Artificial Intelligence Analysis of Gene Expression Predicted the Overall Survival of Mantle Cell Lymphoma and a Large Pan-Cancer Series

Mantle cell lymphoma (MCL) is a subtype of mature B-cell non-Hodgkin lymphoma characterized by a poor prognosis. First, we analyzed a series of 123 cases (GSE93291). An algorithm using multilayer perceptron artificial neural network, radial basis function, gene set enrichment analysis (GSEA), and conventional statistics, correlated 20,862 genes with 28 MCL prognostic genes for dimensionality reduction, to predict the patients’ overall survival and highlight new markers. As a result, 58 genes predicted survival with high accuracy (area under the curve = 0.9). Further reduction identified 10 genes: KIF18A, YBX3, PEMT, GCNA, and POGLUT3 that associated with a poor survival; and SELENOP, AMOTL2, IGFBP7, KCTD12, and ADGRG2 with a favorable survival. Correlation with the proliferation index (Ki67) was also made. Interestingly, these genes, which were related to cell cycle, apoptosis, and metabolism, also predicted the survival of diffuse large B-cell lymphoma (GSE10846, n = 414), and a pan-cancer series of The Cancer Genome Atlas (TCGA, n = 7289), which included the most relevant cancers (lung, breast, colorectal, prostate, stomach, liver, etcetera). Secondly, survival was predicted using 10 oncology panels (transcriptome, cancer progression and pathways, metabolic pathways, immuno-oncology, and host response), and TYMS was highlighted. Finally, using machine learning, C5 tree and Bayesian network had the highest accuracy for prediction and correlation with the LLMPP MCL35 proliferation assay and RGS1 was made. In conclusion, artificial intelligence analysis predicted the overall survival of MCL with high accuracy, and highlighted genes that predicted the survival of a large pan-cancer series

Evaluating zero error noise thresholds by the replica method for Gallager code ensembles

The zero error noise threshold for Gallager code ensemblers were evaluated by using replica method (RM). The RM, which was invented in statistical physics, offered an option for calculating the bound. It was shown that the given approach provided more optimistic evaluations with respect to the evaluations provided by the information theory literature for sparse matrices

The Yamato nakhlite consortium

Among 3550 meteorite samples found near the Yamato Mountains area during the field season of 2000-2001, three meteorites, Yamato (Y) 000593, Y000749, and Y000802 of total weight of about 15 kg, are identified as new paired nakhlites. In ordered to improve our knowledge of the nakhlite parent body, possibly Mars, a coordinated consortium study of the Yamato nakhlites was organized. We here present an outline of the Yamato nakhlite consortium and implications for Martian geological history on the basis of ongoing studies

The diagnosis of delayed expanding traumatic pseudoaneurysm of thoracic aorta caused by self-inflicted penetrating injury with crossbow bolt: A case report

Introduction and importance: Penetrating chest trauma caused by a crossbow bolt is very rare. Herein, we report a successfully treated patient who attempted suicide by directing a crossbow to the chest cavity and developed an expanding pseudoaneurysm of the thoracic aorta during eight-day follow up. Case presentation: A 51-year-old male was admitted to the emergency department after firing a crossbow bolt twice into his left chest. At admission, the patient was hemodynamically stable and maintaining oxygenation. The bolt had already been removed from the body. Contrast-enhanced computed tomography (CT) revealed a cavity pseudoaneurysm 2.5 mm in size in the aortic arch. Three-dimensional reconstruction of the CT demonstrated wound tracts showing probable damage by the bolt. The patient was admitted to the emergency department for careful observation and transferred to the psychiatric ward on day two. Follow-up contrast-enhanced CT on day eight demonstrated rapid expansion of the pseudoaneurysm from 2.5 mm to 4.0 mm in size. We performed thoracic endovascular aortic repair (TEVAR) on day 13. The patient was uneventfully discharged on the 20th hospital day. Clinical discussion: Emergency physicians should be aware that damage to the surrounding tissue may be accompanied by delayed expansion of an aortic pseudoaneurysm, even if the bolts do not cause direct aortic wall injury. Conclusion: This case suggests that understanding the injury mechanism, confirming the tract of the bolts, and carefully exploring traumatic pseudoaneurysm can lead to a less invasive operation due to early detection

Effects of geological structures on rainfall‐runoff responses in headwater catchments in a sedimentary rock mountain

Clarifying rainfall-runoff responses in mountainous areas is essential for disaster prediction as well as water resource management. Although runoff is considered to be significantly affected by topography, some previous studies have reported that geological structures also have significant effects on rainfall-runoff characteristics. Particularly in headwater catchments located in sedimentary rock mountains, dips and strikes may significantly affect rainwater discharge. In this study, the effects of geological structures on rainfall-runoff characteristics were investigated based on observed discharge hydrographs from 12 catchments, which lie radially from the summit of a sedimentary rock mountain. The results obtained were as follows: (1) Even though the topographic wetness index (TWI) distributions of the 12 catchments were similar, there were significant differences in their runoff characteristics; (2) Catchments with average flow direction oriented towards the strike direction (strike-oriented catchments) are characterized by large baseflows; (3) Catchments with average flow direction oriented towards the opposite dip direction (opposite dip-oriented catchments) are steep, and this results in quick storm runoff generation; (4) Catchments with average flow direction oriented toward the dip direction (dip-oriented catchments) are gentle, and this results in delayed storm runoff generation. It was presumed that in strike-oriented catchments, large quantities of groundwater flowing along the bedding planes owing to hydraulic anisotropy, exfiltrate and sustain the large amount of the observed baseflow, that is, in strike-oriented catchments, runoff is directly controlled by geological structures. Conversely, in opposite dip-oriented and dip-oriented catchments, runoff is indirectly controlled by geological structures, that is, geological structures affect slope gradients, which result in differences in storm runoff generation. Thus, this study clearly illustrates that geological structures significantly affect rainfall-runoff responses in headwater catchments located in sedimentary rock mountains

Artificial intelligence and classification of mature lymphoid neoplasms

Hematologists, geneticists, and clinicians came to a multidisciplinary agreement on the classification of lymphoid neoplasms that combines clinical features, histological characteristics, immunophenotype, and molecular pathology analyses. The current classification includes the World Health Organization (WHO) Classification of tumours of haematopoietic and lymphoid tissues revised 4th edition, the International Consensus Classification (ICC) of mature lymphoid neoplasms (report from the Clinical Advisory Committee 2022), and the 5th edition of the proposed WHO Classification of haematolymphoid tumours (lymphoid neoplasms, WHO-HAEM5). This article revises the recent advances in the classification of mature lymphoid neoplasms. Artificial intelligence (AI) has advanced rapidly recently, and its role in medicine is becoming more important as AI integrates computer science and datasets to make predictions or classifications based on complex input data. Summarizing previous research, it is described how several machine learning and neural networks can predict the prognosis of the patients, and classified mature B-cell neoplasms. In addition, new analysis predicted lymphoma subtypes using cell-of-origin markers that hematopathologists use in the clinical routine, including CD3, CD5, CD19, CD79A, MS4A1 (CD20), MME (CD10), BCL6, IRF4 (MUM-1), BCL2, SOX11, MNDA, and FCRL4 (IRTA1). In conclusion, although most categories are similar in both classifications, there are also conceptual differences and differences in the diagnostic criteria for some diseases. It is expected that AI will be incorporated into the lymphoma classification as another bioinformatics tool

Differential quantification of CYP2D6 gene copy number by four different quantitative real-time PCR assays

Copy number variations (CNVs) in the CYP2D6 gene contribute to interindividual variation in drug metabolism. As the most common duplicated allele in Asian populations is the nonfunctional CYP2D6*36 allele, the goal of this study was to identify CNV assays that can differentiate between multiple copies of the CYP2D6*36 allele and multiple copies of other CYP2D6 alleles. We determined CYP2D6 gene copy numbers in 32 individuals with known CYP2D6 CNVs from the Coriell Japanese-Chinese panel using four quantitative real-time PCR assays. These assays target different regions of the CYP2D6 gene: 5'-flanking region, intron 2, intron 6, and exon 9 (Ex9). The specific target site of the Ex9 assay was verified by sequencing the PCR amplicon. Three of the CYP2D6 CNV assays (5'-flanking region, intron 2, and intron 6) estimated CYP2D6 copy numbers that were concordant for all 32 individuals. However, the Ex9 assay was concordant in only 10 of 32 samples. The 10 concordant samples did not contain any CYP2D6*36 alleles and the 22 discordant samples contained at least one CYP2D6*36 allele. In addition, the Ex9 assay accurately quantified all of the non-CYP2D6*36 alleles in all samples. Ex9 amplicon sequencing indicated that it targets a region of CYP2D6 exon 9 that undergoes partial gene-conversion in the CYP2D6*36 allele. In conclusion, CYP2D6 Ex9 CNV assay can be used to determine the copy number of non-CYP2D6*36 alleles. Selective amplification of non-CYP2D6*36 sequence by the Ex9 assay should be useful in determining the number of functional copies of CYP2D6 in Asian populations

Controlled structure of anatase TiO2 nanoparticles by using organic additives in a microwave process

Synthesis of anatase nanoparticles was carried out in a microwave system. Crystal morphology was controlled by organic additives including PAAc (polyacrylic acid) and PVP (polyvinylpyrrolidone). Modified TiO2 particles were compared to the bare TiO2 anatase structure. The synthesis of materials via the microwave system has great advantages due to the short reaction period and low energy requirement and is therefore an environmentally friendly process compared to the hydrothermal process. The decomposition of acetaldehyde was studied to determine the photocatalytic activity of the modified anatase TiO2 material