Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19

Background: We previously reported that impaired type I IFN activity, due to inborn errors of TLR3- and TLR7-dependent type I interferon (IFN) immunity or to autoantibodies against type I IFN, account for 15–20% of cases of life-threatening COVID-19 in unvaccinated patients. Therefore, the determinants of life-threatening COVID-19 remain to be identified in ~ 80% of cases. Methods: We report here a genome-wide rare variant burden association analysis in 3269 unvaccinated patients with life-threatening COVID-19, and 1373 unvaccinated SARS-CoV-2-infected individuals without pneumonia. Among the 928 patients tested for autoantibodies against type I IFN, a quarter (234) were positive and were excluded. Results: No gene reached genome-wide significance. Under a recessive model, the most significant gene with at-risk variants was TLR7, with an OR of 27.68 (95%CI 1.5–528.7, P = 1.1 × 10−4) for biochemically loss-of-function (bLOF) variants. We replicated the enrichment in rare predicted LOF (pLOF) variants at 13 influenza susceptibility loci involved in TLR3-dependent type I IFN immunity (OR = 3.70[95%CI 1.3–8.2], P = 2.1 × 10−4). This enrichment was further strengthened by (1) adding the recently reported TYK2 and TLR7 COVID-19 loci, particularly under a recessive model (OR = 19.65[95%CI 2.1–2635.4], P = 3.4 × 10−3), and (2) considering as pLOF branchpoint variants with potentially strong impacts on splicing among the 15 loci (OR = 4.40[9%CI 2.3–8.4], P = 7.7 × 10−8). Finally, the patients with pLOF/bLOF variants at these 15 loci were significantly younger (mean age [SD] = 43.3 [20.3] years) than the other patients (56.0 [17.3] years; P = 1.68 × 10−5). Conclusions: Rare variants of TLR3- and TLR7-dependent type I IFN immunity genes can underlie life-threatening COVID-19, particularly with recessive inheritance, in patients under 60 years old

Bifurcation diagrams in a class of Kolmogorov systems

We study a two-dimensional Kolmogorov system when its two parameters vary in a small neighbourhood of the value $0.$ The local behavior of the system is described in terms of bifurcation diagrams

Objective Ki-67 Index Quantification In Non-Breast Tumors – Preliminary Data In Timisoara, Romania

INTRODUCTION / BACKGROUND: The immunohistochemical expression of the Ki-67 protein is routinely used for diagnostic and grading purposes of various tumors. The most common use of automation process for Ki-67 quantification is represented by breast tumors. AIMS: We aimed to analyze the accuracy of digital quantification of Ki-67 expression in non-breast tumors. METHODS: We selected all the available Ki-67 stained slides done in 2014 at the County Emergency Hospital Timisoara, Ro- mania, excluding breast tumors. Images of the stained slides (10 images/slide on average, depending on the size of the specimen) were acquired on a Leica DMD108. We performed preprocessing (autolevels) in IrfanView and Ki-67 quantification in Fiji (ImageJ distribution) using ImmunoRatio plugin. RESULTS: Proper image segmentation was identified on 25 cases. The best segmentation was obtained in lymphoid and central nervous system (CNS) tumors. Lower Ki-67 values than the ones manually reported were identified in 16/25 cases (64%). Interestingly, digital quantification showed all 7 lymphoid cases to have a lower Ki-67 index than manually reported, while 6/9 CNS had higher Ki67 indices using automation processing. Valid digital quantification was not possible on skin, cervical and urothelial tumors, as regions of interest could not be defined to restrain the area to be evaluated. CONCLUSION: Our preliminary study shows that ImmunoRatio plugin for Fiji in combination with IrfanView preprocessing are free, easy to use and powerful tools to obtain an objective Ki-67 index in non-mammary tumors: CNS, lymphoid, soft tissue, neuroendocrine tumors, choriocarcinomas and malignant melanomas

Musculo-skeletal tumors incidence and surgical treatment – A single center 5-year retrospective

OBJECTIVE: Muscle-skeletal tumors represent a challenging pathology for orthopedic surgeons worldwide. The extremely invasive character, the local destruction, the high recurrence rate, the high incidence in young patients and the unfavorable prognosis are all very well known. For these patients it is very important to produce an accelerated functional, social and psychological postoperative rehabilitation. We studied 121 cases of muscle-skeletal tumors which were treated in our hospital over a 5 years period. PATIENTS AND METHODS: We noticed a high prevalence in males and mainly between the 2nd-3rd and 5th-7th decades of their life. At our observation, most patients were suffering in advanced stages of malignant lesions. RESULTS: We try to manage amputations below 5%, with a significant reduction in introducing reconstructive surgical methods as a choice of treatment (10 prostheses and 12 cases of filling with acrylic cement or bone substituent increased with internal fixation). In this way we could observe an unusual ratio between benign and malignant tumors, probably caused by the patient’s lack of concern for minimal symptoms. The rural citizen’s addressability towards the medical system is alarmingly low, due to the big gap existing from diagnosis to treatment. CONCLUSIONS: There is still an hard effort to develop better reconstructive techniques for the treatment of muscle-skeletal tumors and more studies must be made in order to achieve this goal

The Impact Of Introducing Virtual Slides As A Replacement For Powerpoint Presentations In The Students’ Microscopy Labs

INTRODUCTION / BACKGROUND: The medical school students in Timisoara, Romania have been studying pathology slides in microscopy labs according to a protocol which uses classical PowerrPoint presentations as guides for understanding the microscopic features of diseases, followed by individual examination of the glass slides under the microscope. AIMS: We aimed to assess the impact of replacing those presentations with virtual slides (VS). METHODS: In the middle of the semester, for the benign tumors microscopy lab, which is presented over the course of 2 weeks, we used 3 VS, while the other 3 slides were presented in the classical PowerPoint manner. All attending students from the 3rd year of the Medical School of the University of Medicine and Pharmacy “Victor Babes” Timisoara were asked to fill out an anonymous questionnaire at the end of the lab, in which they graded the difficulty in identifying lesions, chose the best/least understood lesion and pointed out the best manner of presentation. RESULTS: 431 valid questionnaires were collected. 52.9% of the students indicated one of the 3 VS as the best understood lesion, while 59.62% chose a different VS as a least understood one. One VS was also the top best (113/332 votes) while another the least understood (34/126 votes) lesion. 74.01% students agreed that VS helped them understand the microscopic criteria better, while 74.71% would like VS to be used in the labs to come. CONCLUSION: VS were appreciated by the students as a novelty and a more impressing way of studying pathology slides, but did not dramatically improve the easiness with which they identify and understand the lesions