AXEAP: a software package for X-ray emission data analysis using unsupervised machine learning.

The Argonne X-ray Emission Analysis Package (AXEAP) has been developed to calibrate and process X-ray emission spectroscopy (XES) data collected with a two-dimensional (2D) position-sensitive detector. AXEAP is designed to convert a 2D XES image into an XES spectrum in real time using both calculations and unsupervised machine learning. AXEAP is capable of making this transformation at a rate similar to data collection, allowing real-time comparisons during data collection, reducing the amount of data stored from gigabyte-sized image files to kilobyte-sized text files. With a user-friendly interface, AXEAP includes data processing for non-resonant and resonant XES images from multiple edges and elements. AXEAP is written in MATLAB and can run on common operating systems, including Linux, Windows, and MacOS.

Glucose transporter polymorphisms are associated with clear-cell renal carcinoma.

Clear-cell renal cell carcinoma (CCRCC) is identified by abundant glycogen-rich cytoplasm, due to the aberrant influx and storage of glucose. The objective was to investigate the frequency of polymorphisms of the facilitative glucose transporter (GLUT1). GLUT1 is a downstream target of Hypoxia-inducible factor (HIF-1alpha), a mediator of hypoxia-controlled angiogenesis. In this study, we examine the allelic frequency of polymorphisms in the promoter and the second intron of the GLUT1 gene. Genomic DNA was extracted from normal tissue of 92 patients undergoing nephrectomy for CCRCC, and 99 normal cord blood DNA samples were used to provide control frequencies. The regions of DNA encompassing the polymorphisms were amplified and digested with appropriate endonuclases. The products were separated and viewed by gel electrophoresis. There was a highly significant decrease in the A-2841 genotype (P=0.0004) in the promoter region of those patients with CCRCC compared to the control population. There was also a significant decrease in the T+22999 allele in the intron 2 of those patents with CCRCC (P=0.004) compared to the same control population. This study suggests that GLUT1 is one of a number of genes that may increase susceptibility to developing CCRCC.

Polymorphisms in the hypoxia inducible factor-1alpha gene (HIF1A) are associated with the renal cell carcinoma phenotype.

Hypoxia inducible factor 1 (HIF-1) is a key regulator of the genes involved in the cellular response to hypoxia. HIF consists of alpha and beta subunits, with the alpha subunit being degraded under normoxic conditions and stabilized under hypoxia. We investigated C1772T and G1790A polymorphisms in exon 12 of the HIF gene, which result in an amino acid change from proline 582 to serine and from alanine 588 to threonine, respectively. These polymorphisms are found within the oxygen-dependent degradation domain of the HIF-1alpha protein and may be important in the oxygen regulation of the protein via hydroxylation of the proline residue at position 564 (P564) by HIF-alpha prolyl hydroxylase (HIF-PH). The frequency of these polymorphisms was studied in 160 nontumor DNA samples from patients with renal cell carcinoma (RCC). There was a highly significant increase in the frequency of both the G/A1790 (45.9 vs. 13.5%, P < 0.00001) and C/C1772 (10 vs. 0.7%, P=0.0004) genotypes in patients with RCC compared with normal healthy controls. A decrease was seen for the GG (44.5 vs. 83%, P < 0.00001) and CT (33.8 vs. 55.5%, P=0.0001) genotypes in patients compared with controls. There was a marked increase in the T-A haplotype (22.8 vs. 9.5%, P=0.00008) and an increase in the C-A haplotype (4.9 vs. 1.1%, P=0.02) in patients compared with controls, and a decrease in the T-G haplotype (53.4 vs. 65.1%, P=0.01). No statistical difference was found for the other haplotypes. These findings show that polymorphisms of the HIF1A gene may confer susceptibility to RCC.