IMPatienT: An Integrated Web Application to Digitize, Process and Explore Multimodal PATIENt daTa.

Medical acts, such as imaging, lead to the production of various medical text reports that describe the relevant findings. This induces multimodality in patient data by combining image data with free-text and consequently, multimodal data have become central to drive research and improve diagnoses. However, the exploitation of patient data is problematic as the ecosystem of analysis tools is fragmented according to the type of data (images, text, genetics), the task (processing, exploration) and domain of interest (clinical phenotype, histology). To address the challenges, we developed IMPatienT (Integrated digital Multimodal PATIENt daTa), a simple, flexible and open-source web application to digitize, process and explore multimodal patient data. IMPatienT has a modular architecture allowing to: (i) create a standard vocabulary for a domain, (ii) digitize and process free-text data, (iii) annotate images and perform image segmentation, (iv) generate a visualization dashboard and provide diagnosis decision support. To demonstrate the advantages of IMPatienT, we present a use case on a corpus of 40 simulated muscle biopsy reports of congenital myopathy patients. As IMPatienT provides users with the ability to design their own vocabulary, it can be adapted to any research domain and can be used as a patient registry for exploratory data analysis. A demo instance of the application is available at https://impatient.lbgi.fr/.

Viability predictive factors of the daughter vesicles in hepatic cystic echinococcosis.

INTRODUCTION: Management of cystic echinococcosis (CE) requires knowledge of certain aspects related to the survival of Echinococcus granulosus. The viability of daughter vesicles (DV) is a determining factor in guiding therapeutic indications, particularly for transiently active Cysts type CE3b. PURPOSE: To determine the predictive factors of DV viability and its impact on the therapeutic management of CE3b type. MATERIALS AND METHODS: This is a prospective pilot study with an analytical aim on patients with cystic echinococcosis of the liver type CE2 and CE3b, operated in the General Surgery Department of Habib-Bourguiba Academic Hospital, Sfax-Tunisia for 22 months from March 2018 until December 2019. The unit of the study is the DV. A parasitological study of the DV was done in the parasitology laboratory. RESULTS: During the study period, 27 (40.9%) of 66 operated CE Disease from 21 patients containing 248 DV were explored. The median viability of DV protoscoleces was 16.7%. In bivariate analysis, factors for viability of DV protoscoleces were: fever, acute cholangitis, hyperbilirubinemia, left liver location, rock water and bilious echinococcal fluid (EF), cyst size ≥ 43 mm, Intracystic pressure ≥ 35 mmHg, DV size ≥ 6.5 mm, volume, number of DV/cyst ≥ 5, and opaque wall (p < 0.05). Predictive factors for the Non-viability of DV were: CE3b type, purulent EF, gelatinous EF. In multivariate analysis, only CE2 type, cyst size ≥ 43 mm, number of DV/cyst ≥ 5 and DV size ≥ 6.5 mm were factors significantly associated with the viability of DV protoscoleces. CONCLUSION: CE3b cysts without the criteria of viability of DV protoscoleces may become candidates for the 'Wait-and-Watch' procedure.

Early postoperative intra-axial dissemination of a pediatric extradural and complicated hydatid cyst.

Hydatid disease is very common around the Mediterranean basin and endemic in some parts of the world. Cerebral involvement remains rare, represents only about 2% of all hydatid localizations and mainly affects the pediatric population. Extradural hydatid cyst is very rare or even exceptional when it is associated with or followed by intracerebral disseminations. Here, the authors report a new exceptional case of an early multiple intra-axial hydatid dissemination in a 5-year-old North African male patient from a rural area who underwent surgery 3 months after a primary osteolytic extradural and complicated hydatid cyst with good clinical and radiological outcomes.

A case of pediatric primary osteolytic extradural and complicated hydatid cyst revealed by a skull vault swelling.

Hydatidosis is a parasitic infestation whose etiological agent is the larva of the cestode Echinococcus granulosus. It is a zoonosis, and the human being behaves as an accidental intermediate host in the parasitic cycle with pediatric predominance. The most frequent clinical presentation is hepatic, followed by pulmonary, with cerebral hydatidosis being extremely rare. Imaging is characteristic, generally dealing with single cystic lesion, usually unilocular and less frequently multilocular, located mainly intraaxially. Extradural hydatid cyst, whether primary or secondary, remains very rare or even exceptional. The primary disease remains extremely rare, and its clinical picture is related to the number, size, and location of the lesions. Infection within these cerebral hydatid cysts remains an extremely rare occurrence, and only few cases were reported previously in the literature. The authors report the nosological review of the clinical, imaging, surgical, and histopathological records of a pediatric primary osteolytic extradural and complicated hydatid cyst in a 5-year-old North African male patient coming from a rural area who presented for progressive onset of a painless left parieto-occipital soft swelling without any neurological disorder with good outcomes after surgery. The authors report this case due the fact that it had not been documented before in the pediatric population and to the success of the specialized treatment.

Antifungal, molluscicidal and larvicidal assessment of anemonin and Clematis flammula L. extracts against mollusc Galba truncatula, intermediate host of Fasciola hepatica in Tunisia.

OBJECTIVE: To investigate the potential of anemonin and Clematis flammula (C. flammula) extracts against infective organisms. METHODS: The molluscicidal activities of anemonin and C. flammula extracts against Galba truncatula Müll. (Lymnaeidae) and Fasciola hepatica larval stages contaminating this snail in Tunisia were assessed by testing six groups of snails in 250 mL of extracts and aqueous dechlorinated solutions with different concentrations (ranging from 2.5 to 20.0 mg/L) for 48 h. Besides, the antifungal potential of C. flammula leaves and flowers was evaluated by using the diffusion agar and broth dilution methods against four fungal strains: Aspergillus niger, Pythium catenulatum, Rhizoctonia solani and Fusarium phyllophilum. RESULTS: As a result, hexane and ethyl acetate flower extracts exhibited significant molluscicidal activities with LC50 median lethal concentrations values of 11.87 and 11.65 mg/L, respectively while LC50 value of anemonin was 9.64 mg/L after 48 h exposure. The flower extracts showed a larvicidal effect with a deterioration rate exceeding 35.39% where flower ethyl acetate residue gave a deterioration rate of cercariae close to 97%. Moreover, C. flammula extracts were not noxious to the associated fauna survival. All extracts inhibited the growth of P. catenulatum, the leaves and flowers methanolic extracts had the more important fungicide action with minimum inhibitory concentrations of 1.56 and 3.12 mg/mL together with minimum fungistatic concentrations of 3.12 and 6.25 mg/mL respectively. Only flower extracts were active against Rhizoctonia solani with minimum inhibitory concentrations varying between 0.70 and 1.56 mg/mL and 6.25 mg/mL of minimum fungistatic concentration. Phytochemical tests showed that the antifungal activity may be attributed to the presence of the flavonoids/saponins in the methanolic extracts and the molluscicide effects could be due to the richness of hexane and ethyl acetate extracts on sterols and triterpenoids. CONCLUSIONS: This study emphasizes the important molluscicidal and antiparasitic effects of flower ethyl acetate extracts and anemonin compound as well as the considerable antifungal activities of methanolic extracts. These results improve the therapeutic virtues of C. flammula aerial part extracts.

MOLLUSCICIDAL AND LARVICIDAL ACTIVITIES OF Atriplex inflata AERIAL PARTS AGAINST THE MOLLUSK Galba truncatula, INTERMEDIATE HOST OF Fasciola hepatica / Atividade moluscicida e larvicida das partes aéreas de Atriplex inflata contra o molusco Galba truncatula, hospedeiro intermediário da Fasciola hepatica

Fasciolosis is a widespread parasitosis of farm live-stock in many developing countries. For this reason, it is necessary to search for new substances against parasitic diseases caused by flukes. Indeed, a wide variety of terrestrial plants have been subjected to chemical and pharmacological screening in order to discover their potential for human medicinal use. The molluscicidal and larvicidal activities of Atriplex inflata were tested on Galba truncatula and Fasciola hepatica larval stages infecting this snail in Tunisia. Phytochemical tests were conducted on extracts in order to establish a meaningful relationship with molluscicidal and larvicidal activities. The molluscicidal activity was evaluated by subjecting snails to sample aqueous solutions. Accordingly, hexane, ethyl acetate, methanol and methanol-water (8:2, v-v) were used as extraction solvents. As a result, hexane and ethyl acetate extracts showed potent activity, according to the World Health Organization, giving LC50 = 7.59 mg/L and 6.69 mg/L for hexane extracts of leaves and fruits, respectively. Ethyl acetate extracts gave LC50 = 5.90 mg/L and 7.32 mg/L for leaves and fruits, successively. Molluscicidal activities of powders were less potent on snails, but active according to the World Health Organization. Hexane and ethyl acetate extracts from leaves and fruits gave potent larvicidal activities with a delay rate exceeding 45.50% (45.50- 98.92%). Phytochemical tests showed that these activities may be attributed to the presence of triterpenoids and/or sterols.

Fasciolose é uma parasitose generalizada que ocorre em animais de fazendas em muitos países em desenvolvimento. Por esta razão, é necessária a busca de novas substâncias contra as doenças parasitárias causadas por vermes. De fato, uma grande variedade de plantas terrestres foi objeto de testes farmacológicos e químicos a fim de descobrir o seu potencial para utilização em terapêutica humana. As atividades moluscicida e larvicida de Atriplex inflata foram testadas contra estágios larvários de Galba truncatula e Fasciola hepatica infectando este caracol na Tunísia. Testes fitoquímicos foram realizados com extratos a fim de estabelecer uma relação significativa com as atividades moluscicida e larvicida. A atividade moluscicida foi avaliada submetendo os caracóis a soluções aquosas. Conforme o caso, hexano, acetato de etilo, metanol e metanol-água (8:2, v-v) foram utilizados como solventes de extração. Como resultado, hexano e extratos de acetato apresentaram atividades potentes de acordo com a Organização Mundial de Saúde, resultando em LC50 = 7,59 mg/L e 6,69 mg/L para extratos de hexano de folhas e frutos, respectivamente. Extratos de acetato de etilo resultaram em LC50 = 5,90 mg/L e 7,32 mg/L para as folhas e frutos sucessivamente. Atividades moluscicidas das substâncias sob a forma de pó foram menos potentes em caracóis, mas ativas de acordo com a Organização Mundial de Saúde. Hexano e extratos de acetato de folhas e frutos apresentaram atividade larvicida potente, com uma taxa de atraso superior a 45,50% (45,50-98,92%). Testes fitoquímicos mostraram que estas atividades podem ser atribuídas à presença de triterpenóides e/ou esteróis.

Microsatellite typing of Aspergillus flavus from clinical and environmental avian isolates.

Aspergillosis is one of the most common causes of death in captive birds. Aspergillus fumigatus accounts for approximately 95 % of aspergillosis cases and Aspergillus flavus is the second most frequent organism associated with avian infections. In the present study, the fungi were grown from avian clinical samples (post-mortem lung material) and environmental samples (eggs, food and litter). Microsatellite markers were used to type seven clinical avian isolates and 22 environmental isolates of A. flavus. A. flavus was the only species (28 % prevalence) detected in the avian clinical isolates, whereas this species ranked third (19 %) after members of the genera Penicillium (39 %) and Cladosporium (21 %) in the environmental samples. Upon microsatellite analysis, five to eight distinct alleles were detected for each marker. The marker with the highest discriminatory power had eight alleles and a 0.852 D value. The combination of all six markers yielded a 0.991 D value with 25 distinct genotypes. One clinical avian isolate (lung biopsy) and one environmental isolate (egg) shared the same genotype. Microsatellite typing of A. flavus grown from avian and environmental samples displayed an excellent discriminatory power and 100 % reproducibility. This study showed a clustering of clinical and environmental isolates, which were clearly separated. Based upon these results, aspergillosis in birds may be induced by a great diversity of isolates.

Amphotericin B in vitro resistance is associated with fatal Aspergillus flavus infection.

Whether in vitro antifungal susceptibility findings correlate with the outcome of patients with invasive aspergillosis (IA) remains debated. This study aimed to test whether IA patients' outcomes were associated with in vitro susceptibility results. To do so, we determined the in vitro susceptibility to amphotericin B (AMB) of 37 Aspergillus flavus isolates from 14 patients with haematological malignancies diagnosed with proven or probable IA, of which 13 were treated with AMB deoxycholate. Minimal inhibitory concentrations (MICs) were determined by Etest with the isolates classified as in vitro sensitive (AMB-S) or resistant (AMB-R) if their MICs were < 2 or ≥ 2 mg/l, respectively. The association of the patients' death with primary disease, administered antifungal treatment, and infection with AMB-R A. flavus was tested using generalized estimating equations logistic regression. We assessed AMB-R in 31/37 (84%) isolates. In the patients treated with AMB, the survival rate was 2/3 (67%) and 2/9 (22%) for those infected with AMB-S or AMB-R A. flavus, respectively. Both infection with AMB-R A. flavus (P = 0.014) strain and acute myelocytic leukaemia as the underlying primary disease (P = 0.036) were independent predictors of death. Our findings indicate that in vitro resistance predicts a poor outcome in patients with A. flavus invasive disease treated with AMB. Recent advances in non-culture-based microbiological methods should not discourage efforts to obtain in vitro antifungal susceptibility results, which are critical for the choice of antifungal therapy in patients with IA.

Comparison of PCR-ELISA and Real-Time PCR for invasive aspergillosis diagnosis in patients with hematological malignancies.

This study aimed at comparing a real-time PCR assay and a PCR-ELISA assay of both serum and bronchoalveolar lavage (BAL) samples for the diagnosis of invasive aspergillosis (IA) in patients with hematological malignancies. Using a nested case-control design, 163 patients at risk were prospectively monitored and PCR assays were performed on frozen aliquots of 459 sera which were prospectively sampled twice weekly and 42 BAL specimens sampled from 43 probable and one proven IA cases and 47 matched controls. The data from three patients classified as possible IA were excluded from the nested case-control study. The sensitivity of real-time PCR and PCR-ELISA assays in serum was 73% and 86%, respectively and specificity was 100% for both. In BAL, sensitivity was 64% for real-time PCR, 71% for PCR-ELISA and 86% for Galactomannan antigen (GMA) assays with specificities of 96%, 96%, and 93%, respectively. While slightly less sensitive, the real time-PCR assay was highly specific and considerably faster and more workable than PCR-ELISA. Combining real-time PCR and GMA detection for both serum and BAL samples enhances routine laboratory IA diagnosis.

Detection of antisynthetic mannoside antibodies (ASigmaMA) reveals heterogeneity in the ASCA response of Crohn's disease patients and contributes to differential diagnosis, stratification, and prediction.

OBJECTIVES: Anti-S. cerevisiae mannan antibodies (ASCA) are human antibodies associated with Crohn's disease (CD) reacting with Saccharomyces cerevisiae (S. cerevisiae) mannan polymer. As mannan is a complex and variable repertoire of oligomannoses acting as epitopes, we chemically synthesized (Sigma) two major oligomannose epitopes, Man alpha-1,3 Man alpha-1,2 Man (SigmaMan3) and Man alpha-1,3 Man alpha-1,2 Man alpha-1,2 Man (SigmaMan4), and then explored how antisynthetic mannoside antibodies (ASigmaMA) compare with ASCA as markers of CD. METHODS: The study involved different cohorts of CD and ulcerative colitis (UC) patients and healthy controls who had been studied previously in several medical centers in Europe, the United States, and North Africa to determine the clinical value of ASCA in terms of differential diagnosis, evolution of indeterminate colitis (IC), and serotype-phenotype correlations. The comparison of ASigmaMA and ASCA included a total of 1,365 subjects: 772 CD, 261 UC, 43 IC, and 289 controls. RESULTS: The specificity of ASigmaMA was similar to that of ASCA (89% vs 93%), although the sensitivity was lower (38% vs 55%). Unexpectedly, 24% of the CD patients who were negative for ASCA and/or other CD-associated serologic markers were positive for ASigmaMA. ASigmaMA were associated with colonic involvement in CD (odds ratio [OR] 1.609, 95% confidence interval [CI] 1.033-2.506, P = 0.03) and were 100% predictive of CD in patients with IC. CONCLUSIONS: ASigmaMA reveal the heterogeneity of the antioligomannose antibody response in CD patients and increase the sensitivity of CD diagnosis when combined with ASCA. The subset of ASCA-negative CD patients diagnosed by ASigmaMA had preferentially a colonic involvement, which confirms the high predictive value of ASigmaMA for determining IC evolution toward CD.

[Hydatid cysts of the spigelian lobe (segment I) of the liver: clinical and therapeutic particularities]. / Kystes hydatiques du lobe de Spiegel: particularités cliniques et thérapeutiques.

OBJECTIVE: Hydatid cysts of the spigelian lobe, that is, segment I of the liver, are rare. We analyzed their clinical and therapeutic particularities. METHODS: We conducted a retrospective search for the hydatid cysts of the liver treated surgically in our department from January 1, 1994, through December 31, 2005. Cases were identified and confirmed with the following investigatory techniques: routine abdominal ultrasonography, abdominal computed tomography recommended by the ultrasound operator when a cyst was discovered in segment I, routine intraoperative cholangiography, and three separate serological techniques: electrosyneresis, hemaglutination and ELISA (enzyme-linked-immunosorbent assay)(the latter two being quantitative). The cystic cavity was treated with hypertonic serum. Several surgeons performed different combinations of the following techniques: deroofing, sometimes with omentoplasty, simple drainage, and subtotal pericystectomy. RESULTS: We treated 44 hydatid cysts of segment I surgically in 10 men and 34 women, with a mean age of 40.6 years. Ten patients (22.7%) had a history of hydatid cysts. Symptoms or complications were noted at admission in 45% of cases. Only five cases (11.4%) required emergency surgery. Surgical examination confirmed vascular compression in 17 cases (38.6%) and a biliary fistula in 17 cases (38.6%). Surgical treatment consisted of deroofing in 37 cases (84,1%), with omentoplasty in 23 (54%), subtotal pericystectomy in 3 and simple drainage in 4. Large biliary fistulas (> 5 mm) were treated with bipolar drainage in 2 cases and internal transfistulary drainage in 3. Some hemorrhaging occurred during surgery in 5 cases, and one cyst ruptured in the peritoneal cavity. Albendazole was prescribed postoperatively for nine patients. There was one intraoperative death, secondary to hemorrhage resulting from erosion of the inferior vena cava. Morbidity was 25%. After a mean follow-up of 32 months, five patients had recurrences in the liver but outside segment I. CONCLUSION: Segment I of the liver is a rare site for hydatid disease, and a site where vascular and biliary complications are frequent. Its management requires a good knowledge of the vascular anatomy of the liver and wide experience of hydatid cyst surgery and especially of simple surgical procedures.

Liver cystic echinococcosis: which cysts are correlated with false negative indirect passive hemagglutination (IHA)?

BACKGROUND: It's generally agreed that calcified liver cystic Echinococcosis (CE) is associated with negative serology; the influence of other cystic features on serologic result remains unclear. The aim of this study is to determine predictive factors of negative indirect passive hemagglutination (IHA) in liver CE. METHODS: 119 patients operated on for liver CE, had preoperative IHA. Correlation was studied between serological result and sex, age of patient and number (single vs multiple), size, ultrasonic type (unilocular, multivesicular, degenerative) and intrabiliary rupture of cyst. RESULTS: IHA sensitivity was 74.8%. Univaried analysis showed that false negative serology was correlated with age <10 or >20 years (p < 0.01), single cyst (p < 0.006), cystic size <9 cm (p < 0.03) and unilocular or degenerative cyst in comparison with multivesicular type (p < 0.01 and p < 0.03 respectively). IN CONCLUSION: in liver CE, cystic predictive factors of false negative IHA are single cyst, unilocular or degenerative type and size inferior to 9 cm.

Ethnic and socio-cultural specificities in Tunisia have no impact on the prevalence of anti-Saccharomyces cerevisiae antibodies in Crohn's disease patients, their relatives or associated clinical factors.

BACKGROUND: In Western Europe and the USA, the presence of anti-Saccharomyces cerevisiae antibodies (ASCAs) in Crohn's disease (CD) patients and their healthy relatives suggests that ASCAs may be influenced by genetic and/or environmental factors. OBJECTIVES: To assess the prevalence of ASCAs in Tunisian patients with CD or ulcerative colitis (UC), and unaffected family members, in relation to clinical phenotype. Patients and methods. Seventy-seven patients (39 CD, 38 UC), 66 healthy relatives of CD patients, 16 relatives of UC patients and 70 healthy controls were studied. ASCAs were quantified with a new isotype-specific ELISA test involving an antigenic extract from S. cerevisiae strain W303 and by the original test which detects total immunoglobulins against S. cerevisiae Su1 mannan. RESULTS: The specificity of the two tests was identical (91%). The isotype-specific ASCA W303 test was more sensitive than the ASCA Su1 test for immunoglobulin detection, but some CD patients were positive only with this latter test. A high percentage of patients with CD (72%) and their unaffected family members (35%) were ASCA-positive in contrast to UC patients (16%) and their relatives (0%) and controls (8.6%). ASCAs were shown to be independent of rural or urban living, disease activity, but were associated with ileal location. The antigen of S. cerevisiae strain W303 discriminated patients depending on age at onset or location of the disease. CONCLUSION: This study confirms the antigenic heterogeneity of S. cerevisiae strains in their ability to detect ASCA. It suggests that ASCAs are markers of immunoregulatory disturbance in CD, independently of ethnic/cultural differences between Europe, the USA and North Africa.