Radiation therapy with neutrons and hydrons of the liver region using the MCNP code: المعالجة الاشعاعية بالنترونات والهدرونات لمنطقة الكبد باستخدام الكود MCNP

CT images were read and a 3D model of the tumor was created in the liver area, Then the values ​​of the radiation dose in terms of the depth resulting from (photons, neutrons and protons) were estimated and studied using the code (MCNP) after entering the data into it. The value of the radiation dose in terms of depth and curvature in photons, neutrons and protons radiation therapy was studied, from our findings in the research we note that protons are the best option for radiation therapy for high-depth liver cancer of photons and neutrons due to the lower dose at entry compared to the dose absorbed in the tumor area and its ability to deliver a greater amount of dose of neutrons and photons to the tumor area. We note that the values reached are acceptable for the treatment of tumors at a depth close to the surface. As for a large-depth tumor, it is necessary to increase high-energy radiation doses deep in the tumor area by accelerating proton therapy to protect natural organs from high-energy radiation doses.

Limited allele-specific gene expression in highly polyploid sugarcane

Polyploidy is widespread in plants allowing the different copies of genes to be expressed differently in a tissue specific or developmental specific way. This allele-specific expression (ASE) has been widely reported but the proportion and nature of genes showing this characteristic have not been well defined. We now report an analysis of the frequency and patterns of ASE at the whole genome level in the highly polyploid sugarcane genome. Very high-depth whole genome sequencing and RNA sequencing revealed strong correlations between allelic proportions in the genome and in expressed sequences. This level of sequencing allowed discrimination of each of the possible allele doses in this 12-ploid genome. Most genes were expressed in direct proportion to the frequency of the allele in the genome with examples of polymorphisms being found with every possible discrete level of dose from 1:11 for single copy alleles to 12:0 for monomorphic sites. The rarer cases of ASE were more frequent in the expression of defense-response genes, as well as in some processes related to the biosynthesis of cell walls. ASE was more common in genes with variants that resulted in significant disruption of function. The low level of ASE may reflect the recent origin of polyploid hybrid sugarcane. Much of the ASE present can be attributed to strong selection for resistance to diseases in both nature and domestication.

Population genomic analysis provides strong evidence of the past success and future strategies of South China tiger breeding

The South China tigers (Panthera tigris amoyensis) are extinct in the wild, but viable populations remain in breeding centers and zoos after 60 years of effective conservation efforts. At present, however, the existing genetic variation of these tigers remains unknown. In this study, we assembled a high-quality chromosome-level genome using long-read sequences and re-sequenced 29 high-depth genomes of the South China tigers. We identified two significantly differentiated genomic ancestries in the extant populations, which also harbored some rare genetic variants introgressed from other subspecies, suggesting limited but essential genetic diversity to sustain the South China tigers. The unique pattern of dual ancestry and the genomic resources generated in our study pay the way for a genomics-informed conservation, following the real-time monitoring and controlled exchange of all reproductive South China tigers.

A Deep-Learning Pipeline for TSS Coverage Imputation From Shallow Cell-Free DNA Sequencing

Cell-free DNA (cfDNA) serves as a footprint of the nucleosome occupancy status of transcription start sites (TSSs), and has been subject to wide development for use in noninvasive health monitoring and disease detection. However, the requirement for high sequencing depth limits its clinical use. Here, we introduce a deep-learning pipeline designed for TSS coverage profiles generated from shallow cfDNA sequencing called the Autoencoder of cfDNA TSS (AECT) coverage profile. AECT outperformed existing single-cell sequencing imputation algorithms in terms of improvements to TSS coverage accuracy and the capture of latent biological features that distinguish sex or tumor status. We built classifiers for the detection of breast and rectal cancer using AECT-imputed shallow sequencing data, and their performance was close to that achieved by high-depth sequencing, suggesting that AECT could provide a broadly applicable noninvasive screening approach with high accuracy and at a moderate cost.

NPGREAT: Assembly of the human subtelomere regions with the use of ultralong Nanopore reads and Linked-Reads

Background Human subtelomeric DNA regulates the length and stability of adjacent telomeres that are critical for cellular function, and contains many gene/pseudogene families. Large evolutionarily recent segmental duplications and associated structural variation in human subtelomeres has made complete sequencing and assembly of these regions difficult to impossible for many loci, complicating or precluding a wide range of genetic analyses to investigate their function. Results We present a hybrid assembly method, NanoPore Guided REgional Assembly Tool (NPGREAT), which combines Linked-Read data with ultralong nanopore reads spanning subtelomeric segmental duplications to potentially overcome these difficulties. Linked-Read sets identified by matches with 1-copy subtelomere sequence adjacent to segmental duplications are assembled and extended into the segmental duplication regions using Regional Extension of Assemblies using Linked-Reads (REXTAL). Telomere-containing ultralong nanopore reads are then used to provide contiguity and correct orientation for matching REXTAL sequence contigs as well as identification/correction of any misassemblies (associated primarily with tandem repeats). While we focus on subtelomeres, the method is generally applicable to assembly of segmental duplications and other complex genome regions. Our method was tested for a subset of representative subtelomeres with ultralong nanopore read coverage in GM12878. 10X Linked-Read datasets with high depth of coverage and a TELL-seq Linked-Read dataset with lower depth of coverage were each combined with the ultralong nanopore reads from the same genome to provide improved assemblies. Tandem repeat regions of the short-read assemblies, which are especially prone to misassembly due to collapse of matching tandemly repeated reads, were readily identified and properly sized by comparison with the nanopore reads. Conclusion The NPGREAT method resulted in extension of high-quality assemblies into otherwise inaccessible segmental duplication regions near telomeres, enhancing our ability to accurately assemble human subtelomere DNA. This information will enable improved analyses of the structure, function, and evolution of these key regions.

The Promise of Turning Induced Deformation Process for Synthesizing Magnesium Based Materials with Superior Mechanical Response

In recent times, an alternative synthesis pathway involving severe plastic deformation for Mg-based materials has been explored involving the generation of turnings according to a set of machining parameters and cold compaction into billets followed by hot extrusion. This is known as the turning induced deformation (TID) method and has shown potential to alter the properties of resulting Mg-based materials for the better, not to mention economic benefits arising from this processing method. This work summarizes exploratory efforts involving this method for synthesis of Mg-based materials. The TID method resulted in overall superior properties compared to conventional processing methods, while two distinct parameters (high depth of cut and low cutting speed) were found to have significant positive influence on the final material properties, and as such are considered to be suitable basis on which further exploratory work in this field may be conducted.