The contribution of new US technologies to US differential diagnosis of nonpalpable lesions

Background. Gray-scale ultrasound (US) patterns are still the best indicators of the risk of malignancy and correlation with mammography and guidance to bioptical procedures are still the gold standard in breast diagnosis. But recent technological advancements in ultrasound offer new diagnostic capabilities that integrate conventional US imaging: 3D, CAD, perfusion imaging and elastography. Conclusions. The US technologies allow to differentiate and grade the vascularity of breast lesions (both with conventional technologies and with contrast enhancers) and to evaluate the elastic properties of the normal and pathologic tissues (elastography). Both these technologies are on the way of becoming commer cially available on medium and high-end US instruments. But they must still be considered as research tools because their diagnostic efficacy requires more widely clinicaltesting

Preliminary evaluation of an ELISA kit for the detection of Aldosterone concentration in dog’s urine

Aldosterone is a corticosteroid hormone that plays a pivotal role in homeostatic regulation of water and salt reabsorption, blood volume and pressure. Aldosterone levels tent to rise in humans in hypertension, chronic and acute congestive heart failure (CHF); detrimental effects are opposed by drugs like ACE inhibitors and anti-mineralocorticoid. Aldosterone has a pulsatile secretion, so measurement in serum is less indicative than in urine, where concentration can be indexed to creatinine ratio for estimation of the 24-h aldosterone excretion.Few studies have evaluated aldosterone in canine urine patients, and none by ELISA. Aim of the study was to evaluate a commercial ELISA kit for measuring aldosterone in dog’s urine.Urine was collectedby free catchfrom four dogs. Two were healthy, one was affected by CHF and prescribed anti-mineralocorticoiddaily, one was affected by chronic kidney disease (CKD). Urine was centrifuged (1250g/5 min) and supernatant frozen (-20°C). Aldosterone was measured by a competitive ELISA previously validated for dogs. Twenty-four hours acid hydrolysis was performed on urinary samples before assay.The ELISA standard curve in a semi-log plot was linear between 2.5 and 3.9 ng/mL. Spike-and-recovery, linearity-of-dilution and parallelism experiments showed accuracy inmeasuring aldosterone in dog urine samples. The intra-assay coefficient of variation showed good reproducibility of the assay.Urinary samples are easy to collect, and the ELISA used in this preliminary study seems promising in determining aldosterone in dog urine. Its levels can be of great diagnostic and prognostic value for dogs affected by acute and chronic CHF, in order to assess the best therapeutic strategy. This preliminary analysis will be followed by further studies in patients affected by acute and chronic CHF

Loss of miR-107, miR-181c and miR-29a-3p promote activation of Notch2 signaling in pediatric high-grade gliomas (pHGGs)

The mechanisms by which microRNAs control pediatric high-grade gliomas (pHGGs) have yet to be fully elucidated. Our studies of patient-derived pHGG tissues and of the pHGG cell line KNS42 revealed down-regulation in these tumors of three microRNAs, specifically miR-107, miR-181c, and miR-29a-3p. This down-regulation increases the proliferation of KNS42 cells by de-repressing expression of the Notch2 receptor (Notch2), a validated target of miR-107 and miR-181c and a putative target of miR-29a-3p. Inhibition (either pharmacologic or genetic) of Notch2 or re-expression of the implicated microRNAs (all three combined but also individually) significantly reduced KNS42 cell proliferation. These findings suggest that Notch2 pathway activation plays a critical role in pHGGs growth and reveal a direct epigenetic mechanism that controls Notch2 expression, which could potentially be targeted by novel forms of therapy for these childhood tumors characterized by high-morbidity and high-mortality

The miR-139-5p regulates proliferation of supratentorial paediatric low-grade gliomas by targeting the PI3K/AKT/mTORC1 signalling

Paediatric low-grade gliomas (pLGGs) are a heterogeneous group of brain tumours associated with a high overall survival: however, they are prone to recur and supratentorial lesions are difficult to resect, being associated with high percentage of disease recurrence. Our aim was to shed light on the biology of pLGGs

Testing the performance of the imputation of MHC region in large datasets when using different reference panels

The major histocompatibility complex (MHC) contains a group of genes (~260 genes in ~4Mb) involved in several inflammatory disorders and immune response including the HLA-C gene. So far, the IPD-IMGT/HLA database reports more than 4000 different HLA-C alleles. Given the highly polymorphic nature of the gene, GWAS generally don’t study or study only a small subset of polymorphic sites of the region. Imputation procedures may help in gaining additional information on this region. However, the successful imputation of the MHC region would require a reference panel with detailed information. The main goal of this study is to investigate whether imputation procedures using appropriate reference panels may effectively increase the number of polymorphic sites of the MHC region for association with complex traits. We studied the MHC region imputation performances using 3 different reference panels (Michigan and TOPMed imputation servers): TOPMed-r2, 1000 Genomes (Phase3, v5), and the novel four-digit multi-ethnic HLA panel (v1, 2021). Here, 5 datasets with more than 1000 individuals each underwent imputation. We then focused on the imputation results of the MHC region that surround the HLA-C gene (hg19: 31234948-31241032). Imputation reported a different number of markers for the different reference panels: 482 in 1000G, 365 in TOPMed, and 1272 in HLA-panel. Of note, the HLA panels gave a higher number of imputed markers than the others. We then selected the 104 common markers imputed by all the 3 reference panels. Moreover, 162 markers were found only by 1000G panel, 194 by TOPMed, and 998 by the HLA-panel. The first preliminary comparisons showed a high concordance value for the genotype calling by the 3 different reference sets. The efficiency of the imputation was measured by the R-squared (R2) values stratifying the markers into 3 groups according to the minor allele frequency (MAF). The 104 common markers showed high R2 values (>0.96). As expected, in the other marker groups, the R2 mean values were lower for markers with MAF<0.1 (>0.65 in 1000G, 0.15-0.20 in TOPMed, >0.40 in HLA panel). In conclusion, imputation-based procedures with dedicated HLA panels can produce much more high-quality information than other general purpose reference panels for the MHC region

Pocket-sized genomics and transcriptomics analyses: a look at the newborn BioVRPi project

BioVRPi is a newborn project, started in January 2021, that focuses on Raspberry Pi (RPi) employment in bioinformatics, with particular regards on genomics. In the previous years, some research groups have already reported several examples of applications for RPi, including bioinformatic basic training and proteomics. Our project aims to develop and offer a low-cost, stable, and tested bioinformatic environment for students and researchers involved in genomics and transcriptomics fields. Raspberry Pi is a small single-board low-cost computer that was developed by the Raspberry Pi Foundation since 2012. Its original purpose aimed to facilitate computer science basic teaching in developing countries, but the growing worldwide interest has permitted its constant progress and development. Thanks to its features, RPi can suit several disciplines in need for computational supports and reach almost every, if not all, research group in the world. We tested RPi capabilities on real case studies, relatively to Genome-Wide Association Studies (GWAS) for complex traits in Homo sapiens data and in transcriptomic analyses (RNA-seq) on the Strongyloides stercoralis human parasite samples, using two RPi-4 devices equipped with different amount of RAM (8GB for genomics and 2 GB for transcriptome analyses, respectively), and running a 64-bit Operating System. The analyses leveraged on state-of-art bioinformatic toolset, such as Plink and Plink1.9, SAMtools, Bowtie 2, R, and different R packages, all compiled from source code. Moreover, the GWAS was run according to the golden standard protocols and results from the different platforms were compared. The results showed that RPi are effective devices that can efficiently handle whole GWAS and RNA-seq analyses. Benchmarking showed that the computational time taken by RPi was of the same order of magnitude when compared to the ones from a commonly used bioinformatic computer. At last, BioVRPi project shows how to implement new strategies for bioinformatic analyses, in order to provide a having-fun environment to learn and explore new alternatives in bioinformatic data analysis

Non-equilibrium effects of molecular motors on polymers

We present a generic coarse-grained model to describe molecular motors acting on polymer substrates, mimicking, for example, RNA polymerase on DNA or kinesin on microtubules. The polymer is modeled as a connected chain of beads; motors are represented as freely diffusing beads which, upon encountering the substrate, bind to it through a short-ranged attractive potential. When bound, motors and polymer beads experience an equal and opposite active force, directed tangential to the polymer; this leads to motion of the motors along the polymer contour. The inclusion of explicit motors differentiates our model from other recent active polymer models. We study, by means of Langevin dynamics simulations, the effect of the motor activity on both the conformational and dynamical properties of the substrate. We find that activity leads, in addition to the expected enhancement of polymer diffusion, to an effective reduction of its persistence length. We discover that this effective "softening" is a consequence of the emergence of double-folded branches, or hairpins, and that it can be tuned by changing the number of motors or the force they generate. Finally, we investigate the effect of the motors on the probability of knot formation. Counter-intuitively our simulations reveal that, even though at equilibrium a more flexible substrate would show an increased knotting probability, motor activity leads to a marked decrease in the occurrence of knotted conformations with respect to equilibrium

The bnt162b2 vaccine induces humoral and cellular immune memory to sars-cov-2 Wuhan strain and the Omicron variant in children 5 to 11 years of age

SARS-CoV-2 mRNA vaccines prevent severe COVID-19 by generating immune memory, comprising specific antibodies and memory B and T cells. Although children are at low risk of severe COVID-19, the spreading of highly transmissible variants has led to increasing in COVID-19 cases and hospitalizations also in the youngest, but vaccine coverage remains low. Immunogenicity to mRNA vaccines has not been extensively studied in children 5 to 11 years old. In particular, cellular immunity to the wild-type strain (Wuhan) and the cross-reactive response to the Omicron variant of concern has not been investigated. We assessed the humoral and cellular immune response to the SARS-CoV-2 BNT162b2 vaccine in 27 healthy children. We demonstrated that vaccination induced a potent humoral and cellular immune response in all vaccinees. By using spike-specific memory B cells as a measurable imprint of a previous infection, we found that 50% of the children had signs of a past, undiagnosed infection before vaccination. Children with pre-existent immune memory generated significantly increased levels of specific antibodies, and memory T and B cells, directed against not only the wild type virus but also the omicron variant