Distinguishing between recent balancing selection and incomplete sweep using deep neural networks

Balancing selection is an important adaptive mechanism underpinning a wide range of phenotypes. Despite its relevance, the detection of recent balancing selection from genomic data is challenging as its signatures are qualitatively similar to those left by ongoing positive selection. In this study, we developed and implemented two deep neural networks and tested their performance to predict loci under recent selection, either due to balancing selection or incomplete sweep, from population genomic data. Specifically, we generated forward-in-time simulations to train and test an artificial neural network (ANN) and a convolutional neural network (CNN). ANN received as input multiple summary statistics calculated on the locus of interest, while CNN was applied directly on the matrix of haplotypes. We found that both architectures have high accuracy to identify loci under recent selection. CNN generally outperformed ANN to distinguish between signals of balancing selection and incomplete sweep and was less affected by incorrect training data. We deployed both trained networks on neutral genomic regions in European populations and demonstrated a lower false-positive rate for CNN than ANN. We finally deployed CNN within the MEFV gene region and identified several common variants predicted to be under incomplete sweep in a European population. Notably, two of these variants are functional changes and could modulate susceptibility to familial Mediterranean fever, possibly as a consequence of past adaptation to pathogens. In conclusion, deep neural networks were able to characterize signals of selection on intermediate frequency variants, an analysis currently inaccessible by commonly used strategies

From early stress to 12-month development in very preterm infants: Preliminary findings on epigenetic mechanisms and brain growth

Very preterm (VPT) infants admitted to Neonatal Intensive Care Unit (NICU) are at risk for altered brain growth and less-than-optimal socio-emotional development. Recent research suggests that early NICU-related stress contributes to socio-emotional impairments in VPT infants at 3 months through epigenetic regulation (i.e., DNA methylation) of the serotonin transporter gene (SLC6A4). In the present longitudinal study we assessed: (a) the effects of NICU-related stress and SLC6A4 methylation variations from birth to discharge on brain development at term equivalent age (TEA); (b) the association between brain volume at TEA and socio-emotional development (i.e., Personal-Social scale of Griffith Mental Development Scales, GMDS) at 12 months corrected age (CA). Twenty-four infants had complete data at 12-month-age. SLC6A4 methylation was measured at a specific CpG previously associated with NICU-related stress and socio-emotional stress. Findings confirmed that higher NICU-related stress associated with greater increase of SLC6A4 methylation at NICU discharge. Moreover, higher SLC6A4 discharge methylation was associated with reduced anterior temporal lobe (ATL) volume at TEA, which in turn was significantly associated with less-than-optimal GMDS Personal-Social scale score at 12 months CA. The reduced ATL volume at TEA mediated the pathway linking stress-related increase in SLC6A4 methylation at NICU discharge and socio-emotional development at 12 months CA. These findings suggest that early adversity-related epigenetic changes might contribute to the long-lasting programming of socio-emotional development in VPT infants through epigenetic regulation and structural modifications of the developing brain

Comfort radicalism and NEETs: a conservative praxis

Young people who are not in education, employment or training (NEET) are construed by policy makers as a pressing problem about which something should be done. Such young people's lack of employment is thought to pose difficulties for wider society in relation to social cohesion and inclusion and it is feared that they will become a 'lost generation'. This paper(1) draws upon English research, seeking to historicise the debate whilst acknowledging that these issues have a much wider purchase. The notion of NEETs rests alongside longstanding concerns of the English state and middle classes, addressing unruly male working class youth as well as the moral turpitude of working class girls. Waged labour and domesticity are seen as a means to integrate such groups into society thereby generating social cohesion. The paper places the debate within it socio-economic context and draws on theorisations of cognitive capitalism, Italian workerism, as well as emerging theories of antiwork to analyse these. It concludes by arguing that ‘radical’ approaches to NEETs that point towards inequities embedded in the social structure and call for social democratic solutions veer towards a form of comfort radicalism. Such approaches leave in place the dominance of capitalist relations as well as productivist orientations that celebrate waged labour

Both selective and neutral processes drive GC content evolution in the human genome

Mammalian genomes consist of regions differing in GC content, referred to as isochores or GC-content domains. The scientific debate is still open as to whether such compositional heterogeneity is a selected or neutral trait. RESULTS: Here we analyze SNP allele frequencies, retrotransposon insertion polymorphisms (RIPs), as well as fixed substitutions accumulated in the human lineage since its divergence from chimpanzee to indicate that biased gene conversion (BGC) has been playing a role in within-genome GC content variation. Yet, a distinct contribution to GC content evolution is accounted for by a selective process. Accordingly, we searched for independent evidences that GC content distribution does not conform to neutral expectations. Indeed, after correcting for possible biases, we show that intron GC content and size display isochore-specific correlations. CONCLUSION: We consider that the more parsimonious explanation for our results is that GC content is subjected to the action of both weak selection and BGC in the human genome with features such as nucleosome positioning or chromatin conformation possibly representing the final target of selective processes. This view might reconcile previous contrasting findings and add some theoretical background to recent evidences suggesting that GC content domains display different behaviors with respect to highly regulated biological processes such as developmentally-stage related gene expression and programmed replication timing during neural stem cell differentiation

Maternal sensitivity buffers the association between SLC6A4 methylation and socio-emotional stress response in 3-month-old full term, but not very preterm infants

Background: Very preterm (VPT) infants are hospitalized in Neonatal Intensive Care Units (NICUs) and are exposed to life-saving procedures eliciting pain-related stress. Recent research documented that pain-related stress might result in birth-to-discharge increased methylation of serotonin transporter gene (SLC6A4) in VPT infants, leading to poorer stress regulation at 3 months of age in VPT infants compared to their full-term (FT) counterparts. Maternal sensitivity is thought to support infants' stress response, but its role in moderating the effects of altered SLC6A4 methylation is unknown. Main aim: To assess the role of maternal sensitivity in moderating the association between altered SLC6A4 methylation and stress response in 3-month-old VPT and FT infants. Methods: 53 infants (27 VPTs, 26 FTs) and their mothers were enrolled. SLC6A4 methylation was obtained from peripheral blood samples at NICU discharge for VPT infants and from cord blood at birth for FT infants. At 3 months (age corrected for prematurity), both groups participated to the face-to-face still-face (FFSF) paradigm to measure both infants' stress response (i.e., negative emotionality) and maternal sensitivity. Results: Maternal sensitivity did not significantly differ between VPT and FT infants' mothers. In VPT infants, higher SLC6A4 methylation at hospital discharge associates with higher negative emotionality during the FFSF. In FT infants, SLC6A4 methylation and maternal sensitivity significantly interacted to predict stress response: a positive significant association between SLC6A4 methylation and negative emotionality emerged only in FT infants of less-sensitive mothers. Discussion: Although no differences emerged in caregiving behavior in the two groups of mothers, maternal sensitivity was effective in moderating the effects of SLC6A4 methylation in FT infants, but not in VPT infants at 3 months. Speculatively, the buffering effect of maternal sensitivity observed in FT infants was disrupted by the altered early mother-infant contact due to NICU stay of the VPT group. These findings indirectly support that the effects of maternal sensitivity on infants' socio-emotional development might be time dependent, and that mother-infant interventions in the NICU need to be provided precociously within a narrow sensitive period after VPT birth

Prognostic Value of a 6-Minute Walk Test in Patients With Transthyretin Cardiac Amyloidosis

Background The 6-minute walk test (6MWT) represents a comprehensive functional assessment that is commonly used in patients with heart failure; however, data are lacking in patients with transthyretin cardiac amyloidosis (ATTR-CA). Objectives This study aimed to assess the prognostic importance of the 6MWT in patients with ATTR-CA.Methods A retrospective analysis of patients diagnosed with ATTR-CA at the National Amyloidosis Centre who underwent a baseline 6MWT between 2011 and 2023 identified 2,141 patients, of whom 1,118 had follow-up at 1 year.Results The median baseline 6MWT distance was 347 m (Q1-Q3: 250-428 m) and analysis by quartiles demonstrated an increased death rate with each distance reduction (deaths per 100 person-years: 6.3 vs 9.2 vs 13.6 vs 19.0; log-rank P < 0.001). A 6MWT distance of 35 m) and relative worsening (reduction of >5%) of 6MWT at 1 year was associated with an increased risk of mortality (HR: 1.80; 95% CI: 1.51-2.15; P < 0.001 and HR: 1.89; 95% CI: 1.59-2.24; P < 0.001, respectively), which was similar across the aforementioned subgroups. When combined with established measures of disease progression (N-terminal pro–B-type natriuretic peptide progression and outpatient diuretic intensification), each incremental increase in progression markers was associated with an increased death rate (deaths per 100 person-years: 7.6 vs 13.9 vs 22.4 vs 32.9; log-rank P < 0.001). Conclusions The baseline 6MWT distance can refine risk stratification beyond traditional prognosticators. A worsening 6MWT distance can stratify disease progression and, when combined with established markers, identifies patients at the highest risk of mortality

NUTRITIONAL AND DIGESTIVE EFFECTS OF GASTRECTOMY FOR GASTRIC CANCER

Background: Gastrectomy often leads to malnutrition. Objective: The aim of this study was to analyze nutritional and digestive effects of gastrectomy for cancer. Patients and methods: Gastrectomized patients were studied by nutritional assessment including a weekly nutritional diary exploring digestive symptoms. Results: Thirty-two patients were analyzed after a mean follow-up of 41.8 months. The mean percentage of weight loss was 12.9% \ub1 13.5%. After total gastrectomy, mean weight loss was 22% \ub1 1.2%, against 7.4% \ub111.9% for subtotal gastrectomy (p = 0.002). Moreover, advancing age was related to weight loss (p = 0.02), with a peak around 70 years. The most frequent postprandial symptoms were abdominal swelling (62%) and early satiety (59%). Finally, findings of the present study imply that overm a long follow-up, there are no specific intolerances related to gastrectomy. Conclusions: Patients who have undergone a total gastrectomy and elderly gastrectomized patients are at risk of malnutrition and need postoperative nutritional support

Signatures of Environmental Genetic Adaptation Pinpoint Pathogens as the Main Selective Pressure through Human Evolution

Previous genome-wide scans of positive natural selection in humans have identified a number of non-neutrally evolving genes that play important roles in skin pigmentation, metabolism, or immune function. Recent studies have also shown that a genome-wide pattern of local adaptation can be detected by identifying correlations between patterns of allele frequencies and environmental variables. Despite these observations, the degree to which natural selection is primarily driven by adaptation to local environments, and the role of pathogens or other ecological factors as selective agents, is still under debate. To address this issue, we correlated the spatial allele frequency distribution of a large sample of SNPs from 55 distinct human populations to a set of environmental factors that describe local geographical features such as climate, diet regimes, and pathogen loads. In concordance with previous studies, we detected a significant enrichment of genic SNPs, and particularly non-synonymous SNPs associated with local adaptation. Furthermore, we show that the diversity of the local pathogenic environment is the predominant driver of local adaptation, and that climate, at least as measured here, only plays a relatively minor role. While background demography by far makes the strongest contribution in explaining the genetic variance among populations, we detected about 100 genes which show an unexpectedly strong correlation between allele frequencies and pathogenic environment, after correcting for demography. Conversely, for diet regimes and climatic conditions, no genes show a similar correlation between the environmental factor and allele frequencies. This result is validated using low-coverage sequencing data for multiple populations. Among the loci targeted by pathogen-driven selection, we found an enrichment of genes associated to autoimmune diseases, such as celiac disease, type 1 diabetes, and multiples sclerosis, which lends credence to the hypothesis that some susceptibility alleles for autoimmune diseases may be maintained in human population due to past selective processes

Biopsy confirmation of metastatic sites in breast cancer patients:clinical impact and future perspectives

Determination of hormone receptor (estrogen receptor and progesterone receptor) and human epidermal growth factor receptor 2 status in the primary tumor is clinically relevant to define breast cancer subtypes, clinical outcome,and the choice of therapy. Retrospective and prospective studies suggest that there is substantial discordance in receptor status between primary and recurrent breast cancer. Despite this evidence and current recommendations,the acquisition of tissue from metastatic deposits is not routine practice. As a consequence, therapeutic decisions for treatment in the metastatic setting are based on the features of the primary tumor. Reasons for this attitude include the invasiveness of the procedure and the unreliable outcome of biopsy, in particular for biopsies of lesions at complex visceral sites. Improvements in interventional radiology techniques mean that most metastatic sites are now accessible by minimally invasive methods, including surgery. In our opinion, since biopsies are diagnostic and changes in biological features between the primary and secondary tumors can occur, the routine biopsy of metastatic disease needs to be performed. In this review, we discuss the rationale for biopsy of suspected breast cancer metastases, review issues and caveats surrounding discordance of biomarker status between primary and metastatic tumors, and provide insights for deciding when to perform biopsy of suspected metastases and which one (s) to biopsy. We also speculate on the future translational implications for biopsy of suspected metastatic lesions in the context of clinical trials and the establishment of bio-banks of biopsy material taken from metastatic sites. We believe that such bio-banks will be important for exploring mechanisms of metastasis. In the future,advances in targeted therapy will depend on the availability of metastatic tissue

Deciphering and modelling remyelinating mechanisms induced by clinically-used azole antifungals with exploitable repurposing properties

Recent evidence demonstrated the ability of some antifungals to induce (re)myelination in speci c experimental models. These compounds, already marketed for di erent pathologies, are interesting candidates for a repurposing strategy in neurodegenerative diseases, like multiple sclerosis (MS), characterized by strong demyelination. Our preliminary results show that the inhibition of enzymes involved in retinoic acid (RA) catabolism (CYP26), by miconazole and other azole antifungals, induces an increase of cellular RA concentration and that this increase may be behind the observed oligodendrocyte precursor cell (OPC) maturation and di erentiation. On this basis, our proposal is aimed at studying the molecular mechanisms of azole antifungals used in human pharmacology, both in silico and in vitro, and at identifying the most promising ones according to their ability to increase Myelin Basic Protein (MBP) expression on OPCs and to promote their di erentiation and myelination. In our investigation, the ability of 7 azoles to inhibit CYP26 isozymes was evaluated through molecular docking: in silico results were the basis for the selection of the drugs for the in vitro experiments. The selected azoles were tested in three di erent cell models, characterized by increasing complexity: i) OPC cultures, a maturation assay for myelin-producing cells; ii) OPC-dorsal root ganglion (DRG) neuron co-cultures, a myelination assay; iii) cerebral micromass cultures, a cell di erentiation assay for CNS. In parallel, the e ects of exogenous RA and of an inhibitor of the synthesis of RA (citral), were evaluated as well. In the next phase of the project, the outcomes from the di erent in vitro models will be statistically correlated with the pharmacological treatments. Our results will be useful: 1) for identifying the most promising azole antifungals with respect to their pro-myelinating activity, 2) for clarifying the molecular mechanisms underlying their reparative e ect and 3) for formalizing mathematical models to identify the most active concentrations for the most potent azoles