CustOmics: A versatile deep-learning based strategy for multi-omics integration

The availability of patient cohorts with several types of omics data opens new perspectives for exploring the disease's underlying biological processes and developing predictive models. It also comes with new challenges in computational biology in terms of integrating high-dimensional and heterogeneous data in a fashion that captures the interrelationships between multiple genes and their functions. Deep learning methods offer promising perspectives for integrating multi-omics data. In this paper, we review the existing integration strategies based on autoencoders and propose a new customizable one whose principle relies on a two-phase approach. In the first phase, we adapt the training to each data source independently before learning cross-modality interactions in the second phase. By taking into account each source's singularity, we show that this approach succeeds at taking advantage of all the sources more efficiently than other strategies. Moreover, by adapting our architecture to the computation of Shapley additive explanations, our model can provide interpretable results in a multi-source setting. Using multiple omics sources from different TCGA cohorts, we demonstrate the performance of the proposed method for cancer on test cases for several tasks, such as the classification of tumor types and breast cancer subtypes, as well as survival outcome prediction. We show through our experiments the great performances of our architecture on seven different datasets with various sizes and provide some interpretations of the results obtained. Our code is available on (https://github.com/HakimBenkirane/CustOmics).

A new strategy of management for newborns in a neonatal care unit: A succesful experience from Morocco

Aim of the study: To evaluate if the readmission rates of newborns treated in our unit has been affected by the introduction of new protocols. Materials and Methods: two groups were compared: Group A: newborns readmitted during the period from January 2010 to May 2011, Group B: newborns readmitted during the period from June 2011 until December 2012. Epidemiological data and settings of rehospitalization were collected on a standardized form, the reasons for rehospitalization, and evolution. Results: 105 were readmitted during the first four months of life , the rate of readmission was 1.8%. The difference is not significant between the two periods. The main reasons for readmission are nosocomial infection in 77% and 65% of premature groups A and B respectively, feeding difficulties with dehydration and weight loss, and viral infections in 31% and 21% of premature groups A and B respectively. The death rate was reduced in premature infants in group B (5.8%) compared to preterms of group A (23%). Conclusion: In our study the introduction of a new protocol support has a considerable gain in the number of patients treated, and the mortality reduction without affecting the rates of rehospitalisation.

Home care for antibiotic therapy in the management of maternal-fetal infection: Action research example

Introduction- Given the progress in medical care in neonatology, the development of neonatal medicine evaluation techniques and management of difficulties in our Moroccan context, the need to increase the alternative structures for complete hospitalization (CH) in this discipline, is clear. Purpose- Assess the economic and neonatal outcomes of neonatal infection in case of further outpatient care. Material and methods- This is a prospective, single-center including newborns hospitalized for infection between 1 January 2011 and 31 December 2013. Exclusion criteria were respiratory distress, birth defects, direct admission neonatal resuscitation. Results- 1060 neonates were included. The parturients had a preterm rupture of membranes PRM in 70% of cases. We had found a tinted amniotic fluid in 23% of cases. Mothers had chorioamnionitis in 20% of cases. We noted the presence of vaginal discharge with vaginal itching in 18% of cases. of mictional burns were found in 10% of cases. Breast laboratory tests (urinalysis, vaginal swabs, blood cultures, CRP) was positive in 3% of cases the mean birth weight was 3300.20 grams +/- 600. The average age was +/- 1.4 days 0.45. Thirty percent of the children were exclusively breastfed. 80% of patients were asymptomatic at admission. The clinical signs were found mainly respiratory distress. Mean CRP was 35,12mg / L +/- 3.5. The average duration of the PRM was 9.66 +/- 57.7 hours. The examination at the end of treatment was without abnormalities in 89.2% of cases. CRP control was below 6 mg / l in 48% of cases. The evolution of life on day 28 was favorable in 100% of cases. The average length of hospital treatment was 2.87 +/- 1.145 days; the average duration of treatment as outpatients was 2.74 +/- 1.31 days. 100% of newborns received treatment by parenteral perfusion according the protocol of the center. The average number of hospital days per patient spared protocol averaged 3.21 +/- 0.78 days. The average amount saved per patient was 82.65 +/- 5.51 Euros. Total amount saved over three years was 83,000 Euros. Conclusion- The partial hospitalization seems possible for infected newborns without aggravating their illness. It also contributes significantly to the health economy.

[Massive bilateral adrenal hemorrhage: role of imaging]

Bilateral adrenal hemorrhage is a rare and potentially life threatening situation in adults. The clinical presentation is non-specific, and the diagnosis is based on imaging. The purpose of this report is to provide an illustrative case of spontaneous bilateral adrenal hemorrhage that occurred during pregnancy. The sonographic and computed tomographic findings included large bilateral adrenal hematomas with no evidence of underlying malignancy. Since bilateral adrenal hemorrhage is a rare but potentially life threatening situation, prompt laboratory and imaging evaluation are essential and may reduce both morbidity and mortality.

[Hereditary neuropathy with pressure hypersensitivity or tomaculous neuropathy]

Hereditary neuropathy liability to pressure palsies is characterized by recurring accesses of painless paralysis at the level of various nerves likely to be compressed. This affection remains underdiagnosed because of its usually benign course, sometimes without any symptom. The diagnosis is supported by clinical and electrophysiological data associated with, in the majority of patients, a deletion of one of the alleles coding for protein PMP 22 on the level of the locus 17p11.2.

[Acquired cystic renal disease, bilateral spontaneous renal hemorrhage, and functional renal transplantation. Review of the literature and report of a case]

Presentation of one case of bilateral, retroperitoneal, intracystic and spontaneous renal haematoma in a patient with acquired renal cystic disease (ARCD) and renal transplantation with functioning graft. A literature review is made with regard to the association of ARCD and spontaneous renal haematoma in dialysed patients; also an analysis of the etiopathogenic factors, as well as diagnostic and therapeutical approaches to the above association. No reference has been found in the literature of concomitant ARCD, bilateral spontaneous renal haemorrhage and renal transplantation with functioning graft.

[Leiomyoma of the renal capsule. Presentation of a case and review of the literature]

Leiomyoma of the renal capsule is rare and very difficult to diagnose preoperatively. We report on a patient in whom a solid renal mass had been incidentally detected during ultrasound evaluation for a gastroenterological condition. A CT scan confirmed the presence of a solid mass. The intraoperative biopsy showed it was a benign tumor and conservative surgery was performed. According to the literature, this tumor type has, as yet, not been diagnosed preoperatively. However, some angiographic features may indicate the presence of this condition. This is the fourth case of leiomyoma of the renal capsule reported in the literature and the second case treated by conservative surgery.