bluuebunny/crossref_metadata_2025 huggingface dataset:
Two‐Locus Modeling of Asthma in a Hutterite Pedigree via Markov Chain Monte Carlo
Authors: Luo Yuqun , Lin Shili , Irwin Mark E.
Published: July 2017

Bayesian Markov chain Monte Carlo (MCMC) segregation analysis for asthma was performed on the whole 1,544‐member Hutterite pedigree. Heterogeneous and epistatic two‐locus models and complex one‐locus models were investigated, with trait loci postulated to be linked to markers in regions previously found to be possibly linked to asthma or atopy. The epistatic two‐locus dominant‐dominant model provided the best estimates, among the models investigated, in terms of prediction of population prevalence and relative risk for sibs of the affecteds. © 2001 Wiley‐Liss, Inc.
Incorporating Age at Onset Information into the Transmission/Disequilibrium Test
Authors: Hsu Li , Prentice Ross L. , Zhao Lue Ping , Li Sue
Published: July 2017

In this paper, we proposed two approaches for incorporating the age at onset into the transmission/disequilibrium test (TDT). Trios (affected offspring and their parents) were extracted from the first four replicate data sets of the general population type. Focusing on chromosome 6 where MG6 and MG7 reside, we compared the usual TDT with the newly proposed tests in terms of gene localization. © 2001 Wiley‐Liss, Inc.
Joint Modeling of Genetic Association and Population Stratification Using Latent Class Models
Authors: Ripatti Samuli , Pitkäniemi Janne , Sillanpää Mikko J.
Published: July 2017

We show how latent class log‐linear models can be used to test for an association between a candidate gene and a disease phenotype in a stratified population when the stratification is unobserved. The stratification may arise because of several ethnic groups or immigration and may lead to spurious associations between several loci and the disease. The information about the stratification is drawn from additional markers that are chosen to be independent of the disease and unlinked to the candidate gene and to each other within each population stratum. We use the EM algorithm to simultaneously estimate all the model parameters, including proportions of individuals in the latent population strata. The latent class model is used to test the phenotype association of single nucleotide polymorphism markers in four candidate regions in population‐based case‐control data selected from simulated Genetic Analysis Workshop (GAW) 12 population isolate 30. The analysis clearly demonstrates how the number of false positive associations can be reduced when the model accounts for population stratification. © 2001 Wiley‐Liss, Inc.
A Robust Score Test for Linkage Disequilibrium in General Pedigrees
Authors: Kraft Peter
Published: July 2017

Many family‐based tests of linkage disequilibrium are not valid when related nuclear families from larger pedigrees are used, or when independent nuclear families with multiple cases are used. The Pedigree Disequilibrium Test (PDT) proposed by Martin et al. [Am J Hum Genet 67:146–54, 2000] avoids these problems. This paper sketches an extension of the PDT that can account for measured covariates. Where the PDT is based on allele‐counting methods, this extension is based on conditional logistic regression. Versions of these statistics were used to test for association between disease and two known functional single nucleotide polymorphisms (SNPs) on gene 1 and gene 6 and one inert SNP on gene 7 in the first 25 replicates of the simulated population‐isolate data. The new method was also used to test for linkage disequilibrium after correcting for the effect of the environmental factor E1. The PDT and the conditional logistic extension had similar power to detect the functional SNPs (100% for gene 1, approximately 50% for gene 6) and appropriate type I error rates for the inert SNP. Correcting for E1 slightly increased power to detect the association between gene 6 and disease. © 2001 Wiley‐Liss, Inc.
A Robust Multipoint Linkage Statistic (tlod) for Mapping Complex Trait Loci
Authors: Abkevich Victor , Camp Nicola J. , Gutin Alexander , Farnham James M. , Cannon-Albright Lisa , Thomas Alun
Published: July 2017

Classical parametric two‐point linkage analysis is a powerful analysis tool, however there are clear disadvantages too, including the sensitivity to allele frequency misspecification. Conversely, multipoint linkage analysis is not sensitive to allele frequency misspecification, but it is sensitive to genetic model misspecification. Göring and Terwilliger [Am J Hum Genet 66:1095–106, 2000] proposed a new robust multipoint statistic that increased the robustness of multipoint analyses. In this paper we have referred to this new statistic as the tlod. We applied this new statistic to the Genetic Analysis Workshop (GAW) 12 data using affected status (AFF) as the phenotype of interest. The heterogeneity tlod and two‐point hlod scores correlated highly across the genome (p < 0.0001), as expected, but the het‐tlod had a lower number false positives. In addition, the tlod analysis handled missing data better, as would be expected for a multipoint method. When one‐third of the genotype data was removed (dead people) the tlod analysis was less affected than the two‐point analysis. When tlod scores were compared with multipoint lod scores in true gene locations, the robustness of the tlod to model misspecification was clearly evident. When the “best” replicate from the general population was analyzed, a borderline genome‐wide significant two‐point hlod result (3.6) was found 4 cM from MG6 and MG7 on chromosome 6. The heterogeneity tlod score was lower than the two‐point hlod score (1.8), but greater than the heterogeneity multipoint lod score (0.4). However, when replicate 1 of the isolated population was analyzed none of the true gene locations were identified with either statistic. © 2001 Wiley‐Liss, Inc.
Locus Ordering Based on Crossover Information in Family Haplotypes: Application of a “Minimum Break” Algorithm
Authors: Falk Catherine T.
Published: July 2017

A “minimum break” method, previously applied to radiation hybrid data, is applied to the Genetic Analysis Workshop 12 simulated family data to assess the method's feasibility for ordering dense markers that have been typed in a set of pedigrees of three or more generations. Ordering is based on minimizing the total number of crossovers (“breaks”) in a set of haplotypes where allele origin can be assigned to each specific haplotype, but locus order is unknown. It is shown that, for average locus spacing of about 2 cM and a set of 300 to 600 haplotypes, locus ordering can be reliably determined for sets of at least 50 loci. However, in the absence of crossovers between some pairs (sets) of loci, no unique order can be identified and sets of orders that are equally likely will be recovered. The method presented can be used to obtain reasonable sets of ordered loci that can then be used by other methods to refine the statistical confidence of the locus order. © 2001 Wiley‐Liss, Inc.
Mining Associations Between Genetic Markers, Phenotypes, and Covariates
Authors: Sevon Petteri , Ollikainen Vesa , Onkamo Päivi , Toivonen Hannu T.T. , Mannila Heikki , Kere Juha
Published: July 2017

We used Haplotype Pattern Mining, HPM [Toivonen et al., Am J Hum Genet 67:133–45, 2000], for gene localization in Genetic Analysis Workshop (GAW) 12 isolate data. In HPM, association is analyzed by searching all trait‐associated haplotype patterns. Data mining algorithms are utilized to make the search efficient. The strength of the haplotype‐trait associations is measured by a linear model, into which a pre‐selected set of covariates is incorporated. Marker‐wise patterns of association are used for predicting the disease gene location. Genome‐wide scans of susceptibility genes for affection status as well as for the quantitative traits (Q1–Q5) were performed. First analyses were made with small sample sizes, 63–94 trios per trait, which is compared with a pilot study of a larger complex disease‐mapping project. Subsequently, the analysis was repeated with approximately 600 cases and 600 controls per trait to give higher power to the analyses. With small sample sizes, only the susceptibility genes having the strongest effects on the traits could be localized. The larger sample size gave very good results: all susceptibility genes, except one, could be correctly localized. First experiments on candidate genes suggested that HPM is applicable even to fine mapping of mutations in DNA sequence. © 2001 Wiley‐Liss, Inc.
Localization of the Q1 Mutation by Cladistic Analysis
Authors: Zhu Xiaofeng , Cooper Richard S. , Chen Guanjie , Luke Amy , Elston Robert C.
Published: July 2017

The completion of the human genome project appears to be in sight and enormous new information resources will be available. The challenge now facing the scientific community is to use this information. In this paper, we applied cladistic analysis to the sequenced data in a Genetic Analysis Workshop 12 simulation problem. The Q1 mutation was localized to a 5‐kb segment, in which the true mutation is located. Our analysis shows that cladistic analysis, which summarizes evolutionary history, can be a powerful tool in gene mapping. © 2001 Wiley‐Liss, Inc.
Predicting Quantitative Trait Levels by Modeling SNP Interaction
Authors: Fijal Bonnie A. , Kim Lee-Lian , Buxbaum Sarah G. , Witte John S.
Published: July 2017

Predicting phenotype from genotype is difficult when the phenotype is affected by a gene with numerous weakly penetrant alleles that differ only in the pattern of their single nucleotide polymorphisms (SNPs). While it is probable that SNP interactions affect phenotype, to our knowledge no one has determined the most effective way of evaluating whether SNPs interact and of modeling the interaction. Therefore, to explore this issue, we investigate here three methods of modeling SNP interaction using data from Genetic Analysis Workshop 12. Since major gene 5 (MG5) has sequence information and explains 37% of the variation in quantitative trait 5 (Q5), we focus on using SNPs within MG5 to predict Q5 among individuals who married into the pedigree. As a preliminary screening step, we reduced the number of SNPs from 269 to 34 based on their association with Q5. In our first models we assumed that SNPs affected Q5 in a simple additive manner. These models explained 34% and 15% of the variation in Q5 in women and men, respectively. Our second model was a linear model, which used individual SNPs and simple interaction terms as predictors. These models explained 36% and 16% of the variation in Q5 levels for women and men, respectively. Our last model was a “hit”‐based model which was motivated by the hypothesis that disequilibrium between SNPs may reflect the fact that SNPs affect phenotype by acting in concert with other SNPs within their “disequilibrium set.” Thus, the number of hits within the disequilibrium sets were used as predictors. These models explained 35% and 19% of the variation in Q5 for women and men, respectively. Our results suggest that phenotype can be predicted from complex patterns of weakly penetrant SNPs using relatively simple models. We concluded that SNP interaction either was not included in the simulation model, or had only a weak impact on Q5 levels. © 2001 Wiley‐Liss, Inc.
Sequence Analysis Using Logic Regression
Authors: Kooperberg Charles , Ruczinski Ingo , LeBlanc Michael L. , Hsu Li
Published: July 2017

Logic Regression is a new adaptive regression methodology that attempts to construct predictors as Boolean combinations of (binary) covariates. In this paper we use this algorithm to deal with single‐nucleotide polymorphism (SNP) sequence data. The predictors that are found are interpretable as risk factors of the disease. Significance of these risk factors is assessed using techniques like cross‐validation, permutation tests, and independent test sets. These model selection techniques remain valid when data is dependent, as is the case for the family data used here. In our analysis of the Genetic Analysis Workshop 12 data we identify the exact locations of mutations on gene 1 and gene 6 and a number of mutations on gene 2 that are associated with the affected status, without selecting any false positives. © 2001 Wiley‐Liss, Inc.
Genome Scans for Q1 and Q2 on General Population Replicates Using Loki
Authors: Shmulewitz Dvora , Heath Simon C.
Published: July 2017

The Markov Chain Monte Carlo linkage package Loki was used to perform a genome scan under realistic conditions (using a 10‐cM marker map without marker data on unsampled individuals, analyzing each chromosome separately, and without knowing the answers) for traits Q1 and Q2 on general population replicate 1. Using this approach we detected and correctly localized MG1 for Q1 and MG3 for Q2. We then repeated the analyses on replicate 1 and the “best replicate” (42) adding more information (using marker data on everyone, fitting a polygenic effect, and analyzing multiple chromosomes jointly) to see the effect on the detection of trait loci. We found that adding more data often improves the quality of the linkage signal, and reduces the false positive rate, but did not allow the detection of trait loci missed by the initial analysis. We also investigated the convergence of the sampler by repeating one multi‐chromosome analysis six times with different random number seeds. We concluded that a strategy of performing a single chromosome scan using a moderate number of sampling iterations, followed by a multi‐chromosome analysis of all chromosomes with linkage signals detected in the first scan using a longer sampling run, was an effective way of performing a genome scan on this data set. © 2001 Wiley‐Liss, Inc.
Markov Chain Monte Carlo Linkage Analysis: Effect of Bin Width on the Probability of Linkage
Authors: Slager S.L. , Juo S.H. , Durner M. , Hodge S.E.
Published: July 2017

We analyzed part of the Genetic Analysis Workshop (GAW) 12 simulated data using Monte Carlo Markov chain (MCMC) methods that are implemented in the computer program Loki. The MCMC method reports the “probability of linkage” (PL) across the chromosomal regions of interest. The point of maximum PL can then be taken as a “location estimate” for the location of the quantitative trait locus (QTL). However, Loki does not provide a formal statistical test of linkage. In this paper, we explore how the bin width used in the calculations affects the max PL and the location estimate. We analyzed age at onset (AO) and quantitative trait number 5, Q5, from 26 replicates of the general simulated data in one region where we knew a major gene, MG5, is located. For each trait, we found the max PL and the corresponding location estimate, using four different bin widths. We found that bin width, as expected, does affect the max PL and the location estimate, and we recommend that users of Loki explore how their results vary with different bin widths. © 2001 Wiley‐Liss, Inc.
Bayes Estimates of Haplotype Effects
Authors: Thomas Duncan C. , Morrison John L. , Clayton David G.
Published: July 2017

We describe a Markov chain Monte Carlo implementation of a Bayesian approach to estimating associations of a trait with a large set of haplotypes recently introduced by Clayton and Jones [Am J Hum Genet 65:1161–9, 2000]. The model uses the length of the longest segment in common between any two haplotypes to define the prior correlation structure for the set of haplotype effects, using an intrinsic autocorrelation model. When applied to the Genetic Analysis Workshop 12 data for trait Q1, we found highly significant variation between haplotypes, using either a structured or unstructured covariance matrix. © 2001 Wiley‐Liss, Inc.
Power to Localize the Major Gene for Disease Liability Is Increased After Accounting for the Effects of Related Quantitative Phenotypes
Authors: Arya Rector , Duggirala Ravindaranath , Williams Jeff T. , Almasy Laura , Blangero John
Published: July 2017

We used the simulated general population data for Genetic Analysis Workshop 12 to test whether power to localize the major gene for liability to disease is increased after accounting for the effects of correlated quantitative phenotypes. We performed the multipoint variance‐component linkage analyses for the discrete trait twice: first analysis with age, sex, and EF1 as covariates, and the second analysis with age, sex, EF1, and Q1–Q5 as covariates. Major locus heritability (h2q,) (0.80 ± 0.06) and lod score (6.4) averaged over the number of replicates used are significantly higher in the second analysis compared with the first analysis (h2q= 0.39 ± 0.12, lod = 2.6). Thus, in the present analysis, power to detect linkage and localize the genes for liability to disease appears to be increased after accounting for the effects of five quantitative traits that are correlated with the liability. © 2001 Wiley‐Liss, Inc.
Novel Selection Criteria for Genome Scans of Complex Traits
Authors: Wille Anja , Leal Suzanne M.
Published: July 2017

Due to their oligogenic inheritance, the identification of susceptibility loci for complex traits by classical selection criteria has not been very successful. One way to address this problem is to identify statistics that measure the effect of more than one locus simultaneously. In the approach described here, a p‐value is assigned to a combination of loci under the null hypothesis that none of them is linked to the disease locus. In order to examine the power of this method to detect multiple loci, the Genetic Analysis Workshop 12 general population simulated data set was analyzed using variance component methods. Using the described novel selection criteria resulted in an increase of power, however, a rejection of the null hypothesis has to be interpreted with care. © 2001 Wiley‐Liss, Inc.
Spectrum and immunophenotyping of 653 patients with B‐cell chronic lymphoproliferative disorders in China: A single‐centre analysis
Authors: Miao Yi , Cao Lei , Sun Qian , Li Xiao‐Tong , Wang Yan , Qiao Chun , Wang Li , Wang Rong , Qiu Hai‐Rong , Xu Wei , Li Jian‐Yong , Wu Yu‐Jie , Fan Lei
Published: July 2017

The incidence of B‐cell chronic lymphoproliferative disorders (B‐CLPDs) is significantly lower in China than that in western countries. There have been studies involving small cohorts with conflicting results regarding the spectrum of B‐CLPDs in China, and the types and immunophenotyping of B‐CLPDs in China remain largely unexplored. We conducted a retrospective analysis of 653 cases of B‐CLPDs seen in our centre from 2011 to 2015. Four‐colour flow cytometry was used to determine the expression of each immunological marker, and the diagnostic values of the immunological markers were also investigated. Chronic lymphocytic leukaemia (CLL) was the most common type of B‐CLPD, which was consistent with that in west countries. However, the proportions of CLL (55.9%), follicular lymphoma (2.6%), and hairy cell leukaemia (0.2%) were lower, while the proportion of lymphoplasmacytic lymphoma/WaldenstrÖm macroglobulinaemia (5.4%) was higher in China, as compared with western countries. With respect to immunophenotypic characteristics, CD23 (31.7%) was more frequently expressed in mantle cell lymphoma (MCL) in our cohort than that in western countries. Immunophenotyping was useful in differentiating MCL from CLL or B‐cell prolymphocytic leukaemia and lymphoplasmacytic lymphoma/WaldenstrÖm macroglobulinaemia from splenic marginal zone lymphoma. CD200 was of better diagnostic performance (accuracy: 94.6%) in differentiating CLL from MCL compared with CD23 (accuracy: 93.3%). Some cases of B‐CPLDs, however, had no definite diagnoses, which were diagnosed as CD5+B‐CPLDs unclassified (7.7%) and CD5−B‐CPLDs unclassified (15.8%). This is the largest study that systematically explores the spectrum and immunophenotyping of B‐CLPDs in Asia, confirming that spectrum of B‐CLPDs in China was different from that in western countries. The immunophenotypic features of B‐CLPDs were similar between China and western countries, although a few disparities exist. Cases with no definite diagnoses warrant further studies in the future.
A systematic review of the impact of mindfulness on the well‐being of healthcare professionals
Authors: Lomas Tim , Medina Juan Carlos , Ivtzan Itai , Rupprecht Silke , Eiroa‐Orosa Francisco José
Published: July 2017

Objective

Among efforts to improve the well‐being of healthcare professionals are initiatives based around mindfulness meditation. To understand the value of such initiatives, we conducted a systematic review of empirical studies pertaining to mindfulness in healthcare professionals.

Method

Databases were reviewed from the start of records to January 2016. Eligibility criteria included empirical analyses of mindfulness and well‐being outcomes acquired in relation to practice. 81 papers met the eligibility criteria, comprising a total of 3,805 participants. Studies were principally examined for outcomes such as burnout, distress, anxiety, depression, and stress.

Results

Mindfulness was generally associated with positive outcomes in relation to most measures (although results were more equivocal with respect to some outcomes, most notably burnout).

Conclusion

Overall, mindfulness does appear to improve the well‐being of healthcare professionals. However, the quality of the studies was inconsistent, so further research is needed, particularly high‐quality randomized controlled trials.
Aberrant astrocytic expression of chondroitin sulfate proteoglycan receptors in a rat model of amyotrophic lateral sclerosis
Authors: Shijo Tomomi , Warita Hitoshi , Suzuki Naoki , Kitajima Yasuo , Ikeda Kensuke , Akiyama Tetsuya , Ono Hiroya , Mitsuzawa Shio , Nishiyama Ayumi , Izumi Rumiko , Aoki Masashi
Published: July 2017

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease. Progressive and systemic loss of motor neurons with gliosis in the central nervous system (CNS) is a neuropathological hallmark of ALS. Chondroitin sulfate proteoglycans (CSPGs) are the major components of the extracellular matrix of the mammalian CNS, and they inhibit axonal regeneration physically by participating to form the glial scar. Recently, protein tyrosine phosphatase sigma (PTPσ) and leukocyte common antigen‐related protein were discovered as CSPG receptors that play roles in inhibiting regeneration. Here we examined the expression of CSPG receptors in transgenic female rats overexpressing an ALS‐linked mutant cytosolic Cu/Zn superoxide dismutase gene (SOD1). In contrast to controls, multiple immunofluorescence analyses revealed aberrant expression of CSPG receptors dominantly in reactive astrocytes, while PTPσ expression in neurons decreased in the spinal ventral horns of ALS transgenic rats. The aberrant and progressive astrocytic expression of CSPG receptors and reactive astrocytes themselves may be therapeutic targets for reconstructing a regeneration‐supportive microenvironment under neurodegenerative conditions such as ALS.
Development of resurgent and persistent sodium currents in mesencephalic trigeminal neurons
Authors: Enomoto Akifumi , Seki Soju , Tanaka Susumu , Ishihama Kohji , Yamanishi Tadashi , Kogo Mikihiko , Hamada Suguru
Published: July 2017

Sodium channels play multiple roles in the formation of neural membrane properties in mesencephalic trigeminal (Mes V) neurons and in other neural systems. Mes V neurons exhibit conditional robust high‐frequency spike discharges. As previously reported, resurgent and persistent sodium currents (INaR and INaP, respectively) may carry small currents at subthreshold voltages that contribute to generation of spike firing. These currents play an important role in maintaining and allowing high‐frequency spike discharge during a burst. In the present study, we investigated the developmental changes in tetrodotoxin‐sensitive INaR and INaP underlying high‐frequency spike discharges in Mes V neurons. Whole‐cell patch‐clamp recordings showed that both current densities increased one and a half times from postnatal day (P) 0–6 neurons to P7–14 neurons. Although these neurons do not exhibit subthreshold oscillations or burst discharges with high‐frequency firing, INaR and INaP do exist in Mes V neurons at P0–6. When the spike frequency at rheobase was examined in firing Mes V neurons, the developmental change in firing frequency among P7–14 neurons was significant. INaR and INaP density at −40 mV also increased significantly among P7–14 neurons. The change to an increase in excitability in the P7–14 group could result from this quantitative change in INaP. In neurons older than P7 that exhibit repetitive firing, quantitative increases in INaR and INaP density may be major factors that facilitate and promote high‐frequency firing as a function of age in Mes V neurons.
Raman probing of lipids, proteins, and mitochondria in skeletal myocytes: a case study on obesity
Authors: Brazhe Nadezda A. , Nikelshparg Evelina I. , Prats Clara , Dela Flemming , Sosnovtseva Olga
Published: July 2017

We propose a novel approach to assess simultaneously lipid composition in lipid droplets, the redox state of cytochromes, and the relative amount of [Fe–S] clusters in the electron transport chain in the mitochondria of skeletal myocytes by means of near‐infrared Raman spectroscopy. Mitochondria dysfunction, disruption of oxidative phosphorylation, and change in lipid metabolism may be a consequence of the obesity‐related insulin resistance and diabetes mellitus. Lipid metabolism affects the state of the mitochondrial electron transport chain although these relations are not well understood. We demonstrate the applicability of the proposed approach in a case study of myocytes of an obese patient before and after the gastric bypass surgery in comparison with a healthy lean donor. Ratios from chosen Raman peaks were calculated and compared between the different subjects. We show that the suggested technique allows to estimate qualitatively the relative amount of cholesterol and unsaturated lipids, ordering of lipid phase in lipid droplets, changes in the redox state of c‐type and b‐type cytochromes, and the relative amount of [Fe–S] clusters in the mitochondria of intact myocytes. The proposed approach opens perspectives to uncover relations between the functional state of mitochondrial cytochromes and lipid composition and to develop a monitoring tool once it is applied to a wide cohort of patients. Copyright © 2017 John Wiley & Sons, Ltd.
Enhanced Raman and photoluminescence response in monolayer MoS2 due to laser healing of defects
Authors: Bera Achintya , Muthu D. V. S. , Sood A. K.
Published: July 2017

Bound quasiparticles, negatively charged trions and neutral excitons are associated with the direct optical transitions at the K‐points of the Brillouin zone for monolayer MoS2. The change in the carrier concentration, surrounding dielectric constant, and defect concentration can modulate the photoluminescence and Raman spectra. Here, we show that exposing the monolayer MoS2 in air to a modest laser intensity for a brief period of time enhances simultaneously the photoluminescence intensity associated with both trions and excitons, together with ∼3 to 5 times increase of the Raman intensity of first‐order and second‐order modes. The simultaneous increase of photoluminescence from trions and excitons cannot be understood based only on known scenario of depletion of electron concentration in MoS2 by adsorption of O2 and H2O molecules. This is explained by laser‐induced healing of defect states resulting in reduction of nonradiative Auger processes. This laser healing is corroborated by an observed increase of intensity of both the first‐order and second‐order longitudinal acoustic Raman modes at the M‐point of Brillouin zone by a factor of ∼3 to 5. The A1g mode hardens by ∼1.4 cm−1, whereas the
mode softens by ∼1 cm−1. The second‐order longitudinal acoustic Raman mode at the M‐point of Brillouin zone at ∼440 cm−1 shows an increase in wavenumber by ∼8 cm−1 with laser exposure. These changes are a combined effect of change in electron concentrations and oxygen‐induced lattice displacements. Copyright © 2017 John Wiley & Sons, Ltd.
In situ Raman spectroscopic studies of polyvinyl toluene under laser‐driven shock compression and comparison with hydrostatic experiments
Authors: Rastogi Vinay , Chaurasia S. , Rao Usha , Sijoy C. D. , Poswal H. K. , Mishra V. , Kumar Manmohan , Deo M. N.
Published: July 2017

Shock wave‐induced changes in intra‐molecular vibrations of polyvinyl toluene (PVT) in a confined geometry target assembly are studied over the pressure range of 0–2.25 GPa. A comparative study of the behavior of PVT in the dynamic and quasi‐hydrostatic compression is performed. A 1D radiation hydrodynamic simulation has been performed to calculate the equation of state of the PVT. In present study, the fundamental modes, ν12 mode at 1001 cm−1, ν18a mode at 1031 cm−1 and ν8a mode at 1602 cm−1, of PVT are extensively analyzed. At a pressure of 1.58 GPa, peak shift of 4.24, 5.16 and 6.41 cm−1 for the modes 1001, 1031 and 1602 cm−1, respectively, are observed and are in good agreement with the hydrostatic measurement. Grüneisen parameters are calculated for each modes, which indicates that the primarily volume changes (below 1 GPa) are due to free volume and compression of the inter‐chain bonds, and not because of changes in intermolecular bond lengths. The shock velocity in the sample at pressure 2.25 GPa is calculated as 3.6 ±0.46 km/s by measuring the ratios of the experimental shocked volume to total volume of the sample measured in the time‐resolved measurement and is in good agreement with the simulation result. A comparative study of shock pressure on PVT and polystyrene molecules is also done. These materials are of great interest as they are widely being used as a host material in scintillator detectors, which are used for the measurement of high‐frequency electromagnetic radiation. Copyright © 2017 John Wiley & Sons, Ltd.
Temporal pattern of wildlife‐train collisions in Poland
Authors: Krauze‐Gryz Dagny , Żmihorski Michał , Jasińska Karolina , Kwaśny Łukasz , Werka Joanna
Published: July 2017

The development and modernization of railway infrastructures in many countries has increased the frequency of wildlife‐train collisions. Our objective was to describe the temporal pattern of train accidents related to wild ungulates (i.e., roe deer [Capreolus capreolus], red deer [Cervus elaphus], moose [Alces alces], and wild boar [Sus scrofa]) to determine when the risk of collision is highest. We gathered data on train collisions with wild ungulates throughout Poland between 2012 and 2015 from Polish Railways Polskie Koleje Państwowe SA. We used generalized additive mixed models to investigate whether the number of collisions changed over time. The number of wildlife‐train collisions varied depending on time of year. Most collisions occurred in autumn when animals form winter herds and migrate to and stay in winter refugia. The fewest collisions occurred in summer during breeding season. For all species except red deer, the number of collisions was significantly lower during weekends compared to weekdays. The distribution of collisions with regard to time of day was significantly different from simulated uniform random distribution, with peaks before dawn and after dusk, which reflect activity peaks of ungulates. During the day, the probability of collision was lower, with only single events observed between 0800 and 1600. We observed another collision‐free period after midnight until 0400, probably because train traffic was minimal during this period. Most train collisions with ungulates took place in relatively narrow time windows in terms of time of year and time of day (i.e., 50% of the recorded cases took place in ∼17% of the total time observed). Consequently, mitigation measures of lowering speed limits can be applied during times when the risk of collision is highest. © 2017 The Wildlife Society.
Dynamics of the North–South Capital Flows or Rise of South–South Land Deals? Features of Land Acquisition in Ethiopia
Authors: Teklemariam Dereje , Azadi Hossein , Nyssen Jan , Lanckriet Sil , Asfaha Tesfaalem Ghebreyohannes , Haile Mitiku , Taheri Fatemeh , Witlox Frank
Published: July 2017

Transnational land deals are among the most contested but inadequately understood topics. In this paper, we focus on the features of large‐scale transnational land deals (LSTLDs) in the Global South through an examination of Ethiopia. We apply a mixed method (qualitative and quantitative) research design.Results indicate that in 2005–2015, the government leased nearly 2·47 million ha of the country's approximate total 114 million ha area and offered 11·5 million ha of cultivable land to domestic and transnational investors. We explore the prevalence of LSTLDs deals by companies of the Global South, particularly entrepreneurs from India. Ethiopia's example validates emerging arguments on the rise of South–South investment deals rather than the established explanation of North–South capital flows. However, 75% of the land deals show poor performance. The study shows that LSTLDs have contributed to raising domestic agricultural production but have resulted in non‐performing loans of the banks of the host country. In sum, the land deals have resulted in financial grabbing, where Ethiopian banks end up with non‐performing loans and then must chase investors to settle the approximate €791 million in loans that investors borrowed for their projects. Copyright © 2017 John Wiley & Sons, Ltd.
The role of subduction and gravitational sinking in particle export, carbon sequestration, and the remineralization length scale in the California Current Ecosystem
Authors: Stukel Michael R. , Song Hajoon , Goericke Ralf , Miller Arthur J.
Published: July 2017

Particles and aggregates created in the surface layers of the ocean are transported not only by gravity, but also by the horizontal and vertical advection of the surrounding water. Subduction, in particular, can transport organic matter from the surface ocean to the mesopelagic in a manner that is not likely to be detected by typical in situ carbon export measurements (e.g., sediment traps and 238U‐234Th disequilibrium). To assess the importance of subduction to the biological pump, we combined in situ sediment trap, thorium, primary productivity, and particulate organic carbon (POC) measurements with a data‐assimilative physical circulation model and a Lagrangian particle tracking model. We develop a simple parameterization of two alternative particle sinking processes (Phytoplankton‐Fecal Pellet [PFP] and Aggregation) using results from 13 extensively sampled water parcels in the California Current Ecosystem. Both parameterizations suggested that subduction is an important, at times dominant, mechanism of POC vertical export in the region (median 44% and 23% contribution to total POC export for PFP and Aggregate parameterizations at the 100‐m depth horizon). The percentage contribution of subduction was highly variable across water parcels (ranging from 7% to 90%), with subduction typically more important in offshore, oligotrophic regions. On average the fate of particles that are passively transported out of the surface layer by advection is different from that of particles that sink across the 100‐m depth horizon. Subducted particles were predominantly remineralized shallower than 150 m, while approximately 50% of gravitationally exported POC was remineralized at depths > 500 m.
Outcome of liver transplantation in patients with prior bariatric surgery
Authors: Safwan Mohamed , Collins Kelly M. , Abouljoud Marwan S. , Salgia Reena
Published: July 2017

Nonalcoholic fatty liver disease is becoming the leading cause of disease resulting in liver transplantation (LT). As a result of this trend, more LT candidates are presenting with prior history of bariatric surgery (BS). Over the last decade, 960 patients underwent LT at our institution; 11 (1.1%) had prior BS. The most common type of BS was Roux‐en‐Y gastric bypass (n = 9) with 1 sleeve gastrectomy and 1 jejunoileal bypass. A total of 9 patients underwent LT alone, and 2 underwent simultaneous liver‐kidney transplantation. The most common indication for LT was nonalcoholic steatohepatitis (n = 10) with 5 having additional diagnosis of alcoholic liver disease. The 30‐day reoperation rate was 36.4% (n = 4); indications were bile duct repair (n = 3) and wound repair (n = 1). In the first 6 months after LT, biliary complications were seen in 54.5% (n = 6) of the patients. Both patient and graft survival rates at 1 and 2 years were 81.8% (n = 9) and 72.7% (n = 8), respectively. A total of 8 patients (72.7%) had indications for liver biopsy after LT; significant macrovesicular steatosis was found in 2 (18.2%). In patients with a history of alcohol consumption, 2 (40.0%) relapsed after LT. Two patients (18.2%) had a history of diet‐controlled diabetes before LT; 1 of these patients became insulin dependent after LT. Mean body mass index (BMI) at LT was 31.0 ± 5.7 kg/m2. Mean BMI at 1, 6, and 12 months after LT was 28.3 ± 5.8, 28.0 ± 3.2, and 31.0 ± 6.6 kg/m2, respectively. Mean preoperative albumin was 2.6 ± 0.6 mg/dL. Patients showed improvement in albumin after LT, with mean albumin of 2.7 ± 0.6 and 3.2 ± 0.5 mg/dL at 1 and 3 months, respectively. The liver profile was stable after LT, with mean aspartate aminotransferase of 32.9 ± 18.4 and 26.6 ± 19.8 IU/L and alanine aminotransferase of 28.0 ± 17.5 and 30.2 ± 17.0 IU/L at 6 and 12 months, respectively. In conclusion, outcomes of LT patients with prior BS are comparable with other transplant recipients with regards to patient and graft survival and post‐LT complication rates. Liver Transplantation 23 1415–1421 2017 AASLD.
Dynamic properties of imidazolium orthoborate ionic liquids mixed with polyethylene glycol studied by NMR diffusometry and impedance spectroscopy
Authors: Filippov Andrei , Azancheev Nail , Gibaydullin Amal , Bhattacharyya Shubhankar , Antzutkin Oleg N. , Shah Faiz Ullah
Published: July 2017

We used 1H pulsed field gradient nuclear magnetic resonance to study the self‐diffusion of polyethylene glycol (PEG) with average molecular mass of 200 and ions in mixtures of PEG with imidazolium bis(mandelato)borate (BMB) and imidazolium bis(oxalato)borate ionic liquids (ILs). The IL was mixed with PEG in the concentration range of 0–100 wt%. Within the temperature range of 295 to 353 K, the diffusion coefficient of BMB is slower than that of the imidazolium cation. The diffusion coefficients of PEG, as well as the imidazolium cation and BMB anions, differ under all experimental conditions tested. This demonstrates that the IL in the mixture is present in at least a partially dissociated state. Generally, increasing the concentration of PEG leads to an increase in the diffusion coefficients of PEG and both the ions and decreases their activation energy for diffusion. Nuclear magnetic resonance chemical shift alteration analysis showed that the presence of PEG changes the chemical shifts of both ions but in different directions. Impedance spectroscopy was used to measure the ionic conductivity of the ILs mixed with PEG. Copyright © 2017 John Wiley & Sons, Ltd.
Modeling and Experimentation of RAFT Solution Copolymerization of Styrene and Butyl Acrylate, Effect of Chain Transfer Reactions on Polymer Molecular Weight Distribution
Authors: Jiang Jie , Wang Wen‐Jun , Li Bo‐Geng , Zhu Shiping
Published: July 2017

Chain transfer reactions widely exist in the free radical polymerization and controlled radical polymerization, which can significantly influence polymer molecular weight and molecular weight distribution. In this work, the chain transfer reactions in modeling the reversible addition–fragmentation transfer (RAFT) solution copolymerization are included and the effects of chain transfer rate constant, monomer concentration, and comonomer ratio on the polymerization kinetics and polymer molecular weight development are investigated. The model is verified with the experimental RAFT solution copolymerization of styrene and butyl acrylate, with good agreements achieved. This work has demonstrated that the chain transfer reactions to monomer and solvent can have significant impacts on the number‐average molecular weight (Mn) and dispersity (Ð).
Chemoenzymatic Synthesis in Flow Reactors: A Rapid and Convenient Preparation of Captopril
Authors: De Vitis Valerio , Dall'Oglio Federica , Pinto Andrea , De Micheli Carlo , Molinari Francesco , Conti Paola , Romano Diego , Tamborini Lucia
Published: July 2017

The chemoenzymatic flow synthesis of enantiomerically pure captopril, a widely used antihypertensive drug, is accomplished starting from simple, inexpensive, and readily available reagents. The first step is a heterogeneous biocatalyzed regio‐ and stereoselective oxidation of cheap prochiral 2‐methyl‐1,3‐propandiol, performed in flow using immobilized whole cells of Acetobacter aceti MIM 2000/28, thus avoiding the use of aggressive and environmentally harmful chemical oxidants. The isolation of the highly hydrophilic intermediate (R)‐3‐hydroxy‐2‐methylpropanoic acid is achieved in‐line by using a catch‐and‐release strategy. Then, three sequential high‐throughput chemical steps lead to the isolation of captopril in only 75 min. In‐line quenching and liquid–liquid separation enable breaks in the workflow and other manipulations to be avoided.
Efficient modification with flexible spacing coating for in situ reversible assembly of semirigid macroscopic objects through hierarchical metal coordination
Authors: Akram Raheel , Arshad Anila , Wu Yangxia , Wu Zhanpeng , Wu Dezhen
Published: July 2017

Macroscopic supramolecular assembly plays a key role to bridge the fundamental researches on molecular recognition to the potential applications as supramolecular materials. However, the challenge remains to promote the research from soft hydrogel system to semirigid objects or building blocks. Herein, the concept of flexible spacing coating was employed to modify the model polydimethylsiloxane building blocks, and reversible macroscopic assembly was successfully realized through introducing highly directional, dynamic, and reversible coordinate interactions as driving forces. The driving force for the macroscopic assembly was confirmed by introducing highly competitive ethylene diamine tetra acetic acid solution as an orthodox system to disassemble the assembled blocks. Moreover, the coordinate interaction was further understood through unique in situ measurements of binding forces between building blocks during assembly process. This work of macroscopic supramolecular assembly provides an in situ visible platform, which is significant to clarify the highly fascinating and facile coordinate interactions on the macroscopic assembly behavior.
Morphology and interfacial strength of nonisothermally fusion bonded hard and soft thermoplastics
Authors: Chandran Rajasundar , Plummer Christopher J.G. , Bourban Pierre‐Etienne , Månson Jan‐Anders E.
Published: July 2017

Nonisothermally fusion bonded butt joints were prepared by overmolding thermoplastic elastomers (TPEs) onto isotactic polypropylene (iPP) inserts in order to investigate the effect of processing conditions on the bond strength and interfacial microstructure. The mold temperature (Tm) was the most important factor for bond strength, as determined from interfacial mechanical tests. Extensive melting and recrystallization took place at the surface of the iPP insert at high Tm, promoted by migration of plasticizer from the TPE, whereas the original structure of the iPP remained intact at low Tm. Bond strengths of at least 50% of the cohesive strength of the TPE were nevertheless obtained at low Tm, suggesting intimate contact between the TPE melt and the iPP surface to be sufficient to provide useful adhesive bond strengths in these materials. The influence of pressure was less marked than the Tm, high pressures not being necessary to achieve intimate contact for the bonding times of about 5 s used here. However, the combination of a low bonding pressure with a high Tm typically led to poor quality bonds in thick specimens owing to uncompensated shrinkage during solidification, and voiding at the interface and in the melt zone of the iPP insert. POLYM. ENG. SCI., 58:E82–E92, 2018. © 2017 Society of Plastics Engineers
Crystallization of polyamide 11 during injection molding
Authors: Jariyavidyanont Katalee , Williams Jason L. , Rhoades Alicyn M. , Kühnert Ines , Focke Walter , Androsch René
Published: July 2017

The semicrystalline morphology of injection moldings of polyamide 11 (PA 11) prepared using mold temperatures of 25, 50, and 80°C was investigated. Regardless of the mold temperature, position‐resolved X‐ray diffraction (XRD) and polarized‐light optical microscopy (POM) revealed presence of poor/imperfect α‐crystals with an almost hexagonal arrangement of molecular stems in a nonspherulitic superstructure in the skin, and formation of α‐crystals and spherulites in the core. With increasing mold temperature, the thickness of the skin layer decreased, and the perfection of α‐crystals and the spherulite size in the core increased. The experimental observations are discussed in terms of predicted crystallization temperatures, with the prediction based on cooling‐rate simulations for the various parts of the injection moldings using Moldflow® and analysis of crystallization of the relaxed melt using fast scanning chip calorimetry, XRD, and POM. It is shown that the structure gradient in PA 11 injection moldings can be forecast without considering the effects of shear for this particular polymer. POLYM. ENG. SCI., 58:1053–1061, 2018. © 2017 Society of Plastics Engineers
Synergy of supercritical CO2 and superheated H2O for enhanced processability of polyethersulfone towards open cell foams
Authors: Owusu‐Nkwantabisah Silas , Staudt Claudia , Lesser Alan J.
Published: July 2017

Processing of a high glass transition (Tg) polymer such as polyethersulfone (PES; Tg = 225°C) poses a challenge as it requires high processing temperatures or sometimes toxic solvents. In this work, we report of a facile process using superheated water (shH2O) and supercritical carbon dioxide (scCO2) co‐media. PES solids were foamed in the scCO2/shH2O co‐media or scCO2 alone in a batch process at different temperatures. The scCO2/shH2O produced a synergistic effect and achieved PES foams even at processing temperatures as low as 85°C below the nominal Tg; whereas, scCO2 alone required higher processing temperatures. Moreover, the scCO2/shH2O co‐media produced highly porous PES foams that were at least 23% higher in porosity than what was obtained using scCO2 alone. In addition, the scCO2/shH2O produced open cell foams at some processing conditions; whereas, scCO2 produced closed cell morphologies. Since both CO2 and H2O are innocuous, this approach has potential for use in the preparation of ultrafiltration membranes, which currently require the use of toxic solvents for their fabrication by way of the phase inversion process. Moreover, the use of scCO2/shH2O is a cost‐effective approach for the processing of high Tg polymers at significantly lower temperatures. POLYM. ENG. SCI., 58:1108–1114, 2018. © 2017 Society of Plastics Engineers