bluuebunny/crossref_metadata_2025 huggingface dataset:
Bivariate frequency analysis of nonstationary low‐flow series based on the time‐varying copula
Authors: Jiang Cong , Xiong Lihua , Xu Chong‐Yu , Guo Shenglian
Published: July 2014

Many studies have analysed the nonstationarity in single hydrological variables due to changing environments. Yet, few researches have been done to investigate how the dependence structure between different individual hydrological variables is affected by changing environments. To investigate how the reservoirs have altered the dependence structure between river flows at different locations on the Hanjiang River, a time‐varying copula model, which takes the nonstationarity in the marginal distribution and/or the time variation in dependence structure between different hydrological series into consideration, is presented in this paper to perform a bivariate frequency analysis for the low‐flow series from two neighbouring hydrological gauges. The time‐varying moments model with either time or reservoir index as explanatory variables is applied to build the time‐varying marginal distributions of the two low‐flow series. It's found that both marginal distributions are nonstationary, and the reservoir index yields better performance than the time index in describing the nonstationarities in the marginal distributions. Then, the copula with the dependence parameter expressed as a function of either time or reservoir index is applied to model the variable dependence between the two low‐flow series. The copula with reservoir index as the explanatory variable of the dependence parameter has a better fitting performance than the copula with the constant or the time‐trend dependence parameter. Finally, the effect of the time variation in the joint distribution on three different types of joint return periods (i.e. AND, OR and Kendall) of low flows at two neighbouring hydrological gauges is presented. Copyright © 2014 John Wiley & Sons, Ltd.
Out-of-sample validation for structured expert judgment of Asian carp establishment in Lake Erie
Authors: Cooke Roger M , Wittmann Marion E , Lodge David M , Rothlisberger John D , Rutherford Edward S , Zhang Hongyan , Mason Doran M
Published: July 2014

Structured expert judgment (SEJ) is used to quantify the uncertainty of nonindigenous fish (bighead carp [Hypophthalmichthys nobilis] and silver carp [H. molitrix]) establishment in Lake Erie. The classical model for structured expert judgment model is applied. Forming a weighted combination (called a decision maker) of experts' distributions, with weights derived from performance on a set of calibration variables from the experts' field, exhibits greater statistical accuracy and greater informativeness than simple averaging with equal weights. New methods of cross validation are applied and suggest that performance characteristics relative to equal weighting could be predicted with a small number (1–2) of calibration variables. The performance-based decision maker is somewhat degraded on out-of-sample prediction, but remained superior to the equal weight decision maker in terms of statistical accuracy and informativeness. Integr Environ Assess Manag 2014;10:522–528. © 2014 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals, Inc. on behalf of SETAC.

Key Points

Structured expert judgment is applied to quantify uncertainty in Asian carp establishment in Lake Erie Calibration variables from the experts' field are used to enable performance-based combination In sample validation is applied to the combination of expert judgments and to the experts Out-of-sample validation is applied to the performance-based combination method
Osmotic regulation and tissue localization of the myo‐inositol biosynthesis pathway in tilapia (Oreochromis mossambicus) larvae
Authors: Sacchi Romina , Gardell Alison M. , Chang Nicole , Kültz Dietmar
Published: July 2014

The myo‐inositol biosynthesis (MIB) pathway converts glucose‐6‐phosphate to the compatible osmolyte myo‐inositol, which protects cells from salinity stress. We exposed tilapia larvae just after yolk sac resorption to various hypersaline environments and recorded robust induction of the enzymes that constitute the MIB pathway, myo‐inositol‐phosphate synthase (MIPS), and inositol monophosphatase 1 (IMPA1). Strong up‐regulation of these enzymes is evident at both mRNA (quantitative real‐time PCR) and protein (densitometric analysis of Western blots) levels. The highest level of induction of these enzymes occurs at the highest salinity that larvae were exposed to (90 ppt). Less severe salinity stress causes a proportionately reduced induction of the MIB pathway. Two distinct MIPS mRNA variants are present in tilapia larvae and both are induced at comparable levels for all the salinity challenges tested (34, 70, and 90 ppt). Immunohistochemical localization of IMPA1 protein in sagittal sections of salinity stressed and control larvae identified tissues that are particularly potent in inducing the MIB pathway. These tissues include the skin (epidermis), gills, eye (ciliary epithelium) and heart. In particular, the epidermis directly facing the external milieu showed a very strong induction of IMPA1 immunoreactivity. IMPA1 induction in response to salinity stress was not observed in other tissues suggesting that tilapia larvae may also utilize compatible organic osmolytes other than solely myo‐inositol for osmoprotection. We conclude that the MIB pathway plays an important role in protecting multiple (but not all) tissues of tilapia larvae from hyperosmotic salinity stress. J. Exp. Zool. 321A: 457–466, 2014. © 2014 Wiley Periodicals, Inc.
Computer‐automated focus lateralization of temporal lobe epilepsy using fMRI
Authors: Chiang Sharon , Levin Harvey S. , Haneef Zulfi
Published: July 2014

Purpose

To compare the performance of computer‐automated diagnosis using functional magnetic resonance imaging (fMRI) interictal graph theory (CADFIG) to that achieved in standard clinical practice with MRI, for lateralizing the affected hemisphere in temporal lobe epilepsy (TLE).

Materials and Methods

Interictal resting state fMRI and high‐resolution MRI were performed on 14 left and 10 right TLE patients. Functional topology measures were calculated from fMRI using graph theory, and used to lateralize the epileptogenic hemisphere using quadratic discriminant analysis. Leave‐one‐out cross‐validation prediction accuracy of CADFIG was compared to performance based on expert manual analysis (MA) of MRI, using video EEG as the "gold standard" for focus lateralization.

Results

CADFIG correctly lateralized 95.8% (23/24) of cases, compared to 66.7% (16/24) with expert MA of MRI. Combining MA with CADFIG allowed all cases (24/24) to be correctly lateralized. CADFIG correctly identified the affected hemisphere for all patients (8/8) where MRI failed to lateralize.

Conclusion

CADFIG based on fMRI lateralized the affected hemisphere in TLE with superior performance compared to expert MA of MRI. These results demonstrate that functional patterns in fMRI can be used with automated machine learning for diagnostic lateralization in TLE. Addition of fMRI‐based tests to existing protocols for identifying the affected hemisphere in presurgical assessment can improve diagnostic accuracy and surgical outcome in TLE.J. Magn. Reson. Imaging 2015;41:1689–1694. © 2014 Wiley Periodicals, Inc.
Characterization of the enterovirus 71 VP1 protein as a vaccine candidate
Authors: Zhou Shi‐Li , Ying Xiao‐Ling , Han Xue , Sun Xian‐Xun , Jin Qi , Yang Fan
Published: July 2014

Enterovirus 71 (EV71) is an important agent responsible for hand‐foot‐and‐mouth disease (HFMD), which can cause severe neurological complications and death in children. However, there is no specific treatment for EV71 infection, and a safe and effective vaccine is needed urgently. In this study, an effective and economical method for the production of EV71‐VP1 protein was developed, and the VP1 protein was evaluated in humoral and cellular immune responses as an EV71 vaccine. The results revealed that the VP1 protein induced high titers of cross‐neutralizing antibodies for different EV71 subtypes, and elicited significant splenocyte proliferation. The high levels of IFN‐r and IL‐10 showed the VP1 protein induced a mixed Th1 and Th2 immune response. Vaccinated female mice could confer protection in their neonatal offspring. Compared with the inactivated EV71, the VP1 protein elicited similar humoral and cellular responses, but the engineered protein is safer, less expensive and can be produced more efficiently. Therefore, EV71‐VP1 protein can induce effective immunologic protection against EV71 and is an ideal candidate against EV71 infection.J. Med. Virol. 87:256–262, 2015.© 2014 Wiley Periodicals, Inc.
Artemin augments survival and axon regeneration in axotomized retinal ganglion cells
Authors: Omodaka Kazuko , Kurimoto Takuji , Nakamura Orie , Sato Kota , Yasuda Masayuki , Tanaka Yuji , Himori Noriko , Yokoyama Yu , Nakazawa Toru
Published: July 2014

Artemin, a recently discovered member of the glial cell line‐derived neurotrophic factor (GDNF) family, has neurotrophic effects on damaged neurons, including sympathetic neurons, dopamine neurons, and spiral ganglion neurons both in vivo and in vitro. However, its effects on retinal cells and its intracellular signaling remain relatively unexplored. During development, expression of GFRα3, a specific receptor for artemin, is strong in the immature retina and gradually decreases during maturation, suggesting a possible role in the formation of retinal connections. Optic nerve damage in mature rats causes levels of GFRα3 mRNA to increase tenfold in the retina within 3 days. GFRα3 mRNA levels continue to rise within the first week and then decline. Artemin, a specific ligand for GFRα3, has a neuroprotective effect on axotomized retinal ganglion cells (RGCs) in vivo and in vitro via activation of the extracellular signal‐related kinase− and phosphoinositide 3‐kinase−Akt signaling pathways. Artemin also has a substantial effect on axon regeneration in RGCs both in vivo and in vitro, whereas other GDNF family members do not. Therefore, artemin/GFRα3, but not other GDNF family members, may be of value for optic nerve regeneration in mature mammals. © 2014 Wiley Periodicals, Inc.
Polarized Raman spectroscopy of aligned insulin fibrils
Authors: Sereda Valentin , Lednev Igor K.
Published: July 2014

Amyloid fibrils are associated with many neurodegenerative diseases. The application of conventional techniques of structural biology, X‐ray crystallography and solution NMR, for fibril characterization is limited because of the noncrystalline and insoluble nature of the fibrils. Here, polarized Raman spectroscopy was used to determine the orientation of selected chemical groups in aligned insulin fibrils, specifically of peptide carbonyls. The methodology is solely based on the measurement of the change in Raman scattered intensity as a function of the angle between the incident laser polarization and the aligned fibrils. The order parameters 〈P2〉 and 〈P4〉 of the orientation distribution function were obtained, and the most probable distribution of C=O group orientation was calculated. The results indicate that the peptides' carbonyl groups are oriented at an angle of 13 ± 5° from the fibril axis, which is consistent with previously reported qualitative descriptions of an almost parallel orientation of the C=O groups relative to the main fibril axis. Copyright © 2014 John Wiley & Sons, Ltd.
The role of the American College of Surgeons' cancer program accreditation in influencing oncologic outcomes
Authors: Knutson Allison C. , McNamara Erica J. , McKellar Daniel P. , Kaufman Cary S. , Winchester David P.
Published: July 2014

The multidisciplinary Commission on Cancer (CoC) and National Accreditation Program for Breast Centers (NAPBC), administered by the American College of Surgeons (ACoS), defines evidence and consensus‐based standards, require an operational infrastructure, collect high quality cancer data, and validate compliance with standards through external peer review. A survey of our constituents confirms a high level of agreement that accreditation is regarded as important in improving oncologic outcomes through compliance with standards that include continuous quality improvement. J. Surg. Oncol. 2014 110:611–615. © 2014 Wiley Periodicals, Inc.
Volume‐outcome disparities and informed consent: What should surgeons disclose?
Authors: Stell Lance K.
Published: July 2014

It has been repeatedly shown that higher procedure volumes, by hospital and by physician, are associated with better outcomes. Buttressed by large‐scale selective service purchasing, surgical care for many volume‐sensitive operations has been regionalized. However, the implications of outcome disparity data for obtaining valid patient consent remain uncertain. When the first large scale outcome study appeared showing empirically that outcomes are volume‐related, two prominent bioethicists promptly insisted that such information was material to a reasonable patient's decision whether and where to have a volume‐sensitive operation and that surgeons at low‐volume hospitals should disclose it. More recently, two surgical oncologists have reiterated that argument, most especially when patients are making decisions about pancreatic or esophageal resections. This proposal tantalizingly appeals to the concept of patient empowerment, supposedly showing appropriate respect for the patient's interest in self‐determination by having his surgeon (or physician), rather than others, outline for him personally the risks and benefits associated with surgical care delivered at different hospitals. But on the contrary, a surgeon's conducting a truthful, non‐misleading, non‐confusing informed consent discussion of statistical outcome disparities in the relentlessly shrinking time typically allowed for this conversation is unrealistic as a general requirement. The traditional approach to informed consent is simpler, less fraught and preferable. By law, a surgeon who is licensed to practice independently and who evidences willingness to examine and to offer an operation to a patient conveys (1) an implicit standard of care assurance, and (2) a fiduciary assurance. In other words, it goes without saying that the surgeon holds it out to the patient that s/he possesses the training and skill necessary to perform the offered service with reasonable skill and safety as measured by the applicable standard of care; that s/he will act in good faith and use his/her best medical judgment on the patient's behalf. Liability attaches when patient harm results from a surgeon's failure on either count. It also goes without saying that the surgeon extends similar assurances for care provided by trainees who are under his or her direct supervisory authority and control. The traditional theory of informed consent forestalls requiring desultory discussions of volume‐outcome disparities and will be defended here.J. Surg. Oncol. 2014 110:636–642. © 2014 Wiley Periodicals, Inc.
Artist Authenticity: How Artists’ Passion and Commitment Shape Consumers’ Perceptions and Behavioral Intentions across Genders
Authors: Moulard Julie Guidry , Rice Dan Hamilton , Garrity Carolyn Popp , Mangus Stephanie M.
Published: July 2014

Despite the fact that the art market is a multibillion dollar industry, marketing researchers have yet to fully explore the factors that drive consumers’ purchase intentions toward fine art. This research proposes that information about the artist who created a particular work is an important piece of information that consumers consider. This work is the first to empirically examine the impact of how one such characteristic of the artist, perceived authenticity, affects consumers’ behavioral intentions toward the art. This research, drawing on authenticity research in the arts, marketing, and psychology, builds on the proposed art valuation framework presented by Marshall and Forrest () by testing the effect of consumers’ perceptions of the artist's motives. Empirical data involving 518 respondents were analyzed using structural equation modeling. The results revealed that artist authenticity affected attitude toward the artist, conceptualized as a human brand, which in turn influenced consumers’ evaluation of the artist's work and their behavioral intentions. In addition, this research provides support for the selectivity model by showing woman and men evaluate art differently. Attitude toward the artwork had a stronger effect on behavioral intentions for women compared to men, whereas attitude toward the artist had a stronger effect on behavioral intentions for men compared to women. Overall, the results reveal that consumers use information about that artist's brand in the valuation of the artwork and have important practical implications for the management of the artist's human brand.
Pièces de Résistance? Core and Casual Consumers’ Valuations of Aesthetically Incongruent Artworks
Authors: Althuizen Niek , Sgourev Stoyan V.
Published: July 2014

Research in consumer psychology suggests that there is limited room for acclaimed producers or brands to experiment with the aesthetic appearance and design of their products. This premise is rooted in consumers’ preference for aesthetic congruity and the cognitive difficulty associated with evaluating incongruent offerings. Yet examples of successful artists whose work clearly defies the imperative of congruity do exist. Although these artists are the exception rather than the rule, their success suggests that under certain conditions the audience may tolerate incongruity. The effects of the type of audience and the status of the artist on consumer valuations of aesthetically congruent and incongruent artworks were analyzed in a large within‐subjects experiment. The results show that congruity weighs more heavily for core consumers than for casual consumers, regardless of the status of the artist. Mediation analyses reveal that dislike (affective factor) and difficulty of evaluation (cognitive factor) fully explain the negative effects of incongruity on consumer judgments of aesthetic value, monetary value, and creativity. The positive effects of status are only partially mediated by liking and ease of evaluation. The article concludes with the implications of these findings for psychology and marketing, and specifically for “marketing the arts”.
Repurchase Behavior in the Performing Arts: Do Emotions Matter without Involvement?
Authors: Troilo Gabriele , Cito Maria Cristina , Soscia Isabella
Published: July 2014

Consumer repurchase behavior is a major concern for performing arts organizations because of its impact on their financial sustainability and competitive strength. Consequently, prior research has devoted a huge effort to the investigation of customer loyalty to individual performing arts organizations within a conceptual framework of within‐category competition. However, arts consumption research has highlighted that performing arts organizations also face fierce competition from other categories of artistic and entertainment products, since consumers believe that different product categories are able to provide similar hedonic and entertainment value. Our paper investigates the antecedents of repurchase behavior at the product category level. Specifically, we focus on the interplay between positive emotions and product involvement as predictors of repurchase behavior in the performing arts at the product category level. In this context, we modeled four different types of relationships among positive emotions, product involvement, and repurchase behavior. We then conducted a survey among theatergoers and used structural equation modeling to test the rival models. Our findings indicate that product involvement fully mediates the relation between positive emotions and repurchase behavior in the performing arts.
Can Purchase Behavior Predict Relationship Perceptions and Willingness to Donate?
Authors: Johnson Jennifer Wiggins , Peck Joann , Schweidel David A.
Published: July 2014

As arts organizations frequently seek purchases and donations from the same consumers, one of their challenges is identifying which consumers are likely to become donors in the future. With all of the data currently available, many organizations are looking to their databases to predict future consumer behavior. In the customer relationship management literature, models have been developed that allow organizations to use consumer purchase data to predict future purchase behavior. This goal of this research is to extend this literature to determine whether it is possible to predict consumer willingness to donate using purchase behavior data. It is not expected that purchase behavior data will be nearly as accurate a predictor of future donation behavior as past donation behavior would be. Rather, the goal is simply to determine whether organizations would be able to use purchase behavior data as a proxy for relationship perceptions to improve their ability to identify prospective donors among their consumers. Three commonly used methods of prediction based on past behavior are tested using a combination of purchase behavior data and consumer surveys: a segmentation approach, a recency/frequency/monetary value model, and a Pareto/NBD customer relationship management model. Across all three methods, purchase behavior is found to be a poor predictor of both customer relationship perceptions and willingness to donate to the organization.
Inferring Comonomer Content Using Crystaf: Uncertainty Analysis
Authors: Takeh Arsia , Shanbhag Sachin
Published: July 2014

We estimate the comonomer content in random copolymers, through the use of semi‐empirical models. We extend the model of Anantawaraskul et al. by expanding the number of model parameters from 4 to 9. Using available data on well‐characterized ethylene/1‐hexene copolymers, we randomly select a subset to train the model, and regress model parameters. We test the ability of the parametrized model to infer comonomer content on the rest of the data. We quantify the predictive ability by exploring the effect of the quantity and quality of the training data. The accuracy and precision of the inference improve as the amount of training data increases, and as datasets span the domain more evenly.
A form‐fitted three channel 31P, two channel 1H transceiver coil array for calf muscle studies at 7 T
Authors: Goluch Sigrun , Kuehne Andre , Meyerspeer Martin , Kriegl Roberta , Schmid Albrecht I. , Fiedler Georg B. , Herrmann Tim , Mallow Johannes , Hong Suk‐Min , Cho Zang‐Hee , Bernarding Johannes , Moser Ewald , Laistler Elmar
Published: July 2014

Purpose

To enhance sensitivity and coverage for calf muscle studies, a novel, form‐fitted, three‐channel phosphorus‐31 (31P), two‐channel proton (1H) transceiver coil array for 7 T MR imaging and spectroscopy is presented.

Methods

Electromagnetic simulations employing individually generated voxel models were performed to design a coil array for studying nonpathological muscle metabolism. Static phase combinations of the coil elements' transmit fields were optimized based on homogeneity and efficiency for several voxel models. The best‐performing design was built and tested both on phantoms and in vivo.

Results

Simulations revealed that a shared conductor array for 31P provides more robust interelement decoupling and better homogeneity than an overlap array in this configuration. A static B1+ shim setting that suited various calf anatomies was identified and implemented.

Simulations showed that the 31P array provides signal‐to‐noise ratio (SNR) benefits over a single loop and a birdcage coil of equal radius by factors of 3.2 and 2.6 in the gastrocnemius and by 2.5 and 2.0 in the soleus muscle.

Conclusion

The performance of the coil in terms of B1+ and achievable SNR allows for spatially localized dynamic 31P spectroscopy studies in the human calf. The associated higher specificity with respect to nonlocalized measurements permits distinguishing the functional responses of different muscles. Magn Reson Med 73:2376–2389, 2015. © 2014 Wiley Periodicals, Inc.
Using [1‐13C]lactic acid for hyperpolarized 13C MR cardiac studies
Authors: Chen Albert P. , Lau Justin Y.C. , Alvares Rohan D.A. , Cunningham Charles H.
Published: July 2014

Purpose

Hyperpolarized [1‐13C]lactate in solution may be a clinically relevant and safe substrate for real time MR investigations of key metabolic pathways. The potential of using hyperpolarized [1‐13C]lactate for magnetic resonance studies of cardiac metabolism in vivo was explored.

Methods

Neat [1‐13C]lactic acid was hyperpolarized using the dynamic nuclear polarization process. Cardiac MR spectroscopy experiments were performed in vivo using hyperpolarized [1‐13C]lactate and [1‐13C]pyruvate in solutions.

Results

A high degree of polarization was achieved for [1‐13C]lactate in solution (16.7%). 13C‐bicarbonate was observed in rat hearts in vivo after either hyperpolarized [1‐13C]lactate or hyperpolarized [1‐13C]pyruvate was infused, but lower 13C‐bicarbonate to substrate ratio was observed with hyperpolarized [1‐13C]lactate infusions. The response of 13C‐bicarbonate signal as a function of hyperpolarized [1‐13C]lactate doses was also investigated and a saturation of 13C‐bicarbonate signal was observed at the highest dose of [1‐13C]lactate used (0.69 mmol/kg).

Conclusion

This study demonstrated that the use of neat [1‐13C]lactic acid as the DNP sample is a potential alternative to [1‐13C]pyruvic acid for cardiac hyperpolarized 13C MR studies. Hyperpolarized [1‐13C]lactate may enable noninvasive assessment of cardiac PDH flux in cardiac patients in the near future. Magn Reson Med, 2014. © 2014 Wiley Periodicals, Inc. Magn Reson Med 73:2087–2093, 2015. © 2014 Wiley Periodicals, Inc.
Probing treatment response of glutaminolytic prostate cancer cells to natural drugs with hyperpolarized [5‐13C]glutamine
Authors: Canapè Carolina , Catanzaro Giuseppina , Terreno Enzo , Karlsson Magnus , Lerche Mathilde Hauge , Jensen Pernille Rose
Published: July 2014

Purpose

The correlation between glutamine metabolism and oncogene expression in cancers has led to a renewed interest in the role of glutamine in cancer cell survival. Hyperpolarized [5‐13C]glutamine is evaluated as a potential biomarker for noninvasive metabolic measurements of drug response in prostate cancer cells.

Methods

Hyperpolarized [5‐13C]glutamine is used to measure glutamine metabolism in two prostate cancer cell lines (PC3 and DU145) before and after treatment with the two natural anticancer drugs resveratrol and sulforaphane. An invasive biochemical assay simulating the hyperpolarized experiment is used to independently quantify glutamine metabolism.

Results

Glutamine metabolism is found to be 4 times higher in the more glutaminolytic DU145 cells compared with PC3 cells under proliferating growth conditions by using hyperpolarized [5‐13C]glutamine as a noninvasive probe. A significant decrease in glutamine metabolism occurs upon apoptotic response to treatment with resveratrol and sulforaphane.

Conclusion

Hyperpolarized NMR using [5‐13C]glutamine as a probe permits the noninvasive observation of glutaminolysis in different cell lines and under different treatment conditions. Hyperpolarized [5‐13C]glutamine metabolism thus is a promising biomarker for the noninvasive detection of tumor response to treatment, as it directly monitors one of the hallmarks in cancer metabolism ‐ glutaminolysis ‐ in living cells. Magn Reson Med, 2014. © 2014 Wiley Periodicals, Inc. Magn Reson Med 73:2296–2305, 2015. © 2014 Wiley Periodicals, Inc.
Simple and robust saturation‐based slice selection for ultrashort echo time MRI
Authors: Harkins Kevin D. , Horch R. Adam , Does Mark D.
Published: July 2014

Purpose

To present a new method for localizing signal within a two‐dimensional (2D) slice suitable for ultrashort echo time (UTE) imaging, called saturation‐based UTE (sat‐UTE). The new method digitally subtracts two acquisitions that are nonselectively excited with and without selective saturation of the slice of interest.

Methods

Sat‐UTE was compared with half‐pulse and double‐half pulse excited UTE within phantoms, as well as 3D‐UTE within ex vivo femur and in vivo tibia. Numerical simulations were also used to quantify the effects of slice profile broadening and signal component amplitudes for quantitative UTE.

Results

Sat‐UTE is robust to suppress out‐of‐slice signal, and produces short T2 signal decay curves comparable to 3D‐UTE, but has a lower signal to noise ratio efficiency compared with other slice‐selective methods.

Conclusion

The proposed method is useful for fast, quantitative evaluation of short T2 signals, and is insensitive to gradient performance. Magn Reson Med 73:2204–2211, 2015. © 2014 Wiley Periodicals, Inc.
Triostin A Derived Cyclopeptide as Architectural Template for the Alignment of Four Recognition Units
Authors: Kotyrba Ursula M. , Pröpper Kevin , Sachs Eike-F. , Myanovska Anastasiya , Joppe Tobias , Lissy Friederike , Sheldrick George M. , Koszinowski Konrad , Diederichsen Ulf
Published: July 2014

The DNA bisintercalator triostin A is structurally based on a disulfide‐bridged depsipeptide scaffold that provides preorganization of two quinoxaline units in 10.5 Å distance. Triostin A analogues are synthesized with nucleobase recognition units replacing the quinoxalines and containing two additional recognition units in between. Thus, four nucleobase recognition units are organized on a rigid template, well suited for DNA double strand interactions. The new tetra‐nucleobase binders are synthesized as aza‐TANDEM derivatives lacking the N‐methylation of triostin A and based on a cyclopeptide backbone. Synthesis of two tetra‐nucleobase aza‐TANDEM derivatives is established, DNA interaction analyzed by microscale thermophoresis, cytotoxic activity studied and a nucleobase sequence dependent self‐aggregation investigated by mass spectrometry.
Prenatal diagnosis of chromothripsis, with nine breaks characterized by karyotyping, FISH, microarray and whole‐genome sequencing
Authors: Macera M. J. , Sobrino A. , Levy B. , Jobanputra V. , Aggarwal V. , Mills A. , Esteves C. , Hanscom C. , Pereira S. , Pillalamarri V. , Ordulu Z. , Morton C. C. , Talkowski M. , Warburton D.
Published: July 2014

What's already known about this topic?

Chromothripsis is a recently described phenomenon whereby a single catastrophic event leads to multiple chromosome breaks and subsequent repair through nonhomologous end joining. The result can present karyotypically as a complex rearrangement and occurs both congenitally and in cancer cells.

What does this study add?

We report, to our knowledge, the first case of congenital chromothripsis uncovered prenatally through a combination of G‐banded karyotype analysis and whole‐genome sequencing by jumping libraries. The G‐banded karyotype initially suggested the involvement of five chromosomes and six breakpoints. Whole‐genome sequencing further resolved this event to include nine total breakpoints that disrupt seven independent genes, all in the presence of a normal microarray result. This emphasizes the complementarity that whole‐genome sequencing can provide to the initial karyotype analysis as a reflex test when a rearrangement is detected. We also discuss the dilemma of prognosis with this finding.
The saturated five‐membered heterocyclic molecules as organic hydride donors: a computational study
Authors: Khanna Shweta , Kaur Damanjit , Kaur Rajinder
Published: July 2014

Several five‐membered heterocyclic molecules were studied theoretically as organic hydride donors. The density functional theory and ab initio methods are employed to study the direct one‐step or multistep sequence suggested for the hydride transfer from the selected molecules: H atom/electron, electron/proton/electron or electron/H atom. Out of the three multistep mechanisms, electron/H atom seems to be a probable pathway in the presence of suitable catalyst/photoreaction that can cause ionization. In the lack of such catalyst/photoreaction, the direct hydride transfer seems to be most probable with the presence of suitable hydride acceptor. A detailed mechanism of the hydride transfer from the five‐membered heterocylic compounds is important in understanding chemical and biological reactions and required for scientifically designing and synthesizing new desired five‐membered heterocyclic compounds as organic hydride donor. Copyright © 2014 John Wiley & Sons, Ltd.
The Isolation of Antiprotozoal Compounds from Libyan Propolis
Authors: Siheri Weam , Igoli John O. , Gray Alexander I. , Nasciemento Ticiano G. , Zhang Tong , Fearnley James , Clements Carol J. , Carter Katharine C. , Carruthers John , Edrada‐Ebel RuAngelie , Watson David G.
Published: July 2014

Propolis is increasingly being explored as a source of biologically active compounds. Until now, there has been no study of Libyan propolis. Two samples were collected in North East Libya and tested for their activity against Trypanosoma brucei. Extracts from both samples had quite high activity. One of the samples was fractionated and yielded a number of active fractions. Three of the active fractions contained single compounds, which were found to be 13‐epitorulosal, acetyl‐13‐epi‐cupressic acid and 13‐epi‐cupressic acid, which have been described before in Mediterranean propolis. Two of the compounds had a minimum inhibitory concentration value of 1.56 µg/mL against T. brucei. The active fractions were also tested against macrophages infected with Leishmania donovani, and again moderate to strong activity was observed with the compounds having IC50 values in the range 5.1–21.9 µg/mL. Copyright © 2014 John Wiley & Sons, Ltd.
A comparison between the Local Ensemble Transform Kalman Filter and the Ensemble Square Root Filter for the assimilation of radar data in convective‐scale models
Authors: Thompson Therese E. , Wicker Louis J. , Wang Xuguang , Potvin Corey
Published: July 2014

Two ensemble data assimilation methods are used to assimilate Doppler radar observations into a convection‐allowing model. The analyses and subsequent forecasts from the two systems are compared. The Local Ensemble Transform Kalman Filter (LETKF) simultaneously assimilates all observations that can impact the model state at a given location. It is compared to the Ensemble Square Root Filter (EnSRF), which assimilates observations sequentially and has commonly been used for convective‐scale Doppler radar data assimilation. While the filters should behave the same for ideal systems, a comparison between the serial and simultaneous filters has not previously been explored at the convective scale where significant nonlinear effects are present. Observing System Simulation Experiments (OSSEs) are first used to compare the assimilation systems for the analysis and forecast of a supercell thunderstorm. Both the EnSRF and LETKF produce reasonable analyses from the Doppler velocity and reflectivity observations of the true supercell. Small improvements in analysis errors and system noise from the LETKF simultaneous update do not significantly impact the subsequent forecasts. This result is consistent across a range of localization length‐scales and is independent of the manner in which localization is applied. Tests comparing the EnSRF and LETKF for a real‐data case also have small differences. The magnitudes of these differences are similar to those that arise from the sampling variability associated with a finite ensemble. Overall, the results suggest the EnSRF and LETKF approaches are equally capable methods for radar data assimilation at convective scales.
An improved bulk air–sea surface flux algorithm, including spray‐mediated transfer
Authors: Andreas Edgar L , Mahrt Larry , Vickers Dean
Published: July 2014

A bulk air–sea flux algorithm couples the ocean and the lower atmosphere through flux boundary conditions and can be used in various analyses and in numerical models. The algorithm described here has two features not present in any other existing bulk flux algorithm. First, it has a new air–sea drag relation. Here, for wind speeds above about 9 m s−1, the friction velocity u✻, which is related to the square root of the surface stress, is linearly related to UN10, the neutral‐stability 10 m wind speed. When extrapolated to hurricane‐strength winds, this drag relation has better properties than relations formulated in terms of a drag coefficient or a roughness length. The second unique feature of this flux algorithm is that it recognizes two routes by which heat and moisture cross the air–sea interface: one is the interfacial route, which is controlled by molecular processes right at the air–sea interface; the second is the spray‐mediated route, which is governed by microphysical processes at the surface of sea spray droplets. Through microphysical theory and our analysis of 4000 sets of eddy‐covariance measurements of the scalar fluxes, we separate the measured fluxes into the interfacial and spray contributions and thereby produce the only spray flux algorithm tested and validated against oceanic data. Because all components of our flux algorithm are physics‐based and validated with data for winds up to 25 m s−1, one application is extrapolating this algorithm to hurricane‐strength winds, where sea spray plays a dominant role in scalar transfer.
Large‐eddy simulations of an Arctic mixed‐phase stratiform cloud observed during ISDAC: sensitivity to moisture aloft, surface fluxes and large‐scale forcing
Authors: Savre J. , Ekman A. M. L. , Svensson G. , Tjernström M.
Published: July 2014

Large‐eddy simulation (LES) is used to examine the complex interactions between cloud properties and boundary‐layer structure in Arctic low‐level mixed‐phase clouds using idealised conditions based on the Indirect and Semi‐Direct Aerosol Campaign (ISDAC, April 2008). The persistence of steady mixed‐phase conditions depends mostly on a balance between ice vertical redistribution and ice growth by vapour deposition in such a way that ice crystals cannot accumulate within the cloud layer to consume the available liquid water. An external source of water vapour is necessary to balance the net sink of total water in the cloud layer. Two main local sources of moisture are present: the initial moist surface layer and the free troposphere. In the studied case, the surface layer is found to be the dominant source of vapour to the cloud, the temperature inversion preventing significant entrainment from above. In most of the cases, the simulated boundary layer becomes rapidly well‐mixed despite the stabilising effect of ice sublimation and latent cooling close to the surface. The minor effect of near‐surface latent cooling on stability is connected to the initially moist surface layer limiting ice sublimation. Water vapour supply in the sub‐cloud layer, resulting from entrainment of moisture from aloft, reduces ice sublimation above the surface layer and contributes to the maintenance of some degree of boundary‐layer decoupling. In contrast, moisture surface fluxes reduce sublimation in the surface layer and accelerate cloud–surface coupling. Overall, the persistence of cloud–surface decoupling remains mostly driven by large‐scale heat and moisture advection.
Covariance adjustment on propensity parameters for continuous treatment in linear models
Authors: Yang Wei , Joffe Marshall M. , Hennessy Sean , Feldman Harold I.
Published: July 2014

Propensity scores are widely used to control for confounding when estimating the effect of a binary treatment in observational studies. They have been generalized to ordinal and continuous treatments in the recent literature. Following the definition of propensity function and its parameterizations (called the propensity parameter in this paper) proposed by Imai and van Dyk, we explore sufficient conditions for selecting propensity parameters to control for confounding for continuous treatments in the context of regression‐based adjustment in linear models. Typically, investigators make parametric assumptions about the form of the dose–response function for a continuous treatment. Such assumptions often allow the analyst to use only a subset of the propensity parameters to control confounding. When the treatment is the only predictor in the structural, that is, causal model, it is sufficient to adjust only for the propensity parameters that characterize the expectation of the treatment variable or its functional form. When the structural model includes selected baseline covariates other than the treatment variable, those baseline covariates, in addition to the propensity parameters, must also be adjusted in the model. We demonstrate these points with an example estimating the dose–response relationship for the effect of erythropoietin on hematocrit level in patients with end‐stage renal disease. Copyright © 2014 John Wiley & Sons, Ltd.
Ethnically diverse students' knowledge structures in first‐semester organic chemistry
Authors: Lopez Enrique J. , Shavelson Richard J. , Nandagopal Kiruthiga , Szu Evan , Penn John
Published: July 2014

Chemistry courses remain a challenge for many undergraduate students. In particular, first‐semester organic chemistry has been labeled as a gatekeeper with high attrition rates, especially among students of color. Our study examines a key factor related to conceptual understanding in science and predictive of course outcomes—knowledge structures. Previous research on knowledge structures has focused on differences between experts and novices. Given the increasing ethnic diversity of college classrooms and research indicating unique differences in certain higher order cognitive processes associated cultural practices and ethnicity, it is important to investigate whether similar patterns exist with respect to knowledge structures. Our study utilized concept maps to measure knowledge structures. Two separate analyses where performed to determine whether or not ethnically diverse students' organize their knowledge of organic chemistry content in structurally different ways. The first analysis utilized concept map proposition scoring to examine the influence of prior science achievement and ethnicity on knowledge structures. The second analysis examined holistic map structures to determine whether or not ethnically diverse students show qualitatively distinct structures overall. Results show significant mean differences on concept map proposition scores related to both prior science achievement and ethnic group membership. However, examination of holistic structures revealed that students' qualitative holistic structures did not vary by ethnic group membership. Taken together, our findings suggest that variation in students' knowledge structures are related to prior science achievement across ethnic groups, not qualitative differences in the ways ethnically diverse students' structure knowledge. Implications for teaching and learning in organic chemistry are discussed. © 2014 Wiley Periodicals, Inc. J Res Sci Teach 51: 741–758, 2014
Toxicity of triphenyltin chloride to the rotifer Brachionus koreanus across different levels of biological organization
Authors: Xianliang Yi Andy , Han Jeonghoon , Lee Jae‐Seong , Leung Kenneth M. Y.
Published: July 2014

Although triphenyltin (TPT) compounds are ubiquitous pollutants in urbanised coastal environments in Asian regions, their toxicities to marine organisms are still poorly known. This study was designed to investigate the toxicity of triphenyltin chloride (TPTCl) on the rotifer Brachionus koreanus across different levels of biological organisation. Firstly, we concurrently performed a 24 h static‐acute toxicity test and a 6‐day semi‐static multigenerational life‐cycle test using the rotifer. Our results demonstrated that the 24‐h median lethal concentration of TPTCl for the rotifer was 29.6 μg/L and the 6‐day median effect concentration, based on the population growth inhibition, was 3.31 μg/L. Secondly, we examined the expression of 12 heat shock protein (hsp) genes, four glutathione S‐transferase (GST) genes, one retinoid X receptor (RXR) gene and 13 cytochrome P450 (CYP) genes in the rotifers after exposure to 20 µg/L TPTCl for 24 h. Among these studied genes, hsp90α2, GST‐O and CYP3045C1 were the most significantly up‐regulated genes with a relative expression level up to 32.9, 4.4 and 62.6 folds, respectively. The expression of these three genes in the rotifers showed an increasing trend in the first few hours of TPTCl exposure, peaked at 3 h (hsp90α2 and GST‐O) and 12 h (CYP3045C1) respectively, and then gradually returned to a lower level at 24 h. Such up‐regulations of hsp and GST genes probably offer cellular protection against the TPT‐mediated oxidative stress while the accelerated induction of CYP genes possibly facilitates the detoxification of this toxicant in the rotifer. © 2014 Wiley Periodicals, Inc. Environ Toxicol 31: 13–23, 2016.
Functional repeat‐derived RNAs often originate from retrotransposon‐propagated ncRNAs
Authors: Matylla‐Kulinska Katarzyna , Tafer Hakim , Weiss Adam , Schroeder Renée
Published: July 2014

The human genome is scattered with repetitive sequences, and the ENCODE project revealed that 60–70% of the genomic DNA is transcribed into RNA. As a consequence, the human transcriptome contains a large portion of repeat‐derived RNAs (repRNAs). Here, we present a hypothesis for the evolution of novel functional repeat‐derived RNAs from non‐coding RNAs (ncRNAs) by retrotransposition. Upon amplification, the ncRNAs can diversify in sequence and subsequently evolve new activities, which can result in novel functions. Non‐coding transcripts derived from highly repetitive regions can therefore serve as a reservoir for the evolution of novel functional RNAs. We base our hypothetical model on observations reported for short interspersed nuclear elements derived from 7SL RNA and tRNAs, α satellites derived from snoRNAs and SL RNAs derived from U1 small nuclear RNA. Furthermore, we present novel putative human repeat‐derived ncRNAs obtained by the comparison of the Dfam and Rfam databases, as well as several examples in other species. We hypothesize that novel functional ncRNAs can derive also from other repetitive regions and propose Genomic SELEX as a tool for their identification. WIREs RNA 2014, 5:591–600. doi: 10.1002/wrna.1243

This article is categorized under:

RNA Processing > 3' End Processing

RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms
Noncoding RNAs and the borders of heterochromatin
Authors: Cohen Allison L. , Jia Songtao
Published: July 2014

Eukaryotic genomes contain long stretches of repetitive DNA sequences, which are the preferred sites for the assembly of heterochromatin structures. The formation of heterochromatin results in highly condensed chromosomal domains that limit the accessibility of DNA to the transcription and recombination machinery to maintain genome stability. Heterochromatin has the tendency to spread, and the formation of boundaries that block heterochromatin spreading is required to maintain stable gene expression patterns. Recent work has suggested that noncoding RNAs (ncRNAs) are involved in regulating boundary formation in addition to their well‐established roles in chromatin regulation. Here, we present a review of our current understanding of the involvement of ncRNA at the boundaries of heterochromatin, highlighting their mechanisms of action in different settings. WIREs RNA 2014, 5:835–847. doi: 10.1002/wrna.1249

This article is categorized under:

Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs