Gene structural annotation is a critical step in obtaining biological knowledge from genome sequences yet remains a major challenge in genomics projects. Current de novo Hidden Markov Models are limited in their capacity to model biological complexity; while current pipelines are resource-intensive and their results vary in quality with the available extrinsic data. Here, we build on our previous work in applying Deep Learning to gene calling to make a fully applicable, fast and user friendly tool for predicting primary gene models from DNA sequence alone. The quality is state-of-the-art, with predictions scoring closer by most measures to the references than to predictions from other de novo tools. Helixer's predictions can be used as is or could be integrated in pipelines to boost quality further. Moreover, there is substantial potential for further improvements and advancements in gene calling with Deep Learning. Helixer is open source and available at https://github.com/weberlab-hhu/Helixer A web interface is available at https://www.plabipd.de/helixer_main.html

Breast cancer (BC) is one of the most prevalent forms of cancer in women worldwide. Clinical research indicates that BC patients are at an increased risk for thrombotic events, drastically decreasing their quality-of-life and treatment outcomes. There is ample evidence of this in the literature, but it is mainly focused on metastatic BC. Therefore, coagulopathies of nonmetastatic BC are understudied and require in-depth investigation. In this study, clot kinetics and ultrastructure were used to investigate treatment-naïve, nonmetastatic BC patients using scanning electron microscopy, Thromboelastography®, and confocal laser scanning microscopy. It was demonstrated that nonmetastatic BC patients exhibit minimal ultrastructural alterations of the clot components and no changes in the clot kinetics. However, BC patients presented changes to fibrinogen protein structure, compared to matched controls, using an amyloid-selective stain. Together, these findings suggest that coagulation dysfunction(s) in BC patients with early disease manifest at the microlevel, rather than the macrolevel. This study presents novel insights to a method that are more sensitive to coagulation changes in this specific patient group, emphasizing that the coagulation system may react in different forms to the disease, depending on the progression of the disease itself.

In immunosuppressed patients, a high rate of complications due to opportunistic infection is known. We report the case of a 36 year old patient with ulcerative colitis and a septic complication with ongoing pancytopenia. Due to colonic perforation, colectomy had to be performed. Despite this intervention, the septic constellation persisted. The pancytopenia in peripheral blood counts also persisted with the necessity of repetitive transfusions. A bone marrow biopsy showed an infiltration with Leishmania bodies in macrophages. Tissue culture allowed for typing of the parasites as belonging to the L. donovani/infantum complex, DNA sequencing confirmed infection with L. infantum. This infection must have been contracted during a vacation on Mallorca about 1.5 years earlier. Administration of liposomal amphotericin B cured the patient. Surprisingly, histological examination of the resected colon reveiled the presence of an immunoblastic B-cell lymphoma. In this case, immunosuppression was a prerequisite for the manifestation of leishmaniosis.

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