bluuebunny/crossref_metadata_2025 huggingface dataset:
THE ASSESSMENT OF FINE SEDIMENT ACCUMULATION IN RIVERS USING MACRO‐INVERTEBRATE COMMUNITY RESPONSE
Authors: A. Extence C. , P. CHADD R. , England J. , J. DUNBAR M. , J. WOOD P. , D. TAYLOR E.
Published: September 2011

Increased fine sediment deposition and entrainment in rivers can arise from a combination of factors including low flows, habitat modification and excessive sediment delivery from the catchment. Physical and visual methods have traditionally been used to quantify the volume of deposited fine sediment (<2 mm in size), but here we propose an alternative, the development and utilization of a sediment‐sensitive macro‐invertebrate metric (PSI — Proportion of Sediment‐sensitive Invertebrates) which provides a proxy to describe the extent to which the surface of river beds are composed of, or covered by, fine sediments. Where suitable biomonitoring data exists, the index can be calculated retrospectively to track trends in fine sediment deposition, and its ecological impact, through time. Furthermore, the utilization of reference condition models such as RIVPACS (River InVertebrate Prediction And Classification System), allows site‐specific unimpacted conditions to be defined, opening‐up the possibility of standard classification and assessment systems being developed. In Europe, such systems are vital if the Water Framework Directive is to be implemented. Knowledge regarding spatial differences in sediment/flow interdependencies may provide valuable information on diffuse sources of fine sediment to rivers and we illustrate this with an example from the UK (Laceby Beck). Further UK case studies are presented to show a range of applications, including the demonstration of improvements in habitat heterogeneity following river restoration (rivers Chess and Rib) and the detection of fine sediment impacts downstream of an impoundment (Eye Brook). The PSI metric offers a readily deployable, cost‐effective and hydroecologically relevant methodology for the assessment of fine sediment impacts in rivers. The technique has potential for application outside of the UK and an adaptation of the methodology for use in the Simandou Mountains (Guinea) is used to illustrate this. Copyright © 2011 John Wiley & Sons, Ltd.
QUANTIFYING RIVER ACCRETION IN THE UPPER RIO GRANDE GORGE, NEW MEXICO, BY USING AN ACOUSTIC DOPPLER CURRENT PROFILER
Authors: Kinzli K.‐D. , Shafike N. , Bauer P. , Lundahl A. , Schmidt‐Petersen R. , Harris S. , Lewis G. , Johnson P. , Timmons M.
Published: September 2011

The section of the upper Rio Grande in New Mexico is important to downstream water management and the administration of water rights. It has long been believed that this remote reach of the Rio Grande is characterized by significant groundwater accretions, which contribute to water available for downstream uses. This study focused on the uppermost 30 miles of the Rio Grande in New Mexico seeking to establish locations of groundwater accretions in the reach and document magnitude of gain. In order to quantify the accretion of the upper Rio Grande, an expedition using inflatable kayaks, an acoustic Doppler current profiler (ADCP) and an electromagnetic meter was carried out in the fall of 2008 when natural surface flow was low. The study area covered a stretch of 31 miles. The expedition was able to determine that the total accretion of this stretch of the Rio Grande was 22 ft3s−1 with an average accretion rate of 0.73 ft3s−1 mile−1. Most of the reach exhibited minimal gain or loss, and most of the accretion was centred in Sunshine Valley. One of the most significant results was encountering a large artesian, subaqueous spring, which might be the largest documented spring in New Mexico and contributes nearly 50% of the accretion in the reach. The study was also able to characterize the exact locations of other significant groundwater inputs. In addition to quantifying the accretion of part of the upper Rio Grande, the study provides the framework for using advanced technology in the form of an ADCP to determine river accretions in remote locations. ADCPs offer the benefit of reducing measurement time and measurement error, collect high‐resolution data and are non‐intrusive. Overall, the use of ADCP technology to determine river accretion offers an improvement over traditional methods, and it is the hope of the authors that this technology is utilized for river accretion studies in the future. Copyright © 2011 John Wiley & Sons, Ltd.
Practical round‐optimal blind signatures without random oracles or non‐interactive zero‐knowledge proofs
Authors: Yuan Zhou  , Haifeng Qian
Published: September 2011

Blind signatures are generated by means of a protocol between the signer and a user such that the signer can neither see the message being signed and nor learn any information on the signature being produced. Time/space complexity and security model (random oracle model versus standard model; sequential, parallel, or concurrent security) are commonly used to evaluate blind signature schemes. The paper presents the first round‐optimal blind signatures without random oracles or non‐interactive zero‐knowledge proofs. The proposed blind signature scheme achieves concurrent security and perfect blindness while preserving the efficiency of computation and communication. A novel class of computational problems, called one‐more‐output (OMO) problems, is introduced to prove the unforgeability of the scheme. The paper states the corresponding lower bound of the OMO problem in the generic group model. Such a computational problem might be of independent interests in designing other cryptographic protocol and primitives. Copyright © 2011 John Wiley & Sons, Ltd.
Application of Deadlock Risk Evaluation of Architectural Models
Authors: Monzón Antonio , Fernández José L. , de la Puente Juan A.
Published: September 2011

Software architectural evaluation is a key discipline used to identify, at early stages of a real‐time system (RTS) development, the problems that may arise during its operation. Typical mechanisms supporting concurrency, such as semaphores, mutexes or monitors, usually lead to concurrency problems in execution time that are difficult to be identified, reproduced and solved. For this reason, it is crucial to understand the root causes of these problems and to provide support to identify and mitigate them at early stages of the system lifecycle. This paper aims to present the results of a research work oriented to the development of the tool called ‘Deadlock Risk Evaluation of Architectural Models’ (DREAM) to assess deadlock risk in architectural models of an RTS. A particular architectural style, Pipelines of Processes in Object‐Oriented Architectures–UML (PPOOA) was used to represent platform‐independent models of an RTS architecture supported by the PPOOA –Visio tool. We validated the technique presented here by using several case studies related to RTS development and comparing our results with those from other deadlock detection approaches, supported by different tools. Here we present two of these case studies, one related to avionics and the other to planetary exploration robotics. Copyright © 2011 John Wiley & Sons, Ltd.
Concise Review: Managing Genotoxicity in the Therapeutic Modification of Stem Cells
Authors: Baum Christopher , Modlich Ute , Göhring Gudrun , Schlegelberger Brigitte
Published: September 2011

The therapeutic use of procedures for genetic stem cell modification is limited by potential adverse events related to uncontrolled mutagenesis. Prominent findings have been made in hematopoietic gene therapy, demonstrating the risk of clonal, potentially malignant outgrowth on the basis of mutations acquired during or after therapeutic genome modification. The incidence and the growth rate of insertional mutants have been linked to the “stemness” of the target cells and vector-related features such as the integration pattern, the architecture, and the exact content of transgene cassettes. Milieu factors supporting the survival and expansion of mutants may eventually allow oncogenic progression. Similar concerns apply for medicinal products based on pluripotent stem cells. Focusing on the genetic stress induced by insertional mutagenesis and culture adaptation, we propose four conclusions. (a) Mutations occurring in the production of stem cell-based medicines may be unavoidable and need to be classified according to their risk to trigger the formation of clones that are sufficiently long-lived and mitotically active to acquire secondary transforming mutations. (b) The development of rational prevention strategies depends upon the identification of the specific mutations forming such “dominant clones” (which can also be addressed as cancer stem cell precursors) and a better knowledge of the mechanisms underlying their creation, expansion, and homeostatic control. (c) Quantitative assay systems are required to assess the practical value of preventive actions. (d) Improved approaches for the genetic modification of stem cells can address all critical steps in the origin and growth control of mutants.
Discovery of Nonsteroidal Anti-Inflammatory Drug and Anticancer Drug Enhancing Reprogramming and Induced Pluripotent Stem Cell Generation
Authors: Yang Chao-Shun , Lopez Claudia G. , Rana Tariq M.
Published: September 2011

Recent breakthroughs in creating induced pluripotent stem cells (iPSCs) provide alternative means to obtain embryonic stem-like cells without destroying embryos by introducing four reprogramming factors (Oct3/4, Sox2, and Klf4/c-Myc or Nanog/Lin28) into somatic cells. iPSCs are versatile tools for investigating early developmental processes and could become sources of tissues or cells for regenerative therapies. Here, for the first time, we describe a strategy to analyze genomics datasets of mouse embryonic fibroblasts (MEFs) and embryonic stem cells to identify genes constituting barriers to iPSC reprogramming. We further show that computational chemical biology combined with genomics analysis can be used to identify small molecules regulating reprogramming. Specific downregulation by small interfering RNAs (siRNAs) of several key MEF-specific genes encoding proteins with catalytic or regulatory functions, including WISP1, PRRX1, HMGA2, NFIX, PRKG2, COX2, and TGFβ3, greatly increased reprogramming efficiency. Based on this rationale, we screened only 17 small molecules in reprogramming assays and discovered that the nonsteroidal anti-inflammatory drug Nabumetone and the anticancer drug 4-hydroxytamoxifen can generate iPSCs without Sox2. Nabumetone could also produce iPSCs in the absence of c-Myc or Sox2 without compromising self-renewal and pluripotency of derived iPSCs. In summary, we report a new concept of combining genomics and computational chemical biology to identify new drugs useful for iPSC generation. This hypothesis-driven approach provides an alternative to shot-gun screening and accelerates understanding of molecular mechanisms underlying iPSC induction.
In Situ Genetic Correction of the Sickle Cell Anemia Mutation in Human Induced Pluripotent Stem Cells Using Engineered Zinc Finger Nucleases
Authors: Sebastiano Vittorio , Maeder Morgan L. , Angstman James F. , Haddad Bahareh , Khayter Cyd , Yeo Dana T. , Goodwin Mathew J. , Hawkins John S. , Ramirez Cherie L. , Batista Luis F. Z. , Artandi Steven E. , Wernig Marius , Joung J.Keith
Published: September 2011

The combination of induced pluripotent stem cell (iPSC) technology and targeted gene modification by homologous recombination (HR) represents a promising new approach to generate genetically corrected, patient-derived cells that could be used for autologous transplantation therapies. This strategy has several potential advantages over conventional gene therapy including eliminating the need for immunosuppression, avoiding the risk of insertional mutagenesis by therapeutic vectors, and maintaining expression of the corrected gene by endogenous control elements rather than a constitutive promoter. However, gene targeting in human pluripotent cells has remained challenging and inefficient. Recently, engineered zinc finger nucleases (ZFNs) have been shown to substantially increase HR frequencies in human iPSCs, raising the prospect of using this technology to correct disease causing mutations. Here, we describe the generation of iPSC lines from sickle cell anemia patients and in situ correction of the disease causing mutation using three ZFN pairs made by the publicly available oligomerized pool engineering method (OPEN). Gene-corrected cells retained full pluripotency and a normal karyotype following removal of reprogramming factor and drug-resistance genes. By testing various conditions, we also demonstrated that HR events in human iPSCs can occur as far as 82 bps from a ZFN-induced break. Our approach delineates a roadmap for using ZFNs made by an open-source method to achieve efficient, transgene-free correction of monogenic disease mutations in patient-derived iPSCs. Our results provide an important proof of principle that ZFNs can be used to produce gene-corrected human iPSCs that could be used for therapeutic applications.
Low Level of c-Kit Expression Marks Deeply Quiescent Murine Hematopoietic Stem Cells
Authors: Matsuoka Yoshikazu , Sasaki Yutaka , Nakatsuka Ryusuke , Takahashi Masaya , Iwaki Ryuji , Uemura Yasushi , Sonoda Yoshiaki
Published: September 2011

Although c-kit is expressed highly on murine hematopoietic stem cells (HSCs) and essential for bone marrow (BM) hematopoiesis, the significance of the high level of expression of c-kit on HSCs was not well determined. We show here that CD150+CD48−Lineage−Sca-1+c-kit+ HSCs in adult BM are distributed within the range of roughly a 20-fold difference in the expression level of c-kit, and that c-kit density correlates with the cycling status of the HSC population. This predisposition is more evident in the BM of mice older than 30 weeks. The HSCs in G0 phase express a lower level of c-kit both on the cell surface and inside the cells, which cannot be explained by ligand receptor binding and internalization. It is more likely that the low level of c-kit expression is a unique property of HSCs in G0. Despite functional differences in the c-kit gradient, the HSCs are uniformly hypoxic and accessible to blood perfusion. Therefore, our data indicate the possibility that the hypoxic state of the HSCs is actively regulated, rather than them being passively hypoxic through a simple anatomical isolation from the circulation.
Core Binding Factor Beta Functions in the Maintenance of Stem Cells and Orchestrates Continuous Proliferation and Differentiation in Mouse Incisors
Authors: Kurosaka Hiroshi , Islam Md. Nurul , Kuremoto Koh-ichi , Hayano Satoru , Nakamura Masahiro , Kawanabe Noriaki , Yanagita Takeshi , Rice David P.C. , Harada Hidemitsu , Taniuchi Ichiro , Yamashiro Takashi
Published: September 2011

Rodent incisors grow continuously throughout life, and epithelial progenitor cells are supplied from stem cells in the cervical loop. We report that epithelial Runx genes are involved in the maintenance of epithelial stem cells and their subsequent continuous differentiation and therefore growth of the incisors. Core binding factor β (Cbfb) acts as a binding partner for all Runx proteins, and targeted inactivation of this molecule abrogates the activity of all Runx complexes. Mice deficient in epithelial Cbfb produce short incisors and display marked underdevelopment of the cervical loop and suppressed epithelial Fgf9 expression and mesenchymal Fgf3 and Fgf10 expression in the cervical loop. In culture, FGF9 protein rescues these phenotypes. These findings indicate that epithelial Runx functions to maintain epithelial stem cells and that Fgf9 may be a target gene of Runx signaling. Cbfb mutants also lack enamel formation and display downregulated Shh mRNA expression in cells differentiating into ameloblasts. Furthermore, Fgf9 deficiency results in a proximal shift of the Shh expressing cell population and ectopic FGF9 protein suppresses Shh expression. These findings indicate that Shh as well as Fgf9 expression is maintained by Runx/Cbfb but that Fgf9 antagonizes Shh expression. The present results provide the first genetic evidence that Runx/Cbfb genes function in the maintenance of stem cells in developing incisors by activating Fgf signaling loops between the epithelium and mesenchyme. In addition, Runx genes also orchestrate continuous proliferation and differentiation by maintaining the expression of Fgf9 and Shh mRNA.
TAp63 Is Important for Cardiac Differentiation of Embryonic Stem Cells and Heart Development
Authors: Rouleau Matthieu , Medawar Alain , Hamon Laurent , Shivtiel Shoham , Wolchinsky Zohar , Zhou Huiqing , De Rosa Laura , Candi Eleonora , de la Forest Divonne Stéphanie , Mikkola Marja L. , van Bokhoven Hans , Missero Caterina , Melino Gerry , Pucéat Michel , Aberdam Daniel
Published: September 2011

p63, a member of the p53 family, is essential for skin morphogenesis and epithelial stem cell maintenance. Here, we report an unexpected role of TAp63 in cardiogenesis. p63 null mice exhibit severe defects in embryonic cardiac development, including dilation of both ventricles, a defect in trabeculation and abnormal septation. This was accompanied by myofibrillar disarray, mitochondrial disorganization, and reduction in spontaneous calcium spikes. By the use of embryonic stem cells (ESCs), we show that TAp63 deficiency prevents expression of pivotal cardiac genes and production of cardiomyocytes. TAp63 is expressed by endodermal cells. Coculture of p63-knockdown ESCs with wild-type ESCs, supplementation with Activin A, or overexpression of GATA-6 rescue cardiogenesis. Therefore, TAp63 acts in a non-cell-autonomous manner by modulating expression of endodermal factors. Our findings uncover a critical role for p63 in cardiogenesis that could be related to human heart disease.
Concise Review: Anemia Caused by Viruses
Authors: Morinet Frédéric , Leruez-Ville Marianne , Pillet Sylvie , Fichelson Serge
Published: September 2011

Most of the viruses known to be associated with anemia in human tend to persistently infect their host and are noncytopathic or poorly cytopathic for blood cell progenitors. Infections with Epstein-Barr virus, cytomegalovirus, varicella-zoster virus, human herpes virus 6 (HHV-6), B19 parvovirus, human immunodeficiency virus, hepatitis A and C viruses and the putative viral agent associated with non-A-G post-hepatitis aplastic anemia have been reported in association with anemia. Nevertheless, a direct cytotoxic effect on erythroid progenitors has been clearly demonstrated only for human parvovirus B19 and evocated for HHV-6. A major role for destructive immunity is strongly suspected in the pathogenesis of anemia associated with the other viral infections. Host genes play a role in the occurrence of virus-induced anemia in animal models, and there are some evidences that genetic background could also influence the occurrence of virus-associated anemia in human.
Mechanically Induced Focal Adhesion Assembly Amplifies Anti-Adipogenic Pathways in Mesenchymal Stem Cells
Authors: Sen Buer , Guilluy Christophe , Xie Zhihui , Case Natasha , Styner Maya , Thomas Jacob , Oguz Ipek , Rubin Clinton , Burridge Keith , Rubin Janet
Published: September 2011

The fate of pluripotent mesenchymal stem cells (MSC) is determined through integration of chemical, spatial, and physical signals. The suppression of MSC adipogenesis by mechanical stimuli, which requires Akt-induced inhibition of glycogen synthase kinase 3β (GSK3β) with β-catenin activation, can be enhanced by repetitive dosing within a single day. Here, we demonstrate that reapplication of cyclic strain within a 24-hour period leads to amplification of both Akt activation and its subsequent inhibition of GSK3β, such that total cycle number can be reduced while still inhibiting adipogenesis. Amplification of Akt signaling is facilitated by a dynamic restructuring of the cell in response to mechanical signals, as evidenced by a transient increase in focal adhesion (FA) number and increased RhoA activity. Preventing FA assembly or development of tension blocks activation of Akt by mechanical signals, but not by insulin. This indicates that the FA infrastructure is essential to the physical, but not necessarily the chemical, sensitivity, and responsiveness of the cell. Exploiting the transient nature of cytoskeletal remodeling may represent a process to enhance cell responsiveness to mechanical input and ultimately define the fate of MSCs with a minimal input.
Risk‐based optimal retrofit of a tall steel building by using friction dampers
Authors: Tafakori Ehsan , Banazadeh Mehdi , Jalali Seyed Alireza , Tehranizadeh Mohsen
Published: September 2011

Friction dampers, whose configuration is optimized on the basis of the probabilistic seismic loss associated with a building's damage due to ground motion, were utilized in this study to optimally retrofit a 15‐story steel structure. In line with the concept of performance‐based earthquake engineering (PBEE), a decision‐making procedure based on the monetary seismic loss was incorporated for optimizing the dampers' configuration. A nonlinear numerical model was initially established for representing the structure. In this regard, a brace–damper system was modeled with the buckling of brace elements being addressed accurately and by representing the friction damper's load–displacement relationship on the basis of laboratory evidences. By monitoring the structural deformations in two different response levels, two patterns were established for the distribution of the dampers' strengths throughout the structure, and a number of retrofit alternatives were proposed subsequently. By using incremental dynamic analysis and following the PBEE methodology, the annualized loss (AL), which accounts for all potential damage states in the building and a broad range of seismic intensities, was calculated for each alternative frame. The AL is regarded as a decision variable upon which the best damper configuration is selected. Revealing conclusions were finally made regarding optimal configuration of the damper–brace system. Copyright © 2011 John Wiley & Sons, Ltd.
Estrogen‐like response of perfluorooctyl iodide in male medaka (Oryzias latipes) based on hepatic vitellogenin induction
Authors: Wang Yichen , Zhou Qunfang , Wang Chang , Yin Nuoya , Li Zhuona , Liu Jiyan , Jiang Guibin
Published: September 2011

Using the in vivo male medaka model, we investigated the estrogen‐like response of perfluorooctyl iodide (PFOI) which is a potential source of perfluorinated carboxylic acids. Using real‐time quantitative polymerase chain reaction, the expression levels of related estrogenic genes including estrogenic receptor α (ERα), ERβ, vitellogenin I (VTG I), and VTG II in the livers of male medaka exposed to PFOI were analyzed. The results showed that PFOI upregulated the expression levels of the tested genes in a dose‐dependent manner. VTG protein levels increased in both dose‐ and time‐dependent manners due to PFOI exposure. The results suggested that PFOI is a potential estrogenic compound. © 2011 Wiley Periodicals, Inc. Environ Toxicol 28: 571–578, 2013.
Gallic acid provokes DNA damage and suppresses DNA repair gene expression in human prostate cancer PC‐3 cells
Authors: Liu Kuo‐Ching , Ho Heng‐Chien , Huang An‐Cheng , Ji Bin‐Chuan , Lin Hui‐Yi , Chueh Fu‐Shin , Yang Jai‐Sing , Lu Chi‐Cheng , Chiang Jo‐Hua , Meng Menghsiao , Chung Jing‐Gung
Published: September 2011

Our earlier studies have demonstrated that gallic acid (GA) induced cytotoxic effects including induction of apoptosis and DNA damage and inhibited the cell migration and invasion in human cancer cells. However, GA‐affected DNA damage and repair gene expressions in human prostate cancer cells are still unclear. In this study, we investigated whether or not GA induces DNA damage and inhibits DNA repair gene expression in a human prostate cancer cell line (PC‐3). The results from flow cytometric assay indicated that GA decreased the percentage of viable PC‐3 cells in a dose‐ and time‐dependent manner. PC‐3 cells after exposure to different doses (50, 100, and 200 μM) of GA and various periods of time (12, 24, and 48 h) led to a longer DNA migration smear (comet tail) occurred based on the single cell gel electrophoresis (comet assay). These observations indicated that GA‐induced DNA damage in PC‐3 cells, which also confirmed by 4,6‐diamidino‐2‐phenylindole dihydrochloride staining and DNA agarose gel electrophoresis. Alternatively, results from real‐time polymerase chain reaction assay also indicated that GA inhibited ataxia telangiectasia mutated, ataxia‐telangiectasia and Rad3‐related, O6‐methylguanine‐DNA methyltransferase, DNA‐dependent serine/threonine protein kinase, and p53 mRNA expressions in PC‐3 cells. Taken together, the present study showed that GA caused DNA damage and inhibited DNA repair genes as well as both effects may be the critical factors for GA‐inhibited growth of PC‐3 cells in vitro. © 2011 Wiley Periodicals, Inc. Environ Toxicol 28: 579–587, 2013.
Quercetin attenuates lambda cyhalothrin‐induced reproductive toxicity in male rats
Authors: Ben Abdallah Fatma , Fetoui Hamadi , Zribi Nassira , Fakhfakh Feiza , Keskes Leila
Published: September 2011

The aim of this study was to evaluate the possible protective effects of Quercetin (Qe) against oxidative stress induced by λ cyhalothrin (LTC) in reproductive system. Thirty‐two male rats were divided into four groups. First group was allocated as the control group. Second group was given a Qe alone while the third group received a LTC alone. Animals in the fourth group were given a Qe with LTC. Caudae epididymis was removed for sperm analysis. Lipid peroxidation (LPO), superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx), glutathione‐S‐transferase (GST), and reduced glutathione (GSH) were determined in the testis. Additionally, the different histopathologic changes were observed in the testis of animals. LTC exposure significantly increased the abnormal morphology and LPO. On the contrary, sperm motility, viability and count, levels of GSH, and activities of SOD, CAT, GPx, and GST were significantly decreased compared to controls. Qe with LTC offset the decrease in functional sperm parameters, antioxidants enzymatic activities, and nonenzymatic antioxidant levels when compared with LTC‐treated rats. Furthermore, LTC showed irregular seminiferous tubules containing only Sertoli cells and Qe with LTC caused regular seminiferous tubules showing spermatogenesis at level of spermatocytes. We conclude that LTC‐induced oxidative stress and functional sperm parameters in male rats, and dietary of Qe attenuates the reproductive toxicity of LTC to restore the antioxidant system and sperm parameters in male rats. © 2011 Wiley Periodicals, Inc. Environ Toxicol 28: 673–680, 2013.
Evolution of SR protein and hnRNP splicing regulatory factors
Authors: Busch Anke , Hertel Klemens J.
Published: September 2011

The splicing of pre‐mRNAs is an essential step of gene expression in eukaryotes. Introns are removed from split genes through the activities of the spliceosome, a large ribonuclear machine that is conserved throughout the eukaryotic lineage. While unicellular eukaryotes are characterized by less complex splicing, pre‐mRNA splicing of multicellular organisms is often associated with extensive alternative splicing that significantly enriches their proteome. The alternative selection of splice sites and exons permits multicellular organisms to modulate gene expression patterns in a cell type‐specific fashion, thus contributing to their functional diversification. Alternative splicing is a regulated process that is mainly influenced by the activities of splicing regulators, such as SR proteins or hnRNPs. These modular factors have evolved from a common ancestor through gene duplication events to a diverse group of splicing regulators that mediate exon recognition through their sequence‐specific binding to pre‐mRNAs. Given the strong correlations between intron expansion, the complexity of pre‐mRNA splicing, and the emergence of splicing regulators, it is argued that the increased presence of SR and hnRNP proteins promoted the evolution of alternative splicing through relaxation of the sequence requirements of splice junctions. WIREs RNA 2012, 3:1–12. doi: 10.1002/wrna.100

This article is categorized under:

RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution

RNA Processing > Splicing Regulation/Alternative Splicing
An improved method for whole protein extraction from yeast Saccharomyces cerevisiae
Authors: Zhang Tingting , Lei Jie , Yang Hanjiang , Xu Kun , Wang Rui , Zhang Zhiying
Published: September 2011

A new method for protein extraction from yeast Saccharomyces cerevisiae cells is described. This method involves the use of LiAc and NaOH to enhance the permeability of yeast cell wall prior to protein extraction with SDS‐PAGE sample buffer. It was safe and efficient compared to other methods reported so far in the literature. The proteins extracted with this new method retained their immunoreactive properties and are suitable for most applications in molecular biology studies. Copyright © 2011 John Wiley & Sons, Ltd.
The effect of viscous relaxation on the spatiotemporal stability of capillary jets
Authors: Sevilla Alejandro
Published: September 2011

The linear spatiotemporal stability properties of axisymmetric laminar capillary jets with fully developed initial velocity profiles are studied for large values of both the Reynolds number, $\mathit{Re}= Q/ (\lrm{\pi} a\nu )$, and the Froude number, $\mathit{Fr}= {Q}^{2} / ({\lrm{\pi} }^{2} g{a}^{5} )$, where $a$ is the injector radius, $Q$ the volume flow rate, $\nu $ the kinematic viscosity and $g$ the gravitational acceleration. The downstream development of the basic flow and its stability are addressed with an approximate formulation that takes advantage of the jet slenderness. The base flow is seen to depend on two parameters, namely a Stokes number, $G= \mathit{Re}/ \mathit{Fr}$, and a Weber number, $\mathit{We}= \rho {Q}^{2} / ({\lrm{\pi} }^{2} \sigma {a}^{3} )$, where $\sigma $ is the surface tension coefficient, while its linear stability depends also on the Reynolds number. When non-parallel terms are retained in the local stability problem, the analysis predicts a critical value of the Weber number, ${\mathit{We}}_{c} (G, \mathit{Re})$, below which a pocket of local absolute instability exists within the near field of the jet. The function ${\mathit{We}}_{c} (\mathit{Re})$ is computed for the buoyancy-free jet, showing marked differences with the results previously obtained with uniform velocity profiles. It is seen that, in accounting for gravity effects, it is more convenient to express the parametric dependence of the critical Weber number with use made of the Morton and Bond numbers, $\mathit{Mo}= {\nu }^{4} {\rho }^{3} g/ {\sigma }^{3} $ and $\mathit{Bo}= \rho g{a}^{2} / \sigma $, as replacements for $G$ and $\mathit{Re}$. This alternative formulation is advantageous to describe jets of a given liquid for a known value of $g$, in that the resulting Morton number becomes constant, thereby leaving $\mathit{Bo}$ as the only relevant parameter. The computed function ${\mathit{We}}_{c} (\mathit{Bo})$ for a water jet under Earth gravity is shown to be consistent with the experimental results of Clanet and Lasheras for the transition from jetting to dripping of water jets discharging into air from long injection needles, which cannot be properly described with a uniform velocity profile assumed at the jet exit.
Heat transport by turbulent rotating Rayleigh–Bénard convection and its dependence on the aspect ratio
Authors: Weiss Stephan , Ahlers Guenter
Published: September 2011

We report on the influence of rotation about a vertical axis on heat transport by turbulent Rayleigh–Bénard convection in a cylindrical vessel with an aspect ratio$\Gamma \equiv D/ L= 0. 50$($D$is the diameter and$L$the height of the sample) and compare the results with those for larger$\Gamma $. The working fluid was water at${T}_{m} = 4{0\hspace{0.167em} }^{\ensuremath{\circ} } \mathrm{C} $where the Prandtl number$\mathit{Pr}$ is 4.38. For rotation rates$\Omega \lesssim 1~\mathrm{rad} ~{\mathrm{s} }^{\ensuremath{-} 1} $, corresponding to inverse Rossby numbers$1/ \mathit{Ro}$between zero and twenty, we measured the Nusselt number$\mathit{Nu}$for six Rayleigh numbers$\mathit{Ra}$in the range$2. 2\ensuremath{\times} 1{0}^{9} \lesssim \mathit{Ra}\lesssim 7. 2\ensuremath{\times} 1{0}^{10} $. For small rotation rates and at constant$\mathit{Ra}$, the reduced Nusselt number${\mathit{Nu}}_{red} \equiv \mathit{Nu}(1/ \mathit{Ro})/ \mathit{Nu}(0)$initially increased slightly with increasing$1/ \mathit{Ro}$, but at$1/ \mathit{Ro}= 1/ {\mathit{Ro}}_{0} \simeq 0. 5$it suddenly became constant or decreased slightly depending on$\mathit{Ra}$. At$1/ {\mathit{Ro}}_{c} \approx 0. 85$a second sharp transition occurred in${\mathit{Nu}}_{red} $to a state where${\mathit{Nu}}_{red} $increased with increasing$1/ \mathit{Ro}$. We know from direct numerical simulation that the transition at$1/ {\mathit{Ro}}_{c} $corresponds to the onset of Ekman vortex formation reported before for$\Gamma = 1$at$1/ {\mathit{Ro}}_{c} \simeq 0. 4$and for$\Gamma = 2$at$1/ {\mathit{Ro}}_{c} = 0. 18$(Weisset al.,Phys. Rev. Lett., vol. 105, 2010, 224501). The$\Gamma $-dependence of$1/ {\mathit{Ro}}_{c} $can be explained as a finite-size effect that can be described phenomenologically by a Ginzburg–Landau model; this model is discussed in detail in the present paper. We do not know the origin of the transition at$1/ {\mathit{Ro}}_{0} $. Above$1/ {\mathit{Ro}}_{c} $,${\mathit{Nu}}_{red} $increased with increasing$\Gamma $up to${\ensuremath{\sim} }1/ \mathit{Ro}= 3$. We discuss the$\Gamma $-dependence of${\mathit{Nu}}_{red} $in this range in terms of the average Ekman vortex density as predicted by the model. At even larger$1/ \mathit{Ro}\gtrsim 3$there is a decrease of${\mathit{Nu}}_{red} $that can be attributed to two possible effects. First, the Ekman pumping might become less efficient when the Ekman layer is significantly smaller than the thermal boundary layer, and second, for rather large$1/ \mathit{Ro}$, the Taylor–Proudman effect in combination with boundary conditions suppresses fluid flow in the vertical direction.
Studies on the behaviour of peridomestic and endophagic M form Anopheles gambiae from a rice growing area of Ghana
Authors: Charlwood J.D. , Tomás E.V.E. , Salgueiro P. , Egyir-Yawson A. , Pitts R.J. , Pinto J.
Published: September 2011

The ‘paddy paradox’, the occurrence of large populations of vectors but low amounts of malaria transmission where irrigated rice is grown, was investigated in a village in Ghana where M form Anopheles gambiae are common. Peridomestic and indoor host-seeking mosquitoes were collected in tent traps and light traps over 21 consecutive nights at the start of the rainy season in June 2009 when the population increased exponentially from less than 100 per night to over 1000. Infection rates in the overall mosquito population were 0.3% and in the estimated parous population were 1.9%. Numbers of An. gambiae in the tent trap peaked between midnight and 02:40 am. The majority of insects were taking their first blood meal, as virgins or shortly after mating. More than expected were collected in the light trap during a rainstorm at the start of the rains but overall numbers were not affected. Fewer than expected were collected after a subsequent storm. Recruitment to the adult population decreased over the following days. It is hypothesised that the ‘paddy paradox’ is due to young pre-gravid insects dispersing more widely than gravid ones, not necessarily to low survival in the mosquito.
Current Trends in Online Language Learning
Authors: Blake Robert J.
Published: September 2011

Online language learning (OLL) can take place in Web-facilitated, hybrid, or fully virtual classes. These formats are beginning to attract serious attention from the language profession and, in particular, the field of computer-assisted language learning (CALL). This article traces recent studies of online learning and then focuses in on its application to language learning through tutorial CALL, social computing, and games for language learning. I strive to show that tutorial CALL and computer-mediated communication can complement each other in the service of modern language instruction, along with the inclusion of language games. Although assessment studies of OLL remain sparse, the evidence is steadily mounting that shows that these new formats can provide learning environments conducive to successful second language development when properly integrated into the curriculum.
Teaching Academic Language in L2 Secondary Settings
Authors: Schleppegrell Mary J. , O'Hallaron Catherine L.
Published: September 2011

Research on instruction in academic language in second language (L2) secondary settings is currently emerging as a focus in applied linguistics. Academic language refers to the disciplinary registers that students encounter in the secondary years, and using academic language calls for advanced proficiency in complex language across subject areas, posing challenges for teacher preparation. In this article we summarize recommendations from syntheses of research on adolescent L2 learners and then present reports of recent studies that describe instructional approaches that illuminate the recommended practices in contexts where students who speak languages other than English are learning school subjects in English. Three key instructional dimensions are highlighted: that teachers need knowledge about how language works in their subject areas, that academic language development calls for careful planning across a unit of instruction, and that students need support for engagement in classroom activities that promote the simultaneous learning of language and content. To prepare teachers for this work, secondary teacher education needs to incorporate a focus on language–content relationships in each disciplinary area. More research is needed to better understand and support academic language development, and we call for collaboration and dialogue between educational researchers and applied linguists concerned with these issues.
The Implementation of Communicative and Task-Based Language Teaching in the Asia-Pacific Region
Authors: Butler Yuko Goto
Published: September 2011

Communicative language teaching (CLT) and task-based language teaching (TBLT) have been widely adopted in the Asia-Pacific region, with a number of Asian countries strongly promoting CLT and TBLT in their curricula and English language education policies. Despite their popularity, a number of challenges have arisen in connection with implementing CLT and TBLT in Asian classrooms. The challenges that have emerged include (a) conceptual constraints (e.g., conflicts with local values and misconceptions regarding CLT/TBLT); (b) classroom-level constraints (e.g., various student and teacher-related factors, classroom management practices, and resource availability); and (c) societal-institutional level constraints (e.g., curricula and examination systems). These constraints have led some to argue that successfully implementing CLT and TBLT in Asia requires adaptation to local environments, such that CLT and TBLT become embedded in local practices. Although there have been a growing number of reports of various CLT/TBLT implementation efforts in different Asia-Pacific regions, we still have only a limited understanding of how best to achieve contextually embedded adaptations and how they affect students’ English learning. After reviewing relevant studies, this article suggests potential options for moving forward, including (a) employing more contextually feasible and flexible interpretations of CLT and TBLT, (b) implementing decentralized or innovative language-in-education policies, and (c) creating communities of learning outside of the classroom as well as in the classroom.
Best Practices in Teaching Logographic and Non-Roman Writing Systems to L2 Learners
Authors: Everson Michael E.
Published: September 2011

The past few decades have witnessed a growing interest in how second language (L2) learners come to read in languages employing non-alphabetic writing systems such as Chinese and Japanese and languages employing non-Roman alphabetic systems such as Arabic and Hebrew. Indeed, with efforts afoot to begin more programs in these languages at the K-12 and collegiate levels, in immersion and bilingual settings, and with stated goals for students to eventually attain high levels in reading proficiency, an understanding of this research is critical if program development is to go forward in a principled way. This article discusses some of the theoretical developments that have helped illuminate the cross-orthographic reading process and reports on the relevant research in L2 cross-orthographic reading that has shaped our understanding of the issues involved in learning to read in languages that employ non-Roman alphabetic, logographic, and syllabary systems of writing. The article will also discuss teaching implications, strategies, and classroom practice put forth by reading practitioners, many of which have yet to find consensus.
Teaching American Sign Language to Hearing Adult Learners
Authors: Quinto-Pozos David
Published: September 2011

American Sign Language (ASL) has become a very popular language in high schools, colleges, and universities throughout the U.S., due, in part, to the growing number of schools that allow students to take the language in order to fulfill a foreign or general language requirement. Within the past couple decades, the number of students enrolled in ASL classes has increased dramatically, and there are likely more instructors of ASL at the present time than ever before. ASL and spoken language instruction are similar in some aspects; however, there are also differences between the two (e.g., modality differences involving visual rather than auditory perception and processing, no commonly used writing system in ASL, and the socio-cultural history of deaf-hearing relations). In spite of these differences, minimal research has been done on ASL learning and classroom pedagogy—especially in recent years. This article reports on studies that have been performed recently and it also suggests various themes for future research. In particular, three main areas of research are proposed: the possible role of the socio-political history of the Deaf community in which ASL teaching is situated, linguistic differences between signed and spoken languages, and the use of video and computer-based technologies.
The biology of an Antarctic rhodophyte,Palmaria decipiens: recent advances
Authors: Becker Susanne , Quartino María Liliana , Campana Gabriela Laura , Bucolo Philip , Wiencke Christian , Bischof Kai
Published: September 2011

Palmaria decipiens(Reinsch) R.W. Ricker (1987) represents one of the dominant rhodophyte species in Antarctic coastal ecosystems. Due to its high abundance in the intertidal and upper subtidal it plays a key role in ecosystem structure and function, providing habitat, food and shelter for a multitude of associated organisms. The physiology, reproductive strategy and life cycle ofP. decipiensis considered as being well adapted to the Antarctic environment, which is characterized by permanent low water temperatures and a strong seasonality in light climate. With its obvious ecological significance and adaptive strategiesP. decipienswas frequently studied as a typical representative of an endemic Antarctic macroalga. Here we provide an overview of the recent literature, summarizing the knowledge gained about the alga during the last 25 years. This review focuses on the species life cycle and physiological responses, such as temperature requirements, photosynthetic characteristics, pigment content and protective mechanisms with regard to enhanced ultraviolet radiation (UV-B radiation, 280–315 nm and UV-A radiation, 315–400 nm). The ecology ofP. decipiensis reviewed focussing on grazing activity and abundance patterns. Since most studies onP. decipienshave been conducted at King George Island off the western Antarctic Peninsula this overview serves as a summary of baseline data from an ecosystem particularly prone to environmental change.
Prevalence of ocular signs and subclinical vitamin A deficiency and its determinants among rural pre-school children in India
Authors: Laxmaiah Avula , Nair Madhavan K , Arlappa Nimmathota , Raghu Pullakhandam , Balakrishna Nagalla , Mallikharjuna Rao Kodavanti , Galreddy Chitty , Kumar Sharad , Ravindranath Manachala , Vikas Rao Varaganti , Brahmam Ginnela NV
Published: September 2011

Objective

To assess the magnitude and determinants of vitamin A deficiency (VAD) and coverage of vitamin A supplementation (VAS) among pre-school children.

Design

A community-based cross-sectional study was carried out by adopting a multistage, stratified, random sampling procedure.

Setting

Rural areas of eight states in India.

Subjects

Pre-school children and their mothers were covered.

Results

A total of 71 591 pre-school children were clinically examined for ocular signs of VAD. Serum retinol concentrations in dried blood spots were assessed in a sub-sample of 3954 children using HPLC. The prevalence of Bitot spots was 0·8 %. The total ocular signs were significantly higher (P < 0·001) among boys (2·6 %) compared with girls (1·9 %) and in older children (3–4 years) compared (P < 0·001) with younger (1–2 years), and were also high in children of labourers, scheduled castes and illiterate mothers. The odds of having Bitot spots was highest in children of scheduled caste (OR = 3·8; 95 % CI 2·9, 5·0), labourers (OR = 2·9; 95 % CI 2·1, 3·9), illiterate mothers (OR = 2·7; 95 % CI 2·2, 2·3) and households without a sanitary latrine (OR = 5·9; 95 % CI 4·0, 8·7). Subclinical VAD (serum retinol level <20 μg/dl) was observed in 62 % of children. This was also relatively high among scheduled caste and scheduled tribe children. The rate of coverage of VAS was 58 %.

Conclusions

The study revealed that VAD is a major nutritional problem and coverage of VAS was poor. The important determinants of VAD were illiteracy, low socio-economic status, occupation and poor sanitation. Strengthening the existing VAS programme and focused attention on dietary diversification are essential for prevention of VAD.
The variation of the polarized downwelling radiance distribution with depth in the coastal and clear ocean
Authors: Bhandari Purushottam , Voss Kenneth J. , Logan Luke , Twardowski Michael
Published: September 2011

The spectral polarized radiance distribution provides the most complete description of the light field that can be measured. However, this is a very difficult parameter to measure, particularly near the surface, because of its large dynamic range, changes in the skylight illumination, and waves at the air‐sea interface. To measure the Stokes vector of the downwelling light field, which contains the polarization information, requires the combination of four images acquired simultaneously. To achieve this, we used the downwelling polarized radiance distribution camera system (DPOL) during the Radiance in a Dynamic Ocean (RaDyO) program Santa Barbara Channel and Hawaiian experiments. DPOL consists of four fisheye lenses and a spectral filter changer that allow us to capture the downwelling hemisphere of the polarized radiance distribution at seven wavelengths. Our measurements show that very near the surface, for clear sky conditions, the dominant source of polarization is the refracted sky light. As one progresses in the water column the polarization due to light scattering by the water increases and polarization due to light scattering in the water becomes dominant.