylodiscite tuberculeuse: à propos d'un cas.

We here report the case of a 76-year old patient admitted to Pulmonology Department with tuberculous spondylodiscitis diagnosed on the basis of clinical signs including weight loss, prolonged fever and stabbing lumbar pain occurred 2 months before. The diagnosis was confirmed by lumbar CT scan and by Genexpert TB test on lumbar fluid taken from the abnormal L1 vertebral body, which showed mycobacterium tuberculosis. Three weeks after the beginning of treatment the patient had motor deficit in lower limbs followed by sensory deficit. These abnormalities were confirmed by MRI which showed abnormal L1 somatic signal with collapse of the vertebral body (A). These lesions enhanced after gadolinium injection (B) that also showed posterior cortical rupture with epiduritis. Radiological examination was performed which confirmed the diagnosis of spinal cord compression associated with TB spondylodiscitis. A few days after, the patient had severe sepsis complicated by septic shock after which he died. Spinal compression is rare in patients with spondylodiscitis. It has a high potential for irreversible complications in the absence of early treatment for spinal cord decompression. Surgery and early antibacillar treatment ensure favorable outcome in the medium and long term.

Tuberculosis and impaired IL-23-dependent IFN-γ immunity in humans homozygous for a common TYK2 missense variant.

Inherited IL-12Rß1 and TYK2 deficiencies impair both IL-12- and IL-23-dependent IFN-γ immunity and are rare monogenic causes of tuberculosis, each found in less than 1/600,000 individuals. We show that homozygosity for the common TYK2 P1104A allele, which is found in about 1/600 Europeans and between 1/1000 and 1/10,000 individuals in regions other than East Asia, is more frequent in a cohort of patients with tuberculosis from endemic areas than in ethnicity-adjusted controls (P = 8.37 × 10-8; odds ratio, 89.31; 95% CI, 14.7 to 1725). Moreover, the frequency of P1104A in Europeans has decreased, from about 9% to 4.2%, over the past 4000 years, consistent with purging of this variant by endemic tuberculosis. Surprisingly, we also show that TYK2 P1104A impairs cellular responses to IL-23, but not to IFN-α, IL-10, or even IL-12, which, like IL-23, induces IFN-γ via activation of TYK2 and JAK2. Moreover, TYK2 P1104A is properly docked on cytokine receptors and can be phosphorylated by the proximal JAK, but lacks catalytic activity. Last, we show that the catalytic activity of TYK2 is essential for IL-23, but not IL-12, responses in cells expressing wild-type JAK2. In contrast, the catalytic activity of JAK2 is redundant for both IL-12 and IL-23 responses, because the catalytically inactive P1057A JAK2, which is also docked and phosphorylated, rescues signaling in cells expressing wild-type TYK2. In conclusion, homozygosity for the catalytically inactive P1104A missense variant of TYK2 selectively disrupts the induction of IFN-γ by IL-23 and is a common monogenic etiology of tuberculosis.

[Swelling of the pectoralis muscle revealing isolated muscular tuberculosis]. / Tuméfaction du muscle pectoral révélant une tuberculose musculaire isolée.

Soft tissue tuberculosis is one of the rare forms of extrapulmonary tuberculosis. Furthermore, isolated muscular tuberculosis is exceptional. We here report the original case of a young immunocompetent patient with isolated muscular tuberculosis involving major pectoralis muscle. The diagnosis was mainly based on histology. The patient was successfully treated with anti bacterial therapy only. This rare case study has been combined with a literature review.

[A rare cause of posterior mediastinal tumors: mediastinal hydatid cyst]. / Une cause rare des tumeurs du médiastin postérieur: le kyste hydatique médiastinal.

Mediastinal hydatid cyst is extremely rare even in endemic areas, representing 0-4% of all hydatid cyst locations. We report the case of a 50-year old patient admitted to our Department with a mass in the left dorsal paraspinal region; chest X-ray showed posterior left basal opacity. Chest CT scan showed posterior mediastinal mass located in the left costovertebral gutter extending from D9 to D11. MRI confirmed the existence of a posterior mediastinal mass with endocanalar extension and spinal cord compression, first evoking cystic schwannoma. These radioclinical data were consistent with a neoplastic origin; a transparietal biopsy was performed which showed a paucicellular specimen composed of translucent eosinophilic material with appearance just barely compatible with hydatid cyst. Hydatic serology was positive. The diagnosis of hydatid cyst was retained and the patient underwent thoracotomy which revealed mediastinal hydatid cyst, confirmed by histologic examination. The postoperative course was uneventful. Mediastinal location of hydatid cyst is very rare and poses a problem in differential diagnosis with other mediastinal tumors.

A case of Kartagener syndrome with rhinolalia clausa.

Kartagener syndrome is an autosomal recessive genetic ciliary disorder comprising of a classic triad of sinusitis, situs inversus and bronchiectasis. It's the one of primary ciliary dyskinesia disorders with manifestations present from childhood. Most patients of PCD have situs inversus. We present a case of 18 year-old women with recurrent lower and upper respiratory tracts infections, and rhinolalia clausa.

[Severe pulmonary involvement in hypocomplementemic urticarial vasculitis (HUV)]. / Atteinte pulmonaire sévère au cours de la vascularite hypocomplémentémique urticarienne.

Pulmonary involvement in hypocomplementemic urticarial vasculitis (HUV) or Mac Duffie syndrome is extremely rare with a poor prognosis. We report the case of a 55-year-old female patient treated for HUV over a period of 20 years. The diagnosis was confirmed on the basis of urticarial lesions, ocular inflammation, positive C1q-p test by immunodiffusion, with low rate of C1q. The patient was treated with cycles of cyclophosphamide, corticoids and rituximab as she developed class III dyspnea (NYHA classification ). The clinico-radiological and functional assessment showed thoracic distension and severe obstructive pulmonary disease which found no significant improvement with systemic treatment Aerosol therapy was started and the patient had a marked clinical improvement. Pulmonary involvement in Mac Duffie hypocomplementemic urticarial vasculitis worsens the patient short-term vital prognosis. The knowledge of the different types of pulmonary involvement opens new therapeutic prospects.

Lung findings on thoracic high-resolution computed tomography in patients with ankylosing spondylitis. Correlations with disease duration, clinical findings and pulmonary function testing.

The aim of this study was to identify the spectrum of abnormalities revealed on high-resolution computerized tomography (HRCT) in patients with ankylosing spondylitis (AS), to compare findings with those of plain radiography and pulmonary function testing (PFT), and to look for correlations between lung involvement and AS severity. We prospectively studied 55 consecutive patients with a diagnosis of AS according to the modified New York criteria who attended our department over a period of 2 years. All patients had a detailed rheumatological examination and underwent plain chest radiography, chest HRCT and PFT. HRCT revealed abnormalities in 29 patients (52.7%), whereas plain chest radiography was abnormal in only 2. Abnormalities consisted of interstitial lung disease (ILD) ( n=4), apical fibrosis ( n=5), emphysema ( n=5), bronchiectasis ( n=4), ground glass attenuation ( n=2), and non-specific interstitial abnormalities ( n=26). Only apical fibrosis and bronchiectasis were statistically more frequent with increasing disease duration (significant trend chi(2)test, p=0.0029 and 0.028, respectively). PFT showed a restrictive process in 19 patients (34.5%). No correlation was noted between HRCT and PFT, nor with AS symptomatic and structural severity parameters. However, there was a statistically significant correlation between PFT and AS symptomatic and structural severity parameters. In conclusion,: this study confirms that the chest HRCT of patients with AS showed a great number of abnormalities undetectable by standard X-rays. The high incidence of lung abnormalities emphasizes the importance of excluding such a diagnosis in patients with AS even without respiratory symptoms.

Rapidly fatal Askin's tumor: a case report and literature review.

An 18-year-old male presented with a mass in the right anterior chest wall. Chest Computed tomography revealed a heterogenous mass of 19X13 cm in the right hemithorax with areas of necrosis. There was associated pleural effusion and infiltration of the soft parts of the chest wall. Bronchoscopy showed a tumor in middle lobe bronchus. CT guided biopsy of the mass was performed. Histological examination showed small round tumor cells with scanty cytoplasm, the nuclei are large and hyperchromatic. The tumor cells were positive for CD99 and neuron specific enolase, negative for cytokeratin, leukocyte common antigen and myogenin. Based on these histologic and immunohistochemical findings, the diagnosis of askin's tumor was made. The extension assessment was negative and the patient was given chemotherapy. Two months later, our patient died. Askin's tumor is a rare, highly malignant tumor affecting children and young adults. It is classified as primitive neuroectodermal tumor of the thoracopulmonary region. Prognosis remains poor. In our case, several prognostic factors may explain the shirt 'term survival, despite no distant metastasis were found: important tumor size, impossibility of surgical treatment and pleural effusion.