Development and validation of a machine learning model to predict time to renal replacement therapy in patients with chronic kidney disease.

BACKGROUND: Predicting time to renal replacement therapy (RRT) is important in patients at high risk for end-stage kidney disease. We developed and validated machine learning models for predicting the time to RRT and compared its accuracy with conventional prediction methods that uses the rate of estimated glomerular filtration rate (eGFR) decline. METHODS: Data of adult chronic kidney disease (CKD) patients who underwent hemodialysis at Oita University Hospital from April 2016 to March 2021 were extracted from electronic medical records (N = 135). A new machine learning predictor was compared with the established prediction method that uses the eGFR decline rate and the accuracy of the prediction models was determined using the coefficient of determination (R2). The data were preprocessed and split into training and validation datasets. We created multiple machine learning models using the training data and evaluated their accuracy using validation data. Furthermore, we predicted the time to RRT using a conventional prediction method that uses the eGFR decline rate for patients who had measured eGFR three or more times in two years and evaluated its accuracy. RESULTS: The least absolute shrinkage and selection operator regression model exhibited moderate accuracy with an R2 of 0.60. By contrast, the conventional prediction method was found to be extremely low with an R2 of -17.1. CONCLUSIONS: The significance of this study is that it shows that machine learning can predict time to RRT moderately well with continuous values from data at a single time point. This approach outperforms the conventional prediction method that uses eGFR time series data and presents new avenues for CKD treatment.

Histological classification of Japanese IgA nephropathy with a small number of glomeruli using Bayes' theorem.

In Japan an original pathological classification of IgA nephropathy was used, while Oxford classification of IgA nephropathy was used globally. The Oxford classification requires ≥ 8 glomeruli while the Japanese classification requires ≥ 10. Ninety-nine patients diagnosed with IgA nephropathy were included. To determine the accuracy of histological staging, we calculated the posterior probability using Bayes' theorem and adopted three model of prior distribution. First, the actual staging distribution was reclassified using the beta distribution (reclassified distribution). Second a model with the same distribution (actual distribution) as the actual staging was used. Third, a model assuming that all cases are equally distributed (equal distribution) was used. The median number of collected glomeruli was 12 (8-19). There were 33 cases (33%) wherein the glomerular count was ≤ 9. When only cases with ≥ 10 glomeruli were included, the median posterior probability was 91% (74-99) (actual distribution, 90% [74-98]; equal distribution, 85% [73-96]). Even among the 33 cases with ≤ 9 glomeruli, there were approximately 7 cases in which the posterior probability was ≥ 90% for each model. Using Bayesian probabilistic analysis, it was possible to evaluate the histologic classification of IgA nephropathy, even when the number of obtained glomeruli was ≤ 9.

Glycosylation and Methylation of Quercetin and Myricetin by Cultured Cells of Phytolacca americana.

The glycosylation and methylation of quercetin by cultured plant cells of Phytolacca americana gave quercetin 3-Ο-ß-D-glucoside and isorharnnetin 3-Ο-ß-D- glucoside. Myricetin was glycosylated and methylated to syringetin 3-Ο-ß-D-glucoside by cultured P. americana cells.

Hydroxylation and Glycosylation of Phenylpropanoids by Cultured Cells of Phytolacca americana.

Hydroxylation and glycosylation of cinnamic acid, p-coumaric acid, caffeic acid, and ferulic acid were investigated using cultured plant cells of Phytolacca americana as biocatalysts. Regioselective hydroxylation at the 4-position of cinnamic acid and 3-position of p-coumaric acid was observed. Although cinnamic acid was transformed to mono-glucoside products, di-glycosylation occurred in the case of the biotransformation of p-coumaric acid, caffeic acid, and ferulic acid.

Glycosylation of Chrysin by Cultured Cells of Eucalyptus perriniana.

The biotransformation of chrysin was investigated using cultured plant cells of Eucalyptus perriniana as biocatalysts. Chrysin was glucosylated to chrysin 7- 0-ß-D-glucoside and chrysin 7-ß-p-gentiobioside.

Synthesis and pharmacological evaluation of glycosides of resveratrol, pterostilbene, and piceatannol.

To enhance their water solubility and pharmacological activities, the stilbenes resveratrol, pterostilbene, and piceatannol were glycosylated to their monoglucosides (ß-glucosides) and diglycosides (ß-maltosides) by cultured cells and cyclodextrin glucanotransferase (CGTase). Cultured cells of Phytolacca americana and glucosyltransferase (PaGT) were capable of glucosylation of resveratrol to its 3- and 4'-ß-glucosides. Pterostilbene was slightly transformed into its 4'-ß-glucoside by P. americana cells. Piceatannol was readily converted into piceatannol 4'-ß-glucoside, with the highest yield among the three substrates. The 3- and 4'-ß-glucosides of resveratrol were subjected to further glycosylation by CGTase to give 3- and 4'-ß-maltoside derivatives. The inhibitory action of resveratrol and pterostilbene toward histamine release induced with compound 48/80 from rat peritoneal mast cells was improved by ß-glucosylation and/or ß-maltosylation (i.e., the inhibitory activity for histamine release of the 3- and 4'-ß-glucosides of resveratrol, the 3- and 4'-ß-maltosides of resveratrol, and the 4'-ß-glucoside of pterostilbene was higher than that of the corresponding aglycones, resveratrol and pterostilbene, respectively). In addition, the phosphodiesterase (PDE) inhibitory activity of resveratrol and pterostilbene was enhanced by ß-glucosylation and/or ß-maltosylation (i.e., the PDE inhibitory activities of the 3- and 4'-ß-glucosides of resveratrol, the 4'-ß-maltoside of resveratrol, and the 4'-ß-glucoside of pterostilbene were higher than those of the corresponding aglycones, resveratrol and pterostilbene, respectively).

Regioselective Glycosylation of 3-, 5-, 6-, and 7-Hydroxyflavones by Cultured Plant Cells.

Regioselective glycosylation of 3-, 5-, 6-, and 7-hydroxyflavones was investigated using cultured plant cells of Eucalyptus perriniana and Phytolacca americana as biocatalysts. 3- and 7-Hydroxyflavones were practically glycosylated into the corresponding ß-D-glucosides by E. perriniana and P. americana.

Glycosylation of quercetin with cultured plant cells and cyclodextrin glucanotransferase.

Quercetin was glucosylated by cultured plant cells of lpomoea batatas to its 3- and 7-O-beta-D-glucosides, and 3,7-O-beta-D-diglucoside. On the other hand, further glycosylation of quercetin 3-O-beta-D-glucoside by cyclodextrin glucanotransferase gave the 3-O-beta-maltoside, 3-O-beta-maltotrioside, and 3-O-[beta-maltotetraosides of quercetin.

Downregulation of SAV1 plays a role in pathogenesis of high-grade clear cell renal cell carcinoma.

BACKGROUND: Clinical outcome of patients with high-grade ccRCC (clear cell renal cell carcinoma) remains still poor despite recent advances in treatment strategies. Molecular mechanism of pathogenesis in developing high-grade ccRCC must be clarified. In the present study, we found that SAV1 was significantly downregulated with copy number loss in high-grade ccRCCs. Therefore, we investigated the SAV1 function on cell proliferation and apoptosis in vitro. Furthermore, we attempted to clarify the downstream signaling which is regulated by SAV1. METHODS: We performed array CGH and gene expression analysis of 8 RCC cell lines (786-O, 769-P, KMRC-1, KMRC-2, KMRC-3, KMRC-20, TUHR4TKB, and Caki-2), and expression level of mRNA was confirmed by quantitative RT-PCR (qRT-PCR) analysis. We next re-expressed SAV1 in 786-O cells, and analyzed its colony-forming activity. Then, we transfected siRNAs of SAV1 into the kidney epithelial cell line HK2 and renal proximal tubule epithelial cells (RPTECs), and analyzed their proliferation and apoptosis. Furthermore, the activity of YAP1, which is a downstream molecule of SAV1, was evaluated by western blot analysis, reporter assay and immunohistochemical analysis. RESULTS: We found that SAV1, a component of the Hippo pathway, is frequently downregulated in high-grade ccRCC. SAV1 is located on chromosome 14q22.1, where copy number loss had been observed in 7 of 12 high-grade ccRCCs in our previous study, suggesting that gene copy number loss is responsible for the downregulation of SAV1. Colony-forming activity by 786-O cells, which show homozygous loss of SAV1, was significantly reduced when SAV1 was re-introduced exogenously. Knockdown of SAV1 promoted proliferation of HK2 and RPTEC. Although the phosphorylation level of YAP1 was low in 786-O cells, it was elevated in SAV1-transduced 786-O cells. Furthermore, the transcriptional activity of the YAP1 and TEAD3 complex was inhibited in SAV1-transduced 786-O cells. Immunohistochemistry frequently demonstrated nuclear localization of YAP1 in ccRCC cases with SAV1 downregulation, and it was preferentially detected in high-grade ccRCC. CONCLUSIONS: Taken together, downregulation of SAV1 and the consequent YAP1 activation are involved in the pathogenesis of high-grade ccRCC. It is an attractive hypothesis that Hippo signaling could be candidates for new therapeutic target.

MicroRNA-375 is downregulated in gastric carcinomas and regulates cell survival by targeting PDK1 and 14-3-3zeta.

We investigated expression profiles of microRNA (miRNA) in gastric carcinomas by use of a miRNA microarray platform covering a total of 470 human miRNAs. We identified 39 differentially expressed miRNAs in gastric carcinoma, of which six were significantly downregulated and the other 33 were upregulated. We found that miRNA-375 (miR-375) was the most downregulated and that its ectopic expression in gastric carcinoma cells markedly reduced cell viability via the caspase-mediated apoptosis pathway. Interestingly, we found that expression of miR-375 inhibited expression of PDK1, which is a direct target of miR-375, followed by suppression of Akt phosphorylation. Further analysis by gene expression microarray revealed that 14-3-3zeta, a potent antiapoptotic gene, was significantly downregulated at both the mRNA and protein levels in cells transfected with miR-375. The activity of a luciferase reporter containing the miR-375 binding sequence at the 3' untranslated region (UTR) of 14-3-3zeta mRNA was repressed by the ectopic expression of miR-375, suggesting that miR-375 targets the 3' UTR of 14-3-3zeta. In addition, knockdown of either PDK1 or 14-3-3zeta in gastric carcinoma cells induced caspase activation, which was also observed in miR-375-transfected cells, suggesting that miR-375 may exert its proapoptotic function, at least in part, through the downregulation of PDK1 and 14-3-3zeta. Taken together, we propose that miR-375 is a candidate tumor suppressor miRNA in gastric carcinoma.

Genomic profiling of gastric carcinoma in situ and adenomas by array-based comparative genomic hybridization.

Although genomic copy number aberrations (CNAs) of gastric carcinoma at the advanced stage have already been extensively characterized by array comparative genomic hybridization (array CGH) analysis, those of gastric carcinoma in situ (CIS) are still poorly understood. Furthermore, no reports have demonstrated correlations between CNAs and histopathological features of gastric adenoma. In this study, we investigated CNAs of 20 gastric CISs (Vienna category 4.2) and 20 adenomas including seven low-grade adenomas (LGA; Vienna category 3) and 13 high-grade adenomas (HGA; Vienna category 4.1), using oligonucleotide-based array CGH. The most frequent aberrations in CIS were gains at 8q (85%) and 20q (50%), and losses at 5q (50%) and 17p (50%), suggesting that these CNAs are involved in the development of CIS. We found that the pattern of CNAs in HGA was quite different from that in LGA. The most frequent CNAs in HGA were gains at 8q (62%) and 7pq (54%), whereas those in LGA were gain at 7q21.3-q22.1 (57%) and loss at 5q (43%). Interestingly, gains at 8q and 7pq, both of which occurred most frequently in HGA, were not detected in any cases of LGA. Of note, 8q gain was detected most frequently in both HGA and CIS but was undetected in LGA. Since HGA is believed to have a higher risk of progression to invasive carcinoma than LGA, these data suggest that 8q gain is important for the malignant transformation of gastric adenoma.

A novel diagnostic monoclonal antibody specific for Helicobacter pylori CagA of East Asian type.

Molecular biological and epidemiological studies have suggested that Helicobacter pylori producing East Asian CagA protein variant is more virulent than that producing Western CagA. In the present study, we developed and validated an enzyme-linked immunosorbent assay (ELISA) using a monoclonal antibody specifically recognizing East Asian CagA-positive H. pylori. A total of 32 H. pylori strains were tested and the data were subjected to receiver-operator characteristic (ROC) curve analysis. The accuracy of the test, determined by calculating the area under the curve, was 0.96, which indicated a high level of accuracy. At the ROC optimized cutoff, the sensitivity and specificity of our ELISA method were 88.0% and 100%, respectively. The validated ELISA showed good performance in terms of sensitivity and specificity. These results suggest that this test is suitable for the diagnostic detection of East Asian CagA carrying strains. We also analyzed the localization of the CagA protein in H. pylori-infected gastric mucosa with fluorescence immunohistochemistry, and found that CagA protein expression was up-regulated by adhesion to epithelial cells.

Electrooptics of beta-FeOOH particle in aqueous media 2. Field-strength dependence of decay and steady-state birefringence, and the hydrodynamic and electrooptic properties.

Steady-state and decay birefringence, expressed in terms of the optical phase retardation per cell length delta/d, was measured on beta-FeOOH in aqueous ionic media at 633 nm and at 25 degrees C by an electric square-pulse technique over a wide range of field strength E to ca. 6 kV/cm. The field-strength dependence of both delta/d and field-free rotational relaxation time tau was determined at the sample concentrations between 0.0011 and 0.055 g/L and in the 0.02-2.0 mM NaCl concentration range. Extrapolation of both delta/d and tau values to infinitely high fields (E(2)-->infinity) could yield birefringence- and weight-average quantities, respectively. Observed tau values were decreased at weak fields but leveled off to ca. 0.3 ms at very high fields due to a slight polydispersity regarding the length and volume of particles. The weight-average relaxation time tau(w) was calculated with Perrin's expressions theoretically from the length, width, and volume of beta-FeOOH particles estimated in the dried state from electron micrograph. These quantities were variously averaged. The size distribution was discussed in terms of observed discrete histogram and theoretical (Weibull and Lansing-Kraemer) distribution functions. The sign of observed delta/d value was always positive. The infinitely high-field (delta/d)(infinity) values and the reduced optical anisotropy factor Delta g/n were evaluated by fitting to theoretical orientation functions. The intrinsic birefringence (n3-n1) could be estimated with the mean refractive index n(p) reported in the literature. For the spindle-shaped particle with an axial ratio of ca. 4, the sign of Delta g/n is always positive, whereas the quantity (n3-n1) was either negative (n(p) > 2.35) or positive (n(p) < 2.05) in sign or nearly zero (ca. n(p) = 2.26), depending critically on the n(p) values.