Comparing Three Data Mining Methods to Predict Kidney Transplant Survival

Introduction: One of the most important complications of post-transplant is rejection. Analyzing survival is one of the areas of medical prognosis and data mining, as an effective approach, has the capacity of analyzing and estimating outcomes in advance through discovering appropriate models among data. The present study aims at comparing the effectiveness of C5.0 algorithms, neural network and C & RTree to predict kidney transplant survival before transplant. Method: To detect factors effective in predicting transplant survival, information needs analysis was performed via a researcher-made questionnaire. A checklist was prepared and data of 513 kidney disease patient files were extracted from Sina Urology Research Center. Following CRISP methodology for data mining, IBM SPSS Modeler 14.2, C5.0, C&RTree algorithms and neural network were used. Results: Body Mass Index (BMI), cause of renal dysfunction and duration of dialysis were evaluated in all three models as the most effective factors in transplant survival. C5.0 algorithm with the highest validity (96.77) was the first in estimating kidney transplant survival in patients followed by C&RTree (83.7) and neural network (79.5) models. Conclusion: Among the three models, C5.0 algorithm was the top model with high validity that confirms its strength in predicting survival. The most effective kidney transplant survival factors were detected in this study; therefore, duration of transplant survival (year) can be determined considering the regulations set for a new sample with specific characteristics. © 2016 Leila Shahmoradi, Mostafa Langarizadeh, Gholamreza Pourmand, Ziba Aghsaei fard, and Alireza Borhani

Molecular detection of prostate specific antigen in patients with prostate cancer or benign prostate hyperplasia the first investigation from Iran

Prostate cancer is the second common form of cancer in men. Detection of circulating Prostate Specific Antigen (PSA) transcripts has effectively been used for early diagnosis of prostate cancer cells. This investigation employed a reverse transcriptase polymerase chain reaction (RT-PCR) technique to distinguish the patients with either localized or metastatic prostate cancer (CaP) vs. Benign Prostate Hyperplasia (BPH) and control subjects, as compared with clinical and pathological records. With reservation of ethical issues, blood samples were collected from 60 cases. Based on pathological and clinical findings, 25 patients (20 with localized cancer, 5 with metastatic), 22 with BPH, and 13 healthy (including 3 females) subjects as negative controls, were selected from Shariati, Mehrad, Sina,, Khatam and Atie Hospitals in Tehran, Iran. RT-PCR for a 260 bp PSA transcript was then performed. Clinical and pathological records were used for the assessment and comparison of PSA RT-PCR results. None of the control subjects and BPH (with 7 exceptions) were found positive by RT-PCR (Relative specificity= 72.7). In patients with prostate cancer, 21 out of 25 were found PSA positive (Relative sensitivity= 83.4) and the remaining 3 have been shown to be PSA negative (Positive predictive value= 83.4). All of 5 metastatic patients (100) revealed PSA positive results. Our data reflects the clinical relevance and significance of RT-PCR results as assessed with clinical and pathological examinations. PSA RT-PCR might be used as a powerful means for diagnosis, even when either pathological or clinical findings are negative, and could be employed for further molecular epidemiology surveys

Modern carbonate ooids preserve ambient aqueous REE signatures

Skeletal and non-skeletal components of marine sedimentary rocks have been analyzed for the purpose of reconstructing the rare earth element (REE) and yttrium (Y) compositions of paleo-seawater, but skeletal carbonates frequently have proven to be unreliable recorders of seawater chemistry. Here, we present a systematic multi-technique assessment of rare earth and other trace elements in ooid sands from the modern Great Bahama Bank (GBB–marine) and Great Salt Lake (GSL–continental) based on strong-acid (hydrofluoric and nitric) and weak-acid (acetic) digestions, as well as laser ablation (LA) of ooid cortices and nuclei. The results show that Bahamian ooid cortices possess shale-normalized REE + Y features nearly identical to those of shallow seawater, including limited contamination from siliciclastic REEs. An admixture of even 0.2% of detritally sourced material can modify the primary marine REE + Y patterns by, for example, increasing the light REE (LREE) content. Mean values of LA data for Bahamian ooid cortices exhibit similar REE + Y signatures to those produced by acetic acid digestion, but LA data are generally noisier, primarily as a result of low REE concentrations and the small volume of carbonate ablated in analysis. Screening out samples with ΣREE  0.9 ppm) returns a flat pattern, suggesting similar degrees of LREE depletion controlled by carbonate complexation under similar aqueous alkalinity conditions in Great Salt Lake and Bahamian waters. In summary, ooids can be a reliable proxy for REE + Y characteristics of ambient surficial waters when adopting suitable analytical methods, including laser ablation, that allow the identification and isolation of a contamination signal from siliciclastic detritus

Microchimerism and Renal Transplantation: Doubt Still Persists

Objective: We sought to study microchimerism in a group of kidney transplant recipients. Materials and Methods: In this study, the peripheral blood microchimerism (PBM) after renal transplantation was retrospectively evaluated in 32 male-to-female recipients of living unrelated or cadaveric donor renal transplants. Using a nested polymerase chain reaction (PCR) amplification specific for SRY region of the Y chromosome, microchimerism was detected with a sensitivity of 1:1,000,000. Recipients were compared according to the presence of PBM, acute and chronic rejection episodes, type of allotransplant, recipient and donor age at transplantation, previous male labor or blood transfusion, allograft function (serum creatinine level), and body mass index. Results: Among 32 recipients, 7 (21.9) were positive for PBM upon multiple testing at various posttransplant times. All microchimeric recipients had received kidneys from living unrelated donors. No significant difference was observed with regard to other parameters. In addition the acute rejection rate in the microchimeric group was 3 (42) versus 4 (16) in the nonmicrochimeric recipients (not significant). Conclusion: Our results suggested better establishment of microchimerism after living donor kidney transplantation. However, doubt persists concerning the true effect of microchimerism after renal transplantation. It seems that microchimerism alone has no major protective role upon renal allograft survival. © 2007 Elsevier Inc. All rights reserved

Multiplex SNP typing by bioluminometric assay coupled with terminator incorporation (BATI)

A multiplex single-nucleotide polymorphism (SNP) typing platform using ‘bioluminometric assay coupled with terminator [2′,3′-dideoxynucleoside triphosphates (ddNTPs)] incorporation’ (named ‘BATI’ for short) was developed. All of the reactions are carried out in a single reaction chamber containing target DNAs, DNA polymerase, reagents necessary for converting PPi into ATP and reagents for luciferase reaction. Each of the four ddNTPs is dispensed into the reaction chamber in turn. PPi is released by a nucleotide incorporation reaction and is used to produce ATP when the ddNTP dispensed is complementary to the base in a template. The ATP is used in a luciferase reaction to release visible light. Only 1 nt is incorporated into a template at a time because ddNTPs do not have a 3′ hydroxyl group. This feature greatly simplifies a sequencing spectrum. The luminescence is proportional to the amount of template incorporated. Only one peak appears in the spectrum of a homozygote sample, and two peaks at the same intensity appear for a heterozygote sample. In comparison with pyrosequencing using dNTP, the spectrum obtained by BATI is very simple, and it is very easy to determine SNPs accurately from it. As only one base is extended at a time and the extension signals are quantitative, the observed spectrum pattern is uniquely determined even for a sample containing multiplex SNPs. We have successfully used BATI to type various samples containing plural target sequence areas. The measurements can be carried out with an inexpensive and small luminometer using a photodiode array as the detector. It takes only a few minutes to determine multiplex SNPs. These results indicate that this novel multiplexed approach can significantly decrease the cost of SNP typing and increase the typing throughput with an inexpensive and small luminometer

Mid-Holocene, coral-based sea surface temperatures in the western tropical Atlantic

© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution-NonCommercial‐NoDerivs License. The definitive version was published in Rodriguez, L. G., Cohen, A. L., Ramirez, W., Oppo, D. W., Pourmand, A., Edwards, R. L., Alpert, A. E., & Mollica, N. Mid-Holocene, coral-based sea surface temperatures in the western tropical Atlantic. Paleoceanography and Paleoclimatology, 34(7), (2019): 1234-1245, doi:10.1029/2019PA003571.The Holocene is considered a period of relative climatic stability, but significant proxy data‐model discrepancies exist that preclude consensus regarding the postglacial global temperature trajectory. In particular, a mid‐Holocene Climatic Optimum, ~9,000 to ~5,000 years BP, is evident in Northern Hemisphere marine sediment records, but its absence from model simulations raises key questions about the ability of the models to accurately simulate climate and seasonal biases that may be present in the proxy records. Here we present new mid‐Holocene sea surface temperature (SST) data from the western tropical Atlantic, where twentieth‐century temperature variability and amplitude of warming track the twentieth‐century global ocean. Using a new coral thermometer Sr‐U, we first developed a temporal Sr‐U SST calibration from three modern Atlantic corals and validated the calibration against Sr‐U time series from a fourth modern coral. Two fossil corals from the Enriquillo Valley, Dominican Republic, were screened for diagenesis, U‐series dated to 5,199 ± 26 and 6,427 ± 81 years BP, respectively, and analyzed for Sr/Ca and U/Ca, generating two annually resolved Sr‐U SST records, 27 and 17 years long, respectively. Average SSTs from both corals were significantly cooler than in early instrumental (1870–1920) and late instrumental (1965–2016) periods at this site, by ~0.5 and ~0.75 °C, respectively, a result inconsistent with the extended mid‐Holocene warm period inferred from sediment records. A more complete sampling of Atlantic Holocene corals can resolve this issue with confidence and address questions related to multidecadal and longer‐term variability in Holocene Atlantic climate.This study was supported by NSF OCE 1747746 to Anne Cohen and by NSF OCE 1805618 to Anne Cohen and Delia Oppo. Eric Loss and his crew on Pangaea Exploration's Sea Dragon enabled fieldwork in Martinique, and George P. Lohman, Thomas DeCarlo, and Hanny Rivera assisted with coral coring. Kathryn Pietro and Julia Middleton assisted in the laboratory, and Louis Kerr provided technical support on the SEM at MBL. Gretchen Swarr provided technical support on the Element and iCap ICPMS at WHOI. We also thank Edwin Hernandez, Jose Morales, and Amos Winter for discussion. All data generated in this study will be made publicly available at http://www.ncdc.noaa.gov/data‐ access/paleoclimatology‐data/dataset

Analysis of Short Tandem Repeats by Parallel DNA Threading

The majority of studies employing short tandem repeats (STRs) require investigation of several of these genetic markers. As such, we demonstrate the feasibility of the trinucleotide threading (TnT) approach for scalable analysis of STRs. The TnT method represents a parallel amplification alternative that addresses the obstacles associated with multiplex PCR. In this study, analysis of the STR fragments was performed with capillary gel electrophoresis; however, it should be possible to combine our approach with the massive 454 sequencing platform to considerably increase the number of targeted STRs

Twelve thousand years of dust: The Holocene global dust cycle constrained by natural archives

Mineral dust plays an important role in the climate system by interacting with radiation, clouds, and biogeochemical cycles. In addition, natural archives show that the dust cycle experienced variability in the past in response to global and local climate change. The compilation of the DIRTMAP paleodust datasets in the last two decades provided a target for paleoclimate models that include the dust cycle, following a time slice approach. We propose an innovative framework to organize a paleodust dataset that moves on from the positive experience of DIRTMAP and takes into account new scientific challenges, by providing a concise and accessible dataset of temporally resolved records of dust mass accumulation rates and particle grain-size distributions. We consider data from ice cores, marine sediments, loess/paleosol sequences, lake sediments, and peat bogs for this compilation, with a temporal focus on the Holocene period. This global compilation allows investigation of the potential, uncertainties and confidence level of dust mass accumulation rates reconstructions, and highlights the importance of dust particle size information for accurate and quantitative reconstructions of the dust cycle. After applying criteria that help to establish that the data considered represent changes in dust deposition, 43 paleodust records have been identified, with the highest density of dust deposition data occurring in the North Atlantic region. Although the temporal evolution of dust in the North Atlantic appears consistent across several cores and suggest that minimum dust fluxes are likely observed during the Early to mid-Holocene period (6000–8000 years ago), the magnitude of dust fluxes in these observations is not fully consistent, suggesting that more work needs to be done to synthesize datasets for the Holocene. Based on the data compilation, we used the Community Earth System Model to estimate the mass balance and variability of the global dust cycle during the Holocene, with dust load ranging from 17.1 to 20.5 Tg between 2000 and 10 000 years ago, and a minimum in the Early to Mid-Holocene (6000–8000 years ago)