Single Base Research Articles

Evaluating a multi-step collocation approach for an ensemble climatological dataset of actual evapotranspiration over Italy

Accurate estimations of actual evapotranspiration (ET) are key in a variety of water balance applications, but divergent results can be obtained due to the large range of available methodologies. The use of an ensemble approach is a suitable alternative, as it summarizes multiple sources in an optimized strategy. In this study, an expert-based multi-step collocation (MC) approach is tested to merge six ET datasets, with the aim of reconstructing a spatiotemporally-consistent monthly dataset for Italy in the climatological period 1991–2020. The merged products are: three water balance datasets (BIG BANG, LSA SAF, and LISFLOOD), two residual surface energy balance model datasets (SSEBop, and ALEXI), and the MODIS standard ET product. The merged product is analyzed for spatio-temporal consistency and evaluated using flux observations from 11 sites. On average, the merged product has higher accuracy (mean absolute difference = 0.47 ± 0.17 mm/d, relative difference = 27.9 ± 7.5 %) than any single base dataset, and it is characterized by limited bias (mean bias error = -0.17 ± 0.26 mm/d), high correlation (r = 0.83 ± 0.10), and more uniform performance across sites. The merged ET dataset is accompanied by an estimation of the ensemble spread, which highlights large differences in ET estimates in some areas and periods characterized by severe water stress, such as in southern Italy during the summer. This large spread seems to be mostly driven by systematic differences among datasets, which affect the estimation of the reference climatology, suggesting how inter-model spread can have a defining role in further improving the merging strategies.

Aminoacyl-tRNA synthetases

Aminoacyl-tRNA synthetases hold the key to the genetic code and assign nucleic acid-based codons to amino acids, the building blocks of proteins. In their ability to recognize identity elements on transfer RNAs (tRNAs), some as simple as a single base pair, they ensure that the same proteins are formed each time information embedded in DNA is transcribed into messenger RNA (mRNA) and translated into proteins (Figure 1A). Thus, aminoacyl-tRNA synthetase active sites are conserved; however, since their evolutionary origin, their functions have been co-opted, expanded on and played novel roles during evolution. Below, we provide an overview of the many functions of aminoacyl-tRNA synthetases - from their role in translation, one of the most fundamental processes of all life, to newly discovered, diverse functions.

Mutational signatures in 175 Chinese gastric cancer patients.

Gastric cancer (GC), a molecularly heterogeneous disease, is the third leading cause of cancer death worldwide. The majority of GC cases worldwide occur in East Asia, predominantly China. Mutational Signature Framework offers an elegant approach to identify mutational processes present in tumors. To identify mutational signature patterns, we conducted whole exome sequencing (WES) analysis in Chinese patients with GC. Mutect2 and MutsigCV were used to identify significantly mutated genes in 175 Chinese GC cases using paired tumor-normal tissues. We investigated mutational signatures using Catalogue of Somatic Mutations in Cancer (COSMIC) Version 2 (V2) and Version 3 (V3). We identified 104 mutated genes with P < 0.01. Seven genes (OR6B1, B2M, ELF3, RHOA, RPL22, TP53, ARIDIA) had q < 0.0001, including six previously associated with GC. Mutational signatures (COSMIC-V3) observed include 14 single base substitutions (SBS), one doublet base substitution (DBS) Signature A, and one InDel (ID2). The most frequent SBS signatures (SBS05, SBS01, SBS15, SBS20, SBS40) were also observed in 254 White GC cases from The Cancer Genome Atlas (TCGA) Project. However, SBS01 and SBS20 showed significant differences between Whites vs. All Asians (19.3% vs. 11.3% for SBS 1 (P = 0.012) and 11.4% vs. 5.9% for SBS20 (P = 0.025), respectively). Using COSMIC V2, signatures 6, 15, and 1 were the most frequent in Chinese GC cases. Further, most Chinese GC cases carried multiple signatures. This effort represents the most detailed mutational signatures analysis of GC cases from China to date. Results hold promise for new insights in understanding risk and prognosis factors in GC.

Optimized periphery-core interface increases fitness of the Bacillus subtilisglmS ribozyme.

Like other functional RNAs, ribozymes encode a conserved catalytic center supported by peripheral domains that vary among ribozyme sub-families. To understand how core-periphery interactions contribute to ribozyme fitness, we compared the cleavage kinetics of all single base substitutions at 152 sites across the Bacillus subtilis glmS ribozyme by high-throughput sequencing (k-seq). The in vitro activity map mirrored phylogenetic sequence conservation in glmS ribozymes, indicating that biological fitness reports all biochemically important positions. The k-seq results and folding assays showed that most deleterious mutations lower activity by impairing ribozyme self-assembly. All-atom molecular dynamics simulations of the complete ribozyme revealed how individual mutations in the core or the IL4 peripheral loop introduce a non-native tertiary interface that rewires the catalytic center, eliminating activity. We conclude that the need to avoid non-native helix packing powerfully constrains the evolution of tertiary structure motifs in RNA.

Prediction and functional interpretation of inter-chromosomal genome architecture from DNA sequence with TwinC.

Three-dimensional nuclear DNA architecture comprises well-studied intra-chromosomal (cis) folding and less characterized inter-chromosomal (trans) interfaces. Current predictive models of 3D genome folding can effectively infer pairwise cis-chromatin interactions from the primary DNA sequence but generally ignore trans contacts. There is an unmet need for robust models of trans-genome organization that provide insights into their underlying principles and functional relevance. We present TwinC, an interpretable convolutional neural network model that reliably predicts trans contacts measurable through genome-wide chromatin conformation capture (Hi-C). TwinC uses a paired sequence design from replicate Hi-C experiments to learn single base pair relevance in trans interactions across two stretches of DNA. The method achieves high predictive accuracy (AUROC=0.80) on a cross-chromosomal test set from Hi-C experiments in heart tissue. Mechanistically, the neural network learns the importance of compartments, chromatin accessibility, clustered transcription factor binding and G-quadruplexes in forming trans contacts. In summary, TwinC models and interprets trans genome architecture, shedding light on this poorly understood aspect of gene regulation.

Evidence that DNA polymerase δ proofreads errors made by DNA polymerase α across the Saccharomyces cerevisiae nuclear genome

We show that the rates of single base substitutions, additions, and deletions across the nuclear genome are strongly increased in a strain harboring a mutator variant of DNA polymerase α combined with a mutation that inactivates the 3´-5´ exonuclease activity of DNA polymerase δ. Moreover, tetrad dissections attempting to produce a haploid triple mutant lacking Msh6, which is essential for DNA mismatch repair (MMR) of base•base mismatches made during replication, result in tiny colonies that grow very slowly and appear to be aneuploid and/or defective in oxidative metabolism. These observations are consistent with the hypothesis that during initiation of nuclear DNA replication, single-base mismatches made by naturally exonuclease-deficient DNA polymerase α are extrinsically proofread by DNA polymerase δ, such that in the absence of this proofreading, the mutation rate is strongly elevated. Several implications of these data are discussed, including that the mutational signature of defective extrinsic proofreading in yeast could appear in human tumors.

Design and Technological Aspects of Integrating Multi-Blade Machining and Surface Hardening on a Single Machine Base

Modern mechanical engineering faces high competition in global markets, which requires manufacturers of process equipment to significantly reduce production costs while ensuring high product quality and maximum productivity. Metalworking occupies a significant part of industrial production and consumes a significant share of the world’s energy and natural resources. Improving the technology of manufacturing parts with an emphasis on more efficient use of metalworking machines is necessary to maintain the competitiveness of the domestic machine tool industry. Hybrid metalworking systems based on the principles of multi-purpose integration eliminate the disadvantages of monotechnologies and increase efficiency by reducing time losses and intermediate operations. The purpose of this work is to develop and implement a hybrid machine tool system and an appropriate combined technology for manufacturing machine parts. Theory and methods. Studies of the possible structural composition and layout of hybrid equipment at integration of mechanical and surface-thermal processes were carried out, taking into account the basic provisions of structural synthesis and componentization of metalworking systems. Theoretical studies were carried out using the basic provisions of system analysis, geometric theory of surface formation, design of metalworking machines, methods of finite elements, and mathematical and computer modeling. The mathematical modeling of thermal fields and structural-phase transformations during HEH HFC was carried out in ANSYS (version 19.1) and SYSWELD (version 2010) software packages using numerical methods of solving differential equations of unsteady heat conduction (Fourier equation), carbon diffusion (2nd Fick’s law) and elastic–plastic behavior of the material. The verification of the modeling results was carried out using in situ experiments employing the following: optical and scanning microscopy; and mechanical and X-ray methods of residual stress determination. Formtracer SV-C4500 profilograph profilometer was used in the study for simultaneous measurement of shape deviations and surface roughness. Surface topography was assessed using a Walter UHL VMM 150 V instrumental microscope. The microhardness of the hardened surface layer of the parts was evaluated on a Wolpert Group 402MVD. Results and discussion. The original methodology of structural and kinematic analysis for pre-design studies of hybrid metalworking equipment is presented. Methodological recommendations for the modernization of multi-purpose metal-cutting machine tool are developed, the implementation of which will make it possible to implement high-energy heating with high-frequency currents (HEH HFC) on a standard machine tool system and provide the formation of knowledge-intensive technological equipment with extended functionality. The innovative moment of this work is the development of hybrid metalworking equipment with numerical control and writing a unique postprocessor to it, which allows to realize all functional possibilities of this machine system and the technology of combined processing as a whole. Special tooling and tools providing all the necessary requirements for the process of surface hardening of HEH HFC were designed and manufactured. The conducted complex of works and approbation of the technology of integrated processing in real conditions in comparison with traditional methods of construction of technological process of parts manufacturing allowed to obtain the following results: increase in the productivity of processing by 1.9 times; exclusion of possibility of scrap occurrence at finishing grinding; reduction in auxiliary and preparatory-tasking time; and reduction in inter-operational parts backlogs.

Human and bats genome robustness under COSMIC mutational signatures.

Carcinogenesis is an evolutionary process, and mutations can fix the selected phenotypes in selective microenvironments. Both normal and neoplastic cells are robust to the mutational stressors in the microenvironment to the extent that secure their fitness. To test the robustness of genes under a range of mutagens, we developed a sequential mutation simulator, Sinabro, to simulate single base substitution under a given mutational process. Then, we developed a pipeline to measure the robustness of genes and cells under those mutagenesis processes. We discovered significant human genome robustness to the APOBEC mutational signature SBS2, which is associated with viral defense mechanisms and is implicated in cancer. Robustness evaluations across over 70,000 sequences against 41 signatures showed higher resilience under signatures predominantly causing C-to-T (G-to-A) mutations. Principal component analysis indicates the GC content at the codon's wobble position significantly influences robustness, with increased resilience noted under transition mutations compared to transversions. Then, we tested our results in bats at extremes of the lifespan-to-mass relationship and found the long-lived bat is more robust to APOBEC than the short-lived one. By revealing robustness to APOBEC ranked highest in human (and bats with much more than number of APOBEC) genome, this work bolsters the key potential role of APOBECs in aging and cancer, as well as evolved countermeasures to this innate mutagenic process. It also provides the baseline of the human and bat genome robustness under mutational processes associated with aging and cancer.

Age estimation of burnt human remains through DNA methylation analysis.

The identification of human fire victims is a challenging task in forensic medicine. The heat-induced alterations of biological tissues can make the conventional anthropological analyses difficult. Even if the DNA profile of the victim is achieved, it is possible that no match can be found in a forensic DNA database, thus hindering positive identification. In such cases, any information useful to nail down a possible identity should be collected, such as DNA methylation analysis which could provide useful investigative leads. In the present study, five age-related epigenetic markers (ELOVL2, FHL2, KLF14, C1orf132, and TRIM59) were initially analysed in blood samples of 72 living Italian individuals of known age, using a Single Base Extension (SBE) assay. An age prediction model was built by multiple linear regression including all the markers (Mean Absolute Error, MAE: 3.15 years). This model was tested on 29 blood samples collected during autopsies from burnt human remains, already identified through DNA analysis, providing a MAE of 6.92 years. The model allowed a correct prediction in 79.3% of the cases (95% prediction interval), while six cases were associated with inaccurate predictions (min-max prediction error: 9.8-37.3 years). Among the different sample variables considered to explain these results, only the DNA degradation index was a relevant factor affecting the reliability of the predictions. In conclusion, the SBE typing of blood from burnt remains proved to be a reliable tool to estimate chronological age of most of the samples, also in consideration of its cost-effectiveness and the availability of CE sequencers in every forensic genetics laboratory.

Development of a database structure for the first Geomorphological map of Greece at 1:1,000,000 scale

Geomorphological maps offer researchers multiple advantages when studying an area, as they can provide insights into the formation processes of the observed landforms, as well as their possible evolution in the future. The geodatabase seems to be of primary importance, as it determines the way in which the data will be organized and presented on a map, and thus the map’s functionality. There are not specific guidelines for a database for geomorphological maps, as this would be dependent, inter alia, on the scale of the maps. However, up to this day, there is not a single data base template to be used for geomorphological mapping. In each case, the cartographer/geomorphologist determines the number of fields their layers will have and their type, as well as what information they will contain, depend-ing on the scale they are working on, the variety of landforms of their area, the time and resources available (correspondingly, the accuracy their map will have) and the purpose of its creation. Also, while several countries - not only large ones, but smaller ones as well - do have a geomorphological map at national scale, many countries, Greece among them, do not. On the contrary, only parts of them have been mapped by various researchers, who did not share any common database, which renders the combination of the individual maps difficult. But even in countries with existent national geomorphological maps, a specific and common geodatabase structure was not followed. In this way, there is no uniformity in the data and comparisons between maps, as well as combinations of data are very difficult and require a lot of work. Therefore, as we have initiated a project to create the geomorphological map of the Greek territory at 1:1,000,000 scale, we found that, prior to the beginning of the mapping, it was imperative to create a geodatabase template which we intend to follow, and which can be used as a template for geomorphological mapping at national scale by other countries (researchers and/or authorities). Thus, in this paper, we propose a database template to be used in geomorphological mapping at global scale globally, so that the data and structure of maps share common properties, thus allowing for comparisons and combina-tions of data where necessary.

Prevalence of germline variants in Brazilian pancreatic carcinoma patients

We evaluated the prevalence of pathogenic/likely pathogenic germline variants (PGV) in Brazilian pancreatic adenocarcinoma (PC) patients, that represent a multiethnic population, in a cross-sectional study. We included 192 PC patients unselected for family history of cancer. We evaluated a panel of 113 cancer genes, through genomic DNA sequencing and 46 ancestry-informative markers, through multiplex PCR. The median age was 61 years; 63.5% of the patients presented disease clinical stages III or IV; 8.3% reported personal history of cancer; 4.7% and 16.1% reported first-degree relatives with PC or breast and/or prostate cancer, respectively. Although the main ancestry was European, there was considerable genetic composition admixture. Twelve patients (6.25%) were PGV carriers in PC predisposition genes (ATM, BRCA1, BRCA2, CDKN2A, MSH2, PALB2) and another 25 (13.0%) were PGV carriers in genes with a limited association or not previously associated with PC (ACD, BLM, BRIP1, CHEK2, ERCC4, FANCA, FANCE, FANCM, GALNT12, MITF, MRE11, MUTYH, POLE, RAD51B, RAD51C, RECQL4, SDHA, TERF2IP). The most frequently affected genes were CHEK2, ATM and FANC. In tumor samples from PGV carriers in ACD, BRIP1, MRE11, POLE, SDHA, TERF2IP, which were examined through exome sequencing, the main single base substitutions (SBS) mutational signature was SBS1+5+18, probably associated with age, tobacco smoking and reactive oxygen species. SBS3 associated with homologous repair deficiency was also represented, but on a lower scale. There was no difference in the frequency of PGV carriers between: (a) patients with or without first-degree relatives with cancer; and (b) patients with admixed ancestry versus those with predominantly European ancestry. Furthermore, there was no difference in overall survival between PGV carriers and non-carriers. Therefore, genetic testing should be offered to all Brazilian pancreatic cancer patients, regardless of their ancestry. Genes with limited or previously unrecognized associations with pancreatic cancer should be further investigated to clarify their role in cancer risk.

Clinical Interest in Exome-Based Analysis of Somatic Mutational Signatures for Non-Small Cell Lung Cancer.

Non-small cell lung cancer (NSCLC) remains the leading cause of cancer-related mortality. This study investigates the clinical interest of whole exome sequencing (WES) for analyzing somatic mutational signatures in patients with advanced or metastatic NSCLC treated with the current standard of care. Exome sequencing data and clinical characteristics from 132 patients with advanced or metastatic NSCLC were analyzed. Somatic mutational signatures including single base substitutions (SBSs), double base substitutions (DBSs), and copy number signatures were evaluated. Structural variations including tumor mutational burden (TMB), the number of neoantigens, TCR clonality, homologous recombination deficiency (HRD), copy number alterations (CNAs), and microsatellite instability (MSI) score were determined. The association between these genomic features, NSCLC subtypes, and patient outcomes (progression-free and overall survival) was evaluated. Exome sequencing offers valuable insights into somatic mutational signatures in NSCLC. This study identified specific signatures associated with a poor response to immune checkpoint inhibitor (ICI) therapy and chemotherapy, potentially aiding treatment selection and identifying patients unlikely to benefit from these approaches.

AMAR-seq: Automated Multimodal Sequencing of DNA Methylation, Chromatin Accessibility, and RNA Expression with Single-Cell Resolution.

Parallel single-cell multimodal sequencing is the most intuitive and precise tool for cellular status research. In this study, we propose AMAR-seq to automate methylation, chromatin accessibility, and RNA expression coanalysis with single-cell precision. We validated the accuracy and robustness of AMAR-seq in comparison with standard single-omics methods. The high gene detection rate and genome coverage of AMAR-seq enabled us to establish a genome-wide gene expression regulatory atlas and triple-omics landscape with single base resolution and implement single-cell copy number variation analysis. Applying AMAR-seq to investigate the process of mouse embryonic stem cell differentiation, we revealed the dynamic coupling of the epigenome and transcriptome, which may contribute to unraveling the molecular mechanisms of early embryonic development. Collectively, we propose AMAR-seq for the in-depth and accurate establishment of single-cell multiomics regulatory patterns in a cost-effective, efficient, and automated manner, paving the way for insightful dissection of complex life processes.

Whole-Exome Sequencing Reveals Novel Candidate Driver Mutations and Potential Druggable Mutations in Patients with High-Risk Neuroblastoma.

Neuroblastoma is the most prevalent solid tumor in early childhood, with a 5-year overall survival rate of 40-60% in high-risk cases. Therefore, the identification of novel biomarkers for the diagnosis, prognosis, and therapy of neuroblastoma is crucial for improving the clinical outcomes of these patients. In this study, we conducted the whole-exome sequencing of 48 freshly frozen tumor samples obtained from the Biobank. Somatic variants were identified and selected using a bioinformatics analysis pipeline. The mutational signatures were determined using the Mutalisk online tool. Cancer driver genes and druggable mutations were predicted using the Cancer Genome Interpreter. The most common mutational signature was single base substitution 5. MUC4, MUC16, and FLG were identified as the most frequently mutated genes. Using the Cancer Genome Interpreter, we identified five recurrent cancer driver mutations spanning MUC16, MUC4, ALK, and CTNND1, with the latter being novel and containing a missense mutation, R439C. We also identified 11 putative actionable mutations including NF1 Q1798*, Q2616*, and S636X, ALK F1174L and R1275Q, SETD2 P10L and Q1829E, BRCA1 R612S, NOTCH1 D1670V, ATR S1372L, and FGFR1 N577K. Our findings provide a comprehensive overview of the novel information relevant to the underlying molecular pathogenesis and therapeutic targets of neuroblastoma.

Tuning the stability of DNA tetrahedra with base-stacking interactions.

DNA nanotechnology relies on programmable anchoring of regions of single-stranded DNA through base pair hybridization to create nanoscale objects such as polyhedra, tubes, sheets, and other desired shapes. Recent work from our lab measured the energetics of base-stacking interactions and suggested that terminal stacking interactions between two adjacent strands could be an additional design parameter for DNA nanotechnology. Here, we explore that idea by creating DNA tetrahedra held together with sticky ends that contain identical base pairing interactions but different terminal stacking interactions. Testing all 16 possible combinations, we found that the melting temperature of DNA tetrahedra varied by up to 10 °C from altering a single base stack in the design. These results can inform stacking design to control DNA tetrahedra stability in a substantial and predictable way. To that end, we show that a 4 bp sticky end with weak terminal stacking does not form stable tetrahedra, while strengthening the stacks confers high stability with a 46.8 ± 1.2 °C melting temperature, comparable to a 6 bp sticky end with weak stacking. The results likely apply to other types of DNA nanostructures and suggest that terminal stacking interactions play an integral role in formation and stability of DNA nanostructures.

Genetic diagnostic outcomes from a 10-year research programme in autism in Aotearoa New Zealand

ABSTRACT Autism is a relatively common neurodevelopmental difference with considerable phenotypic heterogeneity impacting cognitive, sensory, and social processing, and often co-occurs with other conditions. Therefore, there is not a one-size-fits-all clinical support pathway for autistic individuals following diagnosis. DNA sequencing technology has enabled the discovery of genes causative of, or associated with, autism. Unsurprisingly, genetic heterogeneity goes hand-in-hand with the phenotypic heterogeneity for this condition; with causative genetic variation ranging from single base pair changes to complex chromosomal rearrangements in more than 100 different genes. This study captures a snapshot (201 individuals) of the autistic population (both clinically referred and self-referred) in Aotearoa New Zealand and documents a decade’s research effort to refine diagnosis using a flexible and customised genome-wide sequencing approach. The diagnostic yield in this phenotypically disparate cohort was 12.9%, with an additional 15.9% of individuals harbouring ‘likely causal’ variants, providing the groundwork to tailor clinical, social, and educational care. Importantly, this study reveals the diagnostic utility of customised genetic screening for autism across a phenotypically diverse autistic population.

A set of Models for Device Positioning in Sixth Generation Networks. Part 1. Methods Survey and Problem Statement

Relevance. Today, terahertz radio systems are considered as a technological basis for integrating methods and means of radio communication and radar in promising sixth-generation networks. If in 4G LTE networks the capabilities of positioning user equipment using the infrastructure of base stations were considered as auxiliary options, then in 5G NR networks, location determination technologies (LDTs) have become full-fledged services, the requirements for which are specified along with communication services. A new trend in positioning in 5G NR networks, compared to 4G LTE networks, has become a single-position assessment of the coordinates and orientation of the user equipment based on signals from a single base station with the ability to distinguish between direct and reflected signals. 6G networks are still in their infancy, but it can already be stated that they mark the next stage in the evolution of digital ecosystems, which is characterized by the convergence of communication technologies, localization and sensing of radio air and the surrounding space by radio engineering means.Purpose. This work opens a research cycle devoted to the review of models, methods and algorithms for positioning devices in 6G networks. The goal of the cycle is to find and justify new radio engineering means for achieving decimeter accuracy in 6G device coordinate estimates. The first part of the cycle provides an overview of the methods and formalization of the model for collecting primary measurements.Method is an analytical review of the state of the problem based on current scientific publications, conceptual modeling, categorical approach, expert combination, comparative analysis, formalization, mathematical and simulation modeling.Results. As a result of the review of device positioning methods during the transition to 6G networks, key performance indicators and LDT scenarios are updated. As a result of the comparative analysis of 5G and 6G networks, new factors, advantages and disadvantages of positioning technologies during the transition from millimeter wave networks to terahertz networks are systematized. A formalized mathematical model for collecting primary measurements is used in the simulation model for assessing the accuracy of device positioning in the second part of the cycle.Novelty. This cycle is the first such study in the Russian scientific segment on network positioning of the sixth generation of the terahertz range, in which the author's version provides an overview of methods and a systematization of a set of new factors of the OMP in communication networks.The theoretical significance of the review-analysis lies in the establishment of both technological obstacles and new opportunities for increasing positioning accuracy during the transition to 6G networks.The practical significance of the formalized mathematical model lies in its subsequent software implementation for numerical justification of the limits of positioning accuracy in 6G networks.

Progress on CRISPR-Cas gene editing technology in sheep production.

Gene editing is a kind of genetic engineering technology that can modify the genome. In recent years, with the rapid development of molecular biotechnology, the clustered regularly interspaced short palindromic repeats associated protein system has been widely used as a powerful gene editing tool due to its high efficiency, accuracy and flexibility. The CRISPR-Cas system makes a significant contribution to different aspects of livestock production by introducing site-specific modifications such as insertions, deletions or single base replacements at specific genomic sites. In terms of sheep production applications, by establishing animal models that improve production economic traits and disease resistance, the function of key genes can be studied to accelerate the improvement of traits, thereby accelerating the improvement of traits. In this review, we summarize the mechanism and function of CRISPR-Cas system and its application in the production of reproductive traits, meat use traits, wool production traits, lactation traits and disease resistance traits of sheep and the establishment of sheep animal models.

Patterns of Locoregional Pancreatic Cancer Recurrence After Total Neoadjuvant Therapy and Implications on Optimal Neoadjuvant Radiation Treatment Volumes

PurposeThis study aimed to generate a map of local recurrences after neoadjuvant chemotherapy and radiation (total neoadjuvant therapy [TNT]) followed by surgical resection for pancreatic ductal adenocarcinoma (PDAC). Such recurrence patterns will serve to inform radiation treatment planning volumes that should be given in the neoadjuvant setting. Methods and MaterialsLocoregional recurrences after TNT followed by surgery treated between 2009 and 2022 were radiologically identified. Recurrences were individually segmented using MIM software and complied in a single base scan. All contour compilations were used to create a threshold contour encompassing 80% of recurrences among all patients, head only, and body/tail only. The distance between organs at risk and the threshold contour were measured to design an optimal clinical target volume contour for patients treated with TNT. Recurrence patterns were also compared with existing adjuvant guidelines to assess coverage. ResultsA database of 484 patients managed with TNT for PDAC was queried. While locoregional recurrences were rare in this cohort, we identified 80 patients with either isolated locoregional or simultaneous local and distant recurrences. Patients with diagnostic imaging at the time of recurrence were identified. The majority of recurrences were partially in the field of published contouring guidelines or volumetric expansions off of vessels, and volumetric coverage was low for all. Common areas of recurrence include the aorticodiaphragmatic junction, retropancreatic duodenal nodal basin, and the region to the right of the superior mesenteric artery. A novel set of proposed neoadjuvant contours was designed to cover the central-most 80% of recurrences. ConclusionsThis is the largest collection of local/regional PDAC recurrences from a cohort of patients treated exclusively with TNT. Patterns of local/regional recurrence using TNT in PDAC vary significantly from those patients with PDAC treated with a surgery-first approach. Novel contouring guidelines presented in this study can help to ensure optimal coverage of high risk regions and avoid reliance on the current adjuvant guidelines to guide treatment planning.

MGFmiRNAloc: Predicting miRNA Subcellular Localization Using Molecular Graph Feature and Convolutional Block Attention Module.

MiRNA has distinct physiological functions at various cellular locations. However, few effective computational methods for predicting the subcellular location of miRNA exist, thereby leaving considerable room for improvement. Accordingly, our study proposes the MGFmiRNAloc simplified molecular input line entry system (SMILES) format as a new approach for predicting the subcellular localization of miRNA. Additionally, the graphical convolutional network (GCN) technique was employed to extract the atomic nodes and topological structure of a single base, thereby constructing RNA sequence molecular map features. Subsequently, the channel attention and spatial attention mechanisms (CBAM) were designed to mine deeper for more efficient information. Finally, the prediction module was used to detect the subcellular localization of miRNA. The 10-fold cross-validation and independent test set experiments demonstrate that MGFmiRNAloc outperforms the most sophisticated methods. The results indicate that the new atomic level feature representation proposed in this study could overcome the limitations of small samples and short miRNA sequences, accurately predict the subcellular localization of miRNAs, and be extended to the subcellular localization of other sequences.