Reassessment of the NF1 Variants of Unknown Significance Found During the 20-Year Activity of a Genetics Diagnostic Laboratory

The finding of variants of uncertain significance (VUS) in the activity of a diagnostic genetic laboratory is a common issue, which is however provisional and needs to be periodically re-evaluated, due to the continuous advancements in our knowledge of the genetic diseases. Neurofibromatosis type 1, caused by the occurrence of heterozygous pathogenic NF1 variants, is a good model for studying the evolution of VUS, due to the widespread use of genetic testing for the disease, the constant enrichment of the international databases with NF1 variants and the full adult penetrance of the disease, which makes genotyping the parents a crucial step in the diagnostic workflow. The present study retrospectively reviewed and reinterpreted the genetic test results of NF1 in a diagnostic genetic laboratory in the period from January 1, 2000 to December 31, 2020. All the VUS were reinterpreted using the 2015 consensus standards and guidelines for the interpretation. Out of 589 NF1 genetic tests which were performed in the period, a total of 85 VUS were found and reinterpreted in 72 cases (84.7%): 21 (29.2%) were reclassified as benign/likely benign, whereas 51 (70.8%) were recoded as pathogenic/likely pathogenic with a significant trend distribution (Chi square test for trend p=0.005). Synonymous VUS have mainly been reclassified as class 1 and 2 (7/8, 87.5%), whereas missense variants have been attributed to class 4 and 5 in 38 out of the 58 cases (65.5%). These findings underline an improvement in the classification of variants over time, suggesting that a reinterpretation of the genetic tests should be routinely performed to support the physicians in the clinical diagnosis of genetic diseases

Use of the polymerase chain reaction to detect Mycobacterium leprae in urine

Leprosy is an infectious disease caused by Mycobacterium leprae. The polymerase chain reaction (PCR) has been applied to detect M. leprae in different clinical samples and urine seems to be attractive for this purpose. PCR was used to improve the sensitivity for diagnosing leprosy by amplifying a 151-bp PCR fragment of the M. leprae pra gene (PCR-Pra) in urine samples. Seventy-three leprosy patients (39 males and 34 females, 14 to 78 years old) were selected for leprosy diagnosis at a reference laboratory in Maringa, PR, Brazil. Of these, 36 were under anti-leprosy multidrug therapy with dapsone and rifampicin for tuberculoid (TT) and dapsone, rifampicin and clofazimine for borderline (BB) and lepromatous (LL) forms. The control group contained 50 healthy individuals without any clinical history of leprosy. DNA isolated from leprosy patients' urine samples was successfully amplified by PCR-Pra in 46.6% (34/73) of the cases. The positivity of PCR-Pra for patients with the TT form was 75% for both patients under treatment and non-treated patients (P = 0.1306). In patients with the LL form, PCR-Pra positivity was 52 and 30% for patients under treatment and non-treated patients, respectively (P = 0.2386). PCR-Pra showed a statistically significant difference in detecting M. leprae between the TT and LL forms of leprosy in patients under treatment (P = 0.0033). Although the current study showed that the proposed PCR-Pra has some limitations in the detection of M. leprae, this method has the potential to be a useful tool for leprosy diagnosis mainly in TT leprosy where the AFB slit-skin smear is always negative.CAPESCAPE

Ag/mgo nanoparticles via gas aggregation nanocluster source for perovskite solar cell engineering

Nanocluster aggregation sources based on magnetron-sputtering represent precise and versatile means to deposit a controlled quantity of metal nanoparticles at selected interfaces. In this work, we exploit this methodology to produce Ag/MgO nanoparticles (NPs) and deposit them on a glass/FTO/TiO2 substrate, which constitutes the mesoscopic front electrode of a monolithic perovskite-based solar cell (PSC). Herein, the Ag NP growth through magnetron sputtering and gas aggregation, subsequently covered with MgO ultrathin layers, is fully characterized in terms of structural and morphological properties while thermal stability and endurance against air-induced oxidation are demonstrated in accordance with PSC manufacturing processes. Finally, once the NP coverage is optimized, the Ag/MgO engineered PSCs demonstrate an overall increase of 5% in terms of device power conversion efficiencies (up to 17.8%)

Recurrent NF1 gene variants and their genotype/phenotype correlations in patients with Neurofibromatosis type I

Neurofibromatosis type I, a genetic condition due to pathogenic variants in the NF1 gene, is burdened by a high rate of complications, including neoplasms, which increase morbidity and mortality for the disease. We retrospectively re-evaluated the NF1 gene variants found in the period 2000\u20132019 and we studied for genotype/phenotype correlations of disease complications and neoplasms 34 variants, which were shared by at least two unrelated families (range 2\u201311) for a total 141 of probands and 21 relatives affected by Neurofibromatosis type I. Recurrent variants could be ascribed to the most common mutational mechanisms (C to T transition, microsatellite slippage, non-homologous recombination). In genotype/phenotype correlations, the variants p.Arg440*, p.Tyr489Cys, and p.Arg1947*, together with the gross gene deletions, displayed the highest rates of complications. When considering neoplasms, carriers of variants falling in the extradomain region at the 5\u2032 end of NF1 had a lower age-related cancer frequency than the rest of the gene sequence, showing a borderline significance (p = 0.045), which was not conserved after correction with covariates. We conclude that (1) hotspots in NF1 occur via different mutational mechanisms, (2) several variants are associated with high rates of complications and cancers, and (3) there is an initial evidence toward a lower cancer risk for carriers of variants in the 5\u2032 end of the NF1 gene although not significant at the multivariate analysis

Asymptomatic HIV-people present different profile of sCD14, sRAGE, DNA damage and vitamins, according to the use of cART and CD4+ T cells restoration.

We aimed to analyze markers of immune activation, inflammation, and oxidative stress in 92 asymptomatic HIV-infected patients according to the adequate (AR, >500 cells/mm(3)) or inadequate (IR, nAR > LTNP > tAR > tIR. Higher levels of 8-isoprostane were observed in nIR. LTNP presented a higher retinol dosage than tAR and less genotoxic damage induced by oxidative stress than the other groups. We suggest that the therapy, despite being related to lesser immune activation and inflammation, alters the vitamin profile and consequently increases the oxidative stress of patients. In addition, the lowest genotoxic index for LTNP indicates that both VL and cART could be responsible for the increased DNA damage. More studies are needed to understand the influence of cART on persistent immune activation and inflammation

Development and validation of a simple questionnaire for the identification of hereditary breast cancer in primary care

<p>Abstract</p> <p>Background</p> <p>Breast cancer is a significant public health problem worldwide and the development of tools to identify individuals at-risk for hereditary breast cancer syndromes, where specific interventions can be proposed to reduce risk, has become increasingly relevant. A previous study in Southern Brazil has shown that a family history suggestive of these syndromes may be prevalent at the primary care level. Development of a simple and sensitive instrument, easily applicable in primary care units, would be particularly helpful in underserved communities in which identification and referral of high-risk individuals is difficult.</p> <p>Methods</p> <p>A simple 7-question instrument about family history of breast, ovarian and colorectal cancer, FHS-7, was developed to screen for individuals with an increased risk for hereditary breast cancer syndromes. FHS-7 was applied to 9218 women during routine visits to primary care units in Southern Brazil. Two consecutive samples of 885 women and 910 women who answered positively to at least one question and negatively to all questions were included, respectively. The sensitivity, specificity and positive and negative predictive values were determined.</p> <p>Results</p> <p>Of the 885 women reporting a positive family history, 211 (23.8%; CI95%: 21.5–26.2) had a pedigree suggestive of a hereditary breast and/or breast and colorectal cancer syndrome. Using as cut point one positive answer, the sensitivity and specificity of the instrument were 87.6% and 56.4%, respectively. Concordance between answers in two different applications was given by a intra-class correlation (ICC) of 0.84 for at least one positive answer. Temporal stability of the instrument was adequate (ICC = 0.65).</p> <p>Conclusion</p> <p>A simple instrument for the identification of the most common hereditary breast cancer syndrome phenotypes, showing good specificity and temporal stability was developed and could be used as a screening tool in primary care to refer at-risk individuals for genetic evaluations.</p

Appropriate model use for predicting elevations and inundation extent for extreme flood events

Flood risk assessment is generally studied using flood simulation models; however, flood risk managers often simplify the computational process; this is called a “simplification strategy”. This study investigates the appropriateness of the “simplification strategy” when used as a flood risk assessment tool for areas prone to flash flooding. The 2004 Boscastle, UK, flash flood was selected as a case study. Three different model structures were considered in this study, including: (1) a shock-capturing model, (2) a regular ADI-type flood model and (3) a diffusion wave model, i.e. a zero-inertia approach. The key findings from this paper strongly suggest that applying the “simplification strategy” is only appropriate for flood simulations with a mild slope and over relatively smooth terrains, whereas in areas susceptible to flash flooding (i.e. steep catchments), following this strategy can lead to significantly erroneous predictions of the main parameters—particularly the peak water levels and the inundation extent. For flood risk assessment of urban areas, where the emergence of flash flooding is possible, it is shown to be necessary to incorporate shock-capturing algorithms in the solution procedure, since these algorithms prevent the formation of spurious oscillations and provide a more realistic simulation of the flood levels

A new well-balanced Hermite weighted essentially non-oscillatory scheme for shallow water equations

Hermite weighted essentially non-oscillatory (HWENO) methods were introduced in the literature, in the context of Euler equations for gas dynamics, to obtain high-order accuracy schemes characterized by high compactness (e.g. Qiu and Shu, J. Comput. Phys. 2003; 193:115). For example, classical fifth-order weighted essentially non-oscillatory (WENO) reconstructions are based on a five-cell stencil whereas the corresponding HWENO reconstructions are based on a narrower three-cell stencil. The compactness of the schemes allows easier treatment of the boundary conditions and of the internal interfaces. To obtain this compactness in HWENO schemes both the conservative variables and their first derivatives are evolved in time, whereas in the original WENO schemes only the conservative variables are evolved. In this work, an HWENO method is applied for the first time to the shallow water equations (SWEs), including the source term due to the bottom slope, to obtain a fourth-order accurate well-balanced compact scheme. Time integration is performed by a strong stability preserving the Runge–Kutta method, which is a five-step and fourth-order accurate method. Besides the classical SWE, the non-homogeneous equations describing the time and space evolution of the conservative variable derivatives are considered here. An original, well-balanced treatment of the source term involved in such equations is developed and tested. Several standard one-dimensional test cases are used to verify the high-order accuracy, the C-property and the good resolution properties of the model

Supercritical flow in sharp bends

The paper deals with the behaviour of supercritical free surface flows in bends, when the usual hypothesis of small width/curvature radius ratio does not hold. In such a case, one dimensional models are not suitable to reproduce the physics of the phenomenon, and two dimensional modelling is required. Here, simplified hypothesis on specific energy distribution or longitudinal velocity component distribution are removed, and a complete two dimensional shallow water mathematical model is adopted. The solution that is proposed here is a numerical one, which is an application of a finite volume method (FVM) computer code, independently developed by the authors. A second order accurate (in time and space) Godunov cell-centered method is adopted, using the Harten, Lax and van Leer (HLL) Riemann solver in order to approximately estimate the momentum fluxes passing through the boundaries of each cell. The scheme is a high resolution one, satisfying the Total Variation Diminishing (TVD) condition. An original new treatment of the source terms relative to the bottom slope is applied, whereas a stabilizing semi-implicit treatment of source terms relative to the friction slope is used. Several aspects concerning the physics of the phenomenon are well reproduced, such as the blocking of the stream when the Froude number of the undisturbed flow is not large enough and the bend is sufficiently sharp. Notwithstanding that, maximum water depth in the bend is systematically underestimated. Such an underestimation seems quite surprising, taking into account that the integration method does not introduce any diffusive effect and that it is fully designed and tested for reproducing sharp discontinuous solutions