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BackgroundStructural variations (SVs) have significant impacts on complex phenotypes by rearranging large amounts of DNA sequence.ResultsWe present a comprehensive SV catalog based on the whole-genome sequence of 1060 pigs (Sus scrofa) representing 101 breeds, covering 9.6% of the pig genome. This catalog includes 42,487 deletions, 37,913 mobile element insertions, 3308 duplications, 1664 inversions, and 45,184 break ends. Estimates of breed ancestry and hybridization using genotyped SVs align well with those from single nucleotide polymorphisms. Geographically stratified deletions are observed, along with known duplications of the KIT gene, responsible for white coat color in European pigs. Additionally, we identify a recent SINE element insertion in MYO5A transcripts of European pigs, potentially influencing alternative splicing patterns and coat color alterations. Furthermore, a Yorkshire-specific copy number gain within ABCG2 is found, impacting chromatin interactions and gene expression across multiple tissues over a stretch of genomic region of ~200 kb. Preliminary investigations into SV's impact on gene expression and traits using the Pig Genotype-Tissue Expression (PigGTEx) data reveal SV associations with regulatory variants and gene-trait pairs. For instance, a 51-bp deletion is linked to the lead eQTL of the lipid metabolism regulating gene FADS3, whose expression in embryo may affect loin muscle area, as revealed by our transcriptome-wide association studies.ConclusionsThis SV catalog serves as a valuable resource for studying diversity, evolutionary history, and functional shaping of the pig genome by processes like domestication, trait-based breeding, and adaptive evolution.

Abstract Background We previously reported in recurrent/metastatic head and neck squamous cell carcinoma (R/M HNSCC) treated with immune checkpoint inhibitors (ICIs), pretreatment higher lactate dehydrogenase (LDH) and absolute (abx) neutrophils as well as lower percent (%) lymphocytes correlated with worse overall survival (OS). In this study we aimed to develop a prognostic signature for HNSCC treated with ICIs using these peripheral blood biomarkers (PBBMs). Methods Adults with R/M HNSCC treated with ICIs at our institution from 08/2012 to 03/2021 with pretreatment PBBMs were included. Follow-up continued until 02/15/2022. The cohort (n = 151) was randomly split into training (n = 100) and testing (n = 51) datasets. A prognostic score incorporating LDH, % lymphocytes, and abx neutrophils was developed from the training dataset using Cox proportional hazards regression. In the training dataset, a grid search identified the optimal cutpoints classifying patients into high, medium, and low-risk groups (trichotomized signature) as well as high vs. low-risk groups (dichotomized signature). The prognostic score, dichotomized and trichotomized signatures were then validated in the testing dataset. Results Training and testing datasets showed no clinically meaningful differences in clinicodemographic characteristics or PBBMs. An OS prognostic model was developed from the training dataset: Risk score = 1.24*log10(LDH) − 1.95*log10(% lymphocytes) + 0.47*log10(abx neutrophils). Optimal risk score cutpoints for the dichotomized and trichotomized signatures were defined in the training dataset, and Kaplan-Meier curves for both dichotomized and trichotomized signatures showed good separation between risk groups. Risk scores were calculated in the testing dataset, where the trichotomized signature demonstrated overlap between low and medium-risk groups but good separation from the high-risk group while the dichotomized signature showed clear separation between low and high-risk groups. Higher risk score correlated with worse OS (HR 2.08, [95%CI 1.17–3.68], p = 0.012). Progression-free survival Kaplan-Meier curves likewise showed excellent separation between dichotomized risk groups in the training and testing datasets. Conclusions We developed a prognostic signature for OS based on 3 previously identified PBBMs for HNSCC treated with ICIs and identified a high-risk group of patients least likely to have survival benefit from ICIs. This signature may improve ICI patient selection and warrants validation in an independent cohort as well as correlation with CPS.

Abstract Thanks to their unique properties such as ultra high porosity and surface area, metal-organic frameworks (MOFs) are highly regarded materials for gas adsorption applications. However, their combinatorial nature results in a vast chemical space, precluding its exploration with traditional techniques. Recently, machine learning (ML) pipelines have been established as the go-to method for large scale screening by means of predictive models. These are typically built in a descriptor-based manner, meaning that the structure must be first coarse-grained into a 1D fingerprint before it is fed to the ML algorithm. As such, the latter can not fully exploit the 3D structural information, potentially resulting in a model of lower quality. In this work, we propose a descriptor-free framework called “AIdsorb”, which can directly process raw structural information for predicting gas adsorption properties. To accomplish that, the structure is first treated as a point cloud and then passed to a deep learning algorithm suitable for point cloud analysis. As a proof of concept, AIdsorb is applied for predicting $$\text {CO}_{2}$$ CO 2 uptake in MOFs, outperforming a conventional pipeline that uses geometric descriptors as input. Additionally, to evaluate the transferability of the proposed framework to different host-guest systems, $$\text {CH}_{4}$$ CH 4 uptake in COFs is examined. Since AIdsorb bases its roots on raw structural information, its applicability extends to all fields of material science.

This study investigates a novel approach toward enhancing the efficacy of Lutetium-177 (Lu-177) radiopharmaceutical therapy by combining it with gold nanoparticles (AuNPs) in the HepG2 hepatic cancer cell line. Lu-177, known for its effective β radiation, also emits gamma rays at energies (113 keV and 208 keV) near the photoelectric absorption range, suggesting potential for targeted and localized radiation enhancement when used in conjunction with AuNPs. Thus, HepG2 cells were treated at two different activity levels (74 MBq and 148 MBq), with Lu-177 alone, with a combination of Lu-177 and AuNPs in two sizes (10 nm and 50 nm), while some received no treatment. Treatment efficacy was assessed by quantifying the radiation enhancement ratio (RER) and the apoptosis levels. The results reveal that combining Lu-177 with AuNPs significantly increases cell death and apoptosis compared to Lu-177 alone, with 10 nm AuNPs demonstrating superior effectiveness. Additionally, varying Lu-177 activity levels influenced the treatment outcomes, with higher activity levels further augmenting the therapeutic impact of combined therapy. These findings underscore the potential of utilizing Lu-177’s beta, but also gamma, emissions, traditionally considered non-therapeutic, for localized radiation enhancement when combined with AuNPs. This novel strategy leverages Lu-177 as an internal irradiator to exploit gamma radiation for a targeted therapeutic advantage without requiring nanoparticle functionalization. The study provides a promising approach to improving radionuclide therapy and sets the stage for future research aimed at optimizing cancer treatments through the combined use of Lu-177 and AuNPs.

Abstract Mammalian DNA replication relies on various DNA helicase and nuclease activities to ensure accurate genetic duplication, but how different helicase and nuclease activities are properly directed remains unclear. Here, we identify the ubiquitin-specific protease, USP50, as a chromatin-associated protein required to promote ongoing replication, fork restart, telomere maintenance, cellular survival following hydroxyurea or pyridostatin treatment, and suppression of DNA breaks near GC-rich sequences. We find that USP50 supports proper WRN-FEN1 localisation at or near stalled replication forks. Nascent DNA in cells lacking USP50 shows increased association of the DNA2 nuclease and RECQL4 and RECQL5 helicases and replication defects in cells lacking USP50, or FEN1 are driven by these proteins. Consequently, suppression of DNA2 or RECQL4/5 improves USP50-depleted cell resistance to agents inducing replicative stress and restores telomere stability. These data define an unexpected regulatory protein that promotes the balance of helicase and nuclease use at ongoing and stalled replication forks.

Abstract We revisit Duff, Okun, and Veneziano’s divergent views on the number of fundamental constants and argue that the issue can be set to rest by having spacetime as the starting point. This procedure disentangles the resolution in what depends on the assumed spacetime (whether relativistic or not) from the theories built over it. By defining that the number of fundamental constants equals the minimal number of independent standards necessary to express all observables, as assumed by Duff, Okun, and Veneziano, it is shown that the same units fixed by the apparatuses used to construct the spacetimes are enough to express all observables of the physical laws defined over them. As a result, the number of fundamental constants equals one in relativistic spacetimes.

Abstract Quarrying of rock aggregates generates produced water that, if not handled properly will be a source of pollution for nearby water bodies, thus affecting the chemistry of the water. This study examined the chemistry, impact of quarrying activities on water resources and the health consequences/risks posed by ingestion of the water by humans in the Akamkpa quarry region in southeastern Nigeria. Thirty (30) water samples consisting of pond water, stream water, hand dug wells, and borehole samples were collected and analyzed for their physicochemical parameters using standard methods. The results obtained from the analyses indicated that the water was moderately acidic, fresh, and not salty, with many parameters below the recommended standards with Ca2+, and HCO3 − being the dominant ions present in the water resources. Rock weathering processes including silicate weathering as illustrated by hydrochemical facies, cross plots, and Gibbs diagrams are the dominant mechanisms influencing the quality and major ions chemistry of the water resources with minor contributions from dissolution, anthropogenic activities, and ion exchange. Ca-Mg-SO4-Cl and Na–K-HCO3 − are the most important water types. Although the water quality index shows that the water is suitable for human use and irrigation, the mean values of As, Cd, Pb, and Se are above the acceptable limits. Additionally, the calculated contamination factor revealed the water resources are moderate to highly contaminated by As, Cd, Cr, Mo, Pb, Sb, and Se, and are therefore unsuitable for consumption with regards to these parameters. However, the residual sodium carbonate and water hazard index (WHI) values showed that 38% to 90% of sites in the quarry area were unsuitable for cultivation, 10–30% were in the low to medium impact category, and 60% were classified as risky and are from high to very high impact category. A non-cancer study of inhabitants living in the vicinity of the quarry area indicated that 6.7% of the sites have values greater than one, indicating that it may endanger the health of the people. Therefore, constant monitoring of the water quality is recommended as long-term use of contaminated water can harm humans, plants, and soils.

The current waste crisis calls for a stable and integrated institutional framework. Policymakers try to untangle the complicated and interconnected acts, regulations, and directives in the European Union (EU). However, it is not a plain sailing to observe and implement the vast regulatory armamentarium of the EU in the circular economy (CE) sectors to achieve sustainable waste management (SWM). Aim of the present study is to showcase the historic – international and European – institutional framework on waste management as well as the main hazardous and special waste streams in order to build an integrated SWM framework. Moreover, CE necessitates for the safeguarding of critical raw materials (CRMs) and energy, in order to blueprint policies for the Net-Zero Age. Hence, the present study would show how CE can establish SWM, even though CE is going to face complex challenges till the conclusion of Agendas 2030 and 2050.

Abstract Sustainable development ensures the longevity of civilization by balancing economic growth, environmental protection, and social equity. The present study evaluates cultural heritage assets via a meta-regression analysis function transfer, in which 85 studies were examined that revealed 106 different willingness-to-pay (WTP) values in the period 1995–2022. The meta-regression methodology enables the valuation of cultural heritage—tangible and intangible—goods and services, as well as cultural values (e.g. aesthetic, spiritual, symbolic, etc.). The utilization of WTP would enable us to compare the two models (i.e., European and non-European) on how much a citizen would value cultural heritage based on non-market valuation. The results would inform policymakers about the importance of cultural heritage assets in the sustainable development agenda. The empirical findings present that the WTP for the European sample is 37.6€ and for the non-European is 60.12€. In essence, the Europeans are influenced mainly by intangible cultural assets, whereas non-Europeans are influenced by oral tradition. Overall, cultural heritage conservation necessitates for proper economic valuation through a holistic approach, in short—the valuation of both tangible and intangible cultural goods and services is imperative for sustainable development.

Abstract Background We recently identified ~ 10,000 correlated regions of systemic interindividual epigenetic variation (CoRSIVs) in the human genome. These methylation variants are amenable to population studies, as DNA methylation measurements in blood provide information on epigenetic regulation throughout the body. Moreover, establishment of DNA methylation at human CoRSIVs is labile to periconceptional influences such as nutrition. Here, we analyze publicly available whole-genome bisulfite sequencing data on multiple tissues of each of two Holstein cows to determine whether CoRSIVs exist in cattle. Results Focusing on genomic blocks with ≥ 5 CpGs and a systemic interindividual variation index of at least 20, our approach identifies 217 cattle CoRSIVs, a subset of which we independently validate by bisulfite pyrosequencing. Similar to human CoRSIVs, those in cattle are strongly associated with genetic variation. Also as in humans, we show that establishment of DNA methylation at cattle CoRSIVs is particularly sensitive to early embryonic environment, in the context of embryo culture during assisted reproduction. Conclusions Our data indicate that CoRSIVs exist in cattle, as in humans, suggesting these systemic epigenetic variants may be common to mammals in general. To the extent that individual epigenetic variation at cattle CoRSIVs affects phenotypic outcomes, assessment of CoRSIV methylation at birth may become an important tool for optimizing agriculturally important traits. Moreover, adjusting embryo culture conditions during assisted reproduction may provide opportunities to tailor agricultural outcomes by engineering CoRSIV methylation profiles.

Abstract Background The prognosis of individual dogs with meningoencephalomyelitis of unknown etiology (MUE) remains difficult to predict. MUE cases with no lesions detected by magnetic resonance imaging (MRI) occur, but it is unknown whether this finding is associated with prognosis. Hypothesis MUE cases without detectable lesions on MRI have a better outcome than cases with detectable lesions. Animals Study included 73 client‐owned dogs with MUE presenting to Purdue University Veterinary Hospital from 2010 to 2020. Methods Retrospective study. Dogs with a clinical diagnosis of MUE were identified by medical record search. MRI reports were reviewed for presence or absence of lesions consistent with MUE. Clinical findings at presentation, treatment, disease‐specific survival, and outcomes including rates of remission and relapse were compared between cases with normal MRI or abnormal MRI. Results Overall, 54 dogs (74%) were classified as abnormal MRI, and 19 dogs (26%) were classified as normal MRI cases. Death caused by MUE occurred in 1/19 (5%) normal MRI dogs and 18/54 (33%) abnormal MRI dogs (P = .016). Median survival was >107 months in both groups, but survival was significantly longer in the normal MRI group (P = .019). On multivariate analysis, abnormal MRI was significantly related to death (hazard ratio, 7.71; 95% confidence interval 1.03‐58.00, P = .0470), whereas significant relationships with death were not identified for either the use of secondary immunosuppressive medications or cerebrospinal fluid nucleated cell count. Conclusions MUE dogs with no detectable lesions on MRI have reduced disease‐related death compared with dogs with abnormal MRI. The presence or absence of MRI lesions in MUE dogs is prognostically relevant.

Abstract A major challenge in Parkinson’s disease is the variability in symptoms and rates of progression, underpinned by heterogeneity of pathological processes. Biomarkers are urgently needed for accurate diagnosis, patient stratification, monitoring disease progression and precise treatment. These were previously lacking, but recently, novel imaging and fluid biomarkers have been developed. Here, we consider new imaging approaches showing sensitivity to brain tissue composition, and examine novel fluid biomarkers showing specificity for pathological processes, including seed amplification assays and extracellular vesicles. We reflect on these biomarkers in the context of new biological staging systems, and on emerging techniques currently in development.