bluuebunny/crossref_metadata_2025 huggingface dataset:
Approximation algorithms and heuristics for a 2‐depot, heterogeneous Hamiltonian path problem
Authors: Doshi Riddhi , Yadlapalli Sai , Rathinam Sivakumar , Darbha Swaroop
Published: February 2011

This article addresses an important routing problem that arises in surveillance applications involving two heterogeneous vehicles. As the addressed routing problem is NP‐Hard, we develop an approximation algorithm and heuristics to solve the problem. Our approach involves solving the routing problem in two main steps: Partitioning and Sequencing. Partitioning involves finding a distinct set of targets to be visited by each vehicle. Sequencing provides the order in which each vehicle must visit the subset of targets assigned to it. The problem of partitioning is tackled by solving a linear program (LP) obtained by relaxing some of the constraints of an integer programming model for the problem. We consider two LP models for partitioning. The first LP model is obtained by mainly relaxing both the integrality and degree constraints, whereas the second model relaxes mainly the integrality constraints. Once the targets are partitioned, the sequencing problem can be solved either by Hoogeveen's algorithm or by the Lin–Kernighan heuristic to yield an approximately optimal solution. Computational results show that the algorithms based on the second LP model, on an average, provided better (closer to the optimum) solutions as compared with those based on the first LP model. We also observed that for both the LP models, the average quality of solutions given by the heuristics were found to be within 4% of the optimum, whereas the average quality of solutions obtained from the approximation algorithms were within 8–20% of the optimum depending on the problem size. Copyright © 2011 John Wiley & Sons, Ltd.
EFFECTS OF FLOW DYNAMICS ON THE AQUATIC‐TERRESTRIAL TRANSITION ZONE (ATTZ) OF LOWER MISSOURI RIVER SANDBARS WITH IMPLICATIONS FOR SELECTED BIOTA
Authors: Tracy‐Smith Emily , Galat David L. , Jacobson Robert B.
Published: February 2011

Sandbars are an important aquatic terrestrial transition zone (ATTZ) in the active channel of rivers that provide a variety of habitat conditions for riverine biota. Channelization and flow regulation in many large rivers have diminished sandbar habitats and their rehabilitation is a priority. We developed sandbar‐specific models of discharge‐area relationships to determine how changes in flow regime affect the area of different habitat types within the submerged sandbar ATTZ (depth) and exposed sandbar ATTZ (elevation) for a representative sample of Lower Missouri River sandbars. We defined six different structural habitat types within the sandbar ATTZ based on depth or exposed elevation ranges that are important to different biota during at least part of their annual cycle for either survival or reproduction. Scenarios included the modelled natural flow regime, current managed flow regime and two environmental flow options, all modelled within the contemporary river active channel. Thirteen point and wing‐dike sandbars were evaluated under four different flow scenarios to explore the effects of flow regime on seasonal habitat availability for foraging of migratory shorebirds and wading birds, nesting of softshell turtles and nursery of riverine fishes. Managed flows provided more foraging habitat for shorebirds and wading birds and more nursery habitat for riverine fishes within the channelized reach sandbar ATTZ than the natural flow regime or modelled environmental flows. Reduced summer flows occurring under natural and environmental flow alternatives increased exposed sandbar nesting habitat for softshell turtle hatchling emergence. Results reveal how management of channelized and flow regulated large rivers could benefit from a modelling framework that couples hydrologic and geomorphic characteristics to predict habitat conditions for a variety of biota. Published in 2011 by John Wiley & Sons, Ltd.
Electron Beam‐Induced Current (EBIC) in solution‐processed solar cells
Authors: Reuter Piet , Rath Thomas , Fischereder Achim , Trimmel Gregor , Hadley Peter
Published: February 2011

Electron Beam‐Induced Current (EBIC) measurements were used to produce 2D maps for investigating the homogeneity of solar cells. These maps are acquired by scanning the electron beam of a scanning electron microscope over a small area and using a programmable sample stage to move the solar cell under the scan area. The electron beam generates electron–hole pairs in the solar cell much like light does in normal solar cell operation. Solution‐processed solar cells where the active layer consisted of purely inorganic or purely organic materials were measured. Since the electron beam irreversibly damages organic material, it was important to ensure that the measurements were made before the materials were altered. SCANNING 33: 1–6, 2011. © 2011 Wiley Periodicals, Inc.
The most recent SSL security attacks: origins, implementation, evaluation, and suggested countermeasures
Authors: El‐Hajj Wassim
Published: February 2011

Attacks have been targeting secure socket layer (SSL) from the time it was created especially because of its utmost importance in securing Web transactions. These attacks are either attacks exploiting vulnerabilities in the SSL protocol itself, or attacks exploiting vulnerabilities in the services that SSL uses, such as certificates and web browsers. While the attacks on SSL itself have been successful, at least in the context of academics or other research, attacks on the services that SSL uses have been successfully exploited in an actual commercial setting; the fact that makes these kinds of attacks extremely dangerous. In this paper, we give a brief overview of the attacks conducted on the implementation of SSL and we analyze in more details the recent attacks that exploit the services SSL uses. Most of these attacks are considered Man in the Middle (MitM) attacks. In particular, we explore the most recent five attacks targeting SSL: SSL sniffing, MD5 collide certificate, SSL striping, SSL Null prefix and online certificate status protocol (OCSP) attack. We discuss the origins of each attack and explain the typical environment that allows for such attacks to occur. We then highlight the implementation phase where we implemented some of the attacks and were able to catch logins, passwords, and any data transmitted between two parties. In addition, we implemented using, Java, our own parsers and decoders to extract the useful data from the captured files and decode them if needed. Since most of the discussed attacks target browsers and the way they manage certificates, we conducted an extensive evaluation on the rate of success of the SSL attacks when various browsers are used. The browsers that were considered are Internet explorer (IE), Mozilla Firefox, Opera, Safari, and Chrome. The alarming results show that all analyzed attacks except for SSL Sniffing can be performed on almost all browsers. Copyright © 2011 John Wiley & Sons, Ltd.
Agent‐based modeling of malware dynamics in heterogeneous environments
Authors: Bose Abhijit , Shin Kang G.
Published: February 2011

The increasing convergence of power‐law networks such as social networking and peer‐to‐peer applications, web‐delivered applications, and mobile platforms makes today's users highly vulnerable to entirely new generations of malware that exploit vulnerabilities in web applications and mobile platforms for new infections, while using the power‐law connectivity for finding new victims. The traditional epidemic models based on assumptions of homogeneity, average‐degree distributions, and perfect‐mixing are inadequate to model this type of malware propagation. In this paper, we study four aspects crucial to modeling malware propagation: application‐level interactions among users of such networks, local network structure, user mobility, and network coordination of malware such as botnets. Since closed‐form solutions of malware propagation considering these aspects are difficult to obtain, we describe an open‐source, flexible agent‐based emulation framework that can be used by malware researchers for studying today's complex malware. The framework, called Agent‐Based Malware Modeling (AMM), allows different applications, network structure, network coordination, and user mobility in either a geographic or a logical domain to study various infection and propagation scenarios. In addition to traditional worms and viruses, the framework also allows modeling network coordination of malware such as botnets. The majority of the parameters used in the framework can be derived from real‐life network traces collected from a network, and therefore, represent realistic malware propagation and infection scenarios. As representative examples, we examine two well‐known malware spreading mechanisms: (i) a malicious virus such as Cabir spreading among the subscribers of a cellular network using Bluetooth and (ii) a hybrid worm that exploit email and file‐sharing to infect users of a social network. In both cases, we identify the parameters most important to the spread of the epidemic based upon our extensive simulation results. Copyright © 2011 John Wiley & Sons, Ltd.
Green approach to prepare silver nanoink with potentially high conductivity for printed electronics
Authors: Tai Yan‐Long , Wang Ying‐Xia , Yang Zhen‐Guo , Chai Zhi‐Qiang
Published: February 2011

A new strategy was described for green preparation of silver nanoink with potentially high conductivity for printed electronics. Silver nanoparticles in the ink were characterized by visible ultraviolet spectrophotometer (UV‐vis), Transmission Electron Microscope (TEM), size distribution analysis (SDA), X‐Ray Diffractomer (XRD) and differential scanning calorimetry (DSC). Silver thin film was investigated by SEM and 4‐point probe. It can be found that silver nanoparticles are of small sizes about 2.1 ± 0.5 nm in diameter, with a low melting point of about 105°. It also can be concluded that continuous silver thin film has formed, and an integrated conductive track has been fabricated. Especially, when the solid content is up to 9 wt.% and the sintering condition is 200° for 30 minutes in air, the resistivity can decrease to 8.1 µΩ·cm, 4.9 times the bulk silver resistivity. In addition, the application of silver nanoink in conductive patterns on polyimide (PI) substrate was also studied by inkjet printing. Copyright © 2011 John Wiley & Sons, Ltd.
Improved Tougaard background calculation by introduction of fittable parameters for the inelastic electron scattering cross‐section in the peak fit of photoelectron spectra with UNIFIT 2011
Authors: Hesse R. , Denecke R.
Published: February 2011

The shape of the background in x‐ray photoemission spectra is strongly affected by scattered electrons from inelastic energy loss processes. A polynomial of low order has very often been applied to model the secondary‐electron background, giving satisfying results in some cases. An improved analysis employing the Tougaard background model has been successfully used to characterize the inelastic loss processes. However, the correct usage of the Tougaard background needs a well defined inelastic electron scattering cross‐section function λ(E) · K(E, T) (λ = inelastic mean free path, E = kinetic energy, T = energy loss). This paper presents a four‐parameter loss function λ(E) · K(E, T) = B · T/(C + C′ · T2)2 + D · T2 with the fitting parameters B, C, C′ and D implemented in the background function allowing the improved estimation of the λ(E) · K(E, T) function for homogenous materials. The fit of the background parameters is carried out parallel to the peak fit. The results will be compared with the parameters recommended by Tougaard. The calculation of inelastic electron scattering cross‐sections of clean surfaces from different materials using UNIFIT 2011 will be demonstrated. Copyright © 2011 John Wiley & Sons, Ltd.
Posterior maximization and averaging for Bayesian working model choice in the continual reassessment method
Authors: Daimon T. , Zohar S. , O'Quigley J.
Published: February 2011

The continual reassessment method (CRM) is a method for estimating the maximum tolerated dose in a dose‐finding study. Traditionally, use is made of a single working model or ‘skeleton’ idealizing an underlying true dose–toxicity relationship. This working model is chosen either by discussion with investigators or published data, before the beginning of the trial or simply on the basis of operating characteristics. To overcome the arbitrariness of the choice of such a single working model, Yin and Yuan (biJ. Am. Statist. Assoc. 2009; 104:954–968) propose a model averaging over a set of working models. Here, instead of averaging, we investigate some alternative Bayesian model criteria that maximize the posterior distribution. We propose three adaptive model‐selecting CRMs using the Bayesian model selection criteria, in which we specify in advance a collection of candidate working models for the dose–toxicity relationship, especially initial guesses of toxicity probabilities, and adaptively select the only one working model among the candidates updated by using the original CRM for each working model, based on the posterior model probability, the posterior predictive loss or the deviance information criteria, during the course of the trial. These approaches were compared via a simulation study with the model averaging approach. Copyright © 2011 John Wiley & Sons, Ltd.
Biocompatibility of Immobilized Aligned Carbon Nanotubes
Authors: Nayagam David A. X. , Williams Richard A. , Chen Jun , Magee Kylie A. , Irwin Jennifer , Tan Justin , Innis Peter , Leung Ronald T. , Finch Sue , Williams Chris E. , Clark Graeme M. , Wallace Gordon G.
Published: February 2011

In vivo host responses to an electrode‐like array of aligned carbon nanotubes (ACNTs) embedded within a biopolymer sheet are reported. This biocompatibility study assesses the suitability of immobilized carbon nanotubes for bionic devices. Inflammatory responses and foreign‐body histiocytic reactions are not substantially elevated when compared to negative controls following 12 weeks implantation. A fibrous capsule isolates the implanted ACNTs from the surrounding muscle tissue. Filamentous nanotube fragments are engulfed by macrophages, and globular debris is incorporated into the fibrous capsule with no further reaction. Scattered leukocytes are observed, adherent to the ACNT surface. These data indicate that there is a minimal local foreign‐body response to immobilized ACNTs, that detached fragments are phagocytosed into an inert material, and that ACNTs do not attract high levels of surface fouling. Collectively, these results suggest that immobilized nanotube structures should be considered for further investigation as bionic components.
Surface‐Tension‐Driven Gradient Generation in a Fluid Stripe for Bench‐Top and Microwell Applications
Authors: Hancock Matthew J. , He Jiankang , Mano João F. , Khademhosseini Ali
Published: February 2011

A simple and inexpensive method is presented employing passive mechanisms to generate centimeters‐long gradients of molecules and particles in under a second with only a coated glass slide and a micropipette. A drop of solution is pipetted onto a fluid stripe held in place on a glass slide by a hydrophobic boundary. The resulting difference in curvature pressure drives the flow and creates a concentration gradient by convection. Experiments and theoretical models characterize the flows and gradient profiles and their dependence on the fluid volumes, properties, and stripe geometry. A bench‐top rapid prototyping method is outlined to allow the user to design and fabricate the coated slides using only tape and hydrophobic spray. The rapid prototyping method is compatible with microwell arrays, allowing soluble gradients to be applied to cells in shear‐protected microwells. The method’s simplicity makes it accessible to virtually any researcher or student and its use of passive mechanisms makes it ideal for field use and compatible with point‐of‐care and global health initiatives.
Combination of a Ptgs2 Inhibitor and an Epidermal Growth Factor Receptor-Signaling Inhibitor Prevents Tumorigenesis of Oligodendrocyte Lineage-Derived Glioma-Initiating Cells
Authors: Hide Takuichiro , Takezaki Tatsuya , Nakatani Yuka , Nakamura Hideo , Kuratsu Jun-ichi , Kondo Toru
Published: February 2011

Recent findings have demonstrated that malignant tumors, including glioblastoma multiforme (GBM), contain cancer-initiating cells (CICs; also known as cancer stem cells), which self-renew and are malignant. However, it remains controversial whether such CICs arise from tissue-specific stem cells, committed precursor cells, or differentiated cells. Here, we sought to examine the origin of the CICs in GBM. We first showed that the overexpression of oncogenic HRasL61 transformed p53-deficient oligodendrocyte precursor cells (OPCs) and neural stem cells (NSCs) into glioma-initiating cell (GIC)-like cells in mice. When as few as 10 of these GIC-like cells were transplanted in vivo, they formed a transplantable GBM with features of human GBM, suggesting that these GIC-like cells were enriched in CICs. DNA microarray analysis showed that widespread genetic reprogramming occurred during the OPCs' transformation: they largely lost their OPC characteristics and acquired NSC ones, including the expression of prominin1, hmga2, ptgs2, and epiregulin. In addition, the combination of a Ptgs2 inhibitor and an epidermal growth factor receptor (EGFR)-signaling inhibitor prevented the tumorigenesis of transformed OPCs and human GICs (hGICs) obtained from anaplastic oligodendroglioma, but not of transformed NSCs or hGICs obtained from GBM. Together, these findings suggest that GBM can arise from either OPCs or NSCs and that the therapeutic targets for GBM might be different, depending on each GIC's cell-of-origin.
Promyelocytic Leukemia Protein in Retinoic Acid-Induced Chromatin Remodeling of Oct4 Gene Promoter
Authors: Chuang Ya-Shan , Huang Wei-Hong , Park Sung Wook , Persaud Shawna D. , Hung Chen-Hsiang , Ho Ping-Chih , Wei Li-Na
Published: February 2011

Promyelocytic leukemia (Pml) protein is required for Oct4 gene expression and the maintenance of its open chromatin conformation in stem cells. In proliferating stem cells, Pml-nuclear body, along with transcription factors TR2, steroidogenic factor 1 (SF1) and Sp1, and Brg1-dependent chromatin remodeling complex (BRGC), associates with conserved region 1 (CR1) of this promoter to maintain a nucleosome-free region for gene activity. Retinoic acid (RA) rapidly downregulates Pml, resulting in the replacement of BRGC with Brm-containing remodeling complex, disassociation of SF1 and Sp1, retaining of TR2, recruitment of receptor-interaction protein 140, G9a and HP1γ, and sequential insertion of two nucleosomes on CR1 that progressively displays repressive heterochromatin marks. This study demonstrates a functional role for Pml in maintaining a specific open chromatin conformation of the Oct4 promoter region for its constant expression in stem cells; and illustrates the mechanism underlying RA-induced chromatin remodeling of Oct4 gene in differentiating cells, in which Pml plays a critical role. The study also demonstrates a novel mode of chromatin remodeling, which occurs by repositioning and sequentially inserting nucleosomes into a specific region of the gene promoter to compact the chromatin in differentiating cells.
Hippocampal mossy fiber long‐term depression in Grm2/3 double knockout mice
Authors: Lyon Louisa , Borel Melodie , CarriÓn Miriam , Kew James N.C. , Corti Corrado , Harrison Paul J. , Burnet Philip W.J. , Paulsen Ole , RodrÍGuez‐Moreno Antonio
Published: February 2011

Group II metabotropic glutamate receptors (mGluR2, encoded by Grm2, and mGluR3, encoded by Grm3) are inhibitory autoreceptors that negatively modulate the adenylate cyclase signaling cascade. Within the hippocampus, mGluR2 is believed to play a key role in the induction of long‐term depression (LTD) at mossy fiber‐CA3 synapses. Here, we used Grm2/3 double knockout (dko) mice to investigate to what extent group II mGluRs are necessary for mossy fiber LTD. Surprisingly, we found that these mice displayed prominent mossy fiber LTD. However, the induction of this form of LTD was sensitive to the external Ca2+ concentration. Mossy fiber LTD in Grm2/3 dko mice was indistinguishable from that in wild‐type mice at 4 mM Ca2+, but largely absent at 2 mM external Ca2+. Mossy fiber LTD in Grm2/3 dko mice was not blocked by the N‐methyl‐D‐aspartic acid (NMDA) receptor antagonist D‐AP5, confirming that the observed response did not reflect NMDA receptor‐dependent LTD in contaminating associational‐commissural fibers, and enabling us to use the NMDA receptor‐mediated EPSC to monitor mossy fiber LTD. Using whole‐cell recordings, we demonstrated that LTD of the NMDA receptor‐mediated EPSC in Grm2/3 dko mice was not affected by intracellular application of BAPTA and CsF to block postsynaptic Ca2+ and G‐protein‐mediated effects. This presynaptic LTD was, however, blocked by the AMPA/kainate receptor antagonist, NBQX. Thus, an activity‐dependent, external Ca2+ concentration‐sensitive form of mossy fiber LTD can be induced in Grm2/3 dko mice. Two mGluR antagonists also failed to block mossy fiber LTD under 4 mM conditions in wild‐type mice, strengthening the conclusion that group II mGluRs are not obligatory for mossy fiber LTD. Synapse, 2011. © 2011 Wiley‐Liss, Inc.
Adapting to crop pest and pathogen risks under a changing climate
Authors: Sutherst Robert W. , Constable Fiona , Finlay Kyla J. , Harrington Richard , Luck Jo , Zalucki Myron P.
Published: February 2011

The need for pest and pathogen management will increase as the intensification of food production proceeds to feed the burgeoning human population. Climate is a significant driver of pest population dynamics, so climate change will require adaptive management strategies to cope with the altered status of pests and pathogens. A hierarchy of analytical tools is required to conduct risk assessments, inform policy and design pest management on scales from regions to landscapes and fields. Such tools include models for predicting potential geographical distributions, seasonal phenology, and population dynamics at a range of spatial and temporal scales. The level of sophistication of such models and databases will be determined by the economic importance of specific species. Many obstacles remain in the way of designing reliable adaptation strategies, and several issues that ensure continuing uncertainty are discussed. Holistic approaches that include nonclimatic drivers of change are needed to address the combination of global change variables. Changed patterns of crop production will determine the pests and pathogens that require greater effort to control. Linked crop‐pest models offer the best opportunities for management of important pests and pathogens. Examples of risk assessments for pests and pathogens are illustrated mostly with cases from Australia, and guidelines for adaptation of pest and pathogen management are reviewed. The plethora of species and strains of pests and pathogens demands a parsimonious approach to risk assessment and adaptation, based on identified needs to inform management. Due to some intractable issues the best approach may often be scenario planning to design systems which will be resilient under any global change. WIREs Clim Change 2011 2 220–237 DOI: 10.1002/wcc.102

This article is categorized under:

Assessing Impacts of Climate Change > Evaluating Future Impacts of Climate Change
Climate change in literature and literary criticism
Authors: Trexler Adam , Johns‐Putra Adeline
Published: February 2011

This article provides an overview of climate change in literature, focusing on the representation of climate change in Anglophone fiction. It then evaluates the way in which these fictional representations are critiqued in literary studies, and considers the extent to which the methods and tools that are currently employed are adequate to this new critical task. We explore how the complexity of climate change as both scientific and cultural phenomenon demands a corresponding degree of complexity in fictional representation. For example, when authors represent climate change as a global, networked, and controversial phenomenon, they move beyond simply employing the environment as a setting and begin to explore its impact on plot and character, producing unconventional narrative trajectories and innovations in characterization. Then, such creative complexity asks of literary scholars a reassessment of methods and approaches. For one thing, it may require a shift in emphasis from literary fiction to genre fiction. It also particularly demands that environmental criticism, or ecocriticism, moves beyond its long‐standing interest in concepts of ‘nature’ and ‘place’, to embrace a new understanding of the local in relation to the global. We suggest, too, that there are synergies to be forged between these revisionary moves in ecocriticism and developments in literary critical theory and historicism, as these critical modes begin to deal with climate change and reimagine themselves in turn.WIREs Clim Change2011 2 185–200 DOI: 10.1002/wcc.105

This article is categorized under:

Trans‐Disciplinary Perspectives > Humanities and the Creative Arts
Coping with the immediate experience of climate: regional variations and indoor trajectories
Authors: Hitchings Russell
Published: February 2011

This article reviews work from across various disciplines that illuminates the changing ways in which people around the world manage their experience of local climate with particular reference to temperature. This topic is important because it has implications for issues that range from the rising energy demands associated with the spread of air‐conditioning to the idea that future societies may eventually forget about the climates outside the buildings into which they have retreated. My purpose is neither to critique the various ways of conceptualizing the relation between human comfort and thermal environment nor to champion any particular argument about the mechanism that guides its development over time. Rather the aim is to integrate a diverse set of studies into an evaluative account that foregrounds the cultural differences and geographical dynamics now characterizing the ways in which people relate to outdoor temperature. Many of us now spend a great deal of our time surrounded by controlled bodies of ambient air which may superficially seem appropriately civilized. Yet this same situation could easily end up making us less willing to experience our local climates and more reliant on some quite resource hungry technologies. Changing practices of coping with outdoor temperature should be examined further. WIREs Clim Change 2011 2 170–184 DOI: 10.1002/wcc.106

This article is categorized under:

Climate, History, Society, Culture > World Historical Perspectives
Topical and mucosal liposomes for vaccine delivery
Authors: Lilia Romero Eder , Morilla Maria Jose
Published: February 2011

Mucosal (and in minor extent transcutanous) stimulation can induce local or distant mucosa secretory IgA. Liposomes and other vesicles as mucosal and transcutaneous adjuvants are attractive alternatives to parenteral vaccination. Liposomes can be massively produced under good manufacturing practices and stored for long periods, at high antigen/vesicle mass ratios. However, their uptake by antigen‐presenting cells (APC) at the inductive sites remains as a major challenge. As neurotoxicity is a major concern in intranasal delivery, complexes between archaeosomes and calcium as well as cationic liposomes complexed with plasmids encoding for antigenic proteins could safely elicit secretory and systemic antigen‐specific immune responses. Oral bilosomes generate intense immune responses that remain to be tested against challenge, but the admixing with toxins or derivatives is mandatory to reduce the amount of antigen. Most of the current experimental designs, however, underestimate the mucus blanket 100‐ to 1000‐fold thicker than a 100‐nm diameter liposome, which has first to be penetrated to access the underlying M cells. Overall, designing mucoadhesive chemoenzymatic resistant liposomes, or selectively targeted to M cells, has produced less relevant results than tailoring the liposomes to make them mucus penetrating. Opposing, the nearly 10 µm thickness stratum corneum interposed between liposomes and underlying APC can be surpassed by ultradeformable liposomes (UDL), with lipid matrices that penetrate up to the limit with the viable epidermis. UDL made of phospholipids and detergents, proved to be better transfection agents than conventional liposomes and niosomes, without the toxicity of ethosomes, in the absence of classical immunomodulators. WIREs Nanomed Nanobiotechnol 2011 3 356–375 DOI: 10.1002/wnan.131

This article is categorized under:

Therapeutic Approaches and Drug Discovery > Nanomedicine for Infectious Disease

Nanotechnology Approaches to Biology > Nanoscale Systems in Biology
Human mitochondrial diseases caused by lack of taurine modification in mitochondrial tRNAs
Authors: Tsutomu Suzuki , Asuteka Nagao , Takeo Suzuki
Published: February 2011

Mitochondrial DNA mutations that cause mitochondrial dysfunction are responsible for a wide spectrum of human diseases, referred to as mitochondrial diseases. Pathogenic point mutations are found frequently in genes encoding mitochondrial (mt) tRNAs, indicating that impaired functioning of mutant mt tRNAs is the primary cause of mitochondrial dysfunction. Our previous studies revealed the absence of posttranscriptional taurine modification at the anticodon wobble uridine in mutant mt tRNAs isolated from cells derived from patients with two major classes of mitochondrial diseases, MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke‐like episodes) and MERRF (myoclonus epilepsy associated with ragged red fibers). Defective taurine modification of the mutant mt tRNAs results in a deficiency in protein synthesis as the cognate codons of the mutant mt tRNA cannot be decoded. These findings represent the first evidence of a molecular pathogenesis caused by an RNA modification disorder. WIREs RNA 2011 2 376–386 DOI: 10.1002/wrna.65

This article is categorized under:

RNA-Based Catalysis > Miscellaneous RNA-Catalyzed Reactions

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

RNA Processing > tRNA Processing
Eukaryotic 5S rRNA biogenesis
Authors: Ciganda Martin , Williams Noreen
Published: February 2011

The ribosome is a large complex containing both protein and RNA which must be assembled in a precise manner to allow proper functioning in the critical role of protein synthesis. 5S rRNA is the smallest of the RNA components of the ribosome, and although it has been studied for decades, we still do not have a clear understanding of its function within the complex ribosome machine. It is the only RNA species that binds ribosomal proteins prior to its assembly into the ribosome. Its transport into the nucleolus requires this interaction. Here we present an overview of some of the key findings concerning the structure and function of 5S rRNA and how its association with specific proteins impacts its localization and function.WIREs RNA2011 2 523–533 DOI: 10.1002/wrna.74

This article is categorized under:

Translation > Translation Mechanisms

RNA Processing > RNA Editing and Modification

RNA Processing > tRNA Processing

RNA in Disease and Development > RNA in Disease
Synthesis and Characterization of Three New Zipper‐like Lanthanide [Ln = TmIII, NdIII, CeIII] Coordination Polymers Containing 1,3‐Benzenedicarboxylate and 2‐Phenyl‐1H‐1,3,7,8‐tetraazacyclopenta[l]phenanthrene Ligands
Authors: Wang Xiang‐Cheng , Liu Chun‐Bo , Chen Jing , Li Xiu‐Ying , Che Guang‐Bo , Yan Yong‐Sheng
Published: February 2011

Reaction of the ligands 2‐phenyl‐1H‐1,3,7,8‐tetraazacyclopenta[l]phenanthrene (PTCP) and benzene‐1,3‐dicarboxylic acid (m‐H2BDC) with Ln2O3 under hydrothermal conditions lead to three isomorphous coordination polymers [Ln2(PTCP)2(m‐BDC)3·H2O]n (Ln = Tm, 1; Nd, 2; Ce, 3). The coordination polymers crystallize in monoclinic, space group P21/m with a = 9.8340(2), b = 17.9140(4), c = 15.6050(3) Å, β = 100.51(3)° for 1, with a = 9.8423(3), b = 18.3562(4), c = 15.6209(3) Å, β = 102.138(3)° for 2, and with a = 9.8620(2), b = 18.4960(4), c = 15.6530(3) Å, β = 102.42(3)° for 3, respectively. The metal ions (Ln3+) are located in an octacoordinated environment and the dinuclear [Ln2O12N4] units act as octahedral secondary building units (SBU), which are bridged in two coordination modes by six m‐BDC ligands to form a three‐strand‐like chain. These chains are decorated by PTCP ligands and form unique three zipper‐like structures, which are further assembled into three‐dimensional supramolecular nets by π···π stacking interactions. Additionally, hydrogen bonds are observed in the structures. Furthermore, compounds 1–3 were studied by IR spectrocopy and thermogravimetric analyses.
Synthesis, Structure, and Magnetic Studies of a New Wheel‐Shaped [LiMnIII6] Cluster
Authors: Yang Pei‐Pei
Published: February 2011

The synthesis, crystal structure, and magnetic properties of a new hexanuclear manganese(III) complex are reported. The complex [LiMn6(L)6]OH·2MeCN·4MeOH·1.5H2O (LiH2L = lithium 2‐{[bis(2‐hydroxyethyl)amino]methyl}‐4‐methylphenate) (1), was obtained from the reaction of one equivalent of LiH2L with Mn(OAc)2 in MeCN/MeOH (v:v/1:1). Single‐crystal X‐ray diffraction shows that six octahedrally coordinated manganese(III) ions define a ring and are linked by twelve bridging oxygen atoms from alkoxo groups. The resulting [Mn6(OCH2)12] skeleton has the remarkable property of acting as a host for a octahedrally coordinated lithium ion in the center of the ring. Variable‐temperature solid‐state magnetic susceptibility studies of 1 in the temperature range 2.0–300 K reveal that the complex has a S = 12 ground state spin, showing ferromagnetic exchange interactions between the constituent manganese(III) ions.
Activation of AMP‐kinase by Policosanol Requires Peroxisomal Metabolism
Authors: Banerjee Subhashis , Ghoshal Sarbani , Porter Todd D.
Published: February 2011

Policosanol, a well‐defined mixture of very long chain primary alcohols that is available as a nutraceutical product, has been reported to lower blood cholesterol levels. The present studies demonstrate that policosanol promotes the phosphorylation of AMP‐kinase and HMG‐CoA reductase in hepatoma cells and in mouse liver after intragastric administration, providing a possible means by which policosanol might lower blood cholesterol levels. Treatment of hepatoma cells with policosanol produced a 2.5‐fold or greater increase in the phosphorylation of AMP‐kinase and HMG‐CoA reductase, and increased the phosphorylation of Ca++/calmodulin‐dependent kinase kinase (CaMKK), an upstream AMP‐kinase kinase. Intragastric administration of policosanol to mice similarly increased the phosphorylation of hepatic HMG‐CoA reductase and AMP‐kinase by greater than 2‐fold. siRNA‐mediated suppression of fatty aldehyde dehydrogenase, fatty acyl‐CoA synthetase 4, and acyl‐CoA acetyltransferase expression in hepatoma cells prevented the phosphorylation of AMP‐kinase and HMG‐CoA reductase by policosanol, indicating that metabolism of these very long chain alcohols to activated fatty acids is necessary for the suppression of cholesterol synthesis, presumably by increasing cellular AMP levels. Subsequent peroxisomal β‐oxidation probably augments this effect.
Nice Teams Finish Last
Authors: Whiteside Dawn
Published: February 2011

Nice Teams Finish Last Brian Cole Miller 2010, AMACOM 224 pages $17.95 softcover
Changing Culture in Interventional Areas to Promote Patient Safety
Authors: Schmidt Terry
Published: February 2011

During the past decade, physicians have begun to perform an increasing number of interventional procedures in various locations outside the traditional OR. Changes in technology and practice have generated the need for a paradigm shift about perioperative practice because these interventional areas have become perioperative centers of care in which patients undergo operative and other invasive procedures. Physicians, nursing staff members, support staff members, and administrators in these interventional areas must consider perioperative practice standards, institutional policies, state practice acts, and regulatory and accreditation requirements when creating policies and procedures. Personnel must be familiar with AORN standards and recommended practices and understand the perioperative practice guidelines related to nurse staffing in invasive procedure areas. Advanced practice nurses and other leaders must use evidence‐based research as the basis for policy and procedure changes.
Sterilization in the Perioperative Setting
Authors: Morris Maxine L.
Published: February 2011

Sterilization in the Perioperative Setting Ciné‐Med producer 2010, CD‐ROM $135 AORN members, $270 nonmembers
Clinical Issues—March 2011
Authors: Ogg Mary J.
Published: February 2011

This Month

First surgical hand scrub of the day

Key words: alcohol‐based surgical hand rub products, surgical hand antisepsis, standardized surgical hand rub protocol.

The correct method for sterilizing towel clips

Key words: ratcheted instruments, instrument hinges, bloodborne pathogens standard, glove tears, percutaneous punctures, instrument stringers.

Patient abandonment

Key words: patient abandonment, patient assignment, nurse‐patient relationship.

Determining shelf life

Key words: event‐related sterility, expiration dates, moisture‐controlled environment, dust‐controlled environment, storage conditions, sterile storage, shelf life, sterile items.
Introduction to the Safe Patient Handling and Movement Series
Authors: Ogg Mary J.
Published: February 2011

Musculoskeletal injuries can occur when the physical work demanded by a job exceeds a worker's ability to respond safely. In perioperative nursing, and nursing in general, patient handling and movement demands commonly lead to injury and are considered high‐risk activities. In 2005, the AORN Workplace Safety Task Force was charged with identifying high‐risk tasks performed in the perioperative area and developing evidence‐based solutions to help establish an ergonomically safe workplace. The work of the task force was incorporated into the “AORN guidance statement: Safe patient handling and movement in the perioperative setting,” which includes seven ergonomic tools to help determine best practices for safe movement and handling of patients, supplies, and equipment in the OR. Members of the AORN Perioperative Environment of Care Task Force have collaborated to author seven articles that help explain the rationale behind and use of these ergonomic tools. The articles will appear in the Journal beginning in this issue.
Cardiovascular Disorders Sourcebook
Authors: Kefer Stephanie
Published: February 2011

Cardiovascular Disorders Sourcebook Amy L. Sutton 4th edition 2010, Omnigraphics 640 pages $93 hardcover
Chlamydomonas reinhardtii as a new model system for studying the molecular basis of the circadian clock
Authors: Matsuo Takuya , Ishiura Masahiro
Published: February 2011

The genome of the unicellular green alga Chlamydomonas reinhardtii has both plant‐like and animal‐like genes. It is of interest to know which types of clock genes this alga has. Recent forward and reverse genetic studies have revealed that its clock has both plant‐like and algal clock components. In addition, since C. reinhardtii is a useful model organism also called “green yeast”, the identification of clock genes will make C. reinhardtii a powerful model for studying the molecular basis of the eukaryotic circadian clock. In this review, we describe our forward genetic approach in C. reinhardtii and discuss some recent findings about its circadian clock.
The hormonal and circadian basis for insect photoperiodic timing
Authors: Schiesari Luca , Kyriacou Charalambos P. , Costa Rodolfo
Published: February 2011

Daylength perception in temperate zones is a critical feature of insect life histories, and leads to developmental changes for resisting unfavourable seasons. The role of the neuroendocrine axis in the photoperiodic response of insects is discussed in relation to the key organs and molecules that are involved. We also discuss the controversial issue of the possible involvement of the circadian clock in photoperiodicity. Drosophila melanogaster has a shallow photoperiodic response that leads to reproductive arrest in adults, yet the unrivalled molecular genetic toolkit available for this model insect should allow the systematic molecular and neurobiological dissection of this complex phenotype.
Setting the clock – by nature: Circadian rhythm in the fruitfly Drosophila melanogaster
Authors: Peschel Nicolai , Helfrich-Förster Charlotte
Published: February 2011

Nowadays humans mainly rely on external, unnatural clocks such as of cell phones and alarm clocks – driven by circuit boards and electricity. Nevertheless, our body is under the control of another timer firmly anchored in our genes. This evolutionary very old biological clock drives most of our physiology and behavior. The genes that control our internal clock are conserved among most living beings. One organism that shares this ancient clock mechanism with us humans is the fruitfly Drosophila melanogaster. Since it turned out that Drosophila is an excellent model, it is no surprise that its clock is very well and intensely investigated. In the following review we want to display an overview of the current understanding of Drosophila's circadian clock.
Acute and chronic hypermethioninemia alter Na+,K+‐ATPase activity in rat hippocampus: prevention by antioxidants
Authors: Stefanello Francieli M. , Ferreira Andréa G.K. , Pereira Talita C.B. , da Cunha Maira J. , Bonan Carla D. , Bogo Maurício R. , Wyse Angela T.S.
Published: February 2011

In the current study we initially investigated the influence of antioxidants (vitamins E plus C) on the effect mediated by acute and chronic administration of methionine (Met) on Na+,K+‐ATPase activity in rat hippocampus. We also verified whether the alterations on the enzyme after administration of Met and/or antioxidants were associated with changes in relative expression of Na+,K+‐ATPase catalytic subunits (isoforms α1, α2 and α3). For acute treatment, young rats received a single subcutaneous injection of Met or saline (control) and were sacrificed 12 h later. In another set of experiments, rats were pretreated for 1 week with daily intraperitoneal administration of vitamins E (40 mg/kg) and C (100 mg/kg) or saline. After that, rats received a single injection of Met or saline and were killed 12 h later. For chronic treatment, Met was administered to rats from the 6th to the 28th day of life; controls and treated rats were sacrificed 12 h after the last injection. In parallel to chronic treatment, rats received a daily intraperitoneal injection of vitamins E and C from the 6th to the 28th day of life and were killed 12 h after the last injection. Results showed that administration of antioxidants partially prevented the inhibition of enzyme activity caused by acute and chronic hypermethioninemia. Besides, we demonstrated that transcription of catalytic subunits of Na+,K+‐ATPase was not altered by chronic and acute exposure to Met and/or vitamins E plus C. These data strongly suggest the oxidative damage as one possible mechanism involved in the reduction of Na+,K+‐ATPase activity caused by hypermethioninemia and if confirmed in human beings, we might propose the use of antioxidants as an adjuvant therapy in hypermethioninemic patients.
Screening for circulating nucleic acids and caspase activity in the peripheral blood as potential diagnostic tools in lung cancer
Authors: Roth Carina , Kasimir-Bauer Sabine , Pantel Klaus , Schwarzenbach Heidi
Published: February 2011

The focus of the current investigational study was to examine whether circulating nucleic acids (i.e., DNA and microRNAs) have the potential to become suitable blood‐based markers for diagnosis and progression of lung cancer. The concentrations of cell‐free DNA and four circulating microRNAs (miR10b, miR34a, miR141 and miR155) as well as the caspase activity were measured in serum of 35 lung cancer patients (19 non‐small‐cell lung cancer, 8 small cell lung cancer patients and 8 patients with indefinite cancer type), 7 patients with benign lung tumors and 28 healthy individuals by PicoGreen, TaqMan MicroRNA, and Caspase‐Glo®3/7 assay, respectively. The data were correlated with the established risk factors for lung cancer progression. The concentrations of cell‐free DNA (p = 0.0001), serum microRNAs (p = 0.0001) and caspase activities (p = 0.0001) significantly discriminated cancer patients from healthy individuals. Serum DNA, caspase activities and RNA levels could not distinguish between patients with benign lung disease and cancer patients. However, the levels of miR10b (p = 0.002), miR141 (p = 0.0001) and miR155 (p = 0.007) were significantly higher in lung cancer patients than those in patients with benign disease. As determined by the Spearman–Rho test, high levels of cell‐free DNA significantly correlated with elevated circulating caspase activities (p = 0.0001). In lung cancer patients high serum miR10b values associated with lymph node metastasis (p < 0.03) and elevated levels of TPA (tissue polypeptide antigen, p = 0.01), whereas high serum miR141 values associated with elevated levels of uPA (urokinase plasminogen activator, p = 0.02).

The findings of our pilot study suggest that the assays for circulating DNA, microRNAs and caspase activities in blood might become novel minimally invasive diagnostic tools for detection and risk assessment of lung cancer, provided that their clinical utility can be confirmed in larger prospective trials.
miRNA expression profiling of mycosis fungoides
Authors: van Kester Marloes S. , Ballabio Erica , Benner Marchina F. , Chen Xiao H. , Saunders Nigel J. , van der Fits Leslie , van Doorn Remco , Vermeer Maarten H. , Willemze Rein , Tensen Cornelis P. , Lawrie Charles H.
Published: February 2011

MicroRNAs (miRNAs) are small RNA species that regulate gene expression post‐transcriptionally and are aberrantly expressed in many malignancies including lymphoma. However, the role of miRNAs in the pathogenesis of T‐cell lymphoid malignancies is poorly understood. Previously we examined the miRNA profile of Sézary syndrome (Sz), a leukemia of skin‐homing memory T cells. In this study we determined the complete miRNome of mycosis fungoides (MF), the most common type of cutaneous T cell lymphoma. The miRNA profile of skin biopsies from 19 patients with tumor stage MF and 12 patients with benign inflammatory dermatoses (eczema and lichen planus) were compared by microarray analysis. We identified 49 miRNAs that are differentially expressed in tumor stage MF compared to benign inflammatory dermatoses using ANOVA analysis (P < 0.05, Benjamini–Hochberg corrected). The majority of the differentially expressed miRNAs (30/49) were up‐regulated in tumor stage MF. The most significant differentially expressed were miR‐155 and miR‐92a (both up‐regulated in tumor stage MF), while miR‐93 showed the highest up‐regulation in tumor stage MF with a fold difference of 5.8. Differential expression of a selection of these miRNAs was validated by miRNA‐Q‐PCR on additional test groups (tumors and controls). None of the miRNAs up‐regulated in tumor stage MF was previously shown to be up‐regulated in Sz, and only 2 of the 19 miRNAs down‐regulated in tumor stage MF were also down‐regulated in Sz. Taken together this report is the first describing the miRNA signature of tumor stage MF.