bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human Relationships Inferred from Genetic Variation
Authors: Lao Oscar , Kayser Manfred 
Published: September 2009

AbstractWe 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

Abstract

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

AbstractThe 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

Abstract

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

Abstract

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

AbstractThe 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

AbstractIn 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

Abstract
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

Abstract
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

Abstract
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

AbstractDistal 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

AbstractGene–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

AbstractThe 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

AbstractThis 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

AbstractAn 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

AbstractEnantiomerically 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.