Effect of cadmium on cytosine hydroxymethylation in gastropod hepatopancreas

5-Hydroxymethylcytosine (5hmC) is an important, yet poorly understood epigenetic DNA modification, especially in invertebrates. Aberrant genome-wide 5hmC levels have been associated with cadmium (Cd) exposure in humans, but such information is lacking for invertebrate bioindicators. Here, we aimed to determine whether this epigenetic mark is present in DNA of the hepatopancreas of the land snail Cantareus aspersus and is responsive to Cd exposure. Adult snails were reared under laboratory conditions and exposed to graded amounts of dietary cadmium for 14 days. Weight gain was used as a sublethal endpoint, whereas survival as a lethal endpoint. Our results are the first to provide evidence for the presence of 5hmC in DNA of terrestrial mollusks; 5hmC levels are generally low with the measured values falling below 0.03%. This is also the first study to investigate the interplay of Cd with DNA hydroxymethylation levels in a non-human animal study system. Cadmium retention in the hepatopancreas of C. aspersus increased from a dietary Cd dose of 1 milligram per kilogram dry weight (mg/kg d. wt). For the same treatment, we identified the only significant elevation in percentage of samples with detectable 5hmC levels despite the lack of significant mortalities and changes in weight gain among treatment groups. These findings indicate that 5hmC is an epigenetic mark that may be responsive to Cd exposure, thereby opening a new aspect to invertebrate environmental epigenetics

Data-driven generation of 4D velocity profiles in the aneurysmal ascending aorta

Background and Objective: Numerical simulations of blood flow are a valuable tool to investigate the pathophysiology of ascending thoratic aortic aneurysms (ATAA). To accurately reproduce in vivo hemodynamics, computational fluid dynamics (CFD) models must employ realistic inflow boundary conditions (BCs). However, the limited availability of in vivo velocity measurements, still makes researchers resort to idealized BCs. The aim of this study was to generate and thoroughly characterize a large dataset of synthetic 4D aortic velocity profiles sampled on a 2D cross-section along the ascending aorta with features similar to clinical cohorts of patients with ATAA. Methods: Time-resolved 3D phase contrast magnetic resonance (4D flow MRI) scans of 30 subjects with ATAA were processed through in-house code to extract anatomically consistent cross-sectional planes along the ascending aorta, ensuring spatial alignment among all planes and interpolating all velocity fields to a reference configuration. Velocity profiles of the clinical cohort were extensively characterized by computing flow morphology descriptors of both spatial and temporal features. By exploiting principal component analysis (PCA), a statistical shape model (SSM) of 4D aortic velocity profiles was built and a dataset of 437 synthetic cases with realistic properties was generated. Results: Comparison between clinical and synthetic datasets showed that the synthetic data presented similar characteristics as the clinical population in terms of key morphological parameters. The average velocity profile qualitatively resembled a parabolic-shaped profile, but was quantitatively characterized by more complex flow patterns which an idealized profile would not replicate. Statistically significant correlations were found between PCA principal modes of variation and flow descriptors. Conclusions: We built a data-driven generative model of 4D aortic inlet velocity profiles, suitable to be used in computational studies of blood flow. The proposed software system also allows to map any of the generated velocity profiles to the inlet plane of any virtual subject given its coordinate set

Greenlight laser™ photovaporization versus transurethral resection of the prostate: A systematic review and meta-analysis

none9GreenLight laser™ photovaporization of the prostate (GLL-PVP) has become a valid alternative to traditional transurethral resection of the prostate (TURP) in men requiring surgery for benign prostatic hyperplasia. We aimed to review systematically the safety and efficacy of studies comparing GLL PVP and TURP in the medium-term. A comprehensive literature search was performed. Twelve studies were identified for meta-analysis. Meta-analyses showed a longer postoperative catheterization time (risk ratio (RR): 1.12, 95% CI:1.09–1.14, p<0.00001) and length of stay (RR: 1.16, 95% CI:1.12–1.19, p<0.00001) in the TURP group; higher risk of transfusion in the TURP group (RR: 6.51, 95% CI: 2,90–14,64 p<0.00001); no difference in the risk of urinary tract infections (RR: 0.83, 95% CI: 0.58–1.18, p=0.30) and transient re-catheterization (RR: 1.11, 95% CI: 0.76–1.60, p=0.60). Regarding reoperation rate, no difference was found in term of postoperative urethral stricture (RR: 1.13, 95% CI: 0.73–1.75, p=0.59) and bladder neck contracture (RR: 0.66, 95% CI: 0.31–1.40, p=0.28). A significantly higher incidence in reoperation for persistent/regrowth adenoma was present in the GLLL-PVP (RR: 0.64, 95% CI: 0.41–0.99, p=0.05). Data at 2-year follow-up showed significant better post-voiding residual (PVR) (MD:-1.42, 95% CI:-2.01,-0.82, p<0.00001) and International Prostate Symptom Score (IPSS) (MD:-0.35, 95% CI:-0.50,-0.20, p<0.00001) after TURP. No difference was found in the mean PVR at 2 years after TURP, in the mean maximum flow rate (Qmax) (MD: 0.30, 95% CI:-0.02–0.61, p=0.06) and quality of life QoL score (MD: 0.05, 95% CI:-0.02–0.42, p=0.13). At 5-year follow-up, data showed better IPSS (MD:-1.70, 95% CI:-2.45,-0.95, p<0.00001), QoL scores (MD:-0.35, 95% CI:-0.69,-0.02, p=0.04) and Qmax (MD: 3.29, 95% CI: 0.19–6.38, p=0.04) after TURP. Data of PVR showed no significant difference (MD:-11.54, 95% CI:-29.55–6.46, p=0.21). In conclusion, our analysis shows that GLL-PVP is a safer and more efficacious procedure than standard TURP in the early and medium-term. However, in the long term period GLL-PVP showed a higher incidence of reoperation rate due to incomplete vaporization/regrowth of prostatic adenoma.openCastellani D.; Pirola G.M.; Rubilotta E.; Gubbiotti M.; Scarcella S.; Maggi M.; Gauhar V.; Teoh J.Y.-C.; Galosi A.B.Castellani, D.; Pirola, G. M.; Rubilotta, E.; Gubbiotti, M.; Scarcella, S.; Maggi, M.; Gauhar, V.; Teoh, J. Y. -C.; Galosi, A. B

On the fixed parameter tractability and approximability of the minimum error correction problem

Haplotype assembly is the computational problem of reconstructing the two parental copies, called haplotypes, of each chromosome starting from sequencing reads, called fragments, possibly affected by sequencing errors. Minimum Error Correction (MEC) is a prominent computational problem for haplotype assembly and, given a set of fragments, aims at reconstructing the two haplotypes by applying the minimum number of base corrections. By using novel combinatorial properties of MEC instances, we are able to provide new results on the fixed-parameter tractability and approximability of MEC. In particular, we show that MEC is in FPT when parameterized by the number of corrections, and, on “gapless” instances, it is in FPT also when parameterized by the length of the fragments, whereas the result known in literature forces the reconstruction of complementary haplotypes. Then, we show that MEC cannot be approximated within any constant factor while it is approximable within factor O(log nm) where nm is the size of the input. Finally, we provide a practical 2-approximation algorithm for the Binary MEC, a variant of MEC that has been applied in the framework of clustering binary data

Real world propensity score matched analysis evaluating the influence of en-bloc vs. non en-bloc techniques, energy and instrumentation on enucleation outcomes for large and very large prostates

Purpose: The primary aim of the study was to evaluate if en-bloc vs. non en-bloc made a difference to intra-, peri- and post-operative surgical outcomes of anatomical endoscopic enucleation (AEEP) in large (> 80 cc) and very large prostates (> 200 cc). The secondary aim was to determine the influence of energy and instruments used. Methods: Data of patients with > 80 cc prostate who underwent surgery between 2019 and 2022 were obtained from 16 surgeons across 13 centres in 9 countries. Propensity score matching (PSM) was used to reduce confounding. Logistic regression was performed to evaluate factors associated with postoperative urinary incontinence (UI). Results: 2512 patients were included with 991 patients undergoing en-bloc and 1521 patients undergoing non-en-bloc. PSM resulted in 481 patients in both groups. Total operation time was longer in the en-bloc group (p 30 days) was similar (2.3% vs. 2.5%; p > 0.99). There were no differences in rates of UI between the two groups. Multivariate analysis revealed that age, Qmax, pre-operative, post-void residual urine (PVRU) and total operative time were predictors of UI. Conclusions: In experienced hands, AEEP in large prostates by the en-bloc technique yields a lower rate of complication and a slightly shorter operative time compared to the non en-bloc approach. However, it does not have an effect on rates of post-operative UI

Photodegradation of Pollutants in Air: Enhanced Properties of Nano-TiO2Prepared by Ultrasound

Nanocrystalline TiO2samples were prepared by promoting the growth of a sol–gel precursor, in the presence of water, under continuous (CW), or pulsed (PW) ultrasound. All the samples turned out to be made of both anatase and brookite polymorphs. Pulsed US treatments determine an increase in the sample surface area and a decrease of the crystallite size, that is also accompanied by a more ordered crystalline structure and the samples appear to be more regular and can be considered to contain a relatively low concentration of lattice defects. These features result in a lower recombination rate between electrons and holes and, therefore, in a good photocatalytic performance toward the degradation of NOxin air. The continuous mode induces, instead, the formation of surface defects (two components are present in XPS Ti 2p3/2region) and consequently yields the best photocatalyst. The analysis of all the characterization data seems to suggest that the relevant parameter imposing the final features of the oxides is the ultrasound total energypervolume (Etot/V) and not the acoustic intensity or the pulsed/continuous mode

Global Burden of Major Chronic Liver Diseases in 2021

Background: This study utilised the Global Burden of Disease data (2010–2021) to analyse the rates and trends in point prevalence, annual incidence and years lived with disability (YLDs) for major chronic liver diseases, such as hepatitis B, hepatitis C, metabolic dysfunction-associated liver disease, cirrhosis and other chronic liver diseases. Methods: Age-standardised rates per 100,000 population for prevalence, annual incidence and YLDs were compared across regions and countries, as well as the socio-demographic index (SDI). Trends were expressed as percentage changes (PC) and estimates were reported with uncertainty intervals (UI). Results: Globally, in 2021, the age-standardised rates per 100,000 population for the prevalence of hepatitis B, hepatitis C, MASLD and cirrhosis and other chronic liver diseases were 3583.6 (95%UI 3293.6–3887.7), 1717.8 (1385.5–2075.3), 15018.1 (13756.5–16361.4) and 20302.6 (18845.2–21791.9) respectively. From 2010 to 2021, the PC in age-standardised prevalence rates were−20.4% for hepatitis B, −5.1% for hepatitis C, +11.2% for MASLD and + 2.6% for cirrhosis and other chronic liver diseases. Over the same period, the PC in age-standardized incidence rates were -24.7%, -6.8%, +3.2%, and +3.0%, respectively. Generally, negative associations, but with fluctuations, were found between age-standardised prevalence rates for hepatitis B, hepatitis C, cirrhosis and other chronic liver diseases and the SDI at a global level. However, MASLD prevalence peaked at moderate SDI levels. Conclusions: The global burden of chronic liver diseases remains substantial. Hepatitis B and C have decreased in prevalence and incidence in the last decade, while MASLD, cirrhosis and other chronic liver diseases have increased, necessitating targeted public health strategies and resource allocation

High performance computing for haplotyping: Models and platforms

\u3cp\u3eThe reconstruction of the haplotype pair for each chromosome is a hot topic in Bioinformatics and Genome Analysis. In Haplotype Assembly (HA), all heterozygous Single Nucleotide Polymorphisms (SNPs) have to be assigned to exactly one of the two chromosomes. In this work, we outline the state-of-the-art on HA approaches and present an in-depth analysis of the computational performance of GenHap, a recent method based on Genetic Algorithms. GenHap was designed to tackle the computational complexity of the HA problem by means of a divide-et-impera strategy that effectively leverages multi-core architectures. In order to evaluate GenHap’s performance, we generated different instances of synthetic (yet realistic) data exploiting empirical error models of four different sequencing platforms (namely, Illumina NovaSeq, Roche/454, PacBio RS II and Oxford Nanopore Technologies MinION). Our results show that the processing time generally decreases along with the read length, involving a lower number of sub-problems to be distributed on multiple cores.\u3c/p\u3