bluuebunny/crossref_metadata_2025 huggingface dataset:
Palaeoecology
Authors: Seppä Heikki
Published: September 2009

The basis of palaeoecological research is to use the fossil remains preserved in sedimentary deposits to investigate the history and long‐term dynamics of taxa, populations, communities and ecosystems. Palaeoecological methods can also be used for reconstructing past climatic conditions and other environmental factors. Palaeoecological records extend from years to millions of years and can therefore be used for testing the hypotheses of neo‐ecology and biogeography under environmental conditions different and more extreme than in the modern Earth. Palaeoecology provides often the only means to investigate species macro‐ and microevolutionary patterns or rates of speciation and extinction, and slow ecological processes, such as the rise and fall of ecosystems and biomes, species adaptation or migration, and population growth or decline rates. Palaeoecological records also provide unique insights for identifying the ancestry and naturalness of modern ecosystems and are increasingly recognized as sources of baseline information in ecosystem management.

Key concepts:

Ecosystem dynamics over long‐time periods, niche conservatism, hypothesis testing, transfer functions, background for ecosystem management.

Biography information: Heikki Seppä has written the text. He is a Quaternary palaeoecologist and palaeoclimatologist.
History of Antimalarial Agents
Authors: Greenwood David
Published: September 2009

Malaria is a debilitating and, in its most severe form, falciparum malaria, a potentially fatal disease. Treatment in the form of powdered bark of the cinchona tree from South America has been available from at least the seventeenth century. Synthetic antimalarial agents were not developed until the twentieth century, stimulated by serious shortages of supply during the two World Wars. The first advances were made in Germany in the interwar period. During and after World War II, further progress was made in Britain and the United States. Inevitably resistance to these agents emerged and became a major problem after the 1960s. Other active chemicals have since been developed, but many have serious side effects and much hope is now pinned on derivatives of a natural product, artemisinin, obtained from sweet wormwood (Artemisia annua) and used for centuries (though not at first for malaria) in traditional Chinese medicine.

Key Concepts

Malaria is a potentially fatal disease affecting millions of people, chiefly in tropical countries.

A treatment in the form of powdered bark of the cinchona tree from northern South America has been available since the seventeenth century.

Cinchona bark contains several antimalarial alkaloids, most importantly quinine.

Synthetic antimalarial agents were first developed in Germany in the 1920s and 1930s.

The first antifolate compound active against malaria, proguanil, was developed in England during World War II.

After World War II, several important synthetic antimalarial compounds, notably chloroquine and pyrimethamine became available for prophylaxis and treatment.

From the 1960s resistance emerged as a major issue and quinine once again became the treatment of choice for serious falciparum malaria.

Derivatives of artemisinin, a natural product used in traditional Chinese medicine, is being now being successfully used in treatment.
Regulatory Genes in Plant Development:
MADS
Authors: Ma Hong
Published: September 2009

MADS‐box genes are found in all major groups of eukaryotes and encode known or putative transcription factors. MADS‐box genes have been phylogenetically defined as type I and type II genes. In plants, type II MADS‐domain proteins typically have the MADS, Intervening, K‐domain,
C
‐terminal (MIKC) domain organization, with conserved MADS and K domains. Many of the plant type II MADS‐box genes have important regulatory functions in development, including the specification of flower organ identities, the control of flowering time, the regulation of meristem identity and the promotion of reproductive organ development. Recent studies have provided further insights into the regulation of MADS‐box genes and uncovered additional functions in controlling the development of various structures, such as embryo, endosperm, gametophyte and roots. In addition, protein physical interaction and genetic studies support the hypothesis that MADS‐box proteins form multimeric protein complexes that regulate specific target genes.
Bacterial Membrane Transport: Superfamilies of Transport Proteins
Authors: Padan Etana
Published: September 2009

The bacterial transport systems enable bacteria to accumulate needed nutrients, extrude unwanted by products and maintain cytoplasmic content of protons and salts conducive to growth and development. Two most widely spread superfamilies of transporters are the ion‐coupled systems that take part in chemiosmotic circuits, and the ABC solute
ATPases
(
adenosine triphosphatases
), whose operation is linked to ATP hydrolysis. The crystal structure of several bacterial transporters has recently been determined, a major breakthrough in the research of transporters. It opened the field to a combined study of structure, function and computation. Several of the structurally deciphered bacterial transporters have eukaryotic orthologues including neurotransmitter transporters that play major roles in health and disease and are major drug targets. Hence, the bacterial transport systems are important both for elucidating the mechanism of transport as well as drug design.

Key concepts:

Crystal structures are essential for understanding the mechanism of transport.

Topology model of transporters obtained from the primary amino acid sequence, the positive‐inside rule and experimental data have been validated by the crystal structure.

Primary transporters utilize external source of energy to drive active transport.

The secondary transporters utilize the energy stored in a pre‐existing gradient to drive transport.

The MFS, major facilitator superfamily, encompasses the largest number of evolutionary related most diverse group of secondary transporters and the extensively studied LacY and GlpT with their crystal structures are educative examples.

Na
+
/H
+
antiporters are essential for sodium and pH homeostasis in all cells and the most studied
Escherichia coli
NhaA with its crystal structure is an educative example.

The sodium‐coupled secondary transporter LeuT is a bacterial homologue of human neurotransmitters transporters and therefore its crystal structure is an essential step in drug design.

The alternating access model is the mechanism of activity of secondary transporters.

The molecules of many secondary transporters exhibit internal symmetry that implies a unique evolution.

The internal symmetry of secondary transporters with the inverted repeats and the interrupted helices in the middle of the membrane is the structural basis of the activity mechanism.
Data Protection Legislation
Authors: Holm Søren
Published: September 2009

Data protection legislation regulates the acquisition, storage, transfer and processing of personal data of all kinds. Human genetic information, whether in digital form or in tissue samples, is by definition personal data and its use will therefore in many cases be governed by data protection legislation. The article introduces the key distinction between data security and wider data protection, and further explores the key legal requirements for data protection. In general, the requirements for legal use of genetic data are informed consent to acquisition and fair processing of any data that are held or generated. The approach to data protection differs between the European Union and the USA and these differences are explained.

Key concepts:

The purpose of data protection legislation is to ensure (1) data security and (2) that data acquisition and processing only occurs in accordance with the law.

Data acquisition usually requires informed consent from the data subject.

There are different rules for the processing of identifiable and nonidentifiable personal data.

There are specific protections in relation to sensitive data, including health data.

Anonymity and nonidentifiability are two different concepts.

Identifiability is only absent if deductive identification is very difficult.

The approach to data protection differs significantly between the European Union and the USA.
Informed Consent: Ethical and Legal Issues
Authors: Holm Søren
Published: September 2009

Informed consent from research participants is a necessary legal and ethical requirement for human genetics research. Valid informed consent relies on giving full information and on the capacity of research participants to consent.

The article describes the historical development of the concept of informed consent in biomedical research and explores its current embedding in international legal documents. It discusses the specific problems of informed consent in fast‐moving research areas and the possible solution in the so‐called ‘broad’ consent. The specific issues raised in relation to consent from minors and other incompetent persons are discussed, as is the research use of old tissue sample and other materials obtained without consent.

Key concepts

Informed consent is a central concept in modern research ethics and law.

Valid consent can only be obtained if the prospective research participant is fully informed and is competent to consent.

In fast‐moving research fields where future research use is difficult to predict, ‘broad’ consent may be used in certain circumstances.

For persons who are incompetent to consent, researchers must often rely on proxy consent (e.g. parents consenting for small children).

A proxy must make a decision to consent based solely on considerations of the best interest of the incompetent person.
Interests of the Future Child
Authors: McLean Sheila AM
Published: September 2009

Modern technology makes it possible for intending parents to make certain choices about the characteristics of their future children, when they seek to establish a pregnancy usingin vitrofertilization (IVF) combined with pre‐implantation genetic diagnosis (PGD). Moreover, choices about whether or not to continue with a pregnancy are also available in those countries where prenatal screening and pregnancy termination are available. Although by and large these decisions are seen as reflecting the rights of people to make free, uncoerced choices (the concept of reproductive liberty) others condemn them either as eugenic or as amounting to killing children. However, increasing emphasis on the commitment to future generations may increasingly impact on the reproductive decisions made by prospective parents. Arguably, the concept of reproductive liberty may be modified by the notion of intergenerational justice.

Key concepts

An understanding of the concept of reproductive liberty.

An understanding of the concept of intergenerational justice.

An understanding of the arguments for and against the use of Pre‐implantation Genetic Diagnosis.
Haemophilias: Gene Therapy
Authors: Callaghan Michael , Kaufman Randal J
Published: September 2009

Haemophilia A and B are the two most common severe congenital bleeding disorders and each is corrected with infusion of a single plasma protein. Preliminary data from animal models and from clinical trials in humans suggest that gene therapy may be effective in the haemophilias. Advances in vector technology combined with improved trangenes and knowledge of factors VIII and IX secretion in target tissues over the past several years have improved the prospects of gene therapy for the haemophilias.

Key Concepts

Understand the roles of factors VIII and IX in the intrinsic coagulation cascade.

Understand that both haemophilia A and B are caused by single gene mutations inherited in an X‐linked recessive pattern.

Understand the clinical features of haemophilia A and B.

Understand that haemophilia A and B are excellent models for gene therapy because of the wide range of protein levels that can be both therapeutic and not toxic.

Understand issues that determine target tissue suitability for gene therapy.

Understand the importance of efficient transgene transfection and secretion and the role of bioengineered transgenes.

Understand the potential for accumulation of unfolded or misfolded protein accumulation with overexpression of a transgene in a target tissue and the possibility of toxicity through induction of the unfolded protein response.

Understand the advantages and disadvantages of available vector technologies including: nonviral delivery systems, retroviral vectors, adenoviral vectors and adeno‐associated viral vectors.

Become familiar with results from gene therapy clinical trials in the haemophilias.

Become aware of the ethical and regulatory considerations in haemophilia gene therapy.
Wetland Communities
Authors: Sharitz Rebecca R , Batzer Darold P
Published: September 2009

Wetland communities are assemblages of individuals of different species (plants, animals, microorganisms) living and interacting together in habitats that have water at or near the surface of the ground, or where the land is flooded by shallow water, for much of the year. These organisms are adapted to life in saturated soil conditions, which can include intermittent flooding, anoxia and potentially harsh water and soil chemistries. Wetland communities may be broadly grouped into coastal, including salt marshes, tidal freshwater marshes and forested mangrove swamps; and inland, including freshwater marshes, freshwater swamps, riparian wetlands (along streams and rivers) and peatlands (including bogs and fens). Hydrological conditions such as the source, depth, flow rate and timing of water presence are the fundamental determinants of the composition and structure of wetland communities.

Key Concepts

Definition and classification of wetland communities.

How wetland and upland communities differ in species richness and composition.

Successional development of wetland communities.

Abiotic and biotic factors affecting wetland community composition.

How competition and facilitation affect wetland plant community composition.

Effects of herbivory and predation on wetland communities.

Threats to wetland communities and wetland losses.
RNA
Silencing and its Suppressors in the Plant‐virus Interplay
Authors: Valli Adrián , López‐Moya Juan José , García Juan Antonio
Published: September 2009

Viruses are obligate intracellular parasites that need to evade the host defences targeted against them. In plants, activation of
ribonucleic acid
(RNA) silencing is among the most powerful responses against viruses. To overcome this defence, both
deoxyribonucleic acid
(DNA) and RNA plant viruses make use of viral products able to interfere with silencing mechanisms, and known collectively as RNA silencing suppressors (RSSs). RSSs present an extraordinary diversity in modes of action, and therefore, their study is providing valuable information about the different silencing pathways in plants. This article reviews our knowledge on RSSs, including the experimental systems used to identify them, and the mechanisms by which they act. Finally, the additional effects that they cause in the network of silencing pathways, and hence the need of a tight control of their activity, are also considered.

Key concepts:

Argonaute: Family of proteins that contain certain conserved domains, such as PIWI domain (found in Piwi, or P‐element‐induced wimpy testis in
Drosophila
, and related proteins) and PAZ domain (found in Piwi, Argonaute and Zwille proteins). Proteins of this family are the main components of RNA silencing effector complexes.

Dicer: Ribonuclease belonging to the RNase III family. Dicer‐like enzymes cleave hairpin or double‐strand RNA molecules into short RNA duplexes of 20–24 nucleotides with a 2‐nucleotides overhang at the 3′ ends, which are key components of the RNA silencing pathways.

microRNA (miRNA): Endogenous single‐strand RNA of 20–21 nucleotides, which derives from a hairpin precursor. miRNAs are incorporated into RISC, guiding it, by base complementary, to silence endogenous mRNAs.

RNA‐dependent RNA polymerase (RdRP, RDR): Enzyme able to synthesize RNA using RNA as template. These enzymes are involved in amplification steps of RNA silencing.

RNA‐induced silencing complex (RISC): Multicomponent complex including an Argonaute protein and a short RNA. RISC can silence mRNAs by endonucleolytic cleavage, decay acceleration and translation inhibition.

RNA‐induced transcriptional silencing complex (RITS): Multicomponent complex including an Argonaute protein and a short RNA that silence gene expression by inhibiting or downregulating the transcription activity.

RNA silencing: General term used to describe different events triggered by small RNAs to induce transcriptional or posttranscriptional gene downregulation in a sequence‐homology manner.

RNA silencing suppressor (RSS): Factor (usually a protein) with the capacity to interfere with the onset of RNA silencing or with its maintenance. The expression of viral RSSs is the most common strategy that plant viruses use to escape from RNA silencing.

Short interfering RNA (siRNA): Small RNA of 20–24 nucleotides derived from Dicer‐mediated cleavage of a double‐stranded RNA precursor. One of the strands of the siRNA is incorporated in RISC or RITS to guide their RNA silencing effector activities.
Analysis of the Amphioxus Genome
Authors: Satoh Noriyuki
Published: September 2009

Amphioxus or cephalochordates are small fish‐like marine invertebrates. The sequenced genome ofBranchiostoma floridaeis approximately 520 Mb in size and estimated to contain approximately 21 900 protein‐coding loci. Comparison of the amphioxus genome with genomes of other animals made a great impact on the resolution of the long‐standing question of the origin of vertebrates. First, chordates are monophyletic group, in which cephalochordates represent the most basal extant chordate lineage, with urochordates sister to vertebrates. Second, there is highly conserved synteny between the cephalochordate and vertebrate genomes. This allows reconstruction of 17 ancestral chordate linkage groups that are conserved in the modern amphioxus and vertebrate genomes. Third, the two rounds of genome‐wide duplications occurred in the vertebrate lineage after their divergence from cephalochordates and urochordates. Fourth, whereas most duplicate genes have been lost, a disproportionate number of genes are retained and involved in developmental processes to produce novel features and complexity of vertebrate biology.

Key concepts

The phylum Chordata consists of the subphyla Cephalochordata (amphioxus), Urochordata (ascidians) and Vertebrata, and these three groups are characterized by possession of a notochord, a hollow dorsal neural tube, a perforated pharyngeal region and a post‐anal tail.

Chordates are monophyletic group in which cephalochordates represent the most basal extant lineage, suggesting a free‐living ancestor of chordates.

Seventeen ancestral chordate linkage groups that are conserved in the modern amphioxus and vertebrate genomes are revealed by highly conserved synteny between the two genomes.

The two rounds of genome‐wide gene duplications occurred in the vertebrate lineage after their divergence from cephalochordates and urochordates.

A disproportionate number of genes which were produced by the genome‐wide duplication are retained and involved in developmental processes to produce novel features and complexity of vertebrate biology.
Recombination Rates in Drosophila
Authors: Stevison Laurie S , Noor Mohamed A F
Published: September 2009

Recombination occurs during meiosis to produce new allelic combinations in natural populations, making it important for studying evolution. The model systemDrosophilahas been crucial for understanding the mechanics underlying recombination and assessing the association between recombination rate and several evolutionary parameters.Drosophilawas the first system in which genetic maps were developed using recombination frequencies between genes. Linkage maps have been subsequently developed in many biological systems, including humans. Fungal systems have been helpful in highlighting the mechanics of recombination and identifying particular enzymes that perform various steps in the process; however, similar proteins have been identified inDrosophila. Further,Drosophilahas been used to determine genetic and environmental conditions that cause variation in recombination rate. Finally,Drosophilahas been instrumental in elucidating associations between local recombination rate and nucleotide diversity, divergence and codon bias, as well as helping determine the causes of these associations.

Key Concepts

Recombination refers to either independent assortment or crossing over, both of which are responsible for introducing genetic variation during meiosis.

Drosophilahas been crucial in the development of genetic mapping techniques, which have been extended to other organismal systems including humans.

Fungal systems have been critical to the discovery of the underlying mechanics of crossing over.

Several key environmental conditions that cause recombination rate variation have been identified primarily inDrosophila.

Recombination rate variation within a genome is in part due to ‘hotspots’ that concentrate double‐strand breaks to particular regions of the genome.

The demonstrated relationship between nucleotide diversity and recombination rate inDrosophilahas been repeated in many organismal systems.

The relationship between recombination rate and genetic divergence has been less repeatable between different organismal systems, due to either mechanical or evolutionary processes.
Human Relationships Inferred from Genetic Variation
Authors: Lao Oscar , Kayser Manfred
Published: September 2009

We humans are a diverse species, both at the phenotypic and the genetic levels. The genetic diversity of current human populations has been shaped by various demographic and evolutionary as well as some cultural factors. Thus, studying how genetic variation is distributed through individuals around the world can provide insights into (i) when and where our human ancestors first appeared on the planet, (ii) the dynamics of admixture with otherHomospecies not existing anymore, (iii) migration waves that brought humans across the world and (iv) processes of adaptations towards environmental and other factors that shaped human genomes and phenotypic traits. Additionally, the quantification of genetic variation between human populations provides data evidence for elucidating whether humans can be classified according to genetically homogeneous groups or not, with implications for medical and forensic studies. Hence, studying human genetic diversity is important for better understanding of our past, presence and future.

Key concepts:

Studying human genetic variation adds important insights for inferring human origins.

Human genetic variation is highest in Africa, and non‐Africans reflect a subset of diversity of Africans.

Most genetic evidence supports a single common origin of modern humans in Africa and a recent spread out of Africa into different regions at different periods of time.

Studying human genetic variation allows to some degree the reconstruction of human migration and adaptation history.

Human genetic variation in Europe is gradually distributed with higher autosomal diversity in the south and lower ones in the north.

European genetic variation implies that Europe was mainly settled from the south to the north and/or that the effective population size was larger in the south than in the north.

Overall genetic variation between individuals is small and most of it is between individuals from the same population, whereas only a small proportion is expressed between continents.

Some strong differences observed in particular loci between individuals from different, for example, continental regions have been driven by local positive selection.

If applications of genetic variation, for example in medicine or forensics, include genomic regions with strong differences among continental groups, population substructure needs to be considered.

It is as error prone to ignore the small proportion of genetic loci with strong differences between individuals from different geographic regions, including coded phenotypes, as it is to extrapolate from them to claim ‘racial’ differences between humans, which do not exist when considering the genome as a whole.
Allele‐specific m
RNA
Splicing in Human
Authors: Nembaware V , Seoighe C
Published: September 2009

Polymorphisms and

de novo

mutations in the genome sequence determine the genetic contribution to human phenotype and disease. Many functionally significant variants, rather than altering an encoded protein, affect the regulation of transcription or posttranscriptional processing, including messenger
ribonucleic acid
(mRNA) splicing. The effects of these mutations can be difficult to determine, yet they make a substantial contribution to human disease and other phenotypes of medical significance, such as interindividual differences in responses to pharmaceuticals. Progress towards understanding the regulation of splicing, coupled with the advent of high‐throughput technologies for interrogating the transcriptome have given rise to new opportunities to investigate allelic differences in mRNA splicing.

Key Concepts

Splicing is a tightly regulated process that can be disrupted by sequence variants (polymorphisms or rare mutations).

Mutations and polymorphisms that affect mRNA splicing are thought to make a major contribution to human genetic diseases.

Alternatively spliced mRNA isoforms are detectable for the majority of human multiexon genes.

The contribution of sequence variants to the diversity of splice isoforms observed for a gene is often overlooked.

Sequence variants that affect splicing can disrupt splicing of constitutively spliced exons or affect the regulation of alternative splicing.

Variants with a quantitative effect on splicing are referred to as splicing quantitative trait loci (sQTLs).

Most examples of allele‐specific splicing involve differences in the relative abundance of isoforms, rather than the creation or loss of an isoform.

Because the balance of alternative splice isoforms is often evolutionarily conserved when the isoforms themselves are conserved, sQTLs of conserved isoforms may frequently have functional implications.
Factor‐Mediated Ribosome Assembly in Bacteria
Authors: Dönhöfer A , Sharma MR , Datta PP , Nierhaus KH , Agrawal RK , Wilson DN
Published: September 2009

The ribosome is a structurally and functionally conserved macromolecular machine responsible for translating messengerribonucleic acid(mRNA) into proteins. Composed of two independently assembled subunits, the bacterial ribosome is approximately 2.5 MDa in size. The process of translation, catalysed by the ribosome, is central to gene expression in the cell. Correspondingly, the regulation of ribosome biogenesis is paramount to cell viability, growth and differentiation. Moreover, the ribosome is the target of numerous clinically relevant therapeutic agents, several of which are known to affect ribosome assembly. Although,in vitroreconstitution of bacterial ribosomal subunits can be achieved using purified ribosomal RNA (rRNA) and r‐protein components, the process occurs at nonphysiological conditions. It is suggested that a specific order of processing and assembly events and regulatory factors is required to achieve fully functional particles. This article focuses on the protein factors that are involved in the process of bacterial ribosome biogenesis.

Key concepts:

This article focuses on the protein factors that are involved in the process of bacterial ribosome biogenesis.
Methanotrophy in Extreme Environments
Authors: Dunfield Peter F
Published: September 2009

Methanotrophy is the ability of a few prokaryotes to grow on methane as a sole energy source. Aerobic methanotrophic bacteria are active in natural environments with pH values ranging from 1 to 11, temperatures ranging from 0 to 72°C and salinities up to 30%. In addition, anaerobic methanotrophs are found in permanently cold ocean sediments at temperatures down to −1°C, and in geothermally heated sediments at temperatures up to 90°C. Several extremophilic species of aerobic methanotrophs have been isolated and studied in pure culture, including thermophiles, psychrophiles, acidophiles, alkaliphiles and halophiles. The knowledge of methanotrophs and their ecology in extreme environments is summarized, with particular attention on bacteria with multiple extremophilic phenotypes that are found in acidic subarctic peatlands and in acidic geothermal springs.

Key concepts

Methane is oxidized by prokaryotes in diverse environments, including some with extreme temperatures, pH values and salinities.

The ecology of extremophilic methanotrophs has been studied using cultivation‐independent molecular methods.

Extremophilic aerobic methanotrophs have been isolated and studied in pure culture, but anaerobic methanotrophs have not yet been isolated.

Some aerobic methanotrophs combine multiple extremophilic phenotypes.

Biogeochemical and molecular ecology studies suggest that sulphate‐reducing methanotrophs are capable of living under a similar range of temperatures as are aerobic methanotrophs.
Microbial Inhibitors of Apoptosis
Authors: Häcker Georg
Published: September 2009

Infection with microbial agents (bacteria, fungi, viruses and parasites) is a challenge to a host cell. The host cell's response to infection is complex and entails changes in the activity of a number of intracellular signalling pathways, commonly including the apoptotic machinery. Microbes, if they have evolved the capacity to infect mammals or other complex hosts, have to be able to deal with such defence systems. The lifestyle of microbes varies substantially – viruses, for instance, depend on an intact cell, whereas many bacteria grow on surfaces and are not sensitive to host cell apoptosis. What we know about microbial interference with host cell apoptosis is in accordance with these lifestyles. Viruses often directly target and inhibit the apoptosis machinery with specific proteins whereas other microbes frequently also interfere with host apoptosis but more indirectly.

Key concepts:

Microbes (bacteria, fungi, viruses and parasites) can vary widely in terms of growth requirements and intimacy of association with host cells.

Apoptosis is commonly induced in cells infected with microbes.

In infections with obligate intracellular agents, apoptosis can be a defence mechanism of the host cell.

A number of viruses carry genes whose products can directly interfere with the host cell's apoptosis apparatus.

Many cells become activated when encountering microbial agents, and this activation may entail the triggering of pro‐survival pathways in the host cell.

Activation of antiapoptotic pathways in immune cells by microbial components is a regulatory mechanism of the immune response.
Electromechanical Impedance Modeling
Authors: Zagrai Andrei N. , Giurgiutiu Victor
Published: September 2009

The electromechanical impedance method is one of the key structural health monitoring (SHM) technologies enabling real‐time in‐service assessment of structural condition. This SHM method utilizes permanently attached piezoelectric wafer active sensors and electromechanical impedance measurements for inferring dynamic characteristics (frequency response) of the host structure. Changes in the impedance signatures serve as a diagnostic for structural damage.

Providing a fundamental consideration of the sensor–structure impedance interaction, this article focuses on the analytical modeling of the sensor and structural dynamics participating in the cumulative impedance response. One‐dimensional models of the sensor and the host structure are discussed first to introduce the reader to the physical mechanisms of the electromechanical impedance method. Under applied harmonic excitation, expansion and contraction of the sensor results in longitudinal and flexural vibrations of the host structure that are accounted for in the model presented. For two‐dimensional structures, an axisymmetric problem is considered and an analytical formulation is derived for the electromechanical impedance as seen at the sensor terminals. Extensional and transverse dynamics of the plate structure are included in the model. Recent developments in impedance modeling are discussed and prospective new trends are suggested.
Acoustic Emission
Authors: Gorman Michael R.
Published: September 2009

In addition to a general summary of the field modal acoustic emission, four new things of significance are presented in this article: (i) how to roughly size fatigue crack depth in metal pressure vessels; (ii) delamination waveforms and relating acoustical energy to delamination size; (iii) a simple formula for predicting the front end frequency of the E wave as a function of plate thickness; (iv) wave shapes for an important range of plate thicknesses.
Time–Frequency Analysis
Authors: Ceravolo Rosario
Published: September 2009

Time–frequency analysis has been recently introduced into many research fields, ranging from seismic signal processing to biomedical engineering. Interest in this representation is motivated by the limitations of classical spectral estimation techniques in analyzing strongly nonstationary behaviors.

Owing to the importance of nonstationary components in vibration signals, several studies have proposed the adoption of time–frequency analysis in structural identification and damage assessment. Many authors have applied linear tools, such as the short‐time Fourier transform and the wavelet transform, or in some cases, their squared magnitudes, known as
spectrogram
and
scalogram
, respectively.

The adoption of a quadratic representation makes it possible to overcome limitations due to the time–frequency resolution, since energetic and correlative transforms are not based on signal segmentation. Specifically, among the quadratic transforms, those belonging to the Cohen class are characterized by their invariance to time and frequency shifts. This property allows for a correct physical interpretation of the mechanical response, thus justifying the interest that many researchers have shown for this approach.

The present article is intended as a comprehensive overview of some recent advances in the field of time–frequency analysis for structural identification. We focus on the shift‐invariant class, including the spectrogram. Other time–frequency analysis techniques include, but are not limited to, wavelet analysis (
see
Wavelet Analysis
) and empirical mode decomposition combined with Hilbert transform (
see
Damage Detection Using the Hilbert–Huang Transform
).
Design Principles for Aerospace Structures
Authors: Telgkamp Jens
Published: September 2009

The development and design of new aircraft structure is today a complex, multidisciplinary challenge. An overview of requirements, dimensioning criteria, and the material‐selection process is given. New ideas are arising for the potential applications of structural health monitoring (SHM) where a variety of benefits for the aircraft structure are possible. An overview is given of ideas to achieve maintenance benefits on current and future aircraft structure, including SHM as a retrofit solution to in‐service aircraft and benefits coming from the early detection of structural damage. Another field of potential application on aircraft is the improvement of structural performance and reduction of weight through the use of SHM to reduce design conservatism. This application places ambitious requirements on the relevant SHM technologies in the fields of robustness, reliability, and durability. Examples are given for weight‐saving ideas on metallic and composite structures, as well as for the integration of structural components and SHM technology.
Multiwire Strands
Authors: di Scalea Francesco Lanza , Bartoli Ivan , Rizzo Piervincenzo , Marzani Alessandro , Sorrivi Elisa , Viola Erasmo
Published: September 2009

Multiwire strands are used in civil structures as prestressing members of posttensioned concrete systems, and tendons of cable‐stayed and suspension bridges. This article discusses the use of ultrasonic guided waves for providing both defect detection and stress monitoring capabilities in the common seven‐wire, 15.34‐mm (0.6‐in.) steel strands using embedded transducers. The semianalytical finite element method is first used to model the multimode and dispersive vibrational behavior of the strand waveguide. Experimentally, magnetostrictive transducers probing the strand as a whole are shown to be sensitive to small notch‐like defects in reflection‐based measurements, which are aided by robust feature extraction and statistical defect classification. Small piezoelectric transducers probing the individual wires comprising the strand are, instead, shown to be suitable to monitor the level of stress applied to the strand. In particular, the ultrasonic transmission between the peripheral wire and the central wire, quantified in terms of ultrasonic energy and frequency, is found to be highly sensitive to the level of stress. The method discussed is currently under laboratory development, and its effectiveness in the field remains to be demonstrated.
Microarray based analysis of 3p25‐p26 deletions (3p‐ syndrome)
Authors: Shuib Salwati , McMullan Dominic , Rattenberry Eleanor , Barber Richard M. , Rahman Fatimah , Zatyka Malgosia , Chapman Cyril , Macdonald Fiona , Latif Farida , Davison Val , Maher Eamonn R.
Published: September 2009

Distal deletion of chromosome 3p25‐pter (3p‐ syndrome) produces a distinct clinical syndrome characterized by low birth weight, mental retardation, telecanthus, ptosis, and micrognathia. Congenital heart disease (CHD), typically atrioventricular septal defect (AVSD) occurs in about a third of patients. Previously we reported on an association between the presence of CHD and the proximal extent of the deletion such that a CHD susceptibility gene was mapped between D3S1263 and D3S3594. In addition, we and others have suggested several candidate genes for the psychomotor retardation usually seen with constitutional 3p25 deletions. In order to further investigate genotype–phenotype correlations in 3p‐ syndrome we analyzed 14 patients with cytogenetically detectable deletions of 3p25 (including one patient with a normal phenotype) using Affymetrix 250K SNP microarrays. Deletion size varied from ∼6 to 12 Mb. Assuming complete penetrance, a candidate critical region for a CHD susceptibility gene was refined to ∼200 kb and a candidate critical region for mental retardation was mapped to an ∼1 Mb interval containing SRGAP3 but other 3p neurodevelopmental genes including CHL1, CNTN4, LRRN1, and ITPR1 mapped outside the candidate critical interval. We suggest that current evidence suggests that SRGAP3 is the major determinant of mental retardation in distal 3p deletions. © 2009 Wiley‐Liss, Inc.
Maternal medication use, carriership of the ABCB1 3435C > T polymorphism and the risk of a child with cleft lip with or without cleft palate
Authors: Bliek Bart J.B. , van Schaik Ron H.N. , van der Heiden Ilse P. , Sayed‐Tabatabaei Fakhredin A. , van Duijn Cock M. , Steegers Eric A.P. , Steegers‐Theunissen Régine P.M. ,   the Eurocran Gene–Environment Interaction Group
Published: September 2009

Gene–environment interactions in the periconceptional period play an increasing role in the pathogenesis of birth defects, including cleft lip and/or cleft palate (CL/P). The P‐glycoprotein, encoded by the ABCB1 gene, is suggested to protect the developing embryo from medication and other xenobiotic exposures. Furthermore, maternal medication use during early pregnancy is a significant risk factor for CL/P offspring. Therefore, the aim of this study is to investigate the association between the maternal and child's functional ABCB1 3435C > T polymorphism, periconceptional medication exposure, and the risk of a child with CL/P. A case–control study was performed among 175 mothers and 98 of their children with CL/P and 83 control mothers and their 65 children. Information on medication and folic acid use was collected. Mothers carrying the 3435TT genotype and using medication showed a 6.2‐fold (95% CI = 1.6–24.2) increased risk of having a child with CL/P compared to mothers carrying the 3435CC genotype and not using medication. Periconceptional folic acid use reduced this risk by approximately 30% (OR = 3.9, 95% CI = 0.9–18.0). Mothers carrying the 3435TT genotype, using medication and not taking folic acid showed the highest risk estimate (OR = 19.2, 95% CI = 1.0–369.2). These data suggest that mothers who carry the ABCB1 3435C > T polymorphism are at significantly increased risk for having offspring with CL/P, especially mothers using medication in the periconceptional period. © 2009 Wiley‐Liss, Inc.
Synthesis and Photophysics of Core‐Substituted Naphthalene Diimides: Fluorophores for Single Molecule Applications
Authors: Bell Toby D. M. , Yap Sheryll , Jani Chintan H. , Bhosale Sheshanath V. , Hofkens Johan , De Schryver Frans C. , Langford Steven J. , Ghiggino Kenneth P.
Published: September 2009

The synthesis and photophysics of two new aminopropenyl naphthalene diimide (SANDI) dyes are reported. A general and convenient method for the synthesis of the precursor mono‐, di‐, and tetrabrominated 1,4,5,8‐naphthalene tetracarboxylic dianhydrides is described. The two core‐substituted SANDIs exhibit many of the photophysical properties required for fluorescence labeling applications including high photostability and high fluorescence quantum yields (>0.5) in the visible region of the spectrum. The emission wavelength is sensitive to the number of substituents on the NDI core, and the fluorescence decay times are in the range of ∼8–12 ns for both compounds in the solvents investigated. Preliminary fluorescence emission data from single molecules of the compounds embedded in poly(methyl methacrylate) films are also reported and show that single molecules have very low yields of photobleaching, particularly the di‐substituted system. Furthermore, only a small proportion (<10 %) of the single molecules studied display fluorescence intermittencies or “blinks” in their photon trajectory. The compounds appear to be excellent candidates for applications at the single molecule level, for example, as FRET labels.
Periodic Mesoporous Organosilicas with Helical and Concentric Circular Pore Architectures
Authors: Yuan Pei , Zhao Lingzhi , Liu Nian , Wei Guangfeng , Zhang Yang , Wang Yunhua , Yu Chengzhong
Published: September 2009

This study systematically investigates periodic mesoporous organosilicas (PMOs) with controlled helical and concentric circular (CC) pore architectures prepared through a basic‐catalyzed sol–gel process by using an achiral cationic surfactant trimethyloctadecylammonium bromide (C18TAB) as a structure‐directing agent, perfluorooctanoic acid (PFOA) as an additive, and 1,2‐bis(triethoxysilyl)ethane (BTEE) as a hybrid silica precursor. By increasing the weight ratio of PFOA/C18TAB, a pore architecture transition of PMO materials from hexagonal‐arrayed, straight longitudinal channels to helical and CC mesostructures is achieved; such a transition has not been observed before in PMO materials. Our discovery is helpful in understanding the supramolecular cooperative assembly of hybrid materials and their structural and morphological evolution, which are important in the future applications of PMO materials.
Gold‐ or Platinum‐Catalyzed Cascade Processes of Alkynol Derivatives Involving Hydroalkoxylation Reactions Followed by Prins‐Type Cyclizations
Authors: Barluenga José , Fernández Amadeo , Diéguez Alejandro , Rodríguez Félix , Fañanás Francisco J.
Published: September 2009

An efficient method for the synthesis of [3.3.1]bicyclic compounds from easily available alkynol derivatives has been developed. The reaction is based on a gold‐ or platinum‐catalyzed tandem process that involves an intramolecular hydroalkoxylation of a triple bond followed by a Prins‐type cyclization. The reaction has been carried out with differently substituted alkynol derivatives and oxygen‐, nitrogen‐, and carbon‐centered nucleophiles. The incorporation of halogen atoms as nucleophiles and elimination reactions has also been studied. Enantiomerically pure [3.3.1]bicyclic systems were easily synthesized from the chiral pool.
Synthesis and Reactivity of Enantiomerically Enriched Thiiranium Ions
Authors: Denmark Scott E. , Vogler Thomas
Published: September 2009

Enantiomerically enriched thiiranium ion 5 has been prepared by silver‐assisted ionization of chloro sulfide 4 at −20 °C. This thiiranium ion is configurationally stable in solution up to room temperature as demonstrated by the stereospecific capture of the ion by various oxygen‐ and nitrogen‐based nucleophiles. Both isolated olefins and weak Lewis bases can promote the racemization of 5 but these processes can also be suppressed at low temperature. Capture of 5 by methanol is faster than the racemization processes.
Aryloxy Phosphoramidate Triesters: a Technology for Delivering Monophosphorylated Nucleosides and Sugars into Cells
Authors: Mehellou Youcef , Balzarini Jan , McGuigan Christopher
Published: September 2009

Prodrug technologies aimed at delivering nucleoside monophosphates into cells (protides) have proved to be effective in improving the therapeutic potential of antiviral and anticancer nucleosides. In these cases, the nucleoside monophosphates are delivered into the cell, where they may then be further converted (phosphorylated) to their active species. Herein, we describe one of these technologies developed in our laboratories, known as the phosphoramidate protide method. In this approach, the charges of the phosphate group are fully masked to provide efficient passive cell‐membrane penetration. Upon entering the cell, the masking groups are enzymatically cleaved to release the phosphorylated biomolecule. The application of this technology to various therapeutic nucleosides has resulted in improved antiviral and anticancer activities, and in some cases it has transformed inactive nucleosides to active ones. Additionally, the phosphoramidate technology has also been applied to numerous antiviral nucleoside phosphonates, and has resulted in at least three phosphoramidate‐based nucleotides progressing to clinical investigations. Furthermore, the phosphoramidate technology has been recently applied to sugars (mainly glucosamine) in order to improve their therapeutic potential. The development of the phosphoramidate technology, mechanism of action and the application of the technology to various monophosphorylated nucleosides and sugars will be reviewed.
Calculated on 1H and 13C NMR chemical shifts of 2,4‐difluorobenzaldehyde isonicotinoylhydrazone and 2,3‐dichlorobenzaldehyde isonicotinoylhydrazone with GIAO, IGAIM, and CSGT models
Authors: Günay N. , Tarcan E. , Avcı D. , Cömert H. , Esmer K. , Atalay Y.
Published: September 2009

The 1H and 13C NMR chemical shifts of the 2,4‐difluorobenzaldehyde isonicotinoylhydrazone (I) and 2,3‐dichlorobenzaldehyde isonicotinoylhydrazone (II) were determined with the help of full spectral analysis. The geometry and electronic structure of the title compounds were investigated at both the ab initio Hartree‐Fock and the B3LYP levels with 6‐31+G(d,p) basis set. The NMR data were calculated by means of the GIAO, CSGT, and IGAIM methods. All quantum‐chemical calculations, including those of NMR data, were performed by ab initio level HF and DFT methods. Excellent agreement between the theoretical and experimental results was found for the HF level 1H and 13C chemical shifts. The parameters of molecular geometry and 1H and 13C chemical shift values of the title compounds (I, II) in the ground state have been calculated and and compared with corresponding experimental result. © 2009 Wiley Periodicals, Inc. Concepts Magn Reson Part A 34A: 297–304, 2009.