bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA
Sequence Analysis
Authors: Gojobori Takashi , Nakagawa So , Clemente Jose C 
Published: September 2009

Abstract

Recent advances in
deoxyribonucleic acid
(DNA) sequencing technology have produced a massive amount of nucleotide sequences, which are stored in DNA databanks and genomic data repositories. Furthermore, comprehensive analyses of transcriptional and genomic elements have uncovered an elaborate system of gene expression that broadens our understanding of fundamental biological phenomena. The analysis of DNA data has therefore become essential to predict gene function or detect regulatory motifs through comparative studies. In this article, DNA databases, homology search tools and sequence alignment methods are surveyed. The concept of distance between genes and how to calculate this measure using DNA or amino acid sequences and introducing several commonly used techniques for phylogenetic analysis and tree evaluation are also described.

Key concepts

Advances in DNA sequencing technology have produced an unprecedented amount of sequence data.

The DNA Data Bank of Japan (DDBJ), the European Bioinformatics Institute (EBI) and the National Center for Biotechnology Information (NCBI) are the three major sequence data repositories. They exchange data periodically, and maintain various services for data search and retrieval.

Similarity searching, alignment of sequences, prediction of function and reconstruction of the evolutionary history (phylogenetic tree) of a group of species are among the most commonly used techniques for sequence analysis.

BLAST (similarity searching), ClustalW (sequence alignment), Pfam (protein domains) and TRANSFAC (transcription factors) are popular tools and resources.

The genetic distance, a measure of evolutionary similarity, is usually calculated as the number of nucleotide or amino acid differences (substitutions) among sequences. Nucleotide substitutions are synonymous (not affecting the codified amino acid) or nonsynonymous (triggering an amino acid change).

Distance‐ and character‐based methods can be used to reconstruct phylogenetic trees. Distance‐based methods reconstruct the tree from an estimation of the evolutionary distance among taxa. Character‐based methods derive the phylogeny directly from the observable state of characters in the taxa.

The bootstrap method is commonly used to determine the quality of an inferred phylogeny.
Comparative Genomic Hybridization
Authors: Tachdjian Gérard 
Published: September 2009

Abstract

Comparative genomic hybridization (CGH) is a modified
in situ
hybridization technique which allows detection and mapping of DNA (
deoxyribonucleic acid
) sequence copy differences between two genomes. In CGH analysis, two differentially labelled genomic DNA (study and reference) are cohybridized to normal metaphase spreads or to microarray. Chromosomal locations of copy number changes in the DNA segments of the study genome are revealed by a variable fluorescence intensity ratio along each target chromosome or DNA sequences. Thus, CGH allows detection and mapping of DNA sequence copy differences between two genomes in a single experiment. Since its development, CGH has been applied as a research tool in the field of cancer cytogenetics to identify genetic changes in many previously unknown regions. CGH is also a powerful tool for detection and identification of unbalanced chromosomal abnormalities in prenatal, postnatal and preimplantation diagnostics. Array CGH is a high‐resolution technique to detect chromosomal DNA copy number variations at a genome‐wide scale.

Key concepts

Comparative genomic hybridization is a modified
in situ
hybridization technique.

CGH allows detection and mapping of DNA sequence copy differences between two genomes.

In CGH analysis, two differentially labelled genomic DNA segments (study and reference) are cohybridized to normal metaphase spreads or to mapped DNA sequences or oligonucleotides arrayed onto glass slides (array CGH).

Chromosomal locations of copy number changes in the DNA segments of the study genome are revealed by a variable fluorescence intensity ratio along each target chromosome.

In CGH on chromosomes, genetic changes are detected and mapped on chromosomes.

CGH allows the detection and characterization of whole and partial aneuploidies.

CGH has been widely used for the study of chromosomal imbalances in tumours.

An important contribution of CGH to cancer research has been in pinpointing putative locations of cancer genes.

In clinical genetics, CGH is increasingly used in diagnosing unbalanced chromosomal rearrangements.

Since its development, CGH has been applied mostly as a research tool in the field of cancer cytogenetics, but it is also used in clinical genetics.
History of Antiulcer Drugs
Authors: Fuccio Lorenzo , Leonardo Henry Eusebi , Bazzoli Franco 
Published: September 2009

Abstract

The therapy of peptic ulcer disease has progressively changed in the last two centuries. Major discoveries were achieved by the possibility to directly visualize the first part of the gastrointestinal tract with endoscopy and by the availability of potent antisecretory agents. Then, since

Helicobacter pylori

was discovered, the cause of this disease was understood and the optimal therapy was found. The cure of the infection was not only able to heal the ulcer but also to cure the disease, interrupting its relapsing behaviour. Initially, dual therapy, a combination of a proton pump inhibitor with an antibiotic, demonstrated an overall efficacy for the eradication of
H. pylori
better than monotherapy, but still not satisfactory. Finally, a triple therapy of proton pump inhibitor, clarithromycin, and either amoxicillin or metronidazole, has been the most widely recommended eradication treatment.

Key concepts

Neutralization of gastric acidity heals peptic ulcer but does not prevent relapse of
Helicobacter pylori
‐related ulcer.

H. pylori

has been clearly related to gastritis, peptic ulcer (gastric and duodenal ulcer), gastric lymphoma and cancer.

Eradication of

H. pylori

infection heals and prevents the peptic ulcer relapse.

The triple therapy of proton pump inhibitor and two antibiotics (clarithromycin and either amoxicillin or metronidazole) is the most widely recommended eradication treatment for

H. pylori

infection.
Bioethics: Institutionalization of
Authors: Engelhardt HT , Iltis Ana Smith , Jotterand Fabrice 
Published: September 2009

Abstract

Bioethics is a recognized discipline in the academy, an established practice within the clinic and a source of guidance for healthcare policy and the conduct of human research. As a complex of theoretical and practical undertakings, bioethics now commands an officially recognized cluster of norm‐setting and behaviour‐guiding roles that have become institutionalized elements of the scholarly, clinical, human research and public policy establishment. The integration of the antecedents of bioethics into these settings began in the 1960s but these activities were recognized under this name only at the end of the 1970s. By 1979, there was an established literature, numerous individuals who called themselves bioethicists, academic programs engaged in bioethics. Attention to bioethics internationally continues to grow, particularly as biotechnological developments raise new questions and concerns.

Key Concepts

The antecedents of bioethics emerged in the 1960s, and then the field took shape under this rubric in the 1970s.

Awareness of past abuses of human research subjects and the need to conduct more research to secure progress in medicine led to a focus on research ethics and the regulation and oversight of research.

Cultural shifts in the 1960s and 1970s that emphasized individual rights led to discussions about patients’ rights and patient‐driven decisions.

The secularization of U.S. society in the 1960s created space for discussions of medical morality among secular scholars who sought a secular source for moral guidance.

Bioethicists provide clinical and research ethics consultations, teach and conduct research in the academy and are involved in the creation of public policy.

Bioethics continues to seek substantive moral insight from secular sources.
Ecosystem Boundaries
Authors: Banks‐Leite Cristina , Ewers Robert M 
Published: September 2009

Abstract

Ecosystem boundaries are zones of transitions between two adjacent habitats. They occur naturally in all biomes but the extent of boundaries has been greatly increased by anthropogenic habitat modification. Transition zones are characterized by a profound change in the composition of plant and animal communities and that transition may be abrupt, gradual or even occur via a series of intermediate habitat types. Naturally occurring ecosystem boundaries sometimes form a unique habitat to which species are specifically adapted, whereas anthropogenically created ecosystem boundaries typically contain a mixture of species from the two adjacent ecosystems and often exert a negative influence on natural habitats. Adjacent ecosystems are connected via flows of energy, material and organisms across ecosystem boundaries, and these flows can exert strong influences on the fertility and productivity of ecosystems. The magnitude of cross‐system fluxes is mediated by a wide range of variables.

Key concepts:

Ecosystem boundaries are the locations exhibiting gradients of change in environmental conditions and a related shift in the composition of plant and/or animal communities.

Naturally occurring ecosystem boundaries can represent unique habitats to which many species are specifically adapted.

Anthropogenically created ecosystem boundaries often support high species diversity, but the combination of species present at edges is very different to the one found deep inside the adjacent ecosystems.

Neighbouring ecosystems experience flows of organisms, materials and energy across the shared boundary.
Cerebral Cortex Evolution and the

ASPM

Gene
Authors: Ali Farhan 
Published: September 2009

Abstract

The cerebral cortex has diversified in many organisms despite having a similar basic plan. Neural cell division at one level and scaling laws at another level can explain interspecies differences in cerebral cortex sizes. Cerebral cortex components are also shaped by adaptive evolution, particularly by ecological and social factors. The genetic basis for brain development has only recently been probed. Guided initially by clinical studies of patients with reduced brain sizes (microcephaly), the gene

ASPM

has been identified as an important candidate involved in cerebral cortex development. Multiple lines of evidence from evolutionary genetics and functional studies have now implicated the gene in cerebral cortex size evolution across diverse organisms. Given the complexities associated with such a large organ, other genes and their expression patterns as well as noncoding DNA may also play a role in cerebral cortex evolution.

Key concepts:

Higher organisms such as mammals and birds show diversity in cerebral cortex size and organization.

This diversity is explained partly by neural cell division and scaling laws that constrain the expansion of the cerebral cortex as a function of body size and development.

Differences in cerebral cortex organization are also explained by adaptive evolution of animals in their unique niches.

Mutations in the gene
ASPM
cause primary microcephaly or reduced brain size in humans.

The gene
ASPM
controls cortical neurogenesis through cell cycle functions in the brain.

There is evidence of accelerated evolution of
ASPM
in humans and other nonhuman primates with enlarged cerebral cortex sizes.

In addition to
ASPM
, other genes particularly those underlying cellular energetics and regulation of gene expression may be involved in cerebral cortex evolution.

The numerous single‐gene, genomic scan and expression studies have its limitations in explaining cerebral cortex evolution.
Regulatory Genes in Ancestral Chordates
Authors: Sasakura Yasunori 
Published: September 2009

Abstract

The phylum ‘Chordate’ includes amphioxus, tunicate and vertebrate. The three groups evolved from a common ancestor. The evolution of chordates is a fascinating subject for biologists, who have long pondered which changes in the genome and genes were critical to the evolution, with no real resolution to this issue. Recent genome projects in the chordates have revealed a repertoire of so‐called regulatory genes, and comparison of these essential genes for development has provided insights into chordate evolution. The ancestral chordate is estimated to have had approximately 80% of the genes in the extant chordate genomes. Some regulatory genes are specific to specific lineages, which may have led to the separation of amphioxus, tunicates and vertebrates.

Key concepts

Small subsets of genes encoding transcription factors and signal transductions play roles as conductors during development. These genes are called regulatory genes. Genetic changes in regulatory genes served as major driving forces for the evolution of chordates. The regulatory genes present in the ancestral chordate can be deduced by comparing the extant chordate genomes. This information is crucial to understand the evolution of chordates.
Evolution of the Chorionic Gonadotropin β Genes in Primates
Authors: Hallast Pille , Laan Maris 
Published: September 2009

Abstract

Several genes associated with reproduction have been duplicated during primate evolution and evolved under positive selection. Chorionic gonadotropin hormone (HCG) produced by trophoblast cells has emerged in primates and assists maternal physiology to establish pregnancy.

CGB

gene, coding for the HCG β subunit has evolved through a duplication of the ancestral
lutenizing hormone
β (

LHB

) gene 55–35 million years ago. Only a few sequence changes in the duplicate locus were required to result in a novel

CGB

gene with different tissue‐specificity and function. Evolution of the

LHB

/

CGB

genomic region has been accompanied by active genome dynamics either as series of additional duplications in Old World monkeys and apes, or as functional modifications of genes in New World monkeys. Duplicated, highly homologous genes with diverged functions are maintained through a balance between selective pressures targeted to their specific functions and evolution

in consort

facilitated by interlocus gene conversion.

Key Concepts

Several genes associated with female and male reproduction have been shown to be duplicated during primate evolution and evolve under positive selection.

Chorionic gonadotropin hormone (HCG) produced by the trophoblast cells has emerged in primates and acts as a key hormone to assist maternal physiology to establish pregnancy.

Primate‐specific

CGB

gene, coding for the β subunit of HCG has emerged through a duplication of the ancestral lutenizing hormone β (

LHB

) gene approximately 55–35 million years ago.

Only a few sequence changes in the duplicate locus were required to result in a novel

CGB

gene with different tissue‐specificity, expression pattern and function.

Evolution of the

LHB

/

CGB

genomic region in primates has been accompanied by active genome dynamics either as a series of additional duplications in the lineage to OWM and apes, or as functional modifications of the gene loci in NWM.

Comparison of the human and chimpanzee

LHB/CGB

gene clusters identified large species‐specific parallel rearrangement events, resulting in lineage‐specific number of

CGB

gene copies (five versus six genes in chimpanzee compared to human).

Duplicated genes tend to evolve

in consort

facilitated by active interlocus gene conversion increasing and preserving sequence similarity among the gene copies.

Intraspecies gene conversion events have led to a higher human–chimpanzee divergence between duplicated

LHB/CGB

genes compared to the available data for unique genomic regions.

Duplicated, highly homologous genes with diverged functions are maintained through balancing interlocus gene conversion activity with selective pressure targeting their specific functions.
Evolution of the
AZFc
Region in Primates
Authors: Yu Yueh‐Hsiang , Yen Pauline H 
Published: September 2009

Abstract

The
Azoospermia Factor c
(
AZFc
) region on the human Y chromosome is one of the most polymorphic regions in the human genome. It encodes several gene families with germ‐cell specific expression and is frequently deleted in infertile men with very low sperm counts or no sperm.
AZFc
consists mainly of very long repeats (amplicons) that have different evolutionary histories. Some of the ampliconic sequences are remnants of the ancient Y chromosome and share homology with the X chromosome. Other sequences arrived on the Y chromosome through segmental duplication and transposition of autosomal sequences or through messenger
ribonucleic acid
(mRNA) retroposition. Subsequent rearrangements such as duplication, inversion and intragenic amplification result in the various structures found on the Y chromosomes of today's primates.

Key Concepts

The
AZFc
region on the human Y chromosome contains several testis‐specific gene families and is essential for normal spermatogenesis.

The
AZFc
region consists mainly of large amplicons and is prone to rearrangement such as deletion, duplication and inversion.

Some ampliconic sequences are remnants of the ancestral Y chromosome and retain sequence similarity with the X chromosome.

Other
AZFc
sequences arrived on the Y chromosome at various time during primate evolution through duplication and transposition of autosomal sequences.

The
CDY
gene within the yellow amplicon arose from retroposition of an ancient autosomal
CDYL
gene and contains no introns.
Modal–Vibration‐Based Damage Identification
Authors: Worden Keith , Friswell Michael I. 
Published: September 2009

AbstractA substantial body of structural health monitoring (SHM) research has been carried out in the context of structural dynamics. In this context, it is natural to make use of features for damage identification, which arise in the normal course of structural dynamic testing. The accepted standard for a dynamic test is amodal analysis, which derives a description of the dynamics in terms of natural frequencies, damping ratios, and modeshapes. This article discusses how such features can be used to extract a damage diagnosis. From a modal test, it is possible to extract the physical matrices that enter the structural equations of motion: mass, damping, and stiffness matrices. This article also describes damage identification strategies based on these matrices.
Probabilistic Approaches to Sensor Layout Design, Data Processing, and Damage Detection
Authors: Mahadevan Sankaran , Jiang Xiaomo , Guratzsch Robert F. 
Published: September 2009

AbstractThis article presents probabilistic methodologies toward the design of a reliable structural health monitoring system, by addressing several types of uncertainties in sensor performance and data, including sensor layout effects and sensor data noise, incompleteness, and variability. The sensor layout is designed to maximize the reliability of damage detection by combining probabilistic finite element analysis, damage detection algorithms, and reliability‐based optimization techniques. A Bayesian discrete wavelet packet transform‐based denoising approach is presented to perform data cleansing prior to damage detection. A nonparametric system identification method is applied when using incomplete sensor data. A Bayesian method is presented to incorporate possible uncertainties in both sensor data and model prediction and to provide a quantitative measure of confidence in structural condition assessment. These methodologies are illustrated for application to an aerospace structure thermal protection system panel and to a five‐story building frame structure, representing two different disciplines.
Energy Harvesting and Wireless Energy Transmission forSHMSensor Nodes
Authors: Farinholt Kevin M. , Park Gyuhae , Farrar Charles R. 
Published: September 2009

AbstractThe concept of wireless sensor nodes and sensor networks has been widely investigated within the field of structural health monitoring (SHM). However, the ability to power sensors, onboard processing, and telemetry components is a significant challenge in many SHM applications. Several energy harvesting techniques, based on piezoelectric and thermoelectric materials, have been proposed and studied to solve such problems. This article summarizes recent advances and research issues in energy harvesting relevant to SHM applications. We also present a feasibility study for using radio frequency (RF) signals to wirelessly deliver energy to power sensing systems. The goal of this study is to provide a method for supplying power to a sensor node periodically so that the SHM system does not rely on an onboard power source.
Integrated Sensor Durability and Reliability
Authors: Blackshire James L. , Jata Kumar V. 
Published: September 2009

AbstractSignificant progress has been made recently in the development of numerous integrated sensing approaches in support of structural health monitoring. To a large degree, however, many of these sensing approaches and methodologies are unproven in fielded, operational environments where the long‐term reliability of the sensors and associated hardware needs to be insured. In this article, some of the physical principles of integrated sensor durability and reliability are covered. In particular, the primary factors that can influence the performance and reliable output of an integrated sensing system are described. The aging, damage, and degradation of a sensing system are also covered. Several specific examples are given, including surface‐bonded piezoelectric sensor disks, direct‐write thermocouples, comparative vacuum sensors, and layered piezoelectric actuator/sensor networks. Lessons learned and opportunities for sensor durability/reliability improvement are also briefly covered.
Structural Health Monitoring—An Introduction and Definitions
Authors: Boller Christian 
Published: September 2009

AbstractStructural health monitoring (SHM) is the lateral integration of a variety of different disciplines in engineering science. Starting from an engineering structural design point of view, it encompasses loads and damage monitoring including the various disciplines being related to this. Once SHM being defined as a system is realized, it needs to be implemented in a structure such that it generates the appropriate benefit in terms of life cycle cost. This article addresses what can be considered as SHM in that regard and how the benefit can be determined using mainly examples taken from aviation.