bluuebunny/crossref_metadata_2025 huggingface dataset:
An Osteopontin-Integrin Interaction Plays a Critical Role in Directing Adipogenesis and Osteogenesis by Mesenchymal Stem Cells
Authors: Chen Qing , Shou Peishun , Zhang Liying , Xu Chunliang , Zheng Chunxing , Han Yanyan , Li Wenzhao , Huang Yin , Zhang Xiaoren , Shao Changshun , Roberts Arthur I. , Rabson Arnold B. , Ren Guangwen , Zhang Yanyun , Wang Ying , Denhardt David T. , Shi Yufang
Published: October 2013

An imbalance between normal adipogenesis and osteogenesis by mesenchymal stem cells (MSCs) has been shown to be related to various human metabolic diseases, such as obesity and osteoporosis; however, the underlying mechanisms remain elusive. We found that the interaction between osteopontin (OPN), an arginine-glycine-aspartate-containing glycoprotein, and integrin αv/β1 plays a critical role in the lineage determination of MSCs. Although OPN is a well-established marker during osteogenesis, its role in MSC differentiation is still unknown. Our study reveals that blockade of OPN function promoted robust adipogenic differentiation, while inhibiting osteogenic differentiation. Re-expression of OPN restored a normal balance between adipogenesis and osteogenesis in OPN−/− MSCs. Retarded bone formation by OPN−/− MSCs was also verified by in vivo implantation with hydroxyapatite-tricalcium phosphate, a bone-forming matrix. The role of extracellular OPN in MSC differentiation was further demonstrated by supplementation and neutralization of OPN. Blocking well-known OPN receptors integrin αv/β1 but not CD44 also affected MSC differentiation. Further studies revealed that OPN inhibits the C/EBPs signaling pathway through integrin αv/β1. Consistent with these in vitro results, OPN−/− mice had a higher fat to total body weight ratio than did wild-type mice. Therefore, our study demonstrates a novel role for OPN-integrin αv/β1 in regulating MSC differentiation. Stem Cells  2014;32:327–337
Concise Review: The Immune Status of Mesenchymal Stem Cells and Its Relevance for Therapeutic Application
Authors: Knaän-Shanzer Shoshan
Published: October 2013

Multipotentiality and anti-inflammatory activity, the two main properties of mesenchymal stem cells (MSCs), underlie their therapeutic prospective. During the past decade, numerous studies in animal models and clinical trials explored the potential of MSCs in the treatment of diseases associated with tissue regeneration and inflammatory control. Other qualities of MSCs: ready accessibility in bone marrow and fat tissue and rapid expansion in culture make the therapeutic use of patients’ own cells feasible. The prevailing belief that MSCs are nonimmunogenic encouraged the use of unrelated donor cells in immune-competent recipients. The data emerging from studies performed with immune-incompatible cells in animal models for a wide-range of human diseases show, however, conflicting results and cast doubt on the immune privileged status of MSCs. Our analysis of the preclinical literature in this review is aimed to gain a better understanding of the therapeutic potential of immune-incompatible MSCs. Emphasis was laid on applications for enhancement of tissue repair in the absence of immune-suppressive therapy. Stem Cells  2014;32:603–608
Loss of Spastin Function Results in Disease-Specific Axonal Defects in Human Pluripotent Stem Cell-Based Models of Hereditary Spastic Paraplegia
Authors: Denton Kyle R. , Lei Ling , Grenier Jeremy , Rodionov Vladimir , Blackstone Craig , Li Xue-Jun
Published: October 2013

Human neuronal models of hereditary spastic paraplegias (HSP) that recapitulate disease-specific axonal pathology hold the key to understanding why certain axons degenerate in patients and to developing therapies. SPG4, the most common form of HSP, is caused by autosomal dominant mutations in the SPAST gene, which encodes the microtubule-severing ATPase spastin. Here, we have generated a human neuronal model of SPG4 by establishing induced pluripotent stem cells (iPSCs) from an SPG4 patient and differentiating these cells into telencephalic glutamatergic neurons. The SPG4 neurons displayed a significant increase in axonal swellings, which stained strongly for mitochondria and tau, indicating the accumulation of axonal transport cargoes. In addition, mitochondrial transport was decreased in SPG4 neurons, revealing that these patient iPSC-derived neurons recapitulate disease-specific axonal phenotypes. Interestingly, spastin protein levels were significantly decreased in SPG4 neurons, supporting a haploinsufficiency mechanism. Furthermore, cortical neurons derived from spastin-knockdown human embryonic stem cells (hESCs) exhibited similar axonal swellings, confirming that the axonal defects can be caused by loss of spastin function. These spastin-knockdown hESCs serve as an additional model for studying HSP. Finally, levels of stabilized acetylated-tubulin were significantly increased in SPG4 neurons. Vinblastine, a microtubule-destabilizing drug, rescued this axonal swelling phenotype in neurons derived from both SPG4 iPSCs and spastin-knockdown hESCs. Thus, this study demonstrates the successful establishment of human pluripotent stem cell-based neuronal models of SPG4, which will be valuable for dissecting the pathogenic cellular mechanisms and screening compounds to rescue the axonal degeneration in HSP. Stem Cells  2014;32:414–423
A Site-Specific Genetic Modification for Induction of Pluripotency and Subsequent Isolation of Derived Lung Alveolar Epithelial Type II Cells
Authors: Yan Qing , Quan Yuan , Sun Huanhuan , Peng Xinmiao , Zou Zhengyun , Alcorn Joseph L. , Wetsel Rick A. , Wang Dachun
Published: October 2013

Human induced pluripotent stem cells (hiPSCs) have great therapeutic potential in repairing defective lung alveoli. However, genetic abnormalities caused by vector integrations and low efficiency in generating hiPSCs, as well as difficulty in obtaining transplantable hiPSC-derived cell types are still major obstacles. Here we report a novel strategy using a single nonviral site-specific targeting vector with a combination of Tet-On inducible gene expression system, Cre/lox P switching gene expression system, and alveolar epithelial type II cell (ATIIC)-specific NeomycinR transgene expression system. With this strategy, a single copy of all of the required transgenes can be specifically knocked into a site immediately downstream of β-2-microglobulin (B2M) gene locus at a high frequency, without causing B2M dysfunction. Thus, the expression of reprogramming factors, Oct4, Sox2, cMyc, and Klf4, can be precisely regulated for efficient reprogramming of somatic cells into random integration-free or genetic mutation-free hiPSCs. The exogenous reprogramming factor transgenes can be subsequently removed after reprogramming by transient expression of Cre recombinase, and the resulting random integration-free and exogenous reprogramming factor-free hiPSCs can be selectively differentiated into a homogenous population of ATIICs. In addition, we show that these hiPSC-derived ATIICs exhibit ultrastructural characteristics and biological functions of normal ATIICs. When transplanted into bleomycin-challenged mice lungs, hiPSC-derived ATIICs efficiently remain and re-epithelialize injured alveoli to restore pulmonary function, preventing lung fibrosis and increasing survival without tumorigenic side effect. This strategy allows for the first time efficient generation of patient-specific ATIICs for possible future clinical applications. Stem Cells  2014;32:402–413
The Transition from Stem Cell to Progenitor Spermatogonia and Male Fertility Requires the SHP2 Protein Tyrosine Phosphatase
Authors: Puri Pawan , Phillips Bart T. , Suzuki Hitomi , Orwig Kyle E. , Rajkovic Aleksandar , Lapinski Philip E. , King Philip D. , Feng Gen-Sheng , Walker William H.
Published: October 2013

SHP2 is a widely expressed protein tyrosine phosphatase required for signal transduction from multiple cell surface receptors. Gain and loss of function SHP2 mutations in humans are known to cause Noonan and LEOPARD syndromes, respectively, that are characterized by numerous pathological conditions including male infertility. Using conditional gene targeting in the mouse, we found that SHP2 is required for maintaining spermatogonial stem cells (SSCs) and the production of germ cells required for male fertility. After deleting SHP2, spermatogenesis was halted at the initial step during which transit-amplifying undifferentiated spermatogonia are produced from SSCs. In the absence of SHP2, proliferation of SSCs and undifferentiated spermatogonia was inhibited, thus germ cells cannot be replenished and SSCs cannot undergo renewal. However, germ cells beyond the undifferentiated spermatogonia stage of development at the time of SHP2 knockout were able to complete their maturation to become sperm. In cultures of SSCs and their progeny, inhibition of SHP2 activity reduced growth factor-mediated intracellular signaling that regulates SSC proliferation and cell fate. Inhibition of SHP2 also decreased the number of SSCs present in culture and caused SSCs to detach from supporting cells. Injection of mice with an SHP2 inhibitor blocked the production of germ cells from SSCs. Together, our studies show that SHP2 is essential for SSCs to maintain fertility and indicates that the pathogenesis of infertility in humans with SHP2 mutations is due to compromised SSC functions that block spermatogenesis. Stem Cells  2014;32:741–753
A generalized fault location method based on voltage sags for distribution network
Authors: Awalin Lilik Jamilatul , Mokhlis Hazlie , Abu Bakar AbHalim , Mohamad Hasmaini , Illias Hazlee A.
Published: October 2013

An enhanced fault location method based on voltage sag profiles for distribution networks is presented in this paper. In other previous methods, only a single measurement has been used. The proposed method can be used with any number of measurements in the network, making it more general. A new ranking approach that addresses multiple possibilities of the faulted section is proposed. Different case studies with various numbers of measurements are performed on a large 11‐kV network with the main feeder consisting of 42 buses to validate the method. The test results show that there is an improvement in terms of accuracy in detecting the faulted section in the first attempt for each additional measurement. Therefore, by utilizing the average value of each measurement, a better accuracy of fault location can be achieved. © 2013 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.
Design of freely configurable safety light curtain using hemispherical mirrors
Authors: Lu Huimin , Serikawa Seiichi
Published: October 2013

Safety light curtains provide reliable and cost‐effective protection against access into hazardous points or areas. However, in practice, peopl still need to adjust the light detection element accurately in order to receive the safe amount of irradiating laser light. In our proposed system, we utilized light emitting diodes (LEDs) as the light source, and designed two hemispherical mirrors to receive the LED light, and used PSoC microcomputer to determine the threshold voltage value. Compared with recent market products, the proposed system is freely configurable, and with no dead zone detection. In addition, compared to the laser light, the LED light has the advantages of no radiation, small electropult, low‐cost, and high efficiency. After conducting sufficient experiments, the proposed system has been found to successfully detect the intruder with 100% recognition rate, which can meet the needs of industrialization. © 2013 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.
Development and external validation of new ultrasound‐based mathematical models for preoperative prediction of high‐risk endometrial cancer
Authors: Van Holsbeke C. , Ameye L. , Testa A. C. , Mascilini F. , Lindqvist P. , Fischerova D. , Frühauf F. , Fransis S. , de Jonge E. , Timmerman D. , Epstein E.
Published: October 2013

Objectives

To develop and validate strategies, using new ultrasound‐based mathematical models, for the prediction of high‐risk endometrial cancer and compare them with strategies using previously developed models or the use of preoperative grading only.

Methods

Women with endometrial cancer were prospectively examined using two‐dimensional (2D) and three‐dimensional (3D) gray‐scale and color Doppler ultrasound imaging. More than 25 ultrasound, demographic and histological variables were analyzed. Two logistic regression models were developed: one ‘objective’ model using mainly objective variables; and one ‘subjective’ model including subjective variables (i.e. subjective impression of myometrial and cervical invasion, preoperative grade and demographic variables). The following strategies were validated: a one‐step strategy using only preoperative grading and two‐step strategies using preoperative grading as the first step and one of the new models, subjective assessment or previously developed models as a second step.

Results

One‐hundred and twenty‐five patients were included in the development set and 211 were included in the validation set. The ‘objective’ model retained preoperative grade and minimal tumor‐free myometrium as variables. The ‘subjective’ model retained preoperative grade and subjective assessment of myometrial invasion. On external validation, the performance of the new models was similar to that on the development set. Sensitivity for the two‐step strategy with the ‘objective’ model was 78% (95% CI, 69–84%) at a cut‐off of 0.50, 82% (95% CI, 74–88%) for the strategy with the ‘subjective’ model and 83% (95% CI, 75–88%) for that with subjective assessment. Specificity was 68% (95% CI, 58–77%), 72% (95% CI, 62–80%) and 71% (95% CI, 61–79%) respectively. The two‐step strategies detected up to twice as many high‐risk cases as preoperative grading only. The new models had a significantly higher sensitivity than did previously developed models, at the same specificity.

Conclusion

Two‐step strategies with ‘new’ ultrasound‐based models predict high‐risk endometrial cancers with good accuracy and do this better than do previously developed models. Copyright © 2013 ISUOG. Published by John Wiley & Sons Ltd.
The expanding tropics: a critical assessment of the observational and modeling studies
Authors: Lucas Christopher , Timbal Bertrand , Nguyen Hanh
Published: October 2013

This review provides comprehensive coverage of the tropical expansion literature to date. The primary focus is on the annual‐ and zonal‐mean behavior of the phenomenon. An idealized model that identifies the mean meridional circulation as a hemisphere‐wide structure with significant tropical–extratropical interaction is introduced as background for the understanding of the expansion and the methodologies used for detection. A variety of metrics from different data sources have been used to identify an expansion of the global tropics since 1979 by 1°–3° latitude in each hemisphere, an average trend of approximately 0.5°–1.0° decade−1. The symmetry of this expansion—whether Northern and Southern hemispheres are expanding at the same rate—is unclear. Limitations of observational datasets, including reanalyses, prevent a more precise determination at this time. General circulation models are able to qualitatively reproduce this expansion, but generally underestimate its magnitude. Multiple factors have been identified as potential drivers of the expansion, including increasing greenhouses gases, stratospheric ozone depletion, and anthropogenic aerosols. No single factor by itself appears to explain the full expansion, perhaps a shortcoming of the models or experiment design. It may be that some combination of these forcings is producing the change, but the relative contribution of each forcing to the expansion is currently unknown. The key issues remaining to be resolved are briefly summarized at the end. WIREs Clim Change 2014, 5:89–112. doi: 10.1002/wcc.251

This article is categorized under:

Paleoclimates and Current Trends > Modern Climate Change

Climate Models and Modeling > Knowledge Generation with Models
A compound event framework for understanding extreme impacts
Authors: Leonard Michael , Westra Seth , Phatak Aloke , Lambert Martin , van den Hurk Bart , McInnes Kathleen , Risbey James , Schuster Sandra , Jakob Doerte , Stafford‐Smith Mark
Published: October 2013

Climate and weather variables such as rainfall, temperature, and pressure are indicators for hazards such as tropical cyclones, floods, and fires. The impact of these events can be due to a single variable being in an extreme state, but more often it is the result of a combination of variables not all of which are necessarily extreme. Here, the combination of variables or events that lead to an extreme impact is referred to as a compound event. Any given compound event will depend upon the nature and number of physical variables, the range of spatial and temporal scales, the strength of dependence between processes, and the perspective of the stakeholder who defines the impact. Modeling compound events is a large, complex, and interdisciplinary undertaking. To facilitate this task we propose the use of influence diagrams for defining, mapping, analyzing, modeling, and communicating the risk of the compound event. Ultimately, a greater appreciation of compound events will lead to further insight and a changed perspective on how impact risks are associated with climate‐related hazards. WIREs Clim Change 2014, 5:113–128. doi: 10.1002/wcc.252

This article is categorized under:

Climate Models and Modeling > Knowledge Generation with Models

Assessing Impacts of Climate Change > Representing Uncertainty
A channel reservation and preemption model using overlapping regions in sector‐based cellular networks
Authors: Sheu Tsang‐Ling , Lin Chia‐Nan , Hwang Jenq‐Neng
Published: October 2013

This paper presents a channel reservation and preemption (CRP) model using overlapping regions in a cellular network with multiple sectors. To fully exploit and reuse the frequencies, directional antennas are installed on base stations (BSs) to divide the coverage into a number of equal‐sized sectors. When traffic is unevenly distributed across the sectors in a BS, channel utilization in every sector may become very different; low‐traffic sectors may be underutilized while high‐traffic sectors may be overutilized. A CRP scheme is thus proposed to more efficiently utilize free channels among sectors. CRP aims at reducing the dropping probabilities of handoff calls. Specifically, when free channels in a sector are not available, a handoff call, instead of being dropped, is allowed to preempt an ongoing call residing in the overlapping region of two adjacent sectors or two neighbor cells. Under CRP, the preempted ongoing call will not be disconnected, because it can switch over its service to the BS of a neighbor cell or to another directional antenna of an adjacent sector. For the purpose of evaluation, we build an analytical model for the proposed CRP using six‐tuple Markov chains. Analytical results show that the proposed CRP can significantly reduce the dropping probabilities of inter‐sector handoff calls, particularly when traffic between two sectors is not evenly distributed. Copyright © 2013 John Wiley & Sons, Ltd.
Subsystem density‐functional theory
Authors: Jacob Christoph R. , Neugebauer Johannes
Published: October 2013

Subsystem density‐functional theory (subsystem DFT) has developed into a powerful alternative to Kohn–Sham DFT for quantum chemical calculations of complex systems. It exploits the idea of representing the total electron density as a sum of subsystem densities. The optimum total density is found by minimizing the total energy with respect to each of the subsystem densities, which breaks down the electronic‐structure problem into effective subsystem problems. This enables calculations on large molecular aggregates and even (bio‐)polymers without system‐specific parameterizations. We provide a concise review of the underlying theory, typical approximations, and embedding approaches related to subsystem DFT such as frozen‐density embedding (FDE). Moreover, we discuss extensions and applications of subsystem DFT and FDE to molecular property calculations, excited states, and wave function in DFT embedding methods. Furthermore, we outline recent developments for reconstruction techniques of embedding potentials arising in subsystem DFT, and for using subsystem DFT to incorporate constraints into DFT calculations.

This article is categorized under:

Structure and Mechanism > Computational Materials Science
Space and language in Williams syndrome: insights from typical development
Authors: Landau Barbara , Ferrara Katrina
Published: October 2013

One of the holy grails of cognitive science is to understand the causal chain that links genes and cognition. Genetic syndromes accompanied by cognitive effects offer natural experiments that can uniquely inform our understanding of this chain. In this article, we discuss the case of Williams syndrome (WS), which is characterized by a set of missing genes on chromosome 7q11.23, and presents with a unique cognitive profile that includes severe spatial impairment along with strikingly fluent and well‐structured language. An early inference from this profile was the idea that a small group of genes could directly target one cognitive system while leaving others unaffected. Recent evidence shows that this inference fails. First, the profile within the spatial domain is varied, with relative strength in some aspects of spatial representation but severe impairment in others. Second, some aspects of language may fail to develop fully, raising the question of how to compare the resilience and fragility of the two key cognitive domains in this syndrome. Third, much research on the profile fails to place findings in the context of typical developmental trajectories. We explore these points and propose a new hypothesis that explains the unusual WS cognitive profile by considering normal mechanisms of cognitive development that undergo change on an extremely prolonged timetable. This hypothesis places the elements of the WS cognitive profile in a new light, refocuses the discussion of the gene–cognition causal chain for WS and other disorders, and more generally, underlines the importance of understanding cognitive structure in both typical and atypical development. WIREs Cogn Sci 2013, 4:693–703. doi: 10.1002/wcs.1258

This article is categorized under:

Psychology > Brain Function and Dysfunction

Psychology > Language

Neuroscience > Development
ART, cognitive science, and technology transfer
Authors: Carpenter Gail A.
Published: October 2013

Three computational examples illustrate how cognitive science can introduce new approaches to the analysis of large datasets. The first example addresses the question: how can a neural system learning from one example at a time absorb information that is inconsistent but correct, as when a family pet is called Spot and dog and animal, while rejecting similar incorrect information, as when the same pet is called wolf? How does this system transform such scattered information into the knowledge that dogs are animals, but not conversely? The second example asks: how can a real‐time system, initially trained with a few labeled examples and a limited feature set, continue to learn from experience when confronted with oceans of additional information, without eroding reliable early memories? How can such individual systems adapt to their unique application contexts? The third example asks: how can a neural system that has made an error refocus attention on environmental features that it had initially ignored? Three models that address these questions, each based on the distributed adaptive resonance theory (dART) neural network, are applied to a spatial testbed created from multimodal remotely sensed data. The article summarizes key design elements of ART models, and provides links to open‐source code for each system and the testbed dataset. WIREs Cogn Sci 2013, 4:707–719. doi: 10.1002/wcs.1260

This article is categorized under:

Computer Science > Machine Learning

Computer Science > Neural Networks

Psychology > Memory
Decision trees
Authors: de Ville Barry
Published: October 2013

Decision trees trace their origins to the era of the early development of written records. This history illustrates a major strength of trees: exceptionally interpretable results which have an intuitive tree‐like display which, in turn, enhances understanding and the dissemination of results. The computational origins of decision trees—sometimes called classification trees or regression trees—are models of biological and cognitive processes. This common heritage drives complementary developments of both statistical decision trees and trees designed for machine learning. The unfolding and progressive elucidation of the various features of trees throughout their early history in the late 20th century is discussed along with the important associated reference points and responsible authors. Statistical approaches, such as a hypothesis testing and various resampling approaches, have coevolved along with machine learning implementations. This had resulted in exceptionally adaptable decision tree tools, appropriate for various statistical and machine learning tasks, across various levels of measurement, with varying levels of data quality. Trees are robust in the presence of missing data and offer multiple ways of incorporating missing data in the resulting models. Although trees are powerful, they are also flexible and easy to use methods. This assures the production of high quality results that require few assumptions to deploy. The treatment ends with a discussion of the most current developments which continue to rely on the synergies and cross‐fertilization between statistical and machine learning communities. Current developments with the emergence of multiple trees and the various resampling approaches that are employed are discussed. WIREs Comput Stat 2013, 5:448–455. doi: 10.1002/wics.1278

This article is categorized under:

Statistical Learning and Exploratory Methods of the Data Sciences > Clustering and Classification

Statistical Learning and Exploratory Methods of the Data Sciences > Pattern Recognition

Statistical Learning and Exploratory Methods of the Data Sciences > Rule-Based Mining
Mapping the world's tropical cyclone rainfall contribution over land using the TRMM Multi‐satellite Precipitation Analysis
Authors: Prat Olivier P. , Nelson Brian R.
Published: October 2013

A study was performed to characterize over land precipitation associated with tropical cyclones (TCs) for basins around the world based upon the International Best Track Archive for Climate Stewardship (IBTrACS). From 1998 to 2009, data from the Tropical Rainfall Measuring Mission (TRMM) Multi‐satellite Precipitation Analysis (TMPA) product 3B42, showed that TCs accounted for 5.5%, 7.5%, 6%, 9.5%, and 8.9% of the annual precipitation for impacted over land areas of the Americas, East Asia, South and West Asia, Oceania, and East Africa respectively, and that TC contribution decreased significantly within the first 150 km from the coast. Locally, TCs contributed on average to more than 25% and up to 61% of the annual precipitation budget over very different climatic areas with arid or tropical characteristics. East Asia represented the higher and most constant TC rain (118 mm yr−1±19%) normalized over the area impacted, while East Africa presented the highest variability (108 mm yr−1±60%), and the Americas displayed the lowest average TC rain (65 mm yr−1±24%) despite a higher TC activity. Furthermore, the maximum monthly TC contribution (8–11%) was found later in the TC season and depended on the peak of TC activity, TC rainfall, and the domain transition between dry and wet regimes if any. Finally, because of their importance in terms of rainfall amount, the contribution of TCs was provided for a selection of 50 urban areas experiencing cyclonic activity. Results showed that for particularly intense years, urban areas prone to cyclonic activity received more than half of their annual rainfall from TCs.
A semiparametric multivariate, multisite weather generator with low‐frequency variability for use in climate risk assessments
Authors: Steinschneider Scott , Brown Casey
Published: October 2013

A multivariate, multisite daily weather generator is presented for use in decision‐centric vulnerability assessments under climate change. The tool is envisioned to be useful for a wide range of socioeconomic and biophysical systems sensitive to different aspects of climate variability and change. The proposed stochastic model has several components, including (1) a wavelet decomposition coupled to an autoregressive model to account for structured, low‐frequency climate oscillations, (2) a Markov chain and k‐nearest‐neighbor (KNN) resampling scheme to simulate spatially distributed, multivariate weather variables over a region, and (3) a quantile mapping procedure to enforce long‐term distributional shifts in weather variables that result from prescribed climate changes. The Markov chain is used to better represent wet and dry spell statistics, while the KNN bootstrap resampler preserves the covariance structure between the weather variables and across space. The wavelet‐based autoregressive model is applied to annual climate over the region and used to modulate the Markov chain and KNN resampling, embedding appropriate low‐frequency structure within the daily weather generation process. Parameters can be altered in any of the components of the proposed model to enable the generation of realistic time series of climate variables that exhibit changes to both lower‐order and higher‐order statistics at long‐term (interannual), mid‐term (seasonal), and short‐term (daily) timescales. The tool can be coupled with impact models in a bottom‐up risk assessment to efficiently and exhaustively explore the potential climate changes under which a system is most vulnerable. An application of the weather generator is presented for the Connecticut River basin to demonstrate the tool's ability to generate a wide range of possible climate sequences over an extensive spatial domain.
An exact series and improved numerical and approximate solutions for the Boussinesq equation
Authors: Chor Tomás , Dias Nelson L. , de Zárate Ailín Ruiz
Published: October 2013

We derive a series solution for the nonlinear Boussinesq equation in terms of the similarity variable of the Boltzmann transformation in a semi‐infinite domain. The first few coefficients of the series have been known for a long time, having been obtained by a truncated inversion of the series solution of the Blasius equation, but no direct recurrence relation was known for the complete series representing the solution of the Boussinesq equation. The series turns out to have a finite radius of convergence, which we estimate with a numerical complex‐plane integration method that identifies the singularities of the solution when the equation is extended to the complex plane. The homogeneous condition at the origin produces a singularity which complicates numerical solutions with Runge‐Kutta methods. We present two variable transformations that circumvent the problem and that are best suited to the complex‐variable and the real‐variable versions of the equation, respectively. Using those tools, an approximate solution accurate to 1.75 × 10−10 and valid for the entire positive real axis is then developed by matching a Padé approximant of the exact series and an asymptotic solution (to overcome the restriction imposed by the finite radius of convergence of the series), along the same lines of the expression proposed by Hogarth and Parlange (1999). The accuracies of all of the existing and the newly proposed solutions are obtained.
Improving computational efficiency in global river models by implementing the local inertial flow equation and a vector‐based river network map
Authors: Yamazaki Dai , de Almeida Gustavo A. M. , Bates Paul D.
Published: October 2013

Global river models are an essential tool for both earth system studies and water resources assessments. As advanced physical processes have been implemented in global river models, increasing computational cost has become problematic for executing ensemble or long‐term simulations. To improve computational efficiency, we here propose the use of a local inertial flow equation combined with a vector‐based river network map. A local inertial equation, a simplified formulation of the shallow water equations, was introduced to replace a diffusion wave equation. A vector‐based river network map which flexibly discretizes river segments was adopted in order to replace the traditional grid‐based map which is based on a Cartesian grid coordinate system. The computational efficiency of the proposed flow routing and river network map was tested by executing hydrodynamic simulations with the CaMa‐Flood global river model. The simulation results suggest that the computational efficiency can be improved by more than 300% by applying the local inertial equation. It can be improved by a further 60% by implementing the vector‐based river network map instead of a grid‐based map. It is found that the vector‐based map with evenly distributed flow distances between calculation units allows longer time steps compared to the grid‐based map because the latter has very short flow distances between calculation units at high latitudes which critically limit time step length. Considering the improvement in simulation speed, the local inertial equation, and a vector‐based river network map are preferable in global hydrodynamic simulations with high computational demands such as ensemble or long‐term experiments.
The emerging role of triple helices in RNA biology
Authors: Conrad Nicholas K.
Published: October 2013

The ability of RNA to form sophisticated secondary and tertiary structures enables it to perform a wide variety of cellular functions. One tertiary structure, the RNA triple helix, was first observed in vitro over 50 years ago, but biological activities for triple helices are only beginning to be appreciated. The recent determination of several RNA structures has implicated triple helices in distinct biological functions. For example, the SAM‐II riboswitch forms a triple helix that creates a highly specific binding pocket for S‐adenosylmethionine. In addition, a triple helix in the conserved pseudoknot domain of the telomerase‐associated RNA TER is essential for telomerase activity. A viral RNA cis‐acting RNA element called the ENE contributes to the nuclear stability of a viral noncoding RNA by forming a triple helix with the poly(A) tail. Finally, a cellular noncoding RNA, MALAT1, includes a triple helix at its 3′‐end that contributes to RNA stability, but surprisingly also supports translation. These examples highlight the diverse roles that RNA triple helices play in biology. Moreover, the dissection of triple helix mechanisms has the potential to uncover fundamental pathways in cell biology. WIREs RNA 2014, 5:15–29. doi: 10.1002/wrna.1194

This article is categorized under:

RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry

RNA Processing > 3' End Processing

RNA Turnover and Surveillance > Regulation of RNA Stability
Recognition modes of RNA tetraloops and tetraloop‐like motifs by RNA‐binding proteins
Authors: Thapar Roopa , Denmon Andria P. , Nikonowicz Edward P.
Published: October 2013

RNA hairpins are the most commonly occurring secondary structural elements in RNAs and serve as nucleation sites for RNA folding, RNA–RNA, and RNA–protein interactions. RNA hairpins are frequently capped by tetraloops, and based on sequence similarity, three broad classes of RNA tetraloops have been defined: GNRA, UNCG, and CUYG. Other classes such as the UYUN tetraloop in histone mRNAs, the UGAA in 16S rRNA, the AUUA tetraloop from the MS2 bacteriophage, and the AGNN tetraloop that binds RNase III have also been characterized. The tetraloop structure is compact and is usually characterized by a paired interaction between the first and fourth nucleotides. The two unpaired nucleotides in the loop are usually involved in base‐stacking or base‐phosphate hydrogen bonding interactions. Several structures of RNA tetraloops, free and complexed to other RNAs or proteins, are now available and these studies have increased our understanding of the diverse mechanisms by which this motif is recognized. RNA tetraloops can mediate RNA–RNA contacts via the tetraloop–receptor motif, kissing hairpin loops, A‐minor interactions, and pseudoknots. While these RNA–RNA interactions are fairly well understood, how RNA‐binding proteins recognize RNA tetraloops and tetraloop‐like motifs remains unclear. In this review, we summarize the structures of RNA tetraloop–protein complexes and the general themes that have emerged on sequence‐ and structure‐specific recognition of RNA tetraloops. We highlight how proteins achieve molecular recognition of this nucleic acid motif, the structural adaptations observed in the tetraloop to accommodate the protein‐binding partner, and the role of dynamics in recognition. WIREs RNA 2014, 5:49–67. doi: 10.1002/wrna.1196

This article is categorized under:

RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry

RNA Interactions with Proteins and Other Molecules > Protein–RNA Recognition

RNA Interactions with Proteins and Other Molecules > RNA–Protein Complexes
Ear‐tag loss rates in American beavers
Authors: Windels Steve K.
Published: October 2013

External marking of American beavers (Castor canadensis) is essential to studies of population dynamics and behavior of individuals. Application of metal ear tags is a common method used to mark beavers but rates and causes of ear‐tag loss have been insufficiently documented. I live‐trapped and tagged 627 beavers in Voyageurs National Park, Minnesota, USA, from 2006 to 2012 with a single, uniquely numbered no. 3 monel ear tag in each ear. Beavers recaptured or recovered via live‐trapping (n = 178), legal harvest outside of the park (n = 55), or death (n = 4) up to 6 years after initial release were inspected for tag loss. An additional 31 beavers were secondarily marked with radiotransmitters and used to test the assumption that loss of one ear tag was independent of loss of the other. Six percent (15 out of 237) of beavers lost a single ear tag. Overall probability of beavers losing a single ear tag was low (3.3%) and did not differ by sex, age class, or method of recapture–recovery. Tag loss was highest within 6 months of initial tagging, but probability of tag loss was not related to time between tagging and recovery up to 6 years after tagging. None of the radioed beavers lost both ear tags, supporting the assumption of independence of ear‐tag loss among individual beavers. Ear‐tag loss rates are sufficiently low that studies of American beavers that rely on mark–recapture methods do not need to account for bias from ear‐tag loss. Published 2013. This article is a U.S. Government work and is in the public domain in the USA.
Nesting burrowing owl density and abundance in the Altamont Pass Wind Resource Area, California
Authors: Smallwood K. Shawn , Neher Lee , Mount Joanne , Culver Renee C. E.
Published: October 2013

About 600 burrowing owls (Athene cunicularia) are killed annually at wind turbines in the Altamont Pass Wind Resource Area (APWRA), California, USA. Understanding the biological significance of this toll requires population data, including an estimate of the number of breeding pairs in the APWRA. An empirical model of breeding density predicted 35–75 pairs within the 16,760 ha of the APWRA, but that prediction proved low in spring 2011, when we detected 78 breeding pairs of burrowing owls in 46 randomly selected plots totaling 2,563 ha. We estimated that 3.201 breeding pairs/km2 occupied the 46 plots we surveyed in April–May. Extrapolating this density to the area of the APWRA led to an estimate of 537 pairs (90% CI = 320–753 pairs) across the APWRA, or 10× the model prediction. Counts of chicks emerged from burrows averaged 1.2 chicks/nest on the 46 plots, but these counts were minimum numbers. We estimated the APWRA supported at least 1,836 burrowing owls in 2011 (90% CI = 1,082–2,590), indicating the local population could conceivably be the sole source of fatalities attributed to wind turbines in the APWRA. Measures to conserve burrowing owls in the APWRA could include ground squirrel conservation and repowering to safer wind turbine models and careful siting to avoid areas densely populated with burrowing owls. More generally, management decisions based on comparisons of breeding‐pair density should also consider whether the density estimates were made in habitat fragments, sites selected for known high density, or in randomly or systematically selected plots sampling large areas, because the type of study area strongly influences the density estimate. © 2013 The Wildlife Society.
Choice of optimal conditions for X‐ray fluorescence analysis of milk products with varying fat content
Authors: Smagunova A. N. , Pashkova G. V.
Published: October 2013

The design of experiments was used to study sources of errors in the sample preparation and to choose optimal conditions for X‐ray fluorescence (XRF) analysis of milk products of varying fat content. The measurements were performed using the conventional wavelength‐dispersive XRF (WDXRF) and the total reflection XRF (TXRF) techniques. For WDXRF, the dried milk samples were pelletized, and the mathematical models were constructed, which described the dependence of XRF intensity on the pelletizing pressure, the pellet weight and the milk fat content. The effect of radiation time on the stability of pressed milk powder samples was also estimated. When applying TXRF, the sample preparation involved diluting milk samples with the ultrapure water, adding the internal standard (Ga) and drying of a sample aliquot on a quartz glass sample carrier. The mathematical models were designed, which described the dependence of the sample preparation error on the dilution ratio and sample aliquot pipetted on the carrier. A physical interpretation of the obtained mathematical models was proposed. Copyright © 2013 John Wiley & Sons, Ltd.
Syntheses, Structures, and Catalytic Activities of Copper(I) Complexes with the Ligand 2(4,5‐Diphenyl‐1H‐imidazol‐2‐yl)­pyridine
Authors: Yang Hua , Liu Yonglu , Hu Dao‐Dao
Published: October 2013

Two copper(I) complexes of compositions [Cu(HL)I]2·EtOH (1) and [Cu(HL)3]I·MeOH (2) were synthesized via the reactions of HL [HL = 2(4,5‐diphenyl‐1H‐imidazol‐2‐yl)pyridine] and CuI in EtOH and MeOH, respectively, under solvothermal conditions. The complexes were characterized by X‐ray single crystal diffraction, IR spectroscopy, and elemental analysis. Compounds 1 and 2 are catalytically active towards ketalization reaction, giving various ketals under mild conditions.
Information & communication technology and true real GDP: economic analysis and findings for selected countries
Authors: Welfens Paul J. J. , Perret Jens K.
Published: October 2013

The expansion of information & communication technology (ICT) is continuing in OECD countries and the world economy – partly due to the ongoing fall of relative ICT prices. The continuing absolute fall of ICT prices and ICT capital prices, respectively, is not adequately considered in the standard analysis of ICT. In the study presented here the ICT investment-GDP ratio is calculated in real terms and it is shown that this ratio is higher (order of magnitude is about 2 percentage points) than the nominal investment-GDP ratio which is misleading the ICT sector, policy makers and society at large. Moreover, we take an innovative look at the digital time budget of private households in selected OECD countries. Assuming that 10 % represents the relevant share of the time budget the digital value-added of private households stands for an unrecorded digital value-added of 2–5 % of gross domestic product; with a share of 20 % of the household’s internet time budget devoted to value-added the hidden internet value-added in the US would be in the range of 4.7–10.4 %. Hence the overall understimation of the ICT sector’s contribution to GDP is considerable and therefore changes in official statistical analysis and the System of National Accounts are required.
Molecular Species of Phospholipids with Very Long Chain Fatty Acids in Skin Fibroblasts of Zellweger Syndrome
Authors: Hama Kotaro , Nagai Toru , Nishizawa Chiho , Ikeda Kazutaka , Morita Masashi , Satoh Noriko , Nakanishi Hiroki , Imanaka Tsuneo , Shimozawa Nobuyuki , Taguchi Ryo , Inoue Keizo , Yokoyama Kazuaki
Published: October 2013

The ratio of C26:0/C22:0 fatty acids in patient lipids is widely accepted as a critical clinical criterion of peroxisomal diseases, such as Zellweger syndrome and X‐linked adrenoleukodystrophy (X‐ALD). However, phospholipid molecular species with very long chain fatty acids (VLCFA) have not been precisely characterized. In the present study, the structures of such molecules in fibroblasts of Zellweger syndrome and X‐ALD were examined using LC–ESI–MS/MS analysis. In fibroblasts from Zellweger patients, a large number of VLCFA‐containing molecular species were detected in several phospholipid classes as well as neutral lipids, including triacylglycerol and cholesteryl esters. Among these lipids, phosphatidylcholine showed the most diversity in the structures of VLCFA‐containing molecular species. Some VLCFA possessed longer carbon chains and/or larger number of double bonds than C26:0‐fatty acid (FA). Similar VLCFA were also found in other phospholipid classes, such as phosphatidylethanolamine and phosphatidylserine. In addition, VLCFA‐containing phospholipid species showed some differences among fibroblasts from Zellweger patients. It appears that phospholipids with VLCFA, with or without double bonds, as well as C26:0‐FA might affect cellular functions, thus leading to the pathogenesis of peroxisomal diseases, such as Zellweger syndrome and X‐ALD.
Structurally-controlled Melt Accumulation: Himalayan Migmatites and Related Deformation – Dhauli Ganga Valley, Garhwal Himalaya
Authors: Jain A. K. , Seth Puneet , Shreshtha Mrinal , Mukherjee P. K. , Singh Keser
Published: October 2013

In the uppermost parts of the Higher Himalayan Crystallines (HHC) of the Great Himalaya, widespread in situ partial melting of sillimanite+K-feldspar gneiss resulted in the formation of migmatite and resultant melt accumulation near the South Tibetan Detachment System (STDS) during various deformation events along the Dhauli Ganga valley in Garhwal. The oldest migmatite phase, designated as the Me1, parallels the main foliation Sm as the stromatite layers and concordant leucogranite bands. Younger melt phases Me2, Me3 and Me5 are recorded along small-scale ductile thrusts, extensional fabric and structureless patches, respectively. It is only the Me4 melting phase that is evidenced by large-scale melt migration along cross-cutting irregular veins. These were possible conduits for migration and accumulation of melt into larger leucogranite bodies like the Malari granite (19.0± 0.5 Ma).