A novel COVID diagnosis and feature extraction based on discrete wavelet model and classification using X-ray and CT images.

Recently, the Covid-19 pandemic has affected several lives of people globally, and there is a need for a massive number of screening tests to diagnose the existence of coronavirus. For the medical specialist, detecting COVID-19 cases is a difficult task. There is a need for fast, cheap and accurate diagnostic tools. The chest X-ray and the computerized tomography (CT) play a significant role in the COVID-19 diagnosis. The advancement of deep learning (DL) approaches helps to introduce a COVID diagnosis system to achieve maximum detection rate with minimum time complexity. This research proposed a discrete wavelet optimized network model for COVID-19 diagnosis and feature extraction to overcome these problems. It consists of three stages pre-processing, feature extraction and classification. The raw images are filtered in the pre-processing phase to eliminate unnecessary noises and improve the image quality using the MMG hybrid filtering technique. The next phase is feature extraction, in this stage, the features are extracted, and the dimensionality of the features is diminished with the aid of a modified discrete wavelet based Mobile Net model. The third stage is the classification here, the convolutional Aquila COVID detection network model is developed to classify normal and COVID-19 positive cases from the collected images of the COVID-CT and chest X-ray dataset. Finally, the performance of the proposed model is compared with some of the existing models in terms of accuracy, specificity, sensitivity, precision, f-score, negative predictive value (NPV) and positive predictive value (PPV), respectively. The proposed model achieves the performance of 99%, 100%, 98.5%, and 99.5% for the CT dataset, and the accomplished accuracy, specificity, sensitivity, and precision values of the proposed model for the X-ray dataset are 98%, 99%, 98% and 97% respectively. In addition, the statistical and cross validation analysis is conducted to validate the effectiveness of the proposed model.

Postpartum infections in a tropical environment: The experience of the infectious diseases department at Fann Teaching Hospital of Dakar (Senegal).

To describe the epidemiology, clinical characteristics, and outcomes of infections in postpartum women admitted to the infectious diseases department at Fann Teaching Hospital. This retrospective descriptive study examined the records of women admitted for infectious diseases within 42 days after childbirth during the five-year period (2007-2011). Data were collected from medical files and analyzed with Sphinx plus2 V5 software. In all, 54 women were admitted for infections during the postpartum period. Their mean age was 27.4 ± 6.2 years. Fifty women (93%) had had vaginal deliveries. The average interval from delivery to admission was 15.4 ± 11.0 days. Tuberculosis (14 cases), vaginitis (13 cases), and severe malaria (7 cases) were the most frequent infectious diseases. The average duration of hospitalization was 12.1 ± 9.0 days. The mortality rate was 30%, with the main causes of death tuberculosis (25 %) and severe pneumonia of unknown causes (25 %). Tropical diseases remain frequent during the postpartum period, with a high lethality rate, as this study shows. Early diagnosis during pregnancy and better follow-up after delivery should be the best ways of reducing morbidity and mortality from these infections.

Connaissances, attitudes et pratiques des personnes vivant avec le VIH dans un centre de prise en charge au Sénégal

L'objectif de cette étude était d'évaluer les connaissances des Personnes Vivant avec le VIH (PVVIH) sur les modes de transmission, la prévention et le traitement de l'infection à VIH, décrire et d'analyser leurs comportements et pratiques depuis l'annonce de leur séropositivité. Méthodologie : Etude transversale à visée descriptive réalisée du 1er juin au 31 octobre 2012, concernant les patients infectés par le VIH, suivis en ambulatoire au Centre de Recherche Clinique et de Formation de Fann. Résultats : Quarante-sept patients, en majorité des femmes (sex-ratio F/M = 3,2) ont été interrogés. Leur âge médian était de 43 ans [extrêmes : 18 ans-63 ans]. Les infections opportunistes constituaient la principale circonstance de dépistage (75%).Les principales sources d'information sur la maladie étaient les médias (75%). La transmission mère-enfant n'était connue que par 17% des patients. Le préservatif était le moyen de prévention le plus cité (77%). Seuls 4 patients ont cité les centres de dépistage volontaire pour le dépistage de l'infection à VIH. Cinquante-quatre pour cent des cas percevaient leur maladie comme une épreuve divine. Par rapport aux attitudes et pratiques face au VIH, 32 patients étaient favorables au partage du statut sérologique mais seuls 29 avaient informé un tiers qui était le conjoint dans 7 cas. Vingt-huit patients étaient sexuellement actifs et 12 exigeaient le port de préservatif. Conclusion : La prise en charge psycho-sociale et sexuelle au cours du suivi est indispensable afin d'améliorer les connaissances des patients sur l'infection à VIH, leurs attitudes et pratiques

[Interest of ambulatory simplified acute physiology score (ASAPS) applied to patients admitted in an intensive care unit of an infectious diseases unit in Dakar]. / Intérêt de l'indice de gravité simplifié ambulatoire (IGSA) appliqué à des patients admis dans l'unité de soins intensifs (USI) d'un service de pathologie infectieuse à Dakar.

The evaluation of patients by a scale of gravity allows a better categorization of patients admitted in intensive care unit (ICU). Our study had for objective to estimate interest of Ambulatory Simplified Acute Physiologic Score (ASAPS) applied to patients admitted in ICU of infectious diseases department of FANN hospital. It was about a descriptive and analytical retrospective study, made from the data found in patients' files admitted into the USI infectious diseases department of FANN hospital in Dakar, from January 1(st), 2009 till December 31st, 2009.The data of 354 patients' files were analyzed. The sex-ratio was 1.77 with an average age of 37.6 years ± 19.4 years old [5-94 years]. The majority of the patients were unemployed paid (39.6%). The most frequent failures were the following ones: neurological (80.5%), cardio-respiratory (16.7%). The average duration of stay was 6.2 days ± 8.2 days going of less than 24 hours to more than 10 weeks. The deaths arose much more at night (53.1%) than in the daytime (46.9%) and the strongest rate of death was recorded in January (61.5%), most low in October (26.7%). The global mortality was 48.3%. The rate of lethality according to the highest main diagnosis was allocated to the AIDS (80.5%). The average ambulatory simplified acute physiology score was 5.3 ± 3.6 with extremes of 0 and 18. The deaths in our series increased with this index (p = 0.000005). The female patients had a rate of lethality higher than that of the men people, 55.5% against 44.2% (p = 0.03). In spite of a predictive score of a high survival (ASAPS < 8), certain number of patients died (n = 105) that is 61.4% of the deaths. The metabolic disturbances, hyperleukocytosis or leukopenia when realised, the presence of a chronic disease, seemed also to influence this lethality. ASAPS only, although interesting, would not good estimate the gravity of patients, where from the necessity thus of a minimum biological balance sheet. It seems better adapted for patients with a high value (ASAPS≥8). This score when it is low, is not correlated, in our study, at a high survival rate as waited in this population.

Initial suboptimal CD4 reconstitution with antiretroviral therapy despite full viral suppression in a cohort of HIV-infected patients in Senegal.

OBJECTIVE: We determined the risk factors and incidence of clinical events associated with suboptimal immune reconstitution (SIR) defined by an increase in CD4 inferior to 50 cells/µL, from inclusion up to six months of antiretroviral treatment (ARVT), in patients with an undetectable viral load (<50 copies/mL). METHODS: Logistic regression and Cox's proportional hazards model were used to examine risk factors for SIR and the association between SIR and the risk of new clinical events or death, respectively after six months of ARVT. RESULTS: One hundred and two (15.5%) of the 657 patients presented with SIR. Age > 40 years (aOR = 1.74, 95% CI = 1.10-2.75), baseline CD4 ≥ 100 cells/µL (aOR = 2.06, 95% CI = 1.24-3.42), ARVT including AZT (aOR = 4.57, 95% CI=1.06-19.76), and the occurrence of a severe opportunistic infection during the first semester of ARVT (aOR = 2.38 95% CI= 1.49-3.80) were associated with SIR. After six months of ARVT and up to seven years of follow-up, 39 patients with SIR had presented with an opportunistic infection or death (rate= 9.78/100 person-years) compared to 168 with a normal recovery (rate = 7.75/100 person-years) but the difference was not statistically significant (aHR = 1.22, 95% CI = 0.85 to 1.74). CONCLUSION: SIR is less common in our country and is not associated with increased mortality or a greater incidence of opportunistic infections after six months of ARVT.

A snapshot of noncommunicable disease profiles and their prescription costs at ten primary healthcare facilities in the in the western half of the Cape Town Metropole

Objectives: There has been a rapid increase in the prevalence of noncommunicable diseases globally. It is thought that this increase will have the greatest impact on developing countries; such as South Africa; where it will adversely affect quality of life and increase healthcare costs. This research was conducted to determine the disease profile and cost of treating patients at 10 facilities in the western half of the Cape Town Metropole.Design: An analytical; cross-sectional study was carried out in order to interpret the cost of the medication in relation to the patient disease profile. Setting and subjects: Data were collected from 10 facilities in the western half of the Cape Town Metropole over a three-month period.Outcome measure: The outcome measure was the disease profile of patients attending the facilities and the cost of prescriptions for these patients.Results: Most patient visits to the community health centres were to treat chronic diseases (82). The disease profile of patients was as follows: 58.96 had hypertension; 19.67 diabetes; 12.14 asthma and chronic obstructive pulmonary disease; and 21.80 arthritis. It was found that 65 of patients with a chronic condition had co-morbidities. The cost of prescriptions was significantly higher (p-value 0.001) for chronic conditions than for acute conditions. The number of comorbidities per patient also influenced the cost of the prescriptions.Conclusion: The results indicated that most of the adults attending public sector facilities in the western half of the Cape Town Metropole have chronic diseases and that the cost of treating these conditions is significantly greater than that of treating acute conditions. An integrated approach to the management of chronic diseases is important in low-resource settings for the efficient utilisation of limited resources

[Current profile of cerebral toxoplasmosis in a hospital setting in Dakar]. / Profil actuel de la toxoplasmose cérébrale en milieu hospitalier à Dakar.

OBJECTIVE: To describe the current epidemiologic, clinical, diagnostic, and prognostic characteristics of cerebral toxoplasmosis in a hospital setting in Dakar. METHODS: This descriptive and analytic study examined the records of all HIV-positive patients with cerebral toxoplasmosis hospitalized at the infectious disease department at Fann (teaching) Hospital from January 2007 through December 2010. The diagnosis was based on clinical and computed tomography criteria completed by a therapeutic test with Cotrimoxazole. RESULTS: There were 26 cases of cerebral toxoplasmosis during the study period. The sex ratio (F/M) was 1.4. The mean age was 41.5 ± 11.2 years. The clinical signs were predominantly fever (88.5%), headache (77.5%), focal signs (64.5%), and disorders of consciousness (61.5%). Brain lesions were most often multiple (64.3%), with mass effects (54.1%) and peripheral edema (77.8%). Seven of the 26 patients died (lethality rate: 29.1%). Impaired consciousness (p = 0.023), high CD8 T-cell counts (p = 0.009), and anemia (p = 0.003) were significantly associated with a higher mortality rate. CONCLUSION: Cerebral toxoplasmosis remains a complication of AIDS in Dakar. Anemia, impaired consciousness, and high CD8(+) T cell counts were factors indicative of poor prognosis.

[Elimination of maternal and neonatal tetanus in Senegal: evolution of survey indicators of 2003-2009]. / Élimination du tétanos maternel et néonatal au Sénégal : évolution des indicateurs de surveillance de 2003 à 2009.

OBJECTIVES: This study aimed to estimate the evolution of the maternal and neonatal tetanus in Senegal from the tetanus vaccination coverage among pregnant women, the proportion of deliveries attended by trained medical personnel and the number of cases of tetanus declared by respective districts, helping to identify districts at high risk of neonatal tetanus (NNT). METHOD: Data analysis of the epidemiological surveillance realized from 2003 to 2009 in 65 districts of Senegal. Data were collected from the reports of vaccination usage and from the Statistical Directories of the National Health Information Services of the Ministry of Health & Prevention. A district is at high risk when the incidence of NNT is ≥1 case per 1 000 Live births (LB). RESULTS: There were 153 reported cases of NNT in Senegal between 2003 and 2009. National incidence decreased from 0.08 to 0.03 case per 1 000 LB (p = 0,0008). The vaccination coverage of the pregnant women by at least two doses of tetanus vaccine (VAT2+) increased from 66% in 2003 to 78% in 2009. The percentage of districts that had reached a vaccination coverage ≥80% was 20% in 2003 compared to 60% in 2009 (p = 0.009). The proportion of deliveries attended by qualified medical staff evolved from 53% in 2003 to 67% in 2009 (p = 0,02). By 2009, the incidence of NNT was less than 1 case per 1,000 LBs in all districts. CONCLUSION: Assessing the elimination of maternal and neonatal tetanus in Senegal shows that progress has been made from 2003 to 2009. This was made possible through the organization of vaccination campaigns for women of childbearing age and the improvements in the conditions of deliveries.

[Efficacy and tolerance of tenofovir-lamivudine-efavirenz combination in HIV-1 patients in Fann Teaching Hospital in Dakar]. / Efficacité et tolérance de l'association ténofovir-lamivudine-éfavirenz chez les patients VIH-1 à la clinique des maladies infectieuses du CHNU de Fann à Dakar.

We conducted a study to evaluate the efficacy and tolerance of the tenofovir (TDF), lamivudine (3TC) and efavirenz (EFV) combination regimen in HIV-1 patients by a descriptive analytical retrospective study of all HIV-1 patients receiving TDF-3TC-EFV combination between 2007 and 2011. Collected data was analysed using EpiInfo™ version 6.04. One hundred patients were included, with an average follow-up duration of 27 months and 19 days (± 21 months and 14 days).We observed an average increase in body weight of about 8 kg per annum, with an average rise in CD4 count of 100/mm(3) by the end of the second year. A reduction in viral load with 71% of patients in therapeutic success at 24 month of treatment was noted. Ninety-two patients presented with at least one side effect, mostly being Grade 1 or 2 (96.36%). Neurological (24 patients) and digestive (20 patients) complaints comprised the commonest reported side effects. Four patients had adverse effects severe enough to warrant a change in treatment regimen, principally due to renal insufficiency. Thirteen subjects died. Patients receiving TDF-3TC-EVF combination therapy need rigorous surveillance because this combination, although efficient, is not without significant adverse effects.

[Access to intermittent preventive treatment (IPt) in a situation of abolition of user's fee: role of economic welfare]. / Accès au traitement préventif intermittent (TPI) dans une situation de gratuité : rôle du bien-être économique.

In Senegal, the free distribution of sulfadoxine pyrimethamine during antenatal care is recommended to remove the disparity in the context of intermittent preventive treatment against malaria. The objective of this study was thus to identify factors influencing access to treatment in a situation of abolition of user fees. It was a cross-sectional and analytical study. It covered a sample of 1906 women aged 15-49 years randomly selected during the national survey on malaria in Senegal. Data were collected during a personal interview. The economic well-being was measured from the characteristics of housing and durable goods. The multivariate analysis was performed using logistic regression. The average age was 27.94 ± 5.34, 64.27% resided in rural area and 71.8% had received no schooling. Among the surveyed women, 23% were in the poorest quintile, while 16.3% were in the richest. Intermittent preventive treatment was performed in 49.3%. IPt were made more in urban areas (OR 1.45 95% [1.17 to 1.72]). It increased with the level of education with an OR of 1.5 and 1.68 in primary and secondary. The completion of the IPt increased with economic welfare. The OR ranged from 1.44 to 2.95 in the second quintile to the richest. Free medication does not necessarily benefit poor people. Other accompanying measures must be developed to facilitate the distribution of drugs particularly at community level with the involvement of people.

[Current profile of HIV-infected patients hospitalized in Dakar (Senegal)]. / Profil actuel des patients infectés par le VIH hospitalisés à Dakar (Sénégal).

Ten years after the introduction of the Senegalese Antiretroviral Drug Access Initiative in 1998, we conducted a retrospective study of the epidemiological and clinical profiles and outcome of HIV-infected patients hospitalized in the Infectious Diseases Clinic of Fann Teaching Hospital in Dakar between 2007 and 2008. During these 2 years, 527 HIV-positive patients were included. The average age of the patients was 41 ± 10 years, and the sex-ratio (F/M) was 1.1; 56% of patients were married. The average interval before admission was 40 ± 57 days. Fever (83%), loss of weight (83%) and cough (54%) were the principal symptoms. Tuberculosis (40.9%) and gastrointestinal candidiasis (38.9%) were the commonest opportunistic infections. Most patients were diagnosed at the AIDS stage (88%) and the CD4+ T lymphocyte count was ≤ 200/mm3 in 86% of cases. Hospital fatality was 44% (231/527). Tuberculosis (36%), bacterial pneumonia (18%) and encephalitis (12%) were the most frequent causes of death. Despite the availability of and free access to antiretroviral drugs in Senegal, the mortality associated with HIV infection remains very high due to late diagnosis. The population must be educated to boost early screening and care.

[Human rabies: diagnostic pitfalls]. / La rage humaine, un diagnostic parfois difficile.

The purpose of this report is to describe two cases of human rabies in Senegal that illustrate possible diagnostic and therapeutic pitfalls even in an endemic area. Although outcome is almost always fatal and interhuman transmission is uncommon, prompt diagnosis of rabies is important since delay increases the risk of exposure to the virus for the entourage.

[Maternal tetanus in Dakar from 2000 to 2007]. / Tétanos maternel à Dakar de 2000 à 2007.

The objective of this study conducted between January 2000 and December 2007 was to assess the current epidemiological, clinical and outcome features of maternal tetanus (MT) observed in the Infectious Diseases Clinic of Fann University Hospital in Dakar, Senegal. A total of 1156 patients were admitted for tetanus during this period including 9 (0.8%) presenting MT. A progressive decrease in the annual number of MT cases was observed. The mean age of MT patients was 28.3 years [range, 18 to 40 years]. Most cases (n=6) involved persons living in suburban areas, as did tetanus in women of childbearing age (WCBA) (51.9% of 129 cases) and in neonates (63.1% of 103 cases) admitted during the same period. All patients had fallen behind the vaccination schedule. Septic abortion (n=7) was the main etiological factor. Although tetanus was graded as moderate in 8 patients (Mollaret stage 2), the death rate was high (44.4%) due to infectious and obstetric complications. This rate was similar to that associated with tetanus in newborns (48.5%), but higher than that associated with tetanus in WCBA (25.6%). The incidence of life-threatening MT is declining in the Infectious Diseases Clinic of Fann University Hospital in Dakar. A systematic immunization program along with campaigns to prevent unwanted pregnancy in women of childbearing age will be needed to eliminate maternal and newborn tetanus in Dakar.

Antimicrobial Activity of 23 Endemic Plants in Madagascar

Purpose: To screen the crude methanol extracts obtained from 23 endemic plants in Madagascar for antimicrobial activity. Methods: In order to assess the antimicrobial properties of the extracts; their minimum inhibitory concentrations (MICs) were obtained using the broth microdilution method. The six test pathogenic species used were Bacillus subtilis; Staphylococcus aureus; Escherichia coli; Salmonella typhi; Pseudomonas aeruginosa and Candida albicans. Bioautography agar overlay test and phytochemical screening were also performed on the most active extracts. Results: From the 23 plants tested; 16 of which are used in traditional medicine; Poivrea phaneropetala Combretaceae); Koehneria madagascariensis (Lythraceae) and Rhopalopilia perrieri (Opiliaceae) exhibited the broad spectrum of activity; being active against all the test organisms; while Monoporus clusiifolius (Myrsinaceae) showed the strongest antifungal activity against Candida albicans with a minimal inhibitory concentration of 0.250 mg/ml. Bioautography and phytochemical analysis of the five active extracts against bacterial strains and of one active extract against C. albicans indicate that the active compounds responsible for antimicrobial activity may be mainly flavonoids and/or terpenes. Conclusion: These preliminary results are the first antimicrobial studies on these of some of them in traditional medicine

[Tetanus in women of childbearing age at the infectious diseases clinic in Dakar]. / Le tétanos de la femme en age de procréer a la clinique des maladies infectieuses de Dakar.

The objective of this article was to describe the epidemiological and outcome features of tetanus in the woman of childbearing age (WCBAT) and compare them with neonatal tetanus (NT) and other tetanus cases in a hospital department in Dakar from 1998 to 2007. A retrospective study was conducted using the files of WCBAT (15 to 49 years old), NT (3 to 28 days old) and other tetanus cases admitted at the Infectious Diseases Clinic, in Fann University Hospital, from 1998 to 2007. 1484 cases of tetanus were admitted in 10 years, with 176 cases of tetanus of WCBAT (11.8%) and 178 cases of NT (11.9%). In comparison with WCBAT the NT annual hospital rate significantly decreased during the study period whereas other tetanus cases rate remained stable. The average age of WCBAT was 26.1 year old and 57.9% were between 15 and 25 years old. The geographical origin was identical for all patients, with more than 71% coming from suburban areas. Most of the WCBAT cases were housewives (50.9%), single women (75%) without updated tetanus immunization (92%). The main portals of entry of WCBAT were injuries and wounds (67.4%) and maternal tetanus cases were rare (8%), mainly post-abortum. At admission, WCBAT cases were less severe than NT cases but more severe than other tetanus cases. The lethality rate of WCBAT cases (28.4%) was significantly lower than NT cases (50%, p = 0.00003), but higher than the other tetanus cases (22.2%; NS). Prognostic factors were: non-identified or intramuscular injection portal of entry and a Mollaret state III at admission. An intensification of the extended immunization program associated with supplementary immunization campaigns targeting women of child bearing age in high risk districts, are necessary to eradicate neonatal and maternal tetanus in Dakar.

[Late diagnosis of HIV infection in the Fann, Dakar clinic of infectious diseases: testing circumstances, therapeutic course of patients, and determining factors]. / Dépistage tardif de l'infection à VIH à la clinique des maladies infectieuses de Fann, Dakar: circonstances de diagnostic, itinéraire thérapeutique des patients et facteurs déterminants.

BACKGROUND AND METHODOLOGY: The delay in the diagnosis of HIV infection is a major obstacle to optimal care for this disease. To deal with this problem, we conducted this study among newly diagnosed HIV patients hospitalized in the Fann University Hospital Infectious Diseases Clinic in Dakar. The epidemiological, clinical, biological and outcome aspects are described and patient history reviewed. A qualitative socio-anthropological study was made to understand and describe the logic of the decision processes in the patient's search for treatment. RESULTS: One hundred patients were included, with a mean age of 39.5+/-11.1 years and a sex-ratio: 1.08. The transmission was mainly heterosexual (90%), and chronic diarrhea (64%) and/or chronic cough (66%) were the principal symptoms leading to diagnosis. The mean delay before diagnosis was 5+/-4.27 months. The major opportunistic diseases were tuberculosis (44 cases) and infectious diarrhea (23 cases). Most patients were diagnosed at the AIDS stage (97%) and the death rate was 30% among hospitalized patients after admission. Sixty-eight percent of patients had consulted at least three times, generally a "traditional practitioner", at first and 43% had been hospitalized at least once. The qualitative investigation revealed that the "representation" or the "feeling of severity" of the disease were the principal justifications for consulting the "traditional practitioner" or the physician, respectively. CONCLUSION: Better information for health workers and global population is necessary for an earlier diagnosis of HIV infection in Dakar.

[Tetanus in neonates and women of child-bearing age in the Dakar hospital infectious diseases unit]. / Tétanos néonatal et de la femme en âge de procréer à la clinique des maladies infectieuses de Dakar.

OBJECTIVES: This study had for aim to describe and compare the epidemiological, clinical and outcome features of tetanus in neonates (NT) and women of child bearing age (WCBAT) in Dakar. PATIENTS AND METHOD: This retrospective study was made on NT (3 to 28 days of age) and WCBAT (15 to 49 years of age) patient files, admitted in the Fann University Hospital Infectious Diseases Clinic from 2000 to 2007. RESULTS: One hundred and thirty-eight WCBAT (11.9%) and 103 NT (8.9%), for a total of 1156 cases of tetanus were admitted. A decrease of the annual rate of these populations was noted over this 8 year period. The majority (59.4%) of WCBAT was between 15 and 25 years of age and the mean age of NT was 9.3 days. Most of the patients in both groups came from suburban areas (78%). The tetanus immunization status was not updated for 92% of WCBAT. The most frequent portals of entry were cutaneous wounds for WCBAT (77.4%) and umbilical stumps for NT (85.4%). On admission, 64% of NT presented with severe tetanus (stage III on the Mollaret scale) compared to 11.6% for WCBAT. The death rate was significantly higher in NT (48.5%) than in WCBAT (26.8%); p=0.0005. CONCLUSION: To eliminate neonatal tetanus, the prognosis of which is worse in Dakar, an intensification of the large vaccination program is needed with supplementary vaccination campaigns including women of child bearing age in areas of risk.