bluuebunny/crossref_metadata_2025 huggingface dataset:
Fast in‐memory XPath search using compressed indexes
Authors: Arroyuelo Diego , Claude Francisco , Maneth Sebastian , Mäkinen Veli , Navarro Gonzalo , Nguyễn Kim , Sirén Jouni , Välimäki Niko
Published: October 2013

Extensible Markup Language (XML) documents consist of text data plus structured data (markup). XPath allows to query both text and structure. Evaluating such hybrid queries is challenging. We present a system for in‐memory evaluation of XPath search queries, that is, queries with text and structure predicates, yet without advanced features such as backward axes, arithmetics, and joins. We show that for this query fragment, which contains Forward Core XPath, our system, dubbed Succinct XML Self‐Index (‘SXSI’), outperforms existing systems by 1–3 orders of magnitude. SXSI is based on state‐of‐the‐art indexes for text and structure data. It combines two novelties. On one hand, it represents the XML data in a compact indexed form, which allows it to handle larger collections in main memory while supporting powerful search and navigation operations over the text and the structure. On the other hand, it features an execution engine that uses tree automata and cleverly chooses evaluation orders that leverage the speeds of the respective indexes. SXSI is modular and allows seamless replacement of its indexes. This is demonstrated through experiments with (1) a text index specialized for search of bio sequences, and (2) a word‐based text index specialized for natural language search. Copyright © 2013 John Wiley & Sons, Ltd.
CPU load prediction for cloud environment based on a dynamic ensemble model
Authors: Cao Jian , Fu Jiwen , Li Minglu , Chen Jinjun
Published: October 2013

Resource performance prediction is becoming more and more important in cloud environment, and CPU load prediction is helpful for system maintenance and application schedule. However, the best predictor often varies from one resource to another. At the same time, CPU load in cloud environment has a wide range of dynamics so that the best predictor for any particular CPU load time series may change over time. Ensemble method, which can use multiple models to obtain better performances, is investigated to support CPU load prediction in this paper. The novel ensemble model proposed consists of two layers. The predictor optimization layer can continuously incorporate new predictor instances and remove those ones with a poor performance. The ensemble layer is responsible for producing the final prediction based on the results of multiple predictor instances. In addition, the ensemble layer can also provide feedbacks to the predictor optimization layer, which helps it to adopt appropriate optimization strategies. Extensive experiments have been performed on CPU load traces collected from an in‐production private cloud environment, and it shows this ensemble model has a better performance than any individual model. Copyright © 2013 John Wiley & Sons, Ltd.
Combining Process Consultation and Structural Interventions
Authors: Lapalme James , Conklin James
Published: October 2013

This article explores the compatibility of a process consulting stance with structural interventions intended to promote significant organizational redesign. Much of the existing literature on process consultation implies that this capacity‐building approach is best suited to relational or process concerns. However, Edgar Schein and other recent commentators have observed that structural issues are not precluded from its purview. Through a case study involving a process consulting stance in relation to a shifting range of structural concerns, this paper argues that the latter offers a feasible way of pursuing structural change. We also show that models focusing on structure allowed us to generate questions for our inquiry process. However, the paper also suggests that it is important to underpin the intervention with a sound grasp of the purpose and affordances of specific structural theories and to be watchful for the significant reserves of resistance that can be aroused when structural issues are tackled. Copyright © 2013 John Wiley & Sons, Ltd.
A new class of semiparametric transformation models based on first hitting times by latent degradation processes
Authors: Choi Sangbum , Doksum Kjell A.
Published: October 2013

In many failure mechanisms, most subjects under study deteriorate physically over time, and thus a depreciation in health may precede failure. A latent stochastic process, called degradation process, may be assumed for modeling such depreciation whereby an event occurs when the process first crosses a threshold. A class of survival regression models can be constructed from the first hitting time of a latent accelerating degradation process, which turns out to be a transformation model in the literature. To characterize these models, we propose to use first‐hitting‐time models for the baseline distribution, specifically inverse Gaussian, Birnbaum–Saunders and gamma distributions, among others. The proposed models have many desirable features, such as a wide variety of shapes of hazard rates, analytical tractability and, most of all, its motivation from a plausible stochastic setting for failure. We estimate the model parameters by the non‐parametric maximum likelihood approach. The estimators are shown to be consistent, asymptotically normal and asymptotically efficient. Simple and stable numerical algorithms are provided to calculate the parameter estimators and estimate their variances. Simulation studies show that the proposed approach is appropriate for practical use. The methodology is illustrated with two real examples. Copyright © 2013 John Wiley & Sons Ltd
HIF1α Modulates Cell Fate Reprogramming Through Early Glycolytic Shift and Upregulation of PDK1–3 and PKM2
Authors: Prigione Alessandro , Rohwer Nadine , Hoffmann Sheila , Mlody Barbara , Drews Katharina , Bukowiecki Raul , Blümlein Katharina , Wanker Erich E. , Ralser Markus , Cramer Thorsten , Adjaye James
Published: October 2013

Reprogramming somatic cells to a pluripotent state drastically reconfigures the cellular anabolic requirements, thus potentially inducing cancer-like metabolic transformation. Accordingly, we and others previously showed that somatic mitochondria and bioenergetics are extensively remodeled upon derivation of induced pluripotent stem cells (iPSCs), as the cells transit from oxidative to glycolytic metabolism. In the attempt to identify possible regulatory mechanisms underlying this metabolic restructuring, we investigated the contributing role of hypoxia-inducible factor one alpha (HIF1α), a master regulator of energy metabolism, in the induction and maintenance of pluripotency. We discovered that the ablation of HIF1α function in dermal fibroblasts dramatically hampers reprogramming efficiency, while small molecule-based activation of HIF1α significantly improves cell fate conversion. Transcriptional and bioenergetic analysis during reprogramming initiation indicated that the transduction of the four factors is sufficient to upregulate the HIF1α target pyruvate dehydrogenase kinase (PDK) one and set in motion the glycolytic shift. However, additional HIF1α activation appears critical in the early upregulation of other HIF1α-associated metabolic regulators, including PDK3 and pyruvate kinase (PK) isoform M2 (PKM2), resulting in increased glycolysis and enhanced reprogramming. Accordingly, elevated levels of PDK1, PDK3, and PKM2 and reduced PK activity could be observed in iPSCs and human embryonic stem cells in the undifferentiated state. Overall, the findings suggest that the early induction of HIF1α targets may be instrumental in iPSC derivation via the activation of a glycolytic program. These findings implicate the HIF1α pathway as an enabling regulator of cellular reprogramming. Stem Cells  2014;32:364–376
MMP-10 Is Required for Efficient Muscle Regeneration in Mouse Models of Injury and Muscular Dystrophy
Authors: Bobadilla Míriam , Sáinz Neira , Rodriguez José Antonio , Abizanda Gloria , Orbe Josune , Martino Alba , García Verdugo José Manuel , Páramo José A. , Prósper Felipe , Pérez-Ruiz Ana
Published: October 2013

Matrix metalloproteinases (MMPs), a family of endopeptidases that are involved in the degradation of extracellular matrix components, have been implicated in skeletal muscle regeneration. Among the MMPs, MMP-2 and MMP-9 are upregulated in Duchenne muscular dystrophy (DMD), a fatal X-linked muscle disorder. However, inhibition or overexpression of specific MMPs in a mouse model of DMD (mdx) has yielded mixed results regarding disease progression, depending on the MMP studied. Here, we have examined the role of MMP-10 in muscle regeneration during injury and muscular dystrophy. We found that skeletal muscle increases MMP-10 protein expression in response to damage (notexin) or disease (mdx mice), suggesting its role in muscle regeneration. In addition, we found that MMP-10-deficient muscles displayed impaired recruitment of endothelial cells, reduced levels of extracellular matrix proteins, diminished collagen deposition, and decreased fiber size, which collectively contributed to delayed muscle regeneration after injury. Also, MMP-10 knockout in mdx mice led to a deteriorated dystrophic phenotype. Moreover, MMP-10 mRNA silencing in injured muscles (wild-type and mdx) reduced muscle regeneration, while addition of recombinant human MMP-10 accelerated muscle repair, suggesting that MMP-10 is required for efficient muscle regeneration. Furthermore, our data suggest that MMP-10-mediated muscle repair is associated with VEGF/Akt signaling. Thus, our findings indicate that MMP-10 is critical for skeletal muscle maintenance and regeneration during injury and disease. Stem Cells  2014;32:447–461
Concise Review: Bridging the Gap: Bone Regeneration Using Skeletal Stem Cell-Based Strategies—Where Are We Now?
Authors: Dawson Jonathan I. , Kanczler Janos , Tare Rahul , Kassem Moustapha , Oreffo Richard O.C.
Published: October 2013

Skeletal stem cells confer to bone its innate capacity for regeneration and repair. Bone regeneration strategies seek to harness and enhance this regenerative capacity for the replacement of tissue damaged or lost through congenital defects, trauma, functional/esthetic problems, and a broad range of diseases associated with an increasingly aged population. This review describes the state of the field and current steps to translate and apply skeletal stem cell biology in the clinic and the problems therein. Challenges are described along with key strategies including the isolation and ex vivo expansion of multipotential populations, the targeting/delivery of regenerative populations to sites of repair, and their differentiation toward bone lineages. Finally, preclinical models of bone repair are discussed along with their implications for clinical translation and the opportunities to harness that knowledge for musculoskeletal regeneration. Stem Cells  2014;32:35–44
Heat Shock Improves Sca-1+ Stem Cell Survival and Directs Ischemic Cardiomyocytes Toward a Prosurvival Phenotype Via Exosomal Transfer: A Critical Role for HSF1/miR-34a/HSP70 Pathway
Authors: Feng Yuliang , Huang Wei , Meng Wei , Jegga Anil G. , Wang Yigang , Cai Wenfeng , Kim Ha Won , Pasha Zeeshan , Wen Zhili , Rao Fang , Modi Rohan M. , Yu Xiyong , Ashraf Muhammad
Published: October 2013

Stem cell-based therapy is a promising intervention for ischemic heart diseases. However, the functional integrity of stem cells is impaired in an ischemic environment. Here, we report a novel finding that heat shock significantly improves Sca-1+stem cell survival in an ischemic environment by the regulation of the triangle: heat shock factor 1 (HSF1), HSF1/miR-34a, and heat shock protein 70 (HSP70). Initially we prove that HSP70 is the key chaperone-mediating cytoprotective effect of heat shock in Sca-1+cells and then we establish miR-34a as a direct repressor of HSP70. We found that HSP70 was downregulated in heat shocked Sca-1+ stem cells (HSSca-1+ cells). Intriguingly, we demonstrate that the downregulation of miR-34a is attributed to HSF1-mediated epigenetic repression through histone H3 Lys27 trimethylation (H3K27me3) on miR-34a promoter. Moreover, we show that heat shock induces exosomal transfer of HSF1 from Sca-1+ cells, which directs ischemic cardiomyocytes toward a prosurvival phenotype by epigenetic repression of miR-34a. In addition, our in vivo study demonstrates that transplantation of HSSca-1+ cells significantly reduces apoptosis, attenuates fibrosis, and improves global heart functions in ischemic myocardium. Hence, our study provides not only novel insights into the effects of heat shock on stem cell survival and paracrine behavior but also may have therapeutic values for stem cell therapy in ischemic heart diseases. Stem Cells  2014;32:462–472
EZH2 and KDM6A Act as an Epigenetic Switch to Regulate Mesenchymal Stem Cell Lineage Specification
Authors: Hemming Sarah , Cakouros Dimitrios , Isenmann Sandra , Cooper Lachlan , Menicanin Danijela , Zannettino Andrew , Gronthos Stan
Published: October 2013

The methyltransferase, Enhancer of Zeste homology 2 (EZH2), trimethylates histone 3 lysine 27 (H3K27me3) on chromatin and this repressive mark is removed by lysine demethylase 6A (KDM6A). Loss of these epigenetic modifiers results in developmental defects. We demonstrate that Ezh2 and Kdm6a transcript levels change during differentiation of multipotential human bone marrow-derived mesenchymal stem cells (MSC). Enforced expression of Ezh2 in MSC promoted adipogenic in vitro and inhibited osteogenic differentiation potential in vitro and in vivo, whereas Kdm6a inhibited adipogenesis in vitro and promoted osteogenic differentiation in vitro and in vivo. Inhibition of EZH2 activity and knockdown of Ezh2 gene expression in human MSC resulted in decreased adipogenesis and increased osteogenesis. Conversely, knockdown of Kdm6a gene expression in MSC leads to increased adipogenesis and decreased osteogenesis. Both Ezh2 and Kdm6a were shown to affect expression of master regulatory genes involved in adipogenesis and osteogenesis and H3K27me3 on the promoters of master regulatory genes. These findings demonstrate an important epigenetic switch centered on H3K27me3 which dictates MSC lineage determination. Stem Cells  2014;32:802–815
Orocline and syntaxes formation during subduction and collision
Authors: Bajolet Flora , Replumaz Anne , Lainé Romain
Published: October 2013

The present work investigates the formation of curved ranges and syntaxes with scaled laboratory experiments. We simulated subduction and collision processes comparable to India‐Asia configuration involving a continental upper plate and a subducting plate composed of an oceanic lithosphere and a continental indenter. The experiments reveal that the shape of the mountain range (concave, straight, or convex) and the development of syntaxes are controlled by the subduction interface, the buoyancy number (Fb) of the upper plate (i.e., thickness and viscosity), and the boundary conditions. Four end‐members regimes of indentation can be defined depending on the range shape and dynamics of the upper plate. The curvature of the range is convex toward the subducting plate with syntaxes for a weak subduction fault and concave without syntaxes for a strong subduction fault. Convex curvature and syntaxes form by overthrusting of upper plate material on the subducting plate, which is faster at the center than at the extremities. They are associated with a rather flat slab (underthrusting) during continental collision. Low‐Fb experiments show less pronounced curvatures associated to thickening comparable to the early stages of the India‐Asia collision. In contrast, a thick and weak upper plate (high Fb) leads to gravity collapse that increases the amplitude of the curvature and lateral escape, similar to the late evolution of the Himalaya‐Tibet system. Important lateral decoupling on the sides of the indenter enhances the indentation and produces sharper syntaxes.
Sea‐level scenarios for evaluating coastal impacts
Authors: Nicholls Robert J. , Hanson Susan E. , Lowe Jason A. , Warrick Richard A. , Lu Xianfu , Long Antony J.
Published: October 2013

Global‐mean sea‐level rise will drive impacts and adaptation needs around the world's coasts over the 21st century and beyond. A key element in assessing these issues is the development of scenarios (or plausible futures) of local relative sea‐level rise to support impact assessment and adaptation planning. This requires combining a number of different but uncertain components of sea level which can be linked to climatic and non‐climatic (i.e., uplift/subsidence of coastal land) factors. A major concern remains about the possibility of significant contributions from the major Greenland and Antarctic ice sheets and this must be factored into the assessments, despite the uncertainty. This paper reviews the different mechanisms which contribute to sea‐level change and considers a methodology for combining the available data to create relative (or local) sea‐level rise scenarios suitable for impact and adaptation assessments across a range of sophistication of analysis. The methods that are developed are pragmatic and consider the different needs of impact assessment, adaptation planning, and long‐term decision making. This includes the requirements of strategic decision makers who rightly focus on low probability but high consequence changes and their consequences. Hence plausible high end sea‐level rise scenarios beyond the conventional Intergovernmental Panel on Climate Change (IPCC) range and which take into account evidence beyond that from the current generation of climate models are developed and their application discussed. Continued review and development of sea‐level scenarios is recommended, starting with assimilating the insights of the forthcoming IPCC AR5 assessment. WIREs Clim Change 2014, 5:129–150. doi: 10.1002/wcc.253

This article is categorized under:

Assessing Impacts of Climate Change > Scenario Development and Application
Long‐range correction for density functional theory
Authors: Tsuneda Takao , Hirao Kimihiko
Published: October 2013

Long‐range correction for exchange functionals in Kohn–Sham density functional theory and its applicability are reviewed. Long‐range correction simply supplements the long‐range exchange effect in exchange functionals by replacing the Hartree–Fock exchange integral with the long‐range part of exchange functionals. Nevertheless, this correction has solved many problems in Kohn–Sham calculations. Using this correction, valence occupied and unoccupied orbital energies are quantitatively reproduced in a comprehensive manner for the first time. Long‐range correction has also solved the underestimations of charge transfer excitation energies and oscillator strengths in time‐dependent Kohn–Sham calculations and has clearly improved poor optical response properties such as hyperpolarizability in coupled‐perturbed Kohn–Sham and finite‐field calculations. Moreover, this correction has drastically improved the reproducibility of van der Waals bonds by simply combining with conventional van der Waals calculation methods. We, therefore, believe that the long‐range correction clearly extends the applicability of the Kohn–Sham method in future quantum chemistry calculations.

This article is categorized under:

Electronic Structure Theory > Density Functional Theory
Aphasias and theories of linguistic representation: representing frequency, hierarchy, constructions, and sequential structure
Authors: Menn Lise , Duffield Cecily Jill
Published: October 2013

Error and preservation patterns in aphasic speech show that the brain makes use of the frequencies of words, constructions, and collocations, as well as category membership and hierarchical structure, during language processing. Frequency effects are evident along two quasi‐independent axes: syntagmatic (the sequential context, e.g., deploying correct functors, categories, and utterance‐level intonation) and paradigmatic (the choice at any given linguistic level, e.g., selecting content words and modifying structures). Frequency along the syntagmatic axis is shown to play a role in errors involving idioms, constructions, and collocations that cross major phrasal boundaries. Along the paradigmatic axis, frequency affects errors involving lexical selection, competing functors and inflected forms (e.g., using plural where singular is required). An account of language representation and processing that encompasses frequency as well as categorization and structure is compatible with what we know about how the brain works: increased experience with a linguistic structure results in increased activation—and strengthening—of the neural networks involved in processing that structure. These claims are supported by the literature on experimental work in normal speakers. Parsimony, plus the unexamined assumption that mental representation is like a written record (entries either present or absent, structure displayable in two dimensions), has been a misleading guide to modeling language representation. The substantial redundancy in representations and processing that is introduced by incorporating both frequency‐based and hierarchy‐based information is in fact appropriate for the brain as a fast, reliable, massively parallel error‐correcting network with very large storage capacity and gradient representation strength. WIREs Cogn Sci 2013, 4:651–663. doi: 10.1002/wcs.1257

This article is categorized under:

Linguistics > Language in Mind and Brain

Linguistics > Linguistic Theory
Rationality
Authors: Sosis Clifford , Bishop Michael A
Published: October 2013

A theory of rationality is a theory that evaluates instances of reasoning as rational, irrational, or (ir)rational to some degree. Theories can be categorized as rule‐based or consequentialist. Rule‐based theories say that rational reasoning accords with certain rules (e.g., of logic or probability). Consequentialist theories say that rational reasoning tends to produce good consequences. For instance, the reliabilist takes rationality to be reasoning that tends to produce mostly true beliefs. The pragmatist takes it to be reasoning that tends to produce mostly useful beliefs. This article reviews some of the features and the challenges of rule‐based, reliabilist, and pragmatist theories of rationality. WIREs Cogn Sci 2014, 5:27–37. doi: 10.1002/wcs.1263

This article is categorized under:

Philosophy > Foundations of Cognitive Science
Changes in the economic value of wind energy and flexible resources at increasing penetration levels in the Rocky Mountain Power Area
Authors: Mills A.D. , Wiser R.H.
Published: October 2013

We use a consistent economic framework to estimate the long‐run economic value of wind while including operational constraints for conventional generation and hourly variation in wind and load. Day‐ahead forecast errors in wind are corrected in the real‐time, after commitment decisions for many thermal generators have already been made. The framework is used to estimate the change in the marginal economic value of wind with increasing penetration in the Rocky Mountain Power Area of the USA. We also evaluate the marginal economic benefit to wind energy of implementing several strategies to manage wind energy variability and uncertainty: more flexible conventional generation, real‐time pricing, low cost bulk energy storage, and increased geographic diversity of wind plant siting. Without mitigation, the marginal economic value of wind is found to decrease by $21 MWh (37% of the marginal value of wind at 0% penetration) as wind penetration increases from 0% to 30%. The decline is largely because of the hourly profile of wind output and day‐ahead wind energy forecast errors; factors whose impact is reduced by the mitigation strategies. With mitigation, the marginal value of wind at the 30% penetration level is $6‐$11 MWh greater than the value without the measures (17‐31% increase in value). Although the marginal value of wind energy decreases with increasing penetration in this region, several different types of mitigation strategies are available and should be investigated in more detail. Copyright © 2013 John Wiley & Sons, Ltd.
Separation and enhancement of gear and bearing signals for the diagnosis of wind turbine transmission systems
Authors: Sawalhi Nader , Randall Robert B. , Forrester David
Published: October 2013

This paper is based on the analysis of a wind turbine vibration data provided by the National Renewable Energy Laboratory under a round robin scheme to diagnose faults in a transmission that had experienced a loss of lubricant for a period. Previously developed techniques were applied, but this is the first time that some were used in combination for a machine covering such a wide speed range and with such a low minimum speed. Another factor was that the gearbox design was far from ‘hunting tooth’, and this gave problems with the diagnosis. The paper describes how the techniques were adapted to solve these problems. The algorithms used for the diagnosis included the extraction of a pseudo‐encoder signal from the vibration signals themselves, to allow order tracking and resampling in the rotation angle domain. This permitted successive resampling over several stages to give synchronous averages for each shaft in the planetary gearbox, allowing diagnostics of the gears on that shaft. Subtraction of all synchronously averaged signals leaves a residual signal containing bearing signals and allowing diagnosis of their faults. This is the first reported case of applying that technique over four separate stages. Bearing diagnosis was carried out using a semi‐automated algorithm based on whitening the residual signal, filtering it to maximize the kurtosis and finally using the Hilbert transform approach to get the spectrum of the squared envelope. The analysis of the gears included using spectrum and cepstrum comparisons between healthy and faulty data. It is shown for the first time that cepstra from the same signal (from spectra in different frequency ranges) gives information about completely different gears at very different speeds. The analysis also involved obtaining synchronous averages for the individual planetary gears and for the sun gear by using software patented by the Australian Defence Science and Technology Organisation. The signal processing tools used for the analysis were shown to be capable of identifying both gear and bearing faults in the wind turbine gearbox, though one bearing fault was missed. Copyright © 2013 John Wiley & Sons, Ltd.
Storage and demand‐side options for integrating wind power
Authors: Tuohy Aidan , Kaun Ben , Entriken Robert
Published: October 2013

With the increased levels of wind power being seen worldwide and the projected further increases over the coming decades, there has been significant attention paid to emerging flexible resources such as storage and demand‐side options as a means to meet many of the challenges associated with wind integration. In particular, these resources could meet the increased flexibility requirements of systems with high wind due to variability and uncertainty of wind across timescales from seconds to minutes to hours or even days. Storage and demand‐side options are both characterized by the ability to respond quickly and accurately, to increase load as well as to provide generation resources and by the fact that they are energy limited in nature. Demand response can contribute to wind integration in different ways, using either price‐ or incentive‐based programs; the extent to which they can be used to integrate wind depends on the nature of the program. Electricity storage comes in many forms, with pumped hydro storage presently accounting for almost all grid storage, along with recent advances in battery and compressed air energy storage. The ability of storage to contribute to integrating wind power is limited mainly by the cost of deployment and the efficiency losses. While these features may not be as significant for demand response, there are significant regulatory and policy barriers in the way of deploying demand‐side options. Both storage and demand‐side resources provide support for wind integration in particular regarding provision of ancillary services and reduction of wind curtailment. WIREs Energy Environ 2014, 3:93–109. doi: 10.1002/wene.92

This article is categorized under:

Wind Power > Economics and Policy

Wind Power > Systems and Infrastructure

Energy Systems Economics > Systems and Infrastructure
Estimation of the base flow recession constant under human interference
Authors: Thomas Brian F. , Vogel Richard M. , Kroll Charles N. , Famiglietti James S.
Published: October 2013

The base flow recession constant, Kb, is used to characterize the interaction of groundwater and surface water systems. Estimation of Kb is critical in many studies including rainfall‐runoff modeling, estimation of low flow statistics at ungaged locations, and base flow separation methods. The performance of several estimators of Kb are compared, including several new approaches which account for the impact of human withdrawals. A traditional semilog estimation approach adapted to incorporate the influence of human withdrawals was preferred over other derivative‐based estimators. Human withdrawals are shown to have a significant impact on the estimation of base flow recessions, even when withdrawals are relatively small. Regional regression models are developed to relate seasonal estimates of Kb to physical, climatic, and anthropogenic characteristics of stream‐aquifer systems. Among the factors considered for explaining the behavior of Kb, both drainage density and human withdrawals have significant and similar explanatory power. We document the importance of incorporating human withdrawals into models of the base flow recession response of a watershed and the systemic downward bias associated with estimates of Kb obtained without consideration of human withdrawals.
Competition and collaboration between RNA‐binding proteins and microRNAs
Authors: Ho J. J. David , Marsden Philip A.
Published: October 2013

Posttranscriptional regulation of mRNA species represents a major regulatory checkpoint in the control of gene expression. Historically, RNA‐binding proteins (RBPs) have been regarded as the primary regulators of mRNA stability and translation. More recently, however, microRNAs have emerged as a class of potent and pervasive posttranscriptional rheostats that similarly affect mRNA stability and translation. The observation that both microRNAs and RBPs regulate mRNA stability and translation has initiated a newer area of research that involves the examination of dynamic interactions between these two important classes of posttranscriptional regulators, the myriad of factors that influence these biological interactions, and ultimately, their effects on target mRNAs. Specifically, microRNAs and RBPs can act synergistically to effect mRNA destabilization and translational inhibition. They can also engage in competition with each other and exert opposing effects on target mRNAs. To date, several key studies have provided critical details regarding the mechanisms and principles of interaction between these molecules. Additionally, these findings raise important questions regarding the regulation of these interactions, including the roles of posttranslational modification, subcellular localization, target inhibition versus activation, and changes in expression levels of these regulatory factors, especially under stimulus‐ and cell‐specific conditions. Indeed, further experimentation is warranted to address these key issues that pertain to the collaboration and competition between microRNAs and RBPs. Significantly, the elucidation of these important details bears critical implications for disease management, especially for those diseases in which these cellular factors are dysregulated. WIREs RNA 2014, 5:69–86. doi: 10.1002/wrna.1197

This article is categorized under:

RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications

RNA Turnover and Surveillance > Regulation of RNA Stability

Regulatory RNAs/RNAi/Riboswitches > RNAi: Mechanisms of Action

Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs
Rule‐based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems
Authors: Chylek Lily A. , Harris Leonard A. , Tung Chang‐Shung , Faeder James R. , Lopez Carlos F. , Hlavacek William S.
Published: October 2013

Rule‐based modeling was developed to address the limitations of traditional approaches for modeling chemical kinetics in cell signaling systems. These systems consist of multiple interacting biomolecules (e.g., proteins), which themselves consist of multiple parts (e.g., domains, linear motifs, and sites of phosphorylation). Consequently, biomolecules that mediate information processing generally have the potential to interact in multiple ways, with the number of possible complexes and posttranslational modification states tending to grow exponentially with the number of binary interactions considered. As a result, only large reaction networks capture all possible consequences of the molecular interactions that occur in a cell signaling system, which is problematic because traditional modeling approaches for chemical kinetics (e.g., ordinary differential equations) require explicit network specification. This problem is circumvented through representation of interactions in terms of local rules. With this approach, network specification is implicit and model specification is concise. Concise representation results in a coarse graining of chemical kinetics, which is introduced because all reactions implied by a rule inherit the rate law associated with that rule. Coarse graining can be appropriate if interactions are modular, and the coarseness of a model can be adjusted as needed. Rules can be specified using specialized model‐specification languages, and recently developed tools designed for specification of rule‐based models allow one to leverage powerful software engineering capabilities. A rule‐based model comprises a set of rules, which can be processed by general‐purpose simulation and analysis tools to achieve different objectives (e.g., to perform either a deterministic or stochastic simulation). WIREs Syst Biol Med 2014, 6:13–36. doi: 10.1002/wsbm.1245

This article is categorized under:

Biological Mechanisms > Cell Signaling

Analytical and Computational Methods > Computational Methods

Models of Systems Properties and Processes > Mechanistic Models
Three Coordination Polymers based on 3,5‐Bis(imidazole‐1‐yl)pyridine and Benzoic Acid: Synthesis, Crystal Structures and Photoluminescent Properties
Authors: Xu Jiakun , Yan Xingchen , Sun Xiaochun , Sun Guolong , Bi Caifeng , Sun Mi
Published: October 2013

Three metal coordination polymers {[Co(L)2(H2O)2]2+·2NO3–}n (1), {[Mn(L)2(H2O)2]2+·2Cl–·3H2O}n (2), and [ZnL(ba)2]n (3) [L = 3,5‐bis(imidazole‐1‐yl)pyridine and Hba = benzoic acid] were synthesized and structurally characterized by IR spectroscopy, elemental analysis, X‐ray powder diffraction, and X‐ray single crystal diffraction. Complex 1 shows a one‐dimensional (1D) chain structure. Adjacent chains are connected by hydrogen bonding and nitrate groups to form a 3D network. Complex 2 features a 2D layer structure. A three‐dimensional network is constructed through the cluster consisting of two chloride ions and three water molecules. Complex 3 shows a 1D zigzag chain structure that further twists together to form a 3D network. The X‐ray powder diffraction patterns were compared with the simulated ones. Moreover, the luminescent properties of 1–3 were investigated in the solid state at room temperature, and the thermogravimetric analyses were carried out to study the thermal stability of the three complexes.
From Chalcogenides to Polychalcogenidehalides – First Identification in Mineral Samples
Authors: Schürmann Ulrich , Duppel Viola , Nilges Tom , Britvin Sergey , Kovalenker Vladimir A. , Kienle Lorenz
Published: October 2013

Mineral samples from the Prasolovskoe epithermal Au‐Ag deposit, Russia, were investigated via transmission electron microscopy (TEM). One component was identified as the mineral kurilite Ag8Te3Se according to the data obtained from electron diffraction (ED) and Fourier transform analyses of high resolution micrographs. Micrometer‐sized grains of kurilite were found next to other noble metal chalcogenide domains like the hessite‐type. The EDX microprobe analyses of the kurilite domains were determined with the chemical composition Ag7.9Au0.1Te2.9Se1.0 which is consistent with kurilite doped by gold. Additionally noble metal polychalcogenidehalides (NMPH) were identified via ED. Monoclinic and tetragonal polymorphs of Ag5Te2Cl were observed for the first time in a mineral sample. One additional component, whose composition equates the kurilite‐type component with regard to Ag, Au, Te, and Se but with a marginal chlorine component, crystallizes in a structure type known from synthetic NMPH, namely Ag23Te12X (X = Cl, Br). This phase as well as the phases Ag10Te4Br3 and Ag20Te10Br2 was found next to each other in an also investigated synthetic sample.
Preparation, Crystal Structure, Vibrational Spectra, and Thermal Behavior of Rb2H2P2O6·2H2O
Authors: Gjikaj Mimoza , Wu Peng , Brockner Wolfgang
Published: October 2013

Single crystals of Rb2H2P2O6·2H2O could be obtained from aqueous solutions of hypodiphosphoric acid and rubidium carbonate. Its crystal structure was determined by X‐ray diffraction and it crystallizes in the monoclinic space group P21/c with Z = 4. The salt‐like title compound consists of [H2P2O6]2– units in staggered P2O6‐skeleton conformation, Rb+ cations, and H2O molecules, held together by intermolecular hydrogen bonds of the type O···O. The vibrational spectra (IR/FIR and Raman) of the rubidium salt were recorded and an assignment of the vibrational modes is proposed based on the point group C2h for the P2O6‐skeleton of the anion. The thermal behavior of Rb2H2P2O6·2H2O is dominated by a complex TG decay indicating a simultaneous H2O delivery coupled with a disproportionation of [H2P2O6]2–, what is also supported by Raman spectra of heated samples.
Wild‐laid versus captive‐laid eggs in the black‐bellied sandgrouse: Is there any effect on chick productivity?
Authors: Aourir M. , Znari M. , Radi M. , Melin J.‐M.
Published: October 2013

Because survival in captivity is a significant determinant of birds available for release and reinforcement of wild populations, we aimed to identify sources of variation in mortality to assess potential impacts of management on chick productivity. We analyzed characteristics of Black‐bellied Sandgrouse eggs collected from the wild and produced by captive pairs. Wild laid‐eggs and pulled captive‐laid eggs were incubated artificially and all chicks were hand‐reared until seven weeks of age. Wild‐laid eggs were significantly bigger, heavier, and denser than captive‐laid eggs which showed a higher variability in size. Fertility, embryo mortality, and fertile egg hatchability were similar for wild‐laid and captive‐laid eggs (67.92% vs. 68%; 15.62% vs. 15.7%, and 80.55% vs. 84.44%, respectively). There were significant positive relationships between egg weigh/volume and chick hatch weight. Mortality of chicks hatched from wild‐laid eggs was much lower than that of chicks from captive‐laid eggs (19.44% vs. 60.5%) during the first week after hatching, but decreased and being nil from the third week. Heavier hatchlings from captive‐laid eggs exhibited higher survival rates which is not the case of hatchlings from wild‐laid eggs. These latter hatchlings had higher survival rates increasing with the age of eggs in relation with the period of natural incubation. The recommended age at which wild‐laid eggs could be collected is at least 13 days for full chick survivability. We concluded that in our experimental captive breeding program of the Black‐bellied Sandgrouse, productivity of viable hatchlings was much better from wild‐laid eggs and as later as these were collected. Zoo Biol. 32:592–599, 2013. © 2013 Wiley Periodicals, Inc.
Calcareous Algal Association from the Lower Paleozoic Tethyan Sedimentary Sequence of the Shiala Formation, Indian Gondwana
Authors: Sinha H. N. , Trampisch C.
Published: October 2013

The Lower Paleozoic rocks of the Shiala Formation of the Tethyan-Tibetan sedimentary sequence of Uttarakhand Garhwal region reveals rich and moderately diverse assemblages of calcareous algae. These assemblages include Dysoporelleae, Cyclocrinitids, Solenoporaceans, Microproblematica and cyanobacteria. Seven species have been identified. Most of the taxa described here are reported for the first time from the Shiala Formation. This formation exposes six different microfacies types. Some of the calcareous algal association occurs in different microfacies types and they are not generally facies dependent.

The presence of calcareous algal age marker forms in the Shiala Formation brackets the upper age limit as Silurian and it is consistent with earlier age as assigned by acritarch biostratigraphy. The recovered flora is broadly comparable with that of the Tarim basin of China, Uzbekistan, Ontario, Scotland, Kazakhstan, Poland, Baltica etc. A possibility of regional link between the present study area and Tarim basin during Ordovician-Silurian time can not be envisaged based on floral similarity of the two basins due to their cosmopolitan affinity in Gondwana, Laurentia, Siberia, Kazakhstania etc. The recovered flora is basically from the euphotic zone(within few dozen meters) of coastal to lagoonal, low to high energy marine waters of deposition in a tropical to warm-temperate palaeoprovince of Ordovician-Silurian time.
Landslide Susceptibility Assessment using Information Value Method in Parts of the Darjeeling Himalayas
Authors: Sarkar Shraban , Roy Archana K. , Martha Tapas R.
Published: October 2013

Landslide susceptibility is the likelihood of a landslide occurrence in an area predicted on the basis of local terrain conditions. Since last few years, researchers have attempted to analyse the probability of landslide occurrences and introduced different methods of landslide susceptibility assessment. The objective of this paper is to assess the landslide susceptibility in parts of the Darjeeling Himalayas using a relatively simple bivariate statistical technique. Seven factor layers with 24 categories, responsible for landslide occurrences in this area, are prepared from Cartosat and Resourcesat - 1 LISS-IV MX data. Each category was given a weight using the Information Value Method. Weighted sum of these values were used to prepare a landslide susceptibility map. The result shows that 8% area was predicted for high, 32% for moderate and remaining 60% for low landslide susceptibility zones. The high value (0.89) of the area under the receiver operating characteristic curve showed the high accuracy of the prediction model.
Inferring the Hydro-Geochemistry of Fluoride Contamination in Bankura District, West Bengal: A Case Study
Authors: Chakrabarti S. , Bhattacharya H. N.
Published: October 2013

In view of the recent reports of fluorosis in many parts of Bankura district, West Bengal, a detailed hydro-geochemical monitoring was carried out in the different blocks of Bankura to find out the level and extent of affectation. It is observed that the sub-surface environment of Bankura is appreciably contaminated with the deadly poison of fluoride. Out of the 3617 tube wells surveyed in 10 affected blocks, 612 sources are detected with fluoride above the desirable limit of 1 mg/l. In addition, down-the-hole rock drilling was performed at 15 different locations in 8 worst affected blocks of Bankura. Nearly 75% of the drill-hole rock chip samples and 62% of sub-surface water samples collected from different depths is found to have fluoride equal to or above 4000 mg/kg and 1 mg/l respectively. Detailed microscopic examination of drill chip samples has indicated diverse rock units in close succession, such as Chotanagpur Gneissic Complex, Singhbhum Group of rocks, anorthosite suite and unclassified metamorphics of Archaean-Proterozoic age. All these rocks have been intruded later by granitic fluids causing mineralization of fluoride to take place. Besides, fluoride is also found derived, to lesser extent, from Older Alluvium which bears different fluoride bearing minerals. Preliminary health surveys have revealed that dental and skeletal fluorosis are prevalent in the study area, which further corroborates with the analytical findings.
Multivariate Statistical Analysis for Assessment of Groundwater Quality in Talcher Coalfield Area, Odisha
Authors: Dhakate Ratnakar , Mahesh J. , Sankaran S. , Rao V. V. S. Gurunadha
Published: October 2013

In order to assess the impact of coal mining on groundwater quality in Talcher Coalfield area, seventeen groundwater samples for pre and post monsoon seasons were collected from borewells/dugwells and analysed for major ions and trace elements. Water quality analysis of major ions and trace elements shows elevated concentration in few groundwater samples. The water quality data was analysed using multivariate statistical techniques viz., factor analysis and cluster analysis. The result clearly shows that the variation in the season is due to recharge of rain water during monsoon. The factor and cluster analysis brought out impact of intensity by mining activity on groundwater regime. Discharge of mining seepage effluents and its interaction with the groundwater contaminate the surrounding groundwater regime. Multivariate statistical techniques are potential tools and provide greater precision for identifying contaminant parameters linkages with mining environment.
Assessment of Groundwater Quality of Lokoja Basement Area, North-Central Nigeria
Authors: Ayuba R. , Omonona O. V. , Onwuka O. S.
Published: October 2013

The hydrochemical characteristics and quality of groundwater in Lokoja basement area have been evaluated based on different indices for assessing groundwater for drinking and irrigation purposes. Twenty groundwater samples were collected and analyzed for physicochemical parameters, major ions and heavy metals. The results revealed that the groundwater is slightly alkaline, with little variations in chemical composition. For example, electrical conductivity (EC) ranges from 242µS/cm to 1835µS/cm. The abundance of the major ions is in the order of Ca2+ >Na+>Mg2+>K+> Fe2+/3+ = HCO3 >Cl- >NO3 >SO4 >PO4. Based on the hydrochemical data, four hydrochemical facies were identified namely, Ca-Mg-HCO3, Na-K-HCO3, Na-K-Cl-SO4 and Ca-Mg-Cl-SO4 and these facies depict groundwater recharge zone, transition flow zone, deep flow zone and mixed water zone respectively. Groundwater from the area is unsuitable for drinking and domestic purposes as some of the ions and heavy metals of health concerns are well above the stipulated guideline values. Irrigation water quality indicators (salinity, Na % and Mg %), reveal that the groundwater is unsuitable for irrigation purposes. Interpreted statistical analysis reveals that the groundwater chemical compositions are controlled predominantly by weathering of litho units of the basement rocks and by drainage from domestic wastes.