Elucidation a possible mechanism of kidney stone formation by using a MetS mouse model and to assess the effectiveness of adiponectin treatment in preventing kidney stones.
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE37173 | GEO | 2013/03/31
SECONDARY ACCESSION(S): PRJNA158609
REPOSITORIES: GEO
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Project description:we performed genome-wide expression analyses for investigating novel genetic environmental changes. 5 samples
2013-03-31 | E-GEOD-37173 | biostudies-arrayexpress
Project description:IntroductionKidney Stone Calculator (KSC) is a free, three-dimensional (3D) planning software for flexible ureteroscopy(fURS) with Holmium:YAG(Ho:YAG) endocorporeal lithotripsy (EL). KSC provides the stone volume (SV) and expected duration of lithotripsy (ExDL) estimations based on non-enhanced-CT scan (NECT) DICOM series. We aimed to provide a preclinical and clinical evaluation of KSC.Patients and methodsA preclinical evaluation measured the SV by three operators (resident, endourology expert and research engineer) among 17 NECT cases. Between January and March 2020, a multicentric, prospective, observational double-blind clinical evaluation was conducted in patients presenting with renal stones treated with Ho:YAG-EL during fURS and preoperative NECT. Demographic and surgical data were collected. The primary endpoint was a significant median difference between ExDL and EffectiveDL (EfDL). Second, efficiency (J/mm3) and efficacy (mm3/min) ratios were calculated.ResultsThe preclinical evaluation showed no significant difference in the SV measurements among operators (p > 0.05). Pearson and Kendall coefficients of 0.99 and 0.98, respectively, were found. Twenty-six patients were included in the clinical evaluation, with a median age of 55 years. In 66% of cases, there was a single stone located in the lower pole, with a density > 1000 Hounsfield Unit observed in 42% and 85% of cases. A 14% [Q1-Q3 (5.4-24.8); p = 0.36] median difference between ExDL and EfDL was noted, which was greater in the case of lower pole stones with no possible relocation (p = 0.008). Median values of 17.6 J/mm3 and 0.4 (0.32-0.56) mm3/s EL were also noted.ConclusionsKidney Stone Calculator is a reproducible and accurate software that allows for an estimation of the stone burden and provides an ExDL for URSf. Defining the influencing factors of EL will improve its ExDL.
| S-EPMC8006641 | biostudies-literature
Project description:Purpose: Ultrasonic propulsion is an investigative modality to noninvasively image and reposition urinary stones. Our goals were to test safety and effectiveness of new acoustic exposure conditions from a new transducer, and to use simultaneous ureteroscopic and ultrasonic observation to quantify stone repositioning. Materials and Methods: During operation, ultrasonic propulsion was applied transcutaneously, whereas stone targets were visualized ureteroscopically. Exposures were 350 kHz frequency, ≤200 W/cm2 focal intensity, and ≤3-second bursts per push. Ureteroscope and ultrasound (US) videos were recorded. Video clips with and without stone motion were randomized and scored for motion ≥3 mm by independent reviewers blinded to the exposures. Subjects were followed with telephone calls, imaging, and chart review for adverse events. Results: The investigative treatment was used in 18 subjects and 19 kidneys. A total of 62 stone targets were treated ranging in size from a collection of "dust" to 15 mm. Subjects received an average of 17 ± 14 propulsion bursts (per kidney) for a total average exposure time of 40 ± 40 seconds. Independent reviewers scored at least one stone movement ≥3 mm in 18 of 19 kidneys (95%) from the ureteroscope videos and in 15 of 19 kidneys (79%) from the US videos. This difference was probably because of motion out of the US imaging plane. Treatment repositioned stones in two cases that would have otherwise required basket repositioning. No serious adverse events were observed with the device or procedure. Conclusions: Ultrasonic propulsion was shown to be safe, and it effectively repositioned stones in 95% of kidneys despite positioning and access restrictions caused by working in an operating room on anesthetized subjects.
| S-EPMC6798799 | biostudies-literature
Project description:We have recently encountered patients incorrectly diagnosed with adenine phosphoribosyltransferase (APRT) deficiency due to misidentification of kidney stones as 2,8-dihydroxyadenine (DHA) stones. The objective of this study was to examine the accuracy of stone analysis for identification of DHA. Medical records of patients referred to the APRT Deficiency Research Program of the Rare Kidney Stone Consortium in 2010-2018 with a diagnosis of APRT deficiency based on kidney stone analysis were reviewed. The diagnosis was verified by measurement of APRT enzyme activity or genetic testing. Attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectra of pure crystalline DHA and a kidney stone obtained from one of the confirmed APRT deficiency cases were generated. The ATR-FTIR spectrum of the kidney stone matched the crystalline DHA spectrum and was used for comparison with available infrared spectra of stone samples from the patients. Of 17 patients referred, 14 had sufficient data available to be included in the study. In all 14 cases, the stone analysis had been performed by FTIR spectroscopy. The diagnosis of APRT deficiency was confirmed in seven cases and rejected in the remaining seven cases. Comparison of the ATR-FTIR spectrum of the DHA stone with the FTIR spectra from three patients who did not have APRT deficiency showed no indication of DHA as a stone component. Misidentification of DHA as a kidney stone component by clinical laboratories appears common among patients referred to our program. Since current clinical protocols used to interpret infrared spectra for stone analysis cannot be considered reliable for the identification of DHA stones, the diagnosis of APRT deficiency must be confirmed by other methods.
| S-EPMC7395965 | biostudies-literature
Project description:The molecular mechanisms by which kidney stones grow are largely unknown. Organic molecules from the urine combine with mineral crystals to form stones, but analysis of the stone matrix has revealed over a thousand different proteins, with no clues as to which are important for stone growth. Molecules that are present in every layer of a stone would be candidates for having an essential function, and thus the analysis of the stone matrix at a microscopic level is necessary. For this purpose, kidney stones were demineralized, sectioned, stained, and imaged by microscopy, using micro CT for precise orientation. Histological staining demonstrated heterogeneity in the density of adjacent layers within stones. Additional results also showed brilliant and unique autofluorescence patterns in decalcified nephroliths, indicating heterogeneous organic composition in adjacent layers. Regions of calcium oxalate (CaOx) stones were dissected using laser microdissection (LMD) for protein analysis. LMD of broad regions of demineralized CaOx stone sections yielded the same proteins as those found in different specimens of pulverized CaOx stones. These innovative methodologies will allow spatial mapping of protein composition within the heterogeneous stone matrix. Proteins that consistently coincide spatially with mineral deposition would be candidates for molecules essential for stone growth. This kind of analysis will be required to assess which of the thousand proteins in the stone matrix may be fundamental for stone growth.
| S-EPMC7786195 | biostudies-literature
Project description:In this study, seven strains of Fusarium graminearum were isolated from wheat, of which six were identified to produce deoxynivalenol and the production of deoxynivalenol was assessed. F. graminearum strain Fg1 was noted to produce 1.0 μg/g deoxynivalenol during the incubation period in the Czapek yeast broth, while none was detected in F. graminearum strain Fg2. Hence, the differences in proteomes and transcriptomes of Fg1 and Fg2 were compared to analyze the mechanism underlying deoxynivalenol production. Among the 66 significantly differentially expressed proteins in Fg1, 39 and 27 were more or less abundant expressed. Functional analysis suggested that the enzymes involved in the methylerythritol 4-phosphate and mevalonate pathways, which provide a substrate for biosynthesis of farnesyl pyrophosphate, a precursor of DON, were activated in Fg1. The transcriptomics data demonstrated that the expression level of a majority of genes, including trichothecene biosynthetic genes, protein kinases, and transcription factors, involved in trichothecene biosynthesis was higher in Fg1 than in Fg2. The results also revealed differential expression profiles of deoxynivalenol biosynthesis genes in strains Fg1 and Fg2, which emphasized their deoxynivalenol producing ability and the underlying mechanism.
| S-EPMC5488034 | biostudies-literature
Project description:Whole shotgun metagenomic sequencing from stool samples from calcium oxalate kidney stone formers and healthy control participants
| PRJEB39576 | ENA
Project description:ImportanceShock wave lithotripsy (SWL) and ureteroscopy (URS) account for more than 90% of procedural interventions for kidney stones, which affect 1 in 11 persons in the United States. Efficacy data for SWL are more than 20 years old. Advances in URS, along with emerging evidence of reduced efficacy of modern lithotripters, have created uncertainty regarding the comparative effectiveness of these 2 treatment options.ObjectiveTo compare the effectiveness of SWL and URS to fragment or remove urinary stones in a large private payer cohort.Design, setting, and participantsWe performed a retrospective cohort study of privately insured beneficiaries who had an emergency department visit for a kidney stone and subsequently underwent SWL or URS. Using an instrumental variable approach to control for observed and unobserved differences between the 2 groups, we created a bivariate probit model to estimate the probability of repeat intervention following an initial procedure.Main outcomes and measuresA second procedure (SWL or URS) within 120 days of an initial intervention to fragment or remove or a kidney stone.ResultsFollowing an acute care visit for a kidney stone, 21 937 patients (45.8%) underwent SWL and 25 914 patients (54.2%) underwent URS to fragment or remove the stone. After the initial URS, 4852 patients (18.7%) underwent an additional fragmentation or removal procedure compared with 5186 patients (23.6%) after the initial SWL (P < .001). After adjusting for observed and unobserved variables, the estimated probabilities of repeat intervention were 11.0%(95%CI, 10.9-11.1) following SWL and 0.3%(95%CI, 0.325-0.329) following URS.Conclusions and relevanceAmong privately insured beneficiaries requiring procedural intervention to remove a symptomatic stone, repeat intervention is more likely following SWL. For the marginal patient (as opposed to the average patient), the probability of repeat intervention is substantially higher.
| S-EPMC9869873 | biostudies-literature
Project description:Protein composition of human kidney matrix stones by nano-LC-MS/MS.
2023-10-24 | PXD033298 | Pride
Project description:Understanding the mechanisms of kidney stone formation, development patterns and associated pathological features are gaining importance due to an increase in the prevalence of the disease and diversity in the presentation of the stone composition. Based on the microstructural characteristics of kidney stones, it may be possible to explain the differences in the pathogenesis of pure and mixed types of stones. In this study, the microstructure and distribution of mineral components of kidney stones of different mineralogy (pure and mixed types) were analyzed. The intact stones removed from patients were investigated using synchrotron radiation X-ray computed microtomography (SR-μCT) and the tomography slice images were reconstructed representing the density and structure distribution at various elevation planes. Infrared (IR) spectroscopes, X-ray diffraction (XRD) and scanning electron microscopy (SEM) were used to confirm the bulk mineral composition in the thin section stones. Observations revealed differences in the micro-morphology of the kidney stones with similar composition in the internal 3-D structure. Calcium oxalate monohydrate stones showed well-organised layering patterns, while uric acid stones showed lower absorption signals with homogenous inner structure. Distinct mineral phases in the mixed types were identified based on the differential absorption rates. The 3-D quantitative analysis of internal porosity and spatial variation between nine different types of stones were compared. The diversity among the microstructure of similar and different types of stones shows that the stone formation is complex and may be governed by both physiological and micro-environmental factors. These factors may predispose a few towards crystal aggregation and stone growth, while, in others the crystals may not establish stable attachment and/or growth.
| S-EPMC6430423 | biostudies-literature