bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genotypic diversity of polyomaviruses circulating among kidney transplant recipients in Kuwait
Authors: Chehadeh Wassim , Nampoory Mangalathillam Raman 
Published: June 2013

AbstractBK virus (BKV) and JC virus (JCV) are human polyomaviruses that cause asymptomatic latent infections. Under immunosuppression, BKV‐associated nephropathy has been documented in Kuwait and elsewhere. Even though different BKV and JCV genotypes with distinct geographical distribution have been described, the genotype of polyomavirus detected in Kuwait is still unknown. The aim of this study was to determine the genotypes of BKV and JCV detected in renal transplant recipients. The detection of polyomavirus DNA was carried out in serum and urine samples of 200 post‐transplant recipients during a 1‐year follow‐up period. Fifty‐one (25.5%) post‐transplant recipients were tested positive for polyomavirus DNA by semi‐nested PCR. JCV DNA could be detected in 29 (57%) patients, and BKV DNA in 22 (43%) patients. In two renal transplant recipients, both BKV and JCV were detected. According to the Bayesian phylogenetic analysis of polyomavirus VP1 sequences, the majority of detected BKV sequences were most closely related to genotypes I and IV, whereas the majority of JCV sequences were most closely related to genotype 3. Polyomavirus VP1 sequences showed strong stability for up to 12 months in most patients; however, in one patient, an amino acid substitution in the BKV VP1 protein was identified over time. The results suggest a close relationship of BKV sequences with the Asian and European strains, and of JCV sequences with the African strains. Long follow‐up studies are needed to investigate the association of polyomavirus polymorphism or genotypic shift with the development of nephropathy. J. Med. Virol. 85:1624–1631, 2013. © 2013 Wiley Periodicals, Inc.
Evaluation of trends and multivariate frequency analysis of droughts in three meteorological subdivisions of western India
Authors: Ganguli Poulomi , Reddy M. Janga 
Published: June 2013

ABSTRACTThis article presents evaluation of trends and multivariate frequency analysis of droughts in three meteorological subdivisions of western India, namely, western Rajasthan, Saurashtra and Kutch and Marathwada regions. These regions are frequently affected by droughts and there is an urgent need for effective planning and management of droughts. Meteorological drought is modelled using Standardized Precipitation Index (SPI) at a time scale of 6 months over 110 years during 1896–2005. Trends in SPI time series are investigated by using nonparametric Mann–Kendall trend test for different time windows: entire study period of 1896–2005 and then splitting into three time windows of 1896–1931, 1932–1966 and 1967–2005. For total study period, the long‐term trend in SPI time series is found to be in an upward direction for the three regions. However, statistically significant downward trend is observed during 1932–1966 for western Rajasthan region, and Saurashtra and Kutch region in the month of June, indicating increase in number of drought occurrences during this period. Further, drought is a multivariate natural calamity characterizing severity, duration and peak; hence, probabilistic assessment of drought characteristics is investigated using copula method. The joint distribution of drought properties is modelled using three fully nested forms of Archimedean copulas: Clayton, Gumbel–Hougaard and Frank and one elliptical class of Student's t copula. On performing various statistical tests as well as upper tail dependence test it is found that Student's t copula better represents trivariate drought properties when compared with other copula families. The joint distribution obtained from the copula is utilized for computation of conditional probabilities and joint return periods. The importance of trivariate frequency analysis of drought is elucidated over univariate and bivariate frequency analysis. Overall, the results of the study could provide valuable insight towards regional drought risk management under changing climate.
Regional temperature change over the Huang‐Huai‐Hai Plain of China: the roles of irrigation versus urbanization
Authors: Shi Wenjiao , Tao Fulu , Liu Jiyuan 
Published: June 2013

ABSTRACTIrrigation and urbanization, two widely occurring land‐use/land‐cover changes, have important influences on regional climate, especially on temperature. The effect of irrigation and urbanization on temperature is separately documented in several studies. However, there are few studies analysing the combined effects of irrigation and urbanization on temperature. In this study, changes in surface temperature were analysed in relation to irrigation and urbanization on the Huang‐Huai‐Hai Plain of China from 1955 to 2007. To better characterize the combined effects of these two processes on temperatures, long‐term weather observations are used along with irrigation and urbanization data sets. The results indicated that irrigation had a significant cooling effect of 0.17–0.20 °C decade−1 on average daily maximum temperature of the hottest 1, 5, and 30 d of each year on the Huang‐Huai‐Hai Plain. Compared with the reference conditions, irrigation also indicated a cooling effect of 0.12 °C decade−1 on summertime daily maximum temperature. In contrast to its effect on maximum temperature, irrigation appeared to induce a warming effect of 0.43 °C/decade on average daily minimum temperature of the coldest 1 d of each year. Where irrigation interfaced with urbanization, the urbanization warming of extreme daily maximum temperature seemed to only partly counteract the irrigation cooling effect. The findings of this study deepen our insight into the effects of irrigation and urbanization on temperature dynamics, and the combined implications for regional climate change. Further efforts to understand irrigation and urbanization effects on climate should not only use observations, but should also be coupled with dynamic land‐use and regional climate models to understand the complex processes and controlling mechanisms.
Precise 14C ages of the Vedde and Saksunarvatn ashes and the Younger Dryas boundaries from western Norway and their comparison with the Greenland Ice Core (GICC05) chronology
Authors: LOHNE ØYSTEIN S. , MANGERUD JAN , BIRKS HILARY H. 
Published: June 2013

ABSTRACTThe Greenland ice cores with the GICC05 chronology represent a standard for late Quaternary climate events and their ages, whereas many other palaeoclimatic archives are dependent on 14C dates. It is therefore critical to know if the ice‐core and the calibrated 14C chronologies are identical, and if not to quantify the offset between them. We present Bayesian age–depth modelling of 118 accelerator mass spectrometry 14C dates from Kråkenes Lake, calibrated using INTCAL09, that provide high precision ages of 12 066 ± 42 and 10 210 ± 35 cal a BP for the Vedde and Saksunarvatn ashes, respectively. The lower and upper Younger Dryas boundaries have ages of 12 710 ± 52 and 11 546 ± 59 cal a BP, respectively. The four dated levels coincide with correlative levels in GICC05 within the dating uncertainties, but are all consistently younger at Kråkenes. The ages of the tephra chronostratigraphic markers suggest a mean offset of ∼70 years to older ages in the GICC05 compared with the INTCAL09 time scale. Responses to small climate changes ∼30 years before the Younger Dryas boundaries at Kråkenes are suggested to correspond to the defined Greenland Stadial 1 boundaries. This suggested difference in timing (30 years) and time scale offset (70 years) mean that the Greenland Stadial 1 boundaries appear ∼100 years older than the Younger Dryas boundaries.
Pleomorphic adenoma of the major salivary glands: Diagnostic utility of FNAB and MRI
Authors: Heaton Chase M. , Chazen J. Levi , van Zante Annemieke , Glastonbury Christine M. , Kezirian Eric J. , Eisele David W. 
Published: June 2013

Objectives/HypothesisPleomorphic adenoma (PA) is the most common, benign tumor of the major salivary glands. Surgical resection is the treatment of choice. Initial preoperative workup of major salivary gland neoplasms often includes fine needle aspiration biopsy (FNAB) and magnetic resonance imaging (MRI) of the head and neck. Our objective was to assess the positive predictive value of FNAB and MRI in the evaluation of PA arising from within the major salivary glands.Study DesignRetrospective chart review.MethodsAll patients with a FNAB diagnosis of PA of the major salivary glands and who underwent surgical excision at our institution from 2001 to 2011 were identified. FNAB slides from these cases were reviewed by a cytopathologist for findings suggestive of PA: fibrillary stroma, mesenchymal elements, plasmacytoid myoepithelial cells, epithelial cells forming ducts or tubules, and the absence of nuclear atypia. For those patients with a preoperative MRI, the MRI studies were reviewed by a neuroradiologist for findings suggestive of PA, including homogenous T2 hyperintensity, well‐circumscribed borders, and solid contrast enhancement. Positive predictive value (PPV) of these specific FNAB and MRI findings were calculated using chi‐squared testing.ResultsOne hundred forty‐six patients met inclusion criteria, and 68 had preoperative MRI. PPV of a FNAB diagnosis of PA was 97.8%. Characteristic features of PA on FNAB (fibrillary stroma, mesenchymal elements, plasmacytoid myoepithelial cells, epithelial cells forming ducts or tubules, and the absence of nuclear atypia) and MRI (homogenous T2 hyperintensity, well‐circumscribed borders, and solid contrast enhancement) all demonstrated PPVs of 95% or greater in patients with FNA diagnosis of PA.ConclusionsPPV of a FNAB diagnosis of PA in the major salivary glands is high. Among patients with a FNAB diagnosis of PA, specific MRI characteristics also have a high PPV. The diagnostic accuracy of these studies in combination allows for the confident preoperative diagnosis of PA.Level of Evidence4. Laryngoscope, 123:3056–3060, 2013
Elevated intracranial pressure in patients with spontaneous cerebrospinal fluid otorrhea
Authors: Allen Kyle P. , Perez Carlos L. , Kutz J. Walter , Gerecci Deniz , Roland Peter S. , Isaacson Brandon 
Published: June 2013

Objectives/HypothesisTo determine the prevalence of elevated intracranial hypertension in patients with spontaneous cerebrospinal fluid otorrhea (SCSFO).Study DesignCase series with chart review at a tertiary care academic medical center following institutional review board approval.MethodsA retrospective review was performed of patients undergoing operative repair of SCSFO between January 2007 and May 2012.ResultsThirty‐eight patients underwent operative repair of SCSFO. Of these, 22 underwent postoperative lumbar puncture with measurement of opening pressure. The opening pressure was elevated (> 20 cm/H20) in eight patients (36.4%). Preoperative magnetic resonance imaging was available for review by a neuroradiologist in 27 patients. Radiographic evidence of elevated intracranial pressure (ICP) was present in 48.1% of patients.ConclusionElevated ICP is common in patients with SCSFO. However, as only a minority of patients have elevated ICP, it is not the sole factor in the development of SCSFO.Level of Evidence4. Laryngoscope, 124:251–254, 2014
Range image of the velopharynx produced using a 3‐D endoscope with pattern projection
Authors: Mishima Katsuaki , Nakano Asuka , Shiraishi Ruriko , Ueyama Yoshiya 
Published: June 2013

Objectives/HypothesisTo measure movements of the velopharynx in detail, a novel method of producing range images of the velopharynx was developed using a 3‐D endoscope. The purpose of this paper is to introduce this system and to clarify its accuracy.Study DesignThe standard errors of repeated measurements, intraclass correlation coefficients (ICC), ICC(1,1) for intrarater reliability, and ICC(2,1) for interrater reliability were measured using a phantom of the nasopharynx.MethodsAn endoscopic measuring system was developed in which a pattern projection system was incorporated into a commercially available 3‐D endoscope. Right and left images of the endoscope were integrated into one video file and digitized at a horizontal and vertical resolution of 640 × 480 pixels, as odd and even scanning lines, respectively. After separation of the video file into right and left images by interlace interpolation, correcting the distortion of the camera images, rectifying, and stereo‐matching range images of the velopharynx were produced. The distances between two points, which were marked at an interval of 5 mm on the uvula and the pharynx of the phantom, were measured.ResultsThe standard errors of repeated measurements were 0.02 horizontally and 0.01 vertically. The ICC(1,1) and ICC(2,1) were 0.83 and 0.94, and both correlation coefficients were considered to be “almost perfect.”ConclusionThe present endoscopic measuring system provided relatively accurate and reliable range images of the velopharynx, and enabled quantitative analysis of movements of the velopharynx.Level of EvidenceN/A. Laryngoscope, 123:E122–E126, 2013
Success of endoscopic pharyngoesophageal dilation after head and neck cancer treatment
Authors: Chapuy Claudia I. , Annino Donald J. , Tishler Roy B. , Haddad Robert I. , Snavely Anna , Goguen Laura A. 
Published: June 2013

Objectives/HypothesisTo assess clinical success and safety of endoscopic pharyngoesophageal dilation after chemoradiation or radiation for head and neck cancer and to identify variables associated with dilation failure.Study DesignCase series with chart review.MethodsBetween 2000 and 2008, a total of 111 patients treated with chemoradiation or radiation for head and neck cancer with subsequent pharyngoesophageal stenosis requiring endoscopic dilation were identified. Patients were evaluated for endoscopic dilation technique, severity of stenosis, technical and clinical success, and intra‐ and postoperative complications. The Diet/GT score (range, 1–5) was utilized to measure swallow success. Variables associated with dilation failure were analyzed by univariate and multivariate logistic regression.ResultsThere were 271 dilations analyzed, with 42 combined antegrade retrograde dilations, 208 dilations over a guidewire, and 21 dilations without guidewire. Intraoperative patency and successful dilation of the stenotic segment was achieved in 95% of patients. A Diet/GT score of 5 (gastrostomy tube removed and soft/regular diet) was attained in 84 of 111 (76%) patients. Safety analysis showed complications occurred in 9% of all dilations. Perforations were noted in 4% of all procedures, with only two esophageal perforations requiring significant intervention. Multiple dilations were associated with an increased risk for perforations. Further logistic regression analyses revealed that the number of dilations was indicating a poor outcome and low Diet/GT score.ConclusionsPharyngoesophageal stenosis, occurring after chemoradiation and radiation treatment, can be successfully and safely treated with endoscopic dilation techniques. Patients with restenosis, requiring multiple dilations, have a higher risk of persistent dysphagia.Level of Evidence4 Laryngoscope, 123:3066–3073, 2013
Genetic variants at chromosome 8q24, colorectal epithelial cell proliferation, and risk for incident, sporadic colorectal adenomas
Authors: Yang Baiyu , Thyagarajan Bharat , Gross Myron D. , Goodman Michael , Sun Yan V. , Bostick Roberd M. 
Published: June 2013

AbstractThree polymorphic sites at chromosome 8q24 (rs7837328, rs10808555, rs6983267) have been associated with risk for colorectal adenomas. It was also previously reported that the single nucleotide polymorphism (SNP) rs6983267 may enhance Wnt signaling, which regulates cell proliferation. To investigate associations between the 8q24 variants and colorectal epithelial cell proliferation in the normal‐appearing colorectal mucosa, as well as with colorectal adenoma, we analyzed data from a previously conducted pilot, colonoscopy‐based case–control study of incident, sporadic colorectal adenoma (n = 90 cases, 132 controls). Proliferation was measured in biopsies of the normal‐appearing mucosa of the rectum, sigmoid colon, and cecum using immunohistochemistry for proliferating cell nuclear antigen (PCNA). The direct associations of each SNP with colorectal adenoma were consistent with those in previous reports. For all three SNPs, proliferation tended to be higher among those homozygous for the risk alleles compared to those heterozygous or homozygous for the nonrisk alleles combined; among the controls, proliferation was 32.1% higher (P = 0.23) for those with the rs10808555 GG genotype, 16.4% higher (P = 0.16) for those with the rs7837328 AA genotype, and 6.5% higher (P = 0.52) for those with the rs6983267 GG genotype. These preliminary findings, which are consistent with previously reported direct associations between genetic variants at chromosome 8q24 and risk for colorectal adenoma, suggest that the genetic variants may also be associated with higher levels of colorectal epithelial cell proliferation, thus providing support for further investigation of the hypothesis that 8q24 variants may increase risk via enhanced Wnt signaling. © 2013 Wiley Periodicals, Inc.
Genetic polymorphisms in RAD23B and XPC modulate DNA repair capacity and breast cancer risk in Puerto Rican women
Authors: Pérez‐Mayoral Julyann , Pacheco‐Torres Alba L. , Morales Luisa , Acosta‐Rodríguez Heidi , Matta Jaime L. , Dutil Julie 
Published: June 2013

AbstractStudies have shown that DNA repair capacity (DRC) is significantly decreased in breast cancer patients, but the molecular causes of inter‐individual variation in DRC are unknown. We hypothesized that genetic variation in the nucleotide excision repair pathway genes can modulate DRC and breast cancer risk in Puerto Rican women. A total of 228 breast cancer cases and 418 controls were recruited throughout Puerto Rico. For all study participants, eight single nucleotide polymorphisms (SNPs) in the genes XPC, XPD, and RAD23B were genotyped using a TaqMan PCR, and the DRC levels of UV induced‐DNA damage was measured in peripheral lymphocytes using a host cell reactivation assay. After adjustment for confounders, RAD23B rs1805329 (Ala249Val) was found to be significantly associated with breast cancer risk under all models tested (P < 0.001). There was also a significant association between breast cancer risk and RAD23B rs10739234 (intronic) under the recessive model (P = 0.003, OR: 2.72, 95% CI: 1.40–5.30). In cases, there was a statistically significant difference in mean DRC per genotype for RAD23B rs1805329 (P < 0.001) and XPC rs2607775 (P = 0.002). When we modeled the combined effect of multiple SNPs that each independently affected DRC on cancer risk, we observed incremental augmentations in risk with increasing number of risk genotypes at those loci (P overall model <0.001). The increase in adverse genotypes was also correlated with a progressive decrease in DRC values. Our data indicate an additive effect of the NER SNPs on DRC and breast cancer risk in Puerto Rican women. © 2013 Wiley Periodicals, Inc.
The Hanes‐Woolf linear QUESP method improves the measurements of fast chemical exchange rates with CEST MRI
Authors: Randtke Edward A. , Chen Liu Qi , Corrales L. Rene , Pagel Mark D. 
Published: June 2013

PurposeContrast agents for chemical exchange saturation transfer MRI often require an accurate measurement of the chemical exchange rate. Many analysis methods have been reported that measure chemical exchange rates. Additional analysis methods were derived as part of this study. This report investigated the accuracy and precision of each analysis method.MethodsChemical exchange saturation transfer spectra were simulated using the Bloch‐McConnell equations modified for chemical exchange. Chemical exchange saturation transfer spectra of iopromide were obtained with a range of saturation times, saturation powers, and concentrations. These simulated and experimental results were used to estimate the chemical exchange rate using the QUESP, QUEST, Omega Plot (LB‐QUESP), EH‐QUESP, HW‐QUESP, LB‐Conc, EH‐Conc, and HW‐Conc methods.ResultsBloch fitting produced the most precise estimates of chemical exchange rates, although substantial expertise and computation time were required to achieve these results. Of the more simplistic analysis methods, the HW‐QUESP method produced the most accurate and precise estimates of fast exchange rates. The QUEST and LB‐QUESP methods produced the most accurate estimates of slow exchange rates, especially with samples that have short T1w relaxation times.ConclusionsHW‐QUESP is a simplistic analysis method that should be used when fast chemical exchange rates need to be estimated from chemical exchange saturation transfer MRI results. Magn Reson Med 71:1603–1612, 2014. © 2013 Wiley Periodicals, Inc.
A comprehensive non‐invasive framework for automated evaluation of acute renal transplant rejection using DCE‐MRI
Authors: Khalifa Fahmi , Abou El‐Ghar Mohamed , Abdollahi Behnaz , Frieboes Hermann B. , El‐Diasty Tarek , El‐Baz Ayman 
Published: June 2013

The objective was to develop a novel and automated comprehensive framework for the non‐invasive identification and classification of kidney non‐rejection and acute rejection transplants using 2D dynamic contrast‐enhanced magnetic resonance imaging (DCE‐MRI).The proposed approach consists of four steps. First, kidney objects are segmented from the surrounding structures with a geometric deformable model. Second, a non‐rigid registration approach is employed to account for any local kidney deformation. In the third step, the cortex of the kidney is extracted in order to determine dynamic agent delivery, since it is the cortex that is primarily affected by the perfusion deficits that underlie the pathophysiology of acute rejection. Finally, we use an analytical function‐based model to fit the dynamic contrast agent kinetic curves in order to determine possible rejection candidates. Five features that map the data from the original data space to the feature space are chosen with a k‐nearest‐neighbor (KNN) classifier to distinguish between acute rejection and non‐rejection transplants. Our study includes 50 transplant patients divided into two groups: 27 patients with stable kidney function and the remainder with impaired kidney function. All of the patients underwent DCE‐MRI, while the patients in the impaired group also underwent ultrasound‐guided fine needle biopsy.We extracted the kidney objects and the renal cortex from DCE‐MRI for accurate medical evaluation with an accuracy of 0.97 ± 0.02 and 0.90 ± 0.03, respectively, using the Dice similarity metric. In a cohort of 50 participants, our framework classified all cases correctly (100%) as rejection or non‐rejection transplant candidates, which is comparable to the gold standard of biopsy but without the associated deleterious side‐effects.Both the 95% confidence interval (CI) statistic and the receiver operating characteristic (ROC) analysis document the ability to separate rejection and non‐rejection groups. The average plateau (AP) signal magnitude and the gamma‐variate model functional parameter α have the best individual discriminating characteristics. Copyright © 2013 John Wiley & Sons, Ltd.